CAR-T DELIVERY OF SYNTHETIC PEPTIDE THERAPEUTICS

CROSS-REFERENCE TO RELATED APPLICATION

The present application is entitled to priority under 35 U.S.C. § 119(e) to U.S.

Provisional Patent Application No. 63/166,073 filed March 25, 2021, which is hereby incorporated by reference in its entirety herein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under CA228455 awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Chimeric antigen receptor T cells (CAR-Ts) have shown significant potential in liquid malingnancies, but responses in solid tumors have been limited thus far. Similarly, bioactive peptide therapeutics have demonstrated promising preclinical activity in vitro and in vivo , but have yet to demonstrate significant clinical benefit. Both therapies face distinct barrers to activity in larger patient populations. In the case of adoptive cell therapies (ACT) such as CAR-T, a variety of local tumor-intrinsic immunosuppressive mechanisms limit anti -tumor efficacy. Likewise, the efficient delivery and localization of peptide therapeutics has proven to be a significant obstacle.

There is a need in the art for improved CAR-T therapies that provide enhanced antitumor activity. The present invention addresses this need.

SUMMARY OF THE INVENTION

In one aspect, the disclosure provides an engineered cell, comprising a chimeric antigen receptor (CAR) and a therapeutic peptide. The CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular domain. The therapeutic peptide is a non-natural therapeutic peptide and the CAR molecule and the therapeutic peptide are expressed from the same expression construct. In another aspect, the disclosure provides an engineered cell comprising a chimeric antigen receptor (CAR) and a therapeutic peptide. The CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular domain, and the therapeutic peptide is a non-natural therapeutic peptide. The therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

In certain embodiments, the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP. In certain embodiments, the therapeutic peptide is a mimetic of a TLR agonist. In certain embodiments, the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL). In certain embodiments, the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic. In certain embodiments, the therapeutic peptide is an inhibitor of poly ADP ribose polymerase (PARP).

In certain embodiments, the non-natural peptide is a peptide that has no more than 90% sequence identity to a naturally occurring peptide. In certain embodiments, the non-natural peptide is a peptide that has no more than 80% sequence identity to a naturally occurring peptide. In certain embodiments, the peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-16.

In certain embodiments, the therapeutic peptide is exported from the engineered cell in an extracellular vesicle. In certain embodiments, the therapeutic peptide is a mimetic of a SCFA that binds to a G protein-coupled receptor (GPCR).

In certain embodiments, the target cell is a tumor cell.

In certain embodiments, the engineered cell is a T cell or an NK cell.

In certain embodiments, the antigen binding domain is selected from the group consisting of an antibody, an antigen binding fragment (Fab), and a single-chain variable fragment (scFv). In certain embodiments, the binding domain is a T cell receptor (TCR).

In certain embodiments, the target antigen is selected from the group consisting of CD 19, CD20, CD22, BCMA, CD123, CD133, EGFR, EGFRvIII, mesothelin, Her2, PSMA, CEA, GD2, IL-13Ra2, glypican-3, CIAX, LI-CAM, CA 125, CTAG1B, Mucin 1, and Folate receptor-alpha. In certain embodiments, the target antigen is expressed on an intestinal cell.

In certain embodiments, the transmembrane domain is a transmembrane domain from a protein selected from the group consisting of CD8 alpha, CD3 zeta, CD3 epsilon, CD28, and ICOS.

In certain embodiments, the intracellular signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD3 zeta, TCR zeta, CD3 epsilon, CD3 gamma, CD3 delta, or ICOS. In certain embodiments, the intracellular signaling domain comprises a functional signaling domain and further comprises a costimulatory domain, wherein the costimulatory domain comprises a functional signaling domain from 4- IBB or CD28.

In certain embodiments, the CAR comprises an anti-CD 19 scFv, a CD8 alpha transmembrane domain, a 4- IBB costimulatory domain, and a CD3 zeta signaling domain.

In certain embodiments, the therapeutic peptide is a SCFA mimetic or is a mimetic of a steroid and/or hormone-like molecule, and wherein the engineered cell has been further modified to reduce activity of one or more effector functions.

In certain embodiments, the engineered cell has been modified to reduce or prevent expression of one or more inflammatory cytokines, expression of Granzyme B, or expression of perforin.

In certain embodiments, the CAR molecule and the therapeutic peptide are expressed from the same expression construct and wherein the expression construct further comprises an RNA molecule that activates a PRR. In certain embodiments, the RNA molecule is 7SL.

In another aspect, the disclosure provides a composition comprising any of the engineered cells contemplated herein.

In another aspect, the disclosure provides a nucleic acid molecule encoding (i) a chimeric antigen receptor (CAR) comprising an antigen binding domain, a transmembrane domain, and an intracellular signaling domain, and (ii) a therapeutic peptide, wherein the therapeutic peptide is a non-natural peptide.

In certain embodiments, a stop codon separates the nucleic acid segment encoding the CAR from the nucleic acid segment encoding the therapeutic peptide.

In certain embodiments, the therapeutic peptide encoded by the nucleic acid molecule has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

In certain embodiments, the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP. In certain embodiments, the therapeutic peptide is a mimetic of a TLR agonist. In certain embodiments, the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL). In certain embodiments, the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic. In certain embodiments, the therapeutic peptide is an inhibitor of poly ADP ribose polymerase (PARP).

In certain embodiments, the nucleic acid encoding the non-natural peptide has no more than 80% sequence identity to a nucleic acid encoding a naturally occurring peptide.

In certain embodiments, the target cell is a tumor cell.

In certain embodiments, the antigen binding domain encoded by the nucleic acid molecule is selected from the group consisting of an antibody, a Fab, and an scFv.

In certain embodiments, the binding domain encoded by the nucleic acid molecule is a

TCR.

In certain embodiments, the binding domain encoded by the nucleic acid molecule binds a target antigen selected from the group consisting of CD19, CD20, CD22, BCMA, CD123, CD133, EGFR, EGFRvIII, mesothelin, Her2, PSMA, CEA, GD2, IL-13Ra2, glypican-3, CIAX, LI-CAM, CA 125, CTAG1B, Mucin 1, and Folate receptor-alpha.

In certain embodiments, the transmembrane domain encoded by the nucleic acid molecule is a transmembrane domain from a protein selected from the group consisting of CD8 alpha, CD3 zeta, CD3 epsilon, CD28, and ICOS.

In certain embodiments, the intracellular signaling domain encoded by the nucleic acid molecule comprises a functional signaling domain of a protein selected from the group consisting of CD3 zeta, TCR zeta, CD3 epsilon, CD3 gamma, CD3 delta, or ICOS. In certain embodiments, the intracellular signaling domain encoded by the nucleic acid molecule comprises a functional signaling domain and further comprises a costimulatory domain, wherein the costimulatory domain comprises a functional signaling domain from 4-1BB or CD28.

In certain embodiments, the nucleic acid molecule encodes a CAR molecule comprising an anti-CD19 scFv, a CD8 alpha transmembrane domain, a 4-1BB costimulatory domain, and a CD3 zeta signaling domain.

In certain embodiments, the nucleic acid molecule further comprises an RNA molecule that activates a PRR. In certain embodiments, the RNA molecule is 7SL.

In another aspect, the disclosure provides a expression vector comprising any of the nucleic acid molecules contemplated herein.

In another aspect, the disclosure provides a method for co-expressing a CAR and a therapeutic peptide in a cell. The method comprises delivering to the cell any of the expression vectors contemplated herein, under conditions such that the CAR and the therapeutic peptide are expressed.

In another aspect, the disclosure provides a cell comprising any of the nucleic acid molecules or any of the the expression vectors contemplated herein.

In another aspect, the disclosure provides a method for treating a disease or disorder in a subject. The method comprises administering to the subject an effective amount of a T cell genetically modified to express a chimeric antigen receptor (CAR). The CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular signaling domain. The method further comprises stimulation of the endogenous immune response against the cancer via a non-natural therapeutic peptide. The non-natural therapeutic peptide is expressed in the modified T cell and/or is administered in combination with the modified T cell. The non-natural therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR),

(v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

In certain embodiments, the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP. In certain embodiments, the therapeutic peptide is a mimetic of a TLR agonist. In certain embodiments, the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL). In certain embodiments, the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic. In certain embodiments, the therapeutic peptide is an inhibitor of poly ADP ribose polymerase (PARP).

In certain embodiments, the non-natural peptide is a peptide that has no more than 80% sequence identity to any naturally occurring peptide.

In certain embodiments, the peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-16.

In certain embodiments, the therapeutic peptide is an immunogenic epitope, and wherein the immunogenic epitope is expressed on the surface of a cancer cell in the subject following the administration to the subject. In certain embodiments, the therapeutic peptide is expressed in the modified T cell, wherein subsequent to administration of the modified T cell to the subject, the therapeutic peptide is exported from the modified T cell in one or more extracellular vesicles. In certain embodiments, the therapeutic peptide is delivered via the one or more extracellular vesicles to one or more antigen presenting cells in the subject.

In another aspect, the disclosure provides a method for enhancing anti-cancer activity of a T cell genetically modified to express a chimeric antigen receptor (CAR). The CAR comprises an antigen binding domain that specifically binds to an antigen expressed on a tumor cell, a transmembrane domain, and a signaling domain. The method comprises co-expressing a non natural therapeutic peptide in the T cell. The non-natural therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide,

(iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

In another aspect, the disclosure provides a method for treating an inflammatory disease, an autoimmune disease, or a cancer in a subject. The method comprises administering to the subject an effective amount of any of the engineered cells or any of the compositions contemplated herein.

In certain embodiments, the cancer is a solid tumor cancer. In certain embodiments, the cancer is selected from the group consisting of lung cancer, small cell lung cancer, non-small cell lung cancer, mesothelioma, pancreatic cancer, breast cancer, ovarian cancer, fallopian tube cancer, cervical cancer, prostate cancer, colorectal cancer, gastric cancer, bladder cancer, esophageal cancer, and melanoma. In certain embodiments, the cancer is a hematological cancer. In certain embodiments, the hematological cancer is a leukemia or lymphoma. In certain embodiments, the hematological cancer is selected from the group consisting of chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL) multiple myeloma, acute lymphoid leukemia (ALL), Hodgkin lymphoma, B-cell acute lymphoid leukemia (BALL), T-cell acute lymphoid leukemia (TALL), small lymphocytic leukemia (SLL), acute myeloid leukemia (AML), B cell prolymphocytic leukemia, blastic plasmacytoid dendritic cell neoplasm, Burkitf s lymphoma, diffuse large B cell lymphoma (DLBCL), chronic myeloid leukemia, myeloproliferative neoplasms, follicular lymphoma, pediatric follicular lymphoma, hairy cell leukemia, small cell- or a large cell-follicular lymphoma, malignant lymphoproliferative conditions, MALT lymphoma (extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue), Marginal zone lymphoma, myelodysplasia, myelodysplastic syndrome, non-

Hodgkin lymphoma, plasmablastic lymphoma, plasmacytoid dendritic cell neoplasm, Waldenstrom macroglobulinemia, splenic marginal zone lymphoma, lymphoplasmacytic lymphoma, and plasma cell myeloma.

In certain embodiments, the autoimmune disease is an inflammatory bowel disease.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing and other features and advantages of the present invention will be more fully understood from the following detailed description of illustrative embodiments taken in conjunction with the accompanying drawings.

FIG. 1 depicts a schematic view of exemplary embodiments of the present disclosure.

FIG. 2 is a schematic of an exemplary CAR construct comprising a CAR molecule (19BBz) and a non-natural peptide (SIINFEKL) (SEQ ID NO: 7), separated by a stop codon.

FIG. 3 depicts flow cytometry plots showing peptide/MHC expression on 19BBz CAR transduced (CAR+) and untransduced (CAR-) cells; and Ova-19BBz CAR transduced (CAR+) and untransduced (CAR-) cells.

FIG. 4 depicts a flow cytometry plot showing that CAR molecule is expressed despite the inclusion of the internal stop codon. CAR expression was determined by staining with an anti human Fab’2 antibody. Proposed peptide transfer event is shown.

FIG. 5 is a schematic of the experimental design for a study assessing inclusion of immunogenic peptide from CAR-T transduced cells into extracellular vesicles and transfer of immunogenic peptide epitopes to tumor cells.

FIG. 6A depicts flow cytometry plots showing peptide/MHC expression on tumor cells (top row) and Granzyme B expression in OT-I T cells (bottom row), incubated with no CAR-T EV, 18 pg EV, 37.5 pg EV, or 75 pg EV.

FIG. 6B depicts flow cytometry plots showing Ki67 expression (top row) and IFNy expression (bottom row) in OT-I T cells incubated with no CAR-T EV, 18 pg EV, 37.5 pg EV, or 75 pg EV.

FIG. 6C depicts quantification of the Ova-19BBz EV data shown in FIG. 6 A, bottom row and FIG. 6B. Ki67 expression (FIG. 6C, left panel), Granzyme B expression (FIG. 6C, middle panel), and IFNy expression (FIG. 6C, right panel) were significantly increased in the presence of EV compared to the equivalent amount of EV from 19BBz (i.e., no Ova peptide) expressing CAR-T cells.

FIG. 7 is a bar graph showing the relative cell death of B16 cells incubated with OT-I T cells and 0 pg EV, 18 pg EV, 37.5 pg EV, or 75 pg EV.

FIG. 8 is a schematic of the study design for an in vivo study of the expression and transfer of immunogenic peptide epitopes in vivo using B16-hCD19 tumor cells.

FIG. 9A shows the expression of peptide/MHC on tumor cells (top two panels) or dendritic cells (bottom two panels) after 19BBz or Ova-19BBz administration to mice implanted with tumor cells.

FIG. 9B shows peptide tetramer staining on CD8+ T cells harvested from tumors following administration of 19BBz (left panel) or Ova-19BBz (middle panel). The tetramer+ cells isolated from the Ova-19BBz group were also Ki67+ (right panel), indicating that the SIINFEKL-specific cells were activated.

FIG. 10A shows the % Ova+ tumor cells (left panel) and the % Ova+ endogenous immune cells (right panel) in 19BBz recipients vs. Ova-19BBz recipients.

FIG. 10B shows the % endogenous T cells staining positively with the Ova tetramer (top left panel) and the % CD8+ T cells expressing the proliferation marker Ki67 (top right panel) in 19BBz recipient mice vs. Ova-19BBz recipient mice. The tumor weight at day 16 in recipient mice is shown in the bottom panel.

FIG. 11 A is a schematic of the study design for an in vivo study of the expression and transfer of immunogenic peptide epitopes in vivo using a 1 : 1 mix of B16-CD19 and B16 WT cells to implant tumors.

FIG. 1 IB shows that the tumor volume (cm ³ ) in animals administered 19BBz was significantly greater than that of animals administered Ova-19BBz at days 21, 24, and 28 post tumor implantation; and that the tumor volume grew more rapidly in 19BBz recipients compared to Ova-19BBz recipients.

FIG. 12A is a schematic of an exemplary CAR construct comprising a CAR molecule (19BBz) and a non-natural peptide (SIINFEKL), separated by a stop codon; and a schematic of an exemplary CAR construct comprising the SIINFEKL peptide, stop codon, 19BBz CAR molecule, and 7SL RNA. The RNA promoter U6 separates the 19BBz CAR molecule and 7SL. Also shown is schematic of the study design for an in vivo study of the expression and transfer of immunogenic peptide epitopes using the Ova-19BBz, 19BBz-7SL, Ova-19BBz-7SL, or control (19BBz) CAR T cells, using a 1 : 1 mix of KP-hCD19 and KP WT cells to implant tumors.

FIG. 12B shows the tumor volume in each group of mice treated with (untreated (Utxl), 19BBz, Ova-19BBz (Ova-19), 19BBz-7SL (19-7SL), or Ova-19BBz-7SL (Ova-19-7SL).

FIG. 12C shows the percent survival over time of mice treated with 19BBz, Ova-19BBz (BBz-Ova), 19BBz-7SL (BBz-7SL), and Ova-19BBz-7SL (Ova-BBz-7SL); or untreated (utx).

FIG. 13 shows the Protein Data Bank crystal structure of the human STING molecule in complex with cGAMP (PDB structure 4EMT; left panel) or the STING structure with cGAMP removed to reveal the isolated active STING structure with an empty cGAMP pocket.

FIG. 14 shows STING with poly-Gly for sampling to create binding peptides (left panel) and STING with a predicted binding peptide present in the cGAMP binding position (right panel). The predicted binding peptide shown is peptide ST2.

FIG. 15 is a schematic depiction of a study design for assessing the activity of the identified STING agonist peptides as measured by CD86 as a DC activation readout (left panel). The right panel of FIG. 15 shows the % CD86+ cells as measured by flow cytometry after incubation with negative control, positive control (cGAMP), or the indicated STING peptide.

FIG. 16 is a schematic depiction of a study design for assessing the effect of the STING agonist peptide when incubated with DCs and OT-1 T cells (left panel). The right panel shows the fold change in Granzyme B, IFNy, and Ki67 in WT cells incubated with liposome encapsulated STING peptide. Liposome-only was used as a negative control. Cells from STING knock out mice (KO) were used in addition to WT, and show that the activation of T cells by ST2 is STING dependent.

FIG. 17 provides schematic depictions of the 19BBz CAR construct and a STING agonist peptide- 19BBz CAR construct comprising STING agonist peptide ST2 and 19BBz (top). The bottom portion shows an exemplary experimental plan for the in vivo assessment of cells expressing the 19BBz-ST2 construct.

FIG. 18 shows that animals that received the 19BBz-STING peptide expressing CAR T cells exhibited significantly improved survival compared to animals that received the traditional 19BBz CAR-T cells. FIG. 19 shows the relative cell death in B16 tumor cells (left panel) or KP tumor cells (right panel) when incubated in the presence of TNF with liposome only (negative control) or the indicated concentration of SMAC mimetic peptide Pepl, Pep3, Pep4, Pep5, or Pep6.

FIG. 20 shows the relative cell death of B16 cells incubated with liposome only (negative control) or the indicated increasing concentrations of SMAC mimetic peptide SMACm6, in the presence or absence of TNF. Concentrations are shown in mM. The efficacy of SMACm6 in inducing cell death is dependent on TNF signaling.

FIG. 21 is a schematic depiction of the CAR-T construct comprising SMACm6 peptide and 19BBz (top), and an experimental design for assessing the effect of EVs released from expanded SMACm CAR-T cells on tumor cell lines (bottom).

FIG. 22 shows the relative cell death of B16 (left panel) or KP (right panel) cells, incubated with the indicated concentrations of EVs from 19BBz or 19BBz-SMACm6 cells.

FIG. 23 shows the tumor volume (cm ³ ; left two panels) and percent survival (right two panels) in animals administered the indicated CAR-T cells (19BBz or 19-SMACm6), with or without anti-CTLA4 therapy.

FIG. 24 is a schematic illustrating PARPi dsDNA triggering of PDL1.

FIG. 25 shows PD-L1 expression in TSA breast cancer cells alter incubation with liposome-encapsulated PARPi peptides (Pepl, Pep2, Pep 1C, or Pep 3), negative control (liposome only), or positive control (PARP inhibitor olaparib).

FIG. 26A shows the design of a 19BBz CAR vector expressing Ova (Ova-19BBz) or Ova plus RN7SL1 (Ova-19-7SL) (top) and representative flow cytometry plots showing detection of SIINFEKL peptide on CAR ⁺ and CAR T cells (bottom).

FIG. 26B shows detection of SIINFEKL peptide on B16 cells loaded with indicated concentrations of EVs from Ova-19BBz CAR-T cells or 19BBz CAR-T cells (Cont) (flow plots, top). OT-I T cells were then added, and activation was measured (flow plots, bottom) and quantitated (dot plots, bottom) using GZMB and Ki67.

FIG. 26C shows SIINFEKL peptide transfer to cancer and immune cells measured in mixed CD19 ⁺ /CD19 B16 tumors following treatment in vivo with 19BBz or Ova-19BBz (Ova) CAR-T cells. Representative flow cytometry plots of cancer cells are shown (left). FIGs. 26D-26E show endogenous Ova-specific T cell expansion measured by tetramer and Ki67 expression (FIG. 26D), and frequency of Ova-specific and Ki67 ⁺ CD8 T cells (FIG. 26E).

FIG. 26F shows growth of heterogenous CD19 ⁺ /CD19 B16 tumors following treatment with indicated CAR-T cells.

FIG. 26G shows growth of heterogenous CD19 ⁺ /CD19 KP mixed tumors following CAR-T cell therapy with anti-CTLA4 plus anti-PDl. 5xl0 ⁵ OT-I T cells were transferred prior to tumor implantation.

FIG. 26H shows relative transfer of Ova peptide from CD45.1 ⁺ CAR T cells to intratumoral CD45.2 ⁺ immune cells versus CD45.2 tumor cells in mixed CD19 and CD19 ⁺ B16 tumors as quantified by flow cytometry for SIINFEKL/MHC-I staining. Each bar represents an individual tumor.

FIG. 27 A depicts the experimental set-up for a study assessing the requirement of MHC-I from CAR-T cells for activating endogenous T cells by delivery of antigen peptide from CAR-T cell extracellular vesicles (EVs).

FIG. 27B shows the expression of indicated T cell activation markers on OT-I T cells after addition of EVs from MHC-I-expressing (top) or MHC-I-deficient (bottom) CAR-T cells under the indicated culture conditions (x-axis).

FIG. 27C shows representative flow cytometry plots of T cell activation markers on OT-I T cells.

FIG 28A depicts the experimental set-up for a study assessing the ability of extracellular vesicles from CAR-T cells engineered to deliver antigen peptide to directly activate endogenous T cells.

FIG. 28B shows representative flow cytometry plots of OT-I CD8 T cells from the upper well for the indicated T cell activation markers (top row) or for OVA/MHC-I transferred from CAR-T cell EVs (bottom row) after addition of the indicated CAR-T cells to the lower well. Two independent replicates are shown. DETAILED DESCRIPTION

Chimeric antigen receptor (CAR) therapies such as CAR-T cells provide new ways to treat diseases such as cancers, but improvements to such therapies are needed. Desirable improvements to CAR therapies include enhancing the potency and/or durability of the immune response against the cancer, harnessing pro-cell death pathways within the tumor cell, identifying new and diverse neoantigens, counteracting or over-riding immune evasion and survival strategies of the tumor cell or in the tumor environment, identifying and using novel tumor antigens to target immune responses to the tumor, and/or otherwise triggering or enhancing anticancer effects.

Enhanced CAR-T therapies that involve expressing a CAR molecule in a cell with an exogenous RNA molecule, such as an RNA molecule that stimulates the immune system, have been explored and offer improved anti-cancer immune activity. However, such approaches cannot utilize many pathways and features of the immune response which cannot be coded on an RNA molecule. The present disclosure provides eloquent methods for addressing this need and demonstrates that the approaches provided herein demonstrate surprisingly high efficacy.

Thus, in certain aspects, the present disclosure provides methods and compositions to deliver multiple anti-tumor immune components to the tumor and tumor microenvironment, tailored to disease-specific needs. In certain embodiments, the present disclosure provides novel therapeutic molecules that are delivered by, and enhance, CAR therapy. The novel therapeutic molecules, in certain embodiments, are synthetic, non-natural peptides. The present disclosure further provides methods for making and using the novel compositions provided herein. The present disclosure further provides compositions and methods for generating immunogenic epitope libraries and transferring immunogenic peptides to tumor cells to enhance anti-cancer immunity.

It is to be understood that the methods described in this disclosure are not limited to particular methods and experimental conditions disclosed herein as such methods and conditions may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.

Furthermore, the experiments described herein, unless otherwise indicated, use conventional molecular and cellular biological and immunological techniques within the skill of the art. Such techniques are well known to the skilled worker, and are explained fully in the literature. See, e.g., Ausubel, el al ., ed., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., NY, N.Y. (1987-2008), including all supplements, Molecular Cloning: A Laboratory Manual (Fourth Edition) by MR Green and J. Sambrook, and Harlow et al., Antibodies: A Laboratory Manual, Chapter 14, Cold Spring Harbor Laboratory, Cold Spring Harbor (2013, 2nd edition).

A. Definitions

Unless otherwise defined, scientific and technical terms used herein have the meanings that are commonly understood by those of ordinary skill in the art. In the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. The use of “or” means “and/or” unless stated otherwise. The use of the term “including,” as well as other forms, such as “includes” and “included,” is not limiting.

Generally, nomenclature used in connection with cell and tissue culture, molecular biology, immunology, microbiology, genetics and protein and nucleic acid chemistry and hybridization described herein is well-known and commonly used in the art. The methods and techniques provided herein are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated. Enzymatic reactions and purification techniques are performed according to manufacturer’s specifications, as commonly accomplished in the art or as described herein. The nomenclatures used in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well- known and commonly used in the art. Standard techniques are used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients.

That the disclosure may be more readily understood, select terms are defined below. The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.

“About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or ±10%, more preferably ±5%, even more preferably ±1%, and still more preferably ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.

“Activation,” as used herein, refers to the state of a T cell that has been sufficiently stimulated to induce detectable cellular proliferation. Activation can also be associated with induced cytokine production, and detectable effector functions. The term “activated T cells” refers to, among other things, T cells that are undergoing cell division.

As used herein, to “alleviate” a disease means reducing the severity of one or more symptoms of the disease.

The term “antigen” as used herein is defined as a molecule that provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both. The skilled artisan will understand that any macromolecule, including virtually all proteins or peptides, can serve as an antigen.

Furthermore, antigens can be derived from recombinant or genomic DNA. A skilled artisan will understand that any DNA, which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an “antigen” as that term is used herein. Furthermore, one skilled in the art will understand that an antigen need not be encoded solely by a full length nucleotide sequence of a gene. It is readily apparent that the present disclosure includes, but is not limited to, the use of partial nucleotide sequences of more than one gene and that these nucleotide sequences are arranged in various combinations to elicit the desired immune response. Moreover, a skilled artisan will understand that an antigen need not be encoded by a “gene” at all. It is readily apparent that an antigen can be generated synthesized or can be derived from a biological sample. Such a biological sample can include, but is not limited to a tissue sample, a tumor sample, a cell or a biological fluid.

As used herein, the term “autologous” is meant to refer to any material derived from the same individual to which it is later to be re-introduced into the individual. A “co-stimulatory molecule” refers to the cognate binding partner on a T cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the T cell, such as, but not limited to, proliferation. Co-stimulatory molecules include, but are not limited to an MHC class I molecule, BTLA and a Toll ligand receptor.

A “co-stimulatory signal”, as used herein, refers to a signal, which in combination with a primary signal, such as TCR/CD3 ligation, leads to T cell proliferation and/or upregulation or downregulation of key molecules.

A “disease” is a state of health of an animal wherein the animal cannot maintain homeostasis, and wherein if the disease is not ameliorated then the animal’s health continues to deteriorate. In contrast, a “disorder” in an animal is a state of health in which the animal is able to maintain homeostasis, but in which the animal’s state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal’s state of health.

The term “downregulation” as used herein refers to the decrease or elimination of gene expression of one or more genes.

“Effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result or provides a therapeutic or prophylactic benefit. Such results may include, but are not limited to an amount that when administered to a mammal, causes a detectable level of immune suppression or tolerance compared to the immune response detected in the absence of the composition of the disclosure. The immune response can be readily assessed by a plethora of art-recognized methods. The skilled artisan would understand that the amount of the composition administered herein varies and can be readily determined based on a number of factors such as the disease or condition being treated, the age and health and physical condition of the mammal being treated, the severity of the disease, the particular compound being administered, and the like.

“Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.

As used herein “endogenous” refers to any material from or produced inside an organism, cell, tissue or system.

The term “epitope” as used herein is defined as a small chemical molecule on an antigen that can elicit an immune response, inducing B and/or T cell responses. An antigen can have one or more epitopes. Most antigens have many epitopes; i.e., they are multivalent. In general, an epitope is roughly about 10 amino acids and/or sugars in size. Preferably, the epitope is about 4- 18 amino acids, more preferably about 5-16 amino acids, and even more most preferably 6-14 amino acids, more preferably about 7-12, and most preferably about 8-10 amino acids. One skilled in the art understands that generally the overall three-dimensional structure, rather than the specific linear sequence of the molecule, is the main criterion of antigenic specificity and therefore distinguishes one epitope from another. Based on the present disclosure, a peptide used in the present invention can be an epitope.

As used herein, the term “exogenous” refers to any material introduced from or produced outside an organism, cell, tissue or system.

The term “expand” as used herein refers to increasing in number, as in an increase in the number of T cells. In one embodiment, the T cells that are expanded ex vivo increase in number relative to the number originally present in the culture. In another embodiment, the T cells that are expanded ex vivo increase in number relative to other cell types in the culture. The term "ex vivo," as used herein, refers to cells that have been removed from a living organism, (e.g., a human) and propagated outside the organism (e.g., in a culture dish, test tube, or bioreactor).

The term “expression” as used herein is defined as the transcription and/or translation of a particular nucleotide sequence driven by its promoter.

“Expression vector” refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., Sendai viruses, lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.

“Identity” as used herein refers to the subunit sequence identity between two polymeric molecules particularly between two amino acid molecules, such as, between two polypeptide molecules. When two amino acid sequences have the same residues at the same positions; e.g., if a position in each of two polypeptide molecules is occupied by an arginine, then they are identical at that position. The identity or extent to which two amino acid sequences have the same residues at the same positions in an alignment is often expressed as a percentage. The identity between two amino acid sequences is a direct function of the number of matching or identical positions; e.g., if half (e.g., five positions in a polymer ten amino acids in length) of the positions in two sequences are identical, the two sequences are 50% identical; if 90% of the positions (e.g., 9 of 10), are matched or identical, the two amino acids sequences are 90% identical.

The term “immune response” as used herein is defined as a cellular response to an antigen that occurs when lymphocytes identify antigenic molecules as foreign and induce the formation of antibodies and/or activate lymphocytes to remove the antigen.

The term “immunosuppressive” is used herein to refer to reducing overall immune response.

“Isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.

A “lentivirus” as used herein refers to a genus of the Retroviridae family. Lentiviruses are unique among the retroviruses in being able to infect non-dividing cells; they can deliver a significant amount of genetic information into the DNA of the host cell, so they are one of the most efficient methods of a gene delivery vector. HIV, SIV, and FIV are all examples of lentiviruses. Vectors derived from lentiviruses offer the means to achieve significant levels of gene transfer in vivo.

By the term “modified” as used herein, is meant a changed state or structure of a molecule or cell of the disclosure. Molecules may be modified in many ways, including chemically, structurally, and functionally. Cells may be modified through the introduction of nucleic acids.

By the term “modulating,” as used herein, is meant mediating a detectable increase or decrease in the level of a response in a subject compared with the level of a response in the subject in the absence of a treatment or compound, and/or compared with the level of a response in an otherwise identical but untreated subject. The term encompasses perturbing and/or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, preferably, a human.

In the context of the present disclosure, the following abbreviations for the commonly occurring nucleic acid bases are used. “A” refers to adenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refers to thymidine, and “U” refers to uridine.

The term “oligonucleotide” typically refers to short polynucleotides. It will be understood that when a nucleotide sequence is represented by a DNA sequence (i.e., A, T, C, G), this also includes an RNA sequence (i.e., A, U, C, G) in which “U” replaces “T.”

Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).

“Parenteral” administration of an immunogenic composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.), or intrastemal injection, or infusion techniques.

