ENHANCING EFFICACY AND SAFETY OF T-CELL-MEDIATED IMMUNOTHERAPY

FIELD OF THE INVENTION

The present document generally relates to the field of cancer, in particular, cell therapies and immunotherapies for the treatment of solid tumors or haematological cancers characterized by the presence of FAP in the tumor microenvironment, in patients.

BACKGROUND

Adoptive cell therapy, also known as cellular immunotherapy, is a form of treatment that uses the cells of the immune system to eliminate pathological cells, such as infected or malignant cells. Some of these approaches involve directly isolating a person’s own immune cells and simply expanding their numbers, whereas others involve genetically engineering immune cells from patients (autologous approach) or donors (allogeneic approach) to boost and/or redirect them towards specific target tissues. In the case of cancer, immune cells, especially immune cytolytic and helper T-lymphocytes, Natural Killers and Macrophages, are particularly powerful against cancer, due to their ability to bind to markers known as antigens on the surface of cancer cells. Cellular immunotherapies take advantage of this natural ability and can be deployed in different ways: Tumor- Infiltrating Lymphocyte (TIL) therapy, Engineered T Cell Receptor (TCR) cell therapy, Chimeric Antigen Receptor (“CAR”) immune cell therapy, and Natural Killer (NK) cell therapy.

Chimeric antigen receptors-expressing immune cells are cells that have been genetically engineered to express chimeric antigen receptors (CARs) usually designed to recognize specific tumor antigens and kill cancer cells that express said tumor antigen(s). These are generally T-cells expressing CARs (“CAR-T cells”), Natural Killer cells expressing CARs (“CAR-NK cells”), or macrophages expressing CARs.

CARs are synthetic receptors consisting of a targeting moiety that is associated with one or more signalling domains in a single or multiple fusion molecule(s). In general, the binding moiety of a CAR can include an antigen-binding domain of a single-chain antibody (“scFv”), comprising the light and heavy variable fragments of a monoclonal antibody joined by a flexible linker. Binding moieties based on receptor or ligand domains have also been used successfully. The signalling domains for first generation CARs are derived from the cytoplasmic region of the CD3zeta (or CD3Q or the Fc receptor gamma chains. First generation CARs have been shown to successfully redirect T-cell cytotoxicity, however, they failed to provide prolonged expansion and anti-tumor activity in vivo. Signalling domains from co-stimulatory molecules including CD28, OX-40 (CD134), ICOS, and 4-1BB (CD137) have been added alone (second generation) or in combination (third generation) to enhance survival and increase proliferation of CAR modified T-cells. CARs have successfully allowed T-cells to be redirected against antigens expressed at the surface of tumor cells from various malignancies including lymphomas and solid tumors (Jena, Dotti et al. Blood (2010) 116(7): 1035-44).

Adoptive immunotherapy, which involves the transfer of autologous or allogeneic antigen-specific T-cells generated ex vivo, is a promising strategy to treat viral infections and cancer as confirmed by the increase in the number of clinical trials involving CAR-T cells.

So far, only autologous CAR T-cells have been approved by the US Food and Drug Administration (FDA) (e.g. Novartis’ anti-CD19 CAR-T tisagenlecleucel (Kymriah™) for the treatment of precursor B-cell acute lymphoblastic leukemia; Kite Pharma’s anti-CD19 CAR-T axicabtagene ciloleucel (Yescarta™) for certain types of large B-cell lymphoma in adult patients expressing CD19 as a marker, anti-BCMA CAR-T idecabtagene vicleucel (Abecma™) for treatment of adult patients with relapsed or refractory multiple myeloma, and anti-CD19 CAR-T lisocabtagene maraleucel (Breyanzi™) for adult patients with relapsed or refractory large B-cell lymphoma, anti- CD19 CAR-T brexucabtagene autoleucel (Tecartus™) for patients with relapsed or refractory mantle cell lymphoma). Allogeneic approaches are more challenging due to the alloreactivity of the cells with respect to the patient’s own immune cells. The most advanced programs involve inactivating endogenous T-cell receptor genes by using specific rare-cutting endonucleases, such as TALE-nucleases, to reduce the alloreactivity of the cells prior to administering them to patients as reported by Poirot et al. (Cancer. Res. (2015) 75 (18): 3853-3864) and Qasim et al. (Science Translational (2017) 9(374)). Meanwhile, inactivation of TCR (e.g. TRAC and/or TRBC) in primary T-cells can be combined with the inactivation of MHC components such as beta-2-microglobulin (B2M) and/or with inactivation of genes encoding checkpoint proteins, such as described for instance in WO 2014/184744.

T-cell mediated anti -tumor cytotoxicity is a promising immunotherapeutic strategy for both leukemia and solid tumors. However, several factors limit the efficacy of tumor-antigen targeted CAR-T therapy against solid tumors, including lack of tumorinfiltrating lymphocytes (TIL) and an immune suppressive tumor microenvironment (TME) (Stern et al. (2020) Cancer Treat Res. 180:297-326).

Most solid tumor microenvironments are characterized by the presence of activated fibroblasts called cancer-associated fibroblasts (CAFs) that express unique surface proteins such as FAP (Kalluri R. Nat Rev Cancer (2016) 16:582-98). CAFs can inhibit TILs and promote immune suppression (Wang et al. (2014) Cancer Immunol Res. 2:154-66).

Fourth -generation CAR T cells have been described, which aim at inducing a pro- inflammatory milieu by engineering CAR-T-cells to release a transgenic cytokine upon CAR signaling in the targeted tumor tissue (Chmieswcki et al. (2020) Adv Cell Gene Then 3:e84 ; Sachdeva et al. (Nature Communications (2019) 10:5100).

Waldhauer et al (MABS (2021)) investigate the effect of immunocytokines to potentiate the efficacy of different immunotherapies.

Despite recent technical advances, the treatment of cancer, particularly treatment of cancers characterized by solid tumors remains a great challenge in healthcare. What is needed are new compositions and treatments that are both effective against solid tumors and safe in patients, in particular that are efficient for targeting the tumor tissues and circumventing the immunosuppressive tumor microenvironment while exhibiting reduced general side effects.

This background information is provided for informational purposes only. No admission is necessarily intended, nor should it be construed, that any of the preceding information constitutes prior art against the present invention.

SUMMARY This document provides methods and materials for treating cancer. For example, this document provides cells (e.g., immune cells such as T cells or NK cells, or iPSCs which can further be differentiated in immune cells) engineered to express a CAR having the ability to bind a tumor antigen and to secrete a stimulatory cytokine with potential effect on both the engineered immune cells and the patient’s immune cells when and where it is the most needed for treating a patient.

It is to be understood that both the foregoing general description of the embodiments and the following detailed description are exemplary, and thus do not restrict the scope of the embodiments.

The methods and materials provided herein are particularly suited for treatment of cancers characterized by the presence of FAP in their tumor microenvironment. The methods and materials provided herein also are particularly suited to achieve a “universal” treatment, where the components of the treatment can be used in many unrelated patients.

In general, one aspect of this document features an engineered cell comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”) placed under the transcriptional control of an exogenous or endogenous constitutive promoter; and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising a Fibroblast Activation Protein (FAP)-binding-domain and a stimulatory cytokine placed under the transcriptional control of an endogenous inducible promoter; wherein said exogenous nucleic acid sequences of a) and b) are integrated in the cell’s genome, and wherein said inducible promoter is inducible upon activation of the cell.

As a consequence, the expression of said fusion protein is induced upon activation of the engineered cell.

In some cases, said FAP-binding-domain can comprise the VH and VL amino acid sequences from a monoclonal anti -FAP antibody.

In some cases, said fusion protein does not comprise an antibody crystallizable fragment (Fc).

In some cases, the tumor antigen targeted by said tumor-CAR is not FAP. In some cases, said fusion protein can comprise a signal peptide that is removed upon or after secretion of the fusion protein outside of the cell.

In some cases, said engineered cell can be an immune cell such as a T-cell, a NK- cell, or a macrophage.

In some cases, said engineered cell can be an engineered T-cell or engineered NK- cell.

In some cases, said engineered cell can be an iPSC that may be an intermediate in the production of an engineered immune cell, such as a T-cell, a NK-cell, or a macrophage, as described herein. In some cases, the engineered cell can be an engineered immune cell that derives from the engineered iPSC after that said iPSC has been submitted to one or more differentiation steps.

Although the various aspects described herein can apply to a situation where the cells are immune cells such as T-cells, these various aspects similarly apply to NK-cells and macrophages and are, thus, included herein.

In some cases, an engineered cell described herein can be a T-cell that has been genetically modified to suppress or repress expression of a T-cell receptor (TCR) (e.g., an endogenous TCR) by inactivation of a gene encoding a TCR component (e.g., a TRAC gene and/or TRBC gene) and, optionally, to suppress or repress expression of at least one gene controlling MHC complex surface presentation, such as B2M and class II major histocompatibility complex transactivator (CIITA), and, optionally, to suppress or repress expression of CD52, and, optionally, to suppress or repress expression of at least one immune checkpoint or receptor thereof, in the T-cell.

In another aspect, this document features an engineered T-cell comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”); and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a Fibroblast Activation Protein (FAP)-binding-domain such as a FAP- binding domain comprising the VH and VL amino acid sequences from a monoclonal anti- FAP antibody (such as a FAPscFv), and (ii) a stimulatory cytokine; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”), and wherein said inducible promoter is inducible upon activation of the T-cell.

In some cases, the exogenous nucleic acid sequence of a) is placed, after integration in the cell’s genome, under the control of an exogenous constitutive promoter.

In some cases, the exogenous nucleic acid sequence of a) is placed, after integration in the cell’s genome, under the control of an endogenous constitutive promoter.

In some cases, the fusion protein comprises: a) a signal peptide that directs the secretion of the fusion protein, wherein said signal peptide is removed after secretion of said fusion protein; b) a FAP-binding-domain, such as a FAP-binding domain comprising the VH and VL amino acid sequences from a monoclonal anti-FAP antibody; c) at least one stimulatory cytokine selected from the group consisting of Interleukin-2 or a variant thereof such as IL-2v, Interleukin-7 or a variant thereof, Interleukin- 12 or a variant thereof, Interleukin- 15 or a variant thereof, Interleukin- 15 in complex with its high affinity receptor IL-15RA, Interleukin- 18 or a variant thereof, Interleukin-23 or a variant thereof.

Optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc).

Optionally, said fusion protein does not comprise a full monoclonal anti-FAP antibody.

In some cases, the tumor-CAR can comprise: a) an extracellular tumor antigen-binding-domain, such as an extracellular tumor antigen-binding-domain comprising the VH and VL amino acid sequences from a monoclonal anti-tumor antigen antibody, b) a hinge selected from a FcyRIII hinge, a CD8a hinge, and an IgGl hinge, c) a transmembrane domain comprising a CD8a transmembrane domain or a CD28 transmembrane domain, and d) a cytoplasmic domain comprising a CD3 zeta signaling domain and a costimulatory domain from 4- IBB or from CD28.

In some cases, the constitutive promoter can be selected from the group consisting of the promoters of EF1A, CD52, GAPDH, CMV, hPGK, UBC, SV40, PGK, CAGG, TRAC, TRBC, TRGC, TRDC, B2M, CD5, CS1, CD45, RPBSA, CD4, and CD8; and/or the inducible promoter can be selected from the group consisting of the promoters of PDCD1, CD25, TIM3, TIGIT, CCL1, NR4A3, EGR3, G0S2, IL22, RGS16, FASLG, RDH10, CSF1, GM-CSF, LAG3, CTLA-4, IL10, NUR77, and FOXP3.

In some cases, the constitutive promoter can be selected from the group consisting of the promoters of EFl A, TRAC, B2M, CD52, CS1, CD45, CD5, and GAPDH. For example, the constitutive promoter can be a EF1A, TRAC, CD52, or B2M promoter. For example, the constitutive promoter can be an EFl A promoter.

In some cases, the inducible promoter can be selected from the group consisting of the promoters ofPDCDl, CD25, GM-CSF, TIM3, and TIGIT. For example, the inducible promoter can be a PDCD1 promoter.

In some cases, the constitutive promoter can be an endogenous TRAC promoter or an exogenous EFl A promoter, and the inducible promoter can be an endogenous PDCD1 promoter.

In some cases, the constitutive promoter can be an exogenous EFl A promoter, and the inducible promoter can be an endogenous PDCD1 promoter.

In some cases, the fusion protein can comprise a FAP-binding-domain comprising the ammo acid sequence of SEQ ID NO: 9, SEQ ID NO: 18, SEQ ID NO: 27, or SEQ ID NO: 36, and/or the tumor-CAR can comprise an extracellular tumor antigen-binding- domain comprising the amino acid sequence of SEQ ID NO: 45, SEQ ID NO: 53, or SEQ ID NO: 61.

In some cases, the fusion protein can comprise a FAP-binding-domain comprising the amino acid sequence of SEQ ID NO: 9 and the tumor-CAR can comprise an extracellular tumor antigen-binding-domain comprising the amino acid sequence of SEQ ID NO: 53 or SEQ ID NO: 61.

In some cases, an engineered T-cell described herein can be a T-cell that has been genetically modified to suppress or repress expression of a T-cell receptor (TCR) (e.g., an endogenous TCR) by inactivation of a gene encoding a TCR component (e.g., a TRAC and/or TRBC) and, optionally, to suppress or repress expression of at least one gene controlling MHC complex surface presentation, such as B2M and CIITA, and, optionally, to suppress or repress expression of CD52, and, optionally, to suppress or repress expression of at least one gene encoding an immune checkpoint or receptor thereof, in the T-cell.

In some cases, the engineered T-cell described herein can be a T-cell that has been genetically modified (i) to suppress or repress expression of a T-cell receptor (TCR) by inactivation of a gene encoding a TCR component (e.g., a TRAC and/or TRBC), (ii) to suppress or repress expression of PD1 or receptor thereof, and optionally (iii) to suppress or repress expression of B2M, and optionally (iv) to suppress or repress expression of CD52, in the T-cell.

In other aspects of the present disclosure the engineered immune cell(s) are NK- cells. Thus, another aspect relates, for instance, to an engineered NK-cell comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”); and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a Fibroblast Activation Protein (FAP)-binding-domain, such as a FAP- binding domain comprising the VH and VL amino acid sequences from a monoclonal anti- FAP antibody (e.g. a FAPscFv), and (ii) a stimulatory cytokine; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”), and wherein said inducible promoter is inducible upon activation of the NK-cell.

In some cases, said engineered NK-cell as described herewith has been genetically modified to suppress or repress expression of at least one gene controlling MHC complex surface presentation, such as B2M and class II major histocompatibility complex transactivator (CIITA), and, optionally, to suppress or repress expression of CD52, and, optionally, to suppress or repress expression of at least one immune checkpoint or receptor thereof, in the NK-cell.

In other aspects of the present disclosure the engineered cell(s) are iPSCs. Thus, another aspect relates, for instance, to an engineered iPSC comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”); and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a Fibroblast Activation Protein (FAP)-binding-domain, such as a FAP- binding domain comprising the VH and VL amino acid sequences from a monoclonal anti- FAP antibody (e.g. a FAPscFv), and (ii) a stimulatory cytokine; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”), and wherein said inducible promoter is inducible upon activation of the immune cell into which said engineered iPSC can further be differentiated.

In some cases, said engineered iPSC as described herewith has been genetically modified to suppress or repress expression of a T-cell receptor (TCR) by inactivation of a gene encoding a TCR component (e.g., a TRAC and/or TRBC), suppress or repress expression of at least one gene controlling MHC complex surface presentation, such as B2M and class II major histocompatibility complex transactivator (CIITA), and, optionally, to suppress or repress expression of CD52, and, optionally, to suppress or repress expression of at least one immune checkpoint or receptor thereof, in the cell.

In some cases, the tumor-CAR can be constitutively expressed in the engineered immune cells (e.g., engineered T-cells) either through lentiviral integration or through nuclease-mediated cDNA insertion at one or more constitutively expressed loci such as one or more of the TRAC, B2M, and CD 52 loci. In some cases, the TRAC and/or B2M loci can be disrupted, for instance by TALE -Nuclease, to inhibit graft versus host disease (GvHD) and increase the engineered immune cells’ persistence (e.g., an engineered T cells’ persistence) in an allogeneic setting.

In some cases, the fusion protein expression is inducible upon activation of the engineered immune cell (e.g., engineered T-cell) and the fusion protein is encoded by an exogenous nucleic acid sequence that can be incorporated in the cell’s genome through nuclease-mediated cDNA insertion at one or more inducible loci.

In some cases, the fusion protein can be encoded by an exogenous nucleic acid sequence that is incorporated in the cell’s genome through nuclease-mediated cDNA insertion at one or more inducible loci selected from the group consisting of PDCD1, CD25, GM-CSF, TIM3, and TIGIT loci; for instance, at the PDCD1 inducible locus.

In some cases, the tumor-antigen targeted by said tumor-CAR can be selected from the group consisting of Mesothelin (e.g. human Mesothelin), MUC1 (e.g. human MUC1), EGFR (e.g. human EGFR), VEGF (e.g. human VEGF), and Trop2 (e.g. human Trop2).

In some cases, the tumor-antigen targeted by said tumor-CAR can be Mesothelin (e.g. human Mesothelin) or MUCl (e.g. human MUC1).

In another aspect, this document features a method of treatment of a cancer characterized by the presence of FAP in the tumor microenvironment comprising administering a therapeutically effective amount of engineered immune cells (e.g., engineered T-cells) comprising (a) an exogenous nucleic acid sequence encoding a tumor- CAR placed under the transcriptional control of an exogenous or endogenous constitutive promoter, and (b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising a FAP-binding domain and a stimulatory cytokine placed under the transcriptional control of an endogenous inducible promoter, as described herein.

In another aspect, this document features a pharmaceutical composition comprising a therapeutically effective amount of engineered immune cells (e.g., engineered T-cells) as described herein.

In another aspect, this document features a composition comprising a therapeutically effective amount of engineered immune cells (e.g., engineered T-cells) as described herein, for use in the treatment of a cancer characterized by the presence of FAP in the tumor microenvironment.

In another aspect, this document features a method of producing a population of cells comprising engineered immune cells (e.g., engineered T-cells), comprising:

(i) providing immune cells from a donor or induced pluripotent stem cells (iPSCs);

(ii) optionally, suppressing or repressing the expression of a T-Cell Receptor (TCR) (e.g., an endogenous TCR) in the cells or its presentation at the cell surface;

(iii) integrating in the cells’ genome an exogenous nucleic acid sequence encoding a tumor-CAR as described herewith placed under the transcriptional control of an exogenous or endogenous constitutive promoter; and

(iv) integrating in the cells’ genome an exogenous nucleic acid sequence encoding a secreted fusion protein comprising a FAP-binding domain and a stimulatory cytokine as described herewith placed under the transcriptional control of an endogenous inducible promoter;

(v) optionally, isolating the engineered cells that do not express a TCR (e.g., an endogenous TCR) at their cell surface; wherein said inducible promoter is inducible upon activation of said engineered immune cells.

In a still other aspect, this document features a set of vectors comprising:

(l)(a) at least one vector comprising an expression cassette comprising a nucleic acid sequence encoding a tumor-CAR as described herewith placed under the transcriptional control of a constitutive promoter, or

(1)(b) at least one vector comprising an expression cassette comprising a nucleic acid sequence encoding a tumor-CAR as described herewith, wherein said nucleic acid sequence encoding the tumor-CAR is placed between a Left-Homology Region and a Right-Homology Region, and wherein said Regions are homologous to an endogenous constitutive locus in a cell; and

(2) at least one vector comprising an expression cassette comprising a nucleic acid sequence encoding a fusion protein comprising a FAP-binding-domain and a stimulatory cytokine as described herewith, wherein said exogenous nucleic acid sequence is placed between a Left-Homology Region and a Right-Homology Region, and wherein said Regions are homologous to an endogenous inducible locus in a cell.

This document also relates to a kit comprising:

(l)(a) at least one vector comprising a nucleic acid sequence comprising a constitutive promoter and, operably linked to said promoter, a nucleic acid sequence encoding a tumor-CAR; and/or

(1)(b) (i) at least one vector comprising an expression cassette comprising a nucleic acid sequence encoding a tumor-CAR, wherein said nucleic acid sequence encoding the tumor-CAR is placed between a Left-Homology Region and a Right-Homology Region, and wherein said Regions are homologous to an endogenous constitutive locus in a cell; and (ii) at least one sequence-specific endonuclease targeting said endogenous constitutive locus; and

(2)(i) at least one vector comprising a nucleic acid sequence encoding a fusion protein comprising a FAP-binding-domain and a stimulatory cytokine, wherein said nucleic acid sequence is placed between a Left-Homology Region and a Right-Homology Region, wherein said Regions are homologous to an endogenous inducible locus in a cell; and (ii) at least one sequence-specific endonuclease targeting said inducible locus.

As used herewith, the endogenous constitutive locus and endogenous inducible locus in a cell refer to loci in a cell that can be transduced with the set of vectors as described, where said vectors constitute means for integrating the defined cassettes in the cell's genome as described.

Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

DESCRIPTION OF THE FIGURES The skilled artisan will understand that the drawings, described below, are for illustration purposes only. The drawings are not intended to limit the scope of the present teachings in any way.

Figure 1: A) Strategy for improving safety and efficacy of CAR-T based treatments using a tumor-targeting CAR expressed constitutively and an immunocytokine (e.g.; FAPscFv-IL2v) expressed under inducible promoter. B) Different approaches to deliver Tumor-CAR in the cell’s genome allowing its expression under a constitutive promoter C) Approach to deliver an immunocytokine (e.g.; FAPscFv-IL2v) in the cell’s genome allowing its expression under an inducible promoter.

Figure 2: A) Strategies for improving safety and efficacy of CAR-T based treatments illustrated in the Examples section. B) Meso-CAR construct is either integrated in the TRAC locus in the cell’s genome (TRAC targeted integration) allowing its expression under the control of the endogenous TCR promoter or is integrated randomly in the cell’s genome using a rLV and its expression is under the control of an exogenous EFlalpha promoter. C) FAPscFv-IL2v construct is integrated at the PDCD1 locus in the cell’s genome (PDCD1 targeted integration).

Figure 3: A) Results of Flow cytometry showing TCRalpha/beta (Y-axis) and Meso-CAR staining (X-axis) of mock electroporated (Mock), Meso-CAR targeted integration at the TRAC locus and PDCD1 knock-out (TRACMesoCARPDCDlKo), TRAC knock-out and FAPscFv-IL2v targeted integration at PDCD1 locus (TRACKOPDCD1FAPSOFV-IL2V) or Meso-CAR targeted integration at the TRAC locus and FAPscFv-IL2v targeted integration at PDCD1 locus (TRACMesoCARPDCDl FAPscFv-IL2v) T cells. B) Results of Flow cytometry post activation showing PD-1 staining (X-axis) after PMA and lonomycin induced activation of indicated T cells. C) Results of His-tag ELISA measuring FAPscFv-IL2v production and secretion after recombinant Mesothelin protein induced activation of the indicated T cells.

Figure 4: A) Schematic depicting the experimental design to investigate the antitumor activity of engineered TRACCAR T cells in xenograft mice model. B) Growth kinetics of mice tumor xenografts treated with mock electroporated (Mock), Meso-CAR targeted integration at the TRAC locus and PDCD1 knock-out (TRACMesoCARPDCDlKo), TRAC knock-out and FAPscFv-IL2v targeted integration at PDCD1 locus (TRACKOPDCD1FAPSOFV-IL2V) or Meso-CAR targeted integration at the TRAC locus and FAPscFv-IL2v targeted integration at PDCD1 locus (TRACMesoCARPDCDl FAPscFv-IL2v) T cells.

