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Title:
METHODS OF PREPARING POPULATIONS OF CELLS AND RETROVIRAL REAGENTS FOR ADOPTIVE CELL IMMUNOTHERAPY
Document Type and Number:
WIPO Patent Application WO/2019/173441
Kind Code:
A1
Abstract:
Disclosed are methods of preparing replication incompetent viruses comprising a vector encoding a T cell receptor (TCR), or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation. Also disclosed are related methods of preparing a population of cells which express the TCR, or antigen-binding portion thereof, isolated or purified populations of cells prepared by the methods, related pharmaceutical compositions, and methods of treating or preventing cancer in a mammal.

Inventors:
FELDMAN, Steven, A. (196 Duane Street, Redwood City, California, 94062, US)
ROSENBERG, Steven, A. (10104 Iron Gate Road, Potomac, Maryland, 20854, US)
Application Number:
US2019/020903
Publication Date:
September 12, 2019
Filing Date:
March 06, 2019
Export Citation:
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Assignee:
THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES (Office of Technology Transfer, National Institutes of Health6011 Executive Boulevard, Suite 325,MSC 766, Bethesda Maryland, 20892-7660, US)
International Classes:
A61K35/17; A61P35/00; C07K14/725; C07K16/30; C12N5/078; C12N15/86
Domestic Patent References:
WO2017192924A12017-11-09
Foreign References:
US20170224800A12017-08-10
US8034334B22011-10-11
US8383099B22013-02-26
US20120244133A12012-09-27
Other References:
ZINAL S. CHHEDA ET AL: "Novel and shared neoantigen derived from histone 3 variant H3.3K27M mutation for glioma T cell therapy", THE JOURNAL OF EXPERIMENTAL MEDICINE, vol. 215, no. 1, 4 December 2017 (2017-12-04), US, pages 141 - 157, XP055585208, ISSN: 0022-1007, DOI: 10.1084/jem.20171046
TAIGO KATO ET AL: "Effective screening of T cells recognizing neoantigens and construction of T-cell receptor-engineered T cells", ONCOTARGET, vol. 9, no. 13, 16 February 2018 (2018-02-16), pages 11009 - 11019, XP055585052, DOI: 10.18632/oncotarget.24232
X WANG ET AL: "Manufacture of tumor- and virus-specific T lymphocytes for adoptive cell therapies", CANCER GENE THERAPY, vol. 22, no. 2, February 2015 (2015-02-01), GB, pages 85 - 94, XP055569768, ISSN: 0929-1903, DOI: 10.1038/cgt.2014.81
ANONYMOUS: "Administration of Autologous T-Cells Genetically Engineered to Express T-Cell Receptors Reactive Against Mutated Neoantigens in People With Metastatic Cancer - Tabular View - ClinicalTrials.gov", 29 January 2018 (2018-01-29), XP055585262, Retrieved from the Internet [retrieved on 20190503]
ZHANG ET AL., J. GENET. GENOMICS, vol. 38, no. 3, 2011, pages 95 - 109
VOELKERDING ET AL., CLINICAL CHEMISTRY, vol. 55, 2009, pages 641 - 658
RONAGHI ET AL., SCIENCE, vol. 281, no. 5375, 1998, pages 363 - 365
"Methods in Molecular Biology", 2010, HUMAN PRESS, article "Antigen Processing and Presentation Protocols"
TURCOTTE ET AL., CLIN. CANCER RES., vol. 20, no. 2, 2013, pages 331 - 43
GROS ET AL., J. CLIN. INVEST., vol. 124, no. 5, 2014, pages 2246 - 59
DUDLEY ET AL., J. IMMUNOTHER., vol. 26, 2003, pages 332 - 42
RIDDELL ET AL., J. IMMUNOL. METHODS, vol. 128, 1990, pages 189 - 201
"Molecular Cloning: A Laboratory Manual", 2012, COLD SPRING HARBOR LABORATORY PRESS
GHANI ET AL., GENE THER., vol. 14, no. 24, 2007, pages 1705 - 11
Attorney, Agent or Firm:
LAWLEY, Stephanie M. et al. (Leydig, Voit & MayerTwo Prudential Plaza, Suite 4900,180 North Stetson Avenu, Chicago Illinois, 60601, US)
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Claims:
CLAIM(S):

1. A method of preparing and testing replication incompetent viruses comprising a vector encoding a T cell receptor (TCR), or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation, the method comprising:

identifying one or more genes in the nucleic acid of a cancer cell of a patient, each gene containing a cancer-specific mutation that encodes a mutated amino acid sequence; inducing autologous antigen presenting cells (APCs) of the patient to present the mutated amino acid sequence;

co-culturing autologous T cells of the patient with the autologous APCs that present the mutated amino acid sequence;

selecting the autologous T cells that (a) were co-cultured with the autologous APCs that present the mutated amino acid sequence and (b) have antigenic specificity for the mutated amino acid sequence presented in the context of a major histocompatability complex (MHC) molecule expressed by the patient;

isolating a nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, from the selected autologous T cells, wherein the TCR, or the antigen-binding portion thereof, has antigenic specificity for the mutated amino acid sequence encoded by the cancer-specific mutation;

inserting the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, into a viral vector;

transfecting packaging cell line 293 GP with the viral vector and a nucleotide sequence that encodes a viral envelope protein;

culturing the transfected cell line 293GP under conditions sufficient to generate a retroviral supernatant comprising replication incompetent viruses, wherein the replication incompetent viruses comprise a vector comprising the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof; and

testing one or both of (i) the replication incompetent viruses and (ii) the transfected cell line 293GP for the presence of one or more adventitious agents.

2. The method according to claim 1, comprising testing both of (i) the replication incompetent viruses and (ii) the transfected cell line 293 GP for the presence of one or more adventitious agents.

3. The method according to claim 1 or 2, further comprising testing one or both of (i) the replication incompetent viruses and (ii) the transfected cell line 293 GP for the presence of one or more of sterility, endotoxin and replication competent retroviruses (RCR).

4. The method according to any one of claims 1-3, wherein the replication incompetent viruses are gammaretroviruses.

5. The method according to any one of claims 1-4, wherein the viral vector is a gammaretroviral vector.

6. The method according to any one of claims 1-4, wherein the viral vector is a pMSGVl vector, a pUMVC vector, a pCL-Eco vector, a pCMV-VSV-G vector, a pMD2.G vector, a pCI-VSVG vector, a pHEF-VSVG vector, a pCAG-Eco vector, or a pCAG-VSVG vector.

7. The method according to any one of claims 1-6, wherein the viral envelope protein is an RD114 envelope protein, a Gibbon ape leukemia virus (GALV) envelope protein, an amphotropic envelope protein, a xenotropic envelope protein, an ectotropic envelope protein, or a vesicular stomatitis virus envelope G protein (VSV-G).

8. A method of preparing a population of cells which express a TCR, or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation, the method comprising:

preparing replication incompetent viruses according to the method of any one of claims 1-7; contacting PBMC of the patient with the replication incompetent viruses under conditions sufficient to transduce the PBMC with the vector comprising the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof; and expressing the TCR, or the antigen-binding portion thereof, by the PBMC, thereby producing the population of cells which express the TCR, or the antigen-binding portion thereof, having antigenic specificity for the mutated amino acid sequence encoded by the cancer-specific mutation.

9. The method according to claim 8, wherein the method produces a population of cells, wherein about 80% to about 90% of the cells in the population produced by the method express the TCR, or the antigen-binding portion thereof.

10. The method according to claim 8 or 9, further comprising testing the population of cells produced by the method for the presence of one or more adventitious agents.

11. The method according to any one of claims 8-10, further comprising testing the population of cells produced by the method for the presence of one or more of sterility, endotoxin and replication competent retroviruses (RCR).

12. An isolated or purified population of cells prepared according to the method of any one of claims 8-11.

13. A pharmaceutical composition comprising the isolated or purified population of cells according to claim 12 and a pharmaceutically acceptable carrier.

14. A population of cells which express a TCR, or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer- specific mutation, which have been prepared by the method according to any one of claims 8- 11, for use in treating or preventing cancer in a mammal. .

Description:
METHODS OF PREPARING POPULATIONS OF CELLS AND RETROVIRAL REAGENTS FOR ADOPTIVE CELL IMMUNOTHERAPY

CROSS-REFERENCE TO RELATED APPLICATION

[0001] This patent application claims the benefit of U.S. Provisional Patent Application No. 62/639,272, filed March 6, 2018, which is incorporated by reference in its entirety herein.

STATEMENT REGARDING

FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

[0002] This invention was made with Government support under project numbers ZLABCO 10985 and ZICBC010989 by the National Institutes of Health, National Cancer Institute. The Government has certain rights in this invention.

BACKGROUND OF THE INVENTION

[0003] Adoptive cell therapy (ACT) using cells that have been genetically engineered to express an anti-cancer antigen T cell receptor (TCR) can produce positive clinical responses in some cancer patients. Nevertheless, obstacles to the successful use of TCR-engineered cells for the widespread treatment of cancer and other diseases remain. For example, the efficiency of the transfer of an exogenous TCR into host cells, e.g., peripheral blood lymphocytes (PBL) may be low. Accordingly, there is a need for improved methods of preparing populations of cells and reagents for adoptive cell therapies.

BRIEF SUMMARY OF THE INVENTION

[0004] An embodiment of the invention provides a method of preparing and testing replication incompetent viruses comprising a vector encoding a T cell receptor (TCR), or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation, the method comprising: identifying one or more genes in the nucleic acid of a cancer cell of a patient, each gene containing a cancer- specific mutation that encodes a mutated amino acid sequence; inducing autologous antigen presenting cells (APCs) of the patient to present the mutated amino acid sequence; co culturing autologous T cells of the patient with the autologous APCs that present the mutated amino acid sequence; selecting the autologous T cells that (a) were co-cultured with the autologous APCs that present the mutated amino acid sequence and (b) have antigenic specificity for the mutated amino acid sequence presented in the context of a major histocompatability complex (MHC) molecule expressed by the patient; isolating a nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, from the selected autologous T cells, wherein the TCR, or the antigen-binding portion thereof, has antigenic specificity for the mutated amino acid sequence encoded by the cancer-specific mutation; inserting the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, into a viral vector; transfecting packaging cell line 293 GP with the viral vector and a nucleotide sequence that encodes a viral envelope protein; culturing the transfected cell line 293GP under conditions sufficient to generate a retroviral supernatant comprising replication incompetent viruses, wherein the replication incompetent viruses comprise a vector comprising the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof; and testing one or both of (i) the replication incompetent viruses and (ii) the transfected cell line 293GP for the presence of one or more adventitious agents.