The term “polynucleotide” as used herein is defined as a chain of nucleotides. Furthermore, nucleic acids are polymers of nucleotides. Thus, nucleic acids and polynucleotides as used herein are interchangeable. One skilled in the art has the general knowledge that nucleic acids are polynucleotides, which can be hydrolyzed into the monomeric “nucleotides.” The monomeric nucleotides can be hydrolyzed into nucleosides. As used herein polynucleotides include, but are not limited to, all nucleic acid sequences which are obtained by any means available in the art, including, without limitation, recombinant means, i.e., the cloning of nucleic acid sequences from a recombinant library or a cell genome, using ordinary cloning technology and PCR, and the like, and by synthetic means.

As used herein, the terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein’s or peptide’s sequence. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides, or a combination thereof.

By the term “specifically binds,” as used herein with respect to an antibody, is meant an antibody which recognizes a specific antigen, but does not substantially recognize or bind other molecules in a sample. For example, an antibody that specifically binds to an antigen from one species may also bind to that antigen from one or more species. But, such cross-species reactivity does not itself alter the classification of an antibody as specific. In another example, an antibody that specifically binds to an antigen may also bind to different allelic forms of the antigen. However, such cross reactivity does not itself alter the classification of an antibody as specific.

In some instances, the terms “specific binding” or “specifically binding,” can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody recognizes and binds to a specific protein structure rather than to proteins generally. If an antibody is specific for epitope “A”, the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled “A” and the antibody, will reduce the amount of labeled A bound to the antibody.

By the term “stimulation,” is meant a primary response induced by binding of a stimulatory molecule (e.g., a TCR/CD3 complex) with its cognate ligand thereby mediating a signal transduction event, such as, but not limited to, signal transduction via the TCR/CD3 complex. Stimulation can mediate altered expression of certain molecules, such as downregulation of TGF-beta, and/or reorganization of cytoskeletal structures, and the like.

A “stimulatory molecule,” as the term is used herein, means a molecule on a T cell that specifically binds with a cognate stimulatory ligand present on an antigen presenting cell.

A “stimulatory ligand,” as used herein, means a ligand that when present on an antigen presenting cell (e.g., an aAPC, a dendritic cell, a B-cell, and the like) can specifically bind with a cognate binding partner (referred to herein as a “stimulatory molecule”) on a T cell, thereby mediating a primary response by the T cell, including, but not limited to, activation, initiation of an immune response, proliferation, and the like. Stimulatory ligands are well-known in the art and encompass, inter alia, an MHC Class I molecule loaded with a peptide, an anti-CD3 antibody, a superagonist anti-CD28 antibody, and a superagonist anti-CD2 antibody.

The term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals). A “subject” or “patient,” as used therein, may be a human or non-human mammal. Non-human mammals include, for example, livestock and pets, such as ovine, bovine, porcine, canine, feline and murine mammals. Preferably, the subject is human.

As used herein, the term “T cell receptor” or “TCR” refers to a complex of membrane proteins that participate in the activation of T cells in response to the presentation of antigen.

The TCR is responsible for recognizing antigens bound to major histocompatibility complex molecules. TCR is composed of a heterodimer of an alpha (a) and beta (b) chain, although in some cells the TCR consists of gamma and delta (g/d) chains. TCRs may exist in alpha/beta and gamma/delta forms, which are structurally similar but have distinct anatomical locations and functions. Each chain is composed of two extracellular domains, a variable and constant domain. In some embodiments, the TCR may be modified on any cell comprising a TCR, including, for example, a helper T cell, a cytotoxic T cell, a memory T cell, regulatory T cell, natural killer T cell, and gamma delta T cell. The term “therapeutic” as used herein means a treatment and/or prophylaxis. A therapeutic effect is obtained by suppression, remission, or eradication of a disease state.

“Transplant” refers to a biocompatible lattice or a donor tissue, organ or cell, to be transplanted. An example of a transplant may include but is not limited to skin cells or tissue, bone marrow, and solid organs such as heart, pancreas, kidney, lung and liver. A transplant can also refer to any material that is to be administered to a host. For example, a transplant can refer to a nucleic acid or a protein.

The term “transfected” or “transformed” or “transduced” as used herein refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell. A “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid. The cell includes the primary subject cell and its progeny.

To “treat” a disease as the term is used herein, means to reduce the frequency or severity of at least one sign or symptom of a disease or disorder experienced by a subject.

A “vector” is a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” includes an autonomously replicating plasmid or a virus. The term should also be construed to include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like. Examples of viral vectors include, but are not limited to, Sendai viral vectors, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like.

Ranges: throughout this disclosure, various aspects of the disclosure can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range.

B. Therapeutic Peptides

As used herein, the term “therapeutic peptide” refers to a peptide that is delivered either by a CAR molecule or in combination with a CAR molecule, and which elicits and/or exerts and/or enhances a therapeutic response in a subject. In certain embodiments, the therapeutic response elicited or exerted or enhanced by the therapeutic peptide is an anti-cancer effect. For example, in certain embodiments, a therapeutic peptide binds to a target and triggers one or more pathways in a cell that increase or enhance an immune response, and/or increase or enhance a prodeath pathway in a tumor cell. In other embodiments, the therapeutic peptide is an immunogenic peptide, e.g., a neoantigen. In certain embodiments, the delivery of the therapeutic peptide via the methods provided herein results in the transfer of an immunogenic peptide to a tumor cell, thereby enhancing the anti-cancer immune response. For example, in certain embodiments, the therapeutic peptide provided herein is an immunogenic peptide, which may be expressed from the same expression vector and/or expressed in conjunction with a CAR molecule. In further embodiments, upon expression of the therapeutic peptide in a cell, the peptide is secreted in extracellular vesicles that are taken up by tumor cells or immune cells (e.g., antigen presenting cells). In certain embodiments, the peptide is secreted in extracellular vesicles, such that the therapeutic peptide is taken up, processed and presented via MHC on the tumor cell.

In certain embodiments, the therapeutic peptides provided herein are synthetic and are non-natural peptides. The non-natural therapeutic peptides provided herein may be novel peptides identified via the methods provided herein or other methods known in the art. In certain embodiments, the therapeutic peptides provided herein are rationally or computationally designed peptides that are capable of binding to a particular target. In certain embodiments, the therapeutic peptides are highly specific for a particular target. In certain embodiments, the therapeutic pathways are designed to act as mimetics, and mimic the binding of a ligand to a receptor. In certain embodiments, the ligand which the therapeutic peptide mimics is not a peptide or protein. In certain embodiments, the therapeutic peptides act as an agonist or an antagonist to trigger a pathway in a cell, e.g., an immune cell. Exemplary targets and pathways are described in detail herein, but the skilled person will recognize that the present disclosure provides methods for enhancing anti-cancer effects through synthetic therapeutic peptides that target any desired pathway.

In certain embodiments, the therapeutic peptide is expressed in the same cell that expresses the CAR molecule. In certain embodiments, the therapeutic peptide and the CAR molecule are encoded on the same expression vector. In certain embodiments, the therapeutic peptide is expressed in the cell that expresses the CAR molecule, and then is secreted from the cell in extracellular vesicles (EV). In certain embodiments, the therapeutic peptide exerts an effect on the cell in which it is expressed (e.g., the cell that expresses the CAR molecule). In certain embodiments, the therapeutic peptide is exported from the cell (e.g., in EV) and exerts an effect in the extracellular space, (e.g., in the tumor microenvironment), or exerts an effect directly or indirectly on neighboring cells such as dendritic cells, T cells, or tumor cells.

In certain embodiments, the non-natural therapeutic peptides provided herein are rationally designed and tested for binding to a target molecule using standard peptide binding assays. In other embodiments, the non-natural therapeutic peptides provided herein are generated using an algorithm and computational peptide binding prediction. In certain embodiments, the crystal structure of a target in complex with its ligand is compared to the crystal structure of the target in the absence of the ligand. The computational program then performs an iterative process of modeling folded peptides for binding prediction. In this manner, synthetic candidate peptides are identified and generated. Synthetic candidate peptides may be tested for target binding. Synthetic candidate peptides may be further tested for functional effects such as immune stimulation, induction of tumor cell death, induction of surrogate markers for immune stimulation and/or cell death, or any other effect relevant to the target. In still other embodiments, the therapeutic peptides provided herein are neoantigens identified via the generation of immunogenic epitope libraries from tumor samples. Candidate synthetic peptides may further be expressed from an expression vector that expresses a CAR as provided herein, and tested for in vivo effects, e.g., in models of cancer.

Table 1: Amino acid sequences of exemplary therapeutic peptides

Amino acid sequences provided herein may be modified. Such modifications may be conservative sequence modifications. “Conservative sequence modifications” refers to amino acid modifications that do not significantly affect or alter the functional characteristics of the protein. Conservative substitutions are ones in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains ( e.g ., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). In certain embodiments, amino acid sequences provided herein may be modified such that they have about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to the reference sequence. Also included within the present disclosure are sequences that are about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% homologous with (or have about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity with) the specific sequences provided herein.

In certain embodiments, the peptides provided herein are non-natural peptides. Non natural peptides include peptides that have, for example and depending on the length of the peptide and the context, no more than 99%, no more than 98%, no more than 97%, no more than 96%, no more than 95%, no more than 94%, no more than 93%, no more than 92%, no more than 91%, no more than 90%, no more than 89%, no more than 88%, no more than 87%, no more than 86%, no more than 85%, no more than 84%, no more than 83%, no more than 82%, no more than 81%, no more than 80%, no more than 79%, no more than 78%, no more than 77%, no more than 76%, no more than 75%, no more than 74%, no more than 73%, no more than 72%, no more than 71%, no more than 70%, no more than 69%, no more than 68%, no more than 67%, no more than 66%, no more than 65%, no more than 64%, no more than 63%, no more than 62%, no more than 61%, or no more than 60% sequence identity to a naturally occurring peptide. With respect to non-natural proteins, directed evolution approaches or generation of de novo peptides have been reported to provide novel and/or distinct functionality compared to the natural protein. For example, mutating a small number of amino acids ( e.g .,

94% or more homology to the natural peptide) has been reported to result in a peptide with distinct functionality relative to the natural peptide (see, e.g., Adriano-Silva el al., Nature 565(186-191) (2019)).

In certain embodiments, the present disclosure provides therapeutic peptides that are contained in extracellular vesicles (EVs). Thus, in certain embodiments, the present disclosure provides EVs comprising any one or more of the therapeutic peptides provided herein. EVs are membranous micro- or nano-sized biological particles that are released by cells and are capable of moving through the inter-cellular space and contacting neighbor cells. In the composition and methods of the present disclosure, in certain embodiments, the therapeutic peptides provided herein are expressed in an immune cell, then packaged into an EV and released from the cell. In certain embodiments, the EVs comprising one or more of the therapeutic peptides provided herein are taken up by neighboring cells such as tumor cells or other immune cells. Once taken up by a neighboring cell, the therapeutic peptide may exert its therapeutic effect, e.g., as an immune stimulating molecule, a modulator of a pro-death or apoptotic pathway, a modulator of DNA repair mechanisms, an antigen presented in the context of MHC, or other effect.

C. Exemplary targets and pathways

The present disclosure advantageously provides compositions and methods for cell-based delivery of therapeutics to target cells, including durable or long-term delivery by cells that express a therapeutic peptide at the desired target tissue. Such methods and compositions vastly improve presently available therapies for disease and disorders that may be or have been treated by delivery of molecules that require repeated administrations. Thus, the present disclosure provides compositions and methods for effectively treating diseases and disorders while avoiding long-term repeated administrations of therapeutics that are often necessary for treatment of certain diseases and disorders.

In certain embodiments, the disease or disorder is a cancer or another cell-proliferation disorder. In such embodiments, the engineered cells provided herein advantageously enhance the immune response and/or elicit a pro-apoptotic program and cell death in cancer cells or other cells associated with the cell-proliferation disorder. In other embodiments, the disease or disorder is an immune-mediated disease such as an autoimmune disease (e.g., an inflammatory bowel disease). In such embodiments, the engineered cells provided herein may be further modified to reduce effector cell function. For example, where an enhanced immune response is undesirable, the engineered cells provided herein may be modified to reduce or eliminate production of one or more inflammatory cytokines, Granzyme B expression, perforin expression, antibody secretion, and/or capacity for proliferation.

One potential immune therapy for cancers and for other cell-proliferation disorders is related to the immune system response to certain danger signals associated with pathogenic infections and/or cellular or tissue damage. The innate immune system has no antigen specificity but does respond to a variety of effector mechanisms, such as the damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs). The receptors that recognize PAMPs are referred to as pattern recognition receptors (PRRs) and include Toll-like receptors (TLRs), nucleotide-binding domain leucine-rich repeat containing proteins (NLRs; also referred to as NOD-like receptors), C-type lectin receptors (CLRs), and RNA helicases of the retinoic acid-inducible gene-1 (RIG-l)-like receptors (RLRs). In certain embodiments, the present disclosure combines such immune stimulatory pathways with CAR-expressing cell therapy to provide an enhanced, targeted therapeutic strategy for treating diseases and disorders such as cancers. In certain embodiments, this is achieved via small molecule and therapeutic peptide mimetics that stimulate danger signal pathways.

Examples of PAMPs and DAMPs include free cytosolic DNA and RNA, e.g., double stranded DNA (dsDNA). Cyclic dinucleotides are second messengers used in signal transduction in a wide variety of bacteria, and are agonists of the innate immune response in mammalian cells. Exemplary cyclic dinucleotides include cyclic guanosine monophosphate (cGMP), cyclic adenosine monophosphate (cAMP), cyclic di-GMP, cyclic-di-AMP, and cyclic AMP-GMP (cAMP-GMP, also known as cGAMP). The main sensor for cytosolic DNA is cGAS (cyclic GMPAMP synthase). Upon recognition of cytosolic DNA, cGAS catalyzes the generation of cGAMP, which strongly binds to the ER-transmembrane adaptor protein Stimulator of Interferon Genes (STING). When STING is bound by cGAMP, it undergoes a conformational change, translocates to a perinuclear compartment and induces the activation of critical transcription factors IRF-3 and NF-KB. This leads to a strong induction of type I interferons and production of pro-inflammatory cytokines such as IL-6, TNF-a and IFN-g. These molecules strongly potentiate T cell activation, for example by enhancing the ability of dendritic cells and macrophages to uptake, process, present and cross-present antigens to T-cells, and by engaging their cognate receptors to trigger the activation of interferon-responsive genes. Thus, stimulation of STING via cGAMP binding, as well as other DAMP and PAMP -triggered pathways, significantly contribute to adaptive immune cell activation.

TLRs are potent inducers of innate immunity and are capable of detecting PAMPs on the cell surface, or in the lumen of intracellular vesicles such as endosomes or lysosomes. Activation of TLRs occurs after ligand (agonist) binding and leads to the recruitment of the adaptor molecules MyD88 and TRIF and subsequent activation of a kinase-driven signaling pathway, resulting in activation of IRF3/7 NF-KB and the inflammatory response as described above. TLR ligands include double-stranded RNA (dsRNA), which indicates the presence of a virus and activates TLR3; DNA containing unmethylated CpG motifs, which are found in viral and bacterial DNA and which activate TLR9; single stranded RNA (ssRNA) and small interfering RNA (siRNA) molecules, which are also virally derived and activate TLR7 and TLR8; flagellin, which is derived from mobile bacteria and which activates TLR5; and lipopolysaccharide (LPS) and monophosphoryl lipid A (MPL) of Gram-negative bacteria, which each activate TLR4.

NLRs are PRRs found in cytosol and are activated by bacterial products such as peptidoglycan fragments and peptides derived from flagellin, the type III secretion system rod components, toxins (e.g., Bacillus anthracis lethal toxin (LT); nigericin ( Streptomyces hygroscopicus ), aerolysin ( Aeromonas hydrophila ), maitotoxin {Marina dinoflagellates ), gramicidin {Bacillus brevis) and a-toxin {Staphylococcus aureus)), and viral double-stranded DNA (dsDNA). NODI and NOD2 are two well characterized NLRs that recognize distinct structural motifs from peptidoglycan. NALP3 and NALPl recognize bacterially derived components such as toxins. IPAF and NAIP5 recognize flagellin. NLR activation leads to formation of an “inflammasome” which involves caspase-1 and which ultimately leads to production of IL-Ib.

RLRs (e.g., RIG-I) typically recognize cytosolic viral dsRNA and then recruit the adaptor IFN-b promoter stimulator 1 (IPS-1; also called MAVS, VISA, and Cardif), leading to phosphorylation of the transcription factors IRF-3 and IRF7 and expression of Type I IFN genes. Absent in melanoma 2 (AIM2) is an interferon-inducible protein that can bind dsDNA in the cytosol and induce autocleavage of caspase-1 and thereby inflammasome activation. C-type lectin receptors (CLRs) such as Dectin-1 bind fungal cell wall components (e.g., b-Glucan) and trigger activation of NF-KB.

In certain embodiments, the present disclosure provides small molecules and/or therapeutic peptides capable of activating an immune response, e.g., an innate immune response pathway including, but not limited to, those described herein. The small molecules and/or therapeutic peptides may be mimetics of molecules that stimulate an innate immune response pathway, such as PRR mimetics, cyclic dinucletoide mimetics, and short chain fatty acid mimetics. In certain embodiments, the present disclosure provides synthetic, non-natural small molecules and synthetic, non-natural therapeutic peptides that are mimetics of any one or more of a bacterial second messenger, TLR agonist, NLR agonist, RLR agonist, CLR agonist, or short chain fatty acid. For example, the provided small molecules and/or therapeutic peptide may be a mimetic of cGAMP, cAMP, cGMP, CpG, LPS, flagellin, a bacterial toxin, peptidoglycan, or butyric acid.

Thus, such compounds have potential use in the treatment of human cancers. Given the potency of STING and other PRR-related pathways in stimulating the immune response, these molecules are associated with highly desirable strategies to target for enhancing existing therapies such as CAR-T cell therapies. However, since the STING binding partner cGAMP is a cyclic dinucleotide, it cannot be encoded on an RNA. Similarly, many other PRRs and related molecules either cannot be encoded on an RNA, and/or their binding partners can be more potently activated using synthetically designed peptide binders. The present disclosure provides novel methods involving peptide mimetics that can be expressed in and/or in conjunction with a CAR expressing cell, and used to stimulate the STING pathway or other immune activation pathways to enhance a CAR therapy.

In certain embodiments, the therapeutic peptide is a PARP inhibitor. Poly (ADP-ribose) polymerase (PARP) is a nuclear and cytoplasmic enzyme involved in cellular processes including DNA repair, genomic stability, and programmed cell death. An important function of PARP is to detect DNA strand breaks and initiate a repair response in the cell. In response to DNA breakage, PARP-1 or PARP -2 binds to single and double DNA nicks. PARP inhibitors are useful as chemosensitizers and radiosensitizers for cancer treatment because radiation therapy and many chemotherapeutic approaches for cancer treatment work by inducing DNA damage. In addition to being involved in DNA repair, PARP may also act as a mediator of cell death. Since PARP functions by breaking down NAD+ into nicotiamide and ADP-ribose to form ADP-ribose polymers, PARP activation can result in substantial depletion of intracellular NAD+, which can result in cell death.

Some cancers are dependent on PARP activity for DNA repair and thus PARP inhibitors have been developed and used as cancer therapeutics. Exemplary PARP inhibitors include olaparib, rucaparib, niraparib, talazoparib, veliparib, and pamiparib. In embodiments, the present disclosure provides novel PARP inhibitors that are synthetically generated small molecules and/or therapeutic peptides. In certain embodiments, the PARP inhibitors provided herein can be used in conjunction with CAR-expressing cell therapy, e.g., in cancer therapy. In certain embodiments, the therapeutic peptide provided herein is a SMAC mimetic. Second mitochondria derived activator of caspase (SMAC) is a proapoptogenic mitochondrial protein that is released into the cytosol in response to certain stimuli of apoptotic response. Once in the cytosol, SMAC interacts with and antagonizes inhibitors of apoptosis proteins (IAPs) to allow apoptosis to proceed via release of caspases. Thus, SMAC sensitizes tumor cells to die by apoptosis. In some cancer cells that have high IAP activity, SMAC activity on its own is able to induce apoptosis. In some cancer cells, SMAC increases the apoptotic effects of cell death factors such as TNF-related apoptosis-inducing ligand (TRAIL). Without wishing to be bound by theory, the SMAC pathway is particularly amenable to combination with CAR-T cell therapies since activated CAR-T cells induce apoptosis of tumor cells in part via cell death triggers such as TRAIL. In certain embodiments, the present disclosure provides novel mimetics of SMAC. In certain embodiments, the SMAC mimetics can be used in conjunction with CAR-expressing cell therapy, e.g., in cancer therapy, to induce cancer cell death.

Short chain fatty acids (SCFAs) are another category of modulators of immunity. SCFAs are free fatty acids containing fewer than 6 carbons. They are produced by gut microbiota as bacterial fermentation products and include formic acid, acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, isovaleric acid, and 2-methylbutanoic acid. SCFAs can regulate immune differentiation and function by binding to metabolite-sensing G protein coupled receptors (e.g., GPR41, GPR43, and GPR109A), expressed on gut epithelial cells, adipocytes, myeloid cells, and/or other cells located in the gut. SCFAs also function through the HD AC inhibitor pathway. SCFAs have been reported to have anti-inflammatory activity in regulating intestinal inflammation, thus helping prevent chronic intestinal inflammatory responses, for example by impacting T cell differentiation and cytokine production indirectly through macrophages, DCs and other cells. SCFAs have been shown to promote production of cytokines such as IL-10 and/or IL-Ib and thus there has been interest in harnessing the effects of SCFAs in inflammatory bowel diseases (IBD). However, delivery of SCFAs, and repetitive dosing that may be required to initiate and/or maintain an effect, presents a challenge. In certain embodiments, the present disclosure provides methods for delivery of SCFA mimetics via a CAR expressing cell therapy. An important advantage of delivery of SCFA mimetics via a CAR expressing cell therapy provided herein is durable expression (e.g, by the CAR-expressing cell) of the SCFA mimetic in the gut microenvironment.

In certain embodiments, the present disclosure provides an engineered cell comprising a CAR construct comprising a CAR and a therapeutic peptide that is a SCFA mimetic. In certain embodiments, the present disclosure provides methods for treating a disorder of the gastrointestinal system comprising administering to a subject in need thereof an engineered cell provided herein comprising a CAR and a therapeutic peptide that is a SCFA mimetic. In certain embodiments, the present disclosure provides methods for treating an inflammatory disorder comprising administering to a subject in need thereof an engineered cell provided herein comprising a CAR and a therapeutic peptide that is a SCFA mimetic. For example, in certain embodiments, the inflammatory disorder is an inflammatory bowel disease (IBD), such as ulcerative colitis or Crohn’s disease. In such contexts, reducing the inflammation that may otherwise be induced by the engineered cell may be desired. Thus, in certain embodiments, the engineered cell has been further modified to knock out and/or reduce expression or activity of one or more effector functions. For example, in certain embodiments, the engineered cell has been modified to knock out or reduce expression of one or more gene required for inflammatory cytokine expression, Granzyme B expression, perforin expression, and/or other effector function associated with inflammation.

In certain embodiments, the therapeutic peptide of the present disclosure is a mimetic of a steroid, hormone, and/or hormone-like molecule. For example, in certain embodiments, the therapeutic peptide is a mimetic of a steroid or hormone that is used in a therapy for a disease or disorder. Exemplary diseases and disorders include growth defect disorders, thyroid disorders, infertility, and cancers such as breast and prostate cancers. Exemplary hormones or hormone-like molecules of which the therapeutic peptides provided herein may be human growth hormone, luteinizing hormone-releasing hormone (LHRH) antagonists, estrogen, estradiol, and progesterone. Exemplary steroids include betamethasone, hydrocortisone, methylprednisolone, prednisolone, and triamcinolone. In certain embodiments, reducing inflammation or avoiding excess inflammation in diseases and disorders amenable to treatment with a steroid, hormone, and/or hormone-like molecule are desired. In such embodiments, the engineered cell may be further modified to knock out and/or reduce expression or activity of one or more effector functions ( e.g ., modified to knock out or reduce expression of one or more gene required for inflammatory cytokine expression, Granzyme B expression, perforin expression, and/or other effector function associated with inflammation).

D. Chimeric Antigen Receptors

The present disclosure provides compositions and methods for engineered cells (e.g. immune cells or precursors thereof, e.g., T cells), comprising a chimeric antigen receptor (CAR) and a therapeutic peptide. Thus, in some embodiments, the immune cell has been genetically modified to express the CAR. CARs of the present disclosure comprise an antigen binding domain, a transmembrane domain, and an intracellular domain.

The antigen binding domain may be operably linked to another domain of the CAR, such as the transmembrane domain or the intracellular domain, both described elsewhere herein, for expression in the cell. In one embodiment, a first nucleic acid sequence encoding the antigen binding domain is operably linked to a second nucleic acid encoding a transmembrane domain, and further operably linked to a third a nucleic acid sequence encoding an intracellular domain.

The antigen binding domains described herein can be combined with any of the transmembrane domains described herein, any of the intracellular domains or cytoplasmic domains described herein, or any of the other domains described herein that may be included in a CAR of the present disclosure. A subject CAR of the present disclosure may also include a hinge domain as described herein. A subject CAR of the present disclosure may also include a spacer domain as described herein. In some embodiments, each of the antigen binding domain, transmembrane domain, and intracellular domain is separated by a linker.

The invention should be construed to include any CAR known in the art and/or disclosed herein. Exemplary CARs include, but are not limited to, those disclosed herein, those disclosed in US8916381B1, US9394368B2, US20140050708A1, US9598489B2, US9365641B2, US20210079059A1, US9783591B2, WO2016028896A1, US9446105B2, WO2016014576A1, US20210284752A1, WO2016014565A2, WO2016014535A1, and US9272002B2, and any other CAR generally disclosed in the art. Antigen Binding Domain

The antigen binding domain of a CAR is an extracellular region of the CAR for binding to a specific target antigen including proteins, carbohydrates, and glycolipids. In some embodiments, the CAR comprises affinity to a target antigen on a target cell. The target antigen may include any type of protein, or epitope thereof, associated with the target cell. For example, the CAR may comprise affinity to a target antigen on a target cell that indicates a particular disease state of the target cell.

In certain embodiments, the target cell antigen is a tumor associated antigen (TAA). Examples of tumor associated antigens (TAAs), include but are not limited to, differentiation antigens such as MART-l/MelanA (MART-I), gplOO (Pmel 17), tyrosinase, TRP-1, TRP-2 and tumor-specific multilineage antigens such as MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, pi 5; overexpressed embryonic antigens such as CEA; overexpressed oncogenes and mutated tumor-suppressor genes such as p53, Ras, HER-2/neu; unique tumor antigens resulting from chromosomal translocations; such as BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR; and viral antigens, such as the Epstein Barr virus antigens EB VA and the human papillomavirus (HPV) antigens E6 and E7. Other large, protein-based antigens include TSP-180, MAGE-4, MAGE-5, MAGE-6, RAGE, NY-ESO, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG- 72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, beta-Catenin, CDK4, Mum-1, p 15, p 16, 43- 9F, 5T4, 791Tgp72, alpha-fetoprotein, beta-HCG, BCA225, BTAA, CA 125, CA 15-3\CA 27.29\BCAA, CA 195, CA 242, CA-50, CAM43, CD68\P1, CO-029, FGF-5, G250, Ga733\EpCAM, HTgp-175, M344, MA-50, MG7-Ag, MOV18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90\Mac-2 binding protein\cyclophilin C-associated protein, TAAL6, TAG72, TLP, and TPS. In a preferred embodiment, the antigen binding domain of the CAR targets an antigen that includes but is not limited to CD19, CD20, CD22, ROR1, Mesothelin, CD33/IL3Ra, c-Met, PSMA, PSCA, Gly colipid F77, EGFRvIII, GD-2, MY-ESO-1 TCR, MAGE A3 TCR, and the like.

In certain embodiments, the target antigen is selected from the group consisting of CD 19, CD20, CD22, BCMA, CD123, CD133, EGFR, EGFRvIII, mesothelin, Her2, PSMA, CEA, GD2, IL-13Ra2, glypican-3, CIAX, LI-CAM, CA 125, CTAG1B, Mucin 1, and Folate receptor-alpha.

In certain embodiments, the target antigen is expressed on an intestinal cell. Depending on the desired antigen to be targeted, the CAR can be engineered to include the appropriate antigen binding domain that is specific to the desired antigen target. For example, if CD 19 is the desired antigen that is to be targeted, an antibody for CD 19 can be used as the antigen bind moiety for incorporation into the CAR.

In one embodiment, the target cell antigen is CD 19. As such, in one embodiment, a CAR of the present disclosure has affinity for CD19 on a target cell. This should not be construed as limiting in any way, as a CAR having affinity for any target antigen is suitable for use in a composition or method of the present disclosure.

As described herein, a CAR of the present disclosure having affinity for a specific target antigen on a target cell may comprise a target-specific binding domain. In some embodiments, the target-specific binding domain is a murine target-specific binding domain, e.g., the target- specific binding domain is of murine origin. In some embodiments, the target-specific binding domain is a human target-specific binding domain, e.g., the target-specific binding domain is of human origin. In one embodiment, a CAR of the present disclosure having affinity for CD 19 on a target cell may comprise a CD 19 binding domain.

In some embodiments, a CAR of the present disclosure may have affinity for one or more target antigens on one or more target cells. In some embodiments, a CAR may have affinity for one or more target antigens on a target cell. In such embodiments, the CAR is a bispecific CAR, or a multispecific CAR. In some embodiments, the CAR comprises one or more target-specific binding domains that confer affinity for one or more target antigens. In some embodiments, the CAR comprises one or more target-specific binding domains that confer affinity for the same target antigen. For example, a CAR comprising one or more target-specific binding domains having affinity for the same target antigen could bind distinct epitopes of the target antigen. When a plurality of target-specific binding domains is present in a CAR, the binding domains may be arranged in tandem and may be separated by linker peptides. For example, in a CAR comprising two target-specific binding domains, the binding domains are connected to each other covalently on a single polypeptide chain, through an oligo- or polypeptide linker, an Fc hinge region, or a membrane hinge region.

In some embodiments, the antigen binding domain is selected from the group consisting of an antibody, an antigen binding fragment (Fab), and a single-chain variable fragment (scFv). In some embodiments, a CD 19 binding domain of the present disclosure is selected from the group consisting of a CD19-specific antibody, a CD19-specific Fab, and a CD19-specific scFv. In one embodiment, a CD 19 binding domain is a CD 19-specific antibody. In one embodiment, a CD19 binding domain is a CD19-specific Fab. In one embodiment, a CD19 binding domain is a CD19-specific scFv.

The antigen binding domain can include any domain that binds to the antigen and may include, but is not limited to, a monoclonal antibody, a polyclonal antibody, a synthetic antibody, a human antibody, a humanized antibody, a non-human antibody, and any fragment thereof. In some embodiments, the antigen binding domain portion comprises a mammalian antibody or a fragment thereof. The choice of antigen binding domain may depend upon the type and number of antigens that are present on the surface of a target cell.

As used herein, the term “single-chain variable fragment” or “scFv” is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of an immunoglobulin (e.g., mouse or human) covalently linked to form a VH::VL heterodimer. The heavy (VH) and light chains (VL) are either joined directly or joined by a peptide-encoding linker, which connects the N- terminus of the VH with the C-terminus of the VL, or the C-terminus of the VH with the N- terminus of the VL. In some embodiments, the antigen binding domain (e.g., CD 19 binding domain) comprises an scFv having the configuration from N-terminus to C-terminus, VH - linker - VL. In some embodiments, the antigen binding domain comprises an scFv having the configuration from N-terminus to C-terminus, VL - linker - VH. Those of skill in the art would be able to select the appropriate configuration for use in the present disclosure.

The linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility. The linker can link the heavy chain variable region and the light chain variable region of the extracellular antigen-binding domain. Non-limiting examples of linkers are disclosed in Shen et ak, Anal. Chem. 80(6): 1910-1917 (2008) and WO 2014/087010, the contents of which are hereby incorporated by reference in their entireties. Various linker sequences are known in the art, including, without limitation, glycine serine (GS) linkers such as (GS)n, (GSGGS)n (SEQ ID NO: 17), (GGGS)n (SEQ ID NO: 18), and (GGGGS)n (SEQ ID NO: 19), where n represents an integer of at least 1. Exemplary linker sequences can comprise amino acid sequences including, without limitation, GGSG (SEQ ID NO:20), GGSGG (SEQ ID NO:21), GSGSG (SEQ ID NO:22), GSGGG (SEQ ID NO:23), GGGSG (SEQ ID NO:24), GSSSG (SEQ ID NO:25), GGGGS (SEQ ID NO:26), GGGGS GGGGS GGGGS (SEQ ID NO:27) and the like. Those of skill in the art would be able to select the appropriate linker sequence for use in the present disclosure. In one embodiment, an antigen binding domain of the present disclosure comprises a heavy chain variable region (VH) and a light chain variable region (VL), wherein the VH and VL is separated by the linker sequence having the amino acid sequence

GGGGSGGGGSGGGGS (SEQ ID NO:27), which may be encoded by the nucleic acid sequence GGTGGCGGTGGCTCGGGCGGTGGTGGGTCGGGTGGCGGCGGATCT (SEQ ID NO:28).

Despite removal of the constant regions and the introduction of a linker, scFv proteins retain the specificity of the original immunoglobulin. Single chain Fv polypeptide antibodies can be expressed from a nucleic acid comprising VH- and VL-encoding sequences as described by Huston, et al. (Proc. Nat. Acad. Sci. USA, 85:5879-5883, 1988). See, also, U.S. Patent Nos. 5,091,513, 5,132,405 and 4,956,778; and U.S. Patent Publication Nos. 20050196754 and 20050196754. Antagonistic scFvs having inhibitory activity have been described (see, e.g., Zhao et al., Hyrbidoma (Larchmt) 200827(6):455-51; Peter et al., J Cachexia Sarcopenia Muscle 2012 August 12; Shieh et al., J Imunol 2009 183(4):2277-85; Giomarelli et al., Thromb Haemost 2007 97(6):955-63; Fife eta., J Clin Invst 2006 116(8):2252-61; Brocks et al., Immunotechnology 1997 3(3): 173-84; Moosmayer et al., Ther Immunol 1995 2(10:31-40). Agonistic scFvs having stimulatory activity have been described (see, e.g., Peter et al., J Bioi Chem 2003 25278(38):36740-7; Xie et al., Nat Biotech 1997 15(8):768-71 ; Ledbetter et al., CritRev Immunol 1997 17(5-6):427-55; Ho et al., BioChim Biophys Acta 2003 1638(3):257-66).

As used herein, “Fab” refers to a fragment of an antibody structure that binds to an antigen but is monovalent and does not have a Fc portion, for example, an antibody digested by the enzyme papain yields two Fab fragments and an Fc fragment (e.g., a heavy (H) chain constant region; Fc region that does not bind to an antigen).

As used herein, “F(ab')2” refers to an antibody fragment generated by pepsin digestion of whole IgG antibodies, wherein this fragment has two antigen binding (ah') (bivalent) regions, wherein each (ah') region comprises two separate amino acid chains, a part of a H chain and a light (L) chain linked by an S — S bond for binding an antigen and where the remaining H chain portions are linked together. A “F(ab')2” fragment can be split into two individual Fab' fragments.

In some embodiments, the antigen binding domain may be derived from the same species in which the CAR will ultimately be used. For example, for use in humans, the antigen binding domain of the CAR may comprise a human antibody or a fragment thereof. In some embodiments, the antigen binding domain may be derived from a different species in which the CAR will ultimately be used. For example, for use in humans, the antigen binding domain of the CAR may comprise a murine antibody or a fragment thereof.

Exemplary antigen binding domains include, but are not limited to, those found in US8916381B1, US9394368B2, US20140050708A1, US9598489B2, US9365641B2, US20210079059A1, US9783591B2, WO2016028896A1, US9446105B2, WO2016014576A1, US20210284752A1, WO2016014565A2, WO2016014535A1, US9272002B2, and any antigen binding domain from any CAR generally disclosed in the art. Additional exemplary antigen binding domains are those having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 41, 42, or 43.

FMC63 (Anti-CD 19) scFv (SEQ ID NO: 41)

ALPVTALLLPLALLLHAARPDIQMTQTTSSLSASLGDRVTISCRASQDISKYLNWYQ QKP DGTVKLLIYHTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGG G TKLEITGGGGSGGGGSGGGGSEVKLQESGPGLVAPSQSLSVTCTVSGVSLPDYGVSWIR QPPRKGLEWLGVIWGSETTYYNSALKSRLTIIKDNSKSQVFLKMNSLQTDDTAIYYCAK HYYY GGS YAMD YW GQGT S VT V S S

M5 (Anti-Mesothelin) scFv (SEQ ID NO: 42)

ALPVTALLLPLALLLHAARPQVQLVQSGAEVEKPGASVKVSCKASGYTFTDYYMHWV RQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVY YC A S GWDFD YW GQGTL VT V S S GGGGS GGGGS GGGGS GGGGSDI VMT QSPSSLSASVG DRVTITCRASQSIRYYLSWYQQKPGKAPKLLIYTASILQNGVPSRFSGSGSGTDFTLTIS SL QPEDF AT YY CLQT YTTPDF GPGTKVEIK

4D5 (Anti-Her2) scFv (SEQ ID NO: 43)

DFQVQIFSFLLISASVIMSRGDIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWY QQK

PGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPP TFGQ GTK VEIKRT GS T S GS GKPGS GEGSE V QL VE S GGGL V QPGGSLRL S C A AS GFNIKDT YIHW VRQ APGKGLEW VARIYPTNGYTRY AD S VKGRFTIS ADT SKNT AYLQMN SLRAEDT AVY Y C SRW GGDGF YAMD VW GQGTL VT V S S

Transmembrane Domain

CARs of the present disclosure may comprise a transmembrane domain that connects the antigen binding domain of the CAR to the intracellular domain of the CAR. The transmembrane domain of a subject CAR is a region that is capable of spanning the plasma membrane of a cell (e.g., an immune cell or precursor thereof). In some embodiments, the transmembrane domain is for insertion into a cell membrane, e.g., a eukaryotic cell membrane. In some embodiments, the transmembrane domain is interposed between the antigen binding domain and the intracellular domain of a CAR.

In some embodiments, the transmembrane domain is naturally associated with one or more of the domains in the CAR. In some embodiments, the transmembrane domain can be selected or modified by one or more amino acid substitutions to avoid binding of such domains to the transmembrane domains of the same or different surface membrane proteins, to minimize interactions with other members of the receptor complex.

The transmembrane domain may be derived either from a natural or a synthetic source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein, e.g., a Type I transmembrane protein. Where the source is synthetic, the transmembrane domain may be any artificial sequence that facilitates insertion of the CAR into a cell membrane, e.g., an artificial hydrophobic sequence. Examples of the transmembrane domain of particular use in this disclosure include, without limitation, transmembrane domains derived from ( i.e . comprise at least the transmembrane region(s) of) the alpha, beta or zeta chain of the T cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD7, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134 (OX-40), CD137 (4-1BB), CD154 (CD40L), Toll-like receptor 1 (TLR1), TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, and TLR9. In some embodiments, the transmembrane domain may be synthetic, in which case it will comprise predominantly hydrophobic residues such as leucine and valine. Preferably a triplet of phenylalanine, tryptophan and valine will be found at each end of a synthetic transmembrane domain. In certain embodiments, the transmembrane domain is selected from the group consisting of CD8 alpha, CD3 zeta, CD3 epsilon, CD28, and ICOS.

The transmembrane domains described herein can be combined with any of the antigen binding domains described herein, any of the intracellular domains described herein, or any of the other domains described herein that may be included in a subject CAR.

In some embodiments, the transmembrane domain further comprises a hinge region. A subject CAR of the present disclosure may also include a hinge region. The hinge region of the CAR is a hydrophilic region which is located between the antigen binding domain and the transmembrane domain. In some embodiments, this domain facilitates proper protein folding for the CAR. The hinge region is an optional component for the CAR. The hinge region may include a domain selected from Fc fragments of antibodies, hinge regions of antibodies, CH2 regions of antibodies, CH3 regions of antibodies, artificial hinge sequences or combinations thereof. Examples of hinge regions include, without limitation, a CD8a hinge, artificial hinges made of polypeptides which may be as small as, three glycines (Gly), as well as CHI and CH3 domains of IgGs (such as human IgG4).

In some embodiments, a subject CAR of the present disclosure includes a hinge region that connects the antigen binding domain with the transmembrane domain, which, in turn, connects to the intracellular domain. The hinge region is preferably capable of supporting the antigen binding domain to recognize and bind to the target antigen on the target cells (see, e.g., Hudecek et al., Cancer Immunol. Res. (2015) 3(2): 125-135). In some embodiments, the hinge region is a flexible domain, thus allowing the antigen binding domain to have a structure to optimally recognize the specific structure and density of the target antigens on a cell such as tumor cell (Hudecek et al., supra). The flexibility of the hinge region permits the hinge region to adopt many different conformations.

In some embodiments, the hinge region is an immunoglobulin heavy chain hinge region. In some embodiments, the hinge region is a hinge region polypeptide derived from a receptor (e.g., a CD8-derived hinge region).

The hinge region can have a length of from about 4 amino acids to about 50 amino acids, e.g., from about 4 aa to about 10 aa, from about 10 aa to about 15 aa, from about 15 aa to about

20 aa, from about 20 aa to about 25 aa, from about 25 aa to about 30 aa, from about 30 aa to about 40 aa, or from about 40 aa to about 50 aa. In some embodiments, the hinge region can have a length of greater than 5 aa, greater than 10 aa, greater than 15 aa, greater than 20 aa, greater than 25 aa, greater than 30 aa, greater than 35 aa, greater than 40 aa, greater than 45 aa, greater than 50 aa, greater than 55 aa, or more.

Suitable hinge regions can be readily selected and can be of any of a number of suitable lengths, such as from 1 amino acid ( e.g ., Gly) to 20 amino acids, from 2 amino acids to 15 amino acids, from 3 amino acids to 12 amino acids, including 4 amino acids to 10 amino acids, 5 amino acids to 9 amino acids, 6 amino acids to 8 amino acids, or 7 amino acids to 8 amino acids, and can be 1, 2, 3, 4, 5, 6, or 7 amino acids. Suitable hinge regions can have a length of greater than 20 amino acids (e.g., 30, 40, 50, 60 or more amino acids).

For example, hinge regions include glycine polymers (G)n, glycine-serine polymers (including, for example, (GS)n, (GSGGS)n (SEQ ID NO: 17) and (GGGS)n (SEQ ID NO: 18), where n is an integer of at least one), glycine-alanine polymers, alanine-serine polymers, and other flexible linkers known in the art. Glycine and glycine-serine polymers can be used; both Gly and Ser are relatively unstructured, and therefore can serve as a neutral tether between components. Glycine polymers can be used; glycine accesses significantly more phi-psi space than even alanine, and is much less restricted than residues with longer side chains (see, e.g., Scheraga, Rev. Computational. Chem. (1992) 2: 73-142). Exemplary hinge regions can comprise amino acid sequences including, but not limited to, GGSG (SEQ ID NO:20), GGSGG (SEQ ID NO:21), GSGSG (SEQ ID NO:22), GSGGG (SEQ ID NO:23), GGGSG (SEQ ID NO:24), GSSSG (SEQ ID NO:25), and the like.

In some embodiments, the hinge region is an immunoglobulin heavy chain hinge region. Immunoglobulin hinge region amino acid sequences are known in the art; see, e.g., Tan et ah, Proc. Natl. Acad. Sci. USA (1990) 87(1): 162-166; and Huck et ah, Nucleic Acids Res. (1986) 14(4): 1779-1789. As non-limiting examples, an immunoglobulin hinge region can include one of the following amino acid sequences: DKTHT (SEQ ID NO:29); CPPC (SEQ ID NO:30); CPEPKSCDTPPPCPR (SEQ ID NO:31) (see, e.g, Glaser et ah, J. Biol. Chem. (2005) 280:41494-41503); ELKTPLGDTTHT (SEQ ID NO:32); KSCDKTHTCP (SEQ ID NO:33); KCCVDCP (SEQ ID NO:34); KYGPPCP (SEQ ID NO:35); EPKSCDKTHTCPPCP (SEQ ID

NO: 36) (human IgGl hinge); ERKCCVECPPCP (SEQ ID NO: 37) (human IgG2 hinge); ELKTPLGDTTHTCPRCP (SEQ ID NO: 38) (human IgG3 hinge); SPNMVPHAHHAQ (SEQ ID NO: 39) (human IgG4 hinge); and the like.

The hinge region can comprise an amino acid sequence of a human IgGl, IgG2, IgG3, or IgG4, hinge region. In one embodiment, the hinge region can include one or more amino acid substitutions and/or insertions and/or deletions compared to a wild-type (naturally-occurring) hinge region. For example, His229 of human IgGl hinge can be substituted with Tyr, so that the hinge region comprises the sequence EPKSCDKTYTCPPCP (SEQ ID NO:40); see, e.g., Yan et al., J. Biol. Chem. (2012) 287: 5891-5897. In one embodiment, the hinge region can comprise an amino acid sequence derived from human CD8, or a variant thereof.

Intracellular Signaling Domain

A subject CAR of the present disclosure also includes an intracellular signaling domain. The terms “intracellular signaling domain” and “intracellular domain” are used interchangeably herein. The intracellular signaling domain of the CAR is responsible for activation of at least one of the effector functions of the cell in which the CAR is expressed (e.g., immune cell). The intracellular signaling domain transduces the effector function signal and directs the cell (e.g., immune cell) to perform its specialized function, e.g., harming and/or destroying a target cell.

Examples of an intracellular domain for use in the disclosure include, but are not limited to, the cytoplasmic portion of a surface receptor, co-stimulatory molecule, and any molecule that acts in concert to initiate signal transduction in the T cell, as well as any derivative or variant of these elements and any synthetic sequence that has the same functional capability.

Examples of the intracellular signaling domain include, without limitation, the z chain of the T cell receptor complex or any of its homologs, e.g., h chain, FcsRFy and b chains, MB 1 (Iga) chain, B29 (Ig) chain, etc., human CD3 zeta chain, CD3 polypeptides (D, d and e), syk family tyrosine kinases (Syk, ZAP 70, etc.), src family tyrosine kinases (Lck, Fyn, Lyn, etc.), and other molecules involved in T cell transduction, such as CD2, CD5 and CD28. In one embodiment, the intracellular signaling domain may be human CD3 zeta chain, FcyRIII, FcsRI, cytoplasmic tails of Fc receptors, an immunoreceptor tyrosine-based activation motif (IT AM) bearing cytoplasmic receptors, and combinations thereof. In one embodiment, the intracellular signaling domain of the CAR includes any portion of one or more co-stimulatory molecules, such as at least one signaling domain from CD2, CD3, CD8, CD27, CD28, ICOS, 4-1BB, PD-1, any derivative or variant thereof, any synthetic sequence thereof that has the same functional capability, and any combination thereof.

Other examples of the intracellular domain include a fragment or domain from one or more molecules or receptors including, but not limited to, TCR, CD3 zeta, CD3 gamma, CD3 delta, CD3 epsilon, CD86, common FcR gamma, FcR beta (Fc Epsilon Rib), CD79a, CD79b, Fcgamma Rlla, DAP10, DAP12, T cell receptor (TCR), CD8, CD27, CD28, 4-1BB (CD137), OX9, 0X40, CD30, CD40, PD-1, ICOS, a KIR family protein, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRFl), CD127, CD 160, CD 19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD l id, ITGAE, CD 103, ITGAL, CD 11 a, LFA-1, IT GAM, CDlib, ITGAX, CD 11c, ITGB1, CD29, ITGB2, CD 18, LFA- 1, ITGB7, TNFR2, TRAN CE/R ANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRT AM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Lyl08), SLAM (SLAMFl, CD 150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, NKG2D, Toll-like receptor 1 (TLR1), TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, other co-stimulatory molecules described herein, any derivative, variant, or fragment thereof, any synthetic sequence of a co- stimulatory molecule that has the same functional capability, and any combination thereof.

Additional examples of intracellular domains include, without limitation, intracellular signaling domains of several types of various other immune signaling receptors, including, but not limited to, first, second, and third generation T cell signaling proteins including CD3, B7 family costimulatory, and Tumor Necrosis Factor Receptor (TNFR) superfamily receptors (see, e.g., Park and Brentjens, J. Clin. Oncol. (2015) 33(6): 651-653). Additionally, intracellular signaling domains may include signaling domains used by NK and NKT cells (see, e.g., Hermanson and Kaufman, Front. Immunol. (2015) 6: 195) such as signaling domains of NKp30

(B7-H6) (see, e.g., Zhang et ak, J. Immunol. (2012) 189(5): 2290-2299), and DAP 12 (see, e.g., Topfer et al., J. Immunol. (2015) 194(7): 3201-3212), NKG2D, NKp44, NKp46, DAP10, and CD3z.

In certain embodiments, the intracellular signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD3 zeta, TCR zeta, CD3 epsilon, CD3 gamma, CD3 delta, or ICOS. In certain embodiments, the intracellular signaling domain comprises a functional signaling domain and further comprises a costimulatory domain, wherein the costimulatory domain comprises a functional signaling domain from 4- IBB or CD28.

Intracellular signaling domains suitable for use in a subject CAR of the present disclosure include any desired signaling domain that provides a distinct and detectable signal ( e.g ., increased production of one or more cytokines by the cell; change in transcription of a target gene; change in activity of a protein; change in cell behavior, e.g., cell death; cellular proliferation; cellular differentiation; cell survival; modulation of cellular signaling responses; etc.) in response to activation of the CAR ( i.e ., activated by antigen and dimerizing agent). In some embodiments, the intracellular signaling domain includes at least one (e.g., one, two, three, four, five, six, etc.) IT AM motifs as described below. In some embodiments, the intracellular signaling domain includes DAP10/CD28 type signaling chains. In some embodiments, the intracellular signaling domain is not covalently attached to the membrane bound CAR, but is instead diffused in the cytoplasm.

Intracellular signaling domains suitable for use in a subject CAR of the present disclosure include immunoreceptor tyrosine-based activation motif (ITAM)-containing intracellular signaling polypeptides. In some embodiments, an IT AM motif is repeated twice in an intracellular signaling domain, where the first and second instances of the ITAM motif are separated from one another by 6 to 8 amino acids. In one embodiment, the intracellular signaling domain of a subject CAR comprises 3 ITAM motifs.

In some embodiments, intracellular signaling domains includes the signaling domains of human immunoglobulin receptors that contain immunoreceptor tyrosine based activation motifs (IT AMs) such as, but not limited to, FcgammaRI, FcgammaRIIA, FcgammaRIIC, FcgammaRIIIA, FcRL5 (see, e.g., Gillis et al., Front. Immunol. (2014) 5:254). A suitable intracellular signaling domain can be an IT AM motif-containing portion that is derived from a polypeptide that contains an ITAM motif. For example, a suitable intracellular signaling domain can be an ITAM motif-containing domain from any ITAM motif-containing protein. Thus, a suitable intracellular signaling domain need not contain the entire sequence of the entire protein from which it is derived. Examples of suitable ITAM motif-containing polypeptides include, but are not limited to: DAP12, FCER1G (Fc epsilon receptor I gamma chain), CD3D (CD3 delta), CD3E (CD3 epsilon), CD3G (CD3 gamma), CD3Z (CD3 zeta), and CD79A (antigen receptor complex-associated protein alpha chain).

In one embodiment, the intracellular signaling domain is derived from DAP12 (also known as TYROBP; TYRO protein tyrosine kinase binding protein; KARAP; PLOSL; DNAX- activation protein 12; KAR-associated protein; TYRO protein tyrosine kinase-binding protein; killer activating receptor associated protein; killer-activating receptor-associated protein; etc.).

In one embodiment, the intracellular signaling domain is derived from FCER1G (also known as FCRG; Fc epsilon receptor I gamma chain; Fc receptor gamma-chain; fc-epsilon Rl-gamma; fcRgamma; fceRl gamma; high affinity immunoglobulin epsilon receptor subunit gamma; immunoglobulin E receptor, high affinity, gamma chain; etc.). In one embodiment, the intracellular signaling domain is derived from T-cell surface glycoprotein CD3 delta chain (also known as CD3D; CD3-DELTA; T3D; CD3 antigen, delta subunit; CD3 delta; CD3d antigen, delta polypeptide (TiT3 complex); OKT3, delta chain; T-cell receptor T3 delta chain; T-cell surface glycoprotein CD3 delta chain; etc.). In one embodiment, the intracellular signaling domain is derived from T-cell surface glycoprotein CD3 epsilon chain (also known as CD3e, T- cell surface antigen T3/Leu-4 epsilon chain, T-cell surface glycoprotein CD3 epsilon chain, AI504783, CD3, CD3epsilon, T3e, etc.). In one embodiment, the intracellular signaling domain is derived from T-cell surface glycoprotein CD3 gamma chain (also known as CD3G, T-cell receptor T3 gamma chain, CD3-GAMMA, T3G, gamma polypeptide (TiT3 complex), etc.). In one embodiment, the intracellular signaling domain is derived from T-cell surface glycoprotein CD3 zeta chain (also known as CD3Z, T-cell receptor T3 zeta chain, CD247, CD3-ZETA,

CD3H, CD3Q, T3Z, TCRZ, etc.). In one embodiment, the intracellular signaling domain is derived from CD79A (also known as B-cell antigen receptor complex-associated protein alpha chain; CD79a antigen (immunoglobulin-associated alpha); MB-1 membrane glycoprotein; ig- alpha; membrane-bound immunoglobulin-associated protein; surface IgM-associated protein; etc.). In one embodiment, an intracellular signaling domain suitable for use in an FN3 CAR of the present disclosure includes a DAP10/CD28 type signaling chain. In one embodiment, an intracellular signaling domain suitable for use in an FN3 CAR of the present disclosure includes a ZAP70 polypeptide. In some embodiments, the intracellular signaling domain includes a cytoplasmic signaling domain of TCR zeta, FcR gamma, FcRbeta, CD3 gamma, CD3 delta,

CD3 epsilon, CD5, CD22, CD79a, CD79b, or CD66d. In one embodiment, the intracellular signaling domain in the CAR includes a cytoplasmic signaling domain of human CD3 zeta.

While usually the entire intracellular signaling domain can be employed, in many cases it is not necessary to use the entire chain. To the extent that a truncated portion of the intracellular signaling domain is used, such truncated portion may be used in place of the intact chain as long as it transduces the effector function signal. The intracellular signaling domain includes any truncated portion of the intracellular signaling domain sufficient to transduce the effector function signal.

The intracellular signaling domains described herein can be combined with any of the antigen binding domains described herein, any of the transmembrane domains described herein, or any of the other domains described herein that may be included in the CAR.

E. Engineered Cells

The present disclosure provides engineered cells ( e.g modified immune cells or precursors thereof; e.g., T cells) comprising a chimeric antigen receptor (CAR) and a therapeutic peptide. In certain embodiments, the therapeutic peptide is a non-natural therapeutic peptide. In certain embodiments, the CAR molecule and the therapeutic peptide are expressed from the same expression construct. Also provided are cells comprising any of the nucleic acid molecules contemplated herein or any of the expression vectors contemplated herein.

In certain embodiments, the cell comprises a therapeutic peptide that has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

In certain embodiments, the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP. In certain embodiments, the therapeutic peptide is a mimetic of a TLR agonist. In certain embodiments, the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL). In certain embodiments, the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic. In certain embodiments, the therapeutic peptide is an inhibitor of poly ADP ribose polymerase (PARP). In certain embodiments, the therapeutic peptide is a mimetic of a SCFA that binds to a G protein-coupled receptor (GPCR). In certain embodiments, the therapeutic peptide is a SCFA mimetic or is a mimetic of a steroid and/or hormone-like molecule, and wherein the engineered cell has been further modified to reduce activity of one or more effector functions.

In certain embodiments, the non-natural peptide is a peptide that has no more than 90% sequence identity to a naturally occurring peptide. In certain embodiments, the non-natural peptide is a peptide that has no more than 80% sequence identity to a naturally occurring peptide. In certain embodiments, the peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-16.

In certain embodiments, the therapeutic peptide is exported from the engineered cell in extracellular vesicles. In certain embodiments, the target cell is a tumor cell. In certain embodiments, the engineered cell is a T cell or an NK cell.

In certain embodiments, the engineered cell has been modified to reduce or prevent expression of one or more inflammatory cytokines, expression of Granzyme B, or expression of perforin.

In certain embodiments, the CAR molecule and the therapeutic peptide are expressed from the same expression construct and wherein the expression construct further comprises an RNA molecule that activates a PRR. In certain embodiments, the RNA molecule is 7SL.

Thus, provided are cells, compositions and methods that enhance immune cells, such as T cells, function in adoptive cell therapy, including those offering improved efficacy, such as by increasing activity and potency of administered genetically engineered cells, while maintaining persistence or exposure to the transferred cells over time. In some embodiments, the genetically engineered cells, exhibit increased expansion and/or persistence when administered in vivo to a subject, as compared to certain available methods. In some embodiments, the provided cells exhibit increased persistence when administered in vivo to a subject. In some embodiments, the persistence of engineered cells, in the subject upon administration is greater as compared to that which would be achieved by alternative methods, such as those involving administration of cells engineered by methods in which T cells do not comprise a CAR and therapeutic peptide. In some embodiments, the persistence is increased at least or about at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold or more.

In some embodiments, the degree or extent of persistence of administered cells can be detected or quantified after administration to a subject. For example, in some aspects, quantitative PCR (qPCR) is used to assess the quantity of cells expressing the CAR and therapeutic peptide in the blood or serum or organ or tissue ( e.g ., disease site) of the subject. In some aspects, persistence is quantified as copies of DNA or plasmid encoding the exogenous receptor per microgram of DNA, or as the number of receptor-expressing cells per microliter of the sample, e.g., of blood or serum, or per total number of peripheral blood mononuclear cells (PBMCs) or white blood cells or T cells per microliter of the sample. In some embodiments, flow cytometric assays detecting cells expressing the receptor generally using antibodies specific for the receptors also can be performed. Cell-based assays may also be used to detect the number or percentage of functional cells, such as cells capable of binding to and/or neutralizing and/or inducing responses, e.g., cytotoxic responses, against cells of the disease or condition or expressing the antigen recognized by the receptor. In any of such embodiments, the extent or level of expression of another marker associated with the CAR can be used to distinguish the administered cells from endogenous cells in a subject.

F. Sources of Cells

In certain embodiments, a source of cells (e.g. immune cells; e.g. T cells) is obtained from a subject for ex vivo manipulation. Sources of target cells for ex vivo manipulation may also include, e.g., autologous or heterologous donor blood, cord blood, or bone marrow. For example the source of immune cells may be from the subject to be treated with the modified immune cells of the disclosure, e.g., the subject's blood, the subject's cord blood, or the subject's bone marrow. Non-limiting examples of subjects include humans, dogs, cats, mice, rats, and transgenic species thereof. Preferably, the subject is a human.

Immune cells can be obtained from a number of sources, including blood, peripheral blood mononuclear cells, bone marrow, lymph node tissue, spleen tissue, umbilical cord, lymph, or lymphoid organs. Immune cells are cells of the immune system, such as cells of the innate or adaptive immunity, e.g., myeloid or lymphoid cells, including lymphocytes, typically T cells and/or NK cells. Other exemplary cells include stem cells, such as multipotent and pluripotent stem cells, including induced pluripotent stem cells (iPSCs). In some aspects, the cells are human cells. With reference to the subject to be treated, the cells may be allogeneic and/or autologous. The cells typically are primary cells, such as those isolated directly from a subject and/or isolated from a subject and frozen.

In certain embodiments, the cell is a T cell, e.g., a CD8+ T cell (e.g., a CD8+ naive T cell, central memory T cell, or effector memory T cell), a CD4+ T cell, a natural killer T cell (NKT cells), a regulatory T cell (Treg), a stem cell memory T cell, a lymphoid progenitor cell a hematopoietic stem cell, a natural killer cell (NK cell) or a dendritic cell. In some embodiments, the cells are monocytes or granulocytes, e.g., myeloid cells, macrophages, neutrophils, dendritic cells, mast cells, eosinophils, and/or basophils. In an embodiment, the target cell is an induced pluripotent stem (iPS) cell or a cell derived from an iPS cell, e.g., an iPS cell generated from a subject, manipulated to alter (e.g., induce a mutation in) or manipulate the expression of one or more target genes, and differentiated into, e.g., a T cell, e.g., a CD8+ T cell (e.g., a CD8+ naive T cell, central memory T cell, or effector memory T cell), a CD4+ T cell, a stem cell memory T cell, a lymphoid progenitor cell or a hematopoietic stem cell.

In some embodiments, the cells include one or more subsets of T cells or other cell types, such as whole T cell populations, CD4+ cells, CD8+ cells, and subpopulations thereof, such as those defined by function, activation state, maturity, potential for differentiation, expansion, recirculation, localization, and/or persistence capacities, antigen- specificity, type of antigen receptor, presence in a particular organ or compartment, marker or cytokine secretion profile, and/or degree of differentiation. Among the sub-types and subpopulations of T cells and/or of CD4+ and/or of CD8+ T cells are naive T (TN) cells, effector T cells (TEFF), memory T cells and sub-types thereof, such as stem cell memory T (TSCM), central memory T (TCM), effector memory T (TEM), or terminally differentiated effector memory T cells, tumor-infiltrating lymphocytes (TIL), immature T cells, mature T cells, helper T cells, cytotoxic T cells, mucosa- associated invariant T (MAIT) cells, naturally occurring and adaptive regulatory T (Treg) cells, helper T cells, such as TH1 cells, TH2 cells, TH3 cells, TH17 cells, TH9 cells, TH22 cells, follicular helper T cells, alpha/beta T cells, and delta/gamma T cells. In certain embodiments, any number of T cell lines available in the art, may be used.

In some embodiments, the methods include isolating immune cells from the subject, preparing, processing, culturing, and/or engineering them. In some embodiments, preparation of the engineered cells includes one or more culture and/or preparation steps. The cells for engineering as described may be isolated from a sample, such as a biological sample, e.g., one obtained from or derived from a subject. In some embodiments, the subject from which the cell is isolated is one having the disease or condition or in need of a cell therapy or to which cell therapy will be administered. The subject in some embodiments is a human in need of a particular therapeutic intervention, such as the adoptive cell therapy for which cells are being isolated, processed, and/or engineered. Accordingly, the cells in some embodiments are primary cells, e.g., primary human cells. The samples include tissue, fluid, and other samples taken directly from the subject, as well as samples resulting from one or more processing steps, such as separation, centrifugation, genetic engineering (e.g. transduction with viral vector), washing, and/or incubation. The biological sample can be a sample obtained directly from a biological source or a sample that is processed. Biological samples include, but are not limited to, body fluids, such as blood, plasma, serum, cerebrospinal fluid, synovial fluid, urine and sweat, tissue and organ samples, including processed samples derived therefrom.