Figure 5: A) Results of Flow cytometry showing TCRalpha/beta (X-axis) staining of TRAC knock-out and PDCD1 knock-out (TRACKOPDCDIKO), Meso-CAR random integration and TRAC and PDCD1 double knock-out (rLv-MesoCAR; TRACKOPDCDIKO), TRAC knock-out and FAPscFv-IL2v targeted integration at PDCD1 locus (TRACKOPDCD1FAPSOFV-IL2V) or Meso-CAR random integration, TRAC knock-out and FAPscFv-IL2v targeted integration at PDCD1 locus (rLv-MesoCAR; TRACKOPDCD1FAPSOFV-IL2V) T cells. B) Results of Flow cytometry showing Meso-CAR (X-axis) staining for the indicated T cells. C) Percentage of targeted integration of FAPscFv-IL2v at PDCD1 locus measured by ddPCR. D) Results of His-tag ELISA showing FAPscFv-IL2v production and secretion after recombinant Mesothelin protein induced activation of the indicated T cells.

Figure 6: A) Results of Flow cytometry showing GFP expression (Y-axis) and human FAP staining (X-axis) of tumor cell lines NCLH226 and NCI-H226-FAP. B) Quantitative representation of flow cytometry analysing dose-dependent binding of recombinant FAPscFv-IL2v protein to NCI-H226-FAP cells, normalized to NCLH226 control cells.

Figure 7: A) Schematic depicting experimental design of serial killing assay to measure anti-tumor cytotoxicity of engineered T-cells. B) Graphical representation of tumor-cell survival as a measure of time following co-incubation of tumor cells with TRAC knock-out and PDCD1 knock-out (TRACKOPDCDIKO), Meso-CAR random integration and TRAC- and PDCD1- double knock-out (rLv-MesoCAR; TRACKOPDCDIKO), TRAC knock-out and FAPscFv-IL2v targeted integration at PDCD1 locus (TRACKOPDCD1FAPSOFV-IL2V), or Meso-CAR random integration and TRAC knock-out and FAPscFv-IL2v targeted integration at PDCD1 locus (rLv-MesoCAR; TRACKOPDCD1FAPSOFV-IL2V) T cells in the serial killing assay. C) Images of surviving NCI- 11226 and NCI-H226-FAP cells expressing GFP reporter at 72 hour time point of serial killing assay post incubation with indicated T cells. D) Graphical representation of NCI- 11226 (left panel) and NCLH226-FAP (right panel) killing kinetics by indicated T cells in the 48h-72h period of serial killing assay. E) Graphical representation of IFN-y released by indicated T cells in co-incubation supernatant with NCI-H226 (left panel) and NCI- H226-FAP (right panel) during the course of serial killing assay.

Figure 8: RNAseq data for CS1-CAR-T cells at t=0 hours (not activated) or 24 hours post activation using recombinant CS1 protein (open symbols). Closed symbols represent genes selected based on expression level (lower than 100 TPM at 0 hours, greater than 50 TPM at 24 hours, and fold change at 24 hours greater than 5).

DETAILED DESCRIPTION

This document provides methods and materials that can be used to harness spatial characteristics of a tumor microenvironment (“TME”) to amplify anti-tumor activity of immunotherapies locally. For example, in some cases, this document provides engineered T-cells expressing tumor-targeting CARs that can be used as a trigger for enhancing the tumoricide activity of said engineered CAR-Ts as well as patient’s immune cells when and where it is needed, thereby enhancing both the therapeutic effect and the safety of targeted cell immunotherapy in the patients.

For the purpose of interpreting this specification, the following definitions will apply and whenever appropriate, terms used in the singular will also include the plural and vice versa. In the event that any definition set forth below conflicts with the usage of that word in any other document, including any document incorporated herein by reference, the definition set forth below shall always control for purposes of interpreting this specification and its associated claims unless a contrary meaning is clearly intended (for example in the document where the term is originally used). The use of “or” means “and/or” unless stated otherwise. As used in the specification and claims, the singular form “a,” “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a cell” includes a plurality of cells, including mixtures thereof. The use of “comprise,” “comprises,” “comprising,” “include,” “includes,” and “including” are interchangeable and not intended to be limiting. Furthermore, where the description of one or more embodiments uses the term “comprising,” those skilled in the art would understand that, in some specific instances, the embodiment or embodiments can be alternatively described using the language “consisting essentially of’ and/or “consisting of’. As used herein, the term “about” means plus or minus 10% of the numerical value of the number with which it is being used.

All methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, with suitable methods and materials being described herein. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will prevail. Further, the materials, methods, and examples are illustrative only and are not intended to be limiting, unless otherwise specified.

The practice of the present invention will employ, unless otherwise indicated, techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, gene editing, and immunology, which belong to the knowledge of the skilled in the art. Such techniques are explained fully in the literature. See, for example, Current Protocols in Molecular Biology (Frederick M. AUSUBEL, 2000, Wiley and son Inc, Library of Congress, USA); Molecular Cloning: A Laboratory Manual, Third Edition, (Sambrook et al, 2001, Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Harries & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the series, Methods In ENZYMOLOGY (J. Abelson and M. Simon, eds. -in-chief, Academic Press, Inc., New York), specifically, Vols.154 and 155 (Wu et al. eds.) and Vol. 185, "Gene Expression Technology" (D. Goeddel, ed.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); and Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).

Unless specifically defined herein, all technical and scientific terms used have the same meaning as commonly understood by a skilled artisan in the fields of gene therapy, biochemistry, genetics, immunology, cancer, molecular biology, and gene editing. Definitions of common terms in molecular biology may be found, for example, in Benjamin Lewin, Genes VII, published by Oxford University Press, 2000 (ISBN 019879276X); Kendrew et al. (eds.); The Encyclopedia of Molecular Biology, published by Blackwell Publishers, 1994 (ISBN 0632021829); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by Wiley, John & Sons, Inc., 1995 (ISBN 0471186341).

As used herein, a "recipient" is a patient that receives a transplant, such as a transplant containing a population of engineered immune cells, e.g. T-cells. The transplanted cells administered to a recipient may be, e.g. autologous, syngeneic, or allogeneic cells.

As used herein, a "donor" is a mammal (e.g. a human) from which one or more cells are isolated prior to administration of the cells, or progeny thereof, into a recipient. The one or more cells may be, e.g. a population of immune cells or hematopoietic stem cells to be engineered, expanded, enriched, or maintained according to the methods described herewith prior to administration of the cells or the progeny thereof into a recipient. In the allogeneic setting contemplated herewith, a “donor” is not the patient to be treated.

"Expansion" in the context of cells refers to the increase in the number of a characteristic cell type, or cell types, from an initial cell population of cells, which may or may not be identical. The initial cells used for expansion may not be the same as the cells generated from expansion.

"Cell population" includes eukaryotic cells, such as mammalian, e.g. human, cells isolated from biological sources, for example, blood product or tissues. A cell population can derive from more than one cell.

As used herein, the term "pharmaceutical composition" refers to the active ingredient in combination with a pharmaceutically acceptable carrier and/or excipient e.g. a carrier and/or excipient commonly used in the pharmaceutical industry. The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of mammals, such as human beings, without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

As used herein, the term "administering," refers to the placement of a compound, cell, or population of cells as disclosed herein into a subject by a method or route which results in at least partial delivery of the agent at a desired site. Pharmaceutical compositions comprising the compounds or cells disclosed herein can be administered by any appropriate route which results in an effective treatment in the patient. The patient who can be treated with the materials and methods disclosed herewith can be a mammal, including a human and a non-human primate.

As used herein, "nucleic acid" or "polynucleotides" refers to nucleotides and/or polynucleotides, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), oligonucleotides, fragments generated by the polymerase chain reaction (PCR), and fragments generated by any of ligation, scission, endonuclease action, and exonuclease action. Nucleic acid molecules can be composed of monomers that are naturally-occurring nucleotides (such as DNA and RNA), or analogs of naturally-occurring nucleotides (e.g. enantiomeric forms of naturally-occurring nucleotides), or a combination of both. Modified nucleotides can have alterations in sugar moieties and/or in pyrimidine or purine base moieties. Sugar modifications include, for example, replacement of one or more hydroxyl groups with halogens, alkyl groups, amines, and azido groups, or sugars can be functionalized as ethers or esters. Moreover, the entire sugar moiety can be replaced with sterically and electronically similar structures, such as aza-sugars and carbocyclic sugar analogs. Examples of modifications in a base moiety include alkylated purines and pyrimidines, acylated purines or pyrimidines, or other well-known heterocyclic substitutes. Nucleic acid monomers can be linked by phosphodiester bonds or analogs of such linkages. Nucleic acids can be either single stranded or double stranded.

The terms "polypeptide," "peptide" and "protein" are used interchangeably to refer to a polymer of amino acid residues. The term also applies to amino acid polymers in which one or more amino acids are chemical analogues or modified derivatives of corresponding naturally-occurring amino acids.

As used herein, the terms "treat," "treatment," "treating," and the like, refer to obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease. "Treatment," as used herein, covers any treatment of a disease in a mammal (e.g. a human), and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, e.g. causing regression of the disease, e.g. to completely or partially remove symptoms of the disease.

The term "subject" or "patient" as used herein includes mammals including nonhuman primates and humans.

An "effective amount" or "therapeutically effective amount" refers to that amount of a composition described herein which, when administered to a subject (e.g. human), is sufficient to aid in treating a disease. The amount of a composition that constitutes a "therapeutically effective amount" will vary depending on the cell preparations, the condition and its severity, the manner of administration, and the age of the subject to be treated, but can be determined routinely by one of ordinary skill in the art having regard to his own knowledge and to this disclosure. When referring to an individual active ingredient or composition, administered alone, a therapeutically effective dose refers to that ingredient or composition alone. When referring to a combination, a therapeutically effective dose refers to combined amounts of the active ingredients, compositions or both that result in the therapeutic effect, whether administered concurrently, simultaneously, or sequentially.

By "vector" is meant a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. A "vector" can include, but is not limited to, a viral vector, a plasmid, an oligonucleotide, a RNA vector or a linear or circular DNA or RNA molecule which may consist of a chromosomal, non-chromosomal, semisynthetic or synthetic nucleic acids. Preferred vectors are those capable of autonomous replication (episomal vector) and/or expression of nucleic acids to which they are linked (expression vectors). Large numbers of suitable vectors are known to those of skill in the art and commercially available. Viral vectors include retrovirus, adenovirus, parvovirus (e.g. adenoassociated viruses (AAV), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g. influenza virus), rhabdovirus (e.g. rabies and vesicular stomatitis virus), paramyxovirus (e.g. measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g. Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g. vaccinia, fowlpox and canarypox). Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example. Examples of retroviruses include avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).

As used herein, the term "locus" is the specific physical location of a DNA sequence (e.g. of a gene) into a genome. The term "locus" can refer to the specific physical location of a rare-cutting endonuclease target sequence on a chromosome. Such a locus can comprise a target sequence that is recognized and/or cleaved by a sequence-specific endonuclease as described herein. It is understood that the locus of interest can not only qualify a nucleic acid sequence that exists in the main body of genetic material (i.e. in a chromosome) of a cell but also a portion of genetic material that can exist independently to said main body of genetic material such as plasmids, episomes, virus, transposons or in organelles such as mitochondria as non-limiting examples.

As used herewith, a nucleic acid sequence is said to be “placed under the transcriptional control of a promoter” if said nucleic acid sequence follows, or is at the 3’ end, of said promoter in such a manner that it is operably linked to said promoter and its transcription is controlled by said promoter.

The term "cleavage" when used in reference to nucleic acid refers to the breakage of the covalent backbone of a polynucleotide. Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events. Double stranded DNA, RNA, or DNA RNA hybrid cleavage can result in the production of either blunt ends or staggered ends. "Sequence identity" refers to the identity between two nucleic acid molecules or polypeptides. It refers to the residues in the two sequences which are the same when the sequences are aligned for maximum correspondence. When a position in the compared sequence is occupied by the same base (or amino acid), then the molecules are identical at that position. A degree of identity between nucleic acid sequences (or amino acid sequences) is a function of the number of identical or matching nucleotides (or amino acids) at positions shared by the aligned nucleic acid sequences (or amino acid sequences). Various alignment algorithms and/or programs may be used to calculate the identity between two sequences, including FASTA, or BLAST which are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with, e.g. default setting. For example, polypeptides having at least 70%, 85%, 90%, 95%, 98% or 99% identity to specific polypeptides described herein and exhibiting substantially the same functions, as well as polynucleotide encoding such polypeptides, are contemplated.

“Fibroblast activation Protein” (“FAP”) is also generally called Prolyl endopeptidase FAP, or Fibroblast Activation Protein alpha (NCBI Gene ID: 2191). In some cases, a FAP polypeptide can be a human FAP polypeptide. Examples of FAP polypeptides that can be targeted by a FAP-binding domain as described herein include, without limitation, a human FAP polypeptide having the amino acid sequence set forth in NCBI Reference Sequence: NP_004451.2.

In one aspect, this document provides an engineered cell comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”); and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising a Fibroblast Activation Protein (FAP)-binding-domain and a stimulatory cytokine, wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”), and wherein said inducible promoter is inducible upon activation of the cell.

In a particular aspect, said fusion protein does not comprise an antibody crystallizable fragment (Fc).

In a particular aspect, said fusion protein does not comprise a full anti -FAP antibody.

In a particular aspect, said Fibroblast Activation Protein -binding-domain comprises the VH and VL amino acid sequences from a monoclonal anti-FAP antibody.

The engineered cell can be any appropriate cell. For example, the cell containing exogenous nucleic acid sequences of a) and b) can be an immune cell such as a T-cell, a NK-cell, or a macrophage. In some cases, the cell containing exogenous nucleic acid sequences of a) and b) can be an iPSC that may be an intermediate in the production of an engineered immune cell, such as a T-cell, a NK-cell, or a macrophage, as described herein.

In some cases, an engineered cell provided herein can be a T-cell that has been genetically modified to suppress or repress expression of T-cell receptors (TCRs) (e.g. endogenous TCRs) at the T-cell surface and, optionally, to suppress or repress expression of at least one gene controlling MHC complex surface presentation such as a B2M gene that encodes a p2m polypeptide and/or a CIITA gene that encodes a CIITA polypeptide, and optionally to suppress or repress expression of a gene encoding a CD52 polypeptide, at the T-cell surface.

In some cases, an engineered cell provided herein can be a NK-cell that has been genetically modified to suppress or repress expression of at least one gene controlling MHC complex surface presentation such as a B2M gene that encodes a p2m polypeptide and/or a CIITA gene that encodes a CIITA polypeptide, and optionally to suppress or repress expression of a gene encoding a CD52 polypeptide, at the NK-cell surface.

In some cases, a p2m polypeptide can be a human p2m polypeptide. Examples of B2M genes encoding p2m polypeptides which expression can be suppressed or repressed as described herein include, without limitation, a human B2M gene (e.g. NCBI Gene ID 567) encoding a 02m polypeptide having the amino acid sequence set forth in GeneBank Accession No. AAA51811.

In some cases, a CIITA polypeptide can be a human CIITA polypeptide. Examples of CIITA genes encoding CIITA polypeptides which expression can be suppressed or repressed as described herein include, without limitation, a human CIITA gene (e.g. NCBI Gene ID 4261) encoding a CIITA polypeptide having the amino acid sequence set forth in GeneBank Accession No. P33076.3 or No. AAU06586.

In some cases, a CD52 polypeptide can be a human CD52 polypeptide. Examples of CD52 genes (e.g. NCBI Gene ID 1043) encoding CD52 polypeptides which expression can be suppressed or repressed as described herein include, without limitation, a human CD52 polypeptide having the amino acid sequence set forth in GeneBank Accession No. AJC 19276.

In some cases, an engineered T-cell described herein can be designed such that the CD52 gene, the B2M gene, or both the CD52 gene and the B2M gene are inactivated.

In some cases, an engineered T-cell described herein can be designed (e.g., genetically modified) to suppress or repress the expression of at least one immune checkpoint protein or receptor thereof. For example, an engineered T-cell described herein can be designed such that the programmed cell death 1 (PDCD1) gene, the CTLA4 gene, or both the PDCD1 gene and the cytotoxic T-lymphocyte associated protein 4 (CTLA4) gene are inactivated.

In some cases, a PD1 polypeptide can be a human PD1 polypeptide. Examples of PDCD1 genes encoding PD1 polypeptides which expression can be suppressed or repressed as described herein include, without limitation, a human PDCD1 gene (e.g. NCBI Gene ID 5133 or ENSG00000188389) encoding a polypeptide having the amino acid sequence set forth in GeneBank Accession No. UMM61402.1.

In some cases, a CTLA4 polypeptide can be a human CTLA4 polypeptide. Examples of CTLA4 genes encoding CTLA4 polypeptides which expression can be suppressed or repressed as described herein include, without limitation, a human CTLA4 gene (e.g. NCBI Gene ID 1493) encoding a CTLA4 polypeptide having the amino acid sequence set forth in GeneBank Accession No. AAL07473. In some cases, an engineered T-cell described herein can be designed such that at least one gene encoding a TCR component, and a PDCD1 gene are inactivated.

In another aspect, this document provides a pharmaceutical composition comprising engineered immune cells as described herewith.

For instance, this document provides a pharmaceutical composition comprising engineered immune cells (e.g., engineered T-cells), comprising: a) an exogenous nucleic acid sequence encoding a tumor-CAR; and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a FAP -binding-domain, such as a FAP-binding domain comprising the VH and VL amino acid sequences from a monoclonal anti-FAP antibody (e.g. a FAPscFv), and (ii) a stimulatory cytokine; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of an endogenous or exogenous constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”), and wherein said inducible promoter is inducible upon activation of the immune cell.

In some cases, a pharmaceutical composition described herein can be for use in the treatment of a cancer characterized by the presence of FAP in the tumor microenvironment.

In another aspect, this document provides methods for treating a cancer characterized by the presence of FAP in the tumor microenvironment, comprising administering, to a patient in need thereof, a therapeutically effective amount of engineered immune cells (e.g., engineered T-cells), comprising: a) an exogenous nucleic acid sequence encoding a tumor-CAR; and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a FAP -binding-domain, such as a FAP-binding domain comprising the VH and VL amino acid sequences from a monoclonal anti-FAP antibody (e.g. a FAPscFv), and (ii) a stimulatory cytokine; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”), and wherein said inducible promoter is inducible upon activation of the immune cell.

The engineered cells and methods described herein can be part of an autologous or part of an allogenic treatment. By autologous, it is meant that cells used for treating patients are originating from said patient. By allogeneic, it is meant that the cells or population of cells used for treating patients are not originating from said patient but from a donor or from a cell line.

In some cases, engineered cells described herein can be administered to patients (e.g. humans) undergoing an immunosuppressive treatment. In some cases, the administered cells can be cells that were made resistant to at least one immunosuppressive agent. In some cases, the immunosuppressive treatment can help the selection and expansion of the engineered immune cells (e.g. engineered T-cells) within the patient.

Any appropriate route of administration can be used to administer cells described herein to a patient, including by aerosol inhalation, injection, ingestion, transfusion, implantation, and/or transplantation. The compositions described herein can be administered to a patient subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous or intralymphatic injection, or intraperitoneally. In some cases, a cell composition described herein can be administered to a patient by intravenous injection, where the cells are capable of migrating to their desired site of action.

While individual needs vary, determination of optimal ranges of effective amounts of a given cell type for a particular disease or conditions within the skill of the art. An effective amount means an amount which provides a therapeutic or prophylactic benefit. The dosage administered will be dependent upon the age, health and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment and the nature of the effect desired. In some cases, the administration of the cells or population of cells can comprise administration of about 10 ⁴ -l 0 ⁹ cells per kg body weight. In some cases, about 10 ⁵ to 10 ⁶ cells/kg body weight, or about 10 ⁵ to 5x10 ⁶ cells/kg body weight, can be administered. All integer values of cell numbers within those ranges are contemplated.

The cells can be administered in one or more doses. In some cases, an effective amount of cells can be administered as a single dose. In some cases, an effective amount of cells can be administered as more than one dose over a period of time. Timing of administration is within the judgment of managing physician and depends on the clinical condition of the patient.

In some cases, administering engineered immune cells (e.g. T-cells) can include treating the patient with a myeloablative and/or immune suppressive regimen to deplete host bone marrow stem cells and prevent rejection. In some cases, the patient can be administered chemotherapy and/or radiation therapy. In some cases, the patient can be administered a reduced dose chemotherapy regimen. In some cases, reduced dose chemotherapy regimen with busulfan at 25% of standard dose can be sufficient to achieve significant engraftment of modified cells while reducing conditioning-related toxicity (Aiuti A. et al. (2013), Science 23; 341 (6148)). A stronger chemotherapy regimen can be based on administration of both busulfan and fludarabine as depleting agents for endogenous HSC. In some cases, the dose of busulfan and fludarabine can be approximately 50% and 30% of the ones employed in standard allogeneic transplantation. In some cases, the cells can be administered following B-cell ablative therapy such as agents that react with CD20, e.g. Rituxan. In some cases, the patient can be administered chemotherapy agents such as fludarabine, external-beam radiation therapy (XRT), cyclophosphamide, or antibodies such as OKT3 directed against CD3 or Alemtuzumab (Campath®, Lemtrada®) directed against CD52. In some cases, the patient can be administered with fludarabine and cyclophosphamide, and, optionally, Alemtuzumab.

In certain cases, the engineered immune cells (e.g. T-cells), can be administered to the subject as combination therapy comprising immunosuppressive agents. Exemplary immunosuppressive agents include sirolimus, tacrolimus, cyclosporine, mycophenolate, anti-thymocyte globulin, corticosteroids, calcineurin inhibitor, anti-metabolite, such as methotrexate, post-transplant cyclophosphamide or any combination thereof. In some cases, the subject can be pretreated with only sirolimus or tacrolimus as prophylaxis against GVHD. In some cases, the cells can be administered to the subject before an immunosuppressive agent. In some cases, the cells can be administered to the subject after an immunosuppressive agent. In some cases, the cells can be administered to the subject concurrently with an immunosuppressive agent. In some cases, the cells can be administered to the subject without an immunosuppressive agent. In some cases, the patient receiving genetically modified cells can receive immunosuppressive agent for less than 6 months, 5 months, 4 months, 3 months, 2 months, 1 month, 3 weeks, 2 weeks, or 1 week.

1. Engineered immune cells comprising a tumor-CAR and a fusion protein such as a FAPscFv-cytokine fusion protein

The type of cells for the engineered cells expressing a) a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”) which expression is constitutive, and b) a secreted fusion protein comprising (i) a Fibroblast Activation Protein-binding-domain and (ii) a stimulatory cytokine, which expression is inducible upon activation of said cells, is not particularly limiting.

1.1. Type of cells

The engineered cells described herewith can be immune cells, including T-cells, NK-cells, and macrophages.

The engineered cells described herewith can also be Induced Pluripotent Stem Cells (“iPSCs”), which can subsequently be differentiated into immune cells as described herewith. The engineered iPSCs as described herewith would, thus, be an intermediate product in the production of engineered immune cells according to the present disclosure.

In some cases, the engineered cells described herewith could be any differentiated cells, which could subsequently be de-differentiated into iPSCs, which in turn could subsequently be differentiated into immune cells as described herewith. The engineered differentiated cells as described herewith would thus be an intermediate product in the production of engineered immune cells according to the present disclosure. The genetic engineering as described herewith can be carried out on the differentiated cells, on the dedifferentiated cells, or on the iPSCs. Methods to produce iPSCs from differentiated cells are well known to the skilled person, they include methods based on nuclear transfer, usage of cell extracts and synthetic molecules, forced expression of defined genes and cytoplasmatic level modifications (Telpalo-Carpio et al (2013) J Stem Cells Regen Med. 9(1): 2-8). Methods to produce immune cells from iPSCs are also well known to the skilled person, they include for instance the use of a serum- and feeder- free in vitro protocol of differentiation into T-cells as disclosed in Themeli et al. (Nature Biotechnology (2013) 31 :928-933) and the protocol of differentiation into NK-cells under a completely chemically-defined condition as described in Matsubara et al. (Biochem Biophys Res Commun. (2019) 515(1): 1-8).