[0005] Another embodiment of the invention provides a method of preparing a population of cells which express a TCR, or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation, the method comprising: preparing replication incompetent viruses according to any of the methods described herein; obtaining peripheral blood mononuclear cells (PBMC) from the patient; contacting the PBMC with the replication incompetent viruses under conditions sufficient to transduce the PBMC with the vector comprising the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof; and expressing the TCR, or the antigen-binding portion thereof, by the PBMC, thereby producing the population of cells which express the TCR, or the antigen-binding portion thereof, having antigenic specificity for the mutated amino acid sequence encoded by the cancer-specific mutation.

[0006] Further embodiments of the invention provide isolated or purified population of cells prepared according to any of the inventive methods, pharmaceutical compositions comprising the same, and related methods of treating or preventing cancer.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S)

[0007] Figure l is a schematic illustrating a method of preparing a population of cells which express a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation (neoantigen) according to an embodiment of the invention.

[0008] Figure 2A presents FACS plots showing the expression of neoantigen-reactive TCRs with a murine constant region (mTCRb) and CD8 by PBMC. The neoantigen-reactive TCRs recognized mutated antigen H3F3B (Vbl6, TCR1) or mutated SKIV2L (Vb20, TCR2). The numbers in the plots are the percentages of cells having each phenotype:

mTCRb+/CD8+, mTCRb+/CD8-, mTCRb-/CD8+, and mTCRb-/CD8-. Untransduced (UT) PBMC served as a negative control.

[0009] Figure 2B is a graph showing the percentage of CD8+ cells transduced with neoantigen-specific TCR Vbl6 or Vb20 which upregulated 4-1BB expression following co culture with autologous APCs pulsed with either wildtype (wt) or mutated (mut) peptide for a given neoantigen (H3F3B or SKIV2L). PBMC transduced with an empty vector served as a negative control.

[0010] Figure 2C is a graph showing the percentage of cells transduced with neoantigen- specific TCR Vbl6 or Vb20 which upregulated IFN-g release (pg/mL) following co-culture with autologous APCs pulsed with either wildtype (wt) or mutated (mut) peptide for a given neoantigen (H3F3B or SKIV2L).

[0011] Figure 3 A is a graph showing the concentration (ng/mL) of residual TCR 1

(triangles) and TCR 2 (squares) vector DNA measured by qPCR after transfection of 293 GP cells and with or without treatment with BENZONASE endonuclease.

[0012] Figure 3B is a graph showing the concentration (ng/mL) of residual

BENZONASE endonuclease measured after BENZONASE endonuclease treatment, after transduction of PBMC with the TCR vector, and after a post-transduction wash during expansion of the numbers of transduced PBMC. 293GP cells were treated with 50U/mL BENZONASE endonuclease at room temperature (RT) (squares) or 37° C (triangles). 293 GP cells treated with no BENZONASE endonuclease served as a negative control (circles).

[0013] Figure 3C is a graph showing the number of copies of RD114 DNA per 0.2 pg of total genomic DNA measured by qPCR at the indicated number of days post-transduction of PBMC. PBMC were transduced with TCR1 without (open circles) or with 50 U/mL

BENZONASE endonuclease treatment at RT (diamonds) or 37° C (▼). PBMC were transduced with TCR2 without (A) or with 50 U/mL BENZONASE endonuclease treatment at RT (closed squares) or 37° C (closed circles). Untransduced PBMC (open squares) served as a negative control. [0014] Figures 4A-4C are graphs showing the amount of IFNy secreted by cells from Patient (Pt) D (Fig. 4A), Pt H (Fig. 4B), or Pt R (Fig. 4C) which were untransduced (light grey bars) or transduced with nb22 TCR following co-culture with B cells pulsed with WT ERBB2IP peptide or mutated ERBB2IP. Controls included T cells cultured alone (no target) and co-cultures with (i) OKT3 antibody and (ii) B cells that have not been pulsed with mutated or wild type peptide. The supernatant used to transduce the cells was treated with 0 (black bars), 25 (checkered bars), or 50 (dark grey bars) U/mL BENZONASE endonuclease.

[0015] Figures 4D-4F are graphs showing the amount of IFNy secreted by cells from Pt D (Fig. 4D), Pt H (Fig. 4E), or Pt R (Fig. 4F) which were untransduced (light grey bars) or transduced with nb5.2 a 26.1 TCR following co-culture with B cells pulsed with WT

ERBB2IP peptide or mutated ERBB2IP. Controls included T cells cultured alone (no target) and co-cultures with (i) OKT3 antibody and (ii) B cells that have not been pulsed with mutated or wild type peptide. The supernatant used to transduce the cells was treated with 0 (black bars), 25 (checkered bars), or 50 (dark grey bars) U/mL BENZONASE endonuclease.

[0016] Figures 4G-4I are graphs showing the amount of IFNy secreted by cells from Pt D (Fig. 4G), Pt H (Fig. 4H), or Pt R (Fig. 41) which were untransduced (light grey bars) or transduced with nb5.2 a 30 TCR following co-culture with B cells pulsed with WT ERBB2IP peptide or mutated ERBB2IP. Controls included T cells cultured alone (no target) and co- cultures with (i) OKT3 antibody and (ii) B cells that have not been pulsed with mutated or wild type peptide. The supernatant used to transduce the cells was treated with 0 (black bars), 25 (checkered bars), or 50 (dark grey bars) U/mL BENZONASE endonuclease.

[0017] Figures 5A-5B are graphs showing the amount of free DNA (ng/mL) measured in the supernatant at the indicated time points during transfection with the nb22 (circles) or nb5.2 a 30 (squares) TCR, including after treatment with 25 (Fig. 5A) or 50 U/mL (Fig. 5B) BENZONASE endonuclease.

[0018] Figures 6A-6B are graphs showing the amount of free DNA (ng/mL) measured in the supernatant at the indicated time points during transfection with the nb22 (circles) or nb5.2 a 30 (squares) TCR, including after treatment with 50 U/mL BENZONASE

endonuclease for 1 hour at 37° C (Fig. 6A) or room temperature (RT) (Fig. 6B).

[0019] Figure 7 is a graph showing the concentration of BENZONASE endonuclease (ng/mL) in transduced cells at the indicated time points during transduction. TCR-transduced cells were prepared using retroviral supernatant prepared with 0 (circles), 25 (squares), or 50 (triangles) U/mL BENZONASE endonuclease. [0020] Figure 8 presents FACS plots showing the expression of neoantigen-reactive TCRs from patient 4217 based on detection of the murine constant region (mTCRP) after transduction into healthy donor PBMC. The neoantigen-reactive TCRs recognized mutated antigen MAP3K2 S153F (4217 MAP3K2 S153F TCR1), UELVD F191L

(4217 UELVD F 191L TCR2), or UEVLD F 191L (4217 UEVLD F 191L TCR3). The numbers in the plots are the percentages of cells having each phenotype: mTCRp+/CD8+ (Q6), mTCRp+/CD8- (Q5), mTCRp-/CD8+ (Q7), and mTCRp-/CD8- (Q8).

[0021] Figure 9 presents FACS plots showing the expression of neoantigen-reactive TCRs from patient 4275 based on detection of the murine constant region (mTCRP) after transduction into healthy donor PBMC. The neoantigen-reactive TCRs recognized mutated antigen GPATCH R954H (4275 GPATCH R954H TCR1), WLS R445G (4275_WLS_ R445G TCR2), or WLS R445G (4275 WLS R445G TCR3). The numbers in the plots are the percentages of cells having each phenotype: mTCRp+/CD8+ (Q6), mTCRp+/CD8- (Q5), mTCRp-/CD8+ (Q7), and mTCRp-/CD8- (Q8).

[0022] Figure 10 presents FACS plots showing the expression of neoantigen-reactive TCRs from patient 4271 based on detection of the murine constant region (mTCRP) after transduction into healthy donor PBMC. The neoantigen-reactive TCRs recognized mutated antigen UPS47 F1156L (4271 UPS47 F1156L TCR2), CHD2 K1351R

(4271 CHD2 K 1351 R TCR4), or WDFY1 E44K (4271 _WDF Y 1 E44K T CR6) . The numbers in the plots are the percentages of cells having each phenotype: mTCRp+/CD8+ (Q6), mTCRp+/CD8- (Q5), mTCRp-/CD8+ (Q7), and mTCRp-/CD8- (Q8).

[0023] Figure 11 presents FACS plots showing the expression of neoantigen-reactive TCRs from patient 4251 based on detection of the murine constant region (mTCRP) after transduction into healthy donor PBMC. The neoantigen-reactive TCRs recognized mutated antigen RNF213 P4766H (425l_RNF2l3_P4766H_TCR2), FMOD S332N

(4251 FMOD S332N TCR6), or TRAFD1 Rl 1L (4251 TRAFD1 R11L TCR8). The numbers in the plots are the percentages of cells having each phenotype: mTCRp+/CD8+ (Q6), mTCRp+/CD8- (Q5), mTCRp-/CD8+ (Q7), and mTCRp-/CD8- (Q8).

[0024] Figure 12 presents a FACS plot showing the expression of a neoantigen-reactive

TCR from patient 4285 based on detection of the murine constant region (mTCRP) after transduction into healthy donor PBMC. The neoantigen-reactive TCR recognized mutated antigen TP53 R175H (4285 TP53 R175H TCR1). The numbers in the plot are the percentages of cells having each phenotype: mTCRp+/CD8+ (Q6), mTCRp+/CD8- (Q5), mTCRp-/CD8+ (Q7), and mTCRp-/CD8- (Q8).

[0025] Figure 13 is a graph showing the concentration (pg/mL) of IFN-g produced following co-culture of healthy donor T cells expressing TCR (post-transduction) with autologous patient B cells pulsed with 10 pg of either mutant or wild type peptide.

DETAILED DESCRIPTION OF THE INVENTION

[0026] An embodiment of the invention provides a method of preparing replication incompetent viruses comprising a vector encoding a TCR, or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer- specific mutation. The invention may provide any one or more of a variety of advantages.