In some aspects, the sample from which the cells are derived or isolated is blood or a blood-derived sample, or is or is derived from an apheresis or leukapheresis product. Exemplary samples include whole blood, peripheral blood mononuclear cells (PBMCs), leukocytes, bone marrow, thymus, tissue biopsy, tumor, leukemia, lymphoma, lymph node, gut associated lymphoid tissue, mucosa associated lymphoid tissue, spleen, other lymphoid tissues, liver, lung, stomach, intestine, colon, kidney, pancreas, breast, bone, prostate, cervix, testes, ovaries, tonsil, or other organ, and/or cells derived therefrom. Samples include, in the context of cell therapy, e.g., adoptive cell therapy, samples from autologous and allogeneic sources.

In some embodiments, the cells are derived from cell lines, e.g., T cell lines. The cells in some embodiments are obtained from a xenogeneic source, for example, from mouse, rat, non human primate, and pig. In some embodiments, isolation of the cells includes one or more preparation and/or non-affinity based cell separation steps. In some examples, cells are washed, centrifuged, and/or incubated in the presence of one or more reagents, for example, to remove unwanted components, enrich for desired components, lyse or remove cells sensitive to particular reagents. In some examples, cells are separated based on one or more property, such as density, adherent properties, size, sensitivity and/or resistance to particular components.

In some examples, cells from the circulating blood of a subject are obtained, e.g., by apheresis or leukapheresis. The samples, in some aspects, contain lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and/or platelets, and in some aspects contains cells other than red blood cells and platelets. In some embodiments, the blood cells collected from the subject are washed, e.g., to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps. In some embodiments, the cells are washed with phosphate buffered saline (PBS). In some aspects, a washing step is accomplished by tangential flow filtration (TFF) according to the manufacturer's instructions. In some embodiments, the cells are resuspended in a variety of biocompatible buffers after washing. In certain embodiments, components of a blood cell sample are removed and the cells directly resuspended in culture media. In some embodiments, the methods include density-based cell separation methods, such as the preparation of white blood cells from peripheral blood by lysing the red blood cells and centrifugation through a Percoll or Ficoll gradient.

In one embodiment, immune are obtained cells from the circulating blood of an individual are obtained by apheresis or leukapheresis. The apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets. The cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media, such as phosphate buffered saline (PBS) or wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations, for subsequent processing steps. After washing, the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca-free, Mg-free PBS. Alternatively, the undesirable components of the apheresis sample may be removed and the cells directly resuspended in culture media.

In some embodiments, the isolation methods include the separation of different cell types based on the expression or presence in the cell of one or more specific molecules, such as surface markers, e.g., surface proteins, intracellular markers, or nucleic acid. In some embodiments, any known method for separation based on such markers may be used. In some embodiments, the separation is affinity- or immunoaffmity-based separation. For example, the isolation in some aspects includes separation of cells and cell populations based on the cells' expression or expression level of one or more markers, typically cell surface markers, for example, by incubation with an antibody or binding partner that specifically binds to such markers, followed generally by washing steps and separation of cells having bound the antibody or binding partner, from those cells having not bound to the antibody or binding partner.

Such separation steps can be based on positive selection, in which the cells having bound the reagents are retained for further use, and/or negative selection, in which the cells having not bound to the antibody or binding partner are retained. In some examples, both fractions are retained for further use. In some aspects, negative selection can be particularly useful where no antibody is available that specifically identifies a cell type in a heterogeneous population, such that separation is best carried out based on markers expressed by cells other than the desired population. The separation need not result in 100% enrichment or removal of a particular cell population or cells expressing a particular marker. For example, positive selection of or enrichment for cells of a particular type, such as those expressing a marker, refers to increasing the number or percentage of such cells, but need not result in a complete absence of cells not expressing the marker. Likewise, negative selection, removal, or depletion of cells of a particular type, such as those expressing a marker, refers to decreasing the number or percentage of such cells, but need not result in a complete removal of all such cells.

In some examples, multiple rounds of separation steps are carried out, where the positively or negatively selected fraction from one step is subjected to another separation step, such as a subsequent positive or negative selection. In some examples, a single separation step can deplete cells expressing multiple markers simultaneously, such as by incubating cells with a plurality of antibodies or binding partners, each specific for a marker targeted for negative selection. Likewise, multiple cell types can simultaneously be positively selected by incubating cells with a plurality of antibodies or binding partners expressed on the various cell types.

In some embodiments, one or more of the T cell populations is enriched for or depleted of cells that are positive for (marker+) or express high levels (marker ¹¹¹⁸¹¹ ) of one or more particular markers, such as surface markers, or that are negative for (marker -) or express relatively low levels (marker ^low ) of one or more markers. For example, in some aspects, specific subpopulations of T cells, such as cells positive or expressing high levels of one or more surface markers, e.g., CD28+, CD62L+, CCR7+, CD27+, CD127+, CD4+, CD8+, CD45RA+, and/or CD45RO+ T cells, are isolated by positive or negative selection techniques. In some cases, such markers are those that are absent or expressed at relatively low levels on certain populations of T cells (such as non-memory cells) but are present or expressed at relatively higher levels on certain other populations of T cells (such as memory cells). In one embodiment, the cells (such as the CD8+ cells or the T cells, e.g., CD3+ cells) are enriched for (i.e., positively selected for) cells that are positive or expressing high surface levels of CD45RO, CCR7, CD28, CD27, CD44, CD 127, and/or CD62L and/or depleted of (e.g., negatively selected for) cells that are positive for or express high surface levels of CD45RA. In some embodiments, cells are enriched for or depleted of cells positive or expressing high surface levels of CD 122, CD95, CD25, CD27, and/or IL7-Ra (CD 127). In some examples, CD8+ T cells are enriched for cells positive for CD45RO (or negative for CD45RA) and for CD62L. For example, CD3+, CD28+ T cells can be positively selected using CD3/CD28 conjugated magnetic beads (e.g., DYNABEADS® M-450 CD3/CD28 T Cell Expander).

In some embodiments, T cells are separated from a PBMC sample by negative selection of markers expressed on non-T cells, such as B cells, monocytes, or other white blood cells, such as CD 14. In some aspects, a CD4+ or CD8+ selection step is used to separate CD4+ helper and CD8+ cytotoxic T cells. Such CD4+ and CD8+ populations can be further sorted into sub populations by positive or negative selection for markers expressed or expressed to a relatively higher degree on one or more naive, memory, and/or effector T cell subpopulations. In some embodiments, CD8+ cells are further enriched for or depleted of naive, central memory, effector memory, and/or central memory stem cells, such as by positive or negative selection based on surface antigens associated with the respective subpopulation. In some embodiments, enrichment for central memory T (TCM) cells is carried out to increase efficacy, such as to improve long term survival, expansion, and/or engraftment following administration, which in some aspects is particularly robust in such sub-populations. In some embodiments, combining TCM-enriched CD8+ T cells and CD4+ T cells further enhances efficacy.

In some embodiments, memory T cells are present in both CD62L+ and CD62L- subsets of CD8+ peripheral blood lymphocytes. PBMC can be enriched for or depleted of CD62L-CD8+ and/or CD62L+CD8+ fractions, such as using anti-CD8 and anti-CD62L antibodies. In some embodiments, a CD4+ T cell population and a CD8+ T cell sub-population, e.g., a sub population enriched for central memory (TCM) cells. In some embodiments, the enrichment for central memory T (TCM) cells is based on positive or high surface expression of CD45RO, CD62L, CCR7, CD28, CD3, and/or CD 127; in some aspects, it is based on negative selection for cells expressing or highly expressing CD45RA and/or granzyme B. In some aspects, isolation of a CD8+ population enriched for TCM cells is carried out by depletion of cells expressing CD4, CD 14, CD45RA, and positive selection or enrichment for cells expressing CD62L. In one aspect, enrichment for central memory T (TCM) cells is carried out starting with a negative fraction of cells selected based on CD4 expression, which is subjected to a negative selection based on expression of CD 14 and CD45RA, and a positive selection based on CD62L. Such selections in some aspects are carried out simultaneously and in other aspects are carried out sequentially, in either order. In some aspects, the same CD4 expression-based selection step used in preparing the CD8+ cell population or subpopulation, also is used to generate the CD4+ cell population or sub-population, such that both the positive and negative fractions from the CD4- based separation are retained and used in subsequent steps of the methods, optionally following one or more further positive or negative selection steps.

CD4+ T helper cells are sorted into naive, central memory, and effector cells by identifying cell populations that have cell surface antigens. CD4+ lymphocytes can be obtained by standard methods. In some embodiments, naive CD4+ T lymphocytes are CD45RO-, CD45RA+, CD62L+, CD4+ T cells. In some embodiments, central memory CD4+ cells are

CD62L+ and CD45RO+. In some embodiments, effector CD4+ cells are CD62L- and CD45RO. In one example, to enrich for CD4+ cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD 14, CD20, CD1 lb, CD 16, HLA-DR, and CD8. In some embodiments, the antibody or binding partner is bound to a solid support or matrix, such as a magnetic bead or paramagnetic bead, to allow for separation of cells for positive and/or negative selection.

In some embodiments, the cells are incubated and/or cultured prior to or in connection with genetic engineering. The incubation steps can include culture, cultivation, stimulation, activation, and/or propagation. In some embodiments, the compositions or cells are incubated in the presence of stimulating conditions or a stimulatory agent. Such conditions include those designed to induce proliferation, expansion, activation, and/or survival of cells in the population, to mimic antigen exposure, and/or to prime the cells for genetic engineering, such as for the introduction of a recombinant antigen receptor. The conditions can include one or more of particular media, temperature, oxygen content, carbon dioxide content, time, agents, e.g., nutrients, amino acids, antibiotics, ions, and/or stimulatory factors, such as cytokines, chemokines, antigens, binding partners, fusion proteins, recombinant soluble receptors, and any other agents designed to activate the cells. In some embodiments, the stimulating conditions or agents include one or more agent, e.g., ligand, which is capable of activating an intracellular signaling domain of a TCR complex. In some aspects, the agent turns on or initiates TCR/CD3 intracellular signaling cascade in a T cell. Such agents can include antibodies, such as those specific for a TCR component and/or costimulatory receptor, e.g., anti-CD3, anti-CD28, for example, bound to solid support such as a bead, and/or one or more cytokines. Optionally, the expansion method may further comprise the step of adding anti-CD3 and/or anti CD28 antibody to the culture medium (e.g., at a concentration of at least about 0.5 ng/ml). In some embodiments, the stimulating agents include IL-2 and/or IL-15, for example, an IL-2 concentration of at least about 10 units/mL.

In another embodiment, T cells are isolated from peripheral blood by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLL™ gradient. Alternatively, T cells can be isolated from an umbilical cord. In any event, a specific subpopulation of T cells can be further isolated by positive or negative selection techniques. The cord blood mononuclear cells so isolated can be depleted of cells expressing certain antigens, including, but not limited to, CD34, CD8, CD14, CD19, and CD56. Depletion of these cells can be accomplished using an isolated antibody, a biological sample comprising an antibody, such as ascites, an antibody bound to a physical support, and a cell bound antibody.

Enrichment of a T cell population by negative selection can be accomplished using a combination of antibodies directed to surface markers unique to the negatively selected cells. A preferred method is cell sorting and/or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected. For example, to enrich for CD4 ⁺ cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CDllb, CD16, HLA-DR, and CD8.

For isolation of a desired population of cells by positive or negative selection, the concentration of cells and surface ( e.g ., particles such as beads) can be varied. In certain embodiments, it may be desirable to significantly decrease the volume in which beads and cells are mixed together (z.e., increase the concentration of cells), to ensure maximum contact of cells and beads. For example, in one embodiment, a concentration of 2 billion cells/ml is used. In one embodiment, a concentration of 1 billion cells/ml is used. In a further embodiment, greater than 100 million cells/ml is used. In a further embodiment, a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/ml is used. In yet another embodiment, a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/ml is used. In further embodiments, concentrations of 125 or 150 million cells/ml can be used. Using high concentrations can result in increased cell yield, cell activation, and cell expansion.

T cells can also be frozen after the washing step, which does not require the monocyte- removal step. While not wishing to be bound by theory, the freeze and subsequent thaw step provides a more uniform product by removing granulocytes and to some extent monocytes in the cell population. After the washing step that removes plasma and platelets, the cells may be suspended in a freezing solution. While many freezing solutions and parameters are known in the art and will be useful in this context, in a non-limiting example, one method involves using PBS containing 20% DMSO and 8% human serum albumin, or other suitable cell freezing media.

The cells are then frozen to -80°C at a rate of 1°C per minute and stored in the vapor phase of a liquid nitrogen storage tank. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at -20°C or in liquid nitrogen.

In one embodiment, the population of T cells is comprised within cells such as peripheral blood mononuclear cells, cord blood cells, a purified population of T cells, and a T cell line. In another embodiment, peripheral blood mononuclear cells comprise the population of T cells. In yet another embodiment, purified T cells comprise the population of T cells.

In certain embodiments, T regulatory cells (Tregs) can be isolated from a sample. The sample can include, but is not limited to, umbilical cord blood or peripheral blood. In certain embodiments, the Tregs are isolated by flow-cytometry sorting. The sample can be enriched for Tregs prior to isolation by any means known in the art. The isolated Tregs can be cryopreserved, and/or expanded prior to use. Methods for isolating Tregs are described in U.S. Patent Numbers: 7,754,482, 8,722,400, and 9,555,105, and U.S. Patent Application No. 13/639,927, contents of which are incorporated herein in their entirety.

G. Nucleic Acids and Expression Vectors

The present disclosure provides a nucleic acid encoding a chimeric antigen receptor (CAR) and a therapeutic peptide. Any of the CARs, disclosed in detail elsewhere herein, are contemplated. In certain embodiments, the therapeutic peptide is a non-natural peptide. Any of the therapueutic pepdites, disclosed in detail elsewhere herein, are contemplated.

In certain embodiments, a stop codon separates the nucleic acid segment encoding the CAR from the nucleic acid segment encoding the therapeutic peptide.

In certain embodiments, a linker may be used to allow for multiple proteins to be encoded by the same nucleic acid sequence ( e.g ., a multi cistronic or bicistronic sequence), which are translated as a polyprotein that is dissociated into separate protein components. In some embodiments, the linker comprises a nucleic acid sequence that encodes for an internal ribosome entry site (IRES). As used herein, “an internal ribosome entry site” or “IRES” refers to an element that promotes direct internal ribosome entry to the initiation codon, such as ATG, of a protein coding region, thereby leading to cap-independent translation of the gene. Various internal ribosome entry sites are known to those of skill in the art, including, without limitation,

IRES obtainable from viral or cellular mRNA sources, e.g., immunogloublin heavy-chain binding protein (BiP); vascular endothelial growth factor (VEGF); fibroblast growth factor 2; insulin-like growth factor; translational initiation factor eIF4G; yeast transcription factors TFIID and HAP4; and IRES obtainable from, e.g., cardiovirus, rhinovirus, aphthovirus, HCV, Friend murine leukemia virus (FrMLV), and Moloney murine leukemia virus (MoMLV). Those of skill in the art would be able to select the appropriate IRES for use in the present disclosure.

In some embodiments, the linker comprises a nucleic acid sequence that encodes for a self-cleaving peptide. As used herein, a “self-cleaving peptide” or “2A peptide” refers to an oligopeptide that allow multiple proteins to be encoded as polyproteins, which dissociate into component proteins upon translation. Use of the term “self-cleaving” is not intended to imply a proteolytic cleavage reaction. Various self-cleaving or 2A peptides are known to those of skill in the art, including, without limitation, those found in members of the Picornaviridae virus family, e.g., foot-and-mouth disease virus (FMDV), equine rhinitis A virus (ERAVO, Thosea asigna virus (TaV), and porcine tescho virus-1 (PTV-1); and carioviruses such as Theilovirus and encephalomyocarditis viruses. 2A peptides derived from FMDV, ER V, PTV-1, and TaV are referred to herein as “F2A,” “E2A,” “P2A,” and “T2A,” respectively. Those of skill in the art would be able to select the appropriate self-cleaving peptide for use in the present disclosure.

In some embodiments, a linker further comprises a nucleic acid sequence that encodes a furin cleavage site. Furin is a ubiquitously expressed protease that resides in the trans-golgi and processes protein precursors before their secretion. Furin cleaves at the COOH- terminus of its consensus recognition sequence. Those of skill in the art would be able to select the appropriate Furin cleavage site for use in the present disclosure.

In some embodiments, the linker comprises a nucleic acid sequence encoding a combination of a Furin cleavage site and a 2A peptide. Examples include, without limitation, a linker comprising a nucleic acid sequence encoding Furin and F2A, a linker comprising a nucleic acid sequence encoding Furin and E2A, a linker comprising a nucleic acid sequence encoding Furin and P2A, a linker comprising a nucleic acid sequence encoding Furin and T2A. Those of skill in the art would be able to select the appropriate combination for use in the present disclosure. In such embodiments, the linker may further comprise a spacer sequence between the Furin and 2A peptide. Various spacer sequences are known in the art, including, without limitation, glycine serine (GS) spacers such as (GS)n, (GSGGS)n (SEQ ID NO: 17) and (GGGS)n (SEQ ID NO: 18), where n represents an integer of at least 1. Exemplary spacer sequences can comprise amino acid sequences including, without limitation, GGSG (SEQ ID NO:20), GGSGG (SEQ ID NO:21), GSGSG (SEQ ID NO:22), GSGGG (SEQ ID NO:23), GGGSG (SEQ ID NO:24), GSSSG (SEQ ID NO:25), and the like. Those of skill in the art would be able to select the appropriate spacer sequence for use in the present disclosure.

In some embodiments, a nucleic acid of the present disclosure may be operably linked to a transcriptional control element, e.g., a promoter, and enhancer, etc. Suitable promoter and enhancer elements are known to those of skill in the art.

In certain embodiments, the nucleic acid encoding a CAR is in operable linkage with a promoter. In certain embodiments, the promoter is a phosphogly cerate kinase- 1 (PGK) promoter.

For expression in a bacterial cell, suitable promoters include, but are not limited to, lacl, lacZ, T3, T7, gpt, lambda P and trc. For expression in a eukaryotic cell, suitable promoters include, but are not limited to, light and/or heavy chain immunoglobulin gene promoter and enhancer elements; cytomegalovirus immediate early promoter; herpes simplex virus thymidine kinase promoter; early and late SV40 promoters; promoter present in long terminal repeats from a retrovirus; mouse metallothionein-I promoter; and various art-known tissue specific promoters. Suitable reversible promoters, including reversible inducible promoters are known in the art.

Such reversible promoters may be isolated and derived from many organisms, e.g., eukaryotes and prokaryotes. Modification of reversible promoters derived from a first organism for use in a second organism, e.g., a first prokaryote and a second a eukaryote, a first eukaryote and a second a prokaryote, etc., is well known in the art. Such reversible promoters, and systems based on such reversible promoters but also comprising additional control proteins, include, but are not limited to, alcohol regulated promoters (e.g., alcohol dehydrogenase I (alcA) gene promoter, promoters responsive to alcohol transactivator proteins (AlcR), etc.), tetracycline regulated promoters, (e.g., promoter systems including Tet Activators, TetON, TetOFF, etc.), steroid regulated promoters (e.g., rat glucocorticoid receptor promoter systems, human estrogen receptor promoter systems, retinoid promoter systems, thyroid promoter systems, ecdysone promoter systems, mifepristone promoter systems, etc.), metal regulated promoters (e.g., metallothionein promoter systems, etc.), pathogenesis-related regulated promoters (e.g., salicylic acid regulated promoters, ethylene regulated promoters, benzothiadiazole regulated promoters, etc.), temperature regulated promoters ( e.g ., heat shock inducible promoters (e.g., HSP-70, HSP-90, soybean heat shock promoter, etc.), light regulated promoters, synthetic inducible promoters, and the like.

In some embodiments, the promoter is a CD8 cell-specific promoter, a CD4 cell-specific promoter, a neutrophil-specific promoter, or an NK-specific promoter. For example, a CD4 gene promoter can be used; see, e.g., Salmon et al. Proc. Natl. Acad. Sci. USA (1993) 90:7739; and Marodon et al. (2003) Blood 101:3416. As another example, a CD8 gene promoter can be used. NK cell-specific expression can be achieved by use of an Ncrl (p46) promoter; see, e.g., Eckelhart et al. Blood (2011) 117:1565.

For expression in a yeast cell, a suitable promoter is a constitutive promoter such as an ADH1 promoter, a PGK1 promoter, an ENO promoter, a PYK1 promoter and the like; or a regulatable promoter such as a GALl promoter, a GAL 10 promoter, an ADH2 promoter, a PHOS promoter, a CUP1 promoter, a GALT promoter, a MET25 promoter, a MET3 promoter, a CYC1 promoter, a HIS3 promoter, an ADH1 promoter, a PGK promoter, a GAPDH promoter, an ADC1 promoter, a TRP1 promoter, a URA3 promoter, a LEU2 promoter, an ENO promoter, a TP1 promoter, and AOX1 (e.g., for use in Pichia). Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. Suitable promoters for use in prokaryotic host cells include, but are not limited to, a bacteriophage T7 RNA polymerase promoter; a trp promoter; a lac operon promoter; a hybrid promoter, e.g., a lac/tac hybrid promoter, a tac/trc hybrid promoter, a trp/lac promoter, a T7/lac promoter; a trc promoter; a tac promoter, and the like; an araBAD promoter; in vivo regulated promoters, such as an ssaG promoter or a related promoter (see, e.g., U.S. Patent Publication No. 20040131637), a pagC promoter (Pulkkinen and Miller, J. Bacteriol. (1991) 173(1): 86-93; Alpuche- Aranda et al., Proc. Natl. Acad. Sci. USA (1992) 89(21): 10079-83), a nirB promoter (Harborne et al. Mol. Micro. (1992) 6:2805-2813), and the like (see, e.g., Dunstan et al., Infect. Immun. (1999) 67:5133-5141; McKelvie et al., Vaccine (2004) 22:3243-3255; and Chatfield et al., Biotechnol. (1992) 10:888- 892); a sigma70 promoter, e.g., a consensus sigma70 promoter (see, e.g., GenBank Accession Nos. AX798980, AX798961, and AX798183); a stationary phase promoter, e.g., a dps promoter, an spv promoter, and the like; a promoter derived from the pathogenicity island SPI-2 (see, e.g., W096/17951); an actA promoter (see, e.g., Shetron-Rama et al., Infect. Immun. (2002) 70:1087- 1096); an rpsM promoter (see, e.g., Valdivia and Falkow Mol. Microbiol. (1996). 22:367); a tet promoter (see, e.g., Hillen, W. and Wissmann, A. (1989) In Saenger, W. and Heinemann, U. (eds), Topics in Molecular and Structural Biology, Protein— Nucleic Acid Interaction. Macmillan, London, UK, Vol. 10, pp. 143-162); an SP6 promoter (see, e.g., Melton et al., Nucl. Acids Res. (1984) 12:7035); and the like. Suitable strong promoters for use in prokaryotes such as Escherichia coli include, but are not limited to Trc, Tac, T5, T7, and PLambda. Non-limiting examples of operators for use in bacterial host cells include a lactose promoter operator (Lacl repressor protein changes conformation when contacted with lactose, thereby preventing the Lad repressor protein from binding to the operator), a tryptophan promoter operator (when complexed with tryptophan, TrpR repressor protein has a conformation that binds the operator; in the absence of tryptophan, the TrpR repressor protein has a conformation that does not bind to the operator), and a tac promoter operator (see, e.g., deBoer et al., Proc. Natl. Acad. Sci. U.S.A. (1983) 80:21-25).

Other examples of suitable promoters include the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto. Other constitutive promoter sequences may also be used, including, but not limited to a simian virus 40 (SV40) early promoter, a mouse mammary tumor virus (MMTV) or human immunodeficiency virus (HIV) long terminal repeat (LTR) promoter, a MoMuLV promoter, an avian leukemia virus promoter, an Epstein-Barr virus immediate early promoter, a Rous sarcoma virus promoter, the EF-1 alpha promoter, as well as human gene promoters such as, but not limited to, an actin promoter, a myosin promoter, a hemoglobin promoter, and a creatine kinase promoter. Further, the disclosure should not be limited to the use of constitutive promoters. Inducible promoters are also contemplated as part of the disclosure. The use of an inducible promoter provides a molecular switch capable of turning on expression of the polynucleotide sequence which it is operatively linked when such expression is desired, or turning off the expression when expression is not desired. Examples of inducible promoters include, but are not limited to a metallothionine promoter, a glucocorticoid promoter, a progesterone promoter, and a tetracycline promoter. In some embodiments, the locus or construct or transgene containing the suitable promoter is irreversibly switched through the induction of an inducible system. Suitable systems for induction of an irreversible switch are well known in the art, e.g., induction of an irreversible switch may make use of a Cre-lox-mediated recombination (see, e.g., Fuhrmann-Benzakein, et ah, Proc. Natl. Acad. Sci. USA (2000) 28:e99, the disclosure of which is incorporated herein by reference). Any suitable combination of recombinase, endonuclease, ligase, recombination sites, etc. known to the art may be used in generating an irreversibly switchable promoter. Methods, mechanisms, and requirements for performing site-specific recombination, described elsewhere herein, find use in generating irreversibly switched promoters and are well known in the art, see, e.g., Grindley et al. Annual Review of Biochemistry (2006) 567-605; and Tropp, Molecular Biology (2012) (Jones & Bartlett Publishers, Sudbury, Mass.), the disclosures of which are incorporated herein by reference.

In some embodiments, a nucleic acid of the present disclosure further comprises a nucleic acid sequence encoding a CAR inducible expression cassette. In one embodiment, the CAR inducible expression cassette is for the production of a transgenic polypeptide product that is released upon CAR signaling. See, e.g., Chmielewski and Abken, Expert Opin. Biol. Ther. (2015) 15(8): 1145-1154; and Abken, Immunotherapy (2015) 7(5): 535-544. In some embodiments, a nucleic acid of the present disclosure further comprises a nucleic acid sequence encoding a cytokine operably linked to a T-cell activation responsive promoter. In some embodiments, the cytokine operably linked to a T-cell activation responsive promoter is present on a separate nucleic acid sequence. In one embodiment, the cytokine is IL-12.

A nucleic acid of the present disclosure may be present within an expression vector and/or a cloning vector. An expression vector can include a selectable marker, an origin of replication, and other features that provide for replication and/or maintenance of the vector. Suitable expression vectors include, e.g., plasmids, viral vectors, and the like. Large numbers of suitable vectors and promoters are known to those of skill in the art; many are commercially available for generating a subject recombinant construct. The following vectors are provided by way of example, and should not be construed in anyway as limiting: Bacterial: pBs, phagescript, PsiX174, pBluescript SK, pBs KS, pNH8a, pNH16a, pNH18a, pNH46a (Stratagene, La Jolla,

Calif., USA); pTrc99A, pKK223-3, pKK233-3, pDR540, and pRIT5 (Pharmacia, Uppsala, Sweden). Eukaryotic: pWLneo, pSV2cat, pOG44, PXR1, pSG (Stratagene) pSVK3, pBPV, pMSG and pSVL (Pharmacia).

Expression vectors generally have convenient restriction sites located near the promoter sequence to provide for the insertion of nucleic acid sequences encoding heterologous proteins.

A selectable marker operative in the expression host may be present. Suitable expression vectors include, but are not limited to, viral vectors (e.g. viral vectors based on vaccinia virus; poliovirus; adenovirus (see, e.g., Li et ah, Invest. Opthalmol. Vis. Sci. (1994) 35: 2543-2549; Borras et ah, Gene Ther. (1999) 6: 515-524; Li and Davidson, Proc. Natl. Acad. Sci. USA (1995) 92: 7700-7704; Sakamoto et ah, H. Gene Ther. (1999) 5: 1088-1097; WO 94/12649, WO 93/03769; WO 93/19191; WO 94/28938; WO 95/11984 and WO 95/00655); adeno-associated virus (see, e.g., Ali et al., Hum. Gene Ther. (1998) 9: 81-86, Flannery et ah, Proc. Natl. Acad.

Sci. USA (1997) 94: 6916-6921; Bennett et al., Invest. Opthalmol. Vis. Sci. (1997) 38: 2857- 2863; Jomary et al., Gene Ther. (1997) 4:683 690, Rolling et al., Hum. Gene Ther. (1999) 10: 641-648; Ali et al., Hum. Mol. Genet. (1996) 5: 591-594; Srivastava in WO 93/09239, Samulski et al., J. Vir. (1989) 63: 3822-3828; Mendelson et al., Virol. (1988) 166: 154-165; and Flotte et al., Proc. Natl. Acad. Sci. USA (1993) 90: 10613-10617); SV40; herpes simplex virus; human immunodeficiency virus (see, e.g., Miyoshi et al., Proc. Natl. Acad. Sci. USA (1997) 94: 10319- 23; Takahashi et al., J. Virol. (1999) 73: 7812-7816); a retroviral vector (e.g., Murine Leukemia Virus, spleen necrosis virus, and vectors derived from retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, human immunodeficiency virus, myeloproliferative sarcoma virus, and mammary tumor virus); and the like.

Additional expression vectors suitable for use are, e.g., without limitation, a lentivirus vector, a gamma retrovirus vector, a foamy virus vector, an adeno-associated virus vector, an adenovirus vector, a pox virus vector, a herpes virus vector, an engineered hybrid virus vector, a transposon mediated vector, and the like. Viral vector technology is well known in the art and is described, for example, in Sambrook et al., 2012, Molecular Cloning: A Laboratory Manual, volumes 1-4, Cold Spring Harbor Press, NY), and in other virology and molecular biology manuals. Viruses, which are useful as vectors include, but are not limited to, retroviruses, adenoviruses, adeno- associated viruses, herpes viruses, and lentiviruses. In general, a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers, (e.g., WO 01/96584; WO 01/29058; and U.S. Pat. No. 6,326,193).

In some embodiments, an expression vector (e.g., a lentiviral vector) may be used to introduce the CAR into an immune cell or precursor thereof (e.g., a T cell). Accordingly, an expression vector (e.g., a lentiviral vector) of the present disclosure may comprise a nucleic acid encoding for a CAR and therapeutic peptide. In some embodiments, the expression vector (e.g., lentiviral vector) will comprise additional elements that will aid in the functional expression of the CAR encoded therein. In some embodiments, an expression vector comprising a nucleic acid encoding for a CAR further comprises a mammalian promoter. In one embodiment, the vector further comprises an elongation-factor- 1 -alpha promoter (EF-la promoter). Use of an EF-la promoter may increase the efficiency in expression of downstream transgenes (e.g., a CAR and therapeutic peptide encoding nucleic acid sequence). Physiologic promoters (e.g., an EF-la promoter) may be less likely to induce integration mediated genotoxicity, and may abrogate the ability of the retroviral vector to transform stem cells. Other physiological promoters suitable for use in a vector (e.g., lentiviral vector) are known to those of skill in the art and may be incorporated into a vector of the present disclosure. In some embodiments, the vector (e.g., lentiviral vector) further comprises a non-requisite cis acting sequence that may improve titers and gene expression. One non-limiting example of a non-requisite cis acting sequence is the central polypurine tract and central termination sequence (cPPT/CTS) which is important for efficient reverse transcription and nuclear import. Other non-requisite cis acting sequences are known to those of skill in the art and may be incorporated into a vector (e.g., lentiviral vector) of the present disclosure. In some embodiments, the vector further comprises a posttranscriptional regulatory element. Posttranscriptional regulatory elements may improve RNA translation, improve transgene expression and stabilize RNA transcripts. One example of a posttranscriptional regulatory element is the woodchuck hepatitis virus posttranscriptional regulatory element (WPRE). Accordingly, in some embodiments a vector for the present disclosure further comprises a WPRE sequence. Various posttranscriptional regulator elements are known to those of skill in the art and may be incorporated into a vector (e.g., lentiviral vector) of the present disclosure. A vector of the present disclosure may further comprise additional elements such as a rev response element (RRE) for RNA transport, packaging sequences, and 5’ and 3’ long terminal repeats (LTRs). The term “long terminal repeat” or “LTR” refers to domains of base pairs located at the ends of retroviral DNAs which comprise U3, R and U5 regions. LTRs generally provide functions required for the expression of retroviral genes (e.g., promotion, initiation and polyadenylation of gene transcripts) and to viral replication. In one embodiment, a vector (e.g., lentiviral vector) of the present disclosure includes a 3’ U3 deleted LTR. Accordingly, a vector (e.g., lentiviral vector) of the present disclosure may comprise any combination of the elements described herein to enhance the efficiency of functional expression of transgenes. For example, a vector (e.g., lentiviral vector) of the present disclosure may comprise a WPRE sequence, cPPT sequence, RRE sequence, 5’LTR, 3’ U3 deleted LTR’ in addition to a nucleic acid encoding for a CAR and therapeutic peptide.