Thus, one aspect relates to an engineered immune cell comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”); and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a Fibroblast Activation Protein (FAP)-binding-domain, such as a FAP- binding domain comprising the VH and VL amino acid sequences from a monoclonal anti- FAP antibody (e.g. a FAPscFv), and (ii) a stimulatory cytokine; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”), and wherein said inducible promoter is inducible upon activation of the immune cell.

In some cases, said immune cell can be a T-cell.

In some cases, said immune cell can be a NK-cell.

In some cases, said immune cell can be a macrophage.

Another aspect relates to an engineered iPSC comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”); and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a Fibroblast Activation Protein (FAP)-binding-domain, such as a FAP- binding domain comprising the VH and VL amino acid sequences from a monoclonal anti- FAP antibody (e.g. a FAPscFv), and (ii) a stimulatory cytokine; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter; wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the promoter of said endogenous inducible locus (“inducible promoter”); and wherein said inducible promoter is inducible upon activation of the iPSC, or upon activation of the immune cell into which said engineered iPSC can further be differentiated.

In some cases, the engineered iPSC described herewith can be an intermediate product in the production of an engineered immune cell as described herewith.

1.2. Tumor -CAR

By “chimeric antigen receptor” or “CAR” is generally meant a synthetic receptor comprising a targeting moiety (also called “binding moiety”) that is associated with one or more signaling domains in a single fusion molecule. As defined herein, the term “chimeric antigen receptor” covers single chain CARs as well as multi-chain CARs. In some cases, the binding moiety of a CAR can comprise an antigen-binding domain of a single-chain antibody (scFv), comprising light chain and heavy chain variable fragments of a monoclonal antibody joined by a flexible linker. Binding moieties based on receptor or ligand domains have also been used successfully. The signaling domains for first generation CARs are derived from the cytoplasmic region of the CD3zeta or the Fc receptor gamma chains. First generation CARs have been shown to successfully redirect T-cell cytotoxicity. However, they failed to provide prolonged expansion and anti-tumor activity in vivo. Signaling domains from co-stimulatory molecules including CD28, OX-40 (CD134), and 4-1BB (CD137) have been added alone (second generation) or in combination (third generation) to enhance survival and increase proliferation of CAR modified T-cells. CARs are not necessarily only single chain polypeptides, as multi-chain CARs are also possible. According to the multi-chain CAR architecture, for instance as described in WO 2014/039523, the signalling domains and co -stimulatory domains are located on different polypeptide chains. Such multi-chain CARs can be derived from FcsRI, by replacing the high affinity IgE binding domain of FcsRI alpha chain by an extracellular ligand-binding domain such as scFv, whereas the N- and/or C-termini tails of FcsRI beta and/or gamma chains are fused to signal transducing domains and costimulatory domains, respectively. The extracellular ligand binding domain has the role of redirecting the immune cell (e.g. T-cell) specificity towards cell targets, while the signal transducing domains activate the immune cell response. CARs are generally expressed in effector immune cells to redirect their immune activity against antigens expressed at the surface of tumor cells from various malignancies including lymphomas and solid tumors. A component of a CAR is any functional subunit of a CAR that is encoded by an exogenous polynucleotide sequence introduced into the cell. For instance, this component can help the interaction with the target antigen, the stability or the localization of the CAR into the cell.

While the CARs of the present disclosure useful in the methods herein are not limited to a specific CAR structure, a nucleic acid that can be used to engineer the immune cells generally encodes a CAR comprising: an extracellular antigen-binding domain that binds to a tumor antigen, a hinge, a transmembrane domain, and an intracellular domain comprising a stimulatory domain and/or a primary signalling domain. Generally, the extracellular antigen-binding domain is a scFv comprising a Heavy variable chain (VH) and a Light variable chain (VL) of an antibody binding to a tumor antigen connected via a Linker. The extracellular antigen-binding domain can also derive from a single domain antibody (e.g. a nanobody) or from an ankyrin repeat domain. Thus, the extracellular antigen-binding domain can comprise one Heavy variable chain and no Light variable chain. Walser et al. (Viruses (2022): 14, 2242) describe ankyrin repeat domains. The transmembrane domain can be, for example, a CD8a transmembrane domain, a CD28 transmembrane domain, or a 4- IBB transmembrane domain. The co-stimulatory domain can be, for example, the 4-1BB co-stimulatory domain or CD28 co-stimulatory domain. The primary signalling domain can be, for example, the CD3(/ signalling domain. The CARs as described herewith also generally comprise a signal peptide to direct the nascent protein to the endoplasmic reticulum and subsequent expression at the engineered cell’s surface. The signal peptide is cleaved after addressing the CAR to the cell surface. The signal peptide comprised in the CARs described herewith can be a CD8a signal peptide, such as one having an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 99% identity with SEQ ID NO: 76, or having an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 99% identity with an alternative signal peptide of SEQ ID NO: 77.

In a broad sense, as used herewith, a tumor-CAR can also be a recombinant TCR recognizing a tumor-expressed peptide/MHC complex. Thus, in some cases, a tumor-CAR as described herewith can be a recombinant TCR a/p comprising an extracellular ligand binding domain and a transmembrane domain without stimulatory and/or co -stimulatory domain. Indeed, typically, recombinant TCR a/p do not contain activation or costimulation domains, they depend on endogenous CD3 chains for activation and endogenous CD28 for costimulation.

Table 1: Sequence of different domains typically present in a CAR

A tumor-CAR comprises an extracellular ligand (or antigen) binding domain that recognizes a tumor antigen. Hence, a tumor-CAR as described herewith comprises an extracellular tumor antigen-binding domain. The term “extracellular antigen binding domain” or “extracellular ligand binding domain” as used herein generally refers to an oligopeptide or polypeptide that is capable of binding a specific antigen, such as a tumor antigen. In some cases, the domain will be capable of interacting with a cell surface molecule, such as a ligand. For example, in some cases, an extracellular antigen-binding domain can be chosen to recognize an antigen that acts as a cell surface marker on target cells associated with a particular disease state. In some cases, said extracellular antigen-binding domain can comprise a single chain antibody fragment (scFv) comprising the heavy (VH) and the light (VL) variable fragments of a target-antigen-specific monoclonal antibody joined by a flexible linker. The antigen binding domain of a CAR expressed on the cell surface of the engineered cells described herein can be any domain that binds to the target antigen and that derives from, for example, a monoclonal antibody, a recombinant antibody, a human antibody, a humanized antibody, and a functional fragment thereof.

As used herewith the term “tumor antigen” is meant to cover “tumor-specific antigens”, “tumor associated antigens”. Tumor-Specific Antigens (TSA) are generally present only on tumor cells and not on any other cell, while Tumor- Associated Antigens (TAA) are present on some tumor cells and also present on some normal cells. “Tumor antigen,” as meant herein, also refers to mutated forms of a protein, which only appears in that form in tumors, while the non-mutated form is observed in non-tumoral tissues.

A tumor antigen can be an antigen specific of, or associated with, a solid tumor. The tumor antigen is not limiting. In some cases, the tumor antigen is selected from the group consisting of CEA, ERBB2, EGFR, GD2, mesothelin, MUC1, PSMA, GD2, PSMA1, LAP3, ANXA3, Tumor-associated glycoprotein 72 (TAG72), MUC16, 5T4, FRa, MUC28z, NKG2D, HRG10, prostate stem cell antigen (PSCA), prostate-specific membrane antigen (PSMA), carboxy-anhydrase-IX (CA-IX), Trop2, claudinl8.2, folate receptor 1 (FOLR1), CXCR2, B7-H3, CD 133, CD24, receptor tyrosine kinase-like orphan receptor 1 -specific (R0R1), EGFR, EGFRvIII, VEGF, erythropoietin-producing hepatocellular carcinoma A2 (EphA2), DLL3, glypican-3, epithelial cell adhesion molecule (EpCAM), GUCY2C (Guanylate Cyclase 2C), doublecortin-like kinase 1 (DCLK1), HER receptors HER1, HER2, HER3, HER4, PEM, A33, G250, carbohydrate antigens Le ^y , Le ^x , Le ^b , STEAP1, CD166, CD24, CD44, E-cadhenn, SPARC, and ERBB3. See, e.g. Marofi et al. Stem Cell Res Ther (2021) 12, 81, which is incorporated by reference herein.

In some cases, the tumor antigen is selected from the group consisting of mesothelin, Trop2, MUC1, EGFR, and VEGF. In some cases, the antigen is selected from the group consisting of Mesothelin, MUC1, and Trop2.

In some cases, the tumor antigen is not FAP. Thus, in some cases, FAP is not the antigen targeted by the tumor-CAR.

A tumor antigen can also be an antigen specific of, or associated with, a haematological cancer characterized by the presence of FAP in the tumor microenvironment such as myelofibrosis, myelodysplastic syndromes, acute myeloid leukemia, non-Hodgkin’s lymphoma, multiple myeloma.

In some cases, the tumor antigen associated with an haematological cancer is selected from the group consisting of BCMA, CD19, CD20, CD22, CD30, CD123, CD70, CD33, CD135, CD44, CD276, CD2, CD3, CD4, CD5, CD7, CD8, CD10, CD37, CD79, CD79a, CD80, CD138, CD47, CRLF2, CD38, CLL-1, NKG2D, CALR, IL1RAP, ILT3, TIM3, CD96, VISTA, CS1, TACI, APRIL, GPRC5D, and CD44v6.

In some cases, the tumor antigen associated with a haematological cancer is selected from the group consisting of BCMA, CD19, CD123, CD20, CD22, CS1, CD138, CD80, CD2, CD3, CD4, CD5, CD7 and CD8.

In some cases, the tumor antigen associated with a haematological cancer is selected from the group consisting of BCMA, CD 19, CD 123, CD20, CD22, and CS1.

Table 2. Sequences of the CDRs comprised in the VH and VL chains of some tumor- CARs

Table 3: Sequences of the ScFv of some tumor-CARs

The tumor-CAR described herewith can comprise:

(a) an extracellular ligand binding-domain comprising the VH and VL amino acid sequences from a monoclonal anti-tumor-antigen antibody, (b) a hinge selected from a FcyRIII hinge, a CD8a hinge and an IgGl hinge,

(c) a transmembrane domain comprising a CD8a transmembrane domain or a CD28 transmembrane domain, and

(d) a cytoplasmic domain comprising a CD3 zeta signaling domain and a costimulatory domain from 4-1BB or from CD28. In some cases, the tumor-CAR can comprise an extracellular binding-domain comprising: a) the H-CDRs of SEQ ID NO: 39, SEQ ID NO: 40, and SEQ ID NO: 41 , and the L-CDRs of SEQ ID NO: 42, SEQ ID NO: 43, and SEQ ID NO: 44, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least 99% identity with amino acid sequence SEQ ID NO: 45; b) the H-CDRs of SEQ ID NO: 47, SEQ ID NO: 48, and SEQ ID NO: 49, and the L-CDRs of SEQ ID NO: 50, SEQ ID NO: 51, and SEQ ID NO: 52, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least 99% identity with amino acid sequence SEQ ID NO: 53; c) the H-CDRs of SEQ ID NO: 55, SEQ ID NO: 56, and SEQ ID NO: 57, and the L-CDRs of SEQ ID NO: 58, SEQ ID NO: 59, and SEQ ID NO: 60, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least 99% identity with amino acid sequence SEQ ID NO: 61 ; or d) the H-CDRs and the L-CDRs comprised in the amino acid sequence of SEQ ID NO: 63, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least 99% identity with amino acid sequence SEQ ID NO: 63.

In some cases, the tumor-CAR can be specific for Mesothelin (Meso-CAR) and can have an amino acid sequence of SEQ ID NO: 62. In some cases, the Meso-CAR can comprise an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 62, and, optionally, the CDRs of SEQ ID NO: 55 to SEQ ID NO: 60.

In some cases, the nucleic acid sequence encoding the Meso-CAR described herewith can comprise a nucleic acid sequence of SEQ ID NO: 100. In some cases, the nucleic acid sequence encoding the Meso-CAR described herewith can comprise a nucleic acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 100, and can encode a Meso-CAR comprising the amino acid sequence of SEQ ID NO: 62.

In some cases, the tumor-CAR can be specific for Trop2 (Trop2-CAR) and can have an amino acid sequence of SEQ ID NO: 46. In some cases, the Trop2-CAR can comprise an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 46, and, optionally, the CDRs of SEQ ID NO: 39 to SEQ ID NO: 44.

In some cases, the nucleic acid sequence encoding the Trop2-CAR described herewith can comprise a nucleic acid sequence of SEQ ID NO: 102. In some cases, the nucleic acid sequence encoding the Trop2-CAR described herewith can comprise a nucleic acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 102, and can encode a Trop2-CAR comprising the amino acid sequence of SEQ ID NO: 46. In some cases, the tumor-CAR can be specific for Mucinl (MUC1-CAR) and can have an amino acid sequence of SEQ ID NO: 54. In some cases, the MUC1-CAR can comprise an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 54, and, optionally, the CDRs of SEQ ID NO: 47 to SEQ ID NO: 52.

In some cases, the nucleic acid sequence encoding the MUC1-CAR described herewith can comprise a nucleic acid sequence of SEQ ID NO: 101. In some cases, the nucleic acid sequence encoding the MUC1-CAR described herewith can comprise a nucleic acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 101, and can encode a MUC1-CAR comprising the amino acid sequence of SEQ ID NO: 54.

In some cases, the tumor-CAR can be specific for CS1 (CS1-CAR) and can have an amino acid sequence of SEQ ID NO: 88. In some cases, the CS1-CAR can comprise an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 88, and, optionally, the CDRs comprised in SEQ ID NO: 88.

1.3 Fusion protein

The engineered immune cells described herewith are able to express and secrete a fusion protein comprising (i) a FAP-binding-domain, and (ii) a stimulatory cytokine.

In some cases, said FAP-binding domain can comprise a single chain antibody fragment (scFv) comprising the heavy (VH) and the light (VL) variable fragments of a FAP-specific monoclonal antibody joined by a flexible linker, which forms a “FAPscFv”. The FAP-binding domain of the fusion protein described herein can be any domain that binds to FAP and that derives from, for example, a monoclonal antibody, a recombinant antibody, a human antibody, a humanized antibody, and a functional fragment thereof. In some cases, an antigen-binding domain (e.g. a FAP-binding domain) can comprise the VH and VL fragments of an antibody but does not comprise an antibody crystallizable fragment (Fc).

It is also contemplated that said FAP-binding domain can derive from a single domain antibody (e.g. a nanobody) or from an ankyrin repeat domain. Thus, the FAP- binding domain can comprise one Heavy variable chain and no Light variable chain. Hence, in some cases, the fusion protein can comprise:

(i) optionally, a signal peptide,

(ii) a FAP -binding-domain, such as a FAP -binding domain comprising the VH and VL amino acid sequences from a monoclonal anti-FAP antibody (e.g. a FAPscFv),

(iii) at least one stimulatory cytokine selected from the group consisting of Interleukin-2 or a variant thereof such as IL-2v, Interleukin-7 or a variant thereof, Interleukin- 12 or a variant thereof, Interleukin- 15 or a variant thereof, Interleukin- 15 in complex with its high affinity receptor IL-15RA, Interleukin- 18 or a variant thereof, and Interleukin-23 or a variant thereof.

In a particular aspect, said fusion protein does not comprise an antibody crystallizable fragment (Fc).

The fusion proteins as described herewith also generally comprise, in their immature form, a signal peptide to direct the nascent protein to the endoplasmic reticulum and allows subsequent secretion outside of the cell. The signal peptide is cleaved after secretion of the fusion protein in the extracellular medium. The signal peptide comprised in the protein fusions described herewith can be, for instance, an IL2 signal sequence (e.g. of SEQ ID NO: 90), an IgE signal sequence (e.g. of SEQ ID NO: 91), a CTLA4 Ig signal sequence (e.g. of SEQ ID NO: 92), or one having an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 99% identity with SEQ ID NO: 90, or one having an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 99% identity with SEQ ID NO: 91, or one having an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 99% identity with SEQ ID NO: 92.

Table 4: Sequences of the VH and VL regions, and corresponding ScFvs of some examples of FAP-binding domains

In some cases, the FAP -binding-domain (such as a FAPscFv) comprises: a) the H-CDRs of SEQ ID NO: 1 , SEQ ID NO: 2, and SEQ ID NO: 3, and the L- CDRs of SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least

99% identity with amino acid sequence SEQ ID NO: 9; b) the H-CDRs of SEQ ID NO: 10, SEQ ID NO: 11, and SEQ ID NO: 12, and the L-CDRs of SEQ ID NO: 13, SEQ ID NO: 14, and SEQ ID NO: 15, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least 99% identity with amino acid sequence SEQ ID NO: 18; c) the H-CDRs of SEQ ID NO: 19, SEQ ID NO: 20, and SEQ ID NO: 21 , and the L-CDRs of SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 24, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least 99% identity with amino acid sequence SEQ ID NO: 27; or d) the H-CDRs of SEQ ID NO: 28, SEQ ID NO: 29, and SEQ ID NO: 30, and the L-CDRs of SEQ ID NO: 31, SEQ ID NO: 32, and SEQ ID NO: 33, and optionally an amino acid sequence having at least 80%, at least 90%, at least 95%, or at least 99% identity with amino acid sequence SEQ ID NO: 36.

In some cases, the FAP -binding-domain (such as a FAPscFv) comprises a VH region comprising SEQ ID NO: 7 and a VL region comprising SEQ ID NO: 8. In some cases, the FAP-binding-domain comprises an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 7 and an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 8. In some cases, the FAP-binding-domain comprises an amino acid sequence comprising complementarity determining regions (CDRs) comprised in SEQ ID NO: 7 and SEQ ID NO: 8. In some cases, the H-CDRs comprised in SEQ ID NO: 7 comprise amino acids sequences of SEQ ID NO: 1 to SEQ ID NO: 3. In some cases, the L-CDRs comprised in SEQ ID NO: 8 comprise amino acids sequences of SEQ ID NO: 4 to SEQ ID NO: 6. In some cases, the FAP-binding-domain comprises (i) the CDRs comprised in SEQ ID NOs: 7 and 8, and (ii) an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 7, and (iii) an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 8.

In some cases, the FAP-binding-domain (such as a FAPscFv) comprises a VH region comprising SEQ ID NO: 16 and a VL region comprising SEQ ID NO: 17. In some cases, the FAP-binding-domain (such as a FAPscFv) comprises an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 16 and an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 17. In some cases, the FAP-binding- domain comprises an amino acid sequence comprising complementarity determining regions (CDRs) comprised in SEQ ID NO: 16 and SEQ ID NO: 17. In some cases, the H- CDRs comprised in SEQ ID NO: 16 comprise amino acids sequences of SEQ ID NO: 10 to SEQ ID NO: 12. In some cases, the L-CDRs comprised in SEQ ID NO: 17 comprise amino acids sequences of SEQ ID NO: 13 to SEQ ID NO: 15. In some cases, the FAP- binding-domain comprises (i) the CDRs comprised in SEQ ID NOs: 16 and 17, and (ii) an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 16, and (iii) an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 17.

In some cases, the FAP-binding-domain (such as a FAPscFv) comprises a VH region comprising SEQ ID NO: 25 and a VL comprising SEQ ID NO: 26. In some cases, the FAP-binding-domain (such as a FAPscFv) comprises an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 25 and an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 26. In some cases, the FAP-binding-domain comprises an amino acid sequence comprising complementarity determining regions (CDRs) comprised in SEQ ID NO: 25 and SEQ ID NO: 26. In some cases, the CDRs comprised in SEQ ID NO: 25 comprise amino acids sequences of SEQ ID NO: 23 to SEQ ID NO: 25. In some cases, the CDRs comprised in SEQ ID NO: 26 comprise amino acids sequences of SEQ ID NO: 26 to SEQ ID NO: 28. In some cases, the FAP-binding-domain comprises (i) the CDRs comprised in SEQ ID NOs: 25 and 26, and (ii) comprising an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 25, and (iii) an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 26.

In some cases, the FAP -binding-domain (such as a FAPscFv) comprises a VH region comprising SEQ ID NO: 34 and a VL comprising SEQ ID NO: 35. In some cases, the FAP -binding-domain (such as a FAPscFv) comprises an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 34 and an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 35 In some cases, the FAP-binding-domain comprises an amino acid sequence comprising complementarity determining regions (CDRs) comprised in SEQ ID NO: 34 and SEQ ID NO: 35. In some cases, the CDRs comprised in SEQ ID NO: 34 comprise amino acids sequences of SEQ ID NO: 28 to SEQ ID NO: 30. In some cases, the CDRs comprised in SEQ ID NO: 35 comprise amino acids sequences of SEQ ID NO: 31 to SEQ ID NO: 33. In some cases, the FAP-binding-domain comprises (i) the CDRs comprised in SEQ ID NOs: 34 and 35, and (ii) comprising an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VH region comprising SEQ ID NO: 34, and (iii) an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a VL region comprising SEQ ID NO: 35.

Table 5: Sequences of the CDRs comprised in the VH and VL chains of some FAP- binding domains (e.g. FAPscFvs)

In some cases, the amino acid sequence comprising a VH region and the amino acid sequence comprising a VL region are separated by one or more linker amino acid residues. The number of amino acids constituting the linker is not necessarily limiting, but in some cases the linker is at least about 5 amino acids in length, such as at least about 10 amino acids in length. In some cases, the linker is between about 10-25 amino acids in length. In some cases, the linker sequence is selected from any one of SEQ ID NOs: 37-38.

In some cases, the FAP-binding-domain comprising the VH region and the VL region from a monoclonal anti-FAP antibody can comprise a sequence selected from any one of SEQ ID NO: 9, SEQ ID NO: 18, SEQ ID NO: 27 and SEQ ID NO: 36. In some cases, the FAP-binding-domain can comprise an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to any one of SEQ ID NO: 9, SEQ ID NO: 18, SEQ ID NO: 27 and SEQ ID NO: 36, and, optionally, the CDRs of SEQ ID NO: 1 to 6, SEQ ID NO: 10 to 15, SEQ ID NO: 19 to 24, and SEQ ID NO: 28 to 33, respectively.

A stimulatory cytokine as defined herewith is a cytokine that influences the maturation, distribution, growth, survival and functions of particular cell populations, in particular CD8+ T cells, CD4+ T cells, Macrophages and NK cells.

A stimulatory cytokine according to the present disclosure includes Interleukin-2 or a variant thereof such as IL-2v, Interleukin-7 or a variant thereof, Interleukin- 12 or a variant thereof, Interleukin- 15 or a variant thereof, Interleukin- 15 in complex with its high affinity receptor IL-15RA, Interleukin- 18 or a variant thereof, and Interleukin -23 or a variant thereof. Variants of Interleukin-2 include mutants which preferentially or exclusively bind to the intermediate-affinity IL-2RPy but not to CD25. According to the present disclosure, a stimulatory cytokine can be a variant of IL-2 that has high affinity for IL-2RPy and low binding to IL-2 Ra such as the variants disclosed in W02012/10747. In some cases, a variant of IL-2 is IL-2v that has the amino acid sequence of SEQ ID NO: 93. IL-2v has been shown to activate NK cells and CD4+/CD8+ T cells, without preferentially activating Tregs (Waldhauer et al. (202V)MAbs. 13(1): 1913791).

The term “variant” applied to a cytokine, in particular an interleukin, as used herewith encompasses any mutant forms of a native cytokine, in particular interleukin. Said mutant form differs from the native protein by at least one amino acid mutation affecting the activity of the native protein, e.g. affecting the interaction of native IL-2 with CD25. This mutation may involve substitution, deletion, or modification of the amino acid residue normally located at the corresponding position in the full-length native protein, as well as addition of one or more amino acid residues, deletion of one or more amino acid residues, or fragments of the full-length native protein. Native proteins of reference can be the human interleukin-2 (IL-2) (Swiss Prot Reference P01585), human interleukin-7 (Swiss Prot Reference Pl 3232), human interleukin- 12 (Swiss Prot Reference P29460 and P29459), human interleukin- 15 (Swiss Prot Reference P40933), human inter leukin- 18 (Swiss Prot Reference Q14116), and human interleukin-23 (Swiss Prot Reference Q9NPL7).

