METHODS FOR IDENTIFYING TCR REPERTOIRE AND COMPOSITIONS AND USES THEREOF

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of US Application 63/331,694, filed April 15, 2022, and US Application 63/341,738, filed May 13, 2022, each of which is herein incorporated by reference in its entirety for all purposes.

BACKGROUND

[0002] Treatment of cancers using adoptive transfer of tumor infiltrating lymphocytes (TILs) represents a powerful approach to therapy for patients. Autologous TIL products are comprised of an unrestricted T-cell receptor (TCR) repertoire and can recognize a broad set of tumor- associated antigens. Current TIL manufacturing processes are limited by length, cost, and other factors. Current predictive models for anti-tumor reactivity have limited positive and negative predictive power, and new predictive models are needed.

SUMMARY

[0003] Provided herein are methods for preparing a therapeutic population of tumor infiltrating lymphocytes (TILs), populations of TILs produced by the methods, and methods of using the TILs to treat cancer in a subject. Biological markers are provided that are predictive of whether a subject treated with the TILs will be responsive or non-responsive.

[0004] In one aspect, provided are methods for identifying a therapeutically effective population of tumor infiltrating lymphocytes (TILs), comprising identifying one or both of the following in a population of TILs: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. In one aspect, provided are methods for identifying a therapeutically effective population of tumor infiltrating lymphocytes (TILs), comprising identifying one or both of the following in a population of TILs: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not MX1+OAS1+ and/or for TILs that are not BBC3+CHAC1+. In one aspect, provided are methods for identifying a therapeutically effective population of tumor infiltrating lymphocytes (TILs), comprising identifying one or both of the following in a population of TILs: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+. [0005] In some such methods, a therapeutically effective population of tumor infiltrating lymphocytes (TILs) is identified by high TCR repertoire clonality. In some such methods, TCR repertoire clonality is measured by bulk TCR RNA sequencing. In some such methods, the high TCR repertoire clonality comprises one or more or all of high TCR P-chain repertoire clonality, high TCR a-chain repertoire clonality, high TCR 8-chain repertoire clonality, and high TCR y- chain repertoire clonality. In some such methods, the high TCR repertoire clonality comprises high TCR P-chain repertoire clonality, and wherein the TCR P-chain repertoire clonality has a Gini coefficient of at least about 0.75, at least about 0.8, or at least about 0.85. In some such methods, the high TCR repertoire clonality comprises high TCR a-chain repertoire clonality, and wherein the TCR a-chain repertoire clonality has a Gini coefficient of at least about 0.7, at least about 0.75, at least about 0.8, or at least about 0.85. In some such methods, the high TCR repertoire clonality comprises high TCR 5-chain repertoire clonality, and wherein the TCR 5- chain repertoire clonality has a Gini coefficient of at least about 0.45, at least about 0.5, at least about 0.55, or at least about 0.6. In some such methods, the high TCR repertoire clonality comprises high TCR y-chain repertoire clonality, and wherein the TCR y-chain repertoire clonality has a Gini coefficient of at least about 0.75 or at least about 0.8.

[0006] In some such methods, TCR repertoire clonality is measured by single-cell TCR RNA sequencing. In some such methods, the high TCR repertoire clonality is in a CD62L+ population of TILs. In some such methods, the TCR repertoire clonality has a Gini coefficient of at least about 0.1, at least about 0.15, or at least about 0.2.

[0007] In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not MX1+OAS1+ and/or for TILs that are not BBC3+CHAC1+. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not C7 TILs. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 3%, less than about 2.5%, or less than about 2% C7 TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not MX1+OAS1+. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 3%, less than about 2.5%, or less than about 2% MX1+OAS1+ TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TTLs that are not C9 TILs. Tn some such methods, a therapeutically effective population of TILs is identified if the population has less than about 1.5% or less than about 1% C9 TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not BBC3+CHAC1+. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 1.5% or less than about 1% BBC3+CHAC1+ TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not C7 TILs and TILs that are not C9 TILs. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either C7 TILs or C9 TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not MX1+0AS1+ and TILs that are not BBC3+CHAC1+. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either MX1+0AS1+ or BBC3+CHAC1+. In some such methods, the percentage of C7 TILs and/or the percentage of C9 TILs is measured by single-cell RNA sequencing analysis. In some such methods, the percentage of MX1+0AS1+ TILs and/or the percentage of BBC3+CHAC1+ TILs is measured by single-cell RNA sequencing analysis.

[0008] In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not LGALS9+. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 3%, less than about 2.5%, or less than about 2% LGALS9+ TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not BBC3+CHAC1+. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 1.5% or less than about 1% BBC3+CHAC1+ TILs. In some such methods, a therapeutically effective population of TILs is identified by enrichment for TILs that are not LGALS9+ and TILs that are not BBC3+CHACl+. In some such methods, a therapeutically effective population of TILs is identified if the population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either LGALS9+ or BBC3+CHAC1+. Tn some such methods, the percentage ofLGALS9+ TTLs and/or the percentage of BBC3+CHAC1+ TILs is measured by single-cell RNA sequencing analysis. [0009] In some such methods, the TILs are from a subject, and the method identifies a therapeutically effective population of TILs for that subject. In some such methods, the TILs are from a tumor biopsy, a lymph node, or ascites. In some such methods, the tumor is from a bladder cancer, a breast cancer, a cancer caused by human papilloma virus, a cervical cancer, a head and neck cancer, a lung cancer, a melanoma, an ovarian cancer, a non-small-cell lung cancer (NSCLC), a renal cancer, or a renal cell carcinoma. In some such methods, the tumor biopsy is from a melanoma.

[0010] In another aspect, provided are isolated therapeutic populations of TILs obtained by any of the above methods. Optionally, the population comprises about 5xl0 ⁹ to about 5xl0 ¹⁰ TILs

[0011] In another aspect, provided are pharmaceutical formulations comprising a pharmaceutically acceptable excipient and the any of the above isolated therapeutic populations of TILs. In another aspect, provided is a cryopreserved bag or an intravenous infusion bag, container, or vessel containing contents comprising the any of the above isolated therapeutic population of TILs.

[0012] In another aspect, provided are methods of treating a cancer in a subject, comprising administering any of the above isolated therapeutic population of TILs or the above pharmaceutical formulation to the subject. Optionally, the TILs are autologous or allogeneic. [0013] In another aspect, provided are methods for treating a cancer in a subject, comprising: (a) performing the method of identifying a therapeutically effective population of TILs according to any of the above methods; and (b) administering a therapeutic amount of the population of TILs to the subject.

[0014] In some such methods, the cancer is a bladder cancer, a breast cancer, a cancer caused by human papilloma virus, a cervical cancer, a head and neck cancer, a head and neck squamous cell carcinoma (HNSCC), a lung cancer, a melanoma, an ovarian cancer, a non-small-cell lung cancer (NSCLC), a renal cancer, or a renal cell carcinoma. In some such methods, the cancer is a melanoma. In some such methods, the subject is a human. In some such methods, the subject is a non-human mammal. In some such methods, the non-human mammal is a primate, a rodent, a rat, a mouse, a domesticated mammal, a domesticated cat, a domesticated dog, a domesticated horse, a guinea pig, a laboratory animal, or a companion animal. Tn some such methods, the subject is an adult or individual having secondary sexual characteristics. In some such methods, he subject is not an adult or not individual having secondary sexual characteristics, or is a child or is a not physically mature mammal.

[0015] In some such methods, the administering is performed more than once. In some such methods, the administering is performed more than once over a course of time, wherein: (1) the course of time is a week and the administering is twice, thrice, four times or five times in the week; (2) the course of time is a month and the administering is twice, thrice of four times in a month; (3) the course of time is three, six, nine, or twelve months and the administering is performed once monthly or once weekly. In some such methods, the administering is intravenous administration.

[0016] In another aspect, provided are methods of predicting whether a subject with a cancer will respond to treatment with a population of tumor infiltrating lymphocytes (TILs). Some such methods comprise: (a) obtaining the population of TILs from the subject; and (b) measuring one or both of the following in the population: (i) TCR repertoire clonality; and (ii) the percentage of C7 TILs and/or the percentage of C9 TILs, wherein the subject is predicted to respond to treatment if the population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. In another aspect, provided are methods of predicting whether a subject with a cancer will respond to treatment with a population of tumor infiltrating lymphocytes (TILs). Some such methods comprise: (a) obtaining the population of TILs from the subject; and (b) measuring one or both of the following in the population: (i) TCR repertoire clonality; and (ii) the percentage of MX1+OAS1+ TILs and/or the percentage of BBC3+CHAC1+ TILs, wherein the subject is predicted to respond to treatment if the population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not MX1+OAS1+ and/or for TILs that are not BBC3+CHAC1+. In another aspect, provided are methods of predicting whether a subject with a cancer will respond to treatment with a population of tumor infiltrating lymphocytes (TILs). Some such methods comprise: (a) obtaining the population of TILs from the subject; and (b) measuring one or both of the following in the population: (i) TCR repertoire clonality; and (ii) the percentage of LGALS9+ TILs and/or the percentage of BBC3+CHAC1+ TILs, wherein the subject is predicted to respond to treatment if the population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+.

[0017] In some such methods, the subject is predicted to respond to treatment if the population has high TCR repertoire clonality. In some such methods, step (b) comprises measuring TCR repertoire clonality by bulk TCR RNA sequencing. In some such methods, the high TCR repertoire clonality comprises one or more or all of high TCR P-chain repertoire clonality, high TCR a-chain repertoire clonality, high TCR 5-chain repertoire clonality, and high TCR y-chain repertoire clonality. In some such methods, the high TCR repertoire clonality comprises high TCR P-chain repertoire clonality, and wherein the TCR P-chain repertoire clonality has a Gini coefficient of at least about 0.75, at least about 0.8, or at least about 0.85. In some such methods, the high TCR repertoire clonality comprises high TCR a-chain repertoire clonality, and wherein the TCR a-chain repertoire clonality has a Gini coefficient of at least about 0.7, at least about 0.75, at least about 0.8, or at least about 0.85. In some such methods, the high TCR repertoire clonality comprises high TCR 8-chain repertoire clonality, and wherein the TCR 6-chain repertoire clonality has a Gini coefficient of at least about 0.45, at least about 0.5, at least about 0.55, or at least about 0.6. In some such methods, the high TCR repertoire clonality comprises high TCR y-chain repertoire clonality, and wherein the TCR y-chain repertoire clonality has a Gini coefficient of at least about 0.75 or at least about 0.8.

[0018] In some such methods, step (b) comprises measuring TCR repertoire clonality by single-cell TCR RNA sequencing. In some such methods, the high TCR repertoire clonality is in a CD62L+ population of TILs. In some such methods, the TCR repertoire clonality has a Gini coefficient of at least about 0.1, at least about 0.15, or at least about 0.2.

[0019] In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not MX1+0AS1+ and/or for TILs that are not BBC3+CHAC1+. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not C7 TILs. In some such methods, the subject is predicted to respond to treatment if the population has less than about 3%, less than about 2.5%, or less than about 2% C7 TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not MXl+OASl+. Tn some such methods, the subject is predicted to respond to treatment if the population has less than about 3%, less than about 2.5%, or less than about 2% MX1+0AS1+ TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not C9 TILs. In some such methods, the subject is predicted to respond to treatment if the population has less than about 1.5% or less than about 1% C9 TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not BBC3+CHAC1+. In some such methods, the subject is predicted to respond to treatment if the population has less than about 1.5% or less than about 1% BBC3+CHAC1 + TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not C7 TILs and TILs that are not C9 TILs. In some such methods, the subject is predicted to respond to treatment if the population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either C7 TILs or C9 TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not MX1+0AS1+ and TILs that are not BBC3+CHAC1+. In some such methods, the subject is predicted to respond to treatment if the population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either MX1+0AS1+ or BBC3+CHAC1+. In some such methods, step (b) comprises measuring the percentage of C7 TILs and/or the percentage of C9 TILs by single-cell RNA sequencing analysis. In some such methods, step (b) comprises measuring the percentage of MX1+0AS1+ TILs and/or the percentage of BBC3+CHAC1+ TILs by single-cell RNA sequencing analysis. [0020] In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1 +. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not LGALS9+. In some such methods, the subject is predicted to respond to treatment if the population has less than about 3%, less than about 2.5%, or less than about 2% LGALS9+ TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not BBC3+CHAC1+. In some such methods, the subject is predicted to respond to treatment if the population has less than about 1.5% or less than about 1% BBC3+CHAC1+ TILs. In some such methods, the subject is predicted to respond to treatment if the population is enriched for TILs that are not LGALS9+ and TILs that are not BBC3+CHAC1+. Tn some such methods, the subject is predicted to respond to treatment if the population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either LGALS9+ or BBC3+CHAC1+. In some such methods, step (b) comprises measuring the percentage of LGALS9+ TILs and/or the percentage of BBC3+CHAC1+ TILs by single-cell RNA sequencing analysis.

[0021] In some such methods, the TILs are from a tumor biopsy, a lymph node, or ascites. In some such methods, the tumor is from a bladder cancer, a breast cancer, a cancer caused by human papilloma virus, a cervical cancer, a head and neck cancer, a lung cancer, a melanoma, an ovarian cancer, a non-small-cell lung cancer (NSCLC), a renal cancer, or a renal cell carcinoma. In some such methods, the tumor biopsy is from a melanoma.

[0022] In some such methods, step (a) comprises: (i) obtaining a refined tumor product by cry opreserving a resected tumor and disaggregating the cryopreserved tumor, disaggregating a resected tumor and cry opreserving the disaggregated tumor, cry opreserving a resected tumor and processing the tumor into multiple tumor fragments, or processing a resected tumor into multiple tumor fragments and cry opreserving the tumor fragments; and (ii) performing a first expansion by culturing the refined resected tumor product in a cell culture medium comprising IL-2 to produce the population of TILs. In some such methods, the cryopreserving comprises: (1) cooling under conditions whereby heat release to, into, around or in an environment including cells, as media crystalizes, is minimized or avoided; (2) continuous cooling, from disaggregation temperature to about -80°C; (3) continuous cooling at a rate of about -2°C / min; (4) continuous cooling, from disaggregation temperature to about -80°C, at a rate of about -2°C / min; or (5) continuous cooling, from disaggregation temperature to about -80°C, or from disaggregation temperature to -80°C at a rate of about -2°C / min, wherein disaggregation temperature comprises a normal body temperature for an animal from which the tumor was resected, or room temperature or 20°C or 25°C , or normal human body temperature approximately 35°C or 36°C or 36.1°C to approximately 37°C or 37.1°C or 37.2° C or 37.3°C or below about 38.3°C. In some such methods, the disaggregating comprises physical disaggregation, enzymatic disaggregation, or physical and enzymatic disaggregation. In some such methods, a single cell suspension is obtained from the refined resected tumor product and used in step (ii), or wherein the refined resected tumor product from step (i) comprises a single cell suspension. In some such methods, the first expansion in step (ii) is performed for about two weeks. Tn some such methods, the culturing in step (ii) includes adding IL-7, IL-12, IL-15, IL-18, IL-21, or a combination thereof. [0023] In some such methods, the method further comprises: (iii) performing a second expansion by culturing the population of TILs in a cell culture medium comprising IL-2.

[0024] In some such methods, the expanding in step (iii) comprises culturing the first population of TILs with IL-2, OKT-3, and antigen presenting cells (APCs). In some such methods, the expanding in step (iii) is performed for about two weeks. In some such methods, the culturing in step (iii) includes adding IL-7, IL-12, IL-15, IL-18, IL-21, or a combination thereof. In some such methods, the method further comprises harvesting and/or cry opreserving the population of TILs.

[0025] In another aspect, provided are isolated therapeutic population of TILs obtained by any of the above methods Optionally, the population comprises about 5xl0 ⁹ to about 5xl0 ¹⁰ TILs.

[0026] In another aspect, provided are pharmaceutical formulations comprising a pharmaceutically acceptable excipient and the any of the above isolated therapeutic populations of TILs. In another aspect, provided is a cryopreserved bag or an intravenous infusion bag, container, or vessel containing contents comprising the any of the above isolated therapeutic population of TILs.

[0027] In another aspect, provided are methods of treating a cancer in a subject, comprising administering any of the above isolated therapeutic population of TILs or the above pharmaceutical formulation to the subject. Optionally, the TILs are autologous or allogeneic. [0028] In another aspect, provided are methods for treating a cancer in a subject, comprising: (a) performing the method of predicting whether a subject with a cancer will respond to treatment with a population of tumor infiltrating lymphocytes (TILs) according to any of the above methods; and (b) administering a therapeutic amount of the population of TILs to the subject predicted to respond to treatment (i.e., if the subject is predicted to respond to treatment). [0029] In some such methods, the cancer is a bladder cancer, a breast cancer, a cancer caused by human papilloma virus, a cervical cancer, a head and neck cancer, a head and neck squamous cell carcinoma (HNSCC), a lung cancer, a melanoma, an ovarian cancer, a non-small-cell lung cancer (NSCLC), a renal cancer, or a renal cell carcinoma. In some such methods, the cancer is a melanoma. In some such methods, the subject is a human. In some such methods, the subject is a non-human mammal. Tn some such methods, the non-human mammal is a primate, a rodent, a rat, a mouse, a domesticated mammal, a domesticated cat, a domesticated dog, a domesticated horse, a guinea pig, a laboratory animal, or a companion animal. In some such methods, the subject is an adult or individual having secondary sexual characteristics. In some such methods, he subject is not an adult or not individual having secondary sexual characteristics, or is a child or is a not physically mature mammal.

[0030] In some such methods, the administering is performed more than once. In some such methods, the administering is performed more than once over a course of time, wherein: (1) the course of time is a week and the administering is twice, thrice, four times or five times in the week; (2) the course of time is a month and the administering is twice, thrice of four times in a month; (3) the course of time is three, six, nine, or twelve months and the administering is performed once monthly or once weekly. In some such methods, the administering is intravenous administration.

[0031] In one aspect, provided are methods for preparing a therapeutic population of tumor infiltrating lymphocytes (TILs). Some such methods comprise: (a) obtaining or receiving a first population of TILs; (b) measuring one or both of the following in the first population: (i) TCR repertoire clonality; and (ii) the percentage of C7 TILs and/or the percentage of C9 TILs; and (c) selecting and expanding the first population to generate the therapeutic population of TILs if the first population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. In one aspect, provided are methods for preparing a therapeutic population of tumor infiltrating lymphocytes (TILs). Some such methods comprise: (a) obtaining or receiving a first population of TILs; (b) measuring one or both of the following in the first population: (i) TCR repertoire clonality; and (ii) the percentage of MX1+OAS1+ TILs and/or the percentage of BBC3+CHAC1+ TILs; and (c) selecting and expanding the first population to generate the therapeutic population of TILs if the first population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not MX1+OAS1+ and/or for TILs that are not BBC3+CHAC1+. In one aspect, provided are methods for preparing a therapeutic population of tumor infiltrating lymphocytes (TILs). Some such methods comprise: (a) obtaining or receiving a first population of TILs; (b) measuring one or both of the following in the first population: (i) TCR repertoire clonality; and (ii) the percentage of LGALS9+ TTLs and/or the percentage of BBC3+CHAC1 + TfLs; and (c) selecting and expanding the first population to generate the therapeutic population of TILs if the first population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+.

[0032] In some such methods, step (c) comprises selecting and expanding the first population if it has high TCR repertoire clonality.

[0033] In some such methods, step (b) comprises measuring TCR repertoire clonality by bulk TCR RNA sequencing. In some such methods, the high TCR repertoire clonality in step (c) comprises one or more or all of high TCR P-chain repertoire clonality, high TCR a-chain repertoire clonality, high TCR 8-chain repertoire clonality, and high TCR y-chain repertoire clonality. Optionally, the high TCR repertoire clonality in step (c) comprises high TCR P-chain repertoire clonality, and the TCR P-chain repertoire clonality has a Gini coefficient of at least about 0.75, at least about 0.8, or at least about 0.85. Optionally, the high TCR repertoire clonality in step (c) comprises high TCR a-chain repertoire clonality, and the TCR a-chain repertoire clonality has a Gini coefficient of at least about 0.7, at least about 0.75, at least about 0.8, or at least about 0.85. Optionally, the high TCR repertoire clonality in step (c) comprises high TCR 8- chain repertoire clonality, and the TCR 8-chain repertoire clonality has a Gini coefficient of at least about 0.45, at least about 0.5, at least about 0.55, or at least about 0.6. Optionally, the high TCR repertoire clonality in step (c) is high TCR y-chain repertoire clonality, and the TCR y- chain repertoire clonality has a Gini coefficient of at least about 0.75 or at least about 0.8.

[0034] In some such methods, step (b) comprises measuring TCR repertoire clonality by single-cell TCR RNA sequencing. Optionally, the high TCR repertoire clonality in step (c) is in a CD62L+ population of TILs. Optionally, the TCR repertoire clonality has a Gini coefficient of at least about 0.1, at least about 0.15, or at least about 0.2.

[0035] In some such methods, step (c) comprises selecting and expanding the first population if it enriched for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. In some such methods, step (c) comprises selecting and expanding the first population if it enriched for TILs that are not MX1+OAS1+ and/or for TILs that are not BBC3+CHAC1+. In some such methods, the first population is enriched for TILs that are not C7 TILs. Optionally, the first population has less than about 3%, less than about 2.5%, or less than about 2% C7 TILs. In some such methods, the first population is enriched for TILs that are not MX1+OAS1+. Optionally, the first population has less than about 3%, less than about 2.5%, or less than about 2% MX1+0AS1 + TILs. In some such methods, the first population is enriched for TILs that are not C9 TILs. Optionally, the first population has less than about 1.5% or less than about 1% C9 TILs. In some such methods, the first population is enriched for TILs that are not BBC3+CHAC1+. Optionally, the first population has less than about 1.5% or less than about 1% BBC3+CHAC1+ TILs. In some such methods, the first population is enriched for TILs that are not C7 TILs and TILs that are not C9 TILs. Optionally, the first population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either C7 TILs or C9 TILs. In some such methods, the first population is enriched for TILs that are not MX1+0AS1+ and TILs that are not BBC3+CHAC1+. Optionally, the first population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either MX1+0AS1+ or BBC3+CHAC1+. In some such methods, step (b) comprises measuring the percentage of C7 TILs and/or the percentage of C9 TILs by single-cell RNA sequencing analysis. In some such methods, step (b) comprises measuring the percentage of MX1+0AS1+ TILs and/or the percentage of BBC3+CHAC1+ TILs by single-cell RNA sequencing analysis.

[0036] In some such methods, step (c) comprises selecting and expanding the first population if it enriched for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+. In some such methods, the first population is enriched for TILs that are not LGALS9+. Optionally, the first population has less than about 3%, less than about 2.5%, or less than about 2% LGALS9+ TILs. In some such methods, the first population is enriched for TILs that are not BBC3+CHAC1+. Optionally, the first population has less than about 1.5% or less than about 1% BBC3+CHAC1+ TILs. In some such methods, the first population is enriched for TILs that are not LGALS9+ and TILs that are not BBC3+CHAC1+. Optionally, the first population has less than about 4.5%, less than about 4%, less than about 3.5%, less than about 3%, or less than about 2.5% TILs that are either LGALS9+ or BBC3+CHAC1+. In some such methods, step (b) comprises measuring the percentage of LGALS9+ TILs and/or the percentage of BBC3+CHAC1+ TILs by single-cell RNA sequencing analysis.

[0037] In some such methods, the TILs originate from a subject. In some such methods, the TILs are from a tumor biopsy, a lymph node, or ascites. In some such methods, the tumor is from a bladder cancer, a breast cancer, a cancer caused by human papilloma virus, a cervical cancer, a head and neck cancer, a lung cancer, a melanoma, an ovarian cancer, a non-small-cell lung cancer (NSCLC), a renal cancer, or a renal cell carcinoma. Optionally, the tumor biopsy is from a melanoma.

[0038] In some such methods, step (a) comprises: (i) obtaining a refined tumor product by cry opreserving a resected tumor and disaggregating the cryopreserved tumor, disaggregating a resected tumor and cry opreserving the disaggregated tumor, cry opreserving a resected tumor and processing the tumor into multiple tumor fragments, or processing a resected tumor into multiple tumor fragments and cry opreserving the tumor fragments; and (ii) performing a first expansion by culturing the refined resected tumor product in a cell culture medium comprising IL-2 to produce the first population of TILs. Optionally, the cryopreserving comprises cooling under conditions whereby heat release to, into, around or in an environment including cells, as media crystalizes, is minimized or avoided. Optionally, the cryopreserving comprises continuous cooling, from disaggregation temperature to about -80°C. Optionally, the cryopreserving comprises continuous cooling at a rate of about -2°C / min. Optionally, the cryopreserving comprises continuous cooling, from disaggregation temperature to about -80°C, at a rate of about -2°C / min. Optionally, the cryopreserving comprises continuous cooling, from disaggregation temperature to about -80°C, or from disaggregation temperature to -80°C at a rate of about -2°C / min, wherein disaggregation temperature comprises a normal body temperature for an animal from which the tumor was resected, or room temperature or 20°C or 25°C , or normal human body temperature approximately 35°C or 36°C or 36.1°C to approximately 37°C or 37.1°C or 37.2°C or 37.3°C or below about 38.3°C.