Vectors of the present disclosure may be self-inactivating vectors. As used herein, the term “self-inactivating vector” refers to vectors in which the 3’ LTR enhancer promoter region (U3 region) has been modified (e.g., by deletion or substitution). A self-inactivating vector may prevent viral transcription beyond the first round of viral replication. Consequently, a self inactivating vector may be capable of infecting and then integrating into a host genome (e.g., a mammalian genome) only once, and cannot be passed further. Accordingly, self-inactivating vectors may greatly reduce the risk of creating a replication-competent virus.

In some embodiments, a nucleic acid of the present disclosure may be RNA, e.g., in vitro synthesized RNA. Methods for in vitro synthesis of RNA are known to those of skill in the art; any known method can be used to synthesize RNA comprising a sequence encoding a CAR and therapeutic peptide of the present disclosure. Methods for introducing RNA into a host cell are known in the art. See, e.g., Zhao et al. Cancer Res. (2010) 15: 9053. Introducing RNA comprising a nucleotide sequence encoding a CAR and therapeutic peptide of the present disclosure into a host cell can be carried out in vitro, ex vivo or in vivo. For example, a host cell (e.g., an NK cell, a cytotoxic T lymphocyte, etc.) can be electroporated in vitro or ex vivo with RNA comprising a nucleotide sequence encoding a CAR and therapeutic peptide of the present disclosure. In order to assess the expression of a polypeptide or portions thereof, the expression vector to be introduced into a cell may also contain either a selectable marker gene or a reporter gene, or both, to facilitate identification and selection of expressing cells from the population of cells sought to be transfected or infected through viral vectors. In some embodiments, the selectable marker may be carried on a separate piece of DNA and used in a co-transfection procedure. Both selectable markers and reporter genes may be flanked with appropriate regulatory sequences to enable expression in the host cells. Useful selectable markers include, without limitation, antibiotic-resistance genes.

Reporter genes are used for identifying potentially transfected cells and for evaluating the functionality of regulatory sequences. In general, a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assessed at a suitable time after the DNA has been introduced into the recipient cells. Suitable reporter genes may include, without limitation, genes encoding luciferase, beta- galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et ah, 2000 FEBS Letters 479: 79-82).

H. Methods of Treatment

The engineered cells (e.g., T cells comprising a CAR and therapeutic peptide) described herein may be included in a composition for immunotherapy. The composition may include a pharmaceutical composition and further include a pharmaceutically acceptable carrier. A therapeutically effective amount of the pharmaceutical composition comprising the engineered T cells may be administered.

In one aspect, the disclosure provides a method for adoptive cell transfer therapy comprising administering to a subject in need thereof an engineered T cell of the present disclosure. In another aspect, the disclosure provides a method of treating a disease or condition in a subject comprising administering to a subject in need thereof a population of engineered T cells.

Methods for administration of immune cells for adoptive cell therapy are known in the art and may be used in connection with the provided methods and compositions. For example, adoptive T cell therapy methods are described, e.g., in US Patent Application Publication No. 2003/0170238 to Gruenberg et al; US Patent No. 4,690,915 to Rosenberg; Rosenberg (2011) Nat Rev Clin Oncol. 8(10):577-85). See, e.g., Themeli et al. (2013) Nat Biotechnol. 31(10): 928-933; Tsukahara et al. (2013) Biochem Biophys Res Commun 438(1): 84-9; Davila et al. (2013) PLoS ONE 8(4): e61338. In some embodiments, the cell therapy, e.g., adoptive T cell therapy is carried out by autologous transfer, in which the cells are isolated and/or otherwise prepared from the subject who is to receive the cell therapy, or from a sample derived from such a subject.

Thus, in some aspects, the cells are derived from a subject, e.g., patient, in need of a treatment and the cells, following isolation and processing are administered to the same subject.

In some embodiments, the cell therapy, e.g., adoptive T cell therapy, is carried out by allogeneic transfer, in which the cells are isolated and/or otherwise prepared from a subject other than a subject who is to receive or who ultimately receives the cell therapy, e.g., a first subject.

In such embodiments, the cells then are administered to a different subject, e.g., a second subject, of the same species. In some embodiments, the first and second subjects are genetically identical. In some embodiments, the first and second subjects are genetically similar. In some embodiments, the second subject expresses the same HLA class or supertype as the first subject.

In some embodiments, the subject has been treated with a therapeutic agent targeting the disease or condition, e.g. the tumor, prior to administration of the cells or composition containing the cells. In some aspects, the subject is refractory or non-responsive to the other therapeutic agent. In some embodiments, the subject has persistent or relapsed disease, e.g., following treatment with another therapeutic intervention, including chemotherapy, radiation, and/or hematopoietic stem cell transplantation (HSCT), e.g., allogenic HSCT. In some embodiments, the administration effectively treats the subject despite the subject having become resistant to another therapy.

In some embodiments, the subject is responsive to the other therapeutic agent, and treatment with the therapeutic agent reduces disease burden. In some aspects, the subject is initially responsive to the therapeutic agent, but exhibits a relapse of the disease or condition over time. In some embodiments, the subject has not relapsed. In some such embodiments, the subject is determined to be at risk for relapse, such as at a high risk of relapse, and thus the cells are administered prophylactically, e.g., to reduce the likelihood of or prevent relapse. In some aspects, the subject has not received prior treatment with another therapeutic agent.

In some embodiments, the subject has persistent or relapsed disease, e.g., following treatment with another therapeutic intervention, including chemotherapy, radiation, and/or hematopoietic stem cell transplantation (HSCT), e.g., allogenic HSCT. In some embodiments, the administration effectively treats the subject despite the subject having become resistant to another therapy.

The engineered cells of the present disclosure can be administered to an animal, preferably a mammal, even more preferably a human, to treat a cancer. In addition, the cells of the present disclosure can be used for the treatment of any condition related to a cancer, especially a cell-mediated immune response against a tumor cell(s), where it is desirable to treat or alleviate the disease. The types of cancers to be treated with the modified cells or pharmaceutical compositions of the disclosure include, carcinoma, blastoma, and sarcoma, and certain leukemia or lymphoid malignancies, benign and malignant tumors, and malignancies e.g., sarcomas, carcinomas, and melanomas. Other exemplary cancers include but are not limited breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, renal cancer, liver cancer, brain cancer, lymphoma, leukemia, lung cancer, thyroid cancer, and the like. The cancers may be non-solid tumors (such as hematological tumors) or solid tumors. Adult tumors/cancers and pediatric tumor s/cancers are also included. In one embodiment, the cancer is a solid tumor or a hematological tumor. In one embodiment, the cancer is a carcinoma. In one embodiment, the cancer is a sarcoma. In one embodiment, the cancer is a leukemia. In one embodiment the cancer is a solid tumor.

Solid tumors are abnormal masses of tissue that usually do not contain cysts or liquid areas. Solid tumors can be benign or malignant. Different types of solid tumors are named for the type of cells that form them (such as sarcomas, carcinomas, and lymphomas). Examples of solid tumors, such as sarcomas and carcinomas, include fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteosarcoma, and other sarcomas, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, lymphoid malignancy, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer, hepatocellular carcinoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, medullary thyroid carcinoma, papillary thyroid carcinoma, pheochromocytomas sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, Wilms' tumor, cervical cancer, testicular tumor, seminoma, bladder carcinoma, melanoma, and CNS tumors (such as a glioma (such as brainstem glioma and mixed gliomas), glioblastoma (also known as glioblastoma multiforme) astrocytoma, CNS lymphoma, germinoma, medulloblastoma, Schwannoma craniopharyogioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, neuroblastoma, retinoblastoma and brain metastases).

Carcinomas that can be amenable to therapy by a method disclosed herein include, but are not limited to, esophageal carcinoma, hepatocellular carcinoma, basal cell carcinoma (a form of skin cancer), squamous cell carcinoma (various tissues), bladder carcinoma, including transitional cell carcinoma (a malignant neoplasm of the bladder), bronchogenic carcinoma, colon carcinoma, colorectal carcinoma, gastric carcinoma, lung carcinoma, including small cell carcinoma and non-small cell carcinoma of the lung, adrenocortical carcinoma, thyroid carcinoma, pancreatic carcinoma, breast carcinoma, ovarian carcinoma, prostate carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinoma, cystadenocarcinoma, medullary carcinoma, renal cell carcinoma, ductal carcinoma in situ or bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical carcinoma, uterine carcinoma, testicular carcinoma, osteogenic carcinoma, epithelial carcinoma, and nasopharyngeal carcinoma.

Sarcomas that can be amenable to therapy by a method disclosed herein include, but are not limited to, fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, chordoma, osteogenic sarcoma, osteosarcoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's sarcoma, leiomyosarcoma, rhabdomyosarcoma, and other soft tissue sarcomas.

In certain exemplary embodiments, the modified immune cells of the disclosure are used to treat a myeloma, or a condition related to myeloma. Examples of myeloma or conditions related thereto include, without limitation, light chain myeloma, non-secretory myeloma, monoclonal gamopathy of undertermined significance (MGUS), plasmacytoma (e.g., solitary, multiple solitary, extramedullary plasmacytoma), amyloidosis, and multiple myeloma. In one embodiment, a method of the present disclosure is used to treat multiple myeloma. In one embodiment, a method of the present disclosure is used to treat refractory myeloma. In one embodiment, a method of the present disclosure is used to treat relapsed myeloma.

In certain exemplary embodiments, the modified immune cells of the disclosure are used to treat a melanoma, or a condition related to melanoma. Examples of melanoma or conditions related thereto include, without limitation, superficial spreading melanoma, nodular melanoma, lentigo maligna melanoma, acral lentiginous melanoma, amelanotic melanoma, or melanoma of the skin ( e.g ., cutaneous, eye, vulva, vagina, rectum melanoma). In one embodiment, a method of the present disclosure is used to treat cutaneous melanoma. In one embodiment, a method of the present disclosure is used to treat refractory melanoma. In one embodiment, a method of the present disclosure is used to treat relapsed melanoma.

In yet other exemplary embodiments, the modified immune cells of the disclosure are used to treat a sarcoma, or a condition related to sarcoma. Examples of sarcoma or conditions related thereto include, without limitation, angiosarcoma, chondrosarcoma, Ewing’s sarcoma, fibrosarcoma, gastrointestinal stromal tumor, leiomyosarcoma, liposarcoma, malignant peripheral nerve sheath tumor, osteosarcoma, pleomorphic sarcoma, rhabdomyosarcoma, and synovial sarcoma. In one embodiment, a method of the present disclosure is used to treat synovial sarcoma. In one embodiment, a method of the present disclosure is used to treat liposarcoma such as myxoid/round cell liposarcoma, differentiated/dedifferentiated liposarcoma, and pleomorphic liposarcoma. In one embodiment, a method of the present disclosure is used to treat myxoid/round cell liposarcoma. In one embodiment, a method of the present disclosure is used to treat a refractory sarcoma. In one embodiment, a method of the present disclosure is used to treat a relapsed sarcoma.

The cells of the disclosure to be administered may be autologous, with respect to the subject undergoing therapy.

The administration of the cells of the disclosure may be carried out in any convenient manner known to those of skill in the art. The cells of the present disclosure may be administered to a subject by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The compositions described herein may be administered to a patient transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous (i.v.) injection, or intraperitoneally. In other instances, the cells of the disclosure are injected directly into a site of inflammation in the subject, a local disease site in the subject, alymph node, an organ, a tumor, and the like.

In some embodiments, the cells are administered at a desired dosage, which in some aspects includes a desired dose or number of cells or cell type(s) and/or a desired ratio of cell types. Thus, the dosage of cells in some embodiments is based on a total number of cells (or number per kg body weight) and a desired ratio of the individual populations or sub-types, such as the CD4+ to CD8+ ratio. In some embodiments, the dosage of cells is based on a desired total number (or number per kg of body weight) of cells in the individual populations or of individual cell types. In some embodiments, the dosage is based on a combination of such features, such as a desired number of total cells, desired ratio, and desired total number of cells in the individual populations.

In some embodiments, the populations or sub-types of cells, such as CD8 ⁺ and CD4 ⁺ T cells, are administered at or within a tolerated difference of a desired dose of total cells, such as a desired dose of T cells. In some aspects, the desired dose is a desired number of cells or a desired number of cells per unit of body weight of the subject to whom the cells are administered, e.g., cells/kg. In some aspects, the desired dose is at or above a minimum number of cells or minimum number of cells per unit of body weight. In some aspects, among the total cells, administered at the desired dose, the individual populations or sub-types are present at or near a desired output ratio (such as CD4 ⁺ to CD8 ⁺ ratio), e.g., within a certain tolerated difference or error of such a ratio.

In some embodiments, the cells are administered at or within a tolerated difference of a desired dose of one or more of the individual populations or sub-types of cells, such as a desired dose of CD4+ cells and/or a desired dose of CD8+ cells. In some aspects, the desired dose is a desired number of cells of the sub-type or population, or a desired number of such cells per unit of body weight of the subject to whom the cells are administered, e.g., cells/kg. In some aspects, the desired dose is at or above a minimum number of cells of the population or subtype, or minimum number of cells of the population or sub-type per unit of body weight. Thus, in some embodiments, the dosage is based on a desired fixed dose of total cells and a desired ratio, and/or based on a desired fixed dose of one or more, e.g., each, of the individual sub-types or sub populations. Thus, in some embodiments, the dosage is based on a desired fixed or minimum dose of T cells and a desired ratio of CD4 ⁺ to CD8 ⁺ cells, and/or is based on a desired fixed or minimum dose of CD4 ⁺ and/or CD8 ⁺ cells.

In certain embodiments, the cells, or individual populations of sub-types of cells, are administered to the subject at a range of about one million to about 100 billion cells, such as, e.g., 1 million to about 50 billion cells (e.g., about 5 million cells, about 25 million cells, about 500 million cells, about 1 billion cells, about 5 billion cells, about 20 billion cells, about 30 billion cells, about 40 billion cells, or a range defined by any two of the foregoing values), such as about 10 million to about 100 billion cells (e.g., about 20 million cells, about 30 million cells, about 40 million cells, about 60 million cells, about 70 million cells, about 80 million cells, about 90 million cells, about 10 billion cells, about 25 billion cells, about 50 billion cells, about 75 billion cells, about 90 billion cells, or a range defined by any two of the foregoing values), and in some cases about 100 million cells to about 50 billion cells (e.g., about 120 million cells, about 250 million cells, about 350 million cells, about 450 million cells, about 650 million cells, about 800 million cells, about 900 million cells, about 3 billion cells, about 30 billion cells, about 45 billion cells) or any value in between these ranges.

In some embodiments, the dose of total cells and/or dose of individual sub-populations of cells is within a range of between at or about lxlO ⁵ cells/kg to about lxlO ¹¹ cells/kg 10 ⁴ and at or about 10 ¹¹ cells/kilograms (kg) body weight, such as between 10 ⁵ and 10 ⁶ cells / kg body weight, for example, at or about 1 x 10 ⁵ cells/kg, 1.5 x 10 ⁵ cells/kg, 2 x 10 ⁵ cells/kg, or 1 x 10 ⁶ cells/kg body weight. For example, in some embodiments, the cells are administered at, or within a certain range of error of, between at or about 10 ⁴ and at or about 10 ⁹ T cells/kilograms (kg) body weight, such as between 10 ⁵ and 10 ⁶ T cells / kg body weight, for example, at or about 1 x 10 ⁵ T cells/kg, 1.5 x 10 ⁵ T cells/kg, 2 x 10 ⁵ T cells/kg, or 1 x 10 ⁶ T cells/kg body weight. In other exemplary embodiments, a suitable dosage range of modified cells for use in a method of the present disclosure includes, without limitation, from about lxlO ⁵ cells/kg to about lxlO ⁶ cells/kg, from about lxlO ⁶ cells/kg to about lxlO ⁷ cells/kg, from about lxlO ⁷ cells/kg about lxlO ⁸ cells/kg, from about lxlO ⁸ cells/kg about lxlO ⁹ cells/kg, from about lxlO ⁹ cells/kg about lxlO ¹⁰ cells/kg, from about lxlO ¹⁰ cells/kg about lxlO ¹¹ cells/kg. In an exemplary embodiment, a suitable dosage for use in a method of the present disclosure is about lxlO ⁸ cells/kg. In an exemplary embodiment, a suitable dosage for use in a method of the present disclosure is about lxlO ⁷ cells/kg. In other embodiments, a suitable dosage is from about lxlO ⁷ total cells to about 5xl0 ⁷ total cells. In some embodiments, a suitable dosage is from about lxlO ⁸ total cells to about 5xl0 ⁸ total cells. In some embodiments, a suitable dosage is from about 1.4xl0 ⁷ total cells to about l.lxlO ⁹ total cells. In an exemplary embodiment, a suitable dosage for use in a method of the present disclosure is about 7xl0 ⁹ total cells.

In some embodiments, the cells are administered at or within a certain range of error of between at or about 10 ⁴ and at or about 10 ⁹ CD4 ⁺ and/or CD8 ⁺ cells/kilograms (kg) body weight, such as between 10 ⁵ and 10 ⁶ CD4 ⁺ and/or CD8 ⁺ cells / kg body weight, for example, at or about 1 x 10 ⁵ CD4 ⁺ and/or CD8 ⁺ cells/kg, 1.5 x 10 ⁵ CD4 ⁺ and/or CD8 ⁺ cells/kg, 2 x 10 ⁵ CD4 ⁺ and/or CD8 ⁺ cells/kg, or 1 x 10 ⁶ CD4 ⁺ and/or CD8 ⁺ cells/kg body weight. In some embodiments, the cells are administered at or within a certain range of error of, greater than, and/or at least about 1 x 10 ⁶ , about 2.5 x 10 ⁶ , about 5 x 10 ⁶ , about 7.5 x 10 ⁶ , or about 9 x 10 ⁶ CD4 ⁺ cells, and/or at least about 1 x 10 ⁶ , about 2.5 x 10 ⁶ , about 5 x 10 ⁶ , about 7.5 x 10 ⁶ , or about 9 x 10 ⁶ CD8+ cells, and/or at least about 1 x 10 ⁶ , about 2.5 x 10 ⁶ , about 5 x 10 ⁶ , about 7.5 x 10 ⁶ , or about 9 x 10 ⁶ T cells. In some embodiments, the cells are administered at or within a certain range of error of between about 10 ⁸ and 10 ¹² or between about 10 ¹⁰ and 10 ¹¹ T cells, between about 10 ⁸ and 10 ¹² or between about 10 ¹⁰ and 10 ¹¹ CD4 ⁺ cells, and/or between about 10 ⁸ and 10 ¹² or between about 10 ¹⁰ and 10 ¹¹ CD8 ⁺ cells.

In some embodiments, the cells are administered at or within a tolerated range of a desired output ratio of multiple cell populations or sub-types, such as CD4+ and CD8+ cells or sub-types. In some aspects, the desired ratio can be a specific ratio or can be a range of ratios, for example, in some embodiments, the desired ratio (e.g., ratio of CD4 ⁺ to CD8 ⁺ cells) is between at or about 5: 1 and at or about 5: 1 (or greater than about 1:5 and less than about 5: 1), or between at or about 1 :3 and at or about 3 : 1 (or greater than about 1 :3 and less than about 3: 1), such as between at or about 2: 1 and at or about 1:5 (or greater than about 1 :5 and less than about 2: 1, such as at or about 5: 1, 4.5: 1, 4: 1, 3.5: 1, 3: 1, 2.5: 1, 2: 1, 1.9: 1, 1.8: 1, 1.7: 1, 1.6: 1, 1.5: 1, 1.4: 1, 1.3: 1, 1.2: 1, 1.1: 1, 1: 1, 1: 1.1, 1: 1.2, 1: 1.3, 1:1.4, 1: 1.5, 1: 1.6, 1: 1.7, 1: 1.8, 1: 1.9:

1:2, 1:2.5, 1:3, 1:3.5, 1:4, 1:4.5, or 1:5. In some aspects, the tolerated difference is within about 1%, about 2%, about 3%, about 4% about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50% of the desired ratio, including any value in between these ranges.

In some embodiments, a dose of modified cells is administered to a subject in need thereof, in a single dose or multiple doses. In some embodiments, a dose of modified cells is administered in multiple doses, e.g., once a week or every 7 days, once every 2 weeks or every 14 days, once every 3 weeks or every 21 days, once every 4 weeks or every 28 days. In an exemplary embodiment, a single dose of modified cells is administered to a subject in need thereof. In an exemplary embodiment, a single dose of modified cells is administered to a subject in need thereof by rapid intravenous infusion.

For the prevention or treatment of disease, the appropriate dosage may depend on the type of disease to be treated, the type of cells or recombinant receptors, the severity and course of the disease, whether the cells are administered for preventive or therapeutic purposes, previous therapy, the subject's clinical history and response to the cells, and the discretion of the attending physician. The compositions and cells are in some embodiments suitably administered to the subject at one time or over a series of treatments.

In some embodiments, the cells are administered as part of a combination treatment, such as simultaneously with or sequentially with, in any order, another therapeutic intervention, such as an antibody or engineered cell or receptor or agent, such as a cytotoxic or therapeutic agent. The cells in some embodiments are co-administered with one or more additional therapeutic agents or in connection with another therapeutic intervention, either simultaneously or sequentially in any order. In some contexts, the cells are co-administered with another therapy sufficiently close in time such that the cell populations enhance the effect of one or more additional therapeutic agents, or vice versa. In some embodiments, the cells are administered prior to the one or more additional therapeutic agents. In some embodiments, the cells are administered after the one or more additional therapeutic agents. In some embodiments, the one or more additional agents includes a cytokine, such as IL-2, for example, to enhance persistence. In some embodiments, the methods comprise administration of a chemotherapeutic agent.

In certain embodiments, the engineered cells of the disclosure (e.g., a modified cell comprising a CAR and therapeutic peptide) may be administered to a subject in combination with an immune checkpoint antibody ( e.g ., an anti-PDl, anti-CTLA-4, or anti-PDLl antibody). For example, the modified cell may be administered in combination with an antibody or antibody fragment targeting, for example, PD-1 (programmed death 1 protein). Examples of anti-PD-1 antibodies include, but are not limited to, pembrolizumab (KEYTRUDA®, formerly lambrolizumab, also known as MK-3475), and nivolumab (BMS-936558, MDX-1106, ONO- 4538, OPDIVA®) or an antigen-binding fragment thereof. In certain embodiments, the modified cell may be administered in combination with an anti-PD-Ll antibody or antigen-binding fragment thereof. Examples of anti-PD-Ll antibodies include, but are not limited to, BMS- 936559, MPDL3280A (TECENTRIQ®, Atezolizumab), and MEDI4736 (Durvalumab, Imfinzi). In certain embodiments, the modified cell may be administered in combination with an anti- CTLA-4 antibody or antigen-binding fragment thereof. An example of an anti- CTLA-4 antibody includes, but is not limited to, Ipilimumab (trade name Yervoy). Other types of immune checkpoint modulators may also be used including, but not limited to, small molecules, siRNA, miRNA, and CRISPR systems. Immune checkpoint modulators may be administered before, after, or concurrently with the modified cell comprising the CAR and therapeutic peptide. In certain embodiments, combination treatment comprising an immune checkpoint modulator may increase the therapeutic efficacy of a therapy comprising a modified cell of the present disclosure.

Following administration of the cells, the biological activity of the engineered cell populations in some embodiments is measured, e.g., by any of a number of known methods. Parameters to assess include specific binding of an engineered or natural T cell or other immune cell to antigen, in vivo , e.g., by imaging, or ex vivo, e.g., by ELISA or flow cytometry. In certain embodiments, the ability of the engineered cells to destroy target cells can be measured using any suitable method known in the art, such as cytotoxicity assays described in, for example, Kochenderfer etal., J. Immunotherapy, 32(7): 689-702 (2009), and Herman et al. J. Immunological Methods, 285(1): 25-40 (2004). In certain embodiments, the biological activity of the cells is measured by assaying expression and/or secretion of one or more cytokines, such as CD 107a, IFNy, IL-2, and TNF. In some aspects the biological activity is measured by assessing clinical outcome, such as reduction in tumor burden or load. In certain embodiments, the subject is provided a secondary treatment. Secondary treatments include but are not limited to chemotherapy, radiation, surgery, and medications.

In some embodiments, the subject can be administered a conditioning therapy prior to CAR T cell therapy. In some embodiments, the conditioning therapy comprises administering an effective amount of cyclophosphamide to the subject. In some embodiments, the conditioning therapy comprises administering an effective amount of fludarabine to the subject. In preferred embodiments, the conditioning therapy comprises administering an effective amount of a combination of cyclophosphamide and fludarabine to the subject. Administration of a conditioning therapy prior to CAR T cell therapy may increase the efficacy of the CAR T cell therapy. Methods of conditioning patients for T cell therapy are described in U.S. Patent No. 9,855,298, which is incorporated herein by reference in its entirety.

In some embodiments, a specific dosage regimen of the present disclosure includes a lymphodepletion step prior to the administration of the modified T cells. In an exemplary embodiment, the lymphodepletion step includes administration of cyclophosphamide and/or fludarabine.

In some embodiments, the lymphodepletion step includes administration of cyclophosphamide at a dose of between about 200 mg/m ² /day and about 2000 mg/m ² /day (e.g., 200 mg/m ² /day, 300 mg/m ² /day, or 500 mg/m ² /day). In an exemplary embodiment, the dose of cyclophosphamide is about 300 mg/m ² /day. In some embodiments, the lymphodepletion step includes administration of fludarabine at a dose of between about 20 mg/m ² /day and about 900 mg/m ² /day (e.g., 20 mg/m ² /day, 25 mg/m ² /day, 30 mg/m ² /day, or 60 mg/m ² /day). In an exemplary embodiment, the dose of fludarabine is about 30 mg/m ² /day.

In some embodiment, the lymphodepletion step includes administration of cyclophosphamide at a dose of between about 200 mg/m ² /day and about 2000 mg/m ² /day (e.g., 200 mg/m ² /day, 300 mg/m ² /day, or 500 mg/m ² /day), and fludarabine at a dose of between about 20 mg/m ² /day and about 900 mg/m ² /day (e.g., 20 mg/m ² /day, 25 mg/m ² /day, 30 mg/m ² /day, or 60 mg/m ² /day). In an exemplary embodiment, the lymphodepletion step includes administration of cyclophosphamide at a dose of about 300 mg/m ² /day, and fludarabine at a dose of about 30 mg/m ² /day. In an exemplary embodiment, the dosing of cyclophosphamide is 300 mg/m ² /day over three days, and the dosing of fludarabine is 30 mg/m ² /day over three days.

Dosing of lymphodepletion chemotherapy may be scheduled on Days -6 to -4 (with a -1 day window, i.e., dosing on Days -7 to -5) relative to T cell ( e.g ., CAR-T, TCR-T, a modified T cell, etc.) infusion on Day 0.

In an exemplary embodiment, for a subject having cancer, the subject receives lymphodepleting chemotherapy including 300 mg/m ² of cyclophosphamide by intravenous infusion 3 days prior to administration of the modified T cells. In an exemplary embodiment, for a subject having cancer, the subject receives lymphodepleting chemotherapy including 300 mg/m ² of cyclophosphamide by intravenous infusion for 3 days prior to administration of the modified T cells.

In an exemplary embodiment, for a subject having cancer, the subject receives lymphodepleting chemotherapy including fludarabine at a dose of between about 20 mg/m ² /day and about 900 mg/m ² /day (e.g., 20 mg/m ² /day, 25 mg/m ² /day, 30 mg/m ² /day, or 60 mg/m ² /day). In an exemplary embodiment, for a subject having cancer, the subject receives lymphodepleting chemotherapy including fludarabine at a dose of 30 mg/m ² for 3 days.

In an exemplary embodiment, for a subject having cancer, the subject receives lymphodepleting chemotherapy including cyclophosphamide at a dose of between about 200 mg/m ² /day and about 2000 mg/m ² /day (e.g., 200 mg/m ² /day, 300 mg/m ² /day, or 500 mg/m ² /day), and fludarabine at a dose of between about 20 mg/m ² /day and about 900 mg/m ² /day (e.g., 20 mg/m ² /day, 25 mg/m ² /day, 30 mg/m ² /day, or 60 mg/m ² /day). In an exemplary embodiment, for a subject having cancer, the subject receives lymphodepleting chemotherapy including cyclophosphamide at a dose of about 300 mg/m ² /day, and fludarabine at a dose of 30 mg/m ² for 3 days.

Cells of the disclosure can be administered in dosages and routes and at times to be determined in appropriate pre-clinical and clinical experimentation and trials. Cell compositions may be administered multiple times at dosages within these ranges. Administration of the cells of the disclosure may be combined with other methods useful to treat the desired disease or condition as determined by those of skill in the art. It is known in the art that one of the adverse effects following infusion of CAR T cells is the onset of immune activation, known as cytokine release syndrome (CRS). CRS is immune activation resulting in elevated inflammatory cytokines. CRS is a known on-target toxicity, development of which likely correlates with efficacy. Clinical and laboratory measures range from mild CRS (constitutional symptoms and/or grade-2 organ toxicity) to severe CRS (sCRS; grade >3 organ toxicity, aggressive clinical intervention, and/or potentially life threatening). Clinical features include: high fever, malaise, fatigue, myalgia, nausea, anorexia, tachycardia/hypotension, capillary leak, cardiac dysfunction, renal impairment, hepatic failure, and disseminated intravascular coagulation. Dramatic elevations of cytokines including interferon-gamma, granulocyte macrophage colony-stimulating factor, IL-10, and IL-6 have been shown following CAR T-cell infusion. One CRS signature is elevation of cytokines including IL-6 (severe elevation), IFN-gamma, TNF-alpha (moderate), and IL-2 (mild). Elevations in clinically available markers of inflammation including ferritin and C-reactive protein (CRP) have also been observed to correlate with the CRS syndrome. The presence of CRS generally correlates with expansion and progressive immune activation of adoptively transferred cells. It has been demonstrated that the degree of CRS severity is dictated by disease burden at the time of infusion as patients with high tumor burden experience a more sCRS.

Accordingly, the disclosure provides for, following the diagnosis of CRS, appropriate CRS management strategies to mitigate the physiological symptoms of uncontrolled inflammation without dampening the antitumor efficacy of the engineered cells ( e.g ., CAR T cells). CRS management strategies are known in the art. For example, systemic corticosteroids may be administered to rapidly reverse symptoms of sCRS (e.g., grade 3 CRS) without compromising initial antitumor response.

In some embodiments, an anti-IL-6R antibody may be administered. An example of an anti-IL-6R antibody is the Food and Drug Administration-approved monoclonal antibody tocilizumab, also known as atlizumab (marketed as Actemra, or RoActemra). Tocilizumab is a humanized monoclonal antibody against the interleukin-6 receptor (IL-6R). Administration of tocilizumab has demonstrated near-immediate reversal of CRS. CRS is generally managed based on the severity of the observed syndrome and interventions are tailored as such. CRS management decisions may be based upon clinical signs and symptoms and response to interventions, not solely on laboratory values alone.