For example, the invention may provide methods of preparing reagents (e.g., viruses) useful for preparing cells which express a TCR, or antigen-binding portions thereof, having antigenic specificity for mutated amino acid sequences encoded by cancer-specific mutations that are unique to the patient (also referred to as“neoantigen(s)”). The inventive methods may produce reagents (e.g., viruses) and populations of cells in a manner which complies with Good Manufacturing Practices (GMP). For example, the reagents (e.g., viruses and packaging cells) may be biosafety tested to industry standards including testing for sterility, residual DNA vector, replication competent retrovirus (RCR), mycoplasma, endotoxin, human viruses and other adventitious agents. The 293GP master cell bank may be fully validated. The inventive methods may include testing the reagents for sterility. In some embodiments, inventive methods which comprise viral transduction of a population of PBMC with a vector encoding the TCR, or antigen binding portion thereof, may generate a cell population with a high frequency (e.g., up to about 90%) of cells which express the TCR, or antigen binding portion thereof. The frequency of cells which express the TCR, or antigen binding portion thereof, obtained using the inventive methods which comprise viral transduction may greatly exceed that which can be achieved using methods of selecting mutation-specific tumor infiltrating lymphocytes (TIL), non-viral techniques such as transposons, or gene editing techniques using zinc finger nucleases, TALENs or CRISPR/Cas genome editing technologies, all of which may suffer from low efficiency gene delivery.

[0027] The method may comprise identifying one or more genes in the nucleic acid of a cancer cell of a patient, each gene containing a cancer-specific mutation that encodes a mutated amino acid sequence. The cancer cell may be obtained from any bodily sample derived from a patient which contains or is expected to contain tumor or cancer cells. The bodily sample may be any tissue sample such as blood, a tissue sample obtained from the primary tumor or from tumor metastases, or any other sample containing tumor or cancer cells. The nucleic acid of the cancer cell may be DNA or RNA.

[0028] In order to identify cancer-specific mutations, the method may further comprise sequencing nucleic acid such as DNA or RNA of normal, noncancerous cells and comparing the sequence of the cancer cell with the sequence of the normal, noncancerous cell. The normal, noncancerous cell may be obtained from the patient or a different individual.

[0029] The cancer-specific mutation may be any mutation in any gene which encodes a mutated amino acid sequence (also referred to as a“non-silent mutation”) and which is expressed in a cancer cell but not in a normal, noncancerous cell. Non-limiting examples of cancer-specific mutations that may be identified in the inventive methods include missense, nonsense, insertion, deletion, duplication, frameshift, and repeat expansion mutations. In an embodiment of the invention, the method comprises identifying at least one gene containing a cancer-specific mutation which encodes a mutated amino acid sequence. However, the number of genes containing such a cancer-specific mutation that may be identified using the inventive methods is not limited and may include more than one gene (for example, about 2, about 3, about 4, about 5, about 10, about 11, about 12, about 13, about 14, about 15, about 20, about 25, about 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 150, about 200, about 400, about 600, about 800, about 1000, about 1500, about 2000 or more, or a range defined by any two of the foregoing values). Likewise, in an embodiment of the invention, the method comprises identifying at least one cancer-specific mutation which encodes a mutated amino acid sequence. However, the number of such cancer-specific mutations that may be identified using the inventive methods is not limited and may include more than one cancer-specific mutation (for example, about 2, about 3, about 4, about 5, about 10, about 11, about 12, about 13, about 14, about 15, about 20, about 25, about 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 150, about 200, about 400, about 600, about 800, about 1000, about 1500, about 2000 or more, or a range defined by any two of the foregoing values). In an embodiment in which more than one cancer-specific mutation is identified, the cancer-specific mutations may be located in the same gene or in different genes.

[0030] In an embodiment, identifying one or more genes in the nucleic acid of a cancer cell comprises sequencing the whole exome, the whole genome, or the whole transcriptome of the cancer cell. Sequencing may be carried out in any suitable manner known in the art. Examples of sequencing techniques that may be useful in the inventive methods include Next Generation Sequencing (NGS) (also referred to as“massively parallel sequencing

technology”) or Third Generation Sequencing. NGS refers to non-Sanger-based high- throughput DNA sequencing technologies. With NGS, millions or billions of DNA strands may be sequenced in parallel, yielding substantially more throughput and minimizing the need for the fragment-cloning methods that are often used in Sanger sequencing of genomes. In NGS, nucleic acid templates may be randomly read in parallel along the entire genome by breaking the entire genome into small pieces. NGS may, advantageously, provide nucleic acid sequence information of a whole genome, exome, or transcriptome in very short time periods, e.g., within about 1 to about 2 weeks, preferably within about 1 to about 7 days, or most preferably, within less than about 24 hours. Multiple NGS platforms which are commercially available or which are described in the literature can be used in the context of the inventive methods, e.g., those described in Zhang et ah, J Genet. Genomics , 38(3): 95- 109 (2011) and Voelkerding et ah, Clinical Chemistry , 55: 641-658 (2009).

[0031] Non-limiting examples of NGS technologies and platforms include sequencing- by-synthesis (also known as“pyrosequencing”) (as implemented, e.g., using the GS-FLX 454 Genome Sequencer, 454 Life Sciences (Branford, CT), ILLUMINA SOLEXA Genome Analyzer (Illumina Inc., San Diego, CA), or the ILLEIMINA HISEQ 2000 Genome Analyzer (Illumina), or as described in, e.g., Ronaghi et ah, Science , 281(5375): 363-365 (1998)), sequencing-by-ligation (as implemented, e.g., using the SOLID platform (Life Technologies Corporation, Carlsbad, CA) or the POLONATOR G.007 platform (Dover Systems, Salem, NH)), single-molecule sequencing (as implemented, e.g., using the PACBIO RS system (Pacific Biosciences (Menlo Park, CA) or the HELISCOPE platform (Helicos Biosciences (Cambridge, MA)), nano-technology for single-molecule sequencing (as implemented, e.g., using the GRIDON platform of Oxford Nanopore Technologies (Oxford, UK), the hybridization-assisted nano-pore sequencing (HANS) platforms developed by Nabsys (Providence, RI), and the ligase-based DNA sequencing platform with DNA nanoball (DNB) technology referred to as probe-anchor ligation (cPAL)), electron microscopy -based technology for single-molecule sequencing, and ion semiconductor sequencing.

[0032] The method may comprise inducing autologous antigen presenting cells (APCs) of the patient to present the mutated amino acid sequence. The APCs may include any cells which present peptide fragments of proteins in association with major histocompatibility complex (MHC) molecules on their cell surface. The APCs may include, for example, any one or more of macrophages, DCs, langerhans cells, B-lymphocytes, and T-cells. Preferably, the APCs are DCs. By using autologous APCs from the patient, the inventive methods may, advantageously, identify TCRs, and antigen-binding portions thereof, that have antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation that is presented in the context of an MHC molecule expressed by the patient. The MHC molecule can be any MHC molecule expressed by the patient including, but not limited to, MHC Class I, MHC Class II, HLA-A, HLA-B, HLA-C, HLA-DM, HLA-DO, HLA-DP, HLA-DQ, and HLA-DR molecules. The inventive methods may, advantageously, identify mutated amino acid sequences presented in the context of any MHC molecule expressed by the patient without using, for example, epitope prediction algorithms to identify MHC molecules or mutated amino acid sequences, which may be useful only for a select few MHC class I alleles and may be constrained by the limited availability of reagents to select mutation-reactive T cells (e.g., an incomplete set of MHC tetramers). Accordingly, in an embodiment of the invention, the inventive methods advantageously identify mutated amino acid sequences presented in the context of any MHC molecule expressed by the patient and are not limited to any particular MHC molecule. Preferably, the autologous APCs are antigen-negative autologous APCs.

[0033] Inducing autologous APCs of the patient to present the mutated amino acid sequence may be carried out using any suitable method known in the art. In an embodiment of the invention, inducing autologous APCs of the patient to present the mutated amino acid sequence comprises pulsing the autologous APCs with peptides comprising the mutated amino acid sequence or a pool of peptides, each peptide in the pool comprising a different mutated amino acid sequence. Each of the mutated amino acid sequences in the pool may be encoded by a gene containing a cancer specific mutation. In this regard, the autologous APCs may be cultured with a peptide or a pool of peptides comprising the mutated amino acid sequence in a manner such that the APCs internalize the peptide(s) and display the mutated amino acid sequence(s), bound to an MHC molecule, on the cell membrane. In an embodiment in which more than one gene is identified, each gene containing a cancer- specific mutation that encodes a mutated amino acid sequence, the method may comprise pulsing the autologous APCs with a pool of peptides, each peptide in the pool comprising a different mutated amino acid sequence. Methods of pulsing APCs are known in the art and are described in, e.g., Solheim (Ed.), Antigen Processing and Presentation Protocols (Methods in Molecular Biology ), Human Press, (2010). The peptide(s) used to pulse the APCs may include the mutated amino acid(s) encoded by the cancer-specific mutation. The peptide(s) may further comprise any suitable number of contiguous amino acids from the endogenous protein encoded by the identified gene on each of the carboxyl side and the amino side of the mutated amino acid(s). The number of contiguous amino acids from the endogenous protein flanking each side of the mutation is not limited and may be, for example, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, or a range defined by any two of the foregoing values. Preferably, the peptide(s) comprise(s) about 12 contiguous amino acids from the endogenous protein on each side of the mutated amino acid(s).

[0034] In an embodiment of the invention, inducing autologous APCs of the patient to present the mutated amino acid sequence comprises introducing a nucleotide sequence encoding the mutated amino acid sequence into the APCs. The nucleotide sequence is introduced into the APCs so that the APCs express and display the mutated amino acid sequence, bound to an MHC molecule, on the cell membrane. The nucleotide sequence encoding the mutated amino acid may be RNA or DNA. Introducing a nucleotide sequence into APCs may be carried out in any of a variety of different ways known in the art as described in, e.g., Solheim et al. supra. Non-limiting examples of techniques that are useful for introducing a nucleotide sequence into APCs include transformation, transduction, transfection, and electroporation. In an embodiment in which more than one gene is identified, the method may comprise preparing more than one nucleotide sequence, each encoding a mutated amino acid sequence encoded by a different gene, and introducing each nucleotide sequence into a different population of autologous APCs. In this regard, multiple populations of autologous APCs, each population expressing and displaying a different mutated amino acid sequence, may be obtained.