As mentioned above, the fusion protein and the tumor-CAR expressed by the engineered immune cells as described herewith have differential expressions as a result of having the exogenous nucleic acid sequence encoding said tumor-CAR placed under the transcriptional control of a constitutive promoter, and the exogenous nucleic acid sequence encoding said fusion protein placed under the transcriptional control of an inducible promoter.

By “constitutive promoter” is generally meant a promoter that is active in all circumstances in a particular cell or cell type comprising said promoter. A constitutive promoter carries out the transcription of its associated gene continuously in the cell. The level of transcription of the gene associated with a constitutive promoter can vary but the transcript and, thus, the gene’s product (when there is one) remain detectable. Examples of constitutive promoters include the human elongation factor la (ELIA) promoter, the cluster of differentiation 52 (CD52) promoter, the Glyceraldehyde-3 -Phosphate Dehydrogenase (GAPDH) promoter, the human cytomegalovirus (CMV) promoter, the human phosphoglycerate promoter (hPGK) promoter, the RPBSA promoter, the human Ubiquitin C (UBC) promoter, the simian virus 40 (SV40) early promoter, the mouse phosphoglycerate kinase 1 (PGK) promoter, and the chicken 0-Actin promoter coupled with CMV early enhancer (CAGG), the T Cell Receptor Alpha Constant region (TRAC or TCRA) promoter, the T Cell Receptor Beta Constant 1 region (TRBC or TCRB) promoter, the T cell receptor gamma constant region 1 or 2 (TRGC1 or TCRG1, TRGC2 or TCRG2) promoter, the T Cell Receptor Delta Constant region (TRDC or TCRD) promoter, the Beta-2 -Microglobulin (B2M) promoter, the cluster of differentiation 5 (CD5) promoter, the CS1 (also called CD319, CRACC and SLAMF7) promoter, the cluster of differentiation 45 (CD45) promoter, the cluster of differentiation 4 (CD4) promoter, the cluster of differentiation 8 (CD8) promoter. A constitutive promoter useful herewith can be identical to a promoter already present (i.e. without genetic engineering as described herewith) in the cell’s genome. This would be the case for the EFl A promoter, the CD52 promoter, the GAPDH promoter, the TRAC promoter, the TRBC promoter, the TRGC promoter, the TRDC promoter, the B2M promoter, and the CD 5 promoter, for example. The constitutive promoter useful herewith can also be absent from the cell’s genome prior to its introduction in the cell by genetic engineering such as would be the case for the synthetic RPBSA promoter (that is a synthetic promoter made up of a fragment of the RPL13a promoter fused to a region of the RPL41 gene), the CMV promoter, the mouse PGK promoter, the SV40 promoter, the CAGG promoter. The constitutive promoter can be added to the cell’s genome as an exogenous polynucleotide or can be an endogenous polynucleotide already present in the cell’s genome independently of the cell’s genetic engineering as described herewith, i.e. without addition to the cell of an exogenous polynucleotide corresponding to this promoter.

By “inducible locus” and by “inducible promoter” is generally meant a locus and a promoter comprised in that locus that become active in the cell comprising said locus or promoter, only in response to a specific stimulus. Therefore, an inducible locus/promoter is active only under certain circumstances. Unless it receives a stimulus, the inducible promoter comprised in said inducible locus stays in an inactive state and the gene associated with the inducible promoter that is in the “off’ state is generally not transcribed, or only weakly. Once the specific stimulus is present, the activator protein binds with the inducible promoter and makes it active to initiate transcription, it is in the “on” state. The transcription of the gene associated with the inducible promoter increases when the inducible promoter passes to an “on” state in response to the specific stimulus. The expression of a gene controlled by an inducible promoter is tightly regulated and its expression decreases rapidly upon removal of the activation signal. In the present disclosure, an inducible promoter is responsive to the cell activation (such as an immune cell, e.g. a T-cell, activation) as defined herewith. For example, promoters that are inducible upon CAR-T cell activation in vitro (e.g. as described in Example 8) fulfil the following criteria: fold change between average expression at 0 hours and average expression at 24 hours is greater than 3, for instance greater than 5.

By “activation of a cell” is generally meant the process by which changes occur in a cell in response to an “activation signal”. An “activation signal” designates a signal or stimulus that is able to, directly or indirectly, activate a cell. In the present disclosure, “activation of a cell”, when applied to an engineered cell comprising a CAR as described herewith, mainly refers to the changes occurring in said engineered cell after an activation signal is generated in the cell upon binding or recognition of an epitope of the tumor antigen by the tumor-CAR expressed by said engineered cell.

At the molecular level, the activation of a cell also corresponds to the activation of inducible promoters. Indeed, an inducible promoter comprises one or more regulatory elements responsive to one or more signaling pathways in the cell, such as the NFAT- regulated signal transduction.

In some cases, the inducible promoter can be responsive to the CD3 zeta signaling. Examples of inducible promoters useful herewith include the promoter of the Programmed Cell Death Protein 1 (PDCD1) gene, Cluster of Differentiation 25 (CD25) gene, T-cell immunoglobulin and mucin-domain containing-3 (TIM3) gene, T Cell Immunoreceptor With Ig And ITIM Domains (TIGIT) gene, C-C Motif Chemokine Ligand 1 (CCL1) gene, Nuclear Receptor Subfamily 4 Group A Member 3 (NR4A3) gene, Early Growth Response 3 (EGR3) gene, G0/G1 Switch 2 (G0S2) gene, Interleukin 22 (IL22) gene, Regulator of G Protein Signaling 16 (RGS16) gene, Fas Ligand (FASLG) gene, Retinol Dehydrogenase 10 (RDH10) gene, Colony Stimulating Factor 1 (CSF1) gene, Colony Stimulating Factor 2 (CSF2, also called GM-CSF) gene, Lymphocyte Activating 3 (LAG3) gene, Cytotoxic T-Lymphocyte Associated Protein 4 (CTLA-4 or CD152) gene, Interleukin- 10 (IL10) gene, Nuclear Receptor Subfamily 4 Group A Member 1 (NR4A1 or NUR77) gene, Forkhead Box P3 (FOXP3) gene. The inducible promoter useful herewith can be identical to a promoter already present (i.e. without genetic engineering as described herewith) in the cell’s genome. This would be the case for the promoter of PDCD1 or the promoter of GM-CSF, for example. The inducible promoter useful herewith can also be absent from the cell’s genome prior to its introduction in the cell by genetic engineering. The inducible promoter can be added to the cell’s genome as an exogenous polynucleotide or can be an endogenous polynucleotide already present in the cell’s genome independently of the cell’s genetic engineering as described herewith, i.e. without addition to the cell of an exogenous polynucleotide corresponding to this promoter.

In some cases, following an activation signal in the engineered cells as described herewith, the frequency of cells expressing the fusion protein in the cell population comprising said engineered immune cells is at least about 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%.

In some cases, the expression of the fusion protein that was induced by the activation signal in the engineered cells returns to its initial basal level or is not detectable after removal, disappearance, or reduction of the activation signal in said engineered immune cells.

1.3.Further features of the engineered cells

In some cases, the engineered immune cells, e.g. T-cells, that have been modified to express a fusion protein comprising a FAP -binding domain and a stimulatory cytokine as well as a CAR directed against the tumor antigen, as described herewith, can have one or more additional modifications.

Additional genetic attributes may be conferred by gene editing in the immune cells in order to improve their therapeutic potency.

In some cases, the engineered cell can be further modified to improve its persistence or its lifespan into the patient, for instance inactivating a gene encoding MHC- I component(s) such as HLA or B2M, such as described in WO 2015/136001 or by Liu et al. (2017, Cell Res 27: 154-157).

Beta-2 microglobulin, also known as 02m, is the light chain of MHC class I molecules, and as such an integral part of the major histocompatibility complex. In human, 02m is encoded by the B2M gene which is located on chromosome 15, as opposed to the other MHC genes which are located as gene cluster on chromosome 6. The human protein is composed of 119 amino acids and has a molecular weight of 11,800 Daltons.

In some cases, inhibition of expression of B2M is achieved by a genome modification, such as through the expression in the cell of a rare-cutting endonuclease able to selectively inactivate by DNA cleavage the gene encoding 02m, such as the human B2M gene (NCBI Reference Sequence: NG_012920.1). Such rare-cutting endonuclease may be a TALE-nuclease, meganuclease, zing-finger nuclease (ZFN), or RNA guided endonuclease (such as Cas9).

In some cases, inhibition of expression of B2M can be achieved by using (e.g. introducing into the T-cell) a nucleic acid molecule that specifically hybridizes (e.g. binds) under cellular conditions with the cellular mRNA and/or genomic DNA encoding 02m, thereby inhibiting transcription and/or translation of the gene. In some cases, the inhibition of expression of B2M is achieved by using (e.g. introducing into the T-cell) an antisense oligonucleotide, ribozyme or interfering RNA (RNAi) molecule. In some cases, such nucleic acid molecule can comprise at least 10 consecutive nucleotides of the complement of the mRNA encoding human 02m.

In some cases, an immune cell (e.g. a T-cell) or a precursor cell is provided which expresses a rare-cutting endonuclease able to selectively inactivate by DNA cleavage the gene encoding 02m. For instance, such cell comprises an exogenous nucleic acid molecule comprising a nucleotide sequence encoding said rare-cutting endonuclease, which may be a TALE-nuclease, meganuclease, zing-finger nuclease (ZFN), or RNA guided endonuclease. Thus, in order to provide less allor eactive immune cells (e.g. T-cells), the method described herewith can further comprise the step of inactivating or mutating B2M gene.

In some cases, the engineered immune cells, e.g. T-cells, have been modified to suppress or repress expression of HLA in said cells. The class I HLA gene cluster in humans comprises three major loci, B, C and A, as well as several minor loci. The class II HLA cluster also comprises three major loci, DP, DQ and DR, and both the class I and class II gene clusters are polymorphic, in that there are several different alleles of both the class I and II genes within the population. There are also several accessory proteins that play a role in HLA functioning as well. The Tapi and Tap2 subunits are parts of the TAP transporter complex that is essential in loading peptide antigens on to the class I HLA complexes, and the LMP2 and LMP7 proteosome subunits play roles in the proteolytic degradation of antigens into peptides for display on the HLA. Reduction in LMP7 has been shown to reduce the amount of MHC class I at the cell surface, perhaps through a lack of stabilization (Fehling et al. (1999) Science 265: 1234-1237). In addition to TAP and LMP, there is the tapasin gene, whose product forms a bridge between the TAP complex and the HLA class I chains and enhances peptide loading. Reduction in tapasin results in cells with impaired MHC class I assembly, reduced cell surface expression of the MHC class I and impaired immune responses (Grandea et al. (2000) Immunity 13:213-222 and Garbi et al. (2000) Nat. Immunol. 1 :234-238). Any of the above genes may be inactivated as part of the present document as disclosed, for instance in WO 2012/012667.

In some cases, the engineered immune cells, e.g. T-cells, have been modified to suppress or repress expression of CUT A in said cells. CIITA is the gene encoding class II major histocompatibility complex transactivator protein.

In some cases, the engineered immune cells, e.g. T-cells, are inactivated in at least one gene selected from the group consisting of RFXANK, RFX5, RFXAP, TAPI, TAP2, ZXDA, ZXDB and ZXDC. Inactivation may, for instance, be achieved by using a genome modification, such as through the expression in the cell of a rare-cutting endonuclease able to selectively inactivate, by DNA cleavage, a gene selected from the group consisting of RFXANK, RFX5, RFXAP, TAPI, TAP2, ZXDA, ZXDB and ZXDC. Such modifications can permit the engineered immune cells to be less alloreactive when infused into patients.

Thus, in one aspect, the engineered cells described herewith can be genetically modified to suppress or repress expression of at least one gene controlling MHC complex surface presentation. A gene controlling MHC complex surface presentation as defined herewith includes B2M, CIITA, HLA, RFXANK, RFX5, RFXAP, TAPI, TAP2, ZXDA, ZXDB and ZXDC. In some cases, said engineered immune cells, e.g. T-cells or NK-cells, have been genetically modified to suppress or repress expression of an immune checkpoint protein and/or the receptor thereof, in said cells, such as PDCD1 or CTLA4 as described in WO 2014/184744. It will be understood by those of ordinary skill in the art, that the term “immune checkpoints” means a group of molecules expressed by T-cells, NK-cells and antigen presenting cells. These molecules effectively serve as "brakes" to down-modulate or inhibit an immune response. Immune checkpoint molecules include, but are not limited to Programmed Death 1 (PD-1, also known as PDCD1 or CD279, e.g. human PD-1 : accession number NM_005018), Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4, also known as CD152, e.g. human CTLA-4: GenBank accession number AF414120.1), LAG3 (also known as CD223, e.g. human LAG3 : accession number NM_002286.5), Tim3 (also known as HAVCR2, e.g. human Tim3: GenBank accession number JX049979.1), BTLA (also known as CD272, e.g. human BTLA: accession number NM_181780.3), BY55 (also known as CD160, e.g. human BY55: GenBank accession number CR541888.1), TIGIT (also known as IVSTM3, e.g. human TIGIT : accession number NM_173799), LAIR1 (also known as CD305, e.g. human LAIR1 : GenBank accession number CR542051.1), SIGLEC10 (e.g. human SIGLEC10: GeneBank accession number AY358337.1), 2B4 (also known as CD244, e.g. human 2B4: accession number NM_001166664.1), PPP2CA (Also known as: NEDLBA, PP2Ac, PP2Calpha, RP-C, e.g. human PPP2CA: NCBI Gene ID 5515), PPP2CB (also known as Also known as: PP2Abeta, e.g. human PPP2CB: NCBI Gene ID 5516), PTPN6 (also known as Also known as: HCP, HCPH, HPTP1C, PTP-1C, SH-PTP1, SHP-1, SHP-1L, SHP1, e.g. human PTPN6: NCBI Gene ID 5777), PTPN22 (NCBI Gene ID 26191), CD96 (NCBI Gene ID 10225), CRTAM (NCBI Gene ID 56253), SIGLEC7 (NCBI Gene ID 27036), SIGLEC9 (NCBI Gene ID 27180), TNFRSF10B (NCBI Gene ID 8795), TNFRSF10A (NCBI Gene ID 8797), CASP8 (NCBI Gene ID 841 ), CASP10 (NCBI Gene ID 843), CASP3 (NCBI Gene ID 836), CASP6 (NCBI Gene ID 839), CASP7 (NCBI Gene ID 840), FADD (NCBI Gene ID 8772), FAS (NCBI Gene ID 355), TGFBRII (NCBI Gene ID 7048), TGFRBRI (NCBI Gene ID 7046), SMAD2 (NCBI Gene ID 4087), SMAD3 (NCBI Gene ID 4088), SMAD4 (NCBI Gene ID 4089), SMAD10, SKI (NCBI Gene ID 6497), SKIL (NCBI Gene ID 6498), TGIF1 (NCBI Gene ID 7050), IL1 ORA (NCBI Gene ID 3587), IL1 ORB (NCBI Gene ID 3588), HM0X2 (NCBI Gene ID 3163), IL6R (NCBI Gene ID 3570), IL6ST (NCBI Gene ID 3572), EIF2AK4 (NCBI Gene ID 440275), CSK (NCBI Gene ID 1445), PAG1 (NCBI Gene ID 55824), SIT1 (NCBI Gene ID 27240), FOXP3 (NCBI Gene ID 50943), PRDM1 (NCBI Gene ID 639), BATF (NCBI Gene ID 10538), GUCY1A2 (NCBI Gene ID 2977), GUCY1A3 (NCBI Gene ID 2977), and GUCY1B2 (NCBI Gene ID 2974) which directly inhibit immune cells. For example, CTLA-4 is a cell-surface protein expressed on certain CD4 and CD8 T-cells; when engaged by its ligands (B7-1 and B7-2) on antigen presenting cells, T-cell activation and effector function are inhibited. In some cases, the engineered T-cells are further genetically modified by inactivating at least one gene encoding a protein involved in the immune checkpoint, such as PD1 and/or CTLA-4 or any immune- checkpoint proteins referred to herein.

In some cases, at least two genes encoding immune checkpoint proteins are inactivated, selected from the group consisting of: CTLA4, PPP2CA, PPP2CB, PTPN6, PTPN22, PDCD1, LAG3, HAVCR2, BTLA, CD160, TIGIT, CD96, CRTAM, LAIR1, SIGLEC7, SIGLEC9, CD244, TNFRSF10B, TNFRSF10A, CASP8, CASP10, CASP3, CASP6, CASP7, FADD, FAS, TGFBRII, TGFRBRI, SMAD2, SMAD3, SMAD4, SMAD10, SKI, SKIL, TGIF1, IL1 ORA, IL1 ORB, HM0X2, IL6R, IL6ST, EIF2AK4, CSK, PAG1, SIT1, FOXP3, PRDM1, BATF, GUCY1A2, GUCY1A3, GUCY1B2, and GUCY1B3.

In some cases, the engineered immune cells, e.g. T-cells, can be modified to confer resistance to at least one immune suppressive or chemotherapy drug, and optionally to comprise a suicide gene.

In some cases, the engineered immune cells, e.g. T-cells, can be further modified to confer resistance to at least one immune suppressive drug, such as by inactivating CD52 that is the target of anti-CD52 antibody (e.g. alemtuzumab), as described for instance in WO 2013/176915.

To improve cancer therapy and selective engraftment of allogeneic immune cells, drug resistance can be conferred to the engineered immune cells to protect them from the toxic side effects of chemotherapy or immunosuppressive agents. In some cases, the engineered immune cell can be further modified to confer resistance to a chemotherapy drug, such as a purine analogue drug, for example by inactivating DCK as described in WO 2015/75195.

Drug resistance of immune cells also permits their enrichment in or ex vivo, as immune cells which express a drug resistance gene, will survive and multiply relative to drug sensitive cells. In some cases, the methods further comprise methods of engineering allogeneic and drug-resistant immune cells for immunotherapy comprising: (a) providing an immune cell, e.g. a T-cell; (b) selecting at least one drug; (c) modifying the cell to confer drug resistance to said cell; and (d) expanding said engineered cell in the presence of said drug. When the immune cell is a T-cell, the preceding steps may be combined with a step of modifying the T-cell, by inactivating at least one gene encoding a T-cell receptor (TCR) component, and then sorting the transformed T-cells, which do not express TCR on their cell surface.

Thus, the engineered immune cells can be further modified to confer a resistance to a drug, such as a chemotherapy agent. The resistance to a drug can be conferred to an immune cell by expressing a drug resistance gene. Variant alleles of several genes such as dihydrofolate reductase (DHFR), inosine monophosphate dehydrogenase 2 (IMPDH2), calcineurin or methylguanine transferase (MGMT) have been identified to confer drug resistance to a cell. In some cases, the drug resistance gene can be expressed in the cell either by introducing a transgene encoding said gene into the cell or by integrating said drug resistance gene into the genome of the cell by homologous recombination.

The resistance to a drug can be conferred to an immune cell by inactivating one or more gene(s) responsible for the cell's sensitivity to the drug (drug sensitizing gene(s)), such as the hypoxanthine-guanine phosphoribosyl transferase (HPRT) gene (Genbank: M26434.1). For instance, HPRT can be inactivated in engineered immune cells to confer resistance to a cytostatic metabolite, the 6-thioguanine (6TG) which is converted by HPRT to cytotoxic thioguanine nucleotide and which is currently used to treat patients with cancer, in particular leukemias (Hacke et al. (2013) Transplantation Proceedings, 45(5): 2040-2044). Another example is the inactivation of the CD3 normally expressed at the surface of the T-cell, which can confer resistance to anti-CD3 antibodies such as teplizumab.

Otherwise, drug resistance can be conferred to the immune cell (e.g. T-cell), by the expression of at least one drug resistance gene. The drug resistance gene refers to a nucleic acid sequence that encodes "resistance" to an agent, such as a chemotherapeutic agent (e.g. methotrexate). In other words, the expression of the drug resistance gene in a cell permits proliferation of the cells in the presence of the agent to a greater extent than the proliferation of a corresponding cell without the drug resistance gene. A drug resistance gene can encode resistance to anti-metabolite, methotrexate, vinblastine, cisplatin, alkylating agents, anthracyclines, cytotoxic antibiotics, anti-immunophilins, their analogs or derivatives, and the like.

Several drug resistance genes have been identified that can potentially be used to confer drug resistance to targeted cells (Takebe et al. (2001) Mol. Ther. 3(1): 88-96); Sugimoto et al. (2003) Mol Cancer Ther. 2 :105-112; Zielske et al. (2003) J. Clin. Invest. 112(10): 1561-70; Nivens et al. (2004) Cancer Chemother Pharmacol 53(2): 107-15; Bardenheuer et al. (2005) Leukemia 19(12): 2281-8 ; Kushman et al. (2007) Carcinogenesis 28(1): 207-14).

One example of drug resistance gene can also be a mutant or modified form of Dihydrofolate reductase (DHFR). DHFR is an enzyme involved in regulating the amount of tetrahydrofolate in the cell and is essential to DNA synthesis. Folate analogs such as methotrexate (MTX) inhibit DHFR and are thus used as anti-neoplastic agents in clinic. Different mutant forms of DHFR which have increased resistance to inhibition by antifolates used in therapy have been described. In some cases, the drug resistance gene can be a nucleic acid sequence encoding a mutant form of human wild type DHFR (GenBank: AAH71996.1) which comprises at least one mutation conferring resistance to an anti-folate treatment, such as methotrexate. In some cases, mutant form of DHFR comprises at least one mutated amino acid at position G15, L22, F31 or F34, for instance at positions L22 or F31 (Schweitzer, Dicker et al. 1990); International application WO94/24277; U.S. Pat. No. 6,642,043).

As used herein, "antifolate agent" or "folate analogs" refers to a molecule directed to interfere with the folate metabolic pathway at some level. Examples of antifolate agents include, e.g. methotrexate (MTX); aminopterin; trimetrexate (Neutrexin™); edatrexate; N10-propargyl-5,8-dideazafolic acid (CB3717); ZD1694 (Tumodex), 5, 8 -dideazaisofolic acid (IAHQ); 5,10-dideazatetrahydrofolic acid (DDATHF); 5-deazafolic acid; PT523 (N alpha-(4-amino-4-deoxypteroyl)-N delta-hemiphthaloyl-L-ornithine); 10-ethyl- 10- deazaaminopterin (DDATHF, lomatrexol); piritrexim; 10-EDAM; ZD 1694; GW1843; Pemetrexate and PDX (10-propargyl-10-deazaaminopterin). Another example of drug resistance gene can also be a mutant or modified form of ionisine-5 '-monophosphate dehydrogenase II (IMPDH2), a rate-limiting enzyme in the de novo synthesis of guanosine nucleotides. The mutant or modified form of IMPDH2 is a IMPDH inhibitor resistance gene. IMPDH inhibitors can be mycophenolic acid (MPA) or its prodrug mycophenolate mofetil (MMF). The mutant IMPDH2 can comprise at least one, for instance two mutations in the MAP binding site of the wild type human IMPDH2 (NP 000875.2) that lead to a significantly increased resistance to IMPDH inhibitor. The mutations can be at positions T333 and/or S351 (Yam et al. (2006) Mol. Ther. 14(2): 236- 44 ; Jonnalagadda et al. (2013) PLoS One 8(6): e65519). In some cases, the threonine residue at position 333 can be replaced with an isoleucine residue and the serine residue at position 351 can be replaced with a tyrosine residue.