Mild to moderate cases generally are treated with symptom management with fluid therapy, non-steroidal anti-inflammatory drug (NSAID) and antihistamines as needed for adequate symptom relief. More severe cases include patients with any degree of hemodynamic instability; with any hemodynamic instability, the administration of tocilizumab is recommended. The first-line management of CRS may be tocilizumab, in some embodiments, at the labeled dose of 8 mg/kg IV over 60 minutes (not to exceed 800 mg/dose); tocilizumab can be repeated Q8 hours. If suboptimal response to the first dose of tocilizumab, additional doses of tocilizumab may be considered. Tocilizumab can be administered alone or in combination with corticosteroid therapy. Patients with continued or progressive CRS symptoms, inadequate clinical improvement in 12-18 hours or poor response to tocilizumab, may be treated with high- dose corticosteroid therapy, generally hydrocortisone 100 mg IV or methylprednisolone 1-2 mg/kg. In patients with more severe hemodynamic instability or more severe respiratory symptoms, patients may be administered high-dose corticosteroid therapy early in the course of the CRS. CRS management guidance may be based on published standards (Lee etal. (2019) Biol Blood Marrow Transplant , doi.org/10.1016/j.bbmt.2018.12.758; Neelapu et al. (2018) Nat Rev Clin Oncology , 15:47; Teachey et al. (2016) Cancer Discov, 6(6):664-679).

Features consistent with Macrophage Activation Syndrome (MAS) or Hemophagocytic lymphohistiocytosis (HLH) have been observed in patients treated with CAR-T therapy (Henter, 2007), coincident with clinical manifestations of the CRS. MAS appears to be a reaction to immune activation that occurs from the CRS, and should therefore be considered a manifestation of CRS. MAS is similar to HLH (also a reaction to immune stimulation). The clinical syndrome of MAS is characterized by high grade non-remitting fever, cytopenias affecting at least two of three lineages, and hepatosplenomegaly. It is associated with high serum ferritin, soluble interleukin-2 receptor, and triglycerides, and a decrease of circulating natural killer (NK) activity.

As such, the engineered cells comprising a CAR and therapeutic peptide of the present disclosure when used in a method of treatment as described herein, enhances the ability of the engineered cells in carrying out their function. Accordingly, the present disclosure provides a method for enhancing a function of an engineered cell ( e.g . immune cell) for use in a method of treatment as described herein.

In one aspect, the disclosure provides a method of treating cancer in a subject in need thereof, comprising administering to the subject any one of the engineered cells disclosed herein. Yet another aspect of the disclosure provides a method of treating cancer in a subject in need thereof, comprising administering to the subject an engineered cell generated by any one of the methods disclosed herein.

Another aspect includes a method for treating a disease or disorder in a subject, comprising administering to the subject an effective amount of a T cell genetically modified to express a chimeric antigen receptor (CAR). The CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular signaling domain. The method further comprises stimulation of the endogenous immune response against the cancer via a non-natural therapeutic peptide. The non-natural therapeutic peptide is expressed in the modified T cell and/or is administered in combination with the modified T cell. The non-natural therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

In certain embodiments, the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP. In certain embodiments, the therapeutic peptide is a mimetic of a TLR agonist. In certain embodiments, the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL). In certain embodiments, the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic. In certain embodiments, the therapeutic peptide is an inhibitor of poly ADP ribose polymerase

(PARP). In certain embodiments, the non-natural peptide is a peptide that has no more than 80% sequence identity to any naturally occurring peptide. In certain embodiments, the peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-16.

In certain embodiments, the therapeutic peptide is an immunogenic epitope, and the immunogenic epitope is expressed on the surface of a cancer cell in the subject following the administration to the subject. In certain embodiments, the therapeutic peptide is expressed in the modified T cell, and subsequent to administration of the modified T cell to the subject, the therapeutic peptide is exported from the modified T cell in one or more extracellular vesicles. In certain embodiments, the therapeutic peptide is delivered via the one or more extracellular vesicles to one or more antigen presenting cells in the subject.

Also provided herein is a method for enhancing anti-cancer activity of a T cell genetically modified to express a chimeric antigen receptor (CAR), wherein the CAR comprises an antigen binding domain that specifically binds to an antigen expressed on a tumor cell, a transmembrane domain, and an intracellular signaling domain. The method comprises co-expressing a non natural therapeutic peptide in the T cell. The non-natural therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

Also provided herein are methods for treating an inflammatory disease, an autoimmune disease, or a cancer in a subject, comprising administering to the subject an effective amount of any of the engineered cells or a compositions contemplated herein.

I. Methods of Producing Engineered Cells

Provided herein are methods for producing or generating an engineered cell ( e.g . immune cell or precursor thereof; e.g., a T cell) of the disclosure for tumor immunotherapy, e.g., adoptive immunotherapy. The cells generally are engineered by introducing one or more nucleic acids encoding the CAR and a therapeutic peptide into the cell. Also provided is a method for co-expressing a CAR and a therapeutic peptide in a cell. The method comprises delivering to the cell any of the expression vectors contemplated herein, under conditions such that the CAR and the therapeutic peptide are expressed.

In some embodiments, the CAR and therapeutic peptide are introduced into a cell by an expression vector. Expression vectors comprising a nucleic acid sequence encoding CAR and therapeutic peptide of the present disclosure are provided herein. Suitable expression vectors include lentivirus vectors, gamma retrovirus vectors, foamy virus vectors, adeno associated virus (AAV) vectors, adenovirus vectors, engineered hybrid viruses, naked DNA, including but not limited to transposon mediated vectors, such as Sleeping Beauty, Piggybak, and Integrases such as Phi31. Some other suitable expression vectors include Herpes simplex virus (HSV) and retrovirus expression vectors.

In certain embodiments, the nucleic acid encoding the CAR is introduced into the cell via viral transduction. In certain embodiments, the viral transduction comprises contacting the immune or precursor cell with a viral vector comprising the nucleic acid encoding a CAR. In certain embodiments, the viral vector is an adeno-associated viral (AAV) vector. In certain embodiments, the AAV vector comprises a 5’ ITR and a 3’TTR. In certain embodiments, the AAV vector comprises a Woodchuck Hepatitis Virus post-transcriptional regulatory element (WPRE). In certain embodiments, the AAV vector comprises a polyadenylation (poly A) sequence. In certain embodiments, the polyA sequence is a bovine growth hormone (BGH) polyA sequence.

Adenovirus expression vectors are based on adenoviruses, which have a low capacity for integration into genomic DNA but a high efficiency for transfecting host cells. Adenovirus expression vectors contain adenovirus sequences sufficient to: (a) support packaging of the expression vector and (b) to ultimately express the CAR in the host cell. In some embodiments, the adenovirus genome is a 36 kb, linear, double stranded DNA, where a foreign DNA sequence ( e.g ., a nucleic acid encoding a CAR) may be inserted to substitute large pieces of adenoviral DNA in order to make the expression vector of the present disclosure (see, e.g., Danthinne and Imperiale, Gene Therapy (2000) 7(20): 1707-1714).

Another expression vector is based on an adeno associated virus (AAV), which takes advantage of the adenovirus coupled systems. This AAV expression vector has a high frequency of integration into the host genome. It can infect nondividing cells, thus making it useful for delivery of genes into mammalian cells, for example, in tissue cultures or in vivo. The AAV vector has a broad host range for infectivity. Details concerning the generation and use of AAV vectors are described in U.S. Patent Nos. 5,139,941 and 4,797,368.

Retrovirus expression vectors are capable of integrating into the host genome, delivering a large amount of foreign genetic material, infecting a broad spectrum of species and cell types and being packaged in special cell lines. The retroviral vector is constructed by inserting a nucleic acid ( e.g ., a nucleic acid encoding a CAR and therapeutic peptide) into the viral genome at certain locations to produce a virus that is replication defective. Though the retroviral vectors are able to infect a broad variety of cell types, integration and stable expression of the a CAR and therapeutic peptide requires the division of host cells.

Lentiviral vectors are derived from lentiviruses, which are complex retroviruses that, in addition to the common retroviral genes gag, pol, and env, contain other genes with regulatory or structural function (see, e.g., U.S. Patent Nos. 6,013,516 and 5,994, 136). Some examples of lentiviruses include the Human Immunodeficiency Viruses (HIV-1, HIV-2) and the Simian Immunodeficiency Virus (SIV). Lentiviral vectors have been generated by multiply attenuating the HIV virulence genes, for example, the genes env, vif, vpr, vpu and nef are deleted making the vector biologically safe. Lentiviral vectors are capable of infecting non-dividing cells and can be used for both in vivo and ex vivo gene transfer and expression, e.g., of a nucleic acid encoding a CAR and therapeutic peptide (see, e.g., U.S. Patent No. 5,994,136).

Expression vectors including a nucleic acid of the present disclosure can be introduced into a host cell by any means known to persons skilled in the art. The expression vectors may include viral sequences for transfection, if desired. Alternatively, the expression vectors may be introduced by fusion, electroporation, biolistics, transfection, lipofection, or the like. The host cell may be grown and expanded in culture before introduction of the expression vectors, followed by the appropriate treatment for introduction and integration of the vectors he host cells are then expanded and may be screened by virtue of a marker present in the vectors.

Various markers that may be used are known in the art, and may include hprt, neomycin resistance, thymidine kinase, hygromycin resistance, etc. As used herein, the terms "cell," "cell line," and "cell culture" may be used interchangeably. In some embodiments, the host cell an immune cell or precursor thereof, e.g., a T cell, an NK cell, or an NKT cell.

The present disclosure also provides genetically engineered cells which include and stably express a CAR of the present disclosure. In some embodiments, the genetically engineered cells are genetically engineered T-lymphocytes (T cells), naive T cells (TN), memory T cells (for example, central memory T cells (TCM), effector memory cells (TEM)), natural killer cells (NK cells), and macrophages capable of giving rise to therapeutically relevant progeny. In certain embodiments, the genetically engineered cells are autologous cells. In certain embodiments, the modified cell is resistant to T cell exhaustion. In certain embodiments, the modified cell is resistant to T cell dysfunction.

Modified cells (e.g., comprising a CAR) may be produced by stably transfecting host cells with an expression vector including a nucleic acid of the present disclosure. Additional methods for generating a modified cell of the present disclosure include, without limitation, chemical transformation methods (e.g., using calcium phosphate, dendrimers, liposomes and/or cationic polymers), non-chemical transformation methods (e.g., electroporation, optical transformation, gene electrotransfer and/or hydrodynamic delivery) and/or particle-based methods (e.g., impalefection, using a gene gun and/or magnetofection). Transfected cells expressing a CAR and therapeutic peptide of the present disclosure may be expanded ex vivo.

Physical methods for introducing an expression vector into host cells include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells including vectors and/or exogenous nucleic acids are well- known in the art. See, e.g., Sambrook et al. (2001), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York. Chemical methods for introducing an expression vector into a host cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes.

Lipids suitable for use can be obtained from commercial sources. For example, dimyristyl phosphatidylcholine (“DMPC”) can be obtained from Sigma, St. Louis, MO; dicetyl phosphate (“DCP”) can be obtained from K & K Laboratories (Plainview, NY); cholesterol (“Choi”) can be obtained from Calbiochem-Behring; dimyristyl phosphatidylglycerol (“DMPG”) and other lipids may be obtained from Avanti Polar Lipids, Inc. (Birmingham, AL). Stock solutions of lipids in chloroform or chloroform/methanol can be stored at about -20°C. Chloroform may be used as the only solvent since it is more readily evaporated than methanol. “Liposome” is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates. Liposomes can be characterized as having vesicular structures with a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh et al., 1991 Glycobiology 5: 505-10). Compositions that have different structures in solution than the normal vesicular structure are also encompassed. For example, the lipids may assume a micellar structure or merely exist as nonuniform aggregates of lipid molecules. Also contemplated are lipofectamine-nucleic acid complexes.

Regardless of the method used to introduce exogenous nucleic acids into a host cell or otherwise expose a cell to the inhibitor of the present disclosure, in order to confirm the presence of the nucleic acids in the host cell, a variety of assays may be performed. Such assays include, for example, molecular biology assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR; biochemistry assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELISAs and Western blots) or by assays described herein to identify agents falling within the scope of the disclosure.

In one embodiment, the nucleic acids introduced into the host cell are RNA. In another embodiment, the RNA is mRNA that comprises in vitro transcribed RNA or synthetic RNA.

The RNA may be produced by in vitro transcription using a polymerase chain reaction (PCR)- generated template. DNA of interest from any source can be directly converted by PCR into a template for in vitro mRNA synthesis using appropriate primers and RNA polymerase. The source of the DNA may be, for example, genomic DNA, plasmid DNA, phage DNA, cDNA, synthetic DNA sequence or any other appropriate source of DNA.

PCR may be used to generate a template for in vitro transcription of mRNA which is then introduced into cells. Methods for performing PCR are well known in the art. Primers for use in PCR are designed to have regions that are substantially complementary to regions of the DNA to be used as a template for the PCR. “Substantially complementary,” as used herein, refers to sequences of nucleotides where a majority or all of the bases in the primer sequence are complementary. Substantially complementary sequences are able to anneal or hybridize with the intended DNA target under annealing conditions used for PCR. The primers can be designed to be substantially complementary to any portion of the DNA template. For example, the primers can be designed to amplify the portion of a gene that is normally transcribed in cells (the open reading frame), including 5' and 3' UTRs. The primers may also be designed to amplify a portion of a gene that encodes a particular domain of interest. In one embodiment, the primers are designed to amplify the coding region of a human cDNA, including all or portions of the 5' and 3' UTRs. Primers useful for PCR are generated by synthetic methods that are well known in the art. “Forward primers” are primers that contain a region of nucleotides that are substantially complementary to nucleotides on the DNA template that are upstream of the DNA sequence that is to be amplified. “Upstream” is used herein to refer to a location 5, to the DNA sequence to be amplified relative to the coding strand. “Reverse primers” are primers that contain a region of nucleotides that are substantially complementary to a double-stranded DNA template that are downstream of the DNA sequence that is to be amplified. “Downstream” is used herein to refer to a location 3' to the DNA sequence to be amplified relative to the coding strand.

Chemical structures that have the ability to promote stability and/or translation efficiency of the RNA may also be used. The RNA preferably has 5' and 3' UTRs. In one embodiment, the 5' UTR is between zero and 3000 nucleotides in length. The length of 5' and 3' UTR sequences to be added to the coding region can be altered by different methods, including, but not limited to, designing primers for PCR that anneal to different regions of the UTRs. Using this approach, one of ordinary skill in the art can modify the 5' and 3' UTR lengths required to achieve optimal translation efficiency following transfection of the transcribed RNA.

The 5' and 3' UTRs can be the naturally occurring, endogenous 5' and 3' UTRs for the gene of interest. Alternatively, UTR sequences that are not endogenous to the gene of interest can be added by incorporating the UTR sequences into the forward and reverse primers or by any other modifications of the template. The use of UTR sequences that are not endogenous to the gene of interest can be useful for modifying the stability and/or translation efficiency of the RNA. For example, it is known that AU-rich elements in 3' UTR sequences can decrease the stability of mRNA. Therefore, 3' UTRs can be selected or designed to increase the stability of the transcribed RNA based on properties of UTRs that are well known in the art.

In one embodiment, the 5' UTR can contain the Kozak sequence of the endogenous gene. Alternatively, when a 5' UTR that is not endogenous to the gene of interest is being added by PCR as described above, a consensus Kozak sequence can be redesigned by adding the 5' UTR sequence. Kozak sequences can increase the efficiency of translation of some RNA transcripts, but does not appear to be required for all RNAs to enable efficient translation. The requirement for Kozak sequences for many mRNAs is known in the art. In other embodiments the 5' UTR can be derived from an RNA virus whose RNA genome is stable in cells. In other embodiments various nucleotide analogues can be used in the 3' or 5' UTR to impede exonuclease degradation of the mRNA.

To enable synthesis of RNA from a DNA template without the need for gene cloning, a promoter of transcription should be attached to the DNA template upstream of the sequence to be transcribed. When a sequence that functions as a promoter for an RNA polymerase is added to the 5' end of the forward primer, the RNA polymerase promoter becomes incorporated into the PCR product upstream of the open reading frame that is to be transcribed. In one embodiment, the promoter is a T7 polymerase promoter, as described elsewhere herein. Other useful promoters include, but are not limited to, T3 and SP6 RNA polymerase promoters. Consensus nucleotide sequences for T7, T3 and SP6 promoters are known in the art.

In one embodiment, the mRNA has both a cap on the 5' end and a 3' poly(A) tail which determine ribosome binding, initiation of translation and stability mRNA in the cell. On a circular DNA template, for instance, plasmid DNA, RNA polymerase produces a long concatameric product which is not suitable for expression in eukaryotic cells. The transcription of plasmid DNA linearized at the end of the 3' UTR results in normal sized mRNA which is not effective in eukaryotic transfection even if it is polyadenylated after transcription.

On a linear DNA template, phage T7 RNA polymerase can extend the 3' end of the transcript beyond the last base of the template (Schenborn and Mierendorf, Nuc Acids Res., 13:6223-36 (1985); Nacheva and Berzal-Herranz, Eur. J. Biochem., 270:1485-65 (2003). The polyA/T segment of the transcriptional DNA template can be produced during PCR by using a reverse primer containing a polyT tail, such as 100T tail (size can be 50-5000 T), or after PCR by any other method, including, but not limited to, DNA ligation or in vitro recombination. Poly(A) tails also provide stability to RNAs and reduce their degradation. Generally, the length of a poly(A) tail positively correlates with the stability of the transcribed RNA. In one embodiment, the poly(A) tail is between 100 and 5000 adenosines.

Poly(A) tails of RNAs can be further extended following in vitro transcription with the use of a poly (A) polymerase, such as E. coli poly A polymerase (E-PAP). In one embodiment, increasing the length of a poly(A) tail from 100 nucleotides to between 300 and 400 nucleotides results in about a two-fold increase in the translation efficiency of the RNA. Additionally, the attachment of different chemical groups to the 3' end can increase mRNA stability. Such attachment can contain modified/artificial nucleotides, aptamers and other compounds. For example, ATP analogs can be incorporated into the poly(A) tail using poly(A) polymerase. ATP analogs can further increase the stability of the RNA.

5' caps also provide stability to RNA molecules. In a preferred embodiment, RNAs produced by the methods disclosed herein include a 5' cap. The 5' cap is provided using techniques known in the art and described herein (Cougot, et al., Trends in Biochem. Sci., 29:436-444 (2001); Stepinski, et al., RNA, 7:1468-95 (2001); Elango, et al ., Biochim. Biophys. Res. Commun., 330:958-966 (2005)).

In some embodiments, the RNA is electroporated into the cells, such as in vitro transcribed RNA. Any solutes suitable for cell electroporation, which can contain factors facilitating cellular permeability and viability such as sugars, peptides, lipids, proteins, antioxidants, and surfactants can be included.

In some embodiments, a nucleic acid encoding a CAR of the present disclosure will be RNA, e.g., in vitro synthesized RNA. Methods for in vitro synthesis of RNA are known in the art; any known method can be used to synthesize RNA comprising a sequence encoding a CAR and therapeutic peptide. Methods for introducing RNA into a host cell are known in the art.

See, e.g., Zhao et al. Cancer Res. (2010) 15: 9053. Introducing RNA comprising a nucleotide sequence encoding a CAR and therapeutic peptide into a host cell can be carried out in vitro, ex vivo or in vivo. For example, a host cell (e.g., an NK cell, a cytotoxic T lymphocyte, etc.) can be electroporated in vitro or ex vivo with RNA comprising a nucleotide sequence encoding a CAR and therapeutic peptide.

The disclosed methods can be applied to the modulation of T cell activity in basic research and therapy, in the fields of cancer, stem cells, acute and chronic infections, and autoimmune diseases, including the assessment of the ability of the genetically modified T cell to kill a target cancer cell.

The methods also provide the ability to control the level of expression over a wide range by changing, for example, the promoter or the amount of input RNA, making it possible to individually regulate the expression level. Furthermore, the PCR-based technique of mRNA production greatly facilitates the design of the mRNAs with different structures and combination of their domains.

One advantage of RNA transfection methods of the disclosure is that RNA transfection is essentially transient and a vector-free. An RNA transgene can be delivered to a lymphocyte and expressed therein following a brief in vitro cell activation, as a minimal expressing cassette without the need for any additional viral sequences. Under these conditions, integration of the transgene into the host cell genome is unlikely. Cloning of cells is not necessary because of the efficiency of transfection of the RNA and its ability to uniformly modify the entire lymphocyte population.

Genetic modification of T cells with in v/Yro-transcribed RNA (IVT-RNA) makes use of two different strategies both of which have been successively tested in various animal models. Cells are transfected with in v/Yro-transcribed RNA by means of lipofection or electroporation. It is desirable to stabilize IVT-RNA using various modifications in order to achieve prolonged expression of transferred IVT-RNA.

Some IVT vectors are known in the literature which are utilized in a standardized manner as template for in vitro transcription and which have been genetically modified in such a way that stabilized RNA transcripts are produced. Currently protocols used in the art are based on a plasmid vector with the following structure: a 5' RNA polymerase promoter enabling RNA transcription, followed by a gene of interest which is flanked either 3' and/or 5' by untranslated regions (UTR), and a 3' polyadenyl cassette containing 50-70 A nucleotides. Prior to in vitro transcription, the circular plasmid is linearized downstream of the polyadenyl cassette by type II restriction enzymes (recognition sequence corresponds to cleavage site). The polyadenyl cassette thus corresponds to the later poly(A) sequence in the transcript. As a result of this procedure, some nucleotides remain as part of the enzyme cleavage site after linearization and extend or mask the poly(A) sequence at the 3' end. It is not clear, whether this nonphysiological overhang affects the amount of protein produced intracellularly from such a construct.

In another aspect, the RNA construct is delivered into the cells by electroporation. See, e.g., the formulations and methodology of electroporation of nucleic acid constructs into mammalian cells as taught in US 2004/0014645, US 2005/0052630A1, US 2005/0070841 Al,

US 2004/0059285A1, US 2004/0092907A1. The various parameters including electric field strength required for electroporation of any known cell type are generally known in the relevant research literature as well as numerous patents and applications in the field. See e.g., U.S. Pat. No. 6,678,556, U.S. Pat. No. 7,171,264, and U.S. Pat. No. 7,173,116. Apparatus for therapeutic application of electroporation are available commercially, e.g., the MedPulser™ DNA Electroporation Therapy System (Inovio/Genetronics, San Diego, Calif.), and are described in patents such as U.S. Pat. No. 6,567,694; U.S. Pat. No. 6,516,223, U.S. Pat. No. 5,993,434, U.S. Pat. No. 6,181,964, U.S. Pat. No. 6,241,701, and U.S. Pat. No. 6,233,482; electroporation may also be used for transfection of cells in vitro as described e.g. in US20070128708A1. Electroporation may also be utilized to deliver nucleic acids into cells in vitro. Accordingly, electroporation-mediated administration into cells of nucleic acids including expression constructs utilizing any of the many available devices and electroporation systems known to those of skill in the art presents an exciting new means for delivering an RNA of interest to a target cell.

In some embodiments, the cells (e.g. T cells) can be incubated or cultivated prior to, during and/or subsequent to introducing the nucleic acid molecule encoding the CAR and therapeutic peptide. In some embodiments, the cells (e.g. T cells) can be incubated or cultivated prior to, during or subsequent to the introduction of the nucleic acid molecule encoding the CAR and therapeutic peptide, such as prior to, during or subsequent to the transduction of the cells with a viral vector (e.g. lentiviral vector) encoding the CAR and therapeutic peptide. In some embodiments, the method includes activating or stimulating cells with a stimulating or activating agent (e.g. anti-CD3/anti-CD28 antibodies) prior to introducing the nucleic acid molecule encoding the CAR and therapeutic peptide. In some embodiments, prior to introducing the agent, the stimulating or activating agent and/or cytokines are not removed. Those of skill in the art will be able to determine the order in which each of the one or more nucleic acid sequences are introduced into the host cell.

J. Expansion of Immune Cells

Whether prior to or after engineering the cells ( e.g . to express a CAR and therapeutic peptide), the cells can be activated and expanded in number using methods as described, for example, in U.S. Patent Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681 ; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and U.S. Publication No. 20060121005. For example, the T cells of the disclosure may be expanded by contact with a surface having attached thereto an agent that stimulates a CD3/TCR complex associated signal and a ligand that stimulates a co-stimulatory molecule on the surface of the T cells. In particular, T cell populations may be stimulated by contact with an anti-CD3 antibody, or antigen-binding fragment thereof, or an anti-CD2 antibody immobilized on a surface, or by contact with a protein kinase C activator (e.g., bryostatin) in conjunction with a calcium ionophore. For co-stimulation of an accessory molecule on the surface of the T cells, a ligand that binds the accessory molecule is used. For example, T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells. Examples of an anti-CD28 antibody include 9.3, B-T3, XR-CD28 (Diaclone, Besancon, France) and these can be used in the disclosure, as can other methods and reagents known in the art (see, e.g., ten Berge et al., Transplant Proc. (1998) 30(8): 3975-3977; Haanen et al., J. Exp. Med. (1999) 190(9): 1319- 1328; and Garland et al., J. Immunol. Methods (1999) 227(1-2): 53-63).

Expanding T cells by the methods disclosed herein can be multiplied by about 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, 200 fold, 300 fold, 400 fold, 500 fold, 600 fold, 700 fold, 800 fold, 900 fold, 1000 fold, 2000 fold, 3000 fold, 4000 fold, 5000 fold, 6000 fold, 7000 fold, 8000 fold, 9000 fold, 10,000 fold, 100,000 fold, 1,000,000 fold,

10,000,000 fold, or greater, and any and all whole or partial integers therebetween. In one embodiment, the T cells expand in the range of about 20 fold to about 50 fold. Following culturing, the T cells can be incubated in cell medium in a culture apparatus for a period of time or until the cells reach confluency or high cell density for optimal passage before passing the cells to another culture apparatus. The culturing apparatus can be of any culture apparatus commonly used for culturing cells in vitro. Preferably, the level of confluence is 70% or greater before passing the cells to another culture apparatus. More preferably, the level of confluence is 90% or greater. A period of time can be any time suitable for the culture of cells in vitro. The T cell medium may be replaced during the culture of the T cells at any time. Preferably, the T cell medium is replaced about every 2 to 3 days. The T cells are then harvested from the culture apparatus whereupon the T cells can be used immediately or cryopreserved to be stored for use at a later time. In one embodiment, the disclosure includes cry opreserving the expanded T cells. The cryopreserved T cells are thawed prior to introducing nucleic acids into the T cell.

In another embodiment, the method comprises isolating T cells and expanding the T cells. In another embodiment, the disclosure further comprises cryopreserving the T cells prior to expansion. In yet another embodiment, the cryopreserved T cells are thawed for electroporation with the RNA encoding the chimeric membrane protein.

Another procedure for ex vivo expansion cells is described in U.S. Pat. No. 5,199,942 (incorporated herein by reference). Expansion, such as described in U.S. Pat. No. 5,199,942 can be an alternative or in addition to other methods of expansion described herein. Briefly, ex vivo culture and expansion of T cells comprises the addition to the cellular growth factors, such as those described in U.S. Pat. No. 5,199,942, or other factors, such as flt3-L, IL-1, IL-3 and c-kit ligand. In one embodiment, expanding the T cells comprises culturing the T cells with a factor selected from the group consisting of flt3-L, IL-1, IL-3 and c-kit ligand.

The culturing step as described herein (contact with agents as described herein or after electroporation) can be very short, for example less than 24 hours such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours. The culturing step as described further herein (contact with agents as described herein) can be longer, for example 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more days.

Various terms are used to describe cells in culture. Cell culture refers generally to cells taken from a living organism and grown under controlled condition. A primary cell culture is a culture of cells, tissues or organs taken directly from an organism and before the first subculture. Cells are expanded in culture when they are placed in a growth medium under conditions that facilitate cell growth and/or division, resulting in a larger population of the cells. When cells are expanded in culture, the rate of cell proliferation is typically measured by the amount of time required for the cells to double in number, otherwise known as the doubling time.

Each round of subculturing is referred to as a passage. When cells are subcultured, they are referred to as having been passaged. A specific population of cells, or a cell line, is sometimes referred to or characterized by the number of times it has been passaged. For example, a cultured cell population that has been passaged ten times may be referred to as a P10 culture. The primary culture, i.e., the first culture following the isolation of cells from tissue, is designated P0. Following the first subculture, the cells are described as a secondary culture (PI or passage 1). After the second subculture, the cells become a tertiary culture (P2 or passage 2), and so on. It will be understood by those of skill in the art that there may be many population doublings during the period of passaging; therefore the number of population doublings of a culture is greater than the passage number. The expansion of cells (i.e., the number of population doublings) during the period between passaging depends on many factors, including but is not limited to the seeding density, substrate, medium, and time between passaging.

In one embodiment, the cells may be cultured for several hours (about 3 hours) to about 14 days or any hourly integer value in between. Conditions appropriate for T cell culture include an appropriate media ( e.g ., Minimal Essential Media or RPMI Media 1640 or, X-vivo 15, (Lonza)) that may contain factors necessary for proliferation and viability, including serum (e.g., fetal bovine or human serum), interleukin-2 (IL-2), insulin, IFN-gamma, IL-4, IL-7, GM-CSF, IL-10, IL-12, IL-15, TGF-beta, and TNF-a or any other additives for the growth of cells known to the skilled artisan. Other additives for the growth of cells include, but are not limited to, surfactant, plasmanate, and reducing agents such as N-acetyl-cysteine and 2-mercaptoethanol. Media can include RPMI 1640, AIM-V, DMEM, MEM, a-MEM, F-12, X-Vivo 15, and X-Vivo 20, Optimizer, with added amino acids, sodium pyruvate, and vitamins, either serum-free or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones, and/or an amount of cytokine(s) sufficient for the growth and expansion of T cells. Antibiotics, e.g., penicillin and streptomycin, are included only in experimental cultures, not in cultures of cells that are to be infused into a subject. The target cells are maintained under conditions necessary to support growth, for example, an appropriate temperature ( e.g ., 37°C) and atmosphere (e.g., air plus 5% CO2).

The medium used to culture the T cells may include an agent that can co-stimulate the T cells. For example, an agent that can stimulate CD3 is an antibody to CD3, and an agent that can stimulate CD28 is an antibody to CD28. A cell isolated by the methods disclosed herein can be expanded approximately 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, 200 fold, 300 fold, 400 fold, 500 fold, 600 fold, 700 fold, 800 fold, 900 fold, 1000 fold, 2000 fold, 3000 fold, 4000 fold, 5000 fold, 6000 fold, 7000 fold, 8000 fold, 9000 fold, 10,000 fold, 100,000 fold, 1,000,000 fold, 10,000,000 fold, or greater. In one embodiment, the T cells expand in the range of about 20 fold to about 50 fold, or more. In one embodiment, human T regulatory cells are expanded via anti-CD3 antibody coated KT64.86 artificial antigen presenting cells (aAPCs). Methods for expanding and activating T cells can be found in U.S. Patent Numbers: 7,754,482, 8,722,400, and 9,555, 105, contents of which are incorporated herein in their entirety.