[0035] In an embodiment in which more than one gene is identified, each gene containing a cancer-specific mutation that encodes a mutated amino acid sequence, the method may comprise introducing a nucleotide sequence encoding the more than one gene. In this regard, in an embodiment of the invention, the nucleotide sequence introduced into the autologous APCs is a tandem minigene (TMG) construct, each minigene comprising a different gene, each gene including a cancer-specific mutation that encodes a mutated amino acid sequence. Each minigene may encode one mutation identified by the inventive methods flanked on each side of the mutation by any suitable number of contiguous amino acids from the endogenous protein encoded by the identified gene, as described herein with respect to other aspects of the invention. The number of minigenes in the construct is not limited and may include for example, about 5, about 10, about 11, about 12, about 13, about 14, about 15, about 20, about 25, or more, or a range defined by any two of the foregoing values. The APCs express the mutated amino acid sequences encoded by the TMG construct and display the mutated amino acid sequences, bound to an MHC molecule, on the cell membranes. In an embodiment, the method may comprise preparing more than one TMG construct, each construct encoding a different set of mutated amino acid sequences encoded by different genes, and introducing each TMG construct into a different population of autologous APCs. In this regard, multiple populations of autologous APCs, each population expressing and displaying mutated amino acid sequences encoded by different TMG constructs, may be obtained.

[0036] The method may comprise co-culturing autologous T cells of the patient with the autologous APCs that present the mutated amino acid sequence. The T cells can be obtained from numerous sources in the patient, including but not limited to tumor, blood, bone marrow, lymph node, the thymus, or other tissues or fluids. The T cells can include any type of T cell and can be of any developmental stage, including but not limited to, CD4+/CD8+ double positive T cells, CD4+ helper T cells, e.g., Thl and Th2 cells, CD8+ T cells (e.g., cytotoxic T cells), tumor infiltrating cells (e.g., tumor infiltrating lymphocytes (TIL)), peripheral blood T cells, memory T cells, naive T cells, and the like. The T cells may be CD8+ T cells, CD4+ T cells, or both CD4+ and CD8+ T cells. The method may comprise co-culturing the autologous T cells and autologous APCs so that the T cells encounter the mutated amino acid sequence presented by the APCs in such a manner that the autologous T cells specifically bind to and immunologically recognize a mutated amino acid sequence presented by the APCs. In an embodiment of the invention, the autologous T cells are co- cultured in direct contact with the autologous APCs.

[0037] The method may comprise selecting the autologous T cells that (a) were co- cultured with the autologous APCs that present the mutated amino acid sequence and (b) have antigenic specificity for the mutated amino acid sequence presented in the context of a MHC molecule expressed by the patient. The phrase“antigenic specificity,” as used herein, means that a TCR, or the antigen-binding portion thereof, expressed by the autologous T cells can specifically bind to and immunologically recognize the mutated amino acid sequence encoded by the cancer-specific mutation. The selecting may comprise identifying the T cells that have antigenic specificity for the mutated amino acid sequence and separating them from T cells that do not have antigenic specificity for the mutated amino acid sequence. Selecting the autologous T cells having antigenic specificity for the mutated amino acid sequence may be carried out in any suitable manner. In an embodiment of the invention, the method comprises expanding the numbers of autologous T cells, e.g., by co-culturing with a T cell growth factor, such as interleukin (IL)-2 or IL-15, or as described herein with respect to other aspects of the invention, prior to selecting the autologous T cells. In an embodiment of the invention, the method does not comprise expanding the numbers of autologous T cells with a T cell growth factor, such as IL-2 or IL-15 prior to selecting the autologous T cells.

[0038] For example, upon co-culture of the autologous T cells with the APCs that present the mutated amino acid sequence, T cells having antigenic specificity for the mutated amino acid sequence may express any one or more of a variety of T cell activation markers which may be used to identify those T cells having antigenic specificity for the mutated amino acid sequence. Such T cell activation markers may include, but are not limited to, programmed cell death 1 (PD-l), lymphocyte-activation gene 3 (LAG-3), T cell immunoglobulin and mucin domain 3 (TIM-3), 4-1BB, 0X40, and CD 107a. Accordingly, in an embodiment of the invention, selecting the autologous T cells that have antigenic specificity for the mutated amino acid sequence comprises selecting the T cells that express any one or more of PD-l, LAG-3, TIM-3, 4-1BB, 0X40, and CDl07a. Cells expressing one or more T cell activation markers may be sorted on the basis of expression of the marker using any of a variety of techniques known in the art such as, for example, fluorescence-activated cell sorting (FACS) or magnetic-activated cell sorting (MACS) as described in, e.g., Turcotte et al, Clin. Cancer Res., 20(2): 331-43 (2013) and Gros et al., J Clin. Invest., 124(5): 2246-59 (2014).

[0039] In another embodiment of the invention, selecting the autologous T cells that have antigenic specificity for the mutated amino acid sequence comprises selecting the T cells (i) that secrete a greater amount of one or more cytokines upon co-culture with APCs that present the mutated amino acid sequence as compared to the amount of the one or more cytokines secreted by a negative control or (ii) in which at least twice as many of the numbers of T cells secrete one or more cytokines upon co-culture with APCs that present the mutated amino acid sequence as compared to the numbers of negative control T cells that secrete the one or more cytokines. The one or more cytokines may comprise any cytokine the secretion of which by a T cell is characteristic of T cell activation (e.g., a TCR expressed by the T cells specifically binding to and immunologically recognizing the mutated amino acid sequence). Non-limiting examples of cytokines, the secretion of which is characteristic of T cell activation, include IFN-g, IL-2, and tumor necrosis factor alpha (TNF-a),

granulocyte/monocyte colony stimulating factor (GM-CSF), IL-4, IL-5, IL-9, IL-10, IL-17, and IL-22.

[0040] For example, a TCR, or an antigen-binding portion thereof, or a T cell expressing the TCR, or the antigen-binding portion thereof, may be considered to have“antigenic specificity” for the mutated amino acid sequence if the T cells, or T cells expressing the TCR, or the antigen-binding portion thereof, secrete at least twice as much IFN-g upon co-culture with (a) antigen-negative APCs pulsed with a concentration of a peptide comprising the mutated amino acid sequence (e.g., about 0.05 ng/mL to about 10 pg/mL, e.g., 0.05 ng/mL, 0.1 ng/mL, 0.5 ng/mL, 1 ng/mL, 5 ng/mL, 100 ng/mL, 1 pg/mL, 5 pg/mL, or 10 pg/mL) or (b) APCs into which a nucleotide sequence encoding the mutated amino acid sequence has been introduced as compared to the amount of IFN-g secreted by a negative control. The negative control may be, for example, (i) T cells expressing the TCR, or the antigen-binding portion thereof, co-cultured with (a) antigen-negative APCs pulsed with the same

concentration of an irrelevant peptide (e.g., the wild-type amino acid sequence, or some other peptide with a different sequence from the mutated amino acid sequence) or (b) APCs into which a nucleotide sequence encoding an irrelevant peptide sequence has been introduced, or (ii) untransduced T cells (e.g., derived from PBMC, which do not express the TCR, or antigen binding portion thereof) co-cultured with (a) antigen-negative APCs pulsed with the same concentration of a peptide comprising the mutated amino acid sequence or (b) APCs into which a nucleotide sequence encoding the mutated amino acid sequence has been introduced. A TCR, or an antigen-binding portion thereof, or a T cell expressing the TCR, or the antigen-binding portion thereof, may also have“antigenic specificity” for the mutated amino acid sequence if T cells, or T cells expressing the TCR, or the antigen-binding portion thereof, secrete a greater amount of IFN-g upon co-culture with antigen-negative APCs pulsed with higher concentrations of a peptide comprising the mutated amino acid sequence as compared to a negative control, for example, any of the negative controls described above. IFN-g secretion may be measured by methods known in the art such as, for example, enzyme- linked immunosorbent assay (ELISA).

[0041] Alternatively or additionally, a TCR, or an antigen-binding portion thereof, or a T cell expressing the TCR, or the antigen-binding portion thereof, may be considered to have “antigenic specificity” for the mutated amino acid sequence if at least twice as many of the numbers of T cells, or T cells expressing the TCR, or the antigen-binding portion thereof, secrete IFN-g upon co-culture with (a) antigen-negative APCs pulsed with a concentration of a peptide comprising the mutated amino acid sequence or (b) APCs into which a nucleotide sequence encoding the mutated amino acid sequence has been introduced as compared to the numbers of negative control T cells that secrete IFN-g. The concentration of peptide and the negative control may be as described herein with respect to other aspects of the invention.

The numbers of cells secreting IFN-g may be measured by methods known in the art such as, for example, ELISPOT.

[0042] While T cells having antigenic specificity for the mutated amino acid sequence may both (1) express any one or more T cells activation markers described herein and (2) secrete a greater amount of one or more cytokines as described herein, in an embodiment of the invention, T cells having antigenic specificity for the mutated amino acid sequence may express any one or more T cell activation markers without secreting a greater amount of one or more cytokines or may secrete a greater amount of one or more cytokines without expressing any one or more T cell activation markers.

[0043] In another embodiment of the invention, selecting the autologous T cells that have antigenic specificity for the mutated amino acid sequence comprises selectively growing the autologous T cells that have antigenic specificity for the mutated amino acid sequence. In this regard, the method may comprise co-culturing the autologous T cells with autologous APCs in such a manner as to favor the growth of the T cells that have antigenic specificity for the mutated amino acid sequence over the T cells that do not have antigenic specificity for the mutated amino acid sequence. Accordingly, a population of T cells may be produced that has a higher proportion of T cells that have antigenic specificity for the mutated amino acid sequence as compared to T cells that do not have antigenic specificity for the mutated amino acid sequence.