[0039] In some such methods, the disaggregating comprises physical disaggregation, enzymatic disaggregation, or physical and enzymatic disaggregation. In some such methods, a single cell suspension is obtained from the refined resected tumor product and used in step (ii), or wherein the refined resected tumor product from step (i) comprises a single cell suspension. [0040] In some such methods, the first expansion in step (ii) is performed for about two weeks. In some such methods, the culturing in step (ii) includes adding IL-7, IL- 12, IL- 15, IL- 18, IL-21, or a combination thereof. In some such methods, the expanding in step (c) comprises culturing the first population of TILs in a cell culture medium comprising IL-2. In some such methods, the expanding in step (c) comprises culturing the first population of TILs with IL-2, OKT-3, and antigen presenting cells (APCs). In some such methods, the expanding in step (c) is performed for about two weeks. Tn some such methods, the culturing in step (c) includes adding IL-7, IL-12, IL-15, IL-18, IL-21, or a combination thereof. In some such methods, the method further comprises harvesting and/or cry opreserving the therapeutic population of TILs.

[0041] In another aspect, provided are isolated therapeutic population of TILs obtained by or obtainable by any of the above methods. In some such populations, the population comprises about 5xl0 ⁹ to about 5xlO ¹⁰ TILs.

[0042] In another aspect, provided are pharmaceutical formulations comprising a pharmaceutically acceptable excipient and any of the above isolated therapeutic populations of TILs.

[0043] In another aspect, provided are cryopreserved bags or intravenous infusion bags, containers, or vessels containing contents comprising any of the above isolated therapeutic populations of TILs.

[0044] In another aspect, provided are methods of treating a cancer in a subject, comprising administering any of above isolated therapeutic population of TILs or the above pharmaceutical formulation to the subject. In some such methods, the TILs are autologous or allogeneic.

[0045] In another aspect, provided are methods of treating a cancer in a subject, comprising: (a) preparing a therapeutic population of TILs according to any of the above methods; and (b) administering a therapeutic amount of the therapeutic population of TILs to the subject with the cancer.

[0046] In some such methods, the cancer is a bladder cancer, a breast cancer, a cancer caused by human papilloma virus, a cervical cancer, a head and neck cancer, a head and neck squamous cell carcinoma (HNSCC), a lung cancer, a melanoma, an ovarian cancer, a non-small-cell lung cancer (NSCLC), a renal cancer, or a renal cell carcinoma. Optionally, the cancer is a melanoma. [0047] In some such methods, the subject is a human. In some such methods, the subject is a non-human mammal. In some such methods, the non-human mammal is a primate, a rodent, a rat, a mouse, a domesticated mammal, a domesticated cat, a domesticated dog, a domesticated horse, a guinea pig, a laboratory animal, or a companion animal. In some such methods, the subject is an adult or individual having secondary sexual characteristics. In some such methods, the subject is not an adult or not individual having secondary sexual characteristics, or is a child or is a not physically mature mammal. [0048] In some such methods, the administering is performed more than once. Tn some such methods, the administering is performed more than once over a course of time, wherein: (1) the course of time is a week and the administering is twice, thrice, four times or five times in the week; (2) the course of time is a month and the administering is twice, thrice of four times in a month; (3) the course of time is three, six, nine, or twelve months and the administering is performed once monthly or once weekly. In some such methods, the administering is intravenous administration.

BRIEF DESCRIPTION OF THE DRAWINGS

[0049] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

[0050] Figure 1A shows TCR P-chain repertoire clonality in TIL product samples in responders and non-responders. Clonality was measured by Gini coefficient on a scale of 0 (even distribution) to 1 (uneven distribution). Statistical significance was assessed by Wilcoxon test. [0051] Figure IB shows correlation of TCR P-chain repertoire clonality with in silico predicted antigen-reactive T cells based on GLIPH2 (grouping of lymphocyte interactions by paratope hotspots 2).

[0052] Figure 1C. Identification of top gene markers associated with more clonally expanded TILs (higher clonality).

[0053] Figures 2A-2B show unsupervised clustering (Figure 2A) of the gene expression profile of individual cells identified cell subpopulations with distinct transcriptional profiles (Figure 2B) previously undescribed in TIL products. UMAP, uniform manifold approximation and projection.

[0054] Figures 3A-3C show the frequency of C7 (MX1+0AS1+; Figure 3A), C9 (BBC3+CHAC1+; Figure 3B), or C7 and C9 (Figure 3C) T-cell subpopulations in TIL product samples. Low abundance of C7 TIL or C9 TIL subpopulations is associated with response (Figures 3A and 3B). Low abundance of the combined C7 and C9 TIL subpopulations is associated with response (Figure 3C).

[0055] Figure 3D shows gene regulatory network analysis of TIL products identified predicted master regulators of C7 and C9 T-cell subpopulations. FDR stands for false discovery rate which is p value adjusted using the Benjamini-Hochberg procedure to account for multiple hypothesis testing.

[0056] Figure 4A shows concordance between TCR repertoire clonality assessed by bulk and single-cell TCR sequencing.

[0057] Figure 4B shows top single-gene-defmed subpopulations whose clonality most significantly correlated with response.

[0058] Figure 4C shows TCR repertoire clonality as assessed by single-cell TCR sequencing in the CD62L+ (SELL+) subpopulation of TILs in responders and non-responders. Clonality was measured by Gini coefficient on a scale of 0 (even distribution) to 1 (uneven distribution). Statistical significance was assessed by Wilcoxon test.

[0059] Figure 5 shows TCR a-chain (top left), TCR -chain (top right), TCR-3 chain (bottom left), and TCR y-chain (bottom right) repertoire clonality in TIL product samples in responders and non-responders. Clonality was measured by Gini coefficient on a scale of 0 (even distribution) to 1 (uneven distribution). Statistical significance was assessed by Wilcoxon test. [0060] Figures 6A-6C show that galectin signaling may be activated in some TIL products. Figure 6A shows pair-wise communication strength among T-cell subpopulations, Figure 6B shows significant ligand-receptor pairs, and Figure 6C shows the expression pattern of significant genes among the T-cell subpopulations.

DEFINITIONS

[0061] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs. [0062] The term “anti-CD3 antibody” refers to an antibody or variant thereof, e.g., a monoclonal antibody and including human, humanized, chimeric, murine or mammalian antibodies which are directed against the CD3 receptor in the T cell antigen receptor of mature human T cells. Anti-CD3 antibodies include OKT-3, also known as muromonab. Anti-CD3 antibodies also include the UHCT1 clone, also known as T3 and CD3. epsilon. Other anti-CD3 antibodies include, for example, otelixizumab, teplizumab, and visilizumab.

[0063] When “an anti-tumor effective amount,” “an tumor-inhibiting effective amount,” or “therapeutic amount” is indicated, the precise amount of the compositions of the present invention to be administered can be determined by a physician with consideration of individual differences in age, weight, tumor size, extent of infection or metastasis, and condition of the patient (subject). It can generally be stated that a pharmaceutical composition comprising the tumor infdtrating lymphocytes (e.g. secondary TILs or genetically modified cytotoxic lymphocytes) described herein may be administered at a dosage of 10 ⁴ to 10 ⁿ cells/kg body weight (e.g., 10 ⁵ to 10 ⁶ , 10 ⁵ to IO ¹⁰ , 10 ⁵ to 10 ¹¹ , 10 ⁶ to IO ¹⁰ , 10 ⁶ to 10 ¹¹ , 10 ⁷ to 10 ¹¹ , 10 ⁷ to IO ¹⁰ , 10 ⁸ to 10 ¹¹ , 10 ⁸ to IO ¹⁰ , 10 ⁹ to 10 ¹¹ , or 10 ⁹ to IO ¹⁰ cells/kg body weight), including all integer values within those ranges. Tumor infiltrating lymphocytes (including in some cases, genetically modified cytotoxic lymphocytes) compositions may also be administered multiple times at these dosages. The tumor infiltrating lymphocytes (including in some cases, genetically) can be administered by using infusion techniques that are commonly known in immunotherapy (see, e.g., Rosenberg et al., New Eng. J. of Med. 319: 1676, 1988). The optimal dosage and treatment regime for a particular patient can readily be determined by one skilled in the art of medicine by monitoring the patient for signs of disease and adjusting the treatment accordingly.

[0064] The terms “co-administration,” “co-administering,” “administered in combination with,” “administering in combination with,” “simultaneous,” and “concurrent,” as used herein, encompass administration of two or more active pharmaceutical ingredients (in a preferred embodiment of the present invention, for example, at least one potassium channel agonist in combination with a plurality of TILs) to a subject so that both active pharmaceutical ingredients and/or their metabolites are present in the subject at the same time. Co-administration includes simultaneous administration in separate compositions, administration at different times in separate compositions, or administration in a composition in which two or more active pharmaceutical ingredients are present. Simultaneous administration in separate compositions and administration in a composition in which both agents are present are preferred.

[0065] Cellularized or cellularization” as used herein refers to the process of disaggregation whereby the solid tissue a multicellular material generally made up of multiple cell lineages/types is broken down into small numbers of cells including but not limited to one cell but could be multiple cells of various lineages or cell types in very small numbers i.e. clump of cells or cell aggregates.

[0066] Closed system” as used herein refers to a system that is closed to the outside environment. Any closed system appropriate for cell culture methods can be employed with the methods of the present invention. Closed systems include, for example, but are not limited to closed G-Rex containers or cell culture bags. Once a tumor segment is added to the closed system, the system is not open to the outside environment until the TILs are ready to be administered to the patient. In an advantageous embodiment, the closed system is the system disclosed in PCT Publication No. WO 2018/130845.

[0067] “Cryopreservation media” or “cryopreservation medium” as used herein refers to any medium that can be used for cry opreservation of cells. Such media can include media comprising 2% to 10% DMSO. Exemplary media include CryoStor CS10, HypoThermosol, Bloodstor BS- 55 as well as combinations thereof.

[0068] The term “cryopreserved TILs” herein is meant that TILs, either primary, bulk, or expanded (REP TILs), are treated and stored in the range of about -190 °C. to -60 °C. General methods for cry opreservation are also described elsewhere herein, including in the Examples. For clarity, “cryopreserved TILs” are distinguishable from frozen tissue samples which may be used as a source of primary TILs.

[0069] “Depletion” as used herein refers to a process of a negative selection that separates the desired cells from the undesired cells which are labelled by one marker-binding fragment coupled to a solid phase.

[0070] “Disaggregation or disaggregate” as used herein refers to the transformation of solid tissue into a single cells or small cell number aggregates where a single cell as a spheroid has a diameter in the range of 5 pm, 6 pm, 7 pm, 8 pm, 9 pm, 10 pm, 20 pm, 30 pm, 40 pm, 50 pm, 60 pm, 70 pm, 80 pm, 90 pm, 100 pm, or more, wherein this is more usually between 7 to 20 pm. [0071] The term “effective amount” or “therapeutically effective amount” refers to that amount of a compound or combination of compounds as described herein that is sufficient to affect the intended application including, but not limited to, disease treatment. A therapeutically effective amount may vary depending upon the intended application (in vitro or in vivo), or the subject and disease condition being treated (e.g., the weight, age and gender of the subject), the severity of the disease condition, or the manner of administration. The term also applies to a dose that will induce a particular response in target cells (e.g., the reduction of platelet adhesion and/or cell migration). The specific dose will vary depending on the particular compounds chosen, the dosing regimen to be followed, whether the compound is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which the compound is carried. [0072] “Engineered” as used herein refers to either addition of nucleic material or factors, which change the tissue derived cell function from their original function to have a new or improved function for its ultimate utility.

[0073] “Enzyme media” as used herein refers to media having enzymatic activity such as collagenase, trypsin, lipase, hyaluronidase, deoxyribonuclease, Liberase HI, pepsin, or mixtures thereof.

[0074] “Filtrate” as used herein refers to the material that passes through a fdter, mesh or membrane.

[0075] “Flexible container” as used herein refers to a flexible packaging system in multiple formats with one or more different types of fdm. Each fdm type is selected to provide specific characteristics to preserve the physical, chemical, and functional characteristics of the sterile fluids, solid tissue derived cellular material and the container integrity depending upon the step of the process.

[0076] “Freezing solution” or “cryopreservation solution” also referred in the field to as the cryoprotectant is a solution that contains cryoprotective additives. These are generally permeable, non-toxic compounds which modify the physical stresses cells are exposed to during freezing in order to minimize freeze damage (i.e., due to ice formation) and are most commonly a % vol/vol of one or more of the following: dimethylsulphoxide (DMSO); ethylene glycol; glycerol; 2-methyl-2,4-pentanediol (MPD); propylene glycol; sucrose; and trehalose.

[0077] The term “hematological malignancy” refers to mammalian cancers and tumors of the hematopoietic and lymphoid tissues, including but not limited to tissues of the blood, bone marrow, lymph nodes, and lymphatic system. Hematological malignancies are also referred to as “liquid tumors.” Hematological malignancies include, but are not limited to, acute lymphoblastic leukemia (ALL), chronic lymphocytic lymphoma (CLL), small lymphocytic lymphoma (SLL), acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute monocytic leukemia (AMoL), Hodgkin's lymphoma, and non-Hodgkin's lymphomas. The term “B cell hematological malignancy” refers to hematological malignancies that affect B cells.

[0078] The term “IL-2” (also referred to herein as “IL2”) refers to the T cell growth factor known as interleukin-2, and includes all forms of IL-2 including human and mammalian forms, conservative amino acid substitutions, glycoforms, biosimilars, and variants thereof. IL-2 is described, e g., in Nelson, J. Immunol. 2004, 172, 3983-88 and Malek, Annu. Rev Immunol. 2008, 26, 453-79, the disclosures of which are incorporated by reference herein. For example, the term IL-2 encompasses human, recombinant forms of IL-2 such as aldesleukin (PROLEUKIN, available commercially from multiple suppliers in 22 million IU per single use vials), as well as the form of recombinant IL-2 commercially supplied by CellGenix, Inc., Portsmouth, N.H., USA (CELLGRO GMP) or ProSpec-Tany TechnoGene Ltd., East Brunswick, N.J., USA (Cat. No. CYT-209-b) and other commercial equivalents from other vendors. Aldesleukin (des-alanyl- 1, serine-125 human IL-2) is a nonglycosylated human recombinant form of IL-2 with a molecular weight of approximately 15 kDa. The term IL-2 also encompasses pegylated forms of IL-2, as described herein, including the pegylated IL2 prodrug NKTR-214, available from Nektar Therapeutics, South San Francisco, Calif., USA. NKTR-214 and pegylated IL-2 suitable for use in the invention is described in U.S. Patent Application Publication No. US 2014/0328791 Al and International Patent Application Publication No. WO 2012/065086 AL Alternative forms of conjugated IL-2 suitable for use in the invention are described in U.S. Pat. Nos. 4,766, 106, 5,206,344, 5,089,261 and 4902,502. Formulations of IL-2 suitable for use in the invention are described in U.S. Pat. No. 6,706,289.

[0079] The term “IL-4” (also referred to herein as “IL4”) refers to the cytokine known as interleukin 4, which is produced by Th2 T cells and by eosinophils, basophils, and mast cells. IL- 4 regulates the differentiation of naive helper T cells (ThO cells) to Th2 T cells. Steinke and Borish, Respir. Res. 2001, 2, 66-70. Upon activation by IL-4, Th2 T cells subsequently produce additional IL-4 in a positive feedback loop. IL-4 also stimulates B cell proliferation and class II MHC expression, and induces class switching to IgE and IgGl expression from B cells. Recombinant human IL-4 suitable for use in the invention is commercially available from multiple suppliers, including ProSpec-Tany TechnoGene Ltd., East Brunswick, N.J., USA (Cat. No. CYT-211) and ThermoFisher Scientific, Inc., Waltham, Mass., USA (human IL-15 recombinant protein, Cat. No. Gibco CTP0043).

[0080] The term “IL-7” (also referred to herein as “IL7”) refers to a glycosylated tissue- derived cytokine known as interleukin 7, which may be obtained from stromal and epithelial cells, as well as from dendritic cells. Fry and Mackall, Blood 2002, 99, 3892-904. IL-7 can stimulate the development of T cells. IL-7 binds to the IL-7 receptor, a heterodimer consisting of IL-7 receptor alpha and common gamma chain receptor, which in a series of signals important for T cell development within the thymus and survival within the periphery. Recombinant human IL-7 suitable for use in the invention is commercially available from multiple suppliers, including ProSpec-Tany TechnoGene Ltd., East Brunswick, N. J., USA (Cat. No. CYT-254) and ThermoFisher Scientific, Inc., Waltham, Mass., USA (human IL-15 recombinant protein, Cat. No. Gibco PHC0071).

[0081] The term “IL-12” (also referred to herein as “IL12”) refers to the T cell growth factor known as interleukin-12. Interleukin (IL)-12 is a secreted heterodimeric cytokine comprised of 2 disulfide- linked glycosylated protein subunits, designated p35 and p40 for their approximate molecular weights. IL-12 is produced primarily by antigen-presenting cells and drives cell- mediated immunity by binding to a two-chain receptor complex that is expressed on the surface of T cells or natural killer (NK) cells. The IL-12 receptor beta-1 (IL-12Rpi) chain binds to the p40 subunit of IL- 12, providing the primary interaction between IL- 12 and its receptor.

However, it is IL-12p35 ligation of the second receptor chain, IL-12RP2, that confers intracellular signaling. IL- 12 signaling concurrent with antigen presentation is thought to invoke T cell differentiation towards the T helper 1 (Thl) phenotype, characterized by interferon gamma (IFNy) production. Thl cells are believed to promote immunity to some intracellular pathogens, generate complement-fixing antibody isotypes, and contribute to tumor immunosurveillance.

Thus, IL-12 is thought to be a significant component to host defense immune mechanisms. IL-12 is part of the IL-12 family of cytokines which also includes IL-23, IL-27, IL-35, IL-39.

[0082] The term “IL- 15” (also referred to herein as “IL 15”) refers to the T cell growth factor known as interleukin- 15, and includes all forms of IL- 15 including human and mammalian forms, conservative amino acid substitutions, glycoforms, biosimilars, and variants thereof. IL- 15 is described, e.g., in Fehniger and Caligiuri, Blood 2001, 97, 14-32, the disclosure of which is incorporated by reference herein. IL-15 shares and y signaling receptor subunits with IL-2. Recombinant human IL-15 is a single, non-glycosylated polypeptide chain containing 114 amino acids (and an N-terminal methionine) with a molecular mass of 12.8 kDa. Recombinant human IL-15 is commercially available from multiple suppliers, including ProSpec-Tany TechnoGene Ltd., East Brunswick, N.J., USA (Cat. No. CYT-230-b) and ThermoFisher Scientific, Inc., Waltham, Mass., USA (human IL-15 recombinant protein, Cat. No. 34-8159-82).

[0083] The term “IL- 18” (also referred to herein as “IL 18”) refers to the T cell growth factor known as interleukin- 15. Interleukin- 18 (IL-18) is a proinflammatory cytokine that belongs to the TL-1 cytokine family, due to its structure, receptor family and signal transduction pathways. Related cytokines include IL-36, IL-37, IL-38.

[0084] The term “IL-21” (also referred to herein as “IL21”) refers to the pleiotropic cytokine protein known as interleukin-21, and includes all forms of IL-21 including human and mammalian forms, conservative amino acid substitutions, glycoforms, biosimilars, and variants thereof. IL-21 is described, e.g., in Spolski and Leonard, Nat. Rev. Drug. Disc. 2014, 13, 379-95, the disclosure of which is incorporated by reference herein. IL-21 is primarily produced by natural killer T cells and activated human CD4 ⁺ T cells. Recombinant human IL-21 is a single, non-glycosylated polypeptide chain containing 132 amino acids with a molecular mass of 15.4 kDa. Recombinant human IL-21 is commercially available from multiple suppliers, including ProSpec-Tany TechnoGene Ltd., East Brunswick, N.I., USA (Cat. No. CYT-408-b) and ThermoFisher Scientific, Inc., Waltham, Mass., USA (human IL-21 recombinant protein, Cat. No. 14-8219-80).

[0085] The term “liquid tumor” refers to an abnormal mass of cells that is fluid in nature. Liquid tumor cancers include, but are not limited to, leukemias, myelomas, and lymphomas, as well as other hematological malignancies. TILs obtained from liquid tumors may also be referred to herein as marrow infiltrating lymphocytes (MILs).

[0086] “Magnetic” in “magnetic particle” as used herein refers to all subtypes of magnetic particles, which can be prepared with methods well known to the skilled person in the art, especially ferromagnetic particles, superparamagnetic particles and paramagnetic particles. “Ferromagnetic” materials are strongly susceptible to magnetic fields and are capable of retaining magnetic properties when the field is removed. “Paramagnetic” materials have only a weak magnetic susceptibility and when the field is removed quickly lose their weak magnetism. “Superparamagnetic” materials are highly magnetically susceptible, i.e. they become strongly magnetic when placed in a magnetic field, but, like paramagnetic materials, rapidly lose their magnetism.

[0087] “Marker” as used herein refers to a cell antigen that is specifically expressed by a certain cell type. Preferentially, the marker is a cell surface marker, so that enrichment, isolation and/or detection of living cells can be performed.

[0088] “Marker-binding fragment” as used herein refers to any moiety that binds preferentially to the desired target molecule of the cell, i.e. the antigen. The term moiety comprises, e.g., an antibody or antibody fragment. The term “antibody” as used herein refers to polyclonal or monoclonal antibodies which can be generated by methods well known to the person skilled in the art. The antibody may be of any species, e.g. murine, rat, sheep, human. For therapeutic purposes, if non-human antigen binding fragments are to be used, these can be humanized by any method known in the art. The antibodies may also be modified antibodies (e.g. oligomers, reduced, oxidized and labelled antibodies). The term “antibody” comprises both intact molecules and antibody fragments, such as Fab, Fab', F(ab')2, Fv and single- chain antibodies. Additionally, the term “marker-binding fragment” includes any moiety other than antibodies or antibody fragments that binds preferentially to the desired target molecule of the cell. Suitable moieties include, without limitation, oligonucleotides known as aptamers that bind to desired target molecules (Hermann and Pantel, 2000: Science 289: 820-825), carbohydrates, lectins or any other antigen binding protein (e g receptor-ligand interaction).

[0089] “Media” means various solutions known in the art of cell culturing, cell handling and stabilization used to reduce cell death, including but not limited to one or more of the following media Organ Preservation Solutions , selective lysis solutions, PBS, DMEM, HBSS, DPBS, RPMI, Iscove’s medium, X-VIVO™, Lactated Ringer's solution, Ringer's acetate, saline, PLASMALYTE™ solution, crystalloid solutions and IV fluids, colloid solutions and IV fluids, five percent dextrose in water (D5W), Hartmann's Solution. The media can be standard cell media like the above mentioned-media or special media for e.g. primary human cell culture (e.g. for endothelia cells, hepatocytes, or keratinocytes) or stem cells (e.g. dendritic cell maturation, hematopoietic expansion, keratinocytes, mesenchymal stem cells or T cell expansion). The media may have supplements or reagents well known in the art, e.g. albumins and transport proteins, amino acids and vitamins, antibiotics, attachments factors, growth factors and cytokines, hormones, metabolic inhibitors or solubilizing agents. Various media are commercially available e. g. from ThermoFisher Scientific or Sigma-Aldrich.

[0090] The term “microenvironment,” as used herein, may refer to the solid or hematological tumor microenvironment as a whole or to an individual subset of cells within the microenvironment. The tumor microenvironment, as used herein, refers to a complex mixture of “cells, soluble factors, signaling molecules, extracellular matrices, and mechanical cues that promote neoplastic transformation, support tumor growth and invasion, protect the tumor from host immunity, foster therapeutic resistance, and provide niches for dominant metastases to thrive,” as described in Swartz, et al., Cancer Res., 2012, 72, 2473. Although tumors express antigens that should be recognized by T cells, tumor clearance by the immune system is rare because of immune suppression by the microenvironment.

[0091] The term “negatively separated” as used herein refers to the active separation of cells which are bound by one marker-binding fragment coupled to a solid phase and these cells are not the required population of cells.

[0092] “Non-labelled” or “untouched” as used herein refers to the cells which are not bound by one marker-binding fragment coupled to a solid phase. The non-labelled, untouched cell fraction contains the desired target cells.

[0093] “Non-target cells” as used herein refers to cells which are specifically bound by one marker-binding fragment which is coupled to a solid phase that is used to remove an unwanted cell type.

[0094] OKT-3” (also referred to herein as “OKT3”) refers to a monoclonal antibody or biosimilar or variant thereof, including human, humanized, chimeric, or murine antibodies, directed against the CD3 receptor in the T cell antigen receptor of mature T cells, and includes commercially-available forms such as OKT-3 (30 ng/mL, MACS GMP CD3 pure, Miltenyi Biotech, Inc., San Diego, Calif, USA) and muromonab or variants, conservative amino acid substitutions, glycoforms, or biosimilars thereof.