Another drug resistance gene is the mutant form of calcineurin. Calcineurin (PP2B) is an ubiquitously expressed serine/threonine protein phosphatase that is involved in many biological processes and which is central to T-cell activation. Calcineurin is a heterodimer composed of a catalytic subunit (CnA; three isoforms) and a regulatory subunit (CnB; two isoforms). After engagement of the T-cell receptor, calcineurin dephosphorylates the transcription factor NF AT, allowing it to translocate to the nucleus and active key target gene such as 1L2. FK506 in complex with FKBP12, or cyclosporine A (CsA) in complex with CyPA block NFAT access to calcineurin's active site, preventing its dephosphorylation and thereby inhibiting T-cell activation (Brewin et al. (2009) Blood 114(23): 4792-803). The drug resistance gene can be a nucleic acid sequence encoding a mutant form of calcineurin resistant to calcineurin inhibitor such as FK506 and/or CsA. In some cases, said mutant form can comprise at least one mutated amino acid of the wild type calcineurin heterodimer at positions: V314, Y341, M347, T351, W352, L354, K360, for instance double mutations at positions T351 and L354 or V314 and Y341. Correspondence of amino acid positions described herein is frequently expressed in terms of the positions of the amino acids of the form of wild-type human calcineurin heterodimer (GenBank: ACX34092.1).

In some cases, said mutant form can comprise at least one mutated amino acid of the wild type calcineurin heterodimer b at positions: V120, N123, L124 or K125, for instance double mutations at positions L124 and K125. Correspondence of amino acid positions described herein is frequently expressed in terms of the positions of the amino acids of the form of wild-type human calcineurin heterodimer b polypeptide (GenBank: ACX34095.1).

Another drug resistance gene is O ⁶ -methylguanine methyltransferase (MGMT) encoding human alkyl guanine transferase (hAGT). AGT is a DNA repair protein that confers resistance to the cytotoxic effects of alkylating agents, such as nitrosoureas and temozolomide (TMZ). 6-benzylguanine (6-BG) is an inhibitor of AGT that potentiates nitrosourea toxicity and is co -administered with TMZ to potentiate the cytotoxic effects of this agent. Several mutant forms of MGMT that encode variants of AGT are highly resistant to inactivation by 6-BG, but retain their ability to repair DNA damage (Maze, Kurpad et al. 1999). In some cases, AGT mutant form can comprise a mutated amino acid of the wild type AGT position P140 (UniProtKB: P16455).

Another drug resistance gene can be multi drug resistance protein 1 (MDR1) gene. This gene encodes a membrane glycoprotein, known as P-gly coprotein (P-GP) involved in the transport of metabolic byproducts across the cell membrane. The P-Gp protein displays broad specificity towards several structurally unrelated chemotherapy agents. Thus, drug resistance can be conferred to cells by the expression of nucleic acid sequence that encodes MDR-1 (NP_000918).

Drug resistance genes can also be cytotoxic antibiotics, such as ble gene or mcrA gene. Ectopic expression of ble gene or mcrA in an immune cell gives a selective advantage when exposed to the chemotherapeutic agent, respectively the bleomycine or the mitomycin C.

With respect to the immunosuppressive agents, the present document describes the possible optional steps of: (a) providing an immune cell such as a T-cell, for instance from a cell culture or from a blood sample, or an induced pluripotent stem cell (iPSC); (b) selecting a gene in said cell expressing a target for an immunosuppressive agent; (c) introducing into said cell an endonuclease able to selectively inactivate by DNA cleavage, for instance by double-strand break, said gene encoding a target for said immunosuppressive agent, (d) expanding said cells, optionally in presence of said immunosuppressive agent. In some cases, said method comprises a further step of inactivating a component of the T-cell receptor (TCR). An immunosuppressive agent is an agent that suppresses immune function by one of several mechanisms of action. In other words, an immunosuppressive agent is a compound which is capable of diminishing the extent and/or voracity of an immune response. As non-limiting examples, an immunosuppressive agent can be a calcineurin inhibitor, a target of rapamycin, an interleukin-2oc-chain blocker, an inhibitor of inosine monophosphate dehydrogenase, an inhibitor of dihydrofolic acid reductase, a corticosteroid or an immunosuppressive antimetabolite. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through inactivation of T-cells or by inhibiting the activation of helper cells. The method described herewith allows conferring immunosuppressive resistance to immune cells (e.g. T-cells), for immunotherapy by inactivating the target of the immunosuppressive agent in said cells. As non-limiting examples, a target for an immunosuppressive agent can be a receptor for an immunosuppressive agent such as CD52, glucocorticoid receptor (GR), a FKBP family gene member and a cyclophilin family gene member.

In immunocompetent hosts, allogeneic cells are normally rapidly rejected by the host immune system. It has been demonstrated that allogeneic leukocytes present in nonirradiated blood products will persist for no more than 5 to 6 days (Boni et al. (2008) Blood 112(12): 4746-54). Thus, to prevent rejection of allogeneic cells, the host's immune system must be effectively suppressed. Glucocorticoid steroids are widely used therapeutically for immunosuppression (Coutinho and Chapman (201 1 ) A7 Z. Cell Endocrinol. 335(1): 2-13). This class of steroid hormones binds to the glucocorticoid receptor (GR) present in the cytosol of T-cells resulting in the translocation into the nucleus and the binding of specific DNA motifs that regulate the expression of a number of genes involved in the immunologic process. Treatment of T-cells with glucocorticoid steroids results in reduced levels of cytokine production leading to T-cell anergy and interfering in T-cell activation. Alemtuzumab, also known as CAMPATH1-H, is a humanized monoclonal antibody targeting CD52, a 12 amino acid glycosylphosphatidyl-inositol-(GPI) linked glycoprotein (Waldmann and Hale (2005) Philos. Trans. R. Soc. Land. B. BiolSci. 360: 1701-11). CD52 is expressed at high levels on T and B lymphocytes and lower levels on monocytes while being absent on granulocytes and bone marrow precursors. Treatment with Alemtuzumab, a humanized monoclonal antibody directed against CD52, has been shown to induce a rapid depletion of circulating lymphocytes and monocytes. It is frequently used in the treatment of T-cell lymphomas and in certain cases as part of a conditioning regimen for transplantation. However, in the case of adoptive immunotherapy the use of immunosuppressive drugs will also have a detrimental effect on the introduced therapeutic immune cells (e.g. T-cells). Therefore, to effectively use an adoptive immunotherapy approach in these conditions, the introduced cells would need to be resistant to the immunosuppressive treatment.

In some cases, the gene that is specific for an immunosuppressive treatment is CD52, and the immunosuppressive treatment comprises a humanized antibody targeting CD52 antigen. In some cases, the gene that is specific for an immunosuppressive treatment is a glucocorticoid receptor (GR) and the immunosuppressive treatment comprises a corticosteroid such as dexamethasone. In some cases, the gene that is specific for an immunosuppressive treatment is a FKBP family gene member or a variant thereof and the immunosuppressive treatment comprises FK506 also known as Tacrolimus or fujimycin. In some cases, the gene that is specific for an immunosuppressive treatment is a FKBP family gene member such as FKBP12 or a variant thereof. In some cases, the gene that is specific for an immunosuppressive treatment is a cyclophilin family gene member or a variant thereof and the immunosuppressive treatment comprises cyclosporine.

Cytokine Release Syndrome (CRS) is the most common adverse event of CAR-T cell therapy. CRS is defined as a clinical syndrome that may occur after cell therapy due to the release of cytokines (substances secreted by immune cells) into the body’s blood stream. It has been shown that inactivation of Granulocyte-macrophage colony-stimulating factor (GM-CSF) can prevent monocyte-dependent release of key cytokine release syndrome mediators (Sachdeva et al. (2019) J. Biol. Chem. 294(14) 5430-5437). Thus, in a further aspect, the engineered immune cells as described herewith have been genetically modified to suppress expression, or cell surface presentation, of GM-CSF.

In some cases, the engineered immune cell as described herewith is one or more of: TCR negative, B2M negative, CIITA negative, PDCD1 negative, GM-CSF negative, CD52 negative; for instance at least TCR negative or at least TCR negative, B2M-negative and CD52-negative. In some cases, to reduce fratricide effect, the engineered immune cell as described herewith does not present at its cell surface the antigen targeted by the tumor-CAR. For example, the engineered immune cell as described herewith can have its CD4 or CD 8 gene inactivated, or its expression inhibited, if the tumor-CAR targets CD4 or CD8, respectively.

2. Methods of producing the engineered cells as described herewith

Another aspect provides a method of producing a population of cells comprising engineered immune cells as described herewith, comprising:

(i) providing immune cells from a donor or induced pluripotent stem cells (iPSCs);

(ii) optionally, suppressing or repressing the expression of a T-Cell Receptor (TCR) in the cells or its presentation at the cells’ surface;

(iii) integrating in the cells’ genome an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”), wherein said exogenous nucleic acid sequence is placed under the transcriptional control of a constitutive promoter after integration;

(iv) integrating in the cells’ genome an exogenous nucleic acid sequence encoding a fusion protein comprising a signal peptide, a FAP -binding-domain (such as a FAP- binding domain comprising the VH and VL amino acid sequences from a monoclonal anti- FAP antibody (e.g. a FAPscFv)) and a stimulatory cytokine, wherein said exogenous nucleic acid sequence is placed under the transcriptional control of an endogenous inducible promoter after integration, optionally wherein said fusion protein does not comprise an antibody crystallizable fragment (Fc); and

(v) optionally, isolating the engineered cells that do not express a TCR at their cell surface. wherein said inducible promoter is inducible upon activation of the engineered immune cells.

The source of the cells provided in step (i), i.e. to be engineered, is not particularly limiting. In some cases, the cells of step (i) can be immune cells originating from a donor or resulting from the differentiation of iPSCs into immune cells. The cells of step (i) can also be iPSCs, which can be differentiated into immune cells after any one of the steps of genetic engineering (ii) to (iv) as disclosed above.

By “immune cell” is meant a cell of hematopoietic origin functionally involved in the initiation and/or execution of innate and/or adaptative immune response, such as typically CD45, CD3, CD8 or CD4 positive cells. Immune cells include dendritic cells, killer dendritic cells, mast cells, macrophages, natural killer cells (NK-cell), cytokine- induced killer cells (CIK cells), B-cells or T-cells selected from the group consisting of cytotoxic T-lymphocytes, or helper T-lymphocytes, gamma delta T-cells, and Natural killer T-cells (“NKT cell).

In some cases, the source of the immune cells (such as T-cells) to be engineered are primary cells, and by “primary cell(s)” are intended cells taken directly from living tissue (e.g. biopsy material) and established for growth in vitro for a limited amount of time, meaning that they can undergo a limited number of population doublings. Primary cells are opposed to continuous tumorigenic or artificially immortalized cell lines. Non-limiting examples of such cell lines are CH0-K1 cells; HEK293 cells; Caco2 cells; U2-OS cells; NIH 3T3 cells; NSO cells; SP2 cells; CHO-S cells; DG44 cells; K-562 cells, U-937 cells; MRC5 cells; IMR90 cells; Jurkat cells; HepG2 cells; HeLa cells; HT-1080 cells; HCT-116 cells; Hu-h7 cells; Huvec cells; and Molt 4 cells.

Primary immune cells can be obtained from a number of non-limiting sources, including peripheral blood mononuclear cells (PBMC), bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and from tumors, such as tumor infiltrating lymphocytes. In some cases, said immune cell can be derived from a healthy donor, from a patient diagnosed with cancer or from a patient diagnosed with an infection. In some cases, said cell is part of a mixed population of immune cells which present different phenotypic characteristics, such as comprising CD4, CD8 and CD56 positive cells. Primary immune cells are provided from donors or patients through a variety of methods known in the art, as for instance by leukapheresis techniques as reviewed by Schwartz J. et al. (Guidelines on the use of therapeutic apheresis in clinical practice-evidence-based approach from the Writing Committee of the American Society for Apheresis: the sixth special issue (2013) J Clin Apher. 28(3):145-284). In the present document, are also regarded as primary immune cells the immune cells derived from stem cells, such as those deriving from induced pluripotent stem cells (iPSCs) (Yamanaka, K. et al. (2008) Science. 322 (5903): 949-53). Lentiviral expression of reprogramming factors has been used to induce multipotent cells from human peripheral blood cells (Staerk et al. (2010) Cell stem cell. 7 (1): 20-4 ; Loh et al. (2010) Cell stem cell. 7 (1): 15-9).

According to some cases, the immune cells can be derived from human embryonic stem cells by techniques well known in the art that do not involve the destruction of human embryos (Chung etal. (2008) Cell Stem Cell 2(2): 113-117).

In some cases, the T-cells can derive from cytotoxic T-lymphocytes or helper T- lymphocytes.

In some cases, the immune cell, e.g. T-cell or NK-cell, can derive from a stem cell. The stem cells can be adult stem cells, embryonic stem cells, such as non-human stem cells, cord blood stem cells, progenitor cells, bone marrow stem cells, induced pluripotent stem cells, totipotent stem cells or hematopoietic stem cells. Representative human cells are CD34+ cells.

In some cases, the immune cells can derive from the group consisting of CD4+ T- lymphocytes and CD8+ T-lymphocytes. Prior to their expansion and genetic modification, the cells can be obtained from a subject through a variety of non-limiting methods. T-cells can be obtained from a number of non-limiting sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors. In certain cases, any number of T-cell lines available and known to those skilled in the art, may be used. In some cases, said cell can be derived from a healthy donor or from a patient diagnosed with cancer. In some cases, said cell is part of a mixed population of cells which present different phenotypic characteristics. In the scope of the disclosure is also encompassed a cell line obtained from a transformed T-cell according to the method previously described. Modified cells resistant to an immunosuppressive treatment and susceptible to be obtained by the previous method are also disclosed herewith.

In some cases, the immune cells (e.g. T-cells or NK cells) to be engineered are allogenic. By “allogeneic” is meant that the cells originate from a donor, from a cell line, or are produced and/or differentiated from stem cells in view of being infused into patients having a different haplotype. Such immune cells are generally engineered to be less allor eactive and/or become more persistent with respect to their patient host. More specifically, the method of engineering the allogeneic cells can comprise the step of reducing or inactivating TCR expression into T-cells, or into the stem cells to be derived into T-cells. This can be obtained by different sequence-specific reagents, such as by gene silencing or gene editing techniques by using for instance nucleases, base editing techniques, shRNA and RNAi as non-limited examples.

In some cases, the immune cells, e.g. T-cells or NK-cells, to be engineered can originate from a human, wherein the human is a donor, not the patient.

In some cases, the engineered T-cells can comprise an inactivated T-cell receptor (TCR) and can have been modified by inactivating at least one component of the TCR, e.g. by using a sequence-specific endonuclease such as a RNA guided endonuclease associated with a specific guide RNA, or using other gene editing approaches such as TALE- nucleases. T cell receptors (TCR) are cell surface receptors that participate in the activation of T-cells in response to the presentation of antigen. The TCR is generally made from two chains, alpha and beta, which assemble to form a heterodimer and associates with the CD3- transducing subunits to form the T-cell receptor complex present on the cell surface. Each alpha and beta chain of the TCR consists of an immunoglobulin-like N-terminal variable (V) and constant (C) region, a hydrophobic transmembrane domain, and a short cytoplasmic region. As for immunoglobulin molecules, the variable region of the alpha and beta chains are generated by V(D)J recombination, creating a large diversity of antigen specificities within the population of T-cells. However, in contrast to immunoglobulins that recognize intact antigen, T-cells are activated by processed peptide fragments in association with an MHC molecule, introducing an extra dimension to antigen recognition by T-cells, known as MHC restriction. Recognition of MHC disparities between the donor and recipient through the T cell receptor leads to T-cell proliferation and the potential development of GvHD. It has been shown that normal surface expression of the TCR depends on the coordinated synthesis and assembly of all seven components of the complex (Ashwell and Klusner (1990) Annu. Rev. Immunol. 8:139-67). The inactivation of TRAC (encoding TCRalpha constant domain) or TRBC (encoding TCRbeta constant domain) can result in the elimination of the TCR from the surface of T-cells preventing recognition of alloantigen and thus GVHD. However, TCR disruption generally results in the elimination of the CD3 signaling component and alters the means of further T-cell expansion.

In some cases, at least 50%, at least 70%, at least 90%, or at least 95% of said engineered T-cells in the population are mutated in their TRAC, TRBC and/or CD3 alleles.

In some cases, the TCR can be inactivated by using specific TALE-nucl eases, better known under the trademark TALEN® (Cellectis, 8, rue de la Croix Jarry, 75013 PARIS). This method has proven to be highly efficient in primary cells using RNA transfection as part of a platform allowing the mass production of allogeneic T-cells. See, e.g. WO 2013/176915, which is incorporated by reference herein in its entirety.

In some cases, the TCR can be inactivated using an RNA guided endonuclease associated with a specific guide RNA. U.S. Patent No. 10,870,864 describes methods for inactivating a TCR in cells using such methods, which is incorporated by reference herein. Engraftment of allogeneic T-cells is possible by inactivating at least one gene encoding a TCR component. In some cases, the TCR is rendered not functional in the cells by inactivating a TRAC gene and/or a TCRB gene. TCR inactivation in allogeneic T-cells aims to prevent or reduce GvHD.

In some cases, the TCR gene can be inactivated by inserting into the TRAC locus of the cell’s genome at least one exogenous polynucleotide encoding a tumor-CAR comprising:

(a) an extracellular tumor antigen-binding-domain comprising the VH and VL amino acid sequences from a monoclonal anti-tumor antigen antibody,

(b) a hinge selected from a FcyRIII hinge, a CD8a hinge and an IgGl hinge,

(c) a CD8a transmembrane domain or a CD28 transmembrane domain, and

(d) a cytoplasmic domain including a CD3 zeta signaling domain and a costimulatory domain from 4- IBB or from CD28.

By inactivating a gene, it is intended that the gene of interest is not expressed in a functional protein form. In some cases, genetic modification of the cells relies on the expression, in provided cells to engineer, of an endonuclease so that it catalyzes cleavage in one targeted gene thereby inactivating the targeted gene. The nucleic acid strand breaks caused by the endonuclease are commonly repaired through the distinct mechanisms of homologous recombination or non-homologous end joining (NHEJ). However, NHEJ is an imperfect repair process that often results in changes to the DNA sequence at the site of the cleavage. Mechanisms involve rejoining of what remains of the two DNA ends through direct re-ligation (Critchlow and Jackson (1998) Trends Biochem Sci. 23(10): 394-8) or via the so-called microhomology-mediated end joining (Betts et al. (2003) J. Immunol. Methods 281(1-2): 65-78; Ma etal. (2003) Mol Cell Biol 23(23): 8820-8). Repair via non- homologous end joining (NHEJ) often results in small insertions or deletions and can be used for the creation of specific gene knockouts. The modification may be a substitution, deletion, or addition of at least one nucleotide. Cells in which a cleavage-induced mutagenesis event, i.e. a mutagenesis event consecutive to an NHEJ event, has occurred can be identified and/or selected by well-known methods in the art.

As the engineered immune cells described herewith can derive from the differentiation of engineered iPSCs as described herewith into said immune cells, another aspect described in the present application concerns a method of producing a population of cells comprising engineered iPSCs as described herewith, comprising:

(i) providing induced pluripotent stem cells (iPSCs);

(ii) optionally, inactivating the potential expression of a T-Cell Receptor (TCR) in the cells or its presentation at the cells’ surface;

(iii) integrating in the cells’ genome an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”), wherein said exogenous nucleic acid sequence is placed under the transcriptional control of a constitutive promoter after integration;

(iv) integrating in the cells’ genome an exogenous nucleic acid sequence encoding a fusion protein comprising a signal peptide, a FAP-binding-domain and a stimulatory cytokine, wherein said exogenous nucleic acid sequence is placed under the transcriptional control of an endogenous inducible promoter after integration; wherein, optionally, said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein, optionally, said FAP-binding domain comprises the VH and VL amino acid sequences from a monoclonal anti-FAP antibody (e.g. a FAPscFv); and wherein said inducible promoter is inducible upon activation of the immune cell into which said engineered iPSC can further be differentiated.

Another aspect, thus, includes a method of producing a population of cells comprising engineered immune cells as described herewith, comprising (i) producing a population of cells comprising engineered iPSCs as described above, and (ii) differentiating said engineered iPSCs into immune cells.

Engineering and gene editing

The methods that can be employed herein to engineer or gene edit cells are not particularly limiting. In some cases, the cells can be contacted with a sequence-specific reagent to modify (e.g. engineer or gene edit) the cells.

By “sequence-specific reagent” is meant any active molecule that has the ability to specifically recognize a selected polynucleotide sequence at a genomic locus, referred to as “target sequence,” which is generally of at least 12 bp, at least 15 bp, or at least 30 pb or 35 bp in length, in view of modifying the expression of said genomic locus. Said expression can be modified by mutation, deletion or insertion into coding or regulatory polynucleotide sequences, by epigenetic change, such as by methylation or histone modification, or by interfering at the transcriptional level by interacting with transcription factors or polymerases.

Examples of sequence-specific reagents are endonucleases, RNA guides, RNAi, methylases, exonucleases, histone deacetylases, end-processing enzymes such as exonucleases, and more particularly cytidine deaminases such as those coupled with the CRISPR/cas9 system to perform base editing (i.e. nucleotide substitution) without necessarily resorting to cleavage by nucleases as described for instance by Hess etal. (Mol Cell. (2017) 68(1): 26-43) and Rees etal. (Nat. Rev. Genet. (2018) 19, 770-788).

According to one aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding a component of the TCR.

According to one aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding 02M. According to one aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding CD52.

According to one aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding PDCD1. According to one aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding LAG3.

According to one aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding HM3.

According to one aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding GM-CSF.

According to another aspect, at least 50%, at least 70%, at least 90%, or at least 95% of the cell population express a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding a component of the TCR, as well as a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding 02M and/or a short hairpin RNA (shRNA) or small interfering (siRNA) directed against a polynucleotide sequence encoding CD3.

In some cases, the sequence-specific reagent can be a sequence-specific nuclease reagent, such as a sequence-specific endonuclease like a rare-cutting endonuclease like TALE Nuclease, or a RNA guide coupled with a guided endonuclease like CRISPR.

The terms “sequence-specific nuclease reagent” include reagents that have nickase or endonuclease activity. The sequence-specific nuclease reagent can be a chimeric polypeptide comprising a DNA binding domain and another domain displaying catalytic activity. Such catalytic activity can be for instance a nuclease to perform gene inactivation, or nickase or double nickase to preferentially perform gene insertion by creating cohesive ends to facilitate gene integration by homologous recombination. The term “endonuclease” generally refers to any wild-type or variant enzyme capable of catalyzing the hydrolysis (cleavage) of bonds between nucleic acids within a DNA or RNA molecule, a DNA molecule. Endonucleases (and, thus, sequence-specific endonucleases) do not cleave the DNA or RNA molecule irrespective of its sequence but recognize and cleave the DNA or RNA molecule at specific polynucleotide sequences, further referred to as “target sequences” or “target sites”. Endonucleases can be classified as rare-cutting endonucleases when having typically a polynucleotide recognition site greater than 10 base pairs (bp) in length, or of 14-55 bp. Rare-cutting endonucleases significantly increase homologous recombination by inducing DNA double-strand breaks (DSBs) at a defined locus thereby allowing gene repair or gene insertion therapies (Pingoud and Silva (2007) Nat. Biotechnol. 25(7): 743-4).

In some cases, the sequence specific-reagent can be a base editor able to perform base editing as described for instance in Komor eta/. (Nature (2019) 533(7603), 420-424) and in Mok etal. (Nature (2020) 583:631-637).

The term “base editor”, as used herein, refers to a catalytic domain capable of making a modification to a base ( e.g. A, T, C, G, or U) within a nucleic acid sequence by converting one base to another (e.g. A to G, A to C, A to T, C to T C to G, C to A, G to A, G to C, G to T, T to A, T to C, T to G). Base editors can include cytidine deaminases that convert target C/G to T/A and adenine base editors that convert target A/T to G/C. Adenosine deaminase can be, for instance, TadA or its variant TadA7.10 as described by Jeong etal. (Nat Biotechnol (2021) 39, 1426-1433). Different members of Apolipoprotein B mRNA editing enzyme (APOBEC) family can be used to convert cytidines to thymidines, such as the murine rAPOBECl and the human APOBEC3G as developed by Lee et al. (Science Advances (2020) 6(29)).