[0044] In an embodiment of the invention, the method further comprises obtaining multiple fragments of a tumor from the patient, separately co-culturing autologous T cells from each of the multiple fragments with the autologous APCs that present the mutated amino acid sequence as described herein with respect to other aspects of the invention, and separately assessing the T cells from each of the multiple fragments for antigenic specificity for the mutated amino acid sequence, as described herein with respect to other aspects of the invention. [0045] In an embodiment of the invention in which T cells are co-cultured with autologous APCs expressing multiple mutated amino acid sequences (e.g., multiple mutated amino acid sequences encoded by a TMG construct or multiple mutated amino acid sequences in a pool of peptides pulsed onto autologous APCs), selecting the autologous T cells may further comprise separately assessing autologous T cells for antigenic specificity for each of the multiple mutated amino acid sequences. For example, the inventive method may further comprise separately inducing autologous APCs of the patient to present each mutated amino acid sequence encoded by the construct (or included in the pool), as described herein with respect to other aspects of the invention (for example, by providing separate APC populations, each presenting a different mutated amino acid sequence encoded by the construct (or included in the pool)). The method may further comprise separately co- culturing autologous T cells of the patient with the different populations of autologous APCs that present each mutated amino acid sequence, as described herein with respect to other aspects of the invention. The method may further comprise separately selecting the autologous T cells that (a) were co-cultured with the autologous APCs that present the mutated amino acid sequence and (b) have antigenic specificity for the mutated amino acid sequence presented in the context of a MHC molecule expressed by the patient, as described herein with respect to other aspects of the invention. In this regard, the method may comprise determining which mutated amino acid sequence encoded by a TMG construct that encodes multiple mutated amino acid sequences (or included in the pool) are immunologically recognized by the autologous T cells (e.g., by process of elimination).

[0046] The method may further comprise isolating a nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, from the selected autologous T cells, wherein the TCR, or the antigen-binding portion thereof, has antigenic specificity for the mutated amino acid sequence encoded by the cancer-specific mutation. In an embodiment of the invention, prior to isolating the nucleotide sequence that encodes the TCR, or the antigen binding portion thereof, the numbers selected autologous T cells that have antigenic specificity for the mutated amino acid sequence may be expanded. Expansion of the numbers of T cells can be accomplished by any of a number of methods as are known in the art as described in, for example, U.S. Patent 8,034,334; U.S. Patent 8,383,099; U.S. Patent

Application Publication No. 2012/0244133; Dudley et al., J Immunother ., 26:332-42 (2003); and Riddell et al., J. Immunol. Methods , 128: 189-201 (1990). In an embodiment, expansion of the numbers of T cells is carried out by culturing the T cells with OKT3 antibody, IL-2, and feeder PBMC (e.g., irradiated allogeneic PBMC). In another embodiment of the invention, the numbers of selected autologous T cells that have antigenic specificity for the mutated amino acid sequence are not expanded prior to isolating the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof. In an embodiment of the invention, the numbers of cells are expanded in gas-permeable GREX flasks (Wilson Wolf

Manufacturing Company, Saint Paul, MN)

[0047] The“the antigen-binding portion” of the TCR, as used herein, refers to any portion comprising contiguous amino acids of the TCR of which it is a part, provided that the antigen-binding portion specifically binds to the mutated amino acid sequence encoded by the gene identified as described herein with respect to other aspects of the invention. The term “antigen-binding portion” refers to any part or fragment of the TCR of the invention, which part or fragment retains the biological activity of the TCR of which it is a part (the parent TCR). Antigen-binding portions encompass, for example, those parts of a TCR that retain the ability to specifically bind to the mutated amino acid sequence, or detect, treat, or prevent cancer, to a similar extent, the same extent, or to a higher extent, as compared to the parent TCR. In reference to the parent TCR, the functional portion can comprise, for instance, about 10%, about 25%, about 30%, about 50%, about 65%, about 80%, about 90%, about 95%, or more, of the parent TCR.

[0048] The antigen-binding portion can comprise an antigen-binding portion of either or both of the a and b chains of the TCR of the invention, such as a portion comprising one or more of the complementarity determining region (CDR)l, CDR2, and CDR3 of the variable region(s) of the a chain and/or b chain of the TCR of the invention. In an embodiment of the invention, the antigen-binding portion can comprise the amino acid sequence of the CDR1 of the a chain (CDRla), the CDR2 of the a chain (CDR2a), the CDR3 of the a chain (CDR3a), the CDR1 of the b chain (CDR^), the CDR2 of the b chain (CDR2b), the CDR3 of the b chain (CDR3b), or any combination thereof. Preferably, the antigen-binding portion comprises the amino acid sequences of CDRla, CDR2a, and CDR3a; the amino acid sequences of CDR^, OOIT2b, and CDR3b; or the amino acid sequences of all of CDRla, CDR2a, CDR3a, CDR^, CDR2b, and CDR3b of the inventive TCR.

[0049] In an embodiment of the invention, the antigen-binding portion can comprise, for instance, the variable region of the inventive TCR comprising a combination of the CDR regions set forth above. In this regard, the antigen-binding portion can comprise the amino acid sequence of the variable region of the a chain (Va), the amino acid sequence of the variable region of the b chain (nb), or the amino acid sequences of both of the Va and nb of the inventive TCR.

[0050] In an embodiment of the invention, the antigen-binding portion may comprise a combination of a variable region and a constant region. In this regard, the antigen-binding portion can comprise the entire length of the a or b chain, or both of the a and b chains, of the inventive TCR.

[0051] Isolating the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, from the selected autologous T cells may be carried out in any suitable manner known in the art. For example, the method may comprise isolating RNA from the autologous T cells and sequencing the TCR, or the antigen-binding portion thereof, using established molecular cloning techniques and reagents such as, for example, 5’ Rapid Amplification of cDNA Ends (RACE) polymerase chain reaction (PCR) using TCR-a and -b chain constant primers.

[0052] In an embodiment of the invention, the method may comprise inserting the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, into a viral recombinant expression vector using established molecular cloning techniques as described in, e.g., Green et al. (Eds.), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; 4th Ed. (2012). For purposes herein, the term "recombinant expression vector" means a genetically-modified oligonucleotide or polynucleotide construct that permits the expression of an mRNA, protein, polypeptide, or peptide by a host cell, when the construct comprises a nucleotide sequence encoding the mRNA, protein, polypeptide, or peptide, and the vector is contacted with the cell under conditions sufficient to have the mRNA, protein, polypeptide, or peptide expressed within the cell. In an embodiment, the vector is not naturally-occurring as a whole. However, parts of the vector can be naturally- occurring. The recombinant expression vector can comprise any type of nucleotides, including, but not limited to DNA and RNA, which can be single-stranded or double- stranded, synthesized or obtained in part from natural sources, and which can contain natural, non-natural or altered nucleotides. The recombinant expression vector can comprise naturally-occurring, non-naturally-occurring internucleotide linkages, or both types of linkages. Preferably, the non-naturally occurring or altered nucleotides or intemucleotide linkages does not hinder the transcription or replication of the vector.

[0053] The viral recombinant expression vector of the invention can be any suitable viral recombinant expression vector, and can be used to transform or transfect any suitable packaging cell line. In an embodiment of the invention, the viral recombinant expression vector is a retroviral vector. Examples of retroviral vectors include alpharetroviral vectors, betaretroviral vectors, deltaretroviral vectors, epsilonretroviral vectors, gammaretroviral vectors, and lentiviral vectors. In a preferred embodiment, the viral recombinant expression vector is a gammaretroviral vector. Examples of retroviral vectors include, but are not limited to, pMSGVl vector, or a pUMVC vector. In an especially preferred embodiment, the gammaretroviral vector is a pMSGVl vector. In an embodiment, the vector is a transient retroviral vector. The vector may be a self-inactivating vector (SIN) or a non-SIN vector. A SIN vector is a viral vector that contains a non-functional or modified 3' Long Terminal Repeat (LTR) sequence. This sequence may be copied to the 5' end of the vector genome during integration, resulting in the inactivation of promoter activity by both LTRs.

[0054] The nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, which is inserted into the recombinant expression vector may be the naturally occurring (i.e., wild-type) nucleotide sequence which encodes the TCR, or the antigen binding portion thereof, which was isolated from the patient. In another embodiment of the invention, the nucleotide sequence may be modified, for example, to increase expression of the TCR or antigen binding portion thereof. In an embodiment of the invention, the nucleotide sequence encoding the TCR which is inserted into the expression vector encodes the variable region of the TCR obtained from the patient, i.e., a human TCR, and the constant region of a murine TCR such that the TCR is“murinized.”

[0055] The method may further comprise transfecting packaging cell line 293 GP with the viral vector and a nucleotide sequence that encodes a viral envelope protein. Transfecting cells with one or more vectors may be carried out in any suitable manner known in the art. See, for example, Green et al, supra. The 293GP cell line is a human embryonic kidney (HEK) 293 -based retroviral packaging cell line stably expressing the Moloney Murine Leukemia Virus gap-pol and amphotropic envelope viral proteins (Ghani et al., Gene Ther ., 14(24): 1705-11 (2007)). The viral envelope protein may be any envelope protein suitable for preparing replication incompetent viruses. Examples of envelope proteins include, but are not limited to, an RD114 envelope protein (e.g., the feline RD114 envelope protein), a Gibbon ape leukemia virus (GALV) envelope protein, an amphotropic envelope protein (e.g., the amphotropic 4070 envelope protein), a xenotropic envelope protein, an ectotropic envelope protein, or a vesicular stomatitis virus envelope G protein (VSV-G). Preferably, the envelope protein is a RD114 envelope protein. In an embodiment of the invention, the transfection may take place in a closed system.

[0056] In an embodiment of the invention, transfecting the packaging cell line 293 GP comprises transfecting the 293GP cells with about 80 to about 200 pg of the viral vector encoding the TCR, or antigen-binding portion thereof (per TCR). Transfecting the packaging cell line 293GP comprises transfecting the 293GP cells with about 40 to about 100 pg of the nucleotide sequence that encodes a viral envelope protein (per TCR). Preferably, transfecting the packaging cell line 293GP comprises transfecting the 293GP cells with about 114 pg of the viral vector encoding the TCR, or antigen-binding portion thereof, and about 57 pg of the nucleotide sequence that encodes a viral envelope protein (per TCR).

[0057] Transfection may be carried out in a vessel (e.g., dish) of any size. For example, transfection may be carried out in a vessel having a size of from about 78.5 cm 2 to about 6320 cm 2 or greater. The amount of vector used for the transfection may be calculated based on the size of the vessel. In an embodiment of the invention, transfecting the packaging cell line 293GP comprises transfecting the 293GP cells with about 0.050 pg to about 0.200 pg of the viral vector encoding the TCR, or antigen-binding portion thereof, per square cm of vessel and about 0.005 pg to about 0.200 pg of the nucleotide sequence that encodes a viral envelope protein per square cm of vessel. These values can be scaled linearly to

accommodate a vessel of any surface area. For example, transfecting the packaging cell line 293GP comprises transfecting the 293GP cells with about 0.114 pg of the viral vector encoding the TCR, or antigen-binding portion thereof, per square cm of vessel and about 0.057 pg of the nucleotide sequence that encodes a viral envelope protein per square cm of vessel.