[0095] ‘Particle” as used herein refers to a solid phase such as colloidal particles, microspheres, nanoparticles, or beads. Methods for generation of such particles are well known in the field of the art. The particles may be magnetic particles or have other selective properties. The particles may be in a solution or suspension or they may be in a lyophilized state prior to use in the present invention. The lyophilized particle is then reconstituted in convenient buffer before contacting the sample to be processed regarding the present invention.

[0096] The terms “peripheral blood mononuclear cells” and “PBMCs” refers to a peripheral blood cell having a round nucleus, including lymphocytes (T cells, B cells, NK cells) and monocytes. Preferably, the peripheral blood mononuclear cells are irradiated allogeneic peripheral blood mononuclear cells. PBMCs are a type of antigen-presenting cell.

[0097] The terms “pharmaceutically acceptable carrier” or “pharmaceutically acceptable excipient” are intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and inert ingredients The use of such pharmaceutically acceptable carriers or pharmaceutically acceptable excipients for active pharmaceutical ingredients is well known in the art. Except insofar as any conventional pharmaceutically acceptable carrier or pharmaceutically acceptable excipient is incompatible with the active pharmaceutical ingredient, its use in the therapeutic compositions of the invention is contemplated. Additional active pharmaceutical ingredients, such as other drugs, can also be incorporated into the described compositions and methods.

[0098] The term “population of cells” (including TILs) herein is meant a number of cells that share common traits. In general, populations generally range from 1 x 10 ⁶ to 1 x 10 ¹² in number, with different TIL populations comprising different numbers.

[0099] “Positively separated” as used herein refers to the active separation of cells which are bound by one marker-binding fragment coupled to a solid phase and these cells are the required population of cells.

[00100] “Negatively separated” as used herein refers to the active separation of cells which are bound by one marker-binding fragment coupled to a solid phase and these cells are not the required population of cells.

[00101] “Purity” as used herein refers to the percentage of the target population or populations desired from the original solid tissue.

[00102] “Rapid expansion” means an increase in the number of antigen-specific TILs of at least about 3-fold (or 4-, 5-, 6-, 7-, 8-, or 9-fold) over a period of a week, more preferably at least about 10-fold (or 20-, 30-, 40-, 50-, 60-, 70-, 800-, or 90-fold) over a period of a week, more preferably at least about 100-fold (or 200-, 300-, 400-, 500-, 600-, 700-, 800-, or 900-fold) over a period of a week, or most preferably at least about 1000-fold or 2000-, 3000-, 4000-, 5000-, 6000-, 7000-, 8000-, or 9000-fold) over a period of a week. A number of rapid expansion protocols are outlined below.

[00103] “Regenerative medicine(s),” “adoptive cell therapy(ies),” or “advanced therapy medicinal product(s)” are used interchangeably herein to refer to cellular material that is used for therapeutic purposes of one or more mammals either by: the action of a part of or all of the cellular material; the supportive actions of a part of or all of the cellular material with the aim to improve the wellbeing of the mammal after application. The therapeutic cells can either be used directly or may require further processing, expansion and/or engineering to provide these actions. [00104] “Sample” as used herein refers to a sample containing cells in any ratio. Preferentially, these cells are viable. In some instances, these cells can also be fixed or frozen cells which may be used for subsequent nucleic acids or protein extraction. The samples may be from animals, especially mammals such as mouse, rats, or humans. Any compressible solid tissue that contains cells can be used. The invention is illustrated mainly through the isolation of hematopoietic and cancer cells from solid tumor tissue. However, the invention relates to a method for isolation of a breadth of cells from any mammalian solid tissue.

[00105] “ Solid phase” as used herein refers to the coupling of the marker-binding fragment, e.g. an antibody, bound to another substrate(s), e.g. particles, fluorophores, haptens like biotin, polymers, or larger surfaces such as culture dishes and microtiter plates. In some cases, the coupling results in direct immobilization of the antigen-binding fragment, e.g. if the antigenbinding fragment is coupled to a larger surface of a culture dish. In other cases, this coupling results in indirect immobilization, e.g. an antigen-binding fragment coupled directly or indirectly (via e.g. biotin) to a magnetic bead is immobilized if said bead is retained in a magnetic field. In further cases the coupling of the antigen-binding fragment to other molecules results not in a direct or indirect immobilization but allows for enrichment, separation, isolation, and detection of cells according to the present invention, e.g. if the marker-binding fragment is coupled to a chemical or physical moiety which then allows discrimination of labelled cells and non-labelled cells, e.g. via flow cytometry methods, like FACS sorting, or fluorescence microscopy.

[00106] “ Solid tissue” as used herein refers to a piece or pieces of animal derived mammalian solid tissue which by its three dimensions i.e. length, breadth and thickness as a geometrical body is larger than the size of multiple individual cell based units and often contains connective materials such as collagen or a similar matrix that make up structure of the tissue whereby said solid tissue cannot flow through tubes or be collected by a syringe or similar small conduit or receptacle and is i.e. with dimensions in the range of 500 pm, 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 1 cm, 2 cm, 3 cm, 4 cm, 5 cm, 10 cm, 20 cm, 30 cm, or more.

[00107] “ Solid tumor” refers to an abnormal mass of tissue that usually does not contain cysts or liquid areas. Solid tumors may be benign or malignant. The term "solid tumor cancer" refers to malignant, neoplastic, or cancerous solid tumors. Solid tumor cancers include, but are not limited to, sarcomas, carcinomas, and lymphomas, such as cancers of the lung, breast, prostate, colon, rectum, and bladder. The tissue structure of solid tumors includes interdependent tissue compartments including the parenchyma (cancer cells) and the supporting stromal cells in which the cancer cells are dispersed and which may provide a supporting microenvironment. In some embodiments, the cancer is selected from cervical cancer, head and neck cancer (including, for example, head and neck squamous cell carcinoma [HNSCC]) glioblastoma, ovarian cancer, sarcoma, pancreatic cancer, bladder cancer, breast cancer, triple negative breast cancer, and nonsmall cell lung carcinoma. The tissue structure of solid tumors includes interdependent tissue compartments including the parenchyma (cancer cells) and the supporting stromal cells in which the cancer cells are dispersed and which may provide a supporting microenvironment.

[00108] By “thawed cryopreserved TILs” herein is meant a population of TILs that was previously cryopreserved and then treated to return to room temperature or higher, including but not limited to cell culture temperatures or temperatures wherein TILs may be administered to a patient.

[00109] The terms “treatment,” “treating,” “treat,” and the like, refer to obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease.

“Treatment,” as used herein, covers any treatment of a disease in a mammal, particularly in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development or progression; and (c) relieving the disease, i.e., causing regression of the disease and/or relieving one or more disease symptoms. “Treatment” is also meant to encompass delivery of an agent in order to provide for a pharmacologic effect, even in the absence of a disease or condition. For example, “treatment” encompasses delivery of a composition that can elicit an immune response or confer immunity in the absence of a disease condition, e.g., in the case of a vaccine.

[00110] By “tumor infiltrating lymphocytes” or “TILs” herein is meant a population of cells originally obtained as white blood cells that have left the bloodstream of a subject and migrated into a tumor. TILs include, but are not limited to, CD8 ⁺ cytotoxic T cells (lymphocytes), Thi and Thi 7 CD4 ⁺ T cells, natural killer cells, dendritic cells, and Ml macrophages. TILs include both primary and secondary TILs. “Primary TILs” are those that are obtained from patient tissue samples as outlined herein (sometimes referred to as “freshly harvested”), and “secondary TILs” are any TIL cell populations that have been expanded or proliferated as discussed herein, including, but not limited to bulk TILs and expanded TILs (“REP TILs” or “post-REP TILs”). TIL cell populations can include genetically modified TILs. TILs can generally be defined either biochemically, using cell surface markers, or functionally, by their ability to infiltrate tumors and effect treatment. TILs can be generally categorized by expressing one or more of the following biomarkers: CD4, CD8, TCR ap, CD27, CD28, CD56, CCR7, CD45Ra, CD62L, CD95, PD-1, and CD25. Additionally and alternatively, TILs can be functionally defined by their ability to infiltrate solid tumors upon reintroduction into a patient. TILS may further be characterized by potency— for example, TILS may be considered potent or functional if in response to TCR engagement they produce, for example, interferon (IFN) release is greater than about 50 pg/mL, greater than about 100 pg/mL, greater than about 150 pg/mL, or greater than about 200 pg/mL, or more preferably individual cells can be Potency through intracellular staining for CD137, CD107a, INF -j TNF-a, and IL-2 following TCR induced stimulation by flow cytometry.

[00111] “Retentate” as used herein refers to the material that does not pass through a filter, mesh or membrane.

[00112] “Ultimate utility” as used herein refers to manufacture of or direct use in regenerative medicines, adoptive cell therapies, ATMPs, diagnostic in vitro studies or scientific research.

[00113] The term “isolated” with respect to cells, tissues, proteins, and nucleic acids includes cells, tissues, proteins, and nucleic acids that are relatively purified with respect to other bacterial, viral, cellular, or other components that may normally be present in situ, up to and including a substantially pure preparation of the cells, tissues, proteins, and nucleic acids. The term “isolated” also includes cells, tissues, proteins, and nucleic acids that have no naturally occurring counterpart, have been chemically synthesized and are thus substantially uncontaminated by other cells, tissues, proteins, and nucleic acids, or has been separated or purified from most other components (e.g., cellular components or organism components) with which they are naturally accompanied (e.g., other cellular proteins, nucleic acids, or cellular or extracellular components).

[00114] Compositions or methods “comprising” or “including” one or more recited elements may include other elements not specifically recited. For example, a composition that “comprises” or “includes” a protein may contain the protein alone or in combination with other ingredients. The transitional phrase “consisting essentially of’ means that the scope of a claim is to be interpreted to encompass the specified elements recited in the claim and those that do not materially affect the basic and novel characteristic(s) of the claimed invention. Thus, the term “consisting essentially of’ when used in a claim of this invention is not intended to be interpreted to be equivalent to “comprising.”

[00115] “Optional” or “optionally” means that the subsequently described event or circumstance may or may not occur and that the description includes instances in which the event or circumstance occurs and instances in which the event or circumstance does not.

[00116] Designation of a range of values includes all integers within or defining the range, and all subranges defined by integers within the range.

[00117] Unless otherwise apparent from the context, the term “about” encompasses values ± 5% of a stated value.

[00118] The term “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).

[00119] The term “or” refers to any one member of a particular list.

[00120] The singular forms of the articles “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a protein” or “at least one protein” can include a plurality of proteins, including mixtures thereof.

[00121] Statistically significant means p <0.05.

DETAILED DESCRIPTION

[00122] Provided herein are methods for identifying a therapeutically effective population of tumor infiltrating lymphocytes (TILs), methods of predicting whether a subject with a cancer will respond to treatment with a population of TILs, methods for preparing a therapeutic population of TILs, populations of TILs produced by the methods, and methods of using the TILs to treat cancer in a subject. Biological markers are provided that are predictive of whether a subject treated with the TILs will be responsive or non-responsive. The biological markers and methods described herein can be used, for example, in combination with the methods disclosed in WO 2021/123832, herein incorporated by reference in its entirety for all purposes.

[00123] T cells are derived from hematopoietic stem cells resident in bone marrow but subsequently migrate to and mature in the thymus. During the process of maturation, T cells undergo a series of selection events, thereby generating a diverse repertoire of T cells. These cells are then released into the peripheral circulation to carry out their specific functions as a part of the adaptive immune system.

[00124] T cells are not a homogeneous group of cells but consist of many lineages, of which the predominant types are defined by the expression of two further cell markers. CD4 expressing T cells are generally termed helper (Th) and are thought to orchestrate many functions of the immune system by cell-cell contact and through the production of mediator molecules called cytokines. CD8 T cells are considered to be cytotoxic (Tc) and are thought to be the cells which perform direct killing of target cells. These activities are all controlled through the T cell receptor/antigen/MHC interaction - consequently, upon successful recognition of a peptide/MHC on a target cell, CD4 and CD8 cells act in concert through cytokine production and cytotoxic activity to eliminate target cells, including virus infected and tumor cells.

[00125] T cells do not recognize intact proteins (antigens) but respond to short, protein fragments presented on the surface of target cells by specific proteins called the Major Histocompatibility Complex (MHC). During the maturation process, T cells express on their cell surface an antigen-specific T cell receptor (TCR), which recognizes these short protein (peptide) antigens presented by MHC molecules. Consequently, only when the correct peptide is presented on the surface of a target cell associated with the correct MHC molecule will the T cell activate its effector functions. Therefore, the frequency of tumor specific T cells are enriched in the tumor making it an ideal source for tumor specific T cells i.e. tumor-infiltrating lymphocytes (TIL) (Andersen et al., Cancer Res. 2012 Apr 1;72(7): 1642-50. doi: 10.1158/0008-5472.CAN- 11-2614. Epub 2012 Feb 6).

[00126] Of course, this is a highly simplified view and represents a short general overview of T cell function. The adaptive immune response does not act in isolation but requires extensive interaction with a range of immune and non-immune cells to facilitate the efficient trafficking of T cells to the required site of activity, to ensure that the correct immune response is initiated and that the immune response is controlled and turned off after it is needed. Therefore, even in patients where the manufactured TIL initiate an immune response to the tumor it may then be supported or dampened by the patient’s own immune system and the tumor microenvironment. [00127] Tumor specific TIL are T cells isolated from a tumor of a patient with primary or metastatic cancer. In most cancer patients circulating tumor-specific T cells can hardly be detected in blood. However, certain cancers such as cutaneous melanoma appear to be immunogenic as it has the ability to induce significant numbers of T cells with anti-tumor activity during the natural course of the tumor growth, especially within the tumor areas (Muul et al., J Immunol. 1987 Feb 1 ; 138(3):989-95). Tumor-reactive T cells “selected as T cell specific for the tumor” can be isolated from tumor material and expanded ex vivo into high numbers. Reports have shown that these cells contain anti -turn or reactivity, which can result in tumor destruction and clinical responses upon reinfusion into the patient (Dudley et al., Science. 2002 Oct 25;298(5594):850-4. Epub 2002 Sep 19). In subsequent trials the importance of T cell characteristics was confirmed and the benefit of “young” rapidly growing cells “Young TILs” was confirmed whereby cells are “not selected for specificity” at all. Remarkably this produces excellent response rates in TIL or CD8 selected TIL of around 50% (Besser et al., Anti cancer Res. 2009 Jan;29(l): 145-54; Dudley et al., Clin Cancer Res. 2010 Dec 15; 16(24):6122-31. doi: 10.1158/1078-0432. CCR-10-1297. Epub 2010 Jul 28).

[00128] Studies by Andersen et al. (Cancer Res. 2012 Apr 1;72(7): 1642-50. doi: 10.1158/0008-5472. CAN-11-2614. Epub 2012 Feb 6) identified that melanoma specific T cells (for known cancer antigens) are enriched within the tumor compared with T cells in the peripheral blood. This supports the dogma that the isolated TIL population are enriched tumor specific T cells resulting in an enhanced anti-tumor activity when compared with early trials in melanoma patients using T cells isolated from peripheral blood and expanded in similar levels of IL2 or intravenous IL-2 alone (LAK cells - Bordignon et al., Haematologica. 1999 Dec; 84(12): 1110-49).

[00129] US Patent No. 10,398,734 relates to methods for expanding TILs and producing therapeutic populations of TILs. The tumor of the ‘734 patent is shipped as a bulk tumor, and the TILs inside the bulk tumor rapidly become oxygen deficient and deteriorate progressively over time. The tumor of the ‘734 patent is also processed to fragments which have deteriorated internal cell populations. Furthermore, the TILs used for manufacturing will only be TILs expanded from tissue fragments and not any TILs retained in the interior. Therefore, the resulting cell population may not reflect the full diversity of the tumor environment.

[00130] Harvesting TILs requires the aseptic disaggregation of solid tissue as a bulk tumor prior to the culture and expansion of the TIL population. The conditions during solid tissue disaggregation and time taken to harvest the cells have a substantial impact on the viability and recovery of the final cellularized material. A solid tissue derived cell suspension that is obtained using conventional methods often includes a wide variety of different cell types, disaggregation media, tissue debris and/or fluids. This may necessitate the use of selective targeting and/or isolation of cell types, for example, prior to manufacture of regenerative medicines, adoptive cell therapies, ATMPs, diagnostic in vitro studies and/or scientific research.

[00131] Currently, selection or enrichment techniques generally utilize one of: size, shape, density, adherence, strong protein-protein interactions (i.e. antibody-antigen interactions). For example, in some instances selection may be conducted by providing a growth supporting environment and by controlling the culture conditions or more complex cell marker interactions associated with semi-permanent or permanent coupling to magnetic or non-magnetic solid or semi-solid phase substrates.

[00132] For enrichment, isolation, or selection, any sorting technology can be used, for example, affinity chromatography or any other antibody-dependent separation technique known in the art. Any ligand-dependent separation technique known in the art may be used in conjunction with both positive and negative separation techniques that rely on the physical properties of the cells. An especially potent sorting technology is magnetic cell sorting. Methods to separate cells magnetically are commercially available e.g. from Thermo Fisher, Miltenyi Biotech, Stemcell Technologies, Cellpro Seattle, Advanced Magnetics, Boston Scientific, or Quad Technologies. For example, monoclonal antibodies can be directly coupled to magnetic polystyrene particles like Dynal M 450 or similar magnetic particles and used, for example for cell separation. The Dynabeads technology is not column based, instead these magnetic beads with attached cells enjoy liquid phase kinetics in a sample tube, and the cells are isolated by placing the tube on a magnetic rack.

[00133] Enriching, sorting and/or detecting cells from a sample includes using monoclonal antibodies in conjunction with colloidal superparamagnetic microparticles having an organic coating of, for example, polysaccharides (e.g. magnetic-activated cell sorting (MACS) technology (Miltenyi Biotec, Bergisch Gladbach, Germany)). Particles (e.g., nanobeads or MicroBeads) can be either directly conjugated to monoclonal antibodies or used in combination with anti-immunoglobulin, avidin, or anti-hapten-specific MicroBeads, or coated with other mammalian molecules with selective binding properties. [00134] Magnetic particle selection technologies such as those described above, allows cells to be positively or negatively separated by incubating them with magnetic nanoparticles coated with antibodies or other moieties directed against a particular surface marker. This causes the cells expressing this marker to attach to the magnetic nanoparticles. Afterwards the cell solution is placed within a solid or flexible container in a strong magnetic field. In this step, the cells attach to the nanoparticles (expressing the marker) and stay on the column, while other cells (not expressing the marker) flow through. With this method, the cells can be separated positively or negatively with respect to the particular marker(s).

[00135] In case of a positive selection the cells expressing the marker(s) of interest, which attached to the magnetic column, are washed out to a separate vessel, after removing the column from the magnetic field.

[00136] In case of a negative selection the antibody or selective moiety used is directed against surface markers(s) which are known to be present on cells that are not of interest. After application of the cells/magnetic nanoparticles solution onto the column the cells expressing these antigens bind to the column and the fraction that goes through is collected, as it contains the cells of interest. As these cells are non-labelled by the selective antibodies or moiety(s) coupled to nanoparticles, they are “untouched”. The known manual or semi-automated solid tissue processing steps are labor-intensive and require a knowledge of the art.

[00137] In addition, where the material is used for therapeutic purposes, the processing requires strict regulated environmental conditions during handling of the cell cultures, for example tissue processing as a part of or prior to disaggregation, enzymatic digestion and transfer into storing devices, or incubation conditions for disaggregation/cellularization and viable tissue yields. Typically, this process would require multiple pieces of laboratory and tissue processing equipment, and personnel with the skills and knowledge of the scientific art with critical stages contained within either hazard containment or tissue processing facility (s) aseptic environment(s) in order to perform the same activity safely and also minimize the risk of contamination(s).

[00138] Viability and recovery of a desired product from tissue may be affected by the conditions during tissue collection, disaggregation, and harvesting of cells. The invention arises from a need to provide improved tissue processing, including an apparatus/device that undertakes said processing that achieves the unmet need described above [00139] Current predictive models for anti-tumor reactivity of TIL therapy infusion product compositions have limited positive and negative predictive power. Provided herein are biological markers that can be used in methods of preparing therapeutic populations of tumor infdtrating lymphocytes (TILs). These biological markers are predictive of whether a subject treated with the TILs will be responsive or non-responsive. Recipients of TIL products with these biological markers are more likely to develop a positive response to the therapy. In some embodiments, the biological markers and methods described herein can be used as part of a prescreening assay prior to treatment of a subject. In some embodiments, the biological markers and methods described herein can be part of a potency assay for TIL products. In some embodiments, the biological markers and methods described herein can be used as a companion diagnostic.

[00140] Provided herein are methods for identifying a therapeutically effective population of tumor infdtrating lymphocytes (TILs). These methods can comprise, for example, identifying one or both of the following in a population of TILs: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. Such methods can further comprise administering a therapeutic amount of the population of TILs to a subject with cancer to treat the cancer in the subject.

[00141] C7 TILs can be characterized in different ways. In some embodiments, C7 TILs have an expression profde as shown in Figure 2B. In some embodiments, C7 TILs have an expression profde as shown in Figure 6C. In some embodiments, C7 TILs have the characteristics shown in Figure 3D (e.g., in some embodiments, C7 TILs are characterized by high expression and/or activity of the predicted master regulators shown in Figure 3D for C7 TILs). In some embodiments, C7 TILs are TILs that are MX1+OAS1+. In some embodiments, C7 TILs are TILs that are LGALS9+. In some embodiments, C7 TILs are TILs that are TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, GZMK-, EOMES-, CD27-, CCR7-, CTLA4-, CHAC1-, KLRC2-, ZNF683-, IL5-, ILI3-, and CD28-. Likewise, C9 TILs can be characterized in different ways. In some embodiments, C9 TILs have an expression profde as shown in Figure 2B. In some embodiments, C9 TILs have the characteristics shown in Figure 3D (e.g., in some embodiments, C9 TILs are characterized by high expression and/or activity of the predicted master regulators shown in Figure 3D for C9 TILs). In some embodiments, C9 TILs are BBC3+CHAC1+. In some embodiments, C9 TILs are CD4-, TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, MKI67-, GZMK-, EOMES-, F0XP3-, CD27-, CCR7-, CTLA4-, KLRC2-, ZNF683-, IL5-, IL13-, CD28-, SELL-, MX 1-, and 0AS1-.

[00142] Provided herein are methods for identifying a therapeutically effective population of tumor infiltrating lymphocytes (TILs). These methods can comprise, for example, identifying one or both of the following in a population of TILs: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. Provided herein are methods for identifying a therapeutically effective population of tumor infiltrating lymphocytes (TILs). These methods can comprise, for example, identifying one or both of the following in a population of TILs: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not MX1+0AS1+ and/or for TILs that are not BBC3+CHAC1+. These methods can comprise, for example, identifying one or both of the following in a population of TILs: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+. Such methods can further comprise administering a therapeutic amount of the population of TILs to a subject with cancer to treat the cancer in the subject.

[00143] Also provided herein are methods of predicting whether a subject with a cancer will respond to treatment with a population of tumor infiltrating lymphocytes (TILs). Such methods can comprise, for example: (a) obtaining the population of TILs from the subject; and (b) measuring one or both of the following in the population: (i) TCR repertoire clonality; and (ii) the percentage of C7 TILs and/or the percentage of C9 TILs, wherein the subject is predicted to respond to treatment if the population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. Such methods can further comprise administering a therapeutic amount of the population of TILs to the subject predicted to respond to treatment (i.e., if the subject is predicted to respond to treatment). Also provided herein are methods of predicting whether a subject with a cancer will respond to treatment with a population of tumor infiltrating lymphocytes (TILs). Such methods can comprise, for example: (a) obtaining the population of TILs from the subject; and (b) measuring one or both of the following in the population: (i) TCR repertoire clonality; and (ii) the percentage of MX1+OAS1+ TILs and/or the percentage of BBC3+CHAC1+ TILs, wherein the subject is predicted to respond to treatment if the population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not MX1+0AS1+ and/or for TILs that are not BBC3+CHAC1+ Such methods can further comprise administering a therapeutic amount of the population of TILs to the subject predicted to respond to treatment (i.e., if the subject is predicted to respond to treatment). Also provided herein are methods of predicting whether a subject with a cancer will respond to treatment with a population of tumor infdtrating lymphocytes (TILs). Such methods can comprise, for example: (a) obtaining the population of TILs from the subject; and (b) measuring one or both of the following in the population: (i) TCR repertoire clonality; and (ii) the percentage of LGALS9+ TILs and/or the percentage of BBC3+CHAC1+ TILs, wherein the subject is predicted to respond to treatment if the population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+. Such methods can further comprise administering a therapeutic amount of the population of TILs to the subject predicted to respond to treatment (i.e., if the subject is predicted to respond to treatment).