In one embodiment, the method of expanding the T cells can further comprise isolating the expanded T cells for further applications. In another embodiment, the method of expanding can further comprise a subsequent electroporation of the expanded T cells followed by culturing. The subsequent electroporation may include introducing a nucleic acid encoding an agent, such as a transducing the expanded T cells, transfecting the expanded T cells, or electroporating the expanded T cells with a nucleic acid, into the expanded population of T cells, wherein the agent further stimulates the T cell. The agent may stimulate the T cells, such as by stimulating further expansion, effector function, or another T cell function.

K. T Cell Receptors

The present disclosure provides compositions and methods for engineered cells (e.g., immune cells or precursors thereof, e.g., T cells) comprising an exogenous T cell receptor (TCR) and a therapeutic peptide. Thus, in some embodiments, the cell has been altered to contain specific T cell receptor (TCR) genes (e.g., a nucleic acid encoding an alpha/beta TCR). TCRs or antigen-binding portions thereof include those that recognize a peptide epitope or T cell epitope of a target polypeptide, such as an antigen of a tumor, viral or autoimmune protein. In certain embodiments, the TCR has binding specificity for a tumor associated antigen, e.g., human NY- ESO-1.

A TCR is a disulfide-linked heterodimeric protein comprised of six different membrane bound chains that participate in the activation of T cells in response to an antigen. There exists alpha/beta TCRs and gamma/delta TCRs. An alpha/beta TCR comprises a TCR alpha chain and a TCR beta chain. T cells expressing a TCR comprising a TCR alpha chain and a TCR beta chain are commonly referred to as alpha/beta T cells. Gamma/delta TCRs comprise a TCR gamma chain and a TCR delta chain. T cells expressing a TCR comprising a TCR gamma chain and a TCR delta chain are commonly referred to as gamma/delta T cells. A TCR of the present disclosure is a TCR comprising a TCR alpha chain and a TCR beta chain.

The TCR alpha chain and the TCR beta chain are each comprised of two extracellular domains, a variable region and a constant region. The TCR alpha chain variable region and the TCR beta chain variable region are required for the affinity of a TCR to a target antigen. Each variable region comprises three hypervariable or complementarity-determining regions (CDRs) which provide for binding to a target antigen. The constant region of the TCR alpha chain and the constant region of the TCR beta chain are proximal to the cell membrane. A TCR further comprises a transmembrane region and a short cytoplasmic tail. CD3 molecules are assembled together with the TCR heterodimer. CD3 molecules comprise a characteristic sequence motif for tyrosine phosphorylation, known as immunoreceptor tyrosine-based activation motifs (ITAMs). Proximal signaling events are mediated through the CD3 molecules, and accordingly, TCR-CD3 complex interaction plays an important role in mediating cell recognition events.

Stimulation of TCR is triggered by major histocompatibility complex molecules (MHCs) on antigen presenting cells that present antigen peptides to T cells and interact with TCRs to induce a series of intracellular signaling cascades. Engagement of the TCR initiates both positive and negative signaling cascades that result in cellular proliferation, cytokine production, and/or activation-induced cell death.

A TCR of the present disclosure can be a wild-type TCR, a high affinity TCR, and/or a chimeric TCR. A high affinity TCR may be the result of modifications to a wild-type TCR that confers a higher affinity for a target antigen compared to the wild-type TCR. A high affinity TCR may be an affinity-matured TCR. Methods for modifying TCRs and/or the affinity- maturation of TCRs are known to those of skill in the art. Techniques for engineering and expressing TCRs include, but are not limited to, the production of TCR heterodimers which include the native disulphide bridge which connects the respective subunits (Garboczi, et al ., (1996), Nature 384(6605): 134-41; Garboczi, etal. , (1996), J Immunol 157(12): 5403-10; Chang etal. , (1994), PNAS USA 91: 11408-11412; Davodeau etal. , (1993), J. Biol. Chem. 268(21): 15455-15460; Golden etal. , (1997), J. Imm. Meth. 206: 163-169; U.S. Pat. No. 6,080,840).

In some embodiments, the exogenous TCR is a full TCR or an antigen-binding portion or antigen-binding fragment thereof. In some embodiments, the TCR is an intact or full-length TCR, including TCRs in the ab form or gd form. In some embodiments, the TCR is an antigen binding portion that is less than a full-length TCR but that binds to a specific peptide bound in an MHC molecule, such as binds to an MHC-peptide complex. In some cases, an antigen-binding portion or fragment of a TCR can contain only a portion of the structural domains of a full-length or intact TCR, but yet is able to bind the peptide epitope, such as MHC-peptide complex, to which the full TCR binds. In some cases, an antigen-binding portion contains the variable domains of a TCR, such as variable a chain and variable b chain of a TCR, sufficient to form a binding site for binding to a specific MHC-peptide complex. Generally, the variable chains of a TCR contain complementarity determining regions (CDRs) involved in recognition of the peptide, MHC and/or MHC-peptide complex.

In some embodiments, the variable domains of the TCR contain hypervariable loops, or CDRs, which generally are the primary contributors to antigen recognition and binding capabilities and specificity. In some embodiments, a CDR of a TCR or combination thereof forms all or substantially all of the antigen-binding site of a given TCR molecule. The various CDRs within a variable region of a TCR chain generally are separated by framework regions (FRs), which generally display less variability among TCR molecules as compared to the CDRs (see, e.g., lores et al, Proc. Nat'l Acad. Sci. U.S. A. 87:9138, 1990; Chothia etal., EMBO J. 7:3745, 1988; see also Lefranc et al., Dev. Comp. Immunol. 27:55, 2003). In some embodiments, CDR3 is the main CDR responsible for antigen binding or specificity, or is the most important among the three CDRs on a given TCR variable region for antigen recognition, and/or for interaction with the processed peptide portion of the peptide-MHC complex. In some contexts, the CDR1 of the alpha chain can interact with the N-terminal part of certain antigenic peptides. In some contexts, CDR1 of the beta chain can interact with the C-terminal part of the peptide. In some contexts, CDR2 contributes most strongly to or is the primary CDR responsible for the interaction with or recognition of the MHC portion of the MHC-peptide complex. In some embodiments, the variable region of the b-chain can contain a further hypervariable region (CDR4 or HVR4), which generally is involved in superantigen binding and not antigen recognition (Kotb (1995) Clinical Microbiology Reviews, 8:411-426).

In some embodiments, a TCR contains a variable alpha domain (V _a ) and/or a variable beta domain (\¾) or antigen-binding fragments thereof. In some embodiments, the a-chain and/or b-chain of a TCR also can contain a constant domain, a transmembrane domain and/or a short cytoplasmic tail (see, e.g., Janeway et al., Immunobiology: The Immune System in Health and Disease, 3 Ed., Current Biology Publications, p. 4:33, 1997). In some embodiments, the a chain constant domain is encoded by the TRAC gene (IMGT nomenclature) or is a variant thereof. In some embodiments, the b chain constant region is encoded by TRBC1 or TRBC2 genes (IMGT nomenclature) or is a variant thereof. In some embodiments, the constant domain is adjacent to the cell membrane. For example, in some cases, the extracellular portion of the TCR formed by the two chains contains two membrane-proximal constant domains, and two membrane-distal variable domains, which variable domains each contain CDRs.

It is within the level of a skilled artisan to determine or identify the various domains or regions of a TCR. In some aspects, residues of a TCR are known or can be identified according to the International Immunogenetics Information System (IMGT) numbering system (see e.g. www.imgt.org; see also, Lefranc et al. (2003) Developmental and Comparative Immunology, 2&;55-77; and The T Cell Factsbook 2nd Edition, Lefranc and LeFranc Academic Press 2001). Using this system, the CDR1 sequences within a TCR Va chain and/or nb chain correspond to the amino acids present between residue numbers 27-38, inclusive, the CDR2 sequences within a TCR Va chain and/or nb chain correspond to the amino acids present between residue numbers 56-65, inclusive, and the CDR3 sequences within a TCR Va chain and/or nb chain correspond to the amino acids present between residue numbers 105-117, inclusive. The IMGT numbering system should not be construed as limiting in any way, as there are other numbering systems known to those of skill in the art, and it is within the level of the skilled artisan to use any of the numbering systems available to identify the various domains or regions of a TCR.

In some embodiments, the TCR may be a heterodimer of two chains a and b (or optionally g and d) that are linked, such as by a disulfide bond or disulfide bonds. In some embodiments, the constant domain of the TCR may contain short connecting sequences in which a cysteine residue forms a disulfide bond, thereby linking the two chains of the TCR. In some embodiments, a TCR may have an additional cysteine residue in each of the a and b chains, such that the TCR contains two disulfide bonds in the constant domains. In some embodiments, each of the constant and variable domains contain disulfide bonds formed by cysteine residues.

In some embodiments, the TCR for engineering cells as described is one generated from a known TCR sequence(s), such as sequences of na,b chains, for which a substantially full- length coding sequence is readily available. Methods for obtaining full-length TCR sequences, including V chain sequences, from cell sources are well known. In some embodiments, nucleic acids encoding the TCR can be obtained from a variety of sources, such as by polymerase chain reaction (PCR) amplification of TCR-encoding nucleic acids within or isolated from a given cell or cells, or synthesis of publicly available TCR DNA sequences. In some embodiments, the TCR is obtained from a biological source, such as from cells such as from a T cell (e.g. cytotoxic T cell), T cell hybridomas or other publicly available source. In some embodiments, the T cells can be obtained from in vivo isolated cells. In some embodiments, the T cells can be a cultured T cell hybridoma or clone. In some embodiments, the TCR or antigen-binding portion thereof can be synthetically generated from knowledge of the sequence of the TCR. In some embodiments, a high-affinity T cell clone for a target antigen (e.g., a cancer antigen) is identified, isolated from a patient, and introduced into the cells. In some embodiments, the TCR clone for a target antigen has been generated in transgenic mice engineered with human immune system genes (e.g., the human leukocyte antigen system, or HLA). See, e.g., tumor antigens (see, e.g., Parkhurst et al. (2009) Clin Cancer Res. 15: 169-180 and Cohen et al. (2005) J Immunol. 175:5799-5808. In some embodiments, phage display is used to isolate TCRs against a target antigen (see, e.g., Varela-Rohena et al. (2008) Nat Med. 14: 1390-1395 and Li (2005) Nat Biotechnol. 23:349-354.

In some embodiments, the TCR or antigen-binding portion thereof is one that has been modified or engineered. In some embodiments, directed evolution methods are used to generate TCRs with altered properties, such as with higher affinity for a specific MHC-peptide complex. In some embodiments, directed evolution is achieved by display methods including, but not limited to, yeast display (Holler et al. (2003) Nat Immunol, 4, 55-62; Holler et al. (2000) Proc Natl Acad Sci U S A, 97, 5387-92), phage display (Li etal. (2005) Nat Biotechnol, 23, 349-54), or T cell display (Chervin et al. (2008) J Immunol Methods, 339, 175-84). In some embodiments, display approaches involve engineering, or modifying, a known, parent or reference TCR. For example, in some cases, a wild-type TCR can be used as a template for producing mutagenized TCRs in which in one or more residues of the CDRs are mutated, and mutants with an desired altered property, such as higher affinity for a desired target antigen, are selected.

In some embodiments as described, the TCR can contain an introduced disulfide bond or bonds. In some embodiments, the native disulfide bonds are not present. In some embodiments, the one or more of the native cysteines (e.g. in the constant domain of the a chain and b chain) that form a native interchain disulfide bond are substituted with another residue, such as with a serine or alanine. In some embodiments, an introduced disulfide bond can be formed by mutating non-cysteine residues on the alpha and beta chains, such as in the constant domain of the a chain and b chain, to cysteine. Exemplary non-native disulfide bonds of a TCR are described in published International PCT No. W02006/000830 and W02006/037960. In some embodiments, cysteines can be introduced at residue Thr48 of the a chain and Ser57 of the b chain, at residue Thr45 of the a chain and Ser77 of the b chain, at residue TyrlO of the a chain and Serl7 of the b chain, at residue Thr45 of the a chain and Asp59 of the b chain and/or at residue Serl5 of the a chain and Glul5 of the b chain. In some embodiments, the presence of non-native cysteine residues (e.g. resulting in one or more non-native disulfide bonds) in a recombinant TCR can favor production of the desired recombinant TCR in a cell in which it is introduced over expression of a mismatched TCR pair containing a native TCR chain.

In some embodiments, the TCR chains contain a transmembrane domain. In some embodiments, the transmembrane domain is positively charged. In some cases, the TCR chain contains a cytoplasmic tail. In some aspects, each chain (e.g. alpha or beta) of the TCR can possess one N-terminal immunoglobulin variable domain, one immunoglobulin constant domain, a transmembrane region, and a short cytoplasmic tail at the C-terminal end. In some embodiments, a TCR, for example via the cytoplasmic tail, is associated with invariant proteins of the CD3 complex involved in mediating signal transduction. In some cases, the structure allows the TCR to associate with other molecules like CD3 and subunits thereof. For example, a TCR containing constant domains with a transmembrane region may anchor the protein in the cell membrane and associate with invariant subunits of the CD3 signaling apparatus or complex. The intracellular tails of CD3 signaling subunits ( e.g . CD3y, CD35, CD3s and CD3z chains) contain one or more immunoreceptor tyrosine-based activation motif or IT AM that are involved in the signaling capacity of the TCR complex.

In some embodiments, the TCR is a full-length TCR. In some embodiments, the TCR is an antigen-binding portion. In some embodiments, the TCR is a dimeric TCR (dTCR). In some embodiments, the TCR is a single-chain TCR (sc-TCR). A TCR may be cell-bound or in soluble form. In some embodiments, for purposes of the provided methods, the TCR is in cell-bound form expressed on the surface of a cell. In some embodiments a dTCR contains a first polypeptide wherein a sequence corresponding to a TCR a chain variable region sequence is fused to the N terminus of a sequence corresponding to a TCR a chain constant region extracellular sequence, and a second polypeptide wherein a sequence corresponding to a TCR b chain variable region sequence is fused to the N terminus a sequence corresponding to a TCR b chain constant region extracellular sequence, the first and second polypeptides being linked by a disulfide bond. In some embodiments, the bond can correspond to the native interchain disulfide bond present in native dimeric ab TCRs. In some embodiments, the interchain disulfide bonds are not present in a native TCR. For example, in some embodiments, one or more cysteines can be incorporated into the constant region extracellular sequences of dTCR polypeptide pair. In some cases, both a native and a non-native disulfide bond may be desirable. In some embodiments, the TCR contains a transmembrane sequence to anchor to the membrane. In some embodiments, a dTCR contains a TCR a chain containing a variable a domain, a constant a domain and a first dimerization motif attached to the C-terminus of the constant a domain, and a TCR b chain comprising a variable b domain, a constant b domain and a first dimerization motif attached to the C-terminus of the constant b domain, wherein the first and second dimerization motifs easily interact to form a covalent bond between an amino acid in the first dimerization motif and an amino acid in the second dimerization motif linking the TCR a chain and TCR b chain together.

In some embodiments, the TCR is a scTCR, which is a single amino acid strand containing an a chain and a b chain that is able to bind to MHC -peptide complexes. Typically, a scTCR can be generated using methods known to those of skill in the art, See e.g., International published PCT Nos. WO 96/13593, WO 96/18105, W099/18129, WO04/033685, W02006/037960, WO2011/044186; U.S. Patent No. 7,569,664; and Schlueter, C. J. et al. J. Mol. Biol. 256, 859 (1996). In some embodiments, a scTCR contains a first segment constituted by an amino acid sequence corresponding to a TCR a chain variable region, a second segment constituted by an amino acid sequence corresponding to a TCR b chain variable region sequence fused to the N terminus of an amino acid sequence corresponding to a TCR b chain constant domain extracellular sequence, and a linker sequence linking the C terminus of the first segment to the N terminus of the second segment. In some embodiments, a scTCR contains a first segment constituted by an amino acid sequence corresponding to a TCR b chain variable region, a second segment constituted by an amino acid sequence corresponding to a TCR a chain variable region sequence fused to the N terminus of an amino acid sequence corresponding to a TCR a chain constant domain extracellular sequence, and a linker sequence linking the C terminus of the first segment to the N terminus of the second segment. In some embodiments, a scTCR contains a first segment constituted by an a chain variable region sequence fused to the N terminus of an a chain extracellular constant domain sequence, and a second segment constituted by a b chain variable region sequence fused to the N terminus of a sequence b chain extracellular constant and transmembrane sequence, and, optionally, a linker sequence linking the C terminus of the first segment to the N terminus of the second segment. In some embodiments, a scTCR contains a first segment constituted by a TCR b chain variable region sequence fused to the N terminus of a b chain extracellular constant domain sequence, and a second segment constituted by an a chain variable region sequence fused to the N terminus of a sequence comprising an a chain extracellular constant domain sequence and transmembrane sequence, and, optionally, a linker sequence linking the C terminus of the first segment to the N terminus of the second segment. In some embodiments, for the scTCR to bind an MHC-peptide complex, the a and b chains must be paired so that the variable region sequences thereof are orientated for such binding. Various methods of promoting pairing of an a and b in a scTCR are well known in the art. In some embodiments, a linker sequence is included that links the a and b chains to form the single polypeptide strand. In some embodiments, the linker should have sufficient length to span the distance between the C terminus of the a chain and the N terminus of the b chain, or vice versa, while also ensuring that the linker length is not so long so that it blocks or reduces bonding of the scTCR to the target peptide-MHC complex. In some embodiments, the linker of a scTCRs that links the first and second TCR segments can be any linker capable of forming a single polypeptide strand, while retaining TCR binding specificity. In some embodiments, the linker sequence may, for example, have the formula -P-AA-P-, wherein P is proline and AA represents an amino acid sequence wherein the amino acids are glycine and serine. In some embodiments, the first and second segments are paired so that the variable region sequences thereof are orientated for such binding. Hence, in some cases, the linker has a sufficient length to span the distance between the C terminus of the first segment and the N terminus of the second segment, or vice versa, but is not too long to block or reduces bonding of the scTCR to the target ligand. In some embodiments, the linker can contain from or from about 10 to 45 amino acids, such as 10 to 30 amino acids or 26 to 41 amino acids residues, for example 29, 30, 31 or 32 amino acids. In some embodiments, a scTCR contains a disulfide bond between residues of the single amino acid strand, which, in some cases, can promote stability of the pairing between the a and b regions of the single chain molecule (see e.g. U.S. Patent No. 7,569,664). In some embodiments, the scTCR contains a covalent disulfide bond linking a residue of the immunoglobulin region of the constant domain of the a chain to a residue of the immunoglobulin region of the constant domain of the b chain of the single chain molecule. In some embodiments, the disulfide bond corresponds to the native disulfide bond present in a native dTCR. In some embodiments, the disulfide bond in a native TCR is not present. In some embodiments, the disulfide bond is an introduced non-native disulfide bond, for example, by incorporating one or more cysteines into the constant region extracellular sequences of the first and second chain regions of the scTCR polypeptide. Exemplary cysteine mutations include any as described above. In some cases, both a native and a non-native disulfide bond may be present.

In some embodiments, any of the TCRs, including a dTCR or scTCR, can be linked to signaling domains that yield an active TCR on the surface of a T cell. In some embodiments, the TCR is expressed on the surface of cells. In some embodiments, the TCR does contain a sequence corresponding to a transmembrane sequence. In some embodiments, the transmembrane domain can be a Ca or CP transmembrane domain. In some embodiments, the transmembrane domain can be from a non-TCR origin, for example, a transmembrane region from CD3z, CD28 or B7.1. In some embodiments, the TCR does contain a sequence corresponding to cytoplasmic sequences. In some embodiments, the TCR contains a CD3z signaling domain. In some embodiments, the TCR is capable of forming a TCR complex with CD3. In some embodiments, the TCR or antigen binding portion thereof may be a recombinantly produced natural protein or mutated form thereof in which one or more property, such as binding characteristic, has been altered. In some embodiments, a TCR may be derived from one of various animal species, such as human, mouse, rat, or other mammal.

In some embodiments, the TCR comprises affinity to a target antigen on a target cell. The target antigen may include any type of protein, or epitope thereof, associated with the target cell. For example, the TCR may comprise affinity to a target antigen on a target cell that indicates a particular disease state of the target cell. In some embodiments, the target antigen is processed and presented by MHCs.

L. Pharmaceutical Compositions and Formulations

Also provided are populations of cells ( e.g . immune cells; e.g. T cells) of the disclosure, compositions containing such cells and/or enriched for such cells, such as in which cells expressing the CAR and therapeutic peptide make up at least 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more of the total cells in the composition or cells of a certain type such as T cells or CD8+ or CD4+ cells. Among the compositions are pharmaceutical compositions and formulations for administration, such as for adoptive cell therapy. Also provided are therapeutic methods for administering the cells and compositions to subjects, e.g., patients.

Also provided are compositions including the cells for administration, including pharmaceutical compositions and formulations, such as unit dose form compositions including the number of cells for administration in a given dose or fraction thereof. The pharmaceutical compositions and formulations generally include one or more optional pharmaceutically acceptable carrier or excipient. In some embodiments, the composition includes at least one additional therapeutic agent.

The term "pharmaceutical formulation" refers to a preparation which is in such form as to permit the biological activity of an active ingredient contained therein to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered. A "pharmaceutically acceptable carrier" refers to an ingredient in a pharmaceutical formulation, other than an active ingredient, which is nontoxic to a subject. A pharmaceutically acceptable carrier includes, but is not limited to, a buffer, excipient, stabilizer, or preservative. In some aspects, the choice of carrier is determined in part by the particular cell and/or by the method of administration. Accordingly, there are a variety of suitable formulations. For example, the pharmaceutical composition can contain preservatives. Suitable preservatives may include, for example, methylparaben, propylparaben, sodium benzoate, and benzalkonium chloride. In some aspects, a mixture of two or more preservatives is used. The preservative or mixtures thereof are typically present in an amount of about 0.0001% to about 2% by weight of the total composition. Carriers are described, e.g., by Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980). Pharmaceutically acceptable carriers are generally nontoxic to recipients at the dosages and concentrations employed, and include, but are not limited to: buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride; benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g. Zn-protein complexes); and/or non-ionic surfactants such as polyethylene glycol (PEG). Buffering agents in some aspects are included in the compositions. Suitable buffering agents include, for example, citric acid, sodium citrate, phosphoric acid, potassium phosphate, and various other acids and salts. In some aspects, a mixture of two or more buffering agents is used. The buffering agent or mixtures thereof are typically present in an amount of about 0.001% to about 4% by weight of the total composition. Methods for preparing administrable pharmaceutical compositions are known. Exemplary methods are described in more detail in, for example, Remington: The Science and Practice of Pharmacy, Lippincott Williams & Wilkins; 21st ed. (May 1, 2005).

The formulations can include aqueous solutions. The formulation or composition may also contain more than one active ingredient useful for the particular indication, disease, or condition being treated with the cells, preferably those with activities complementary to the cells, where the respective activities do not adversely affect one another. Such active ingredients are suitably present in combination in amounts that are effective for the purpose intended. Thus, in some embodiments, the pharmaceutical composition further includes other pharmaceutically active agents or drugs, such as chemotherapeutic agents, e.g., asparaginase, busulfan, carboplatin, cisplatin, daunorubicin, doxorubicin, fluorouracil, gemcitabine, hydroxyurea, methotrexate, paclitaxel, rituximab, vinblastine, and/or vincristine. The pharmaceutical composition in some embodiments contains the cells in amounts effective to treat or prevent the disease or condition, such as a therapeutically effective or prophylactically effective amount. Therapeutic or prophylactic efficacy in some embodiments is monitored by periodic assessment of treated subjects. The desired dosage can be delivered by a single bolus administration of the cells, by multiple bolus administrations of the cells, or by continuous infusion administration of the cells.

Formulations include those for oral, intravenous, intraperitoneal, subcutaneous, pulmonary, transdermal, intramuscular, intranasal, buccal, sublingual, or suppository administration. In some embodiments, the cell populations are administered parenterally. The term "parenteral," as used herein, includes intravenous, intramuscular, subcutaneous, rectal, vaginal, and intraperitoneal administration. In some embodiments, the cells are administered to the subject using peripheral systemic delivery by intravenous, intraperitoneal, or subcutaneous injection. Compositions in some embodiments are provided as sterile liquid preparations, e.g., isotonic aqueous solutions, suspensions, emulsions, dispersions, or viscous compositions, which may in some aspects be buffered to a selected pH. Liquid preparations are normally easier to prepare than gels, other viscous compositions, and solid compositions. Additionally, liquid compositions are somewhat more convenient to administer, especially by injection. Viscous compositions, on the other hand, can be formulated within the appropriate viscosity range to provide longer contact periods with specific tissues. Liquid or viscous compositions can comprise carriers, which can be a solvent or dispersing medium containing, for example, water, saline, phosphate buffered saline, polyoi (for example, glycerol, propylene glycol, liquid polyethylene glycol) and suitable mixtures thereof.

Sterile injectable solutions can be prepared by incorporating the cells in a solvent, such as in admixture with a suitable carrier, diluent, or excipient such as sterile water, physiological saline, glucose, dextrose, or the like. The compositions can contain auxiliary substances such as wetting, dispersing, or emulsifying agents ( e.g ., methylcellulose), pH buffering agents, gelling or viscosity enhancing additives, preservatives, flavoring agents, and/or colors, depending upon the route of administration and the preparation desired. Standard texts may in some aspects be consulted to prepare suitable preparations.

Various additives which enhance the stability and sterility of the compositions, including antimicrobial preservatives, antioxidants, chelating agents, and buffers, can be added. Prevention of the action of microorganisms can be ensured by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, and sorbic acid. Prolonged absorption of the injectable pharmaceutical form can be brought about by the use of agents delaying absorption, for example, aluminum monostearate and gelatin.

The formulations to be used for in vivo administration are generally sterile. Sterility may be readily accomplished, e.g., by filtration through sterile filtration membranes.

M. Enumerated Embodiments

The following enumerated embodiments are provided, the numbering of which is not to be construed as designating levels of importance.

Embodiment 1 provides an engineered cell, comprising a chimeric antigen receptor

(CAR) and a therapeutic peptide, wherein the CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular domain, and wherein the therapeutic peptide is a non-natural therapeutic peptide; wherein the CAR molecule and the therapeutic peptide are expressed from the same expression construct.

Embodiment 2 provides an engineered cell comprising a chimeric antigen receptor (CAR) and a therapeutic peptide, wherein the CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular domain, and wherein the therapeutic peptide is a non-natural therapeutic peptide, and wherein the therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

Embodiment 3 provides the engineered cell of any preceding embodiment, wherein the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP.

Embodiment 4 provides the engineered cell of embodiment 1 or 2, wherein the therapeutic peptide is a mimetic of a TLR agonist.

Embodiment 5 provides the engineered cell of embodiment 4, wherein the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL).

Embodiment 6 provides the engineered cell of embodiment 1 or 2, wherein the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic.

Embodiment 7 provides the engineered cell of embodiment 1 or 2, wherein the therapeutic peptide is an inhibitor of poly ADP ribose polymerase (PARP).

Embodiment 8 provides the engineered cell of any one of embodiments 1-7, wherein the non-natural peptide is a peptide that has no more than 90% sequence identity to a naturally occurring peptide. Embodiment 9 provides the engineered cell of any one of embodiments 1-7, wherein the non-natural peptide is a peptide that has no more than 80% sequence identity to a naturally occurring peptide.

Embodiment 10 provides the engineered cell of any one of embodiments 1-9, wherein the peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-16.

Embodiment 11 provides the engineered cell of any one of embodiments 1-10, wherein the therapeutic peptide is exported from the engineered cell in extracellular vesicles.

Embodiment 12 provides the engineered cell of any one of embodiments 1-11, wherein the therapeutic peptide is a mimetic of a SCFA that binds to a G protein-coupled receptor (GPCR).

Embodiment 13 provides the engineered cell of any one of embodiments 1-12, wherein the target cell is a tumor cell.

Embodiment 14 provides the engineered cell of any one of embodiments 1-13, wherein the engineered cell is a T cell or an NIC cell.

Embodiment 15 provides the engineered cell of any one of embodiments 1-14 wherein the antigen binding domain is selected from the group consisting of an antibody, an antigen binding fragment (Fab), and a single-chain variable fragment (scFv).

Embodiment 16 provides the engineered cell of any one of embodiments 1-14, wherein the binding domain is a T cell receptor (TCR).

Embodiment 17 provides the engineered cell of any one of embodiments 1-16, wherein the target antigen is selected from the group consisting of CD19, CD20, CD22, BCMA, CD123, CD133, EGFR, EGFRvIII, mesothelin, Her2, PSMA, CEA, GD2, IL-13Ra2, glypican-3, CIAX, LI-CAM, CA 125, CTAG1B, Mucin 1, and Folate receptor-alpha.

Embodiment 18 provides the engineered cell of embodiment 17, wherein the target antigen is expressed on an intestinal cell.

Embodiment 19 provides the engineered cell of any one of embodiments 1-18, wherein the transmembrane domain is a transmembrane domain from a protein selected from the group consisting of CD8 alpha, CD3 zeta, CD3 epsilon, CD28, and ICOS. Embodiment 20 provides the engineered cell of any one of embodiments 1-19, wherein the intracellular signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD3 zeta, TCR zeta, CD3 epsilon, CD3 gamma, CD3 delta, or ICOS.

Embodiment 21 provides the engineered cell of any one of embodiments 1-19, wherein the intracellular signaling domain comprises a functional signaling domain and further comprises a costimulatory domain, wherein the costimulatory domain comprises a functional signaling domain from 4-1BB or CD28.

Embodiment 22 provides the engineered cell of any one of embodiments 1-21, wherein the CAR comprises an anti-CD19 scFv, a CD8 alpha transmembrane domain, a 4-1BB costimulatory domain, and a CD3 zeta signaling domain.

Embodiment 23 provides the engineered cell of any one of embodiments 1-13, wherein the therapeutic peptide is a SCFA mimetic or is a mimetic of a steroid and/or hormone-like molecule, and wherein the engineered cell has been further modified to reduce activity of one or more effector functions.

Embodiment 24 provides the engineered cell of embodiment 23, wherein the engineered cell has been modified to reduce or prevent expression of one or more inflammatory cytokines, expression of Granzyme B, or expression of perforin.

Embodiment 25 provides the engineered cell of any one of embodiments 1-24, wherein the CAR molecule and the therapeutic peptide are expressed from the same expression construct and wherein the expression construct further comprises an RNA molecule that activates a PRR.

Embodiment 26 provides the engineered cell of embodiment 25, wherein the RNA molecule is 7SL.

Embodiment 27 provides a composition comprising the engineered cell of any one of embodiments 1-26.

Embodiment 28 provides a nucleic acid molecule encoding (i) a chimeric antigen receptor (CAR) comprising an antigen binding domain, a transmembrane domain, and an intracellular signaling domain, and (ii) a therapeutic peptide, wherein the therapeutic peptide is a non-natural peptide. Embodiment 29 provides the nucleic acid molecule of embodiment 28, wherein a stop codon separates the nucleic acid segment encoding the CAR from the nucleic acid segment encoding the therapeutic peptide.

Embodiment 30 provides the nucleic acid molecule of embodiment 28 or 29, wherein the therapeutic peptide encoded by the nucleic acid molecule has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

Embodiment 31 provides the nucleic acid molecule of embodiment 30, wherein the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP.

Embodiment 32 provides the nucleic acid molecule of embodiment 30, wherein the therapeutic peptide is a mimetic of a TLR agonist.

Embodiment 33 provides the nucleic acid molecule of embodiment 32, wherein the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL).

Embodiment 34 provides the nucleic acid molecule of embodiment 30, wherein the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic.

Embodiment 35 provides the nucleic acid molecule of embodiment 30, wherein the therapeutic peptide is an inhibitor of poly ADP ribose polymerase (PARP).