In some cases, base editor catalytic domain can convert C to T (cytidine deaminase) and catalyzes the chemical reaction “cytosine + H2O -> uracil + NEB” or “5 -methylcytosine + H2O -> thymine + NE .” As it may be apparent from the reaction formula, such chemical reactions result in a C to U/T nucleobase change. In the context of a gene, such a nucleotide change, or mutation, may in turn lead to an amino acid change in the protein, which may affect the protein’s function, e.g. loss-of-function or gain-of-function. The sequence specific-reagents as defined herewith include TALE-base editors (BE), which can be generated by the fusion of transcription activator-like effector array proteins (TALE) with a base editor catalytic domain. The base editor catalytic domain can be a double-stranded DNA deaminase (“DddA”) that precisely makes nucleotide changes and/or corrects pathogenic mutations, rather than destroying DNA by double-strand breaks (DSBs). For instance, Mok et al. (Nature (2020) 583:631-637) recently developed TALE base editor by using the bacterial cytidine deaminase toxin DddAtox, from Burkohlderia cenocepacia, that has been split into non-toxic halves which have been fused to the C- terminus of paired (left and right) TALE binding domains, respectively, to form heterodimeric TALE base editors. In such setting, the deaminase DddAtox becomes active when its two halves, linked to their respective TALE binding domains, co-localize at a predetermined genomic locus. The split “DddA-N half and “DddA-C half’ can be obtained by cleaving the full DddAtox protein (SEQ ID NO: 87) at positions 1333 or 1397.

In some cases, such TALE-base editors can also comprise a domain that inhibits uracil glycosylase referred to as “UGI”, and/or a nuclear localization signal. The term “uracil glycosylase inhibitor” or “UGI,” as used herein, refers to a protein that is capable of inhibiting an uracil-DNA glycosylase base-excision repair enzyme. In some cases, a UGI domain can comprise a wild-type UGI or a canonical UGI. In some cases, the UGI proteins can include fragments of UGI and proteins homologous to a UGI or a UGI fragment, which are useful to improve the specificity of base editing performed at a predetermined locus.

The methods and material provided herein aim to improve the therapeutic potential of immune cells through gene editing techniques, especially by gene targeted integration.

After integration in the cell’s genome, an exogenous nucleic acid sequence encoding a tumor-CAR is placed under the transcriptional control of an exogenous or endogenous constitutive promoter. After integration in the cell’s genome, an exogenous nucleic acid sequence encoding a fusion protein comprising a FAP-binding domain and a stimulatory cytokine is placed under the transcriptional control of an endogenous inducible promoter.

The exogenous nucleic acid sequence encoding a tumor-CAR as described herewith can be integrated in the cell’s genome through random integration (such as through lentiviral vector integration) or through gene targeting integration (such as through sequence-specific endonuclease-mediated cDNA insertion at a targeted locus in the cells’ genome).

The exogenous nucleic acid sequence encoding a fusion protein as described herewith can be integrated in the cell’s genome through gene targeting integration (such as through sequence-specific endonuclease-mediated cDNA insertion at a targeted locus in the cells’ genome).

In one instance, the exogenous nucleic acid sequence encoding a tumor-CAR as described herewith is integrated in the cell’s genome through random integration (such as through lentiviral vector integration) and the exogenous nucleic acid sequence encoding a fusion protein as described herewith is integrated in the cell’s genome through gene targeting integration (such as through sequence-specific endonuclease-mediated cDNA insertion at a targeted locus in the cells’ genome).

In another instance, the exogenous nucleic acid sequence encoding a tumor-CAR as described herewith is integrated in the cell’s genome through gene targeting integration (such as through sequence-specific endonuclease-mediated cDNA insertion at a targeted locus in the cells’ genome) and the exogenous nucleic acid sequence encoding a fusion protein as described herewith is integrated in the cell’s genome through gene targeting integration (such as through sequence-specific endonuclease-mediated cDNA insertion at targeted loci in the cells’ genome).

By “gene targeting integration” is meant any known site-specific methods allowing to insert, replace or correct a genomic coding sequence into a living cell.

In some cases, the gene targeted integration involves homologous gene recombination at the locus of the targeted gene to result in the insertion of, or replacement of the targeted gene by, at least one exogenous nucleotide sequence, such as a sequence of several nucleotides (i.e. polynucleotide), e.g. a coding sequence.

By “DNA target,” “DNA target sequence,” “target DNA sequence,” “nucleic acid target sequence,” “target sequence,” or “processing site” is intended a polynucleotide sequence that can be targeted and processed by a sequence-specific nuclease reagent as described herewith. These terms refer to a specific DNA location, such as a genomic location in a cell, but also to a portion of genetic material that can exist independently to the main body of genetic material such as plasmids, episomes, virus, transposons or in organelles such as mitochondria as non-limiting example. As non-limiting examples of RNA guided target sequences, are those genome sequences that can hybridize the guide RNA which directs the RNA guided endonuclease to a desired locus.

“Rare-cutting endonucleases” are sequence-specific endonuclease reagents of choice, insofar as their recognition sequences generally range from 10 to 50 successive base pairs, for instance from 12 to 30 bp or from 14 to 20 bp.

In some cases, said sequence-specific endonuclease reagent can be a nucleic acid encoding an “engineered” or “programmable” rare-cutting endonuclease, such as a homing endonuclease as described for instance by Arnould et al. (W02004067736), a zinc finger nuclease (ZFN) as described, for instance, by Urnov et al. (Nature (2005) 435:646-651), a TALE -Nuclease as described, for instance, by Mussolino et al. (Nucl. Acids Res. (2011) 39(21):9283-9293), or a MegaTAL nuclease as described, for instance by Boissel et al. (Nucleic Acids Research (2013) 42(4):2591-2601).

In some cases, the endonuclease reagent can be a RNA-guide to be used in conjunction with a RNA guided endonuclease, such as Cas9 or Cpfl , as per, inter alia, the teaching by Doudna and Charpentier (Science (2014) 346 (6213):! 077), which is incorporated herein by reference.

In some cases, the endonuclease reagent can be transiently expressed into the cells, meaning that said reagent is not supposed to integrate into the genome or persist over a long period of time, such as would be the case of RNA, such as mRNA, proteins or complexes mixing proteins and nucleic acids (e.g. ribonucleoproteins).

An endonuclease under mRNA form can be synthetized with a cap to enhance its stability according to techniques well known in the art, as described, for instance, by Kore etal. (J Am Chem Soc. (2009) 131(18):6364-5).

The nucleases, polynucleotides encoding these nucleases, donor polynucleotides and compositions comprising the proteins and/or polynucleotides described herein for genetically modifying the cells may be delivered in vivo or ex vivo by any suitable means.

In some cases, polypeptides may be synthesized in situ in a cell as a result of the introduction of polynucleotides encoding the polypeptides into the cell. In some cases, the polypeptides can be produced outside the cell and then introduced into the cell. Methods for introducing a polynucleotide construct into cells are known in the art and include, as non-limiting examples, stable transformation methods wherein the polynucleotide construct is integrated into the genome of the cell, transient transformation methods wherein the polynucleotide construct is not integrated into the genome of the cell and virus mediated methods. In some cases, the polynucleotides can be introduced into a cell by recombinant viral vectors (e.g. retroviruses, adenoviruses), liposomes and the like. For example, transient transformation methods include, for example micro injection, electroporation or particle bombardment. The polynucleotides can be included in vectors, such as plasmids or virus, in view of being expressed in cells.

In some cases, the cells can be transfected with a nucleic acid encoding an endonuclease reagent. In some cases, 80% of the endonuclease reagent is degraded by 30 hours, for instance by 24 or by 20 hours after transfection.

In some cases, nucleases and/or donor constructs as described herein can also be delivered using vectors containing sequences encoding one or more of the CRISPR/Cas system(s), zinc finger or TALEN protein(s).

Any vector systems may be used including, but not limited to, plasmid vectors, retroviral vectors, lentiviral vectors, adenovirus vectors, poxvirus vectors; herpesvirus vectors and adeno-associated virus vectors, etc. See, also, U.S. Pat. Nos. 6,534,261; 6,607,882; 6,824,978; 6,933,113; 6,979,539; 7,013,219; and 7,163,824, incorporated by reference herein in their entireties. Furthermore, it will be apparent that any of these vectors may comprise one or more of the sequences needed for treatment. Thus, when one or more nucleases and a donor construct are introduced into the cell, the nucleases and/or donor polynucleotide may be carried on the same vector or on different vectors. When multiple vectors are used, each vector may comprise a sequence encoding one or multiple nucleases and/or donor constructs.

Any appropriate viral and non-viral based gene transfer methods can be used to introduce nucleic acids encoding nucleases and donor constructs in cells (e.g. mammalian cells) and target tissues.

Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. For a review of gene therapy procedures, see Anderson, Science 256:808-813 (1992); Nabel & Feigner, TIBTECH 11 :211-217 (1993); Mitam & Caskey, TIBTECH 11 :162-166 (1993); Dillon, TIBTECH 11 :167-175 (1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology 6(10): 1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience 8:35-36 (1995); Kremer & Perri caudet, British Medical Bulletin 51(1): 31-44 (1995); Haddada et al., in Current Topics in Microbiology and Immunology, Doerfler and Bohm (eds.) (1995); and Yu et al., Gene Therapy 1 :13-26 (1994).

In some cases, methods of non-viral delivery of nucleic acids include electroporation, lipofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, poly cation or lipid: nucleic acid conjugates, naked DNA, naked RNA, capped RNA, artificial virions, and agent-enhanced uptake of DNA. Sonoporation using, e.g. the Sonitron 2000 system (Rich-Mar) can also be used for delivery of nucleic acids.

In general, electroporation steps that are used to transfect primary immune cells, such as PBMCs are typically performed in closed chambers comprising parallel plate electrodes producing a pulse electric field between said parallel plate electrodes greater than 100 volts/cm and less than 5,000 volts/cm, substantially uniform throughout the treatment volume such as described in WO 2004/083379, which is incorporated by reference, especially from page 23, line 25 to page 29, line 11. One such electroporation chamber can have a geometric factor (cm ) defined by the quotient of the electrode gap squared (cm2) divided by the chamber volume (cm ³ ), wherein the geometric factor is less than or equal to 0.1 cm , wherein the suspension of the cells and the sequence-specific reagent is in a medium which is adjusted such that the medium has conductivity in a range spanning 0.01 to 1.0 milliSiemens. In general, the suspension of cells undergoes one or more pulsed electric fields. With the method, the treatment volume of the suspension is scalable, and the time of treatment of the cells in the chamber is substantially uniform.

In some cases, different transgenes or multiple copies of the transgene can be included in one vector. The vector can comprise a nucleic acid sequence encoding ribosomal skip sequence such as a sequence encoding a 2A peptide. 2A peptides, which were identified in the Aphthovirus subgroup of picornaviruses, causes a ribosomal "skip" from one codon to the next without the formation of a peptide bond between the two amino acids encoded by the codons (see Donnelly et al., J. of General Virology 82: 1013-1025 (2001); Donnelly et al., J. of Gen. Virology 78: 13-21 (1997); Doronina et al., Mol. And. Cell. Biology 28(13): 4227-4239 (2008); Atkins etal., RNA 13: 803-810 (2007)).

By "codon" is meant three nucleotides on an mRNA (or on the sense strand of a DNA molecule) that are translated by a ribosome into one amino acid residue. Thus, two polypeptides can be synthesized from a single, contiguous open reading frame within an mRNA when the polypeptides are separated by a 2A oligopeptide sequence that is in frame. Such ribosomal skip mechanisms are well known in the art and are known to be used by several vectors for the expression of several proteins encoded by a single messenger RNA.

In some cases, a polynucleotide encoding a sequence-specific reagent can be mRNA which is introduced directly into the cells, for example by electroporation. In some cases, the cells can be electroporated using cytoPulse technology which allows, by the use of pulsed electric fields, to transiently permeabilize living cells for delivery of material into the cells. The technology, based on the use of PulseAgile (BTX Havard Apparatus, 84 October Hill Road, Holliston, Mass. 01746, USA) electroporation waveforms grants the precise control of pulse duration, intensity as well as the interval between pulses (see U.S. Pat. No. 6,010,613 and published International Application WO 2004/083379). All these parameters can be modified in order to reach the best conditions for high transfection efficiency with minimal mortality. The first high electric field pulses allow pore formation, while subsequent lower electric field pulses allow moving the polynucleotide into the cell.

Additional exemplary nucleic acid delivery systems include those provided by Amaxa Biosystems (Cologne, Germany), Maxcyte, Inc. (Rockville, Md.), BTX Molecular Delivery Systems (Holliston, Mass.) and Copernicus Therapeutics Inc., (see for example U.S. Pat. No. 6,008,336). Lipofection is described in e.g. U.S. Pat. Nos. 5,049,386; 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g. Transfectam and Lipofectin). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Feigner, WO 91/17424, WO 91/16024.

The preparation of lipid: nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g. Crystal, Science 270:404-410 (1995); Blaese et al., Cancer Gene Ther. 2:291-297 (1995); Behr et al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res. 52:4817- 4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).

In some cases, the donor sequence and/or sequence-specific reagent can be encoded by a viral vector. In some cases, adenoviral based systems can be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and high levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus ("AAV") vectors are also used to transduce cells with target nucleic acids, e.g. in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g. West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994). Construction of recombinant AAV vectors are described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin etal., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, etal., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al., J. Virol. 63:03822-3828 (1989).

Recombinant adeno-associated virus vectors (rAAV) are a promising alternative gene delivery system based on the defective and nonpathogenic parvovirus adeno- associated type 2 virus. All vectors are derived from a plasmid that retains only the AAV 145 bp inverted terminal repeats flanking the transgene expression cassette. Efficient gene transfer and stable transgene delivery due to integration into the genomes of the transduced cell are key features for this vector system (Wagner etal., Lancet 351:9117 1702-3 (1998), Kearns et al., Gene Ther. 9:748-55 (1996)). Other AAV serotypes, including but non- limiting example, AAV1, AAV3, AAV4, AAV5, AAV6, AAV8, AAV 8.2, AAV9, and AAV rhl 0 and pseudotyped AAV such as AAV2/8, AAV2/5 and AAV2/6 can also be used in accordance with the present disclosure.

In some cases, the cells can be administered with an effective amount of one or more caspase inhibitors in combination with an AAV vector.

In some cases, the donor sequence and/or sequence-specific reagent can be encoded by a recombinant lentiviral vector (rLV). An integrase-deficient lentivirus (IDLV) can also be employed herewith. IDLV derived from the regular integrating lentivirus but has loss-of-function mutations in its lentiviral integrase protein, which prevent proviral DNA insertion into the transduced cell’s genome.

The nuclease-encoding sequences and donor constructs can be delivered using the same or different systems. For example, a donor polynucleotide can be carried by a viral vector, while the one or more nucleases can be delivered as mRNA compositions.

In some cases, one or more reagents can be delivered to cells using nanoparticles. In some cases, nanoparticles are coated with ligands, such as antibodies, having a specific affinity towards HSC surface proteins, such as CD105 (Uniprot #P17813). In some cases, the nanoparticles are biodegradable polymeric nanoparticles in which the sequencespecific reagents under polynucleotide form are complexed with a polymer of polybeta amino ester and coated with polyglutamic acid (PGA).

Due to their higher specificity, TALE-nuclease have proven to be particularly appropriate sequence-specific nuclease reagents for therapeutic applications, especially under heterodimeric forms, i.e. working by pairs with a “right” monomer (also referred to as “5”’ or “forward”) and ‘left” monomer (also referred to as “3 ”” or “reverse”) as reported for instance by Mussolino et al. (Nucl. Acids Res. (2014) 42(10): 6762-6773).

As previously stated, the sequence-specific reagent can be under the form of nucleic acids, such as under DNA or RNA form encoding a rare cutting endonuclease or a subunit thereof, but they can also be part of conjugates involving polynucleotide(s) and polypeptide(s) such as so-called “ribonucleoproteins.” Such conjugates can be formed with reagents as Cas9 or Cpfl (RNA-guided endonucleases) as respectively described by Zetsche etal. (Cell (2015) 163(3): 759-771), which involve RNA or DNA guides that can be complexed with their respective nucleases.

“Exogenous sequence” refers to any nucleotide or nucleic acid sequence that was not initially present at the selected locus. This sequence may be homologous to, or a copy of, a genomic sequence, or be a foreign sequence introduced into the cell. By opposition, “endogenous sequence” means a cell genomic sequence initially present at a locus.

As used herewith, a “donor construct” or “donor polynucleotide” comprises the exogenous nucleotide sequence to be inserted in the cell’s genome either randomly at any locus or at, or replacing, the targeted locus. A donor construct can comprise a nucleotide sequence encoding a CAR or a fusion protein described herewith and, optionally, a promoter controlling the transcription of said CAR or fusion protein.

In some cases, the donor construct can be a vector comprising a constitutive exogenous promoter and, operably linked to said promoter, an exogenous nucleic acid sequence encoding a tumor-CAR, as described herewith. In this case, the donor construct can be integrated in the cell’s genome randomly at any locus and the tumor-CAR transcription is controlled by said constitutive exogenous promoter.

In some cases, the donor construct can be a vector comprising an exogenous nucleic acid sequence encoding a tumor-CAR flanked by Left- and Right- Homologous Arms (or “Left- and Right- Homologous Regions”) (also called “5'- and 3'-Homology Arms (or Regions)”, respectively) which have homology to the targeted locus, the expression of which is constitutive as described herewith. In some cases, the vector does not comprise a promoter sequence and the donor construct can be integrated in the cell’s genome by homologous recombination at the targeted constitutively expressed locus so that the tumor- CAR transcription is controlled by the constitutive (endogenous) promoter of said targeted locus. In some cases, the vector further comprises a constitutive exogenous promoter sequence and the “cassette” comprising the promoter sequence and the exogenous nucleic acid sequence encoding a tumor-CAR is flanked by Left- and Right- Homologous Arms which have homology to the targeted locus. In these later cases, the donor construct can be integrated in the cell’s genome by homologous recombination at the targeted locus but the tumor-CAR transcription is controlled by the constitutive exogenous promoter provided by the vector.

In some cases, the donor construct can be a vector comprising an exogenous nucleic acid sequence encoding a fusion protein as described herewith flanked by Left- and Right- Homologous Arms which have homology to the targeted locus, which is an inducible locus. In general, such a vector does not comprise a promoter sequence and the donor construct can be integrated in the cell’s genome by homologous recombination at the targeted inducible locus so that the fusion protein transcription is controlled by the inducible (endogenous) promoter of said targeted locus. When the donor construct does not comprise a promoter, the donor construct can comprise, in addition to the CAR coding sequence or fusion protein coding sequence, an Internal Ribosome Entry Site (IRES) or "self-cleaving" 2A peptides, such as T2A, P2A, E2A or F2A, so as to allow production of a functional CAR or fusion protein, respectively.

Stable expression of proteins, in particular tumor-CAR and fusion protein as described herewith, in the above-described immune cells, such as T-cells, can be achieved using, for example, viral vectors (e.g. lentiviral vectors, retroviral vectors, Adeno- Associated Virus (AAV) vectors) or transposon/transposase systems or plasmids or PCR products integration. Other approaches include direct mRNA electroporation.

Non-limitative examples of TALE-nuclease targeting the endogenous genes expressing PDCD1, TRAC, CD52, and B2M are provided in Table 6. The invention can be practiced as described herein with such polynucleotides or polypeptides having at least 70%, for instance at least 80%, at least 90% or at least 95% or 99% identity with the sequences referred to in Table 6.

Table 6: Examples of TALE-nucleases and their target sequences

In some cases, the integration of the donor construct by homologous recombination at the targeted locus results in the reduction or suppression of the production of the targeted gene’s product.

Therefore, in some cases, any of the donor constructs as described herewith can be integrated at a locus encoding TCR, HLA, B2M, PDCD1, CTLA4, TIM3, LAG3, CD69, IL2Ra, GM-CSF and/or CD52. As a consequence, in these cases, the targeted gene’s expression is reduced or suppressed.

For instance, in some cases, a polynucleotide encoding the tumor-CAR as described herewith is integrated at the endogenous TRAC, B2M, or CD52 locus in the genome of said engineered immune cell, e.g. T-cell. In some cases, a polynucleotide encoding the fusion protein as described herewith is integrated at the endogenous PDCD 1 , CD25, GM-CSF, TIM3, or TIGIT locus in the genome of said engineered immune cell (e.g. T-cell).

Gene targeted insertion of the sequences encoding CARs or fusion proteins and/or other exogenous genetic sequences can be performed using AAV vectors, especially vectors from the AAV6 family or chimeric vectors AAV2/6 previously described by Sharma et al. (Brain Research Bulletin. (2010) 81 (2-3): 273-278).

One aspect thus relates to the transduction of such AAV vectors encoding a tumor- CAR or a fusion protein as described herewith, in human primary immune cells, such as primary T-cells, in conjunction with the expression of sequence-specific endonuclease reagents, such as TALE endonucleases, to increase gene integration at the loci previously cited.

Another aspect relates to the transduction of a recombinant lentiviral vector (rLV) encoding a CAR, such as a tumor-CAR as described herewith, in human primary immune cells, in particular primary T-cells, that can be performed before or after introduction of a sequence-specific endonuclease reagent, such as a TALE endonuclease, to inactivate the genes previously cited (e.g. TRAC, TRBC, CD3, HLA, B2M, PDCD1, CTLA4, TIM3, LAG3, CD69, IL2Ra, GM-CSF and/or CD52).

In some cases, sequence-specific endonuclease reagents can be introduced into the cells by transfection, such as by electroporation of mRNA encoding said sequence-specific endonuclease reagents. Accordingly, it is provided a method for inserting an exogenous nucleic acid sequence coding for a tumor-CAR or a fusion protein as described herein, at one of the previously cited locus in the cell’s genome, which comprises at least one of the following steps: transducing into said cell an AAV vector comprising an exogenous nucleic acid sequence encoding a tumor-CAR or a fusion protein as described herein and the sequences homologous to the targeted endogenous DNA sequence, and expressing a sequence-specific endonuclease reagent that cleaves said endogenous sequence at the locus of insertion.

The obtained insertion of the exogenous nucleic acid sequence may result into the introduction of genetic material and replacement of the endogenous sequence, and, thus, inactivation of the endogenous locus.

Another object relates to the AAV vector used in the method, which can comprise an exogenous coding sequence that is “promoterless”, the coding sequence being any of those referred to in this specification.

Many other vectors known in the art, such as plasmids, episomal vectors, linear DNA matrices, etc. can also be used to perform gene insertions at those loci by following present teachings.

The DNA vector used for random integration as described herewith can comprise the exogenous nucleic acid to be inserted comprising (i) a constitutive promoter and, operably linked to said promoter, a sequence encoding a tumor-CAR, as described herewith.

It is to be understood that, as it derives from the meaning of the term “exogenous sequence” provided herewith, the sequences comprised in the DNA vector to be integrated are necessarily “exogenous” since it is intended that they are added to the cell’s genome. Thus, in this situation the adjective “exogenous” could have been omitted.

According to another aspect, when said CAR is a multi-chain CAR, the nucleic acid under (1) further comprises an Internal Ribosome Entry Site (IRES) or "self-cleaving" 2A peptides, such as T2A, P2A, E2A or F2A, so that the exogenous coding sequence inserted is multi-cistronic. The IRES or 2A Peptide can precede or follow said exogenous coding sequence. The exogenous polynucleotide sequences encoding said tumor-CAR and/or fusion protein as described herein can also be introduced into the immune cells, e.g. T-cells or NK-cells, or into iPSCs, by using a viral vector, such as lentiviral vectors. The present disclosure thus provides with viral vectors encoding tumor-CARs and/or fusion proteins as described herein.