[00144] Also provided herein are methods for preparing a therapeutic population of tumor infdtrating lymphocytes (TILs). These methods can comprise, for example: (a) obtaining or receiving a first population of TILs; (b) measuring one or both of the following in the first population: (i) TCR repertoire clonality; and (ii) the percentage of C7 TILs and/or the percentage of C9 TILs; and (c) selecting and expanding the first population to generate the therapeutic population of TILs if the first population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not C7 TILs and/or for TILs that are not C9 TILs. As described in more detail elsewhere herein, the methods can further administering a therapeutic amount of the therapeutic population of TILs to a subject with a cancer to treat the subject. Also provided herein are methods for preparing a therapeutic population of tumor infiltrating lymphocytes (TILs). These methods can comprise, for example: (a) obtaining or receiving a first population of TILs; (b) measuring one or both of the following in the first population: (i) TCR repertoire clonality; and (ii) the percentage of MX1+0AS1+ TILs and/or the percentage of BBC3+CHAC1+ TILs; and (c) selecting and expanding the first population to generate the therapeutic population of TILs if the first population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not MX1+0AS1+ and/or for TILs that are not BBC3+CHAC1+. As described in more detail elsewhere herein, the methods can further administering a therapeutic amount of the therapeutic population of TILs to a subject with a cancer to treat the subject. Also provided herein are methods for preparing a therapeutic population of tumor infiltrating lymphocytes (TILs). These methods can comprise, for example: (a) obtaining or receiving a first population of TILs; (b) measuring one or both of the following in the first population: (i) TCR repertoire clonality; and (ii) the percentage of LGALS9+ TILs and/or the percentage of BBC3+CHAC1+ TILs; and (c) selecting and expanding the first population to generate the therapeutic population of TILs if the first population has one or both of the following characteristics: (i) high TCR repertoire clonality; and (ii) enrichment for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+. As described in more detail elsewhere herein, the methods can further administering a therapeutic amount of the therapeutic population of TILs to a subject with a cancer to treat the subject.

[00145] In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR repertoire clonality. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not C7 TILs and/or for TILs that are not C9 TILs (e.g., enriched for TILs that are not C7 TILs, enriched for TILs that are not C9 TILs, or enriched for TILs that are not C7 TILs and for TILs that are not C9 TILs). In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR repertoire clonality and if they are enriched for TILs that are not C7 TILs and/or for TILs that are not C9 TILs (e.g., enriched for TILs that are not C7 TILs, enriched for TILs that are not C9 TILs, or enriched for TILs that are not C7 TILs and for TILs that are not C9 TILs). In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not MX1+0AS1+ and/or for TILs that are not BBC3+CHAC1+ (e.g., enriched for TILs that are not MX1+0AS1+, enriched for TILs that are not BBC3+CHAC1+, or enriched for TILs that are not MX1+0AS1+ and for TILs that are not BBC3+CHAC1+). In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR repertoire clonality and if they are enriched for TILs that are not MX1+0AS1+ and/or for TILs that are not BBC3+CHAC1+ (e.g., enriched for TILs that are not MX1+0AS1+, enriched for TILs that are not BBC3+CHAC1+, or enriched for TILs that are not MX1+0AS1+ and for TILs that are not BBC3+CHAC1+). In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TTLs) if they have high TCR repertoire clonality. Tn some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+ (e.g., enriched for TILs that are not LGALS9+, enriched for TILs that are not BBC3+CHAC1+, or enriched for TILs that are not LGALS9+ and for TILs that are not BBC3+CHAC1+). In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR repertoire clonality and if they are enriched for TILs that are not LGALS9+ and/or for TILs that are not BBC3+CHAC1+ (e.g., enriched for TILs that are not LGALS9+, enriched for TILs that are not BBC3+CHAC1+, or enriched for TILs that are not LGALS9+ and for TILs that are not BBC3+CHAC1+).

[00146] TCR repertoire clonality can be measured, for example, by bulk TCR RNA sequencing in a population of TILs (i.e., bulk analysis of TCR use in a population). The TCR repertoire clonality that is measured can be one or more or all of TCR P-chain repertoire clonality, TCR a-chain repertoire clonality, TCR 5-chain repertoire clonality, and TCR y-chain repertoire clonality. In one embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR a-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR 5-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR y-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality and high TCR a-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality and high TCR 5-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality and high TCR y-chain repertoire clonality In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TTLs) if they have high TCR a-chain repertoire clonality and high TCR 8-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR a-chain repertoire clonality and high TCR y-chain repertoire clonality TILs are selected and expanded if they have high. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR 8-chain repertoire clonality and high TCR y-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality, high TCR a-chain repertoire clonality, and high TCR 8-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality, high TCR a-chain repertoire clonality, and high TCR y-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality, high TCR 8-chain repertoire clonality, and high TCR y-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR a-chain repertoire clonality, high TCR 8-chain repertoire clonality, and high TCR y-chain repertoire clonality. In another embodiment, TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they have high TCR P-chain repertoire clonality, high TCR a-chain repertoire clonality, high TCR 8-chain repertoire clonality, and high TCR y-chain repertoire clonality are measured.

[00147] For CD8+ cytotoxic T lymphocytes (CTLs), the clonotypic T-cell receptor (TCR) recognizes “non-self ’ peptides (p) in complex with “self’ class I MHC glycoproteins (MHCI). To recognize and respond to the vast array of novel pMHCI determinants encountered by a given individual (or population), the adaptive immune system uses the recombination of variable (V), junctional (J), diversity (D), and constant (C) somatic gene segments to establish an extraordinary spectrum of TCRs. Most of the observed TCR diversity results from imprecise joining of these gene segments and the addition of non-template-encoded nucleotides at V(D)J junctions. The consequence is that TCR diversity is principally a function of the CDR3 regions, meaning that clonal uniqueness is reliably defined by the TCRaP CDR3 sequences. Therefore, the TCR P-chain repertoire clonality can, for example, refer to the TCR P-chain CDR3 repertoire clonality. Likewise, the TCR a-chain repertoire clonality can, for example, refer to the TCR a- chain CDR3 repertoire clonality. Likewise, the TCR 8-chain repertoire clonality can, for example, refer to the TCR 8-chain CDR3 repertoire clonality. Likewise, the TCR y-chain repertoire clonality can, for example, refer to the TCR y-chain CDR3 repertoire clonality.

[00148] TCR repertoire clonality can be represented by a Gini coefficient. The Gini coefficient is commonly used in economics and ecology to determine the degree to which some commodity is distributed among individuals and is, as such, a direct measure of equality of distribution. This approach can be used to measure the equality of distribution for individual TCR clones in TIL populations. See, e.g., Thomas et al. (2013) Proc. Natl. Acad. Sci. U.S.A. 110(5): 1839-1844, herein incorporated by reference in its entirety for all purposes. The Gini coefficient yields a value between 0 and 1 : a Gini coefficient of 0 represents a perfectly even distribution, and a higher value represents a less even distribution. The quantity varies between 0 and 1, with 1 representing extreme inequality and 0 representing an equal distribution of sequences across all clonotypes

[00149] In some methods, high TCR P-chain repertoire clonality means a Gini coefficient of at least about 0.75 or at least 0.75. In some methods, high TCR P-chain repertoire clonality means a Gini coefficient of at least about 0.8 or at least 0.8. In some methods, high TCR P-chain repertoire clonality means a Gini coefficient of at least about 0.85 or at least 0.85.

[00150] In some methods, high TCR a-chain repertoire clonality means a Gini coefficient of at least about 0.7 or at least 0.7. In some methods, high TCR a-chain repertoire clonality means a Gini coefficient of at least about 0.75 or at least 0.75. In some methods, high TCR a-chain repertoire clonality means a Gini coefficient of at least about 0.8 or at least 0.8. In some methods, high TCR a-chain repertoire clonality means a Gini coefficient of at least about 0.85 or at least 0.85.

[00151] In some methods, high TCR 6-chain repertoire clonality means a Gini coefficient of at least about 0.45 or at least 0.45. In some methods, high TCR 8-chain repertoire clonality means a Gini coefficient of at least about 0.5 or at least 0.5. In some methods, high TCR 8-chain repertoire clonality means a Gini coefficient of at least about 0.55 or at least 0.55. In some methods, high TCR S-chain repertoire clonality means a Gini coefficient of at least about 0.6 or at least 0.6.

[00152] In some methods, high TCR y-chain repertoire clonality means a Gini coefficient of at least about 0.75 or at least 0.75. In some methods, high TCR y-chain repertoire clonality means a Gini coefficient of at least about 0.8 or at least 0.8.

[00153] While in some methods TCR repertoire clonality can be measured, for example, by bulk TCR RNA sequencing in a population of TILs (i.e., bulk analysis of TCR use in a population), in other methods TCR repertoire clonality can be measured by single-cell TCR RNA sequencing. As one example, identical clones in single-cell TCR RNA sequences can be clones that have identical TCR a-chain CDR3 and TCR P-chain CDR3 amino acid sequences. Clones that have identical TCR a-chain CDR3 amino acid sequences but different TCR P-chain CDR3 amino acid sequences would be considered different clones.

[00154] In some methods, the high TCR repertoire clonality can be in a subpopulation of TILs. For example, TCR repertoire clonality can be measured in CD62L+ TILs. In some methods, high TCR repertoire clonality in a CD62L+ population of TILs as measured by singlecell sequencing can mean a Gini coefficient of at least about 0.1 or at least 0.1. In some methods, high TCR repertoire clonality in a CD62L+ population of TILs as measured by single-cell sequencing can mean a Gini coefficient of at least about 0.15 or at least 0.15. In some methods, high TCR repertoire clonality in a CD62L+ population of TILs as measured by single-cell sequencing can mean a Gini coefficient of at least about 0.2 or at least 0.2.

[00155] In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not C7 TILs. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not C9 TILs. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not C7 TILs and for TILs that are not C9 TILs. The percentage of TILs in a population that are C7 TILs and/or percentage of TILs in a population that are C9 TILs can be measured by any suitable means. For example, single-cell RNA sequencing analysis can be used.

[00156] C7 TILs can be characterized in different ways. In some embodiments, C7 TILs have an expression profile as shown in Figure 2B. In some embodiments, C7 TILs have an expression profile as shown in Figure 6C. Tn some embodiments, C7 TILs have the characteristics shown in Figure 3D (e.g., in some embodiments, C7 TILs are characterized by high expression and/or activity of the predicted master regulators shown in Figure 3D for C7 TILs). In some embodiments, C7 TILs are TILs that are MX1+0AS1+. In some embodiments, C7 TILs are TILs that are LGALS9+. In some embodiments, C7 TILs are TILs that are TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, GZMK-, EOMES-, CD27-, CCR7-, CTLA4-, CHAC1-, KLRC2-, ZNF683-, IL5-, IL13-, and CD28-. Likewise, C9 TILs can be characterized in different ways. In some embodiments, C9 TILs have an expression profile as shown in Figure 2B. In some embodiments, C9 TILs have the characteristics shown in Figure 3D (e.g., in some embodiments, C9 TILs are characterized by high expression and/or activity of the predicted master regulators shown in Figure 3D for C9 TILs). In some embodiments, C9 TILs are BBC3+CHAC1+. In some embodiments, C9 TILs are CD4-, TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, MKI67-, GZMK-, EOMES-, FOXP3-, CD27-, CCR7-, CTLA4-, KLRC2-, ZNF683-, IL5-, IL13-, CD28-, SELL-, MX 1-, and OAS 1-.

[00157] In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not MX1+OAS1+. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not BBC3+CHAC1+. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not MX1+OAS1+ and for TILs that are not BBC3+CHAC1+. The percentage of TILs in a population that are MX1+OAS1+ TILs and/or percentage of TILs in a population that are BBC3+CHAC1+ TILs can be measured by any suitable means. For example, single-cell RNA sequencing analysis can be used.

[00158] MX1 (NCBI GenelD 4599) encodes interferon-induced GTP -binding protein Mxl (UniProt ID P20591). Interferon-induced GTP -binding protein Mxl is an interferon-induced dynamin-like GTPase with antiviral activity against a wide range of RNA viruses and some DNA viruses. Its target viruses include negative-stranded RNA viruses and HBV through binding and inactivation of their ribonucleocapsid.

[00159] OAS1 (NCBI GenelD 4938) encodes 2' -5 '-oligoadenylate synthase 1 (UniProt ID P00973). 2'-5'-oligoadenylate synthase 1 is an interferon-induced, dsRNA-activated antiviral enzyme which plays a critical role in cellular innate antiviral response. Tn addition, it may also play a role in other cellular processes such as apoptosis, cell growth, differentiation and gene regulation. Synthesizes higher oligomers of 2'-5'-oligoadenylates (2-5A) from ATP which then bind to the inactive monomeric form of ribonuclease L (RNase L) leading to its dimerization and subsequent activation. Activation of RNase L leads to degradation of cellular as well as viral RNA, resulting in the inhibition of protein synthesis, thus terminating viral replication.

[00160] BBC3 (NCBI GenelD 27113) encodes Bcl-2-binding component 3 (UniProt ID Q9BXH1). Bcl-2-binding component 3 is an essential mediator of p53/TP53-dependent and p53/TP53-independent apoptosis. It promotes partial unfolding of BCL2L1 and dissociation of BCL2L1 from p53/TP53, releasing the bound p53/TP53 to induce apoptosis.

[00161] CHAC1 (NCBI GenelD 79094) encodes glutathione-specific gammaglutamylcyclotransferase 1 (UniProt ID Q9BUX1). Glutathione-specific gammaglutamylcyclotransferase 1 catalyzes the cleavage of glutathione into 5-oxo-L-proline and a Cys- Gly dipeptide. It acts specifically on glutathione, but not on other gamma-glutamyl peptides. Glutathione depletion is an important factor for apoptosis initiation and execution. Glutathionespecific gamma-glutamylcyclotransferase 1 acts as a pro-apoptotic component of the unfolded protein response pathway by mediating the pro-apoptotic effects of the ATF4-ATF3- DDIT3/CHOP cascade. It is a negative regulator of the Notch signaling pathway involved in embryonic neurogenesis. It acts by inhibiting Notch cleavage by furin, maintaining Notch in an immature inactive form, thereby promoting neurogenesis in embryos.

[00162] In some methods, a population of TILs is considered enriched for TILs that are not MX1+0AS1+ if it has less than about 3% MX1+0AS1+ TILs or less than 3% MX1+0AS1+ TILs. In some methods, a population of TILs is considered enriched for TILs that are not MX1+0AS1+ if it has less than about 2.5% MX1+0AS1+ TILs or less than 2.5% MX1+0AS1+ TILs. In some methods, a population of TILs is considered enriched for TILs that are not MX1+0AS1+ if it has less than about 2% MX1+0AS1+ TILs or less than 2% MX1+0AS1+ TILs.

[00163] In some methods, a population of TILs is considered enriched for TILs that are not BBC3+CHAC1+ if it has less than about 1.5% BBC3+CHAC1+ TILs or less than 1.5% BBC3+CHAC1+ TILs. In some methods, a population of TILs is considered enriched for TILs that are not BBC3+CHAC1+ TILs if it has less than about 1% BBC3+CHAC1+ TILs or less than 1% BBC3+CHAC1+ TILs.

[00164] In some methods, a population of TILs is considered enriched for TILs that are not MX1+0AS1+ and not BBC3+CHAC1+ if it has less than about 4.5% TILs that are either MX1+0AS1+ or BBC3+CHAC1+ or less than 4.5% TILs that are either MX1+OAS1+ or BBC3+CHAC1+. In some methods, a population of TILs is considered enriched for TILs that are not MX1+OAS 1+ and not BBC3+CHAC 1+ if it has less than about 4% TILs that are either MX1+OAS1+ or BBC3+CHAC1+ or less than 4% TILs that are either MX1+OAS1+ or BBC3+CHAC1+. In some methods, a population of TILs is considered enriched for TILs that are not MX1+OAS1+ and not BBC3+CHAC1+ if it has less than about 3.5% TILs that are either MX1+0AS1+ or BBC3+CHAC1+ or less than 3.5% TILs that are either MX1+OAS1+ or BBC3+CHAC1+. In some methods, a population of TILs is considered enriched for TILs that are not MX1+OAS1+ and not BBC3+CHAC1+ if it has less than about 3% TILs that are either MX1+0AS1+ or BBC3+CHAC1+ or less than 3% TILs that are either MX1+OAS1+ or BBC3+CHAC1+. In some methods, a population of TILs is considered enriched for TILs that are not MX1+OAS1+ and not BBC3+CHAC1+ if it has less than about 2.5% TILs that are either MX1+OAS1+ or BBC3+CHAC1+ or less than 2.5% TILs that are either MX1+OAS1+ or BBC3+CHAC1+.

[00165] In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not LGALS9+. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not BBC3+CHAC1+. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not LGALS9+ and for TILs that are not BBC3+CHAC1+. The percentage of TILs in a population that are LGALS9+ TILs and/or percentage of TILs in a population that are BBC3+CHAC1+ TILs can be measured by any suitable means. For example, single-cell RNA sequencing analysis can be used.

[00166] LGALS9 (NCBI GenelD 3965) encodes galectin-9 (UniProt ID 000182). Gal ectin-9 binds galactosides and has high affinity for Forssman pentasaccharide. Galectin-9 is a ligand for HAVCR2/TIM3, and binding to HAVCR2 induces T-helper type 1 lymphocyte (Thl) death. Gal ectin-9 is a ligand for P4HB; the interaction retains P4HB at the cell surface of Th2 T-helper cells, increasing disulfide reductase activity at the plasma membrane, altering the plasma membrane redox state, and enhancing cell migration. It is also a ligand for CD44; the interaction enhances binding of SMAD3 to the F0XP3 promoter, leading to up-regulation of F0XP3 expression and increased induced regulatory T (iTreg) cell stability and suppressive function. Galectin-9 promotes ability of mesenchymal stromal cells to suppress T-cell proliferation and expands regulatory T-cells and induces cytotoxic T-cell apoptosis following virus infection. Galectin-9 activates ERK1/2 phosphorylation, inducing cytokine (IL-6, IL-8, IL-12) and chemokine (CCL2) production in mast and dendritic cells; it inhibits degranulation and induces apoptosis of mast cells; and it induces maturation and migration of dendritic cells. Galectin-9 can also inhibit natural killer (NK) cell function.

[00167] In some methods, a population of TILs is considered enriched for TILs that are not

LGALS9+ if it has less than about 3% LGALS9+ TILs or less than 3% LGALS9+ TILs. In some methods, a population of TILs is considered enriched for TILs that are not LGALS9+ if it has less than about 2.5% LGALS9+ TILs or less than 2.5% LGALS9+ TILs. In some methods, a population of TILs is considered enriched for TILs that are not LGALS9+ if it has less than about 2% LGALS9+ TILs or less than 2% LGALS9+ TILs.

[00168] In some methods, a population of TILs is considered enriched for TILs that are not

LGALS9+ and not BBC3+CHAC1+ if it has less than about 4.5% TILs that are either LGALS9+ or BBC3+CHAC1+ or less than 4.5% TILs that are either LGALS9+ or BBC3+CHAC1+. In some methods, a population of TILs is considered enriched for TILs that are not LGALS9+ and not BBC3+CHAC1+ if it has less than about 4% TILs that are either LGALS9+ or BBC3+CHAC1+ or less than 4% TILs that are either LGALS9+ or BBC3+CHAC1+. In some methods, a population of TILs is considered enriched for TILs that are not LGALS9+ and not BBC3+CHAC1+ if it has less than about 3.5% TILs that are either LGALS9+ or BBC3+CHAC1+ or less than 3.5% TILs that are either LGALS9+ or BBC3+CHAC1+. In some methods, a population of TILs is considered enriched for TILs that are not LGALS9+ and not BBC3+CHAC1+ if it has less than about 3% TILs that are either LGALS9+ or BBC3+CHAC1+ or less than 3% TILs that are either LGALS9+ or BBC3+CHAC 1+. In some methods, a population of TILs is considered enriched for TILs that are not LGALS9+ and not BBC3+CHAC1 + if it has less than about 2.5% TILs that are either LGALS9+ or BBC3+CHAC1+ or less than 2.5% TILs that are either LGALS9+ or BBC3+CHAC1+.

[00169] In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not TRDC- , FOS-, FOSB-, TNFRSF9-, IFNG-, GZMK-, EOMES-, CD27-, CCR7-, CTLA4-, CHAC1-, KLRC2-, ZNF683-, IL5-, IL13-, and CD28-, that are not LGALS9+, and/or that are not MX1+0AS1+. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not CD4-, TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, MKI67-, GZMK-, EOMES-, FOXP3-, CD27-, CCR7-, CTLA4-, KLRC2-, ZNF683-, IL5-, IL13-, CD28-, SELL-, MX1-, and OAS1- and/or that are not BBC3+CHAC1+. In some methods, the TILs are identified or are selected and expanded (or a subject is predicted to respond to treatment with the TILs) if they are enriched for TILs that are not TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, GZMK-, EOMES-, CD27-, CCR7-, CTLA4-, CHAC1-, KLRC2-, ZNF683-, IL5-, IL13-, and CD28-, that are not LGALS9+, and/or that are not MX1+0AS1+ and for TILs that are not CD4-, TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, MKI67-, GZMK-, EOMES-, FOXP3-, CD27-, CCR7-, CTLA4-, KLRC2-, ZNF683-, IL5-, IL13-, CD28-, SELL-, MX1-, and OAS1- and/or that are not BBC3+CHAC1+. The percentage of TILs in a population that are TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, GZMK-, EOMES-, CD27-, CCR7-, CTLA4-, CHAC1-, KLRC2-, ZNF683-, IL5-, IL13-, and CD28-, that are LGALS9+, and/or that are MX1+OAS1+ and/or percentage of TILs in a population that are CD4-, TRDC-, FOS-, FOSB-, TNFRSF9-, IFNG-, MKI67-, GZMK-, EOMES-, FOXP3-, CD27- , CCR7-, CTLA4-, KLRC2-, ZNF683-, IL5-, IL13-, CD28-, SELL-, MX1-, and OAS1- and/or that are BBC3+CHACl+can be measured by any suitable means. For example, single-cell RNA sequencing analysis can be used.

[00170] TRDC (NCBI GenelD 28526) encodes T cell receptor delta constant (UniProt ID B7Z8K6). This is the constant region of T cell receptor (TR) delta chain that participates in the antigen recognition. Gamma-delta TRs recognize a variety of self and foreign non-peptide antigens frequently expressed at the epithelial boundaries between the host and external environment, including endogenous lipids presented by MH-like protein CD ID and phosphoantigens presented by butyrophilin-like molecule BTN3A1. Upon antigen recognition, gamma-delta TR induces rapid, innate-like immune responses involved in pathogen clearance and tissue repair. Binding of gamma-delta TR complex to antigen triggers phosphorylation of immunoreceptor tyrosine-based activation motifs (IT AMs) in the CD3 chains by the LCK and FYN kinases, allowing the recruitment, phosphorylation, and activation of ZAP70 that facilitates phosphorylation of the scaffolding proteins LCP2 and LAT. This leads to the formation of a supram olecular si nalosome that recruits the phospholipase PLCG1, resulting in calcium mobilization and ERK activation, ultimately leading to T cell expansion and differentiation into effector cells. Gamma-delta TRs are produced through somatic rearrangement of a limited repertoire of variable (V), diversity (D), and joining (J) genes. The potential diversity of gammadelta TRs is conferred by the unique ability to rearrange (D) genes in tandem and to utilize all three reading frames. The combinatorial diversity is considerably increased by the sequence exonuclease trimming and random nucleotide (N) region additions which occur during the V- (D)-J rearrangements.

[00171] FOS (NCBI GenelD 2353) encodes the nuclear phosphoprotein c-Fos (UniProt ID P01100). c-Fos forms a tight but non-covalently linked complex with the JUN/AP-1 transcription factor. In the heterodimer, FOS and JUN/AP-1 basic regions each seems to interact with symmetrical DNA half sites. On TGF-beta activation, forms a multimeric SMAD3/SMAD4/JUN/FOS complex at the APl/SMAD-binding site to regulate TGF-beta- mediated signaling. It also has a critical function in regulating the development of cells destined to form and maintain the skeleton. It is thought to have an important role in signal transduction, cell proliferation and differentiation. In growing cells, c-Fos activates phospholipid synthesis, possibly by activating CDS1 and PI4K2A. This activity requires Tyr-dephosphorylation and association with the endoplasmic reticulum.

[00172] FOSB (NCBI GenelD 2354) encodes FosB (UniProt ID P53539). FosB heterodimerizes with proteins of the JUN family to form an AP-1 transcription factor complex, thereby enhancing their DNA binding activity to gene promoters containing an AP-1 consensus sequence 5'-TGA[GC]TCA-3' and enhancing their transcriptional activity. As part of the AP-1 complex, it facilitates enhancer selection together with cell-type-specific transcription factors by collaboratively binding to nucleosomal enhancers and recruiting the SWI/SNF (BAF) chromatin remodeling complex to establish accessible chromatin. Together with JUN, FosB plays a role in activation-induced cell death of T cells by binding to the AP-1 promoter site of FASLG/CD95L, and inducing its transcription in response to activation of the TCR/CD3 signaling pathway. [00173] TNFRSF9 (NCBT GeneTD 3604) encodes tumor necrosis factor receptor superfamily member 9 (UniProt ID Q07011). Tumor necrosis factor receptor superfamily member 9 is a receptor for TNFSF9/4-1BBL, and it may be active during T cell activation.