[0058] Transfecting the packaging cell line 293 GP may comprise culturing the 293 GP cells in the presence of one or more of the viral vector, the nucleotide sequence that encodes a viral envelope protein, cell medium supplement, and transfection reagent for a period of time and under conditions sufficient to transfect the cells. The transfection may be carried out using any suitable transfection reagent and any suitable technique. Examples of suitable transfection reagents may include, but are not limited to, calcium phosphate precipitates, cationic lipids and liposomes, polyamines, polyethylenimine (PEI), histone proteins, and polylysine complexes. Examples of suitable transfection techniques include, but are not limited to, calcium phosphate precipitation, DEAE-dextran-mediated transfection, lipofection, electroporation and microinjection. For example, transfecting the packaging cell line 293 GP may comprise culturing the 293 GP cells in the presence of the viral vector, the nucleotide sequence that encodes a viral envelope protein, fetal bovine serum (FBS) and LIPOFECTAMINE transfection reagent (Thermo Fisher Scientific, Waltham, MA) for a period of time and under conditions sufficient to transfect the cells. The time period may be, for example, about 24 to about 75 hours, e.g., about 40 to about 50 hours, or, preferably, about 48 hours. In an embodiment of the invention, the cells are transfected in suspension.

[0059] The method may further comprise culturing the transfected cell line 293 GP under conditions sufficient to generate a retroviral supernatant comprising replication incompetent viruses, wherein the replication incompetent viruses comprise a vector comprising the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof. As used herein, the term“replication incompetent viruses” refer to viruses that contain a viral envelope and have the ability to infect cells but are not replication competent. In an embodiment of the invention, the replication incompetent viruses are retroviruses. Examples of retroviruses include alpharetroviruses, betaretroviruses, deltaretroviruses,

epsilonretroviruses, gammaretroviruses, and lentiviruses. In a preferred embodiment, the replication incompetent viruses are gammaretroviruses.

[0060] In an embodiment of the invention, the method comprises harvesting the supernatant comprising replication incompetent viruses. The supernatant may be treated with an endonuclease which degrades free DNA and RNA which may be present in the

supernatant. An example of such an endonuclease is BENZONASE nuclease (Sigma Aldrich, St. Louis, MO). The supernatant may be treated with the endonuclease for any period of time and under such conditions so as to degrade free DNA and RNA. For example, the supernatant may be treated with the endonuclease for about 0.5 to about 3 hours at a temperature of about 37° C. Preferably, the supernatant is treated with the endonuclease for about 1 hour at a temperature of about 37° C. The amount of free DNA and RNA may be reduced or eliminated.

[0061] In an embodiment of the invention, the method comprises filtering the

supernatant. The filtering may be carried out as a step-filtration. The filtration may reduce or eliminate residual 293GP packaging cells and/or aggregates from the supernatant.

[0062] The method may, optionally, further comprise freezing the supernatant, e.g., in aliquots.

[0063] The method may further comprise testing one or both of (i) the replication incompetent viruses and (ii) the transfected cell line 293 GP for the presence of one or more adventitious agents. Adventitious agents may include any of a variety of microorganisms that may have been unintentionally introduced into the manufacturing process of a biological medicinal product. Examples of adventitious agents may include, but are not limited to, bacteria, fungi, mycoplasma, spiroplasma, mycobacteria, rickettsia, protozoa, parasites, transmissible spongiform encephalopathy (TSE) agents, and replication competent viruses (e.g., SV40 and adenovirus El A). In an embodiment, the method may comprise testing both of (i) the replication incompetent viruses and (ii) the transfected cell line 293 GP for the presence of one or more adventitious agents. In an embodiment of the invention, the method further comprises testing one or both of (i) the replication incompetent viruses and (ii) the transfected cell line 293 GP for the presence of one or more of sterility, residual DNA vector, endotoxin and replication competent retroviruses (RCR). A master cell bank (MCB) may also be produced and tested for RCR. By producing a MCB, testing on those cells may not need to performed more than once. Assays for RCR may include the use of antibodies for specific retroviruses and/or qPCR for DNA signatures of retroviruses.

[0064] The replication incompetent viruses prepared by the inventive methods may be useful for preparing cells for adoptive cell therapies. In this regard, an embodiment of the invention provides a method of preparing a population of cells that express a TCR, or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation. The method may comprise preparing replication incompetent viruses according to any of the methods described herein with respect to other aspects of the invention.

[0065] The method may further comprise obtaining PBMC from the patient. In an embodiment of the invention, the PBMC include T cells. The T cells may be any type of T cell, for example, any of those described herein with respect to other aspects of the invention.

[0066] The method may further comprise contacting the PBMC with the replication incompetent viruses under conditions sufficient to transduce the PBMC with the vector comprising the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof. The PBMC may be physically contacted with the replication incompetent viruses such that the replication incompetent viruses introduce the nucleotide sequence that encodes the TCR, or the antigen-binding portion thereof, into the genome of the PBMC. In an embodiment of the invention, the method comprises diluting the viruses about 2-fold prior to contacting the PBMC with the viruses. PBMC may be contacted with the viruses on plates, e.g., plates coated with RETRONECTIN reagent. [0067] Transduction of the PBMC may be carried out in any suitable vessel, e.g., a multiwell plate or bag. In an embodiment of the invention, the transduction of the PBMC is carried out in a closed system. In an embodiment of the invention, about lxlO 6 to about 3xl0 6 PBMC may be transduced in each well of the multi well plate. In an embodiment of the invention, about 5 to about 10 multi -well plates may be employed per TCR. Preferably, about 2xl0 6 PBMC may be transduced in each well of the multiwell plate (for a total of about 9.6xl0 7 cells). In an embodiment of the invention, about 8 multi-well plates may be employed per TCR.

[0068] The method may further comprise expressing the TCR, or the antigen-binding portion thereof, by the PBMC, thereby producing the population of cells which express the TCR, or the antigen-binding portion thereof, having antigenic specificity for the mutated amino acid sequence encoded by the cancer-specific mutation.

[0069] The method may further comprise confirming that transduction of the PBMC was successful. Confirming that transduction of the PBMC may be carried out in a variety of different ways. For example, expression of the TCR (e.g., a murine TCR constant region) may be detected by fluorescence activated cell sorting (FACS).

[0070] In an embodiment of the invention, the method further comprises expanding the numbers of PBMC that express the TCR, or the antigen-binding portion thereof. The numbers of PBMC may be expanded, for example, as described herein with respect to other aspects of the invention. The numbers of cells expressing different TCRs may be expanded separately. In this regard, the inventive methods may, advantageously, generate a large number of T cells having antigenic specificity for the mutated amino acid sequence.

[0071] The inventive methods may, advantageously, transduce the PBMC with the nucleotide sequence that encodes the TCR, or the antigen binding portion thereof, with high efficiency. In an embodiment of the invention, the method produces a population of cells, wherein about 80% to about 100% of the cells in the population produced by the method express the TCR, or the antigen-binding portion thereof. In an embodiment of the invention, about 80% to about 99%, about 80% to about 98%, about 80% to about 97%, about 80% to about 96%, about 80% to about 95%, about 80% to about 94%, about 80% to about 93%, about 80% to about 92%, about 80% to about 91%, about 80% to about 90%, or about 85% to about 95%, or more of the cells in the population produced by the method express the TCR.

[0072] In an embodiment of the invention, the method may further comprise testing the population of cells produced by the method for the presence of one or more adventitious agents. The adventitious agents may be as described herein with respect to other aspects of the invention. In an embodiment of the invention, the method may further comprise testing the population of cells produced by the method for the presence of one or more of sterility, endotoxin, residual endonuclease, e.g., BENZONASE nuclease, and RCR.

[0073] Another embodiment of the invention provides an isolated or purified population of cells prepared according to any of the methods described herein with respect to other aspects of the invention. The population of cells can be a heterogeneous population comprising the PBMC expressing the isolated TCR, or the antigen-binding portion thereof, in addition to at least one other cell, e.g., a host cell (e.g., a PBMC), which does not express the isolated TCR, or the antigen-binding portion thereof, or a cell other than a T cell, e.g., a B cell, a macrophage, a neutrophil, an erythrocyte, a hepatocyte, an endothelial cell, an epithelial cells, a muscle cell, a brain cell, etc. Alternatively, the population of cells can be a substantially homogeneous population, in which the population comprises mainly of PBMC (e.g., consisting essentially of) expressing the isolated TCR, or the antigen-binding portion thereof. The population also can be a clonal population of cells, in which all cells of the population are clones of a single PBMC expressing the isolated TCR, or the antigen-binding portion thereof, such that all cells of the population express the isolated TCR, or the antigen binding portion thereof. In one embodiment of the invention, the population of cells is a clonal population comprising PBMC expressing the isolated TCR, or the antigen-binding portion thereof, as described herein. By introducing the nucleotide sequence encoding the isolated TCR, or the antigen binding portion thereof, into PBMC, the inventive methods may, advantageously, provide a population of cells that comprises a high proportion of PBMC cells that express the isolated TCR and have antigenic specificity for the mutated amino acid sequence. In an embodiment of the invention, about 80% to about 100% of the cells in the population express the TCR, or the antigen-binding portion thereof. In an embodiment of the invention, about 80% to about 99%, about 80% to about 98%, about 80% to about 97%, about 80% to about 96%, about 80% to about 95%, about 80% to about 94%, about 80% to about 93%, about 80% to about 92%, about 80% to about 91%, about 80% to about 90%, or about 85% to about 95%, or more of the cells in the population express the TCR. Without being bound to a particular theory or mechanism, it is believed that populations of cells that comprise a high proportion of PBMC cells that express the isolated TCR and have antigenic specificity for the mutated amino acid sequence have a lower proportion of irrelevant cells that may hinder the function of the PBMC, e.g., the ability of the PBMC to target the destruction of cancer cells and/or treat or prevent cancer.