In some cases, lentiviral or AAV vectors as contemplated herewith can comprise sequences encoding a CAR separated by a T2A or P2A sequence, as forming one transcriptional unit. In lentiviral vectors said sequences coding for the tumor-CAR as described herewith can form an expression cassette transcribed under control of a constitutive exogenous promoter, such as a EFl alpha promoter derived from the human EFl Al gene.

In some cases, the engineered cells are made by a process comprising random integration, in the genome of said cells, of a lentiviral vector comprising a constitutive promoter sequence and a polynucleotide encoding a tumor-CAR as described herewith.

In some cases, the engineered cells are made by a process comprising targeted integration of the exogenous sequences encoding the tumor-CAR.

In some cases, the engineered cells are made by a process comprising targeted integration of the exogenous sequences encoding the fusion protein as described herewith.

Thus, in some cases, the engineered cells are made by a process comprising targeted integration, in the genome of said cells, of a polynucleotide encoding a tumor- CAR as described herewith through sequence-specific endonuclease-mediated cDNA insertion at a constitutively expressed locus in the cells’ genome. In these cases, said cDNA comprises a polynucleotide encoding a tumor-CAR as described herewith and the constitutively expressed locus is a locus controlled by an endogenous constitutive promoter as defined herewith. In these cases, the expression of said tumor-CAR is controlled by said endogenous constitutive promoter.

In some cases, the engineered cells are made by a process comprising targeted integration, in the genome of said cells, of a polynucleotide comprising an exogenous constitutive promoter and, operably linked to said promoter, an exogenous nucleic acid sequence encoding a tumor-CAR as described herewith, through sequence-specific endonuclease-mediated insertion at any targeted locus in the cells’ genome. In these cases, expression of said tumor-CAR is controlled by said exogenous constitutive promoter.

In some cases, the engineered cells are made by a process comprising targeted integration, in the genome of said cells, of a polynucleotide encoding a fusion protein as described herewith through sequence-specific endonuclease-mediated cDNA insertion at an inducible locus in the cells’ genome. In these cases, said cDNA comprises a polynucleotide encoding a fusion protein as described herewith and the inducible locus is controlled by an inducible promoter as defined herewith. In these cases, the expression of said fusion protein is controlled by said endogenous inducible promoter.

Another aspect relates to a set of vectors or a kit for producing the engineered immune cells or iPSCs as described herewith.

In one aspect is provided a set of vectors comprising at least one vector comprising a nucleic acid sequence encoding a tumor-CAR as described herein allowing its integration in the cell’s genome under the transcriptional control of an endogenous or exogenous constitutive promoter, and at least one vector comprising a nucleic acid sequence encoding a fusion protein as described herein allowing its integration in the cell’s genome under the transcriptional control of an inducible endogenous promoter.

In one aspect is provided a set of vectors comprising:

(l)(a) at least one vector comprising an exogenous nucleic acid sequence comprising a constitutive promoter and, operably linked to said promoter, a nucleic acid sequence encoding a tumor-CAR, or

(1)(b)) at least one vector comprising an expression cassette comprising an exogenous nucleic acid sequence encoding a tumor-CAR, wherein said exogenous nucleic acid sequence encoding the tumor-CAR is placed between a Left-Homology Region and a Right-Homology Region, and wherein said Regions are homologous to an endogenous constitutive locus in a cell, and

(2) at least one vector comprising an expression cassette comprising an exogenous nucleic acid sequence encoding a secreted fusion protein comprising a FAP-binding- domain and a stimulatory cytokine, wherein optionally said fusion protein does not comprise an antibody crystallizable fragment (Fc), wherein said exogenous nucleic acid sequence encoding the fusion protein is placed between a Left-Homology Region and a Right-Homology Region, and wherein said Regions are homologous to an endogenous inducible locus in a cell.

As used herewith, the endogenous constitutive locus and endogenous inducible locus in a cell refer to loci present in the genome of a cell that can be transduced with the set of vectors defined, where said vectors constitute means for integrating the defined cassettes in said cell’s genome as described.

In another aspect is provided a kit comprising:

(a) at least one vector comprising a nucleic acid sequence comprising an exogenous constitutive promoter and, operably linked to said promoter, a nucleic acid sequence encoding a tumor-CAR; and

(b) at least one vector comprising a nucleic acid sequence encoding a secreted fusion protein comprising a FAP-binding-domain and a stimulatory cytokine, wherein optionally said fusion protein does not comprise an antibody crystallizable fragment (Fc), wherein said nucleic acid sequence encoding the fusion protein is placed between a Left- Homology Region and a Right-Homology Region, wherein said Regions are homologous to the locus targeted by the endonuclease of (c); and

(c) at least one sequence-specific endonuclease targeting one endogenous inducible locus.

In another aspect is provided a kit comprising:

(a) at least one vector comprising an expression cassette comprising an exogenous nucleic acid sequence encoding a tumor-CAR, wherein said exogenous nucleic acid sequence encoding the tumor-CAR is placed between a Left-Homology Region and a Right-Homology Region, and wherein said Regions are homologous to the locus targeted by the endonuclease of (b);

(b) at least one sequence-specific endonuclease targeting one endogenous constitutive locus;

(c) at least one vector comprising a nucleic acid sequence encoding a secreted fusion protein comprising a FAP-binding-domain and a stimulatory cytokine, wherein optionally said fusion protein does not comprise an antibody crystallizable fragment (Fc), wherein said nucleic acid sequence encoding the fusion protein is placed between a Left- Homology Region and a Right-Homology Region, wherein said Regions are homologous to the locus targeted by the endonuclease of (d); and

(d) at least one sequence-specific endonuclease targeting one endogenous inducible locus.

In some of the kits described herewith, said exogenous constitutive promoter is selected from the group consisting of an EFl A promoter, a CD52 promoter, a GAPDH promoter, a CMV promoter, an hPGK promoter, a UBC promoter, a SV40 promoter, a PGK promoter, a CAGG promoter, a TRAC promoter, a TRBC promoter, a TRGC promoter, a TRDC promoter, a B2M promoter, a CD5 promoter, a CS1 promoter, a CD45 promoter, a RPBSA promoter, a CD4 promoter, and a CD8 promoter; and/or said endogenous constitutive locus is selected from the group consisting of EFl A, CD52, GAPDH, hPGK, UBC, TRAC, TRBC, TRGC, TRDC, B2M, CD5, CS1, CD45, CD4, and CD8 loci.

In some of the kits described herewith, said inducible locus is selected from the group consisting of PDCD1, CD25, TIM3, TIGIT, CCL1, NR4A3, EGR3, G0S2, IL22, RGS16, FASLG, RDH10, CSF1, GM-CSF, LAG3, CTLA-4, IL10, NUR77, and FOXP3 loci.

In some of the kits, the sequence-specific endonuclease targeting one constitutive locus is a TALE nuclease. In some cases, said TALE nuclease can target one endogenous constitutively expressed locus selected from the group consisting of EFl A, CD52, GAPDH, hPGK, UBC, TRAC, TRBC, TRGC, TRDC, B2M, CD5, CS1, CD45, CD4, and CD8 loci. In some cases, said TALE nuclease can target one endogenous constitutively expressed locus selected from the group consisting of EFl A, TRAC, B2M, CD52, CS1, CD45, CD5, and GAPDH loci. In some cases, said TALE nuclease can target one endogenous constitutively expressed locus selected from the group consisting of EFl A, TRAC, B2M, and CD52 loci.

In some of the kits, the sequence-specific endonuclease targeting one inducible locus is a TALE nuclease. In some cases, said TALE nuclease can target one inducible locus selected from the group consisting ofPDCDl, CD25, TIM3, TIGIT, CCL1, NR4A3, EGR3, G0S2, IL22, RGS16, FASLG, RDH10, CSF1, GM-CSF, LAG3, CTLA-4, IL10, NUR77, and FOXP3 loci. In some cases, said TALE nuclease can target one inducible locus selected from the group consisting of PDCD1, CD25, GM-CSF, TIM3, and TIGIT loci. In some cases, said TALE can target one inducible locus that is PDCD1 locus.

In some instances, when a vector of said kits does not comprise a promoter controlling the transcription of the exogenous nucleic acid sequence comprised in the vector, the transcription of said exogenous nucleic acid sequence will be controlled by the endogenous promoter of the targeted endogenous locus, after integration in the cell’s genome.

In some instances, when a vector of said kits comprises a promoter controlling the transcription of the exogenous nucleic acid sequence comprised in the vector, the transcription of said exogenous nucleic acid sequence will be controlled by the exogenous promoter, after integration in the cell’s genome.

In another aspect is provided a kit comprising:

(a) at least one vector comprising a nucleic acid sequence comprising a constitutive promoter and, operably linked to said promoter, a nucleic acid sequence encoding a tumor-CAR as described herewith; and

(b) at least one vector comprising a nucleic acid sequence encoding a fusion protein as described herewith placed between a Left-Homology Region and a Right- Homology Region, wherein said Regions are homologous to the locus targeted by the endonuclease of (c), and

(c) at least one sequence-specific endonuclease targeting one inducible locus selected from the group consisting of PDCD1, CD25, TIM3, TIGIT, CCL1, NR4A3, EGR3, G0S2, IL22, RGS16, FASLG, RDH10, CSF1, GM-CSF, LAG3, CTLA-4, IL10, NUR77, and FOXP3 loci.

In another aspect is provided a kit comprising:

(a) at least one vector comprising a nucleic acid sequence encoding a tumor- CAR as described herewith placed between a Left-Homology Region and a Right- Homology Region, wherein said Regions are homologous to the locus targeted by the endonuclease of (b);

(b) at least one sequence-specific endonuclease targeting one constitutively expressed locus selected from the group consisting of EFl A, CD52, GAPDH, hPGK, UBC, TRAC, TRBC, TRGC, TRDC, B2M, CD5, CS1, CD45, CD4, and CD8 loci; (c) at least one vector comprising a nucleic acid sequence encoding a fusion protein as described herewith placed between a Left-Homology Region and a Right- Homology Region, wherein said Regions are homologous to the locus targeted by the endonuclease of (d), and

(d) at least one sequence-specific endonuclease targeting one inducible locus selected from the group consisting of PDCD1, CD25, TIM3, TIGIT, CCL1, NR4A3, EGR3, G0S2, IL22, RGS16, FASLG, RDH10, CSF1, GM-CSF, LAG3, CTLA-4, IL10, NUR77, and FOXP3 loci.

In another aspect is provided a kit comprising:

(a) at least one vector comprising a cassette comprising a constitutive promoter and, operably linked to said promoter, a nucleic acid sequence encoding a tumor-CAR as described herewith; wherein said constitutive promoter is selected from the group consisting of EFl A, CD52, GAPDH, hPGK, UBC, TRAC, TRBC, TRGC, TRDC, B2M, CD5, CS1, CD45, RPBSA, CD4, and CD8, wherein said cassette of (a) is placed between a Left-Homology Region and a Right-Homology Region, wherein said Regions are homologous to the locus targeted by the endonuclease of (b);

(b) at least one sequence-specific endonuclease targeting a locus,

(c) at least one vector comprising a nucleic acid sequence encoding a fusion protein as described herewith placed between a Left-Homology Region and a Right- Homology Region, wherein said Regions are homologous to the locus targeted by the endonuclease of (d), and

(d) at least one sequence-specific endonuclease targeting one inducible locus selected from the group consisting of PDCD1, CD25, TIM3, TIGIT, CCL1, NR4A3, EGR3, G0S2, IL22, RGS16, FASLG, RDH10, CSF1, GM-CSF, LAG3, CTLA-4, IL10, NUR77, and FOXP3 loci.

In this later aspect, as the tumor-CAR is under the control of the specified exogenous promoter, there is no limitation regarding said targeted locus of (b). Thus, in this later aspect said targeted locus of (b) can be inducible or constitutively expressed.

Activation and expansion of immune cells Whether prior to or after genetic modification, the immune cells described herewith can be activated or expanded, even if they can activate or proliferate independently of antigen binding mechanisms. T-cells, for example, can be activated and expanded 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 7,572,631. T-cells can be expanded in vitro or in vivo. T-cells are generally expanded by contact with an agent that stimulates a CD3 TCR complex and a co-stimulatory molecule on the surface of the T- cells to create an activation signal for the T-cell. For example, chemicals such as calcium ionophore A23187, phorbol 12-myristate 13 -acetate (PMA), or mitogenic lectins like phytohemagglutinin (PHA) can be used to create an activation signal for the T-cell.

As non-limiting examples, T-cell populations may be stimulated in vitro such as 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, a population of 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. Conditions appropriate for T-cell culture include an appropriate media (e.g. Minimal Essential Media or RPMI Media 1640 or, X-vivo 5, (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-g , IL-4, IL-7, GM-CSF, IL-10, IL-12, IL-15, TGFp, and TNF- 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-mercaptoethanoi. Media can include RPMI 1640, A1M-V, DMEM, MEM, a-MEM, F-12, X-Vivo 1, and X-Vivo 20, OptTmizer, 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). T-cells that have been exposed to varied stimulation times may exhibit different characteristics.

In some cases, said cells can be expanded by co-culturing with tissue or cells. Said cells can also be expanded in vivo, for example in the subject’s blood after administrating said cell into the subject.

Any biological activity exhibited by the engineered immune cell expressing a CAR can be determined, including, for instance, cytokine production and secretion, degranulation, proliferation, or any combination thereof.

In some instances, the biological activity determined in step (iii) is cytokine secretion, cell proliferation, or both.

The biological activities can be measured by methods well known by the skilled person, such as by in vitro and/or ex vivo methods.

Secretion of any cytokine can be measured, e.g. secretion of IFNy, TNFa, can be determined. Standard methods to determine cytokine secretion includes ELISA, flow cytometry. These methods are described for instance in Sachdeva et al. (Front Biosci, 2007, 12:4682-95) and Pike et al. (2016) (Methods in Molecular Biology, vol 1458. Humana Press, New York, NY).

The level of cytokine secretion can be measured, for instance, as the maximum level of cytokine (e.g. IFNy) secreted per CAR-expressing immune cell (e.g. CAR-T cell), e.g. maximum amount of IFNy secreted per CAR-T cell.

To evaluate “degranulation,” standard methods can be used, including for instance CD 107a degranulation assay or measurement of secreted Granzyme B or Perforin (such as described in Lorenzo-Herrero et al, (Methods Mol Biol (2019) 1884: 119-130), Betts et al. Methods in Cell Biology (2004) 75:497-512).

To evaluate “proliferation” activity, standard methods can be carried out, which are mainly based on methods involving measurement of DNA synthesis, detection of proliferation-specific markers, measurement of successive cell divisions by the use of cell membrane binding dyes, measurement of cellular DNA content and measurement of cellular metabolism. In some cases, the methods described herewith allow producing engineered T-cells within a limited time frame of about 15 to 30 days, for instance between 15 and 20 days or between 18 and 20 days so that the cells keep their full immune therapeutic potential, especially with respect to their cytotoxic activity.

These cells can be from or be members of populations of cells, which can originate from a single donor or patient. In some cases, these populations of cells can be expanded under closed culture recipients to comply with highest manufacturing practices requirements and can be frozen prior to infusion into a patient, thereby providing “off the shelf’ or “ready to use” therapeutic compositions.

In some cases, a significant number of cells originating from the same leukapheresis can be obtained, which can be important to obtain sufficient doses for treating a patient. Although variations between populations of cells originating from various donors may be observed, the number of immune cells procured by a leukapheresis is generally about from 10 ⁸ to IO ¹⁰ cells of PBMC. PBMC comprises several types of cells: granulocytes, monocytes and lymphocytes, among which from 30 to 60 % of T-cells, which generally represents between 10 ⁸ to 10 ⁹ of primary T-cells from one donor.

In some cases, methods described herewith generally end up with a population of engineered cells that reaches generally more than about 10 ⁸ T-cells, more generally more than about 10 ⁹ T-cells, even more generally more than about 10 ¹⁰ T-cells, and usually more than 10 ¹¹ T-cells. In some cases, the T-cells are gene edited in at least at two different loci.

Such compositions or populations of engineered cells can therefore be used as a therapeutic; especially for treating any of the cancers herein, for example for the treatment of solid tumors in patients such as melanomas, neuroblastomas, gliomas or carcinomas such as lung, breast, colon, prostate or ovary tumors in a patient in need thereof

Also encompassed herewith is a therapeutically effective population of immune cells comprising at least 30%, at least 50%, or at least 80% of engineered cells as described herewith.

The present document discloses, for instance, populations of primary TCR negative immune cells, such as T-cells, originating from a single donor, wherein at least 20%, at least 30%, at least 50%, at least 90%, at least 95%, at least 96%, or at least 97% of the cells in said population have been genetically modified using sequence-specific reagents to become TCR negative.

By “TCR negative immune cell” is meant an immune cell, such as a T-cell or NK- cell, in which expression of TCR is not detectable by standard methods based on antibodies such as Flow-cytometry, Western-blot, ELISA. TCR negative immune cells include immune cells which have two of the endogenous alleles encoding a component of the T- cell receptor that have been genetically modified (e.g. disrupted), so that TCR presence at the cell surface of said engineered cells is suppressed and/or not detectable. TCR negative immune cells also include immune cells which, in their natural non-engineered state, generally do not express TCR gene, such as is the case of NK cells.

By “CD 52 negative immune cell” is meant an immune cell, such as a T-cell or NK- cell, in which expression of CD52 is not detectable by standard methods based on antibodies such as Flow-cytometry, Western-blot, ELISA. CD52 negative immune cells include immune cells which have two of the endogenous alleles encoding CD52 that have been genetically modified (e.g. disrupted), so that CD52 presence at the cell surface of said engineered cells is suppressed and/or not detectable.

By “B2M negative immune cell” is meant an immune cell, such as a T-cell or NK- cell, in which expression of p2M is not detectable by standard methods based on antibodies such as Flow-cytometry, Western-blot, ELISA. B2M negative immune cells include immune cells which have two of the endogenous alleles encoding p2M that have been genetically modified (e.g. disrupted), so that p2M presence at the cell surface of said engineered cells is suppressed and/or not detectable.

By “PDCD1 negative immune cell” is meant an immune cell, such as a T-cell or NK-cell, in which expression of PD1 is not detectable by standard methods based on antibodies such as Flow-cytometry, Western-blot, ELISA. PDCD1 negative immune cells include immune cells which have two of the endogenous alleles encoding PD1 that have been genetically modified (e.g. disrupted), so that PD1 presence at the cell surface of said engineered cells is suppressed and/or not detectable.

By “GM-CSF negative immune cell” is meant an immune cell, such as a T-cell or NK-cell, in which expression of GM-CSF is not detectable by standard methods based on antibodies such as Flow-cytometry, Western-blot, ELISA. GM-CSF negative immune cells include immune cells which have two of the endogenous alleles encoding GM-CSF that have been genetically modified (e.g. disrupted), so that GM-CSF presence at the cell surface of said engineered cells is suppressed and/or not detectable.

Methods of treatment and products for use in immunotherapy

An aspect relates to a pharmaceutical composition comprising a therapeutically effective amount of immune cells as described herewith.

Also described herewith is a composition comprising a therapeutically effective amount of immune cells as described herewith, for use in the treatment of a cancer, such as a cancer characterized by the presence of FAP in the tumor microenvironment.

Also contemplated herewith is a method of treatment of a cancer, such as a cancer characterized by the presence of FAP in the tumor microenvironment, comprising administering a therapeutically effective amount of engineered immune cells as described herewith.

The cancer that can be treated with the compositions, cells, or method of treatment described herewith are not limiting.

Said cancer can be a solid tumor or an haematological cancer.

Said cancer expressing a solid tumor antigen can be selected from any one of breast cancer, ovarian cancer, endometrial cancer, cervical cancer, bladder cancer, renal cancer, melanoma, lung cancer, prostate cancer, testicular cancer, mesothelioma, thyroid cancer, brain cancer, esophageal cancer, gastric cancer, pancreatic cancer, colorectal cancer, or liver cancer.

Examples of said cancer expressing a solid tumor antigen include breast cancer (e.g. triple-negative breast cancer), pancreatic cancer, and lung cancer (e.g. malignant pleural mesothelioma).

Said haematological cancer characterized by the presence of FAP in the tumor microenvironment can be selected from the group consisting of myelofibrosis, myelodysplastic syndromes, acute myeloid leukemia, non-Hodgkin’s lymphoma, multiple myeloma.

All of the above listed cancers can be treated with the engineered immune cells or the pharmaceutical composition described herein. The cancers advantageously treated with the engineered immune cells or pharmaceutical composition described herein are those for which the tumor antigen to be targeted is also present in normal healthy tissues.

In some cases, the cancer is an ovarian cancer and the tumor antigen is selected from one or more of mesothelin, glycoprotein 72 (TAG72), MUC16, Her2, 5T4, and FRa.

In some cases, the cancer is a breast cancer and the tumor antigen is selected from one or more of MUC28z, NKG2D, HRG10, and HER2.

In some cases, the cancer is a prostate cancer and the tumor antigen is selected from one or more of prostate stem cell antigen (PSCA) and prostate-specific membrane antigen (PSMA).

In some cases, the cancer is a renal cancer and the tumor antigen is carboxy- anhydrase-IX (CA-IX).

In some cases, the cancer is a gastric cancer and the tumor antigen is selected from one or more of Trop2, claudinl8.2, NKG2D, folate receptor 1 (FOLR1), and HER2.

In some cases, the cancer is a pancreatic cancer and the tumor antigen is selected from one or more of mesothelin, MUC1, CXCR2, B7-H3, CD133, CD24, PSCA, CEA, and Her-2.

In some cases, the cancer is a lung cancer and the tumor antigen is selected from one or more of mesothelin, receptor tyrosine kinase-like orphan receptor 1 -specific (R0R1), EGFRvIII, erythropoietin-producing hepatocellular carcinoma A2 (EphA2), PSCA, MUC1, and DLL3.

In some cases, the cancer is a liver cancer and the tumor antigen is selected from one or more of MUC1, CEA, glypican-3, and epithelial cell adhesion molecule (EPC AM).

In some cases, the cancer is a colorectal cancer and the tumor antigen is selected from one or more of MUC1, NKG2D, CD133, GUCY2C (Guanylate Cyclase 2C), TAG- 72 Doublecortin-like kinase 1 (DCLK1), and CEA.

In some cases, the haematological cancer is myelofibrosis and the tumor antigen is CALR.

In some cases, the haematological cancer is myelodysplastic syndromes and the tumor antigen is selected from one or more of CD123, CD33, and NKG2D. In some cases, the haematological cancer is acute myeloid leukemia and the tumor antigen is selected from one or more of CD123, CLL-1, IL1RAP, CD33, CD135, CD70, CD44, CD276, ILT3, CD7, CD47, TIM3, CD96, and VISTA.

In some cases, the haematological cancer is acute lymphocytic leukemia and the tumor antigen is selected from one or more of CD19, CD22, CD79a, CD10, CD2, CD3, CD4, CD5, CD7, CD8, CRLF2, and CD38.

In some cases, the haematological cancer is non-Hodgkin’s lymphoma and the tumor antigen is selected from one or more of CD19, CD20, CD22, CD80, CD37, CD79, CD30, CD70, and CD38.

In some cases, the haematological cancer is multiple myeloma and the tumor antigen is selected from one or more of BCMA, CD19, CD138, CS1, CD38, TACI, APRIL, GPRC5D, and CD44v6.

The treatments involving the engineered primary immune cells described herewith can be ameliorating, curative or prophylactic.

In some cases, the patient can undergo preparative lymphodepletion - the temporary ablation of the immune system- prior to administration of the engineered T- cells. In some cases, the lymphodepletion is only partial and not a complete ablation of the patient’s immune system. In some cases, a combination of IL-2 treatment and preparative lymphodepletion can enhance persistence of a cellular therapeutic.

In some cases, the engineered immune cells, such as T-cells, described herewith can be administered in an amount of about 10 ⁶ to 10 ⁹ cells/kg, with or without a course of lymphodepletion, for example by administering cyclophosphamide and/or fludarabine, and/or alemtuzumab.