[00174] IFNG (NCBI GenelD 3458) encodes interferon gamma (UniProt ID P01579). It is a type II interferon produced by immune cells such as T-cells and NK cells that plays crucial roles in antimicrobial, antiviral, and antitumor responses by activating effector immune cells and enhancing antigen presentation. Interferon gamma primarily signals through the JAK-STAT pathway after interaction with its receptor IFNGR1 to affect gene regulation. IFNG plays a role in class I antigen presentation pathway by inducing a replacement of catalytic proteasome subunits with immunoproteasome subunits. In turn, it increases the quantity, quality, and repertoire of peptides for class I MHC loading. IFNG increases the efficiency of peptide generation by inducing the expression of activator PA28 that associates with the proteasome and alters its proteolytic cleavage preference. In addition, it up-regulates MHC II complexes on the cell surface by promoting expression of several key molecules such as cathepsins B/CTSB, H/CTSH, and L/CTSL.

[00175] GZMK (NCBI GenelD 3003) encodes granzyme K (UniProt ID P49863). Granzyme K is a member of a group of related serine proteases from the cytoplasmic granules of cytotoxic lymphocytes.

[00176] EOMES (NCBI GenelD 8320) encodes eomesodermin homolog (UniProt ID 095936). Eomesodermin homolog functions as a transcriptional activator playing a crucial role during development, particularly in trophoblast differentiation and later in gastrulation, regulating both mesoderm delamination and endoderm specification. It plays a role in brain development, being required for the specification and the proliferation of the intermediate progenitor cells and their progeny in the cerebral cortex. EOMES is also involved in the differentiation of CD8+ T-cells during immune response regulating the expression of lytic effector genes.

[00177] CD27 (NCBI GenelD 939) encodes the cluster of differentiation 27 antigen (UniProt ID P26842). CD27 is a receptor for CD70/CD27L. It may play a role in survival of activated T- cells, and it may also play a role in apoptosis through association with SIVA1. [00178] CCR7 (NCBT GeneTD 1236) encodes the C-C motif chemokine receptor 7 (UniProt ID P32248). CCR7 is the receptor for the MIP-3-beta chemokine, and probable mediator of EBV effects on B-lymphocytes or of normal lymphocyte functions.

[00179] CTLA4 (NCBI GenelD 1493) encodes cytotoxic T-lymphocyte associated protein 4 (UniProt ID P16410). CTLA4 is an inhibitory receptor acting as a major negative regulator of T- cell responses. The affinity of CTLA4 for its natural B7 family ligands, CD80 and CD86, is considerably stronger than the affinity of their cognate stimulatory co-receptor CD28.

[00180] KLRC2 (NCBI GenelD 3822) encodes NKG2-C type II integral membrane protein (killer cell lectin-like receptor C2; UniProt ID P26717). NKG2-C type II integral membrane protein is an immune activating receptor involved in self-/non-self-discrimination. In complex with KLRD1 on cytotoxic lymphocyte subsets, it recognizes non-classical major histocompatibility (MHC) class lb HLA-E loaded with signal sequence-derived peptides from non-classical MHC class lb HLA-G molecules, likely playing a role in the generation and effector functions of adaptive natural killer (NK) cells and in maternal-fetal tolerance during pregnancy. It regulates the effector functions of terminally differentiated cytotoxic lymphocyte subsets, and in particular may play a role in adaptive NK cell response to viral infection. Upon HLA-E-peptide binding, it transmits intracellular signals via the adapter protein TYROBP/DAP12, triggering the phosphorylation of proximal signaling molecules and cell activation.

[00181] ZNF683 (NCBI GenelD 257101) encodes zinc finger protein 683, also known as tissue-resident T-cell transcription regulator protein (UniProt ID Q8IZ20). Tissue-resident T-cell transcription regulator protein is a transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T-cell types such as tissueresident memory T (Trm), natural killer (trNK), and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs. It plays a role in the development, retention, and longterm establishment of adaptive and innate tissue-resident lymphocyte T cell types in non- lymphoid organs, such as the skin and gut, but also in other non-barrier tissues like liver and kidney, and therefore may provide immediate immunological protection against reactivating infections or viral reinfection. Tissue-resident T-cell transcription regulator protein plays a role in the differentiation of both thymic and peripheral NKT cells. It negatively regulates the accumulation of interferon-gamma (TFN-gamma) in NKT cells at steady state or after antigenic stimulation and positively regulates granzyme B production in NKT cells after innate stimulation. It associates with the transcriptional repressor PRDM1/BLIMP1 to chromatin at gene promoter regions.

[00182] IL5 (NCBI GenelD 3567) encodes interleukin-5 (UniProt ID P05113). Interleukin-5 is a cytokine that induces terminal differentiation of late-developing B-cells to immunoglobulin secreting cells.

[00183] IL13 (NCBI GenelD 3596) encodes interleukin- 13 (UniProt ID P35225). Interleukin- 13 is a cytokine that inhibits inflammatory cytokine production. It synergizes with IL2 in regulating interferon-gamma synthesis and may be critical in regulating inflammatory and immune responses.

[00184] CD28 (NCBI GenelD 940) encodes T-cell-specific surface glycoprotein CD28 (UniProt ID P10747). CD28 is involved in T-cell activation, the induction of cell proliferation, and cytokine production and promotion of T-cell survival. It enhances the production of IL4 and IL10 in T-cells in conjunction with TCR/CD3 ligation and CD40L co-stimulation.

[00185] CD4 (NCBI GenelD 920) encodes T-cell surface glycoprotein CD4 (UniProt ID P01730). CD4 is an integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, it functions primarily as a co-receptor for the MHC class II molecule:peptide complex. The antigens presented by class II peptides are derived from extracellular proteins while class I peptides are derived from cytosolic proteins. CD4 interacts simultaneously with the T-cell receptor (TCR) and the MHC class II presented by antigen presenting cells (APCs). In turn, it recruits the Src kinase LCK to the vicinity of the TCR-CD3 complex. LCK then initiates different intracellular signaling pathways by phosphorylating various substrates ultimately leading to lymphokine production, motility, adhesion, and activation of T-helper cells. In other cells such as macrophages or NK cells, CD4 plays a role in differentiation/activation, cytokine expression, and cell migration in a TCR/LCK-independent pathway. CD4 also participates in the development of T-helper cells in the thymus and triggers the differentiation of monocytes into functional mature macrophages.

[00186] MKI67 (NCBI GenelD 4288) encodes proliferation marker protein Ki-67 (UniProt ID P46013). Ki-67 is required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly. It associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface. Ki-67 prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier. The protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility.

[00187] FOXP3 (NCBI GenelD 50943) encodes forkhead box protein P3 (UniProt ID Q9BZS1). FOXP3 is a transcriptional regulator that is crucial for the development and inhibitory function of regulatory T-cells (Tregs). It can act either as a transcriptional repressor or a transcriptional activator depending on its interactions with other transcription factors, histone acetylases, and deacetylases. FOXP3 plays an essential role in maintaining homeostasis of the immune system by allowing the acquisition of full suppressive function and stability of the Treg lineage, and by directly modulating the expansion and function of conventional T-cells. FOXP3 inhibits cytokine production and T-cell effector function by repressing the activity of two key transcription factors, RELA and NFATC2. It mediates transcriptional repression of IL2 via its association with histone acetylase KAT5 and histone deacetylase HDAC7, and can activate the expression of TNFRSF18, IL2RA and CTLA4 and repress the expression of IL2 and IFNG via its association with transcription factor RUNX1. FOXP3 inhibits the differentiation of IL17-producing helper T-cells (Thl7) by antagonizing RORC function, leading to downregulation of IL17 expression, favoring Treg development. FOXP3 also inhibits the transcriptional activator activity of RORA.

[00188] SELL (NCBI GenelD 6402) encodes L-selectin (UniProt ID P14151). L-selectin is a calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells. It mediates the adherence of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes and promotes initial tethering and rolling of leukocytes in endothelia. [00189] LGALS9 (NCBI GenelD 3965) encodes galectin-9 (UniProt ID 000182). Gal ectin-9 binds galactosides and has high affinity for Forssman pentasaccharide. Galectin-9 is a ligand for HAVCR2/TIM3, and binding to HAVCR2 induces T-helper type 1 lymphocyte (Thl) death. Galectin-9 is a ligand for P4HB; the interaction retains P4HB at the cell surface of Th2 T-helper cells, increasing disulfide reductase activity at the plasma membrane, altering the plasma membrane redox state, and enhancing cell migration. It is also a ligand for CD44; the interaction enhances binding of SMAD3 to the FOXP3 promoter, leading to up-regulation of FOXP3 expression and increased induced regulatory T (iTreg) cell stability and suppressive function. Galectin-9 promotes ability of mesenchymal stromal cells to suppress T-cell proliferation and expands regulatory T-cells and induces cytotoxic T-cell apoptosis following virus infection. Galectin-9 activates ERK1/2 phosphorylation, inducing cytokine (IL-6, IL-8, IL-12) and chemokine (CCL2) production in mast and dendritic cells; it inhibits degranulation and induces apoptosis of mast cells; and it induces maturation and migration of dendritic cells. Galectin-9 can also inhibit natural killer (NK) cell function.

[00190] In some embodiments, C7 TILs have the characteristics shown in Figure 3D (e.g., in some embodiments, C7 TILs are characterized by high expression and/or activity of the predicted master regulators shown in Figure 3D for C7 TILs). For example, C7 TILs can be characterized by high expression and/or activity of one or more or all of IRF7, ETV7, ETV3, ASH2L, PML, STAT2, SPI1, IRF9, STAT1, and IRF4. In some embodiments, C9 TILs have the characteristics shown in Figure 3D (e.g., in some embodiments, C9 TILs are characterized by high expression and/or activity of the predicted master regulators shown in Figure 3D for C9 TILs). For example, C9 TILs can be characterized by high expression and/or activity of one or more or all of POLR3A, JDP2, ZNF337, ETV2, ETV3L, SOX18, CEBPG, CREB3L4, CEBPB, and FOXD1.

[00191] Interferon regulatory factor 7 (Uniprot ID Q92985) is encoded by IRF7 (NCBI GenelD 3665). Interferon regulatory factor 7 is a key transcriptional regulator of type I interferon (IFN)-dependent immune responses and plays a critical role in the innate immune response against DNA and RNA viruses. It regulates the transcription of type I IFN genes (IFN-alpha and IFN-beta) and IFN-stimulated genes (ISG) by binding to an interferon-stimulated response element (ISRE) in their promoters.

[00192] Transcription factor ETV7 (ETS translocation variant 7; ETS variant transcription factor; Uniprot ID Q9Y603) is encoded by ETV7 (NCBI GenelD 51513). Transcription factor ETV7 is a transcriptional repressor that binds to the DNA sequence 5'-CCGGAAGT-3'.

[00193] ETS translocation variant 3 (Uniprot ID P41162) is encoded by ETV3 (NCBI GenelD 2117). ETS translocation variant 3 is a transcriptional repressor that contributes to growth arrest during terminal macrophage differentiation by repressing target genes involved in Ras-dependent proliferation. It also represses MMP1 promoter activity. [00194] Setl/Ash2 histone methyltransferase complex subunit ASH2 (ASH2 like, histone lysine methyltransferase complex subunit; Uniprot ID Q9UBL3) is encoded by ASH2L (NCBI GenelD 9070). ASH2 is a component of the Setl/Ash2 histone methyltransferase (HMT) complex, a complex that specifically methylates 'Lys-4' of histone H3, but not if the neighboring 'Lys-9' residue is already methylated.

[00195] Protein PML (PML nuclear body scaffold; promyelocytic leukemia protein; Uniprot ID P29590) is encoded by PML (NCBI GenelD 5371). PML functions via its association with PML-nuclear bodies (PML-NBs) in a wide range of important cellular processes, including tumor suppression, transcriptional regulation, apoptosis, senescence, DNA damage response, and viral defense mechanisms. It acts as the scaffold of PML-NBs allowing other proteins to shuttle in and out, a process which is regulated by SUMO-mediated modifications and interactions.

[00196] Signal transducer and activator of transcription 2 (Uniprot ID P52630) is encoded by STAT2 (NCBI GenelD 6773). STAT2 mediates signaling by type I interferons (IFN-alpha and IFN-beta). Following type I IFN binding to cell surface receptors, Jak kinases (TYK2 and JAK1) are activated, leading to tyrosine phosphorylation of STAT1 and STAT2. The phosphorylated STATs dimerize, associate with IRF9/ISGF3G to form a complex termed ISGF3 transcription factor, and then enter the nucleus. ISGF3 binds to the IFN stimulated response element (ISRE) to activate the transcription of interferon stimulated genes, which drive the cell in an antiviral state. [00197] Transcription factor PU.1 (Spi-1 proto-oncogene; Uniprot ID Pl 7947) is encoded by SPI1 (NCBI GenelD 6688). Transcription factor PU.l binds to the PU-box, a purine-rich DNA sequence (5'-GAGGAA-3') that can act as a lymphoid-specific enhancer. This protein is a transcriptional activator that may be specifically involved in the differentiation or activation of macrophages or B-cells.

[00198] Interferon regulatory factor 9 (Uniprot ID Q00978) is encoded by IRF9 (NCBI GenelD 10379). Interferon regulatory factor 9 is a transcription factor that plays an essential role in anti-viral immunity. It mediates signaling by type I IFNs (IFN-alpha and IFN-beta). Following type I IFN binding to cell surface receptors, Jak kinases (TYK2 and JAK1) are activated, leading to tyrosine phosphorylation of STAT1 and STAT2. IRF9/ISGF3G associates with the phosphorylated STATLSTAT2 dimer to form a complex termed ISGF3 transcription factor, that enters the nucleus. ISGF3 binds to the IFN stimulated response element (ISRE) to activate the transcription of interferon stimulated genes, which drive the cell in an antiviral state. [00199] Signal transducer and activator of transcription 1 (Uniprot ID P42224) is encoded by STAT1 (NCBI GenelD 6772). STAT1 mediates cellular responses to interferons (IFNs), cytokine KITLG/SCF and other cytokines and other growth factors. Following type I IFN (IFN-alpha and IFN-beta) binding to cell surface receptors, signaling via protein kinases leads to activation of Jak kinases (TYK2 and JAK1) and to tyrosine phosphorylation of STAT1 and STAT2. The phosphorylated STATs dimerize and associate with ISGF3G/IRF-9 to form a complex termed ISGF3 transcription factor that enters the nucleus. ISGF3 binds to the IFN stimulated response element (ISRE) to activate the transcription of IFN-stimulated genes (ISG), which drive the cell in an antiviral state. In response to type II IFN (IFN-gamma), STAT1 is tyrosine- and serine- phosphorylated. It then forms a homodimer termed IFN-gamma-activated factor (GAF), migrates into the nucleus, and binds to the IFN gamma activated sequence (GAS) to drive the expression of the target genes, inducing a cellular antiviral state. It becomes activated in response to KITLG/SCF and KIT signaling.

[00200] Interferon regulatory factor 4 (Uniprot ID QI 5306) is encoded by IRF4 (NCBI GenelD 3662). Interferon regulatory factor 4 is a transcriptional activator. IRF4 binds to the interferon-stimulated response element (ISRE) of the MHC class I promoter. It also binds the immunoglobulin lambda light chain enhancer, together with PU.1.

[00201] POLR3A (DNA-directed RNA polymerase III subunit RPC1; UniProt ID 014802) is encoded by POLR3A (NCBI GenelD 11128). It is a DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [00202] lun dimerization protein 2 (Uniprot ID Q8WYK2) is encoded by JDP2 (NCBI GenelD 122953). Jun dimerization protein 2 is a component of the AP-1 transcription factor that represses transactivation mediated by the Jun family of proteins. It is involved in a variety of transcriptional responses associated with AP-1, such as UV-induced apoptosis, cell differentiation, tumorigenesis, and tumor suppression. JDP2 can also function as a repressor by recruiting histone deacetylase 3/HDAC3 to the promoter region of JUN.

[00203] Zinc finger protein 337 (Uniprot ID Q9Y3M9) is encoded by ZNF337 (NCBI GenelD 26152). Zinc finger protein 337 may be involved in transcriptional regulation.

[00204] ETS translocation variant 2 (Uniprot ID 000321) is encoded by ETV2 (NCBI GenelD 2116). ETS translocation variant 2 binds to DNA sequences containing the consensus pentanucleotide 5'-CGGA[AT]-3'. [00205] ETS translocation variant 3 -like protein (ETS variant transcription factor 3 like; Uniprot ID Q6ZN32) is encoded by ETV3L (NCBI GenelD 440695). ETS translocation variant 3 -like protein is a transcriptional regulator.

[00206] SRY-box transcription factor 18 (Uniprot ID P35713) is encoded by S0X18 (NCBI GenelD 54345). SRY-box transcription factor 18 is a transcriptional activator that binds to the consensus sequence 5'-AACAAAG-3' in the promoter of target genes and plays an essential role in embryonic cardiovascular development and lymphangiogenesis. It activates transcription of PROXI and other genes coding for lymphatic endothelial markers. SOX18 also plays an essential role in triggering the differentiation of lymph vessels, but it is not required for the maintenance of differentiated lymphatic endothelial cells. It plays an important role in postnatal angiogenesis, where it is functionally redundant with SOX17. Interaction with MEF2C enhances transcriptional activation of SOX18.

[00207] CCAAT/enhancer-binding protein gamma (Uniprot ID P53567) is encoded by CEBPG (NCBI GenelD 1054). CEBPG is a transcription factor that binds to the promoter and the enhancer regions of several target genes, including the enhancer element PRE-I (positive regulatory element-I) of the IL-4 gene, the promoter and the enhancer of the immunoglobulin heavy chain, and binds to GPE1, a cis-acting element in the G-CSF gene promoter.

[00208] Cyclic AMP -responsive element-binding protein 3 -like protein 4 (Uniprot ID Q8TEY5) is encoded by CREB3L4 (NCBI GenelD 148327). CREB3L4 is a transcriptional activator that may play a role in the unfolded protein response. It binds to the UPR element (UPRE) but not to CRE element. CREB3L4 preferentially binds DNA with to the consensus sequence 5'-T[GT]ACGT[GA][GT]-3' and has transcriptional activation activity from UPRE. [00209] CCAAT/enhancer-binding protein beta (Uniprot ID P17676) is encoded by CEBPB (NCBI GenelD 1051). CEBPB is an important transcription factor regulating the expression of genes involved in immune and inflammatory responses. It also plays a significant role in adipogenesis, as well as in the gluconeogenic pathway, liver regeneration, and hematopoiesis. The consensus recognition site is 5'-T[TG]NNGNAA[TG]-3'. Its functional capacity is governed by protein interactions and post-translational protein modifications.

[00210] Forkhead box protein DI (Uniprot ID Q16676) is encoded by F0XD1 (NCBI GenelD 2297). Forkhead box protein DI is a transcription factor involved in regulation of gene expression in a variety of processes, including formation of positional identity in the developing retina, regionalization of the optic chiasm, morphogenesis of the kidney, and neuralization of ectodermal cells.

[00211] As described in more detail elsewhere herein, the TILs can originate from a subject. For example, the TILs can be from a tumor biopsy, a lymph node, or ascites. The tumor can be, for example, from a bladder cancer, a breast cancer, a cancer caused by human papilloma virus, a cervical cancer, a head and neck cancer, a lung cancer, a melanoma, an ovarian cancer, a nonsmall -cell lung cancer (NSCLC), a renal cancer, or a renal cell carcinoma. In a specific example, the tumor biopsy is from a melanoma.

[00212] Obtaining or receiving a first population of TILs can comprise obtaining a refined tumor product as described in more detail elsewhere herein. For example, this can comprise obtaining a refined tumor product by cry opreserving a resected tumor and disaggregating the cryopreserved tumor. Alternatively, this can comprise obtaining a refined tumor product by disaggregating a resected tumor and cry opreserving the disaggregated tumor. Alternatively, this can comprise obtaining a refined tumor product by cry opreserving a resected tumor and processing the tumor into multiple tumor fragments. Alternatively, this can comprise obtaining a refined tumor product by processing a resected tumor into multiple tumor fragments and cry opreserving the tumor fragments. Optionally, the cry opreserving comprises cooling under conditions whereby heat release to, into, around or in an environment including cells, as media crystalizes, is minimized or avoided. Optionally, the cryopreserving comprises continuous cooling, from disaggregation temperature to about -80°C. Optionally, the cryopreserving comprises continuous cooling at a rate of about -2°C / min. Optionally, the cryopreserving comprises continuous cooling, from disaggregation temperature to about -80°C, at a rate of about -2°C / min. Optionally, the cryopreserving comprises continuous cooling, from disaggregation temperature to about -80°C, or from disaggregation temperature to -80°C at a rate of about -2°C / min, wherein disaggregation temperature comprises a normal body temperature for an animal from which the tumor was resected, or room temperature or 20°C or 25°C , or normal human body temperature approximately 35°C or 36°C or 36.1°C to approximately 37°C or 37.1°C or 37.2°C or 37.3°C or below about 38.3°C. The disaggregating can comprise, for example, physical disaggregation, enzymatic disaggregation, or physical and enzymatic disaggregation. In some methods, a single cell suspension is obtained from the refined resected tumor product, or the refined resected tumor product comprises a single cell suspension. [00213] Obtaining or receiving a first population of TTLs can further comprise performing a first expansion as described in more detail elsewhere herein. For example, it can comprise performing a first expansion by culturing the refined resected tumor product in a cell culture medium comprising IL-2 to produce the first population of TILs. The first expansion can be performed for any suitable period of time as described elsewhere herein. For example, the first expansion step can be performed for about two weeks. In some methods, the culturing in step (ii) includes adding IL-7, IL-12, IL-15, IL-18, IL-21, or a combination thereof.

[00214] Likewise, the expanding in step (c) after selecting can be for any suitable amount of time and under any suitable conditions. For example, in some methods, the expanding comprises culturing the first population of TILs in a cell culture medium comprising IL-2. In some methods, the expanding comprises culturing the first population of TILs with additional IL-2, OKT-3, and antigen presenting cells (APCs). In some methods, the expanding in step (c) is performed for about two weeks. In some methods, the culturing in step (c) includes adding IL-7, IL- 12, IL- 15, IL- 18, IL-21, or a combination thereof. In some methods, the method further comprises harvesting and/or cry opreserving the therapeutic population of TILs.

[00215] As disclosed in more detail elsewhere herein, also provided are isolated therapeutic population of TILs obtained by or obtainable by any of the above methods, pharmaceutical formulations comprising a pharmaceutically acceptable excipient and any of the above isolated therapeutic populations of TILs, cryopreserved bags or intravenous infusion bags, containers, or vessels containing contents comprising any of the above isolated therapeutic populations of TILs, and methods of treating a cancer in a subject, comprising administering any of above isolated therapeutic population of TILs or the above pharmaceutical formulation to the subject. [00216] In some embodiments, the present invention relates to a method for isolating a therapeutic population of cryopreserved unmodified tumor infiltrating lymphocytes (UTIL) which may comprise: (a) resecting a tumor from a subject; (b) storing the resected tumor in a single use aseptic kit, wherein the aseptic kit comprises: a disaggregation module for receipt and processing of material comprising solid mammalian tissue; an optional enrichment module for filtration of disaggregated solid tissue material and segregation of non-disaggregated tissue and filtrate; and a stabilization module for optionally further processing and/or storing disaggregated product material, wherein each of the modules comprises one or more flexible containers connected by one or more conduits adapted to enable flow of the tissue material there between; and wherein each of the modules comprises one or more ports to permit aseptic input of media and/or reagents into the one or more flexible containers; (c) aseptically disaggregating the resected tumor in the disaggregation module thereby producing a disaggregated tumor, wherein the resected tumor is sufficiently disaggregated if it can be cryopreserved with a minimum of cell damage; (d) cry opreserving the disaggregated tumor in the stabilization module; (e) performing a first expansion by culturing the disaggregated tumor in a cell culture medium comprising IL-2 to produce a first population of UTILs; (f) optionally performing a second expansion by culturing the first population of UTILs with additional IL-2, OKT-3, and antigen presenting cells (APCs), to produce a second population of TILs; (g) harvesting and/or cry opreserving the second population of UTILs.

[00217] The disaggregation may comprise physical disaggregation, enzymatic disaggregation, or physical and enzymatic disaggregation. In an advantageous embodiment, the disaggregated tumor is cellularized or purified.

[00218] In some embodiments, the present invention relates to tumor infiltrating lymphocytes (TILs) in particular unmodified TILs (UTILs), which may be isolated from tumors of a cancer patient or a metastatic cancer patient, involving autologous TILs generated from and returned to the same cancer patient. The present invention also relates to methods for isolating a therapeutic population of cryopreserved TILs or UTILs and to TILs and UTILs obtained or obtainable via use of a device comprising a single use aseptic kit for processing of a resected tumor by the methods described herein.