[0074] The inventive populations of cells can be formulated into a composition, such as a pharmaceutical composition. In this regard, the invention provides a pharmaceutical composition comprising any of the inventive populations of cells described herein and a pharmaceutically acceptable carrier. The inventive pharmaceutical composition can comprise a population of cells in combination with another pharmaceutically active agent(s) or drug(s), such as a chemotherapeutic agents, e.g., asparaginase, busulfan, carboplatin, cisplatin, daunorubicin, doxorubicin, fluorouracil, gemcitabine, hydroxyurea, methotrexate, paclitaxel, rituximab, vinblastine, vincristine, etc.

[0075] Preferably, the carrier is a pharmaceutically acceptable carrier. With respect to pharmaceutical compositions, the carrier can be any of those conventionally used for the particular inventive population of cells under consideration. Such pharmaceutically acceptable carriers are well-known to those skilled in the art and are readily available to the public. It is preferred that the pharmaceutically acceptable carrier be one which has no detrimental side effects or toxicity under the conditions of use.

[0076] The choice of carrier will be determined in part by the particular population of cells, as well as by the particular method used to administer the population of cells.

Accordingly, there are a variety of suitable formulations of the pharmaceutical composition of the invention. Suitable formulations may include any of those for oral, parenteral, subcutaneous, intravenous, intramuscular, intratumoral, intraarterial, intrathecal, or interperitoneal administration. More than one route can be used to administer the inventive population of cells, and in certain instances, a particular route can provide a more immediate and more effective response than another route.

[0077] Preferably, the inventive population of cells is administered by injection, e.g., intravenously. When the inventive population of cells is to be administered, the

pharmaceutically acceptable carrier for the cells for injection may include any isotonic carrier such as, for example, normal saline (about 0.90% w/v of NaCl in water, about 300 mOsm/L NaCl in water, or about 9.0 g NaCl per liter of water), NORMOSOL R electrolyte solution (Abbott, Chicago, IL), PLASMA-LYTE A (Baxter, Deerfield, IL), about 5% dextrose in water, or Ringer's lactate. In an embodiment, the pharmaceutically acceptable carrier is supplemented with human serum albumin. [0078] It is contemplated that the inventive populations of cells and pharmaceutical compositions can be used in methods of treating or preventing cancer. Without being bound to a particular theory or mechanism, the TCRs, or the antigen-binding portions thereof, are believed to bind specifically to a mutated amino acid sequence encoded by a cancer-specific mutation, such that the TCR, or the antigen-binding portion thereof, when expressed by a cell, is able to mediate an immune response against a target cell expressing the mutated amino acid sequence. In this regard, an embodiment of the invention provides a method of treating or preventing cancer in a mammal, comprising preparing a population of cells which express a TCR, or an antigen-binding portion thereof, having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation by any of the methods described herein with respect to other aspects of the invention; and administering the population of cells produced by the method to the mammal in an amount sufficient to treat or prevent cancer in the mammal. The population of cells to be administered to the mammal may be included in a pharmaceutical composition, as described herein with respect to other aspects of the invention.

[0079] In an embodiment of the invention, cells expressing multiple different TCRs identified by the inventive methods may be pooled into a single pharmaceutical composition for administration. For example, the pharmaceutical composition may comprise greater than about lxlO 8 cells expressing each TCR, preferably greater than about lxlO 9 cells expressing each TCR.

[0080] The terms "treat," and "prevent" as well as words stemming therefrom, as used herein, do not necessarily imply 100% or complete treatment or prevention. Rather, there are varying degrees of treatment or prevention of which one of ordinary skill in the art recognizes as having a potential benefit or therapeutic effect. In this respect, the inventive methods can provide any amount of any level of treatment or prevention of cancer in a mammal.

Furthermore, the treatment or prevention provided by the inventive method can include treatment or prevention of one or more conditions or symptoms of the cancer being treated or prevented. For example, treatment or prevention can include promoting the regression of a tumor. Also, for purposes herein, "prevention" can encompass delaying the onset of the cancer, or a symptom or condition thereof.

[0081] For purposes of the invention, the amount or dose of the inventive population of cells or pharmaceutical composition administered (e.g., numbers of cells when the inventive population of cells is administered) should be sufficient to effect, e.g., a therapeutic or prophylactic response, in the mammal over a reasonable time frame. For example, the dose of the inventive population of cells or pharmaceutical composition should be sufficient to bind to a mutated amino acid sequence encoded by a cancer-specific mutation, or detect, treat or prevent cancer in a period of from about 2 hours or longer, e.g., 12 to 24 or more hours, from the time of administration. In certain embodiments, the time period could be even longer. The dose will be determined by the efficacy of the particular population of cells or pharmaceutical composition administered and the condition of the mammal (e.g., human), as well as the body weight of the mammal (e.g., human) to be treated.

[0082] Many assays for determining an administered dose are known in the art. For purposes of the invention, an assay, which comprises comparing the extent to which target cells are lysed or IFN-g is secreted by T cells expressing the TCR, or the antigen-binding portion thereof, upon administration of a given dose of such T cells to a mammal among a set of mammals of which is each given a different dose of the T cells, could be used to determine a starting dose to be administered to a mammal. The extent to which target cells are lysed or IFN-g is secreted upon administration of a certain dose can be assayed by methods known in the art.

[0083] The dose of the inventive population of cells or pharmaceutical composition also will be determined by the existence, nature and extent of any adverse side effects that might accompany the administration of a particular inventive population of cells or pharmaceutical composition. Typically, the attending physician will decide the dosage of the inventive population of cells or pharmaceutical composition with which to treat each individual patient, taking into consideration a variety of factors, such as age, body weight, general health, diet, sex, inventive population of cells or pharmaceutical composition to be administered, route of administration, and the severity of the condition being treated.

[0084] In an embodiment in which the inventive population of cells is to be administered, the number of cells administered per infusion may vary, for example, in the range of one million to 100 billion cells; however, amounts below or above this exemplary range are within the scope of the invention. For example, the daily dose of inventive host cells can be about 1 million to about 150 billion cells (e.g., about 5 million cells, about 25 million cells, about 500 million cells, about 1 billion cells, about 5 billion cells, about 20 billion cells, about 30 billion cells, about 40 billion cells, about 60 billion cells, about 80 billion cells, about 100 billion cells, about 120 billion cells, about 130 billion cells, about 150 billion cells, or a range defined by any two of the foregoing values), preferably about 10 million to about 130 billion cells (e.g., about 20 million cells, about 30 million cells, about 40 million cells, about 60 million cells, about 70 million cells, about 80 million cells, about 90 million cells, about 10 billion cells, about 25 billion cells, about 50 billion cells, about 75 billion cells, about 90 billion cells, about 100 billion cells, about 110 billion cells, about 120 billion cells, about 130 billion cells, or a range defined by any two of the foregoing values), more preferably about 100 million cells to about 130 billion cells (e.g., about 120 million cells, about 250 million cells, about 350 million cells, about 450 million cells, about 650 million cells, about 800 million cells, about 900 million cells, about 3 billion cells, about 30 billion cells, about 45 billion cells, about 50 billion cells, about 75 billion cells, about 90 billion cells, about 100 billion cells, about 110 billion cells, about 120 billion cells, about 130 billion cells, or a range defined by any two of the foregoing values).

[0085] Another embodiment of the invention provides any of the isolated populations of cells or pharmaceutical compositions described herein for use in treating or preventing cancer in a mammal.

[0086] The cancer may, advantageously, be any cancer, including any of acute lymphocytic cancer, acute myeloid leukemia, alveolar rhabdomyosarcoma, bone cancer, brain cancer, breast cancer, cancer of the anus, anal canal, or anorectum, cancer of the eye, cancer of the intrahepatic bile duct, cancer of the joints, cancer of the neck, gallbladder, or pleura, cancer of the nose, nasal cavity, or middle ear, cancer of the oral cavity, cancer of the vagina, cancer of the vulva, cholangiocarcinoma, chronic lymphocytic leukemia, chronic myeloid cancer, colon cancer, esophageal cancer, uterine cervical cancer, gastrointestinal carcinoid tumor, glioma, Hodgkin lymphoma, hypopharynx cancer, kidney cancer, larynx cancer, liver cancer, lung cancer, malignant mesothelioma, melanoma, multiple myeloma, nasopharynx cancer, non-Hodgkin lymphoma, cancer of the oropharynx, ovarian cancer, cancer of the penis, pancreatic cancer, peritoneum, omentum, and mesentery cancer, pharynx cancer, prostate cancer, rectal cancer, renal cancer, skin cancer, small intestine cancer, soft tissue cancer, stomach cancer, testicular cancer, thyroid cancer, cancer of the uterus, ureter cancer, urinary bladder cancer, solid tumors, and liquid tumors. The cancer may be an epithelial cancer. In an embodiment, the cancer is cholangiocarcinoma, melanoma, colon cancer, or rectal cancer.

[0087] The mammal referred to in the inventive methods can be any mammal. As used herein, the term "mammal" refers to any mammal, including, but not limited to, mammals of the order Rodentia, such as mice and hamsters, and mammals of the order Logomorpha, such as rabbits. It is preferred that the mammals are from the order Carnivora, including Felines (cats) and Canines (dogs). Preferably, the mammals are from the order Artiodactyla, including Bovines (cows) and Swines (pigs) or of the order Perssodactyla, including Equines (horses). Preferably, the mammals are of the order Primates, Ceboids, or Simoids (monkeys) or of the order Anthropoids (humans and apes). A more preferred mammal is the human. In an especially preferred embodiment, the mammal is the patient expressing the cancer-specific mutation.

[0088] The following examples further illustrate the invention but, of course, should not be construed as in any way limiting its scope.

EXAMPLES

[0089] A nucleotide sequence that encodes a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation was isolated as follows for the experiments described in Examples 1-9. One or more genes were identified in the nucleic acid of a cancer cell of a patient. Each gene contained a cancer-specific mutation that encodes a mutated amino acid sequence. Autologous APCs of the patient were induced to present the mutated amino acid sequence. Autologous T cells of the patient were co-cultured with the autologous APCs that present the mutated amino acid sequence. The autologous T cells that (a) were co-cultured with the autologous APCs that present the mutated amino acid sequence and (b) have antigenic specificity for the mutated amino acid sequence presented in the context of a MHC molecule expressed by the patient were selected. A nucleotide sequence that encodes the TCR was isolated from the selected autologous T cells. The nucleotide sequence was inserted into a viral vector.

EXAMPLE 1

[0090] This example demonstrates a method of preparing a population of cells which express a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation.