In some cases, the cells or population of cells comprising the engineered immune cells, such as T-cells, described herewith are administered in an amount of about 10 ⁴ - 10 ⁹ cells per kg body weight, from about 10 ⁵ to 5x10 ⁶ cells/kg body weight, or from about 10 ⁵ to 10 ⁶ cells/kg body weight, including all integer values of cell numbers within those ranges. Dosing in CAR-T cell therapies may for example involve administration of from 10 ⁵ or 10 ⁶ to 10 ⁹ cells/kg, with or without a course of lymphodepletion, for example with fludarabine, cyclophosphamide or alemtuzumab, or any combination thereof. The cells or population of cells can be administered in one or more doses. In some cases, the effective amount of cells are administered as a single dose. In some cases, the effective amount of cells are administered as more than one dose over a period of time. Timing of administration is within the judgment of managing physician and depends on the clinical condition of the patient. The cells or population of cells may be obtained from any source, such as a blood bank or a donor. While individual needs vary, determination of optimal ranges of effective amounts of a given cell type for a particular disease or conditions are within the skill of one in the art.

An effective amount of engineered immune cells, such as CAR-T cells, means an amount which provides a therapeutic or prophylactic benefit. The dosage administered will be dependent upon the age, health and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment and the nature of the effect desired.

The treatment with the engineered immune cells described herewith may be carried out in further combination with one or more therapies against cancer selected from the group of antibodies therapy, chemotherapy, cytokines therapy, dendritic cell therapy, gene therapy, hormone therapy, laser light therapy and radiation therapy.

For example, the treatment with the engineered immune cells as described herewith can be carried out in combination with the administration of an immune checkpoint antagonist, that can be administered intravenously in an amount of about 200 mg to 400 mg including all integer values within those ranges.

What is described herewith with engineered T-cells comprising an inactivated TCR and expressing a tumor-CAR constitutively and a fusion protein comprising a FAP- binding -domain and a stimulatory cytokine upon activation of the T-cells can equally be applied to engineered Natural Killer cells expressing a tumor-CAR constitutively and a fusion protein comprising a FAP -binding-domain and a stimulatory cytokine upon activation of the NK cells.

Such engineered NK cells are naturally TCR negative. The NK cells described herewith can originate from a donor or from a cell line such as NK92 cell line. In some cases, the engineered NK cells derive from engineered iPSCs as described herewith which have been differentiated into NK cells. Optionally, said engineered NK cells have a reduced expression of 02M gene mediated by gene inactivation and/or by gene silencing and/or by inserting into the 02M locus of said NK-cells’ genome at least one exogenous polynucleotide encoding a CAR as defined herewith.

Said engineered NK cells may have a reduced expression of CD 52 gene mediated by gene inactivation and/or by gene silencing and/or by inserting into the CD52 locus of said NK-cells’ genome at least one exogenous polynucleotide encoding a CAR as defined herewith.

In some cases, said engineered NK cells comprise either the CD52 or the 02M gene inactivated.

Thus, is also provided herewith an engineered NK-cell comprising: a) an exogenous nucleic acid sequence encoding a chimeric antigen receptor (CAR) targeting a tumor antigen (“tumor-CAR”) ; and b) an exogenous nucleic acid sequence encoding a secreted fusion protein comprising (i) a Fibroblast Activation Protein (FAP)-binding-domain comprising the VH and VL amino acid sequences from a monoclonal anti-FAP antibody (such as a FAPscFv), and (ii) a stimulatory cytokine, wherein optionally said fusion protein does not comprise an antibody crystallizable fragment (Fc); wherein said exogenous nucleic acid sequence of a) is integrated in the cell’s genome and is placed under the transcriptional control of a constitutive promoter, wherein said exogenous nucleic acid sequence of b) is integrated in the cell’s genome at an endogenous inducible locus and is placed under the transcriptional control of the inducible promoter of said endogenous locus, and wherein the expression of said fusion protein is inducible upon activation of the NK cell; and wherein, optionally, the NK-cell has been genetically modified to suppress or repress expression of at least one gene controlling MHC complex surface presentation, such as B2M or CIITA, in the NK-cell.

Similar tumor-CARs and fusion proteins as described herewith can be expressed in said NK cells to produce engineered tumor-CAR/fusion proteins expressing-NK cells, which can be used in methods of treatment of a cancer characterized by the presence of FAP in the tumor microenvironment, such as solid tumor and haematological cancers, as described herewith.

Thus, are also described herewith a pharmaceutical composition comprising engineered NK-cells comprising (i) an exogenous nucleic acid sequence encoding a tumor- CAR placed under the transcriptional control of an exogenous or endogenous constitutive promoter, (ii) an exogenous nucleic acid sequence encoding a fusion protein comprising a FAP-binding-domain and a stimulatory cytokine placed under the transcriptional control of an endogenous inducible promoter, and (iii) optionally comprising an inactivated 02M gene. Optionally, said fusion protein to be expressed and secreted by said engineered NK- cells does not comprise an antibody crystallizable fragment (Fc).

A still other aspect described herewith is a pharmaceutical composition as described above for use in the treatment of a cancer characterized by the presence of FAP in the tumor microenvironment, such as solid tumors and haematological cancers; wherein said exogenous nucleic acid sequences a) and b) are integrated in the cell’s genome, and wherein the expression of the fusion protein is inducible upon activation of the NK cell.

The above written description provides a manner and process of making and using the invention such that any person skilled in the art is enabled to make and use the same, this enablement being provided in particular for the subject matter of the appended claims, which make up a part of the original description.

Where a numerical limit or range is stated herein, the endpoints are included. Also, all values and subranges within a numerical limit or range are specifically included as if explicitly written out.

Having generally described this invention, a further understanding can be obtained by reference to certain specific examples, which are provided herein for purposes of illustration only, and are not intended to limit the scope of the claimed invention.

EXAMPLES

Example 1 : Materials

TALE-nuclease targeting TRAC and PDCD1 TALEN-mRNA targeting TRAC (SEQ ID NO: 66 and SEQ ID NO: 67) and PDCD1 (SEQ ID NO: 64 and SEQ ID NO: 65) were produced by Trilink.

A A V constructs

Meso-C AR construct was inserted in frame with TRAC locus and peptide 2A (SEQ ID NO: 103) in an AAV vector. The TRAC-FAP-CAR donor construct is composed of 300 bp of the TRAC left and right Homology arms, a self-cleaving 2 A peptide allowing the expression of the Meso-CAR of amino acid sequence SEQ ID NO: 62.

FAPscFv-IL2v construct was inserted in frame with PDCD1 locus and peptide 2A (SEQ ID NO: 104) in an AAV vector. The PDCDl-FAPscFv-IL2v donor construct is composed of 300 bp of the PDCD1- left and right Homology arms, a self-cleaving 2A peptide allowing the expression of FAPscFv-IL2v fused to a (His)e tag at its C-terminal. Additionally, the FAPscFv-IL2v is followed by another 2A peptide and truncated surface protein DLNGFR. DLNGFR expression is used as a reporter for matrix insertion at PDCD1 locus. This construct comprises a nucleic acid encoding the IL2 signal sequence (SEQ ID NO: 90) directing secretion of the fusion protein outside the cell.

AAV vectors were produced by Vigene. rLV constructs

Meso-CAR expression cassette was inserted randomly in the genome using recombinant lentiviral vector comprising the Meso-CAR coding sequence (SEQ ID NO: 100) under the control of the EFl A promoter (SEQ ID NO: 105). The lentivirus particles were produced by Flash Therapeutics.

Example 2: Generation of CAR-T cells having a constitutive expression of a Meso- CAR and an inducible expression of an FAPscFv-IL2v protein, by AAV transduction

This Example describes the generation of universal CAR-T cells having a constitutive expression of a Meso-CAR and an inducible expression of a FAPscFv-IL2v protein. The Meso-CAR construct was inserted at the endogenous TRAC locus, whereas the FAPscFv-IL2v construct was inserted at the endogenous PDCD1 locus. The expression of Meso-CAR and FAPscFv-IL2v was driven by the endogenous TRAC promoter and the PDCD1 promoter, respectively (Figure 2A, B and C).

Engineered CAR-T cells

Cryopreserved PBMC were thawed at 37°C, washed and re-suspended in OpTmizer medium supplemented with AB human serum (5%) for overnight incubation at 37°C in 5% CO2 incubator. Cells were then activated with Transact in OpTmizer medium supplemented with AB human serum (5%) and recombinant human interleukin-2 (rhIL-2, 350 lU/mL) in a CO2 incubator (culture medium). Three days after activation, T cells were electroporated with 5 pg of each TALEN® arm mRNAs specific for TRAC (SEQ ID NO: 66 and SEQ ID NO: 67) or PDCD1 (SEQ ID NO: 64 and SEQ ID NO: 65). Transfection was performed using Pulse Agile technology by applying two 0.1 mS pulses at 800V followed by four 0.2 mS pulses at 130 V in 0.4 cm gap cuvettes in Cytoporation buffer T (BTX Harvard Apparatus, Holliston, Massachusetts). The electroporated cells were then immediately transferred into prewarmed Optmizer serum-free media and incubated at 37°C for 15 min. The cells were then concentrated and incubated in the presence of TRAC- Meso-CAR AAV particles (MOI= 1.1E5 vg/cells) and PDCDl-FAPscFv-IL2v AAV particles (MOI = 1.1E5 vg/cells), comprising the donor constructs depicted in Figures 2B and 2C respectively. After 2 h of culture at 30°C, OpTmizer media supplemented by 10% AB serum and IL-2 was added to the cell suspension, and the mix was incubated for 16 h under the same culture conditions. Cells were subsequently cultivated at 37°C in the presence of 5% CO2. Cells were thereafter cultivated at 37°C in the presence of 5% CO2 and analyzed for TRAC, PD1, FAP-CAR and MESO-CAR expression. These cells were analysed for TRAC knockout, Meso-CAR expression (Figure 3A) and PDCD1 knockout post activation with PMA (20 pM)/Ionomycin (800 ng/ml) for 24 h by flow cytometry (Figure 3B). More than 90% of TRAC knockout could be achieved and approximately 30% of the edited T-cells expressed Meso-CAR (Figure 3A). In addition, PDCD1 positive cells were reduced from 70% (in Mock control) down to 15 to 20% (Figure 3B). To determine expression and secretion of FAPscFv-IL2v upon MesoCAR activation, cells were incubated on Mesothelin protein (2 ug/ml; Lake Pharma) coated 24-well plates for 48 hours. Secreted FAPscFv-IL2v protein in the cell culture supernatants was detected using a His tag ELISA detection kit (Genscript, Catalog no. L00436). FAPscFv-IL2v protein was detected at a concentration of 18 ng/mL in the TRACMesoCARPDCDlFAPsoFv- iL2v cell supernatant (Figure 3C).

Example 3: Improved cytotoxic activity of CAR-T cells having a constitutive expression of a MESO-CAR and an inducible secretion of FAPscFv-IL2v in vivo

To demonstrate, in vivo, increased CAR-T anti-tumor activity upon FAPscFv-IL2v expression with this strategy, 8 -week-old, female NSG mice were orthotopically implanted with 3 x 10 ⁶ human triple-negative breast cancer cell line HCC70-NanoLuc-GFP mixed with 3 x 10 ⁶ human triple-negative breast tumor derived cancer-associated fibroblasts in the left inguinal mammary fat pad. 24 days post tumor implantation, tumor-bearing mice were intravenously injected with 5 x 10 ⁶ mock transfected, TRACMesoCARPDCDlKo, TRACMesoCARPDCDlFAPsoFv-iL2v or TRACKOPDCD1 FAPSOFV-IL2V T cells. Mice were monitored for tumor growth post-CAR-T injection for 3 weeks (Figure 4A). Inducible expression of FAPscFv-IL2v in TRACMesoCAR T cells significantly decreased tumor growth, relative to TRACMBSOCAR T cells alone (Figure 4B). Additionally, the PDCD1 FAPscFv-iL2v insertion had no effect on tumor progression in the absence of TRACMSSOCAR, indicative of the stringency of induction (Figure 4B).

Overall, our results demonstrate a clear advantage of combining FAPscFv-IL2v immune-stimulation with anti -tumor CAR activity for attaining maximal tumor regression.

Example 4. Generation of CAR-T cells having a constitutive expression of a MesoCAR by lentiviral transduction and an inducible expression of FAPscFv-IL2v by AAV-mediated targeted integration

T cells were electroporated with TALEN to knockout TRAC and PDCD1 genes, transduced with lentivirus to constitutively express a CAR directed against Mesothelin protein and with the AAV for targeted integration of FAPscFv-IL2v at PDCD1 locus.

To express a Meso-CAR on the surface of primary T cells, cryopreserved PBMC were thawed at 37°C, washed and re-suspended in OpTmizer medium supplemented with AB human serum (5%) for overnight incubation at 37°C in 5% CO2 incubator. Cells were then activated with Transact in OpTmizer medium supplemented with AB human serum (5%) and recombinant human interleukin-2 (rhIL-2, 350 lU/ml) in a CO2 incubator (culture medium). Same day as activation, T cells were transduced with lentiviral particle containing anti-Mesothelin CAR coding sequence (SEQ ID NO: 100) expressed under the control of an EFl A promoter at an MOI of 10.

Four days after transduction, Meso-CAR-T cells were electroporated with 5 pg of each TALEN® arm mRNAs specific for TRAC (SEQ ID NO: 66 and SEQ ID NO: 67) or PDCD1 (SEQ ID NO: 64 and SEQ ID NO: 65). Transfection was performed using Pulse Agile technology by applying two 0.1 mS pulses at 800V followed by four 0.2 mS pulses at 130 V in 0.4 cm gap cuvettes in Cytoporation buffer T (BTX Harvard Apparatus, Holliston, Massachusetts). The electroporated cells were then immediately transferred into prewarmed Optmizer serum-free media and incubated at 37°C for 15 min. The cells were then concentrated and incubated in the presence of PDCDl-FAPscFv-IL2v AAV particles (MOI = 1.1E5 vg/cells), comprising the donor constructs depicted in Figure 2C. After 2 h of culture at 30°C, OpTmizer media supplemented by 10% AB serum and IL-2 was added to the cell suspension, and the mix was incubated for 16 h under the same culture conditions. Cells were subsequently cultivated at 37°C in the presence of 5% CO2.

These cells were analysed for TRAC knockout and Meso-CAR expression by flow cytometry. More than 90% of TRAC knockout could be achieved (Figure 5A) and more than 30% of the edited T-cells expressed Meso-CAR (Figure 5B). Additionally, FAPscFv- IL2v integration at PDCD1 locus was assessed using digital droplet PCR (ddPCR) and expression and secretion of FAPscFv-IL2v upon MesoCAR activation was determined by incubating cells on Mesothelin protein (2 ug/ml; Lake Pharma) coated 24-well plates for 48 hours. Secreted FAPscFv-IL2v protein in the cell culture supernatants was detected using a His tag ELISA detection kit (Genscript, Catalog no. L00436). FAPscFv-IL2v expression matrix was integrated at the PDCD1 locus at an allelic frequency of approximately 8% (Figure 5C) and FAPscFv-IL2v protein was detected at a concentrations of 3-4 ng/mL only in the rLv-MesoCAR;TRACKoPDCDl FAPscFv-IL2v cell supernatant (Figure 5D).

Example 5. Assessment of FAPscFv-IL2v binding to FAP positive tumor cells To validate the binding and activity of FAPscFv-IL2v immunocytokine, we generated a human FAP-expressing cell line by transducing mesothelioma tumor cells NCI-H226 (ATCC, CRL5826) expressing GFP and Luciferase reporter genes with lentiviral particles containing human FAP gene expressed under the control of CMV promoter. NCI-H226-FAP cell line expressed human FAP in upwards of 40% cell population (Figure 6 A) as assessed by flow cytometry, recapitulating the heterogeneity of FAP expression in solid tumors. This cell line was further used to determine FAP -binding ability of FAPscFv-IL2v. (His)e-tagged recombinant FAPscFv-IL2v protein synthesized by Lake Pharma was incubated at different concentrations with NCLH226-FAP or control NCLH226 cells. FAPscFv-IL2v bound cellular fraction was then detected using APC fluor conjugated anti-His antibody and subsequent analysis by Flow Cytometry.

As depicted in Figure 6B, FAPscFv-IL2v binds to human FAP-expressing NCI- 11226 cells in a dose dependent manner, with saturating concentration being reached at 100 ng/ml. This result validates that the recombinant FAPscFv-IL2v fusion protein can successfully bind to human FAP protein in a specific manner.

Example 6. Anti-tumor cytotoxic activity of CAR-T cells having a constitutive expression of a Meso-CAR and an inducible expression of FAPscFv-IL2v

This example demonstrates that combining a constitutive expression of a MesoCAR with an inducible expression of immunocytokine FAPscFv-IL2v enhances the specific killing of tumor cells. Engineered T-cells produced in Example 5 were used.

Serial Killing assay procedure

To assess the antitumor activity of engineered T cells, a serial killing assay was performed as outlined in Figure 7A. Adherent tumor cell lines NCLH226 or NCLH226- FAP expressing reporter genes GFP and Luciferase were plated at a density of 5 x 10 ⁴ cells per well in a total volume of 0.5 ml ofDMEM media supplemented with 10% FBS (Day 0). 24 hours later TRACKOPDCDIKO, TRACKOPDCDI FAPSCFV-IL2V, rLv-MesoCAR; TRACKOPDCDI KO or rLv-MesoCAR; TRACKOPDCDI FAPSCFV-IL2V engineered T-cells were added to the tumor cells at an effector CAR ⁺ T-cell: Tumor cell ratio of 2:1. The mixture was incubated for 24 hours in an Incucyte ZOOM Live-Cell analyser which measured live tumor cell GFP signal every 2 hours. Subsequently, suspension T cells were collected from the well supernatant, spun down, resuspended in 0.1 ml DM1M+1O%FBS media and added to a fresh well of tumor cells plated as described above. Simultaneously, the first 24h T cell cytotoxicity was determined by measuring luciferase activity of surviving tumor cells on Day 0 plate. This protocol was repeated up to a period of 5 days.

Cytolytic activity of rLv-MesoCAR; TRACKOPDCD 1 FAP _S CFV-IL2V T-cells against NCI-H226 and NCI-H226-FAP tumor cells

Highest anti-tumor cytotoxicity upon repeated challenge of engineered T -cells with tumor cells was observed for the rLv-MesoCAR; TRACKOPDCD 1FAP _SC FV-IL2V T-cells, which secreted the FAPscFv-IL2v immunocytokine upon tumor cell exposure (Figure 7B). Higher anti-tumor cytotoxicity of rLv-MesoCAR; TRACKOPDCD 1FAP _SC FV-IL2V T-cells was observed as early as 24 hours post tumor cell dosing and persisted throughout the course of the assay, relative to rLv-MesoCAR; TRACKOPDCD IKO T cells, which in contrast displayed lower cytotoxicity and eventual sub-optimal tumor cell clearance.

Furthermore, anti-tumor cytotoxicity of rLv-MesoCAR; TRACKOPDCD I FAPSOFV- IL2V was more enhanced when the target NCI-H266 expressed human FAP protein (NCI- H226-FAP), demonstrating an advantage of FAP -anchoring for mediating FAPscFv-IL2v immune stimulation (Figure 7B).

Since maximum cytotoxic activity was recorded during the 48h-72h period, we analysed the killing kinetics of the engineered T cells during this period by assessing the time course of GFP signal changes, as measured by Incucyte ZOOM. As depicted in Figures 7C, 7D FAPscFv-IL2v-expressing rLv-MesoCAR; TRACKOPDCDI FAPscFv-IL2v T cells elicited a faster tumor cell clearance than control rLv-MesoCAR; TRACKOPCDCIKO T cells, particularly against the NCI-H226-FAP tumor cells (Figure 7D). This was further validated by increased and persistent IFNy secretion by rLv-MesoCAR; TRACKOPDCDI FAPSCFV-IL2V T cells during the course of the assay, as determined by ELISA (Figure 7E).

Overall, our results illustrate a clear functional advantage of FAPscFv-IL2v secretion for boosting anti -tumor cytotoxicity and persistent activity of MesoCAR T-cells, relative to MesoCAR T-cell alone especially when FAP is expressed in the microenvironment.

Example 7. Safety measurement in vivo

To demonstrate increased anti -tumor activity with simultaneous decrease in systemic toxicity of this strategy relative to IL-2 cytokine therapy in vivo, 8 weeks old, female NSG mice are orthotopically implanted with 3 x 10 ⁶ human triple-negative breast cancer cell line HCC70-NanoLuc-GFP mixed with 3 x 10 ⁶ human triple-negative breast tumor derived cancer-associated fibroblasts in the left inguinal mammary fat pad. 21 days post tumor implantation, tumor-bearing mice are intravenously (TV.) injected with 8 x 10 ⁶ CAR ⁺ rLv-MesoCAR; TRACKOPDCDIKO or rLv-MesoCAR; TRACKOPDCDI FAPscFv-IL2v engineered T-cells. 8 x 10 ⁶ TRACKOPDCDIKO or TRACKOPDCDI FAP _SC FV-IL2V T cells are injected in two additional cohorts as controls. For systemic toxicity comparison, one tumor-bearing mice cohort is I.V. injected with 8 x 10 ⁶ CAR ⁺ rLv-MesoCAR; TRACKOPDCDI KO T cells and is dosed with recombinant human IL-2 0.4 mg/kg, c|d^ 3 every 9 days for 3 cycles, via intraperitoneal injection, i.p.). Mice weight is monitored closely through the course of the study. Tumor volumes are measured once a week and 40 days post treatment initiation, animals are euthanized, lungs and liver are harvested and analysed for vascular leak syndrome (VLS) by Evans blue dye staining.

Recombinant IL-2 dosing boosts CAR-T activity, but also results in systemic toxicity, as indicated by rapid weight loss and VLS in peripheral organs. On the other hand, rLv-MesoCAR; TRACKOPDCDI FAPSCFV-IL2V boosts tumor clearance without inducing systemic toxicity, owing to the two levels of control programmed in the system: (1) tumorsite specific production of FAPscFv-IL2v, and (2) FAP anchoring of FAPscFv-IL2v which prevents its systemic accumulation.

Example 8: Identification of some promoters inducible upon CAR-T cells activation

Anti-CSl-CART cells were produced using an 18-day process as briefly described below.

Human PBMCs were thawed and activated using TransAct beads. 3 days later, the cells were electroporated with mRNA encoding TRAC- (SEQ ID NO: 66 and SEQ ID NO: 67) and CS1- (SEQ ID NO: 74 and SEQ ID NO: 75) specific TALE-Nucleases. 2 days later, the cells were transduced with a lentiviral vector driving expression of CS1 -specific second generation CAR (SEQ ID NO: 88), followed by an in vitro expansion phase and magnetic depletion of remaining alpha/betaTCR-positive cells. At the end of the production process, the CAR-T cells were filled into vials and stored frozen.

A fraction of CS1 -CAR-T cells were thawed and CAR+ T cells were sorted by flow- activated cell sorting (FACS) using CAR-specific reagent (“unactivated cell sample”).

In parallel, another fraction of CS1 -CAR-T cells were thawed and activated using platebound CS1 recombinant protein (SEQ ID NO: 89). 24 h after activation, CAR+ T cells were FACS-sorted (“activated cell sample”).

Unactivated and activated samples from 2 independent donors were analyzed by RNA- seq.

To identify activation induced genes, genes were selected that fulfill the following criteria:

- maximum expression level at 0 h is lower than 100 TPM (transcripts per kilobase million);

- minimum expression level at 24 h is greater than 50 TPM; and

- fold change between average expression at 0 h and average expression at 24 h is greater than 5.

These criteria led to the identification of 159 genes (represented in Figure 8). From this list, based on literature, we identified the ones that adversely affect T cell proliferation, tumor infiltration or function. Some of those are presented in Table 7.

Table 7. Examples of genes induced upon T-cell activation