[00219] In general, TILs may initially be obtained from a patient tumor sample (“primary TILs”) and then expanded into a larger population for further manipulation as described herein, cryopreserved, restimulated as outlined herein and optionally evaluated for phenotype and metabolic parameters as an indication of TIL health.

[00220] A patient tumor sample may be obtained using methods known in the art, generally via surgical resection, needle biopsy or other means for obtaining a sample that contains a mixture of tumor and TIL cells. In general, the tumor sample may be from any solid tumor, including primary tumors, invasive tumors or metastatic tumors. The tumor sample may also be a liquid tumor, such as a tumor obtained from a hematological malignancy. The solid tumor may be of any cancer type, including, but not limited to, breast, ovary, cervical, pancreatic, prostate, colorectal, lung, brain, renal, stomach, and skin (including but not limited to squamous cell carcinoma, basal cell carcinoma, and melanoma). Tn some embodiments, TTLs are obtained from malignant melanoma tumors, as these have been reported to have particularly high levels of TILs.

[00221] The production can generally involve a two-stage process. In stage 1, initial tumor material is dissected, placed in the aseptic kit having a disaggregation module, enzymatically digesting and/or fragmenting, and homogenizing the tumor in the disaggregation module to provide a single cell suspension. While the homogenized cells can be further purified within the aseptic kit in a separate enrichment module to remove components such as no longer required reagents; cell debris; non-disaggregated tissue, the cells can be directly cryopreserved to stabilize the starting material for TIL manufacture and storage in the stabilization module of the aseptic kit until Stage 2 is required. Stage 2 generally involves growth of the TILs out of the resected tumor starting material (2 weeks), followed by a rapid expansion process of the TIL cells (rapid expansion protocol “REP” - 2 weeks). The final product is washed and harvested prior to suspension in buffered saline, 8.5% HAS and 10% DMSO and cryopreserved to form a solid aseptic product that is thawed prior to infusion as a single dose with no further modification.

[00222] There are at least three separate elements to the treatment that can potentially contribute to therapeutic activity. The core element is the TILs (i.e., tumor-derived T cells), which can target and eliminate tumor cells by a variety of methods utilized by T cells as a part of their normal function. These methods include direct methods (i.e. perforin-mediated cytotoxicity) and indirect methods (i .e. cytokine production). Which of these methods is the most important to in vivo anti-tumor effects is unclear although mouse models suggest that the production of interferon gamma is critical for effective therapy. The two other elements which contribute to the therapy are pre-conditioning chemotherapy and high dose intravenous IL-2. These two elements are thought to act by supporting engraftment of T cells in the patient after infusion: initially through conditioning chemotherapy which removes competing and regulating immune cells; followed by the IL -2 component which supports survival of T cells.

[00223] The structure of the cell therapy product is created by growing the TIL directly out of an enzyme digested tumor mass by means of growth supporting cell culture media and a T cell supporting growth factor Interleukin-2 (IL-2). This enables tumor specific T cells to selectively survive and grow out of the tumor cell mixture, while T cells that do not recognize tumor antigens will not be stimulated and be selectively lost. The product comprises an autologous T- cell based product where the T cells have been derived from a patient’s own cancer tissue and rapidly expanded to form a pure T cell population and T cells as defined by CD3 surface marker. [00224] In brief, TILs, in particular UTILs, may be produced in a two-stage process using a tumor biopsy as the starting material: Stage 1 (generally performed over 2-3 hours) initial collection and processing of tumor material using dissection, enzymatic digestion and homogenization via use of a kit and a semi-automatic device to produce a single cell suspension which can be directly cryopreserved using the stabilization module of the kit to stabilize the starting material for subsequent manufacture and Stage 2 which can occur days or years later. Stage 2 may be performed over 4 weeks, which may be a continuous process starting with thawing of the product of Stage 1 and growth of the TIL out of the tumor starting material (about 2 weeks) followed by a rapid expansion process of the TIL cells (about 2 weeks) to increase the number of cells and therefore dose. The TILs, in particular UTILs, are concentrated and washed prior to formulation as a liquid suspension of cells. The aseptic drug product may be cryopreserved in a bag that will be thawed prior to intravenous infusion as a single dose with no further modification.

[00225] For enzymatic digestion, a cell suspension (containing both T cells and tumor cells) can be generated from the resected metastatic tumor using an enzyme mixture of DNase 1 and Collagenase (Type IV). The combination of the repeated mechanical compression exposes additional surfaces for the enzymes to access and the enzymatic reaction speed up the process of turning a solid tissue into a cell suspension prior to optional cry opreservation. In one embodiment upon completion of the disaggregation step a DMSO based cryoprotectant is added just prior to a controlled rate freezing cycle. In some embodiments, the enzymatic breakdown of the solid tissue may be by the selection and provision of one or more media enzyme solutions such as collagenase, trypsin, lipase, hyaluronidase, deoxyribonuclease, Liberase Hl, pepsin, or any mixture thereof. Enzymatic digestion of the resected metastatic tumor can occur in the disaggregation flexible containers of the semi-automatic device.

[00226] By way of example, in another embodiment of the method of the invention, where the disaggregation process is being supplemented with enzymatic digestion the media formulation for enzymatic digestion must be supplemented with enzymes that aid in protein breakdown causing the cell to cell boundaries to break down. [00227] Various liquid formulations known in the art of cell culturing or cell handling can be used as the liquid formulation used for cell disaggregation and enzymatic digestion of solid tissues, including but not limited to one or more of the following media Organ Preservation Solutions, selective lysis solutions, PBS, DMEM, HBSS, DPBS, RPMI, Iscove’s medium, XVIVO™, AIM-V™, Lactated Ringer's solution, Ringer's acetate, saline, PLASMALYTE™ solution, crystalloid solutions and IV fluids, colloid solutions and IV fluids, five percent dextrose in water (D5W), Hartmann's Solution, DMEM, HBSS, DPBS, RPMI, AIM-V™, Iscove’s medium, XVIVO™, each can be optionally supplemented with additional cell supporting factors e.g. with fetal calf serum, human serum or serum substitutes or other nutrients or cytokines to aid in cell recovery and survival or specific cell depletion. The media can be standard cell media like the above mentioned media or special media for e.g. primary human cell culture (e.g. for endothelia cells, hepatocytes or keratinocytes) or stem cells (e.g. dendritic cell maturation, hematopoietic expansion, keratinocytes, mesenchymal stem cells or T cells). The media may have supplements or reagents well known in the art, e.g. albumins and transport proteins, amino acids and vitamins, metal-ion(s), antibiotics, attachments factors, de-attachment factors, surfactants, growth factors and cytokines, hormones or solubilizing agents. Various media are commercially available e.g. from ThermoFisher, Lonza, or Sigma-Aldrich or similar media manufacturers and suppliers.

[00228] The liquid formulation required for enzymatic digestion must have sufficient calcium ions present in the of at least 0.1 mM up to 50 mM with an optimal range of 2 to 7 mM ideally 5 mM.

[00229] The solid tissue to be digested can be washed after disaggregation with a liquid formulation containing chelating agents EGTA and EDTA to remove adhesion factors and inhibitory proteins prior to washing and removal of EDTA and EGTA prior to enzymatic digestion.

[00230] The liquid formulation required for enzymatic digestion is more optimal with minimal chelating agents EGTA and EDTA which can severely inhibit enzyme activity by removing calcium ions required for enzyme stability and activity. In addition, 0- mercaptoethanol, cysteine and 8-hydroxyquinoline-5-sulfonate are other known inhibitory substances. [00231] Processing of tumor material using dissection, enzymatic digestion and homogenization produces a single cell suspension of TILs, in particular UTILs, which can be directly cryopreserved to stabilize the starting material for subsequent processing via the first expansion of the cell suspension of TILs, in particular UTILs, in IL-2 to obtain a first population of TILs, in particular UTILs.

[00232] The methods can also comprise the step of ciyopreserving the disaggregated tumor, e.g. the cell suspension. Cryopreserving the disaggregated tumor is carried out on the same day as carrying out the step of aseptically disaggregating a tumor resected from a subject thereby producing a disaggregated tumor, wherein the resected tumor is sufficiently disaggregated if it can be cryopreserved without cell damage. For example, cryopreserving is carried out 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, or 22 hours following the step of disaggregating the tumor.

Cry opreservation of the disaggregated tumor, as a single cell suspension obtained from the enzymatic disaggregation in the disaggregation module of the semi-automatic device, is carried out by cooling or maintaining the suspension at a temperature between 8 °C and at least -80 °C. Disaggregation could be as quick as 5 mins but most usually 45 mins to 1 hour and the cry opreservation can be a quick as 60 mins or up to 150 mins. In one embodiment, the methods include storing the cryopreserved disaggregated tumor. As described in preferred embodiments, the device comprises at least one cell container for cry opreservation wherein the containers are a flexible container manufactured from resilient deformable material. In this embodiment of the device, the final container is either transferred directly to a freezer -20 to -190 °C or more optimally located in the controlled rate freezing apparatus either associated with the device or supplied separately (manufactured by for example Planer Products or Asymptote Ltd) in which the temperature of the freezing chamber and the flexible storage container(s) employed to contain the enriched disaggregated solid tissue container is controlled either by: injecting a cold gas (normally nitrogen for example Planer products); or by removing heat away from the controlled cooling surface(s). Both methods result in the ability to accurately control with an error of less than 1 °C or more preferable 0.1 °C the freezing process at the required rate for the specific cell(s) to be frozen based on the freezing solution and the desired viability of the product. This cryopreservation process must consider the ice nucleation temperature which is ideally as close as possible to the melting temperature of the freezing solution. Followed by crystal growth in an aqueous solution, water is removed from the system as ice, and the concentration of the residual unfrozen solution increases. As the temperature is lowered, more ice forms, decreasing the residual non-frozen fraction which further increases in concentration. In aqueous solutions, there exists a large temperature range in which ice co-exists with a concentrated aqueous solution. Eventually through temperature reduction the solution reaches the glass transition state at which point the freezing solution and cells move from a viscous solution to a solid-like state below this temperature the cells can undergo no further biological changes and hence are stabilized, for years potentially decades, until required.

[00233] Ice nucleation and crystal growth involves release of heat to the freezing solution and the cellular microenvironment and it is desirable to maintain cooling of cells and freezing solution even as the freezing fluid resists temperature changes while undergoing phase change. Depending on whether disaggregation includes enzymatic disaggregation, and what is the optimal temperature of enzymatic digestion for a given enzyme, enzyme concentration and tissue type, temperatures at the start of cry opreservation include, without limitation, 40°C, 39°C, 38°C, 37°C, 36°C, 35°C, 34°C, 33°C, 32°C, 31°C, 30°C, 29°C, 28°C, 27°C, 26°C, 25°C, 24°C, 23°C, 22°C, 21°C, and 20°C, i.e., temperatures ranging from a mammalian body temperature to room temperature, and further include temperatures below room temperature, including but not limited to refrigeration temperatures such as, without limitation, 19°C, 18°C, 17°C, 16°C, 15°C, 14°C, 13°C, 12°C, 11°C, 10°C, 9°C, 8°C, 7°C, 6°C, 5°C, 4°C, 3°C, and 2°C. Target temperatures for cryogenic cooling include, without limitation, -60°C, -65°C, -70°C, -75°C, -80°C, -85°C, -90°C, and temperatures in between as well as colder temperatures down to the temperature of liquid nitrogen vapor storage (-195.79°C). In certain embodiments, the methods and devices used according to the invention are designed or programmed to minimize the time from physiological temperature or digestion temperature to cryostorage temperature. In certain embodiments, the methods and devices used according to the invention for cry opreservation are advantageously designed and programmed for cooling under conditions whereby heat release to, into, around or in an environment including cells, as media crystalizes, is minimized or avoided. In certain embodiments, the methods and devices used according to the invention for cryopreservation are advantageously designed and programmed for cooling under conditions whereby heat release to, into, around or in an environment including cells, as media crystalizes, is minimized or avoided, for example by maintaining a pre-determined rate of temperature change of the cry opreservation media even as nucleation and crystallization of the media releases heat that resists temperature change. Tn certain embodiments, regulating or programming a rate of temperature change includes regulating the rate of heat extraction from the cry opreservation sample to maintain a predetermined rate of temperature change. In certain embodiments, the cooling rate of the cry opreservation sample is maintained by measuring the temperature of the cry opreservation sample and adjusting the rate of heat extraction through a phase change by a feedback process. In certain embodiments, the cooling rate of the cryopreservation sample is maintained by anticipating a phase change and increasing the rate of heat extraction at the anticipated time of the phase change. In certain embodiments, methods are designed and/or devices programmed for continuous cooling from disaggregation temperature down to a cryogenic target temperature. Exemplary programmed cooling rates include, without limitation, -0.5°C/min, -l°C/min, - 1.5°C/min, -2°C/min, or -2.5°C/min. The cooling rates are program targets and may vary over a cooling cycle. The cooling rates may vary, for example by ± 0.1°C/min, ± 0.2°C/min, ± 0.3°C/min, ± 0.4°C/min, or ± 0.5°C/min. In an embodiment of the invention, the cry opreservation temperature is -80°C ± 10°C and the device is programmed to reduce temperature by l°C/min or 1.5°C/min or 2°C/min or l°C/min ± 0.5°C/min or 1.5°C/min ± 0.5°C/min or 2°C/min ± 0.5°C/min.

[00234] It will be evident that accurate controlled cooling of TILs is desired. Accordingly, to optimized measurement and control of heat transfer from the TILs, it is advantageous to employ optimize surface to volume ratios, employ cassettes to house cryopreservation containers and facilitate heat transfer, and optimally locate temperature sensors.

[00235] Cryopreservation may be employed throughout TIL manufacture including but not limited to i) cry opreservation of a processed tumor sample for use at a later time by thawing and TIL expansion, ii) cry opreservation of a processed tumor sample for use at a later time by thawing and use of tumor cells, iii) cryopreservation of a processed tumor sample for later analysis, iv) cry opreservation of a pre-REP expansion culture for use at a later time by thawing and REP expansion, v) cryopreservation of a portion of a pre-REP expansion culture (such as but not limited to a predetermined portion or to excess cells above a predetermined amount from a pre-REP culture) for use at a later time by thawing and REP expansion, vi) cryopreservation of a post-REP culture for use at a later time in a subsequent pre-REP expansion or REP, or vii) cry opreservation of a post-REP culture for use at a later time by thawing and administering to a subject. [00236] Cryopreserved TIL intermediates, products, and samples may be washed upon thawing prior to use. In certain embodiments cryopreserved tumor digests are thawed, diluted in growth media, and washed one or more times. In certain embodiments, washing comprises centrifugation and growth media change. In certain embodiments, washing comprises fdtration and growth media change. In certain embodiments, wash media is mixed into then withdrawn from a closed TIL container, such as a bag or dish and replaced by fresh media. The wash may be automated in a closed system or containers for TILs, wash media, and other components interconnected by tubes and valves.

[00237] In certain embodiments, to increase proportions of TILs, TIL subsets. TIL viability, and or TIL potency, upon thawing, dilution, and optional wash, cryopreserved TILs are held in culture prior to outgrowth (i.e. pre-REP expansion). In certain embodiments, the hold time is chosen to maximize total viable cells or fold expansion measured by CD3 In certain embodiments, the hold time may comprise or consist of from 2 to 4 hr. or from 4 to 6 hrs. or from 6 to 9 hrs. or from 9 to 12 hr. or from 12 to 18 hr. or from 18 to 24 hr.

[00238] In some embodiments, the present methods provide for obtaining young TILs, which are capable of increased replication cycles upon administration to a subject/patient and as such may provide additional therapeutic benefits over older TILs (i.e., TILs which have further undergone more rounds of replication prior to administration to a subject/patient). Features of young TILs have been described in the literature, for example Donia, at al., Scandinavian Journal of Immunology, 75: 157-167 (2012); Dudley et al., Clin Cancer Res, 16:6122-6131 (2010); Huang et al., J Immunother, 28(3):258-267 (2005); Besser et al., Clin Cancer Res, 19(17):OF1- OF9 (2013); Besser et al., J Immunother 32:415-423 (2009); Robbins, et al., J Immunol 2004; 173:7125-7130; Shen et al., J Immunother, 30: 123-129 (2007); Zhou, et al., J Immunother, 28:53-62 (2005); and Tran, et al., J Immunother, 31:742-751 (2008), all of which are incorporated herein by reference in their entireties.

[00239] The diverse antigen receptors of T and B lymphocytes are produced by somatic recombination of a limited, but large number of gene segments. These gene segments: V (variable), D (diversity), J (joining), and C (constant), determine the binding specificity and downstream applications of immunoglobulins and T-cell receptors (TCRs). The present invention provides a method for generating TILs which exhibit and increase the T-cell repertoire diversity. In some embodiments, the TILs obtained by the present method exhibit an increase in the T-cell repertoire diversity. Tn some embodiments, the TTLs obtained by the present method exhibit an increase in the T-cell repertoire diversity as compared to freshly harvested TILs and/or TILs prepared using other methods than those provide. In some embodiments, the TILs obtained by the present method exhibit an increase in the T-cell repertoire diversity as compared to freshly harvested TILs and/or TILs. In some embodiments, the TILs obtained in the first expansion exhibit an increase in the T-cell repertoire diversity. In some embodiments, the increase in diversity is an increase in the immunoglobulin diversity and/or the T-cell receptor diversity. In some embodiments, the diversity is in the immunoglobulin is in the immunoglobulin heavy chain. In some embodiments, the diversity is in the immunoglobulin is in the immunoglobulin light chain. In some embodiments, the diversity is in the T-cell receptor. In some embodiments, the diversity is in one of the T-cell receptors selected from the group consisting of alpha, beta, gamma, and delta receptors. In some embodiments, there is an increase in the expression of T- cell receptor (TCR) alpha and/or beta. In some embodiments, there is an increase in the expression of T-cell receptor (TCR) alpha. In some embodiments, there is an increase in the expression of T-cell receptor (TCR) beta. In some embodiments, there is an increase in the expression of TCRab (i.e., TCRa/p).

[00240] The methods of the invention can also comprise the step of performing a first expansion by culturing the disaggregated tumor in a cell culture medium comprising IL-2 to produce a first population of TILs, in particular UTILs. The cells resulting from the steps described above are cultured in serum containing IL-2 under conditions that favor the growth of TILs over tumor and other cells. In some embodiments, the tumor digests are incubated in 2 ml wells in media comprising inactivated human AB serum with 6000 lU/mL of IL-2. This primary cell population is cultured for a period of days, generally from 3 to 14 days, resulting in a bulk TIL population, generally about IxlO ⁸ bulk TIL cells. In some embodiments, this primary cell population is cultured for a period of 7 to 14 days, resulting in a bulk TIL population, generally about IxlO ⁸ bulk TIL cells. In some embodiments, this primary cell population is cultured for a period of 10 to 14 days, resulting in a bulk TIL population, generally about IxlO ⁸ bulk TIL cells. In some embodiments, this primary cell population is cultured for a period of about 11 days, resulting in a bulk TIL population, generally about IxlO ⁸ bulk TIL cells.

[00241] In a preferred embodiment, expansion of TILs may be performed using an initial bulk TIL expansion step as described below and herein, followed by a second expansion (including rapid expansion protocol (REP) steps and followed by restimulation REP steps) as described below and herein.

[00242] In an advantageous embodiment, the cryopreserved disaggregated tumor tissue is thawed and resuspended 1 :9 in T cell media (T cell culture media contract manufactured for Immetacyte supplemented with the following additives 10% FBS and 3000 ZU/mL IL-2) prior to filtration through an inline 100-270 pm filter and centrifugation in a 50 mL centrifuge tube prior to resuspension in 20 mL. A sample may be taken for flow cytometry analysis to quantify a number of HLA-A, B, C and CD58 ⁺ , and DRAQ7 cells. In some embodiments this may be seeded using an alternative manual (such as but not limited to a hemocytometer) or alternative automated total viable cell counting device such as but not limited to NucleoCounter™; Guava®; automated blood analysis and counter; pipette based cell counter such as but not limited to Scepter™.

[00243] In one embodiment, resuspended cryopreserved disaggregated tumor tissue is cultured in serum containing IL -2 under conditions that favor the growth of TILs over tumor and other cells. In some embodiments, the tumor digests are incubated in 2 mL wells in media comprising inactivated human AB serum (or, in some cases, as outlined herein, in the presence of an artificial antigen-presenting [aAPC] cell population) with 6000 lU/mL of IL-2. This primary cell population is cultured for a period of days, generally from 10 to 14 days, resulting in a bulk TIL population, generally about IxlO ⁸ bulk TIL cells. In some embodiments, the growth media during the first expansion comprises IL-2 or a variant thereof. In some embodiments, the IL is recombinant human IL-2 (rhIL-2). In some embodiments the IL-2 stock solution has a specific activity of 20-30xl0 ⁶ lU/mg for a 1 mg vial. In some embodiments the IL-2 stock solution has a specific activity of 20xl0 ⁶ lU/mg for a 1 mg vial. In some embodiments the IL-2 stock solution has a specific activity of 25x10 ⁶ lU/mg for a 1 mg vial. In some embodiments the IL-2 stock solution has a specific activity of 30xl0 ⁶ lU/mg for a 1 mg vial. In some embodiments, the IL-2 stock solution has a final concentration of 4-8xl0 ⁶ lU/mg of IL-2. In some embodiments, the IL-2 stock solution has a final concentration of 5-7xl0 ⁶ lU/mg of IL-2. In some embodiments, the IL-2 stock solution has a final concentration of 6x10 ⁶ lU/mg of IL-2. In some embodiments, the first expansion culture media comprises about 10,000 lU/mL of IL-2, about 9,000 lU/mL of IL-2, about 8,000 lU/mL of IL-2, about 7,000 lU/mL of IL-2, about 6000 lU/mL of IL-2 or about 5,000 lU/mL of IL-2. In some embodiments, the first expansion culture media comprises about 9,000 TU/mL of IL-2 to about 5,000 TU/mL of TL-2. Tn some embodiments, the first expansion culture media comprises about 8,000 lU/mL of IL-2 to about 6,000 lU/mL of IL-2. In some embodiments, the first expansion culture media comprises about 7,000 lU/mL of IL-2 to about 6,000 lU/mL of IL-2. In some embodiments, the first expansion culture media comprises about 6,000 lU/mL of IL-2. In an embodiment, the cell culture medium further comprises IL-2. In some embodiments, the cell culture medium comprises about 3000 lU/mL of IL-2. In an embodiment, the cell culture medium further comprises IL-2. In a preferred embodiment, the cell culture medium comprises about 3000 lU/mL of IL-2. In an embodiment, the cell culture medium comprises about 1000 lU/mL, about 1500 lU/mL, about 2000 lU/mL, about 2500 lU/mL, about 3000 lU/mL, about 3500 lU/mL, about 4000 lU/mL, about 4500 lU/mL, about 5000 lU/mL, about 5500 lU/mL, about 6000 lU/mL, about 6500 lU/mL, about 7000 lU/mL, about 7500 lU/mL, or about 8000 lU/mL of IL-2. In an embodiment, the cell culture medium comprises between 1000 and 2000 lU/mL, between 2000 and 3000 lU/mL, between 3000 and 4000 lU/mL, between 4000 and 5000 lU/mL, between 5000 and 6000 lU/mL, between 6000 and 7000 lU/mL, between 7000 and 8000 lU/mL, or about 8000 lU/mL of IL-2. [00244] In some embodiments, first expansion culture media comprises about 500 lU/mL of IL-12, about 400 lU/mL of IL-12, about 300 lU/mL of IL-12, about 200 lU/mL of IL-12, about 180 lU/mL of IL-12, about 160 lU/mL of IL-12, about 140 lU/mL of IL-12, about 120 lU/mL of IL-12, or about 100 lU/mL of IL-12. In some embodiments, the first expansion culture media comprises about 500 HJ/mL of IL-12 to about 100 lU/mL of IL-12. In some embodiments, the first expansion culture media comprises about 400 lU/mL of IL-12 to about 100 lU/mL of IL-12. In some embodiments, the first expansion culture media comprises about 300 lU/mL of IL-12 to about 100 lU/mL of IL-12. In some embodiments, the first expansion culture media comprises about 200 lU/mL of IL-12. In some embodiments, the cell culture medium comprises about 180 lU/mL of IL-12. In an embodiment, the cell culture medium further comprises IL-12. In a preferred embodiment, the cell culture medium comprises about 180 lU/mL of IL-12.