Embodiment 36 provides the nucleic acid molecule of any one of embodiments 28-35, wherein the nucleic acid encoding the non-natural peptide has no more than 80% sequence identity to a nucleic acid encoding a naturally occurring peptide.

Embodiment 37 provides the nucleic acid molecule of any one of embodiments 28-36, wherein the target cell is a tumor cell. Embodiment 38 provides the nucleic acid molecule of any one of embodiments 28-37, wherein the antigen binding domain encoded by the nucleic acid molecule is selected from the group consisting of an antibody, a Fab, and an scFv.

Embodiment 39 provides the nucleic acid molecule of any one of embodiments 28-37, wherein the binding domain encoded by the nucleic acid molecule is a TCR.

Embodiment 40 provides the nucleic acid molecule of any one of embodiments 28-39, wherein the binding domain encoded by the nucleic acid molecule binds a target antigen selected from the group consisting of CD19, CD20, CD22, BCMA, CD123, CD133, EGFR, EGFRvIII, mesothelin, Her2, PSMA, CEA, GD2, IL-13Ra2, glypican-3, CIAX, LI-CAM, CA 125, CTAG1B, Mucin 1, and Folate receptor-alpha.

Embodiment 41 provides the nucleic acid molecule of any one of embodiments 28-40, wherein the transmembrane domain encoded by the nucleic acid molecule is a transmembrane domain from a protein selected from the group consisting of CD8 alpha, CD3 zeta, CD3 epsilon, CD28, and ICOS.

Embodiment 42 provides the nucleic acid molecule of any one of embodiments 28-41, wherein the intracellular signaling domain encoded by the nucleic acid molecule comprises a functional signaling domain of a protein selected from the group consisting of CD3 zeta, TCR zeta, CD3 epsilon, CD3 gamma, CD3 delta, or ICOS.

Embodiment 43 provides the nucleic acid molecule of any one of embodiments 28-42, wherein the intracellular signaling domain encoded by the nucleic acid molecule comprises a functional signaling domain and further comprises a costimulatory domain, wherein the costimulatory domain comprises a functional signaling domain from 4-1BB or CD28.

Embodiment 44 provides the nucleic acid molecule of any one of embodiments 28-43, wherein the nucleic acid molecule encodes a CAR molecule comprising an anti-CD 19 scFv, a CD8 alpha transmembrane domain, a 4- IBB costimulatory domain, and a CD3 zeta signaling domain.

Embodiment 45 provides the nucleic acid molecule of any one of embodiments 28-44, further comprising an RNA molecule that activates a PRR.

Embodiment 46 provides the engineered cell of embodiment 45, wherein the RNA molecule is 7SL. Embodiment 47 provides an expression vector comprising the nucleic acid molecule of any one of embodiments 28-46.

Embodiment 48 provides a method for co-expressing a CAR and a therapeutic peptide in a cell, the method comprising delivering to the cell the expression vector of embodiment 47, under conditions such that the CAR and the therapeutic peptide are expressed.

Embodiment 49 provides a cell comprising the nucleic acid molecule of any one of embodiments 28-45 or the expression vector of embodiment 47.

Embodiment 50 provides a method for treating a disease or disorder in a subject, comprising administering to the subject an effective amount of a T cell genetically modified to express a chimeric antigen receptor (CAR), wherein the CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular signaling domain, and wherein the method further comprises stimulation of the endogenous immune response against the cancer via a non-natural therapeutic peptide, wherein the non-natural therapeutic peptide is expressed in the modified T cell and/or is administered in combination with the modified T cell, and wherein the non-natural therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

Embodiment 51 provides the method of embodiment 50, wherein the therapeutic peptide is a mimetic of cGAMP, cAMP, or cGMP.

Embodiment 52 provides the method of embodiment 50, wherein the therapeutic peptide is a mimetic of a TLR agonist.

Embodiment 53 provides the method of embodiment 50, wherein the therapeutic peptide is a mimetic of flagellin, a CpG motif, peptidoglycan, lipopolysaccharide (LPS), or monophosphoryl lipid A (MPL). Embodiment 54 provides the method of embodiment 50, wherein the therapeutic peptide is a second mitochondria derived activator of caspase (SMAC) mimetic.

Embodiment 55 provides the method of embodiment 50, wherein the therapeutic peptide is an inhibitor of poly ADP ribose polymerase (PARP).

Embodiment 56 provides the method of claim 50, wherein the non-natural peptide is a peptide that has no more than 80% sequence identity to any naturally occurring peptide.

Embodiment 57 provides the method of embodiment 50, wherein the peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-16.

Embodiment 58 provides the method of embodiment 50, wherein the therapeutic peptide is an immunogenic epitope, and wherein the immunogenic epitope is expressed on the surface of a cancer cell in the subject following the administration to the subject.

Embodiment 59 provides the method of any one of embodiments 51-58, wherein the therapeutic peptide is expressed in the modified T cell, wherein subsequent to administration of the modified T cell to the subject, the therapeutic peptide is exported from the modified T cell in one or more extracellular vesicles.

Embodiment 60 provides the method of embodiment 59, wherein the therapeutic peptide is delivered via the one or more extracellular vesicles to one or more antigen presenting cells in the subject.

Embodiment 61 provides a method for enhancing anti-cancer activity of a T cell genetically modified to express a chimeric antigen receptor (CAR), wherein the CAR comprises an antigen binding domain that specifically binds to an antigen expressed on a tumor cell, a transmembrane domain, and a signaling domain, wherein the method comprises co-expressing a non-natural therapeutic peptide in the T cell, and wherein the non-natural therapeutic peptide has one or more of the following properties: (i) the therapeutic peptide is an activator of the stimulator of interferon genes (STING) pathway, (ii) the therapeutic peptide is a mimetic of a cyclic dinucleotide, (iii) the therapeutic peptide is a mimetic of a short chain fatty acid (SCFA), (iv) the therapeutic peptide is an agonist of a pattern recognition receptor (PRR), (v) the therapeutic peptide is a mimetic of a steroid/hormone-like molecule, (vi) the therapeutic peptide promotes apoptosis of the target cell, (vii) the therapeutic peptide is an immunogenic epitope, and/or (viii) the therapeutic peptide blocks one or more mechanism of DNA repair in the target cell.

Embodiment 62 provides a method for treating an inflammatory disease, an autoimmune disease, or a cancer in a subject, comprising administering to the subject an effective amount of an engineered cell according to any one of embodiments 1-26 or a composition according to embodiment 27 or a cell according to embodiment 49.

Embodiment 63 provides the method of any one of embodiments 50-61, wherein the cancer is a solid tumor cancer.

Embodiment 64 provides the method of embodiment 63, wherein the cancer is selected from the group consisting of lung cancer, small cell lung cancer, non-small cell lung cancer, mesothelioma, pancreatic cancer, breast cancer, ovarian cancer, fallopian tube cancer, cervical cancer, prostate cancer, colorectal cancer, gastric cancer, bladder cancer, esophageal cancer, and melanoma.

Embodiment 65 provides the method of any one of embodiments 50-61, wherein the cancer is a hematological cancer.

Embodiment 66 provides the method of embodiment 65, wherein the hematological cancer is a leukemia or lymphoma.

Embodiment 67 provides the method of embodiment 65, wherein the hematological cancer is selected from the group consisting of chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL) multiple myeloma, acute lymphoid leukemia (ALL), Hodgkin lymphoma, B- cell acute lymphoid leukemia (BALL), T-cell acute lymphoid leukemia (TALL), small lymphocytic leukemia (SLL), acute myeloid leukemia (AML), B cell prolymphocytic leukemia, blastic plasmacytoid dendritic cell neoplasm, Burkitf s lymphoma, diffuse large B cell lymphoma (DLBCL), chronic myeloid leukemia, myeloproliferative neoplasms, follicular lymphoma, pediatric follicular lymphoma, hairy cell leukemia, small cell- or a large cell-follicular lymphoma, malignant lymphoproliferative conditions, MALT lymphoma (extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue), Marginal zone lymphoma, myelodysplasia, myelodysplastic syndrome, non-Hodgkin lymphoma, plasmablastic lymphoma, plasmacytoid dendritic cell neoplasm, Waldenstrom macroglobulinemia, splenic marginal zone lymphoma, lymphoplasmacytic lymphoma, and plasma cell myeloma. Embodiment 68 provides the method of embodiment 62, wherein the autoimmune disease is an inflammatory bowel disease.

The contents of the articles, patents, and patent applications, and all other documents and electronically available information mentioned or cited herein, are hereby incorporated by reference in their entirety to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference. Applicants reserve the right to physically incorporate into this application any and all materials and information from any such articles, patents, patent applications, or other physical and electronic documents.

While the present disclosure has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the disclosure. It will be readily apparent to those skilled in the art that other suitable modifications and adaptations of the methods described herein may be made using suitable equivalents without departing from the scope of the embodiments disclosed herein. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present disclosure. All such modifications are intended to be within the scope of the claims appended hereto. Having now described certain embodiments in detail, the same will be more clearly understood by reference to the following examples, which are included for purposes of illustration only and are not intended to be limiting.

EXPERIMENTAL EXAMPLES

The invention is now described with reference to the following Examples. These Examples are provided for the purpose of illustration only, and the invention is not limited to these Examples, but rather encompasses all variations that are evident as a result of the teachings provided herein. Example 1: CAR-T cells engineered to express and transfer immunogenic peptide epitopes

A study was conducted to assess whether CAR-T cells can be engineered to express and transfer immunogenic peptide epitopes. The SIINFEKL peptide (SEQ ID NO: 7) was utilized as a test peptide. FIG. 2 provides a schematic view of the viral construct for SIINFEKL peptide delivery. The construct includes a 19BBz CAR molecule (anti-CD 19 scFv, and 4- IBB and CD3 zeta intracellular domains) and the SIINFEKL peptide (“Ova-19BBz CAR”). The short length of the peptide allows for an internal stop codon, which facilitates efficient expression of both the peptide and the CAR molecule. The construct for SIINFEKL peptide as shown in FIG. 2 was incorporated into CD3+ T cells isolated from a subject. Cells were subsequently assessed by flow cytometry to determine if the CAR and/or the peptide was expressed on the engineered cells. FIG. 3 shows that both peptide and the CAR molecule were efficiently expressed. Peptide expression was detected by SIINFEKL peptide/MHC-specific antibody. Moreover, peptide/MHC complexes were detected not only on CAR+ cells, but also on untransduced (non-CAR expressing) cells, indicating successful transfer of the antigenic peptide to other cells in the population (FIG. 4).

Further studies were conducted to assess the transfer of the antigenic peptide from CAR expressing cells to tumor cells and/or immune cells. As shown in the schematic depiction in FIG. 5, Ova-19BBz CAR T cells were expanded in culture and cells and EVs were harvested after expansion. For expansion, T cells were isolated from mouse splenocytes using a negative selection T cell isolation kit. Following isolation, T cells were stimulated with CD3/CD28 beads, and 24 hours later, the retrovirus (on a MSGV backbone) encoding the indicated CAR molecules was introduced. 48 hours after transduction, cells were de-beaded and checked for CAR transduction.

Extracellular vesicles (EV) were harvested from the media via ultracentrifugation. EVs were then incubated with B 16 cells (a melanoma cell line) in vitro at various concentrations, along with 1 x 10 ⁶ OT-I T cells, which are specific for SIINFEKL. Peptide/MHC loading and OT-I T cell activation were assessed by flow cytometry 72 hours later. T cell activation was determined by staining for Granzyme B. As shown in FIG. 6 A, a dose response of increasing Ova/MHC expression on the tumor, as well as increasing Granzyme B expression in OT-I T cells, was observed with increasing concentrations of EV from Ova-CAR-T expressing cells. As shown in FIG. 6B, similarly, Ki67 (proliferation) and IFNy expression on OT-1 T cells was increased in the presence of EV released from Ova-CAR-T expressing cells, in a dose-dependent manner. FIG. 6C provides a quantification of Ki67 expression (left panel), Granzyme B expression (middle panel), and IFNy expression shown in FIGs. 6A and 6B. The data showed that the CAR-T cells expressed the peptide and transferred it to tumor cells, where it was presented in the context of MHC. Further, this peptide transfer enhanced the anti-tumor T cell response in a dose-dependent and statistically significant manner.

Utilizing the same experimental setup (FIG. 5), tumor cell death was also assessed by flow cytometry at various concentrations of Ova-CAR T EV loading. The relative cell death is shown in FIG. 7. At increasing concentrations of EV (0, 18, 37.5, and 75pg), incubation of B16 cells with the EV and OT-I T cells resulted in statistically significant increases in levels of tumor cell death. Thus, the in vitro studies indicated that CAR-T cells engineered to express an immunogenic peptide can transfer the immunogenic peptide to tumor cells and elicit enhanced T cell responses and tumor death compared to CAR-T cells that do not express the immunogenic peptide.

To test whether the CAR-T cells express and transfer the immunogenic peptide epitope in vivo , mice were implanted with a 1:1 mix of B16 WT and B16-hCD19 tumor cells (50,000 cells) and subsequently treated with 4.5 x 10 ⁶ Ova-19BBz CAR-T cells at day 12, as depicted in FIG.

8. Four days later, tumors were harvested and peptide loading of tumor cells and DCs was assessed by flow cytometry. The results are provided in FIG. 9A. In animals that received control CAR-T cells (19BBz), no peptide/MHC loading was detected in tumor cells or dendritic cells (gated on live cells/CD45.2+, F4/80-, CDllc+/MHCII+). However, peptide/MHC positive cells were detected in both tumor cells and dendritic cells isolated from animals that received Ova- 19BBz CAR-T cells. The Ova peptide loading also resulted in the expansion of Ova-specific CD8+ T cells, as detected by positive tetramer staining in Ova-19BBz recipients (FIG. 9B, middle panel) compared to 19BBz control recipients (FIG. 9B, left panel). The tetramer positive, Ova-specific T cells also were positive for Ki67, indicating activation (FIG. 9B, right panel).

FIG. 10A shows the percent of Ova+ tumor cells (left panel) and endogenous immune cells (right panel) in 19BBz and Ova-19BBz recipient mice. As above, animals that received control 19BBz cells, no Ova+ tumor or endogenous immune cells were detected, whereas a significant number of tumor and endogenous immune cells presented Ova in Ova-19BBz recipients. Quantification of the % of endogenous T cells stained positively for the Ova tetramer and of the % of CD8 T cells expressing Ki67 is provided in FIG. 10B, top two panels. The tumor weight in the two different groups at day 16 is shown in FIG. 10B, bottom panel. The tumor weight in Ova-19BBz recipients was significantly less than the tumor weight in 19BBz recipients (p=0.002).

Using a similar in vivo experimental setup, but using 1:1 mix of B16-hCD16 and B16 WT cells to implant tumors, the ability of Ova-19BBz CAR-T cells to control tumor growth in vivo was further assessed. Mice were implanted with the B16-hCD19 / B16 tumor cell mix and subsequently treated with Ova-19BBz CAR-T cells or control 19BBz CAR-T cells at 12 days postimplantation (FIG. 11 A). Growth of tumor cells was monitored over time and measured as tumor volume (cm ³ ). FIG. 1 IB shows that by day 21 after tumor implantation (8 days after CAR- T cell administration), tumor volume was significantly greater in 19BBz groups vs. Ova-19BBz groups. The difference in tumor volume between the two groups continued to increase over time at days 24 and 28 after tumor implantation (p < 0.001).

Taken together, the studies showed that incorporating an immunogenic peptide epitope into the CAR construct, and expressing the CAR molecule and peptide in a cell, can enhance CAR-T therapy by transferring the immunogenic peptide to tumor cells and dendritic cells, enhancing the anti-tumor T cell response. This immunogenic peptide transfer translates to enhanced antigen specific T cell activation and anti-tumor activity, including significant inhibition of tumor size. Thus, the studies showed that a method of expressing an immunogenic peptide in conjunction with a CAR-T cell therapy significantly improves the efficacy of the CAR-T cell therapy.

To investigate the effect of Ova-19BBz CAR-T cells in the context of a less immunogenic cancer, mice were implanted with mixed KP tumors and subsequently treated with Ova-19BBz CAR-T cells at days 5 and 12 in combination with an anti-CTLA4 and anti-PDl antibody at days 8, 11, and 14 post-implantation (FIG. 12A). Growth and survival was monitored. In addition, the study was designed to assess the effects in the less immunogenic cancer of a CAR containing a combination of the Ova peptide and the RNA RN7SL1 (7SL); see construct in FIG. 12A. 7SL is a highly structured RNA that functions as an intratumoral PAMP and activates PRR signaling. 7SL CAR-T cells ( e.g ., BBz-7SL) have been discussed, e.g., in International Patent Application No. PCT/US2019/012675 and Johnson et al ., ./. Immunol vol. 202(1) 134-4 (2019). As shown in FIGs. 12B and 12C, in the context of the far less immunogenic KP tumors, the combination of the Ova peptide with the 7SL PAMP resulted in significantly reduced tumor volume over time and significantly improved survival, compared to 19BBz CAR-T cells, as well as compared to Ova-19BBz or BBz-7SL CAR-T cells. Therefore, the combination of the immunogenic peptide and 7SL significantly improved the anti -turn or effect of CAR-T cells in this context.

Many solid human tumors lack sufficient neoantigens and/or an adequate anti-tumor T cell repertoire, either of which might limit endogenous T cell responses initiated by CAR-T cells expressing RN7SL1. To address this, CAR-T cells were engineered to co-deliver RN7SL1 with peptide antigens of choice. As proof of concept, 19BBz CAR-T cells were engineered to express the SIINFEKL peptide alone (Ova-19BBz) or with RN7SL1 (Ova-19-7SL) (FIG. 26A, top). Using an antibody that detects SIINFEKL in complex with MHC class I (Porgador et al., (1997) Immunity 6, 715-726), it was confirmed that this peptide is effectively presented on Ova-19BBz CAR-T cells and is also detected on CAR T cells (FIG. 26A, bottom), demonstrating successful expression and deployment of this peptide antigen. Indeed, when EVs from Ova-19BBz CAR-T cell cultures were incubated with B16 tumor cells, a dose-dependent increase in SIINFEKL presentation by MHC class I on cancer cells was observed (FIG. 26B, top row, left plot), and addition of naive OT-I T cells showed increasing T cell activation (FIG. 26B). Parallel in vivo experiments reveal that Ova-19BBz CAR-T cells deliver SIINFEKL for presentation on MHC class I by tumor cells and CD45.2+ immune cells (FIG. 26C), promote the expansion of Ki67 ⁺ Ova-specific and total endogenous CD8 T cells (FIGs. 26D-26E), and improve control of mixed CD19 ⁺ and CD19 B16 tumors (FIG. 26F). Unlike RNA delivery by CAR-T cells, SIINFEKL delivery was not obviously biased toward immune cells (FIG. 26H). Thus, CAR-T cells can be engineered to deliver peptide antigens that are effectively presented by tumor and immune cells.

Having verified that CAR-T cells can effectively deliver Ova peptide, 19BBz CAR-T cells that co-express SIINFEKL and RN7SL1 were tested and their efficacy assessed against a low mutational burden tumor model for CAR antigen loss (FIG. 26G). For this, mice were implanted with tumors comprised of a 1:1 mix of human CD19 ⁺ and CD 19 KP lung cancer cells

(DuPage et al., (2011) Cancer Cell 19, 72-85) and 5xl0 ⁵ OT-I T cells were adoptively transferred to control for the presence of a preexisting T cell pool. 19BBz CAR-T cells or 19BBz CAR-T cells that deliver either SIINFEKL or RN7SL1 had little effect. This suggests that in a poorly immunogenic heterogenous tumor, autonomous CAR function, recruitment of endogenous immunity, or provision of neoantigen without enhancing adjuvanticity are all individually insufficient. However, combining these functions by simultaneous CAR-T cell delivery of RN7SL1 plus SIINFEKL significantly delays tumor growth. Thus, these data suggest that multi-armored CAR-T cells can co-deploy peptide antigens with RN7SL1 to further recruit endogenous immunity, making CAR-T cells less susceptible to CAR antigen loss, even if tumors with heterogenous CAR antigen expression lack adequate neoantigens.

Example 2: Novel STING agonist peptides and CAR-T cells engineered to target the STING pathway

Studies were carried out to assess the ability of computationally developed de novo therapeutic peptides to be delivered via, and enhance the effectiveness of, CAR-T cells. To develop the therapeutic peptides, the present inventors utilized a computational peptide binding prediction algorithm. The algorithm takes unfolded peptides and folds them into novel peptides using iterative, computational prediction of binding to specified sites (see, e.g., Obarska-Koshina et al ., “PepComposer: computational design of peptides binding to a given protein surface.” Nucleic Acid Research 2016 Jul 8;44(W1): W522-8).

The STING pathway was selected as a pathway target given its powerful ability to trigger immune responses. STING is triggered by a cyclic di -nucleotide, cGAMP, which cannot be encoded in an expression vector for expression in a cell along with a CAR molecule. As an initial step, peptides were generated that bind the STING binding site that is occupied by cGAMP. Novel peptides that bind the STING structure were identified by removing cGAMP from a structure of the STING-cGAMP active complex as represented in the crystal structure provided by Protein Data Bank (structure 4EMT), to obtain a structure of the isolated active STING without cGAMP (FIG. 13). Peptide binding in the vacated cGAMP pocket was predicted by monte-carlo side-chain substitution. FIG. 14, left panel, shows the STING structure with poly glycine peptide for representative sampling peptide binding. FIG. 14, right panel, shows the STING structure with a predicted STING binding peptide bound within the cGAMP pocket. The peptide shown in the structure is peptide ST2 (SEQ ID NO: 3: LFILSG).

Six cGAMP mimetic peptides (also referred to herein as STING peptides) were selected to test for activity. An initial screen for bone marrow dendritic cell (BMDC) stimulation revealed that the 6 STING peptides generated via the computational method were active. BDMCs were prepared by harvesting bone marrow from mouse hindlimbs and culturing in media (RPMI +

10% FBS in 30 ng/mL GM-CSF) for 4 days. BMDCs were then stimulated with potential STING agonist peptides encapsulated in liposomes (Lipofectamine 2000) and returned to culture with GM-CSF for 48 hours. BMDCs were then evaluated for expression of CD86 by flow cytometry as a surrogate for STING activity. A schematic of the study design is provided in the left panel of FIG. 15.

The results are provided in the right panel of FIG. 15. The peptides tested were peptides STIC, ST1, ST2, ST3, ST4, and ST5 (SEQ ID NOs: 1, 2, 3, 4, 5, and 6, respectively) (Table 1). The native ligand cGAMP was used as a positive control. The study showed that all 5 peptides increased CD86 expression in BMDCs at statistically significant levels over negative control.

ST2 peptide induced the highest CD86 expression of the peptides tested.

Activity of the STING agonist peptide ST2 was further characterized. BMDCs from wild type (WT) or STING knock-out (KO) mice were prepared as described above. Following stimulation with ST2, cells were loaded with Ova (SIINFEKL) peptide and then extensively washed to remove residual peptide. OT-I T cells specific for the Ova peptide were then added to BMDC cultures to assess DC activity and ability to stimulate CD8 T cell responses. OT-I T cell expression of Granzyme B (an indicator of cell killing activity), Ki67 (an indicator of cell proliferation), and IFNy were assessed by flow cytometry 48 hours later. As shown in FIG. 16, stimulation of DCs with ST2 peptide significantly increased T cell stimulation as measured by all three of Granzyme B, Ki67, and IFNy in WT cells. Granzyme B, Ki67, and IFNy were not significantly increased over liposome-only controls in STING KO cells, indicating that the activity of ST2 requires the STING pathway. Thus, the results showed that STING peptide enhances T cell function through DCs, via a STING-dependent mechanism.

Next, a study was conducted to determine if delivery of the novel STING peptides provided herein by CAR-T cells would enhance the anti-cancer activity of the CAR-T therapy. FIG. 17, top panel, provides a schematic view of the CAR-T constructs used in the study. A 19BBz CAR construct was used as a control to generate CD 19 CAR-T cells (“19BBz”). A 19BBz CAR construct further comprising the ST2 peptide was also prepared, in which a stop codon separated the nucleic acid segment encoding the ST2 peptide and the nucleic acid encoding the 19BBz CAR molecule, to generate CD19 CAR-T cells with ST2 peptide (“19BBz- STING Peptide”).

A schematic view of the study design is provided in FIG. 17, bottom panel. Mice were implanted with B16-hCD19 tumors and treated with CAR-T cells at days 5 and 12, and with anti-CTLA4 antibody at days 8, 11, and 14. Percent survival was monitored over 80 days. Animals that received the 19BBz-STING Peptide CAR-T cells exhibited significantly improved survival compared to mice that received CAR-T cells without ST2 peptide (FIG. 18; p=0.036).

Taken together, the studies showed that novel STING peptides, generated via computational binding analysis, are capable of acting as potent cGAMP mimetic peptides and enhancing immune responses against cancer antigens. The presence of the cGAMP mimetic, STING agonist peptides in the context of a CAR-T cell therapy significantly improved the anti cancer effect of the CAR-T cells. Thus, the present disclosure provides novel methods for improving CAR-T cell therapy via exploitation of a potent pathway of the immune system that cannot be delivered by CAR-T cells through previously known or conventional means.

Example 3 : SMAC mimetic peptides in combination with CAR-T cell therapy

Activation of SMAC enhances apoptosis and is particularly effective in inducing cell death when in the presence of cell death signals. SMAC mimetic small molecules have been tested in cancer but on their own, they have not demonstrated efficacy in clinical studies. Without wishing to be bound by theory, the poor efficacy of SMAC small molecules in clinical studies may be due in whole or in part to the absence of a cell death trigger ( e.g ., activation of the TNF/TRAIL pathway) which may be required for optimal SMAC activity.

SMAC peptides were generated using a rational design strategy. Peptides with the best binding and potency (as measured by induction of cell death) in a dose response assay were selected for testing. SMAC mimetic peptide compositions were encapsulated in liposomes and transfected into B 16 or KP (lung adenocarcinoma) cells in vitro at various concentrations in the presence of 20 ng/mL of TNF. 24 hours later, cell death was assessed by flow cytometry. An exemplary data set is provided in FIG. 19. Peptide 6 (SMACm6; SEQ ID NO: 8) was selected for further analysis based on dose response in multiple cell lines.

The SMACm6 mimetic peptides were encapsulated in liposomes and transfected into B16 or KP cells in vitro at various concentrations with or without 20 ng/mL TNF. As shown in FIG. 20, in the absence of TNF, no cell death was observed. In the presence of TNF, increasing concentrations of encapsulated SMACm6 resulted in increasing relative cell death. Thus, the data showed that the SMAC mimetic peptide induces TNF-dependent cell death of tumor cells in vitro.

A SMACm CAR-T construct was generated as shown in FIG. 21 and expressed in T cells. SMACm CAR-T cells were expanded in culture. After cell culture, EVs were harvested from the media via ultracentrifugation. EVs were then incubated with indicated cells in vitro at various concentrations with 20 ng/mL TNF. 24 hours later, cell death was assessed by flow cytometry. The results are provided in FIG. 22, and indicate that in both tumor cell types, SMACm6 EVs significantly enhanced cell death.

Moreover, the SMACm CAR-T EVs enhanced tumor control in vivo. Mice were implanted with 50,000 B16-hCD19 tumors and treated with 2 x 10 ⁶ SMACm6 CAR-T cells per dose at days 5 and 12 post implantation, as well as with anti-CTLA4 antibody in some groups at days 8, 11, and 14. Tumor growth was measured over time. The results of the study showed that the SMACm CAR-T cells significantly reduced tumor volume and significantly increased survival compared to control 19BBz CAR-T cells, in the presence or the absence of anti-CTLA4 antibody as an immune checkpoint blocker (FIG. 23).

Thus, the study showed that a peptide that triggers a TNF-dependent cell death pathway that has shown limited utility as a target in clinical studies but can act as a potent mediator of cell death in certain contexts, can be delivered by CAR-T cell therapy and significantly improve the efficacy of the CAR-T cell therapy by increasing cell death in target tumor cells. Moreover, the improvement in tumor volume and survival was achieved in the CAR-T cell + SMAC mimetic peptide groups regardless of the presence or absence of an immune checkpoint inhibitor. Example 4: PARP inhibitors in combination with CAR-T cell therapy

PARP inhibitors enhance cell stress by blocking DNA damage repair (DDR) and inducing cell death. Reduction in DDR is associated with enhanced anti-tumor immunity mediated by damage-associated molecular pattern molecule (DAMP) production, as well as increased neoantigen prevalence. The present inventors sought to generate and identify PARPi mimetic peptides as part of a strategy for targeting PARP in the anti-cancer methods and compositions provided herein.

PARP inhibitor peptides were computationally designed using methods as described in Example 2. Resulting PARP inhibitor (PARPi) mimetic peptides were encapsulated in liposomes and transfected into TSA breast cancer cells in vitro. 48 hours later, PD-L1 was assessed by flow cytometry as a readout of a DNA damage response. The results of the study are shown in FIG.

25. The PARPi mimetic peptides (Pepl, PeplC, Pep2, and Pep3; SEQ ID NOs: 13, 14, 15, and 16, respectively) increased PD-L1 expression. The PARP inhibitor olaparib was used as a positive control. The PARPi mimetic peptides increased PD-L1 expression to a similar level compared to the olaparib. Thus, the study showed that the computationally designed, novel PARPi mimetic peptides induce a DNA damage response that will lead to cancer cell death. In embodiments, the PARPi mimetic peptides may be introduced into a CAR construct for delivery to the tumor microenvironment via an engineered CAR-T cell.

Example 5: MHC-I from CAR-T cells is required for activating endogenous T cells by delivery of antigen peptide from CAR-T cell extracellular vesicles (EVs)

CAR-T cells with MHC-I or without MHC-I (generated from wildtype or B2M KO CD4 T cells), expressing OVA-19BBz or control CAR, were used to isolate EVs (FIG. 27A). These EVs were then added to a co-culture of OT-I CD8 T cells (OVA-specific) with either wildtype B16 cancer cells or B16 cells deficient for MHC-I (B2M KO). Flow cytometry for T cell activation markers expressed by OT-I T cells was performed 48 hours later. Expression of indicated T cell activation markers on OT-I T cells after addition of EVs from MHC-I-expressing or MHC-I-deficient CAR-T cells under the indicated culture conditions is shown in FIG. 27B, top and bottom, respectively. Representative flow cytometry plots of T cell activation markers on OT-I T cells are shown in FIG. 27C. The data demonstrated that MHC-I from CAR-T cells is required for activating endogenous T cells by delivery of antigen peptide from CAR-T cell extracellular vesicles (EVs).

Example 6: Extracellular vesicles from CAR-T cells engineered to deliver antigen peptide can directly activate endogenous T cells

A transwell filter was used to separate OT-I CD8 T cells (FIG. 28A, upper well) from CAR-T cells (FIG. 28A, lower well) that were untransduced or expressed either OVA-199BBz CAR or a control 19BBz CAR. The filter separating the wells had a pore size of 0.4 microns that allowed passage of extracellular vesicles (EVs) but not cells (FIG. 28 A). Representative flow cytometry plots are shown in FIG. 28B of OT-I CD8 T cells from the upper well for the indicated T cell activation markers or for OVA/MHC-I transferred from CAR-T cell EVs after addition of the indicated CAR-T cells to the lower well. Results demonstrated that extracellular vesicles from CAR-T cells engineered to deliver antigen peptide can directly activate endogenous T cells.

Other Embodiments

The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

The disclosures of each and every patent, patent application, and publication cited herein are hereby incorporated herein by reference in their entirety. While this invention has been disclosed with reference to specific embodiments, it is apparent that other embodiments and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such embodiments and equivalent variations.