[0091] A schematic illustrating a method of preparing a population of cells which express a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer- specific mutation (neoantigen) according to an embodiment of the invention is presented in Figure 1. The human constant regions of the TCR were replaced with murine constant regions. As shown in Figure 1, packaging cell line 293GP was transfected with the viral vector and a nucleotide sequence that encodes a viral envelope protein. The transfected cell line 293 GP was cultured under conditions sufficient to generate a retroviral supernatant comprising replication incompetent viruses, wherein the replication incompetent viruses comprise a vector comprising the nucleotide sequence that encodes the TCR. The replication incompetent viruses (in the supernatant) were tested for safety. The PBMC were contacted with the replication incompetent viruses under conditions sufficient to transduce the PBMC with the vector comprising the nucleotide sequence that encodes the TCR. The population of cells produced by the method was tested for safety.

EXAMPLE 2

[0092] This example demonstrates the pre-clinical validation of good laboratory practice (GLP) preparations for transient gammaretovrial vector production.

[0093] Autologous PBMC were transduced with a transient gammaretoviral vector produced as described in Example 1 (Figure 1) and encoding TCR1 or TCR2. The transduced PBMC were then co-cultured with autologous APCs pulsed with either wildtype (wt) or mutated (mut) peptide for a given neoantigen. The neoantigen-reactive TCR1 (Vbl6) recognized mutated antigen H3F3B. The neoantigen-reactive TCR2 (Vb20) recognized mutated SKIV2L (Vb20, TCR2).

[0094] The expression of the neoantigen-reactive TCRs by the PBMC was measured by fluorescence-activated cell sorting (FACS). The results are shown in Figure 2 A. As shown in Figure 2A, efficient expression of the neoantigen-reactive TCRs by PBMC was obtained.

[0095] Following co-culture, cells were assessed by FACS for upregulation of 4-1BB (a marker of T cell activation) and specific release of IFNy by enzyme-linked immunosorbent assay (ELISA). The results are shown in Figures 2B and 2C. Specific upregulation of 4-1BB (Fig. 2B) and IFNy release (Fig. 2C) was observed following recognition of the respective target mutated antigen (mutated H3F3B for Vbl6 (TCR1) and mutated SKIV2L for Vb20 (TCR2)).

EXAMPLE 3

[0096] This example demonstrates safety characteristics of the gammaretroviral vector transiently produced as described in Example 1.

[0097] Gammaretroviral vector encoding the TCR1 or TCR2 of Example 2 was manufactured by transient transfection of 293GP cells as described in Example 1 (Figure 1). Samples were taken after transfection with or without BENZONASE endonuclease treatment. Residual vector DNA was measured by quantitative polymerase chain reaction (qPCR).

[0098] The results are shown in Figure 3 A. As shown in Figure 3 A, residual vector was degraded to undetectable levels following BENZONASE endonuclease treatment.

[0099] BENZONASE endonuclease levels were measured after BENZONASE

endonuclease treatment, after transduction of PBMC with the TCR vector, and after a post- transduction wash during expansion of the numbers of transduced PBMC. The results are shown in Figure 3B. As shown in Figure 3B, residual BENZONASE endonuclease was removed from the cells after the post-transduction wash during expansion.

[0100] PBMC transduced with either TCR1 or TCR2 were cultured for up to 1 month. Cell samples were taken and cryopreserved at the time points indicated in Figure 3C.

Samples were then tested for replication competent retrovirus (RCR) at Indiana ETniversity Vector Production Facility following an amplification phase and the RD1 l4-specific qPCR.

[0101] The results are shown in Figure 3C. As shown in Figure 3C, carryover of RD114 vector was detected early in the process, but continued to decrease to almost undetectable levels, even in samples not treated with BENZONASE endonuclease. These results suggested that the RD114 vector was naturally degraded during the cell expansion process. No RCR was detected, as the RD114 qPCR signal dropped over time and did not rebound.

EXAMPLE 4

[0102] This example demonstrates a method of preparing a population of cells which express a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation.

[0103] A population of cells which express a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation was prepared as follows:

Transfection

[0104] Day 0: 293GP cells were plated.

[0105] Day 1 : the plated 293GP cells were transfected with a retroviral vector encoding the RD114 envelope protein and a viral vector encoding a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation.

[0106] Day 2: The cell medium was changed. [0107] Day 3 : The supernatant was harvested and treated with BENZONASE endonuclease. PBMC were transduced.

Transduction

[0108] Day 1 : PBMC were stimulated.

[0109] Day 3 : PBMC were transduced.

[0110] Day 4: Transduced cells were washed.

[0111] Day 8: TCR expression was measured by FACS.

[0112] Day 9 : Co-culture of T cells (expressing the TCR having antigenic specificity for a mutated amino acid sequence) with antigen-positive target cells.

EXAMPLE 5

[0113] This example demonstrates that PBMC transduced as described in Example 4 secrete IFNy in the presence of target antigen.

[0114] Retroviral supernatant was prepared as described in Example 4. The supernatant was treated with 0, 25, or 50 U/mL BENZONASE endonuclease.

[0115] The supernatant was used to transfect PBMC from three patients (Patients D, H, and R) with one of three TCRs (nb22, nb5.2 a 26.1, or nb5.2 a 30) which recognize mutated ERBBIP2 as also described in Example 4.

[0116] ETntransduced or transduced cells were co-cultured with B cells pulsed overnight with wild type ERBBIP2 or mutated ERBBIP2. IFNy secretion was measured. Controls included T cells cultured alone (no target) and co-cultures with (i) OKT3 antibody and (ii) B cells that have not been pulsed with mutated or wild type peptide.

[0117] The results are shown in Figures 4A-4I. As shown in Figures 4A-4I, the transduced cells secreted IFNY in the presence of antigen.

EXAMPLE 6

[0118] This example demonstrates the reduction of free DNA from the retroviral supernatant produced in Example 4.

[0119] Retroviral supernatant was prepared as described in Example 4 with retroviral vectors encoding the Ub22 or Ub5.2 a 30 TCR. The supernatant was treated with 0, 25, or 50 U/mL BENZONASE endonuclease. Free DNA in the supernatant and in a 100 mL dose was measured by qPCR. The results are shown in Table 1A (Ub5.2 a 30) and Table 1B (Ub22).

TABLE 1 A

TABLE 1B

[0120] Free DNA in the supernatant was also measured by qPCR at the time points during transfection shown in Figures 5 A and 5B (Days 1, 2, and 3 of transfection, respectively), including after treatment with 25 or 50 U/mL BENZONASE endonuclease. The results are shown in Figure 5A (25 U/mL) and Figure 5B (50 U/mL).

[0121] The BENZONASE endonuclease treatments shown in Tables 1 A and 1B do not satisfy the WO recommendation of less than 10 ng/patient dose.

EXAMPLE 7

[0122] This example demonstrates the reduction of free DNA from the retroviral supernatant produced in Example 4.

[0123] Retroviral supernatant was prepared as described in Example 4 with retroviral vectors encoding the nb22 or nb5.2 a 30 TCR. The supernatant was treated with 0 or 50 U/mL BENZONASE endonuclease. Free DNA in the supernatant and in a 100 mL dose was measured by qPCR. The results are shown in Table 2A (Ub5.2 a 30) and Table 2B (Ub22). TABLE 2 A

TABLE 2B

[0124] Free DNA in the supernatant was also measured by qPCR at the time points during transfection shown in Figures 6A and 6B (Days 1, 2, and 3 of transfection, respectively), including after treatment with 50 U/mL BENZONASE endonuclease for 1 hour at RT or 37° C. The results are shown in Figure 6 A (37° C) and Figure 6B (RT).

[0125] The BENZONASE endonuclease treatments shown in Tables 2A and 2B satisfy the WO recommendation of less than 10 ng/patient dose.

EXAMPLE 8

[0126] This example demonstrates the reduction of BENZONASE endonuclease from the transduced cells produced in Example 4.

[0127] TCR-transduced cells were prepared as described in Example 4 using retroviral supernatant prepared using 0, 25, or 50 U/mL BENZONASE endonuclease. The

concentration of BENZONASE endonuclease in the transduced cells was measured by ELISA at the time points shown in Figure 7. The results are shown in Figure 7. After the wash, the concentration of BENZONASE endonuclease was below the detection limit of the ELISA (0.2 ng/mL). EXAMPLE 9

[0128] This example demonstrates a method of preparing a population of cells which expresses a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation.

[0129] One or more TCRs having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation (neoantigen) were identified and isolated from 5 patients (Patients 4217, 4275, 4271, 4251, and 4285). The human constant region of the TCR was replaced with a murine constant region. A viral vector (pMSGV) encoding the TCR with the murine constant region was prepared.

[0130] Packaging cell line 293GP was transfected with the viral vector and a nucleotide sequence that encodes a viral envelope protein (RD114) at a Contract Manufacturing

Organization (CMO) and using calcium phosphate (CaPhos). The transfected cell line 293 GP was cultured under conditions sufficient to generate a retroviral supernatant comprising replication incompetent viruses, wherein the replication incompetent viruses comprise a vector comprising the nucleotide sequence that encodes the TCR. Healthy donor PBMC were contacted with the replication incompetent viruses under conditions sufficient to transduce the PBMC with the vector comprising the nucleotide sequence that encodes the TCR.

[0131] Expression of the mTCRP constant region was detected by flow cytometry. The results are shown in Figures 8-12. As shown in Figures 8-12, the transductions satisfied the clinical criteria to use in cell therapy manufacturing, which is >30% transduction efficiency.

EXAMPLE 10

[0132] This example demonstrates the specificity and potency of the TCR-transduced healthy donor T cells of Example 9.

[0133] The TCR-transduced healthy donor T cells of Example 9 were co-cultured overnight with autologous patient B cells pulsed with 10 pg of either mutant or wild type peptide. IFN-g release was measured by ELISA assay and reported in pg/mL. The results are shown in Figure 13. As shown in Figure 13, the TCR-transduced healthy donor T cells of Example 9 specifically recognized the target mutated antigen. [0134] All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.

[0135] The use of the terms“a” and“an” and“the” and“at least one” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The use of the term“at least one” followed by a list of one or more items (for example,“at least one of A and B”) is to be construed to mean one item selected from the listed items (A or B) or any combination of two or more of the listed items (A and B), unless otherwise indicated herein or clearly

contradicted by context. The terms“comprising,”“having,”“including,” and“containing” are to be construed as open-ended terms (i.e., meaning“including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g.,“such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.

[0136] Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.