[00245] In some embodiments, first expansion culture media comprises about 500 lU/mL of IL-15, about 400 lU/mL of IL-15, about 300 lU/mL of IL-15, about 200 lU/mL of IL-15, about 180 lU/mL of IL-15, about 160 lU/mL of IL-15, about 140 lU/mL of IL-15, about 120 lU/mL of IL-15, or about 100 lU/mL of IL-15. In some embodiments, the first expansion culture media comprises about 500 lU/mL of IL-15 to about 100 lU/mL of IL-15. In some embodiments, the first expansion culture media comprises about 400 TU/mL of TL-15 to about 100 lU/mL of IL-15. In some embodiments, the first expansion culture media comprises about 300 lU/mL of IL-15 to about 100 lU/mL of IL- 15. In some embodiments, the first expansion culture media comprises about 200 lU/mL of IL-15. In some embodiments, the cell culture medium comprises about 180 lU/mL of IL-15. In an embodiment, the cell culture medium further comprises IL-15. In a preferred embodiment, the cell culture medium comprises about 180 lU/mL of IL-15.

[00246] In some embodiments, first expansion culture media comprises about 500 lU/mL of IL-18, about 400 lU/mL of IL-18, about 300 lU/mL of IL-18, about 200 lU/mL of IL-18, about 180 lU/mL of IL- 18, about 160 lU/mL of IL- 18, about 140 lU/mL of IL- 18, about 120 lU/mL of IL- 18, or about 100 lU/mL of IL-18. In some embodiments, the first expansion culture media comprises about 500 lU/mL of IL-18 to about 100 lU/mL of IL-18. In some embodiments, the first expansion culture media comprises about 400 TU/mL of IL-18 to about 100 lU/mL of IL-18. In some embodiments, the first expansion culture media comprises about 300 lU/mL of IL-18 to about 100 lU/mL of IL-18. In some embodiments, the first expansion culture media comprises about 200 lU/mL of IL- 18. In some embodiments, the cell culture medium comprises about 180 lU/mL of IL-18. In an embodiment, the cell culture medium further comprises IL-18. In a preferred embodiment, the cell culture medium comprises about 180 lU/mL of IL-18.

[00247] In some embodiments, first expansion culture media comprises about 20 lU/mL of IL-21, about 15 lU/mL of IL-21, about 12 lU/mL of IL-21, about 10 lU/mL of IL-21, about 5 lU/mL of IL-21, about 4 lU/mL of IL-21, about 3 lU/mL of IL-21, about 2 lU/mL of IL-21, about 1 lU/mL of IL-21, or about 0.5 lU/mL of IL-2L In some embodiments, the first expansion culture media comprises about 20 lU/mL of IL-21 to about 0.5 lU/mL of IL-21. In some embodiments, the first expansion culture media comprises about 15 lU/mL of IL-21 to about 0.5 lU/mL of IL-21. In some embodiments, the first expansion culture media comprises about 12 lU/mL of IL-21 to about 0.5 lU/mL of IL-2 L In some embodiments, the first expansion culture media comprises about 10 lU/mL of IL-21 to about 0.5 lU/mL of IL-21. In some embodiments, the first expansion culture media comprises about 5 lU/mL of IL-21 to about 1 lU/mL of IL -21. In some embodiments, the first expansion culture media comprises about 2 lU/mL of IL-21. In some embodiments, the cell culture medium comprises about 1 lU/mL of IL-21. In some embodiments, the cell culture medium comprises about 0.5 lU/mL of IL-2L In an embodiment, the cell culture medium further comprises IL-21 . Tn a preferred embodiment, the cell culture medium comprises about 1 TU/mL of IL-21.

[00248] Also contemplated for the culture media are combinations of interleukins, such as but not limited to, IL-2, IL-12, IL-15, IL-18 and IL-2L Other cytokines are also contemplated, such as IL-23, IL-27, IL-35, IL-39, IL-18, IL-36, IL-37, IL-38, IFN-alpha, IFN-beta, IFN-gamma or a combination thereof along with IL-2, IL-12, IL-15, IL-18 and IL-2L Antibodies, such as Th2 blocking reagents, are also contemplated, such as but not limited to, IL-4 (aIL4), anti-IL-4 (a!L4R), anti-IL-5R (aIL5R), anti-IL-5 (aIL5), anti-IL13R (aIL13R), or anti-IL13 (aIL13).

[00249] In some embodiments, the first TIL expansion can proceed for 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days. In some embodiments, the first TIL expansion can proceed for 1 day to 14 days. In some embodiments, the first TIL expansion can proceed for 2 days to 14 days. In some embodiments, the first TIL expansion can proceed for 3 days to 14 days. In some embodiments, the first TIL expansion can proceed for 4 days to 14 days. In some embodiments, the first TIL expansion can proceed for 5 days to 14 days. In some embodiments, the first TIL expansion can proceed for 6 days to 14 days. In some embodiments, the first TIL expansion can proceed for 7 days to 14 days. In some embodiments, the first TIL expansion can proceed for 8 days to 14 days. In some embodiments, the first TIL expansion can proceed for 9 days to 14 days. In some embodiments, the first TIL expansion can proceed for 10 days to 14 days. In some embodiments, the first TIL expansion can proceed for 11 days to 14 days. In some embodiments, the first TIL expansion can proceed for 12 days to 14 days. In some embodiments, the first TIL expansion can proceed for 13 days to 14 days. In some embodiments, the first TIL expansion can proceed for 14 days. In some embodiments, the first TIL expansion can proceed for 1 day to 13 days. In some embodiments, the first TIL expansion can proceed for 2 days to 13 days. In some embodiments, the first TIL expansion can proceed for 3 days to 13 days. In some embodiments, the first TIL expansion can proceed for 4 days to 13 days. In some embodiments, the first TIL expansion can proceed for 5 days to 13 days. In some embodiments, the first TIL expansion can proceed for 6 days to 13 days. In some embodiments, the first TIL expansion can proceed for 7 days to 13 days. In some embodiments, the first TIL expansion can proceed for 8 days to 13 days. In some embodiments, the first TIL expansion can proceed for 9 days to 13 days. In some embodiments, the first TIL expansion can proceed for 10 days to 13 days. In some embodiments, the first TIL expansion can proceed for 11 days to 13 days. Tn some embodiments, the first TIL expansion can proceed for 12 days to 13 days. In some embodiments, the first TIL expansion can proceed for 1 day to 12 days. In some embodiments, the first TIL expansion can proceed for 2 days to 12 days. In some embodiments, the first TIL expansion can proceed for 3 days to 12 days. In some embodiments, the first TIL expansion can proceed for 4 days to 12 days. In some embodiments, the first TIL expansion can proceed for 5 days to 12 days. In some embodiments, the first TIL expansion can proceed for 6 days to 12 days. In some embodiments, the first TIL expansion can proceed for 7 days to 12 days. In some embodiments, the first TIL expansion can proceed for 8 days to 12 days. In some embodiments, the first TIL expansion can proceed for 9 days to 12 days. In some embodiments, the first TIL expansion can proceed for 10 days to 12 days. In some embodiments, the first TIL expansion can proceed for 11 days to 12 days. In some embodiments, the first TIL expansion can proceed for 1 day to 11 days. In some embodiments, the first TIL expansion can proceed for 2 days to 11 days. In some embodiments, the first TIL expansion can proceed for 3 days to 11 days. In some embodiments, the first TIL expansion can proceed for 4 days to 11 days. In some embodiments, the first TIL expansion can proceed for 5 days to 11 days. In some embodiments, the first TIL expansion can proceed for 6 days to 11 days. In some embodiments, the first TIL expansion can proceed for 7 days to 11 days. In some embodiments, the first TIL expansion can proceed for 8 days to 11 days. In some embodiments, the first TIL expansion can proceed for 9 days to 11 days. In some embodiments, the first TIL expansion can proceed for 10 days to 11 days. In some embodiments, the first TIL expansion can proceed for 11 days. In some embodiments, REP day 10 is 3 days following electroporation.

[00250] In some embodiments, a combination of IL-2, IL-7, IL-15, and/or IL-21 are employed as a combination during the first expansion. In some embodiments, IL-2, IL-7, IL-15, and/or IL- 21 as well as any combinations thereof can be included during the first expansion. In some embodiments, a combination of IL-2, IL-15, and IL-21 are employed as a combination during the first expansion.

[00251] In some embodiments, the first expansion is performed in a closed system bioreactor. In some embodiments, a closed system is employed for the TIL expansion, as described herein. In some embodiments, a single bioreactor is employed. In some embodiments, the single bioreactor employed is example a G-REX-10 or a G-REX-100 or advantageously the device of WO 2018/130845. In some embodiments, the closed system bioreactor is a single bioreactor. [00252] Advantageously, the TIL population obtained from the first expansion, referred to as the second TIL population, can be subjected to a second expansion (which can include expansions sometimes referred to as REP. Similarly, in the case where genetically modified TILs will be used in therapy, the first TIL population (sometimes referred to as the bulk TIL population) or the second TIL population (which can in some embodiments include populations referred to as the REP TIL populations) can be subjected to genetic modifications for suitable treatments prior to expansion or after the first expansion and prior to the second expansion.

[00253] In certain embodiments, the PBMCs are cryopreserved. Cryopreservation enables prescreening and PBMC inventory maintenance and reduces the number of donors needed for TIL manufacture.

[00254] Disaggregated tumor tissue can be thawed. In some embodiments, the TILs obtained from the first expansion are stored until phenotyped for selection. In some embodiments, the TILs obtained from the first are not stored and proceed directly to the second expansion. Thus, the methods comprise the step of performing a second expansion by culturing the first population of TILs, in particular UTILs, with additional IL-2, OKT-3, and antigen presenting cells (APCs), to produce a second population of TILs. In some embodiments, the TILs obtained from the first expansion are not cryopreserved after the first expansion and prior to the second expansion. In some embodiments, the transition from the first expansion to the second expansion occurs at about 3 days, 4, days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days after the cryopreserved 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs at about 3 days to 21 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs at about 4 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs at about 4 days to 10 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs at about 7 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs at about 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments the seeding of the REP culture occurs 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20 or 21 days after the cryopreserved disaggregated tumor tissue is thawed.

[00255] In some embodiments, the transition from the first expansion to the second expansion occurs at 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 1 day to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the first TIL expansion can proceed for 2 days to 14 days. In some embodiments, the transition from the first expansion to the second expansion occurs 3 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 4 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 5 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 6 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 7 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 8 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 9 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 10 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 11 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 12 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 13 days to 14 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 14 days after the cryopreserved disaggregated tumor tissue is thawed. Tn some embodiments, the transition from the first expansion to the second expansion occurs 1 day to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 2 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 3 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 4 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 5 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 6 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 7 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 8 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 9 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 10 days to 11 days after the cryopreserved disaggregated tumor tissue is thawed. In some embodiments, the transition from the first expansion to the second expansion occurs 11 days after the cryopreserved disaggregated tumor tissue is thawed.

[00256] In some embodiments, the TILs or a portion of the TILs from the first expansion are cryopreserved. In certain embodiments, the TILs are divided in two or more portions, one or more portion proceeding to the second expansion, and one or more portion cryopreserved to be used in a later second expansion. In certain embodiments, the number of cells at the end of the first expansion is determined and the culture divided accordingly. In certain embodiments, the average potency of the TILs from the first expansion is determined and the culture is divided accordingly. In certain embodiments, an predetermined minimum number or optimal number of TILs proceeds to the second expansion and the remaining TILs are cryopreserved, and later thawed and used in a further second expansion. In certain embodiments, depending on the number and/or activity of left-over TILs, the cryopreserved TILs, can alternatively be used in a first expansion followed by a second expansion.

[00257] In some embodiments, the TILs are not stored after the first expansion and prior to the second expansion, and the TILs proceed directly to the second. In some embodiments, the transition occurs in closed system, as described herein. In some embodiments, the TILs from the first expansion, the second population of TILs, proceeds directly into the second expansion with no transition period.

[00258] In some embodiments, the transition from the first expansion to the second expansion is performed in a closed system bioreactor. In some embodiments, a closed system is employed for the TIL expansion, as described herein. In some embodiments, a single bioreactor is employed. In some embodiments, the single bioreactor employed is for example a G-REX-10 or a G-REX-100 or Xuri WAVE bioreactor. In some embodiments, the closed system bioreactor is a single bioreactor.

[00259] In some embodiments, the TIL cell population is expanded in number after harvest and initial bulk processing. This further expansion is referred to herein as the second expansion, which can include expansion processes generally referred to in the art as a rapid expansion process. The second expansion is generally accomplished using a culture media comprising a number of components, including feeder cells, a cytokine source, and an anti-CD3 antibody, in a gas-permeable or gas exchanging container.

[00260] In some embodiments, the second expansion or second TIL expansion of TIL can be performed using any TIL culture flasks or containers known by those of skill in the art. In some embodiments, the second TIL expansion can proceed for 0 days, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days. In some embodiments, the second TIL expansion can proceed for about 7 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 8 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 9 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 10 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 11 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 12 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 13 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 14 days. In

15 some embodiments, the second TIL expansion can proceed for about 7 days to about 13 days. Tn some embodiments, the second TIL expansion can proceed for about 8 days to about 13 days. In some embodiments, the second TIL expansion can proceed for about 9 days to about 13 days. In some embodiments, the second TIL expansion can proceed for about 10 days to about 13 days.

In some embodiments, the second TIL expansion can proceed for about 11 days to about 13 days. In some embodiments, the second TIL expansion can proceed for about 12 days to about 13 days. In some embodiments, the second TIL expansion can proceed for about 7 days to about

12 days. In some embodiments, the second TIL expansion can proceed for about 8 days to about

12 days. In some embodiments, the second TIL expansion can proceed for about 9 days to about

12 days. In some embodiments, the second TIL expansion can proceed for about 10 days to about 12 days. In some embodiments, the second TIL expansion can proceed for about 11 days to about 12 days. In some embodiments, the second TIL expansion can proceed for about 12 days. In some embodiments, the second TIL expansion can proceed for about 13 days. In some embodiments, the second TIL expansion can proceed for about 14 days.

[00261] In an embodiment, the second expansion can be performed in a gas permeable container using the methods of the present disclosure. For example, TILs can be rapidly expanded using non-specific T-cell receptor stimulation in the presence of interleukin-2 (IL-2) or interleukin-7 (IL-7) or interleukin- 15 (IL-15); or interleukin- 12 (IL-12). The non-specific T-cell receptor stimulus can include, for example, an anti-CD3 antibody, such as about 30 ng/ml of OKT3, a mouse monoclonal anti-CD3 antibody (commercially available from Ortho-McNeil, Raritan, N.J. or Miltenyi Biotech, Auburn, Calif.) or clone UHCT-1 (commercially available from BioLegend, San Diego, Calif, USA). TILs can be expanded to induce further stimulation of the TILs in vitro by including one or more antigens during the second expansion, including antigenic portions thereof, such as epitope(s), of the cancer, which can be optionally expressed from a vector, such as a human leukocyte antigen A2 (HLA-A2) binding peptide, e.g., 0.3 pM MART-1 :26-35 (27 L) or gpl 00:209-217 (210M), optionally in the presence of a T-cell growth factor, such as 300 lU/mL IL-2 or IL-15. Other suitable antigens may include, e.g., NY-ESO-1, TRP-1, TRP-2, tyrosinase cancer antigen, MAGE- A3, SSX-2, and VEGFR2, or antigenic portions thereof. TIL may also be rapidly expanded by re-stimulation with the same antigen(s) of the cancer pulsed onto HLA-A2-expressing antigen-presenting cells. Alternatively, the TILs can be further re-stimulated with, e.g., example, irradiated, autologous lymphocytes or with irradiated HLA-A2+ allogeneic lymphocytes and TL-2. Tn some embodiments, the re-stimulation occurs as part of the second expansion. In some embodiments, the second expansion occurs in the presence of irradiated, autologous lymphocytes or with irradiated HLA-A2+ allogeneic lymphocytes and IL-2.

[00262] In an embodiment, the cell culture medium further comprises IL-2. In some embodiments, the cell culture medium comprises about 3000 lU/mL of IL-2. In an embodiment, the cell culture medium comprises about 100 lU/mL, about 200 lU/mL, about 300 lU/mL, about 400 lU/mL, about 500 lU/mL, about 600 lU/mL, about 700 lU/mL, about 800 lU/mL, about 900 lU/mL, 1000 lU/mL, about 1500 lU/mL, about 2000 lU/mL, about 2500 lU/mL, about 3000 lU/mL, about 3500 lU/mL, about 4000 lU/mL, about 4500 lU/mL, about 5000 lU/mL, about 5500 lU/mL, about 6000 lU/mL, about 6500 lU/mL, about 7000 lU/mL, about 7500 lU/mL, or about 8000 lU/mL of IL-2. In an embodiment, the cell culture medium comprises between 1000 and 2000 lU/mL, between 2000 and 3000 lU/mL, between 3000 and 4000 lU/mL, between 4000 and 5000 lU/mL, between 5000 and 6000 lU/mL, between 6000 and 7000 lU/mL, between 7000 and 8000 lU/mL, or between 8000 lU/mL of IL-2.

[00263] In an embodiment, the cell culture medium comprises OKT3 antibody. In some embodiments, the cell culture medium comprises about 30 ng/mL of OKT3 antibody. In an embodiment, the cell culture medium comprises about 0.1 ng/mL, about 0.5 ng/mL, about 1 ng/mL, about 2.5 ng/mL, about 5 ng/mL, about 7.5 ng/mL, about 10 ng/mL, about 15 ng/mL, about 20 ng/mL, about 25 ng/mL, about 30 ng/mL, about 35 ng/mL, about 40 ng/mL, about 50 ng/mL, about 60 ng/mL, about 70 ng/mL, about 80 ng/mL, about 90 ng/mL, about 100 ng/mL, about 200 ng/mL, about 500 ng/mL, and about 1 pg/mL of OKT3 antibody. In an embodiment, the cell culture medium comprises between 0.1 ng/mL and 1 ng/mL, between 1 ng/mL and 5 ng/mL, between 5 ng/mL and 10 ng/mL, between 10 ng/mL and 20 ng/mL, between 20 ng/mL and 30 ng/mL, between 30 ng/mL and 40 ng/mL, between 40 ng/mL and 50 ng/mL, and between 50 ng/mL and 100 ng/mL of OKT3 antibody.

[00264] In some embodiments, a combination of IL-2, IL-7, IL-15, and/or IL-21 are employed as a combination during the second expansion. In some embodiments, IL-2, IL-7, IL-15, and/or IL-21 as well as any combinations thereof can be included during the second expansion. In some embodiments, a combination of IL-2, IL-15, and IL-21 are employed as a combination during the second expansion. Tn some embodiments, IL-2, TL-15, and TL-21 as well as any combinations thereof can be included.

[00265] In some embodiments, the second expansion can be conducted in a supplemented cell culture medium comprising IL-2, OKT-3, and antigen-presenting feeder cells. In some embodiments, the second expansion occurs in a supplemented cell culture medium. In some embodiments, the supplemented cell culture medium comprises IL-2, OKL-3, and antigen- presenting feeder cells. In some embodiments, the second cell culture medium comprises IL-2, OKT-3, and antigen-presenting cells (APCs; also referred to as antigen-presenting feeder cells). In some embodiments, the second expansion occurs in a cell culture medium comprising IL-2, OKT-3, and antigen-presenting feeder cells (i.e., antigen presenting cells).

[00266] In some embodiments, the second expansion culture media comprises about 500 lU/mL of IL-15, about 400 lU/mL of IL-15, about 300 lU/mL of IL-15, about 200 lU/mL of IL- 15, about 180 lU/mL of IL-15, about 160 lU/mL of IL-15, about 140 lU/mL of IL-15, about 120 lU/mL of IL-15, or about 100 lU/mL of IL-15. In some embodiments, the second expansion culture media comprises about 500 lU/mL of IL-15 to about 100 lU/mL of IL-15. In some embodiments, the second expansion culture media comprises about 400 lU/mL of IL- 15 to about 100 lU/mL of IL-15. In some embodiments, the second expansion culture media comprises about 300 lU/mL of IL- 15 to about 100 lU/mL of IL- 15. In some embodiments, the second expansion culture media comprises about 200 lU/mL of IL-15. In some embodiments, the cell culture medium comprises about 180 lU/mL of IL-15. In an embodiment, the cell culture medium further comprises IL-15. In a preferred embodiment, the cell culture medium comprises about 180 lU/mL of IL-15.

[00267] In some embodiments, the second expansion culture media comprises about 20 lU/mL of IL-21, about 15 lU/mL of IL-21, about 12 lU/mL of IL-21, about 10 lU/mL of IL-21, about 5 lU/mL of IL-21, about 4 lU/mL of IL-21, about 3 lU/mL of IL-21, about 2 lU/mL of IL- 21, about 1 lU/mL of IL-21, or about 0.5 lU/mL of IL-21. In some embodiments, the second expansion culture media comprises about 20 lU/mL of IL-21 to about 0.5 lU/mL of IL-21. In some embodiments, the second expansion culture media comprises about 15 lU/mL of IL-21 to about 0.5 lU/mL of IL-21. In some embodiments, the second expansion culture media comprises about 12 lU/mL of IL-21 to about 0.5 lU/mL of IL-21. In some embodiments, the second expansion culture media comprises about 10 lU/mL of IL-21 to about 0.5 lU/mL of IL-21. In some embodiments, the second expansion culture media comprises about 5 TU/mL of IL-21 to about 1 lU/mL of IL-21. In some embodiments, the second expansion culture media comprises about 2 lU/mL of IL-21. In some embodiments, the cell culture medium comprises about 1 lU/mL of IL-21. In some embodiments, the cell culture medium comprises about 0.5 lU/mL of IL-21. In an embodiment, the cell culture medium further comprises IL-21. In a preferred embodiment, the cell culture medium comprises about 1 lU/mL of IL-21.

[00268] In some embodiments the antigen-presenting feeder cells (APCs) are PBMCs. In an embodiment, the ratio of TILs to PBMCs and/or antigen-presenting cells in the rapid expansion and/or the second expansion is about 1 to 25, about 1 to 50, about 1 to 100, about 1 to 125, about 1 to 150, about 1 to 175, about 1 to 200, about 1 to 225, about 1 to 250, about 1 to 275, about 1 to 300, about 1 to 325, about 1 to 350, about 1 to 375, about 1 to 400, or about 1 to 500. In an embodiment, the ratio of TILs to PBMCs in the rapid expansion and/or the second expansion is between 1 to 50 and 1 to 300. In an embodiment, the ratio of TILs to PBMCs in the rapid expansion and/or the second expansion is between 1 to 100 and 1 to 200.

[00269] In some embodiments, the second expansion (which can include processes referred to as the REP process) is shortened to 0-14 days. In some embodiments, the second expansion is shortened to 7-11 days.

[00270] In the present invention, sets of containers, which are interconnected and have specific separate functions maintain an aseptically closed system to process, optionally enrich but stabilize the disaggregated and cellularized tumor. Essentially the invention provides a rapid pre-sterilized environment to minimize the time required and risk of contamination or operator exposure during the processing of the resected tumor.

[00271] The aseptic kit allows for closed solid tissue processing, eliminating the risk of contamination of the final cellularized product compared to standard non-closed tissue processing, especially when the process is performed within a tissue retrieval/procurement site and requires storage prior to final cell processing for its ultimate utility. In addition, safety of the operator is increased due to reduction of direct contact with biological hazardous material, which may contain infectious organisms such as viruses. The kit also enables either all of or a portion of the finally processed cellularized material to be stabilized for either transport or storage prior to being processed for its ultimate utility. [00272] The invention will enable the resected tumor to be processed at the time of resection, or later if required, without impact upon the retrieval procedure or the viability of the cellularized tumor.

[00273] In some embodiments, an optional enrichment via a form of physical purification to reduce impurities such as no longer required reagents; cell debris; non-disaggregated tumor tissue and fats can be employed. The aseptic kit can have an optional enrichment module, prior to stabilization, for this purpose. A single cell or small cell number aggregates can be enriched for stabilization after disaggregation by excluding particles and fluids of less than 5 pm or incompletely disaggregated material of or around 200 pm across or larger but this will vary upon the tissue and the efficiency of disaggregation and various embodiments in the form of tissue specific kits may be employed depending upon the tissue or ultimate utility of the disaggregated tumor.

[00274] In another embodiment, a single cell suspension is provided after step (c).

[00275] In another embodiment, the first population of UTILs requires about 1-250 million

UTILs, including 1-20 million UTILS, 20-40 million UTILS, 40-60 million UTILS, 60-80 million UTILS, 80-100 million UTILS, 100-125 million UTILS, 125-150 million UTILS, 150- 200 million UTILS, or 200-250 million UTILS.

[00276] In another embodiment, step (e) may further comprise growth of the UTILs out of the resected tumor starting material followed by the rapid expansion of step (f).

[00277] In another embodiment, step (e) may be performed for about two weeks and step (f) may be performed for about two weeks.

[00278] In another embodiment, additional step (h) involves suspending the second population of UTILs. The suspending may be in buffered saline, human serum albumin, and/or dimethylsulfoxide (DMSO).

[00279] The present invention also may comprise a therapeutic population of cryopreserved UTILs obtained by any of the herein disclosed methods. The therapeutic population may comprise about 5xl0 ⁹ to 5xl0 ¹⁰ of T cells.

[00280] The present invention also encompasses a cryopreserved bag of the herein disclosed therapeutic population. The cryopreserved bag may be for use in intravenous infusion.

[00281] The present invention also encompasses a method for treating cancer which may comprise administering the herein disclosed therapeutic population or the herein disclosed cryopreserved bag. The present invention also encompasses the herein disclosed therapeutic population, pharmaceutical composition or cryopreserved bag for use in the treatment of cancer. The cancer may be bladder cancer, breast cancer, cancer caused by human papilloma virus, cervical cancer, head and neck cancer (including head and neck squamous cell carcinoma (HNSCC), lung cancer (including non-small-cell lung cancer (NSCLC)), melanoma, ovarian cancer, renal cancer, or renal cell carcinoma.

[00282] In another embodiment, the one or more flexible containers of the aseptic kit comprise a resilient deformable material.

[00283] In another embodiment, the one or more flexible containers of the disaggregation module of the aseptic kit comprises one or more sealable openings. The one or more flexible containers of the disaggregation module and/or the stabilization module may also comprise a heat sealable weld.

[00284] In another embodiment, the one or more flexible containers of the aseptic kit comprises internally rounded edges.

[00285] In another embodiment, the one or more flexible containers of the disaggregation module of the aseptic kit comprises disaggregation surfaces adapted to mechanically crush and shear the solid tumor therein.

[00286] In another embodiment, the one or more flexible containers of the enrichment module of the aseptic kit comprises a filter that retains a retentate of cellularized disaggregated solid tumor.

[00287] In another embodiment, the one or more flexible containers of the stabilization module of the aseptic kit comprises media formulation for storage of viable cells in solution or in a cryopreserved state.

[00288] In another embodiment, the aseptic kit further comprises a digital, electronic, or electromagnetic tag identifier. The tag identifier can relate to a specific program that defines a type of disaggregation and/or enrichment and/or stabilization process, one or more types of media used in said processes, including an optional freezing solution suitable for controlled rate freezing.

[00289] In another embodiment, the same flexible container can form part of one or more of the disaggregation module, the stabilization module, and the optional enrichment modules. [00290] In another embodiment, the disaggregation module of the aseptic kit comprises a first flexible container for receipt of the tissue to be processed.

[00291] In another embodiment, the disaggregation module of the aseptic kit comprises a second flexible container comprising the media for disaggregation.

[00292] In another embodiment, the optional enrichment module of the aseptic kit comprises the first flexible container and a third flexible container for receiving the enriched filtrate.

[00293] In another embodiment, both the disaggregation module and the stabilization module of the aseptic kit comprise the second flexible container and the second flexible container comprises digestion media and stabilization media.

[00294] In another embodiment, the stabilization module of the aseptic kit comprises a fourth flexible container comprising stabilization media.

[00295] In another embodiment, the stabilization module of the aseptic kit also comprises the first flexible container and/or third flexible container for storing and/or undergoing cry opreservation.

[00296] The present invention also provides for a method for isolating a therapeutic population of cryopreserved TILs comprising: (a) resecting a tumor from a subject; (b) storing the resected tumor in a single use aseptic kit, wherein the aseptic kit comprises: a disaggregation module for receipt and processing of material comprising solid mammalian tissue; an optional enrichment module for filtration of disaggregated solid tissue material and segregation of nondisaggregated tissue and filtrate; and a stabilization module for optionally further processing and/or storing disaggregated product material, wherein each of the modules comprises one or more flexible containers connected by one or more conduits adapted to enable flow of the tissue material there between; and wherein each of the modules comprises one or more ports to permit aseptic input of media and/or reagents into the one or more flexible containers; (c) aseptically disaggregating the resected tumor in the disaggregation module thereby producing a disaggregated tumor, wherein the resected tumor is sufficiently disaggregated if it can be cryopreserved without cell damage; (d) cryopreserving the disaggregated tumor in the stabilization module; (e) performing a first expansion by culturing the disaggregated tumor in a cell culture medium comprising IL-2 to produce a first population of TILs; (f) optionally performing a second expansion by culturing the first population of TILs with additional IL-2, OKT-3, and a TIL activator, to produce a second population of TTLs; (g) harvesting and/or cry opreserving the second population of TILs.

[00297] In certain non-limiting embodiments, the TIL activator comprises an antigen presenting cell (APC), or an artificial antigen presenting cell (aAPC), or an antigen fragment or complex or an antibody.

[00298] In another embodiment, the automated device further comprises a radio frequency identification tag reader for recognition of the aseptic kit so that it may be scanned and recognized during automated processing, such as within the automated device in embodiments of the present invention. Crucially the tag provides information about the conditions and steps required to be auto processed, so simply by scanning the kit, any automated system used with the kit to process the tissue can be undertaken without further intervention or contamination. Once the tissue sample has been placed in the disaggregation module, it can for example be sealed, manually or automatically, before processing begins. The programmable processor of the automated device can also recognize the aseptic kit via the tag and subsequently can execute the kit program defining the type of disaggregation, enrichment, and stabilization processes, and the respective media types required for said processes, which include an optional freezing solution suitable for controlled rate freezing. The programmable processor of the automated device is adaptable to communicate with and control the disaggregation module, the enrichment module, and/or the stabilization module. Put another way, the kit is therefore readable by an automated device used to execute a specific fully automatic method for processing the tumor when inserted into such a device.

[00299] The programmable processor of the automated device can control the disaggregation module to enable a physical and/or biological breakdown of the solid tissue material. This breakdown can be a physical or enzymatic breakdown of the solid tissue material. Enzymatic breakdown of the solid tissue material can be by one or more media enzyme solutions selected from the group consisting of collagenase, trypsin, lipase, hyaluronidase, deoxyribonuclease, Liberase HI, pepsin, and mixtures thereof.

[00300] In another embodiment, the programmable processor controls disaggregation surfaces within the disaggregation flexible containers that mechanically crush and shear the solid tissue. In some embodiments, the disaggregation surfaces are controlled by mechanical pistons. [00301] In another embodiment, the programmable processor controls the stabilization module to cry opreserve the enriched disaggregated solid tissue in the container. This may be achieved using a programmable temperature setting, a condition which is determined by reading the tag of the kit inserted in the device.

[00302] In another embodiment, to undertake different functions of the process, one or more of the additional components of the device and/or kit are provided and may be available in any combination. This may include: sensors capable of recognizing whether a disaggregation process has been completed in the disaggregation module prior to transfer of the disaggregated solid tissue to the optional enrichment module; weight sensors to determine an amount of media required in the containers of one or more of the disaggregation module; the enrichment module; and/or the stabilization module and control the transfer of material between respective containers; sensors to control temperature within the containers of the one or more of the disaggregation module; the enrichment module; and/or the stabilization module; at least one bubble sensor to control transfer of media between the input and output ports of each container in the module; at least one pump, optionally a peristaltic pump, to control transfer of media between the input and output ports; pressure sensors to assess the pressure within the enrichment module; one or more valves to control a tangential flow filtration process within the enrichment module; and/or one or more clamps to control the transfer of media between the input and output ports of each module.

[00303] In another embodiment, the programmable processor of the automated device is adapted to maintain an optimal storage temperature range in the stabilization module until the container is removed; or executes a controlled freezing step. This allows the UTILs to be stored for short periods (minutes to days) or stored for long periods (multiple days to years) prior to their ultimate utility depending on the type or stabilization process used with the stabilization module.

[00304] In another embodiment, the automated device further comprises a user interface. The interface can comprise a display screen to display instructions that guide a user to input parameters, confirm pre-programmed steps, warn of errors, or combinations thereof.

[00305] In another embodiment, the automated device is adapted to be transportable and thus may comprise dimensions that permit easy maneuverability and/or aid movement such as wheels, tires, and/or handles. [00306] The present invention also provides a semi-automatic aseptic tissue processing method for isolating a therapeutic population of cryopreserved UTILs comprising the steps of: (a) automatically determining aseptic disaggregation tissue processing steps and their associated conditions from a digital, electronic, or electromagnetic tag identifier associated with an aseptic processing kit, wherein the aseptic kit comprises: a disaggregation module for receipt and processing of material comprising solid mammalian tissue; an optional enrichment module for filtration of disaggregated solid tissue material and segregation of non-disaggregated tissue and filtrate; and a stabilization module for optionally further processing and/or storing disaggregated product material, wherein each of the modules comprises one or more flexible containers connected by one or more conduits adapted to enable flow of the tissue material there between; and wherein each of the modules comprises one or more ports to permit aseptic input of media and/or reagents into the one or more flexible containers; (b) resecting a tumor from a subject; (c) placing the tumor into the flexible plastic container of the disaggregation module of the aseptic kit; (d) processing the tumor by automatically executing the one or more tissue processing steps by communicating with and controlling: the disaggregation module; wherein the resected tumor is aseptically disaggregated thereby producing a disaggregated tumor, wherein the resected tumor is sufficiently disaggregated if it can be cryopreserved without cell damage; the optional enrichment module wherein the disaggregated tumor is filtered to remove disaggregated solid tissue material and to segregate non-disaggregated tissue and filtrate; the stabilization module wherein the disaggregated tumor is cryopreserved; (e) performing a first expansion by culturing the disaggregated tumor in a cell culture medium comprising IL-2 to produce a first population of UTILs; (f) optionally performing a second expansion by culturing the first population of UTILs with additional IL-2, OKT-3, and antigen presenting cells (APCs), to produce a second population of TILs; (g) harvesting and/or cryopreserving the second population of UTILs.

[00307] Flexible containers such as bags, may be used to process tissue materials. Processing may include treatments that may separate or breakdown tissue, for example, physical breakdown may be accomplished using agitation, e.g., gentle agitation, a biological and/or enzymatic breakdown may include enzymatic digestion, and/or extraction of components of the tissue materials in the bag.

[00308] A flexible container, such as a bag, for processing tissue may include one or more layers made of a sealable polymer having at least three edges of the flexible container which are sealed during manufacturing and an open edge on the flexible container through which tissue material is inserted during use. One or more connectors may be used to couple the flexible container to at least one element through tubing. After tissue is placed in the flexible container, a section of the flexible container proximate the open edge may be sealed or welded to form a seal. The seal may have a width of at least a three mm and be positioned substantially parallel to the open edge and spaced away from the open edge of the flexible container. In some instances, the seal may have a width greater than about five mm. For example, a bag may be sealed after tissue is placed inside to have a seal of least 5 mm positioned proximate the open edge of the bag. The seal may be parallel to the open edge and spaced away from the open edge of the bag.

[00309] The flexible container may be further secured using a clamp having protrusions and positioned proximate the seal and spaced further from the open edge of the flexible container than the seal.

[00310] In some instances, the seal and the flexible container are constructed such that the flexible container can withstand a 100 N force applied to the flexible container during use. Using a clamp in conjunction with such a seal may be advantageous in some instances depending on the type of material used and/or a structure of the seal. Thus, during use of a flexible container, such as a bag, a combination of a seal and a clamp may be capable of withstanding a 100 N force applied to the flexible container.

[00311] In some instances, the seal and the flexible container are constructed such that the flexible container can withstand a 75 N force applied to the flexible container during use. Using a clamp in conjunction with such a seal may be advantageous in some instances depending on the type of material used and/or a structure of the seal. Thus, during use of a flexible container, such as a bag, a combination of a seal and a clamp may be capable of withstanding a 75 N force applied to the flexible container.

[00312] A flexible container may be used to hold tissue during processing such as disaggregation of the tissue material.

[00313] In some embodiments, a flexible container, such as a bag, may be used for disaggregation of the tissue material, filtration of disaggregated tissue material, and/or segregation of non-disaggregated tissue and filtrate.

[00314] Flexible containers such as bags may be formed from a resilient deformable material. Materials for use in flexible containers, such as bags may be selected for one or more properties including but not limited to sealability such as sealability due to heat welding, or use of radio frequency energy, gas permeability, flexibility for example low temperature flexibility (e.g., at - 150°C, or -195 °C), elasticity for example low temperature elasticity, chemical resistance, optical clarity, biocompatibility such as cytotoxicity, hemolytic activity, resistance to leaching, having low particulates, high transmissions rates for particular gases (e.g., Oxygen and/or Carbon dioxide), and/or complying with regulatory requirements.

[00315] Flexible containers, such as bags, may include indicators. Indicators may be used to identify samples, patients from whom the samples were derived, and/or to track progress of a particular sample through a treatment process. In some instances, indicators may be scanned by an automated or semi-automated system to track progress of a sample.

[00316] Marks may be used on a flexible container, such as a bag, to identify where the bag should be placed, treated, sealed, or any other action that may be taken with respect to a bag that includes tissue. Each bag may include multiple marks for sealing.

[00317] An open end of the bag may be sealed after tissue is inserted in the bag. Any seal may be formed using a sealing device (e.g., heater sealer) operating at a predetermined pressure, a predetermined temperature, and predetermined time frame.

[00318] In some instances, a flexible container, such as a bag may be used as a disaggregation container for use as part of a disaggregation element that may also include a disaggregation device. In some embodiments, media and/or enzymes may be added to a bag within a disaggregation element of a device. For example, a bag may be used with a device that mechanically crushes tissue material placed in the flexible container.

[00319] In some embodiments, tissue in a flexible container such as a bag may be sheared during disaggregation. In particular, the flexible container may be configured to shear the tissue material.

[00320] Flexible containers may be used in a semi-automated or an automated process for the aseptic disaggregation, stabilization and/or optional enrichment of mammalian cells or cell aggregates.

[00321] A kit for extraction of a desired material from tissue may include a disaggregation element in which at least some tissue is treated to form a processed fluid, an enrichment element (e.g., a filter) capable of enriching at least some of the processed fluid to form the desired material, a stabilization element capable of storing a portion of the desired material, and an indicator tag positioned on at least one of the disaggregation element, the enrichment element, or the stabilization element capable of providing at least one of a source of tissue, a status of the tissue with respect to the process, or a identifier.

[00322] The desired material may be biological material or components of a particular size. For example, the desired material may be tumor infiltrating lymphocytes (TILs).

[00323] Different types of media may be used in the various processes conducted by the disaggregation element and the stabilization element. For example, a cry opreservation media may be provided to the kit and used in the stabilization element to control a rate freezing.

[00324] Kit for use in a device where a disaggregation element may include a first flexible container and the stabilization element may include a second flexible container.

[00325] An automated device for semi -automated aseptic disaggregation and/or enrichment and/or stabilization of cells or cell aggregates from mammalian solid tissue may include a programmable processor and a kit that includes the flexible container described herein. The automated device may further include an indicator tag reader. For example, an indicator tag reader may be positioned at any element (e.g., disaggregation, enriching, or stabilization of tissue material in the kit).

[00326] In some instances, an automated device may further include radio frequency identification tag reader to recognize samples in flexible containers in the kit.

[00327] An automated device may include a programmable processor that is capable of recognizing indicators positioned on components of the kit such as a bag via an indicator tag such as a QR code. After determining which sample is in the bag, the programmable processor subsequently executes a program defining the type of disaggregation, enrichment, and stabilization processes and provides the respective media types required for those processes. [00328] A kit for use in an automated device may include a disaggregation flexible container or bag. The programmable processor may control a disaggregation element and disaggregation flexible container to enable a physical and/or biological breakdown of the solid tissue.

[00329] A programmable processor may control elements of an automated device such that disaggregation surfaces positioned proximate a disaggregation flexible container may mechanically crush and shear the solid tissue in the disaggregation flexible container, optionally wherein the disaggregation surfaces are mechanical pistons. [00330] Disaggregation elements of a system may be controlled by a processor such that tissue in the disaggregation flexible container to enable a physical and enzymatic breakdown of the solid tissue. One or more media enzyme solutions selected from collagenase, trypsin, lipase, hyaluronidase, deoxyribonuclease, Liberase HI, pepsin, or mixtures thereof may be provided to the disaggregation flexible container to aid in enzymatic breakdown of tissue.

[00331] A system may include a kit that includes a disaggregation flexible container and a stabilization flexible container and a programmable processor. The programmable processor may be adapted to control one or more of: the disaggregation element; the enrichment element, and the stabilization element.

[00332] A programmable processor may control a stabilization element to cryopreserve the enriched disaggregated solid tissue in the stabilization container. In some embodiments, a predetermined temperature may be programmed.

[00333] An automated device may include additional components in a multitude of combinations. Components may include sensors capable of recognizing whether a disaggregation process has been completed in the disaggregation module prior to transfer of the disaggregated solid tissue to the optional enrichment element, weight sensors to determine an amount of media required in the containers of one or more of the disaggregation element, an enrichment element, and/or the stabilization element and control the transfer of material between respective containers, sensors to control temperature within the containers of the one or more of the disaggregation element; the enrichment element; and/or the stabilization element; at least one bubble sensor to control the transfer of media between the input and output ports of each container in the element; at least one pump, optionally a peristaltic pump, to control the transfer of media between the input and output ports; pressure sensors to assess the pressure within the enrichment element; one or more valves to control a tangential flow fdtration process within the enrichment element; and/or one or more clamps to control the transfer of media between the input and output ports of each element.

[00334] An automated device may include a programmable processor is adapted to maintain an optimal storage temperature range in the stabilization module until the container is removed. In an embodiment, the programmable processor may execute a controlled freezing step. [00335] In some instances, an automated device may include a user interface. An interface of an automated device may include a display screen to display instructions that guide a user to input parameters, confirm pre-programmed steps, warn of errors, or combinations thereof [00336] An automated device as described herein may be adapted to be transportable.

[00337] An automatic tissue processing method may include automatically determining conditions for processing steps and the associated conditions from a digital, electronic or electromagnetic tag indicator associated with a component of a kit. During use a tissue sample may be placed into a flexible container of the kit having at least one open edge. After positioning tissue in the flexible container, the open edge may be sealed. During use tissue may be processed by automatically executing one or more tissue processing steps by communicating information associated with the indicator and controlling conditions near the flexible container and/or positions of the flexible container. Further, addition of materials to the kit may be controlled based on information associated with indicators. At least some of the processed tissue may be filtered such that a filtered fluid is generated. At least some of the filtered fluid may be provided to a cryopreservative flexible container to stabilize the desired material present in the filtered fluid.

[00338] Processing as described herein may include agitation, extraction, and enzymatic digestion of at least a portion of the tissue sample in the flexible container. In some instances, this processing of tissue may result in the extraction of a desired material from a tissue sample. For example, tumor infiltrating lymphocytes (TILs) may be extracted from a tissue sample. [00339] Flexible containers, such as bags, for use in the methods described herein may include heat-sealable material.

[00340] Tissue processing and extraction from the tissue materials using a cryopreservation kit may result isolation of the desired material. In particular, materials such as tumor infiltrating lymphocytes (TILs) may be the desired material.

[00341] In some instances, a cryopreservation kit and/or components thereof described herein may be single use in an automated and/or a semi-automated process for the disaggregation, enrichment, and/or stabilization of cells or cell aggregates. In some embodiments, bags for use in a cry opreservation kit such as a collection bag may in some embodiments be used for multiple processes. For example, collection bags may be repeatedly sealed in different locations to create separate compartments for processing of a tissue sample such as a biopsy sample and/or solid tissue.

[00342] Flexible containers, such as bags, for use in the invention described herein include a collection bag and a cry opreservation bag may include at least a portion made from a predetermined material such as a thermoplastic, polyolefin polymer, ethylene vinyl acetate (EVA), blends such as copolymers, for example, a vinyl acetate and polyolefin polymer blend (i.e., OriGen Biomedical EVO film), a material that includes EVA, and/or coextruded layers of sealable plastics. A collection bag, such as a tissue collection bag of the invention may include a bag for receiving tissue made from a predetermined material such as ethylene vinyl acetate (EVA) and/or a material including EVA. Materials for use in the bag may be selected for specific properties. In an embodiment, bags, including collection bags may be made substantially from a vinyl acetate and polyolefin polymer blend. For example, a property of interest that may be used to select a material for cryopreservation kit component such as a collection bag and/or the associated tubing may relate to heat sealing.

[00343] Materials for use in the bag may be selected for a specific property and/or a selection of properties, for example, sealability such as heat sealability, gas permeability, flexibility for example low temperature flexibility, elasticity for example low temperature elasticity, chemical resistance, optical clarity, biocompatibility such as cytotoxicity, hemolytic activity, resistance to leaching, having low particulates.

[00344] In some embodiments, materials may be selected for specific properties for use in a coextruded material to form at least one layer of a bag. Layers may be constructed such that when constructed an interior layer of the bag is relatively biocompatible, that is the material on an inner surface of the bag is stable and does not leach into the contents of the bag.

[00345] For example, a property of interest that may be used to select a material for kit component such as a collection bag, a cry opreservation bag, and/or the associated tubing may relate to sealing, for example heat sealing.

[00346] Bags, such as collection bags and/or cryopreservation bags, and any associated tubing may be generally clear, transparent, translucent, any color desired, or a combination thereof. Tissue collection bags and/or tubing may be generally fabricated in ways analogous to the fabrication of closed and/or sealed blood and/or cryopreservation bags and the associated tubing. Tubing in the invention may be constructed from any desired material including, but not limited to polyvinyl chloride (PVC). For example, PVC may be a desired material as PVC is advantageous for welding and/or sealing.

[00347] In some embodiments, at least one end of a collection bag may be open for receiving tissue. In particular, in an embodiment, a tissue sample, for example from a biopsy may be placed in the bag through the open end, for example, a top end. In some cases, the biopsy sample may be cancerous tissue from an animal (e.g., domestic animal such as dog or cat) or a human. [00348] After tissue is positioned in the bag, the bag may be sealed, and then may be processed. Processing may include agitation, e.g., gentle agitation, extraction, and/or enzymatic digestion of the tissue in the bag. Tissue processing and extraction of a desired material, such as tumor infdtrating lymphocytes (TILs), can be in a closed system. Advantageous or preferred embodiments may include indicators to identify the patient from whom the tissue was collected and/or marks to show where the collection bag may be clamped, sealed, acted upon by a device, and/or affixed in place in an instrument.

[00349] In some embodiments, bag may be formed from a sealable material. For example, bag may be formed from materials including, but not limited to polymers such as synthetic polymers including aliphatic or semi-aromatic polyamides (e.g., Nylon), ethylene-vinyl acetate (EVA) and blends thereof, thermoplastic polyurethanes (TPU), polyethylenes (PE), a vinyl acetate and polyolefin polymer blends, and/or combinations of polymers. Portions of a bag may be sealed and/or welded with energy such as heat, radio frequency energy, high frequency (HF) energy, dielectric energy, and/or any other method known in the art.

[00350] A collection bag may be used as a processing and/or disaggregation bag. Collection bags may have width in a range from about 4 cm to about 12 cm and a width in a range from about 10 cm to about 30 cm. For example, a collection bag for use in processing may have a width of about 7.8 cm and a length of about 20 cm. In particular, a bag may be heat sealable, for example, using an EVA polymer or blends thereof, a vinyl acetate and polyolefin polymer blend, and/or one or more polyamides (Nylon).

[00351] Indicators may include, but are not limited to codes, letters, words, names, alphanumeric codes, numbers, images, bar codes, quick response (QR) codes, tags, trackers such as smart tracker tags or bluetooth trackers, and/or any indicator known in the art. In some embodiments, indicators may be printed on, etched on, and/or adhered to a surface of a component of a kit. Indicators may also be positioned on a bag using an adhesive, for example, a sticker or tracker may be placed on a bag and/or on multiple bags. Collection bags and/or cry opreservation kit may include multiple indicators such as numeric codes and/or QR codes. [00352] Indicators, for example QR codes, tags such as smart tags, and/or trackers may be used to identify a sample within a bag as well as to instruct a device's processor such that the device runs a specific program according to a type of disaggregation, enrichment, and/or stabilization processes that are conducted in cryopreservation kits. Different types of media may be used in these processes, for example, enzyme media, tumor digest media and/or cry opreservation media which may allow for a controlled rate of freezing. In some embodiments, cry opreservation kit and/or components thereof may include indicators that may be readable by an automated device. The device may then execute a specific fully automatic method for processing tissue when inserted to such a device. The invention is particularly useful in a sample processing, particularly automated processing. In some instances, the cryopreservation kit and/or components thereof described herein may be single use in an automated and/or a semi-automated process for the disaggregation, enrichment, and/or stabilization of cells or cell aggregates. In some embodiments, bags for use in a cryopreservation kit such as a collection bag may in some embodiments be used for multiple processes. For example, collection bags may be repeatedly sealed in different locations to create separate compartments for processing of a tissue sample such as a biopsy sample and/or solid tissue.

[00353] Further, marks may be placed at various locations on bags, such as tissue collection bags to indicate where the bags may be sealed, clamped, and/or affixed to an object. In some embodiments, marks showing where a bag may be clamped, sealed, and/or affixed to an object, such as instrument, may be positioned on the bag prior to use. For example, one or more marks may be positioned on a bag during manufacturing.

[00354] Positioners may be used to ensure that tissue material in bags can be treated properly during use, for example, positioning proximate an instrument. In some systems, the positioners may facilitate the use of the bags described herein in automated systems. In particular, positioners may be used to move bag through an automated system.

[00355] Use of an indicator, such as a QR code may allow for tracking of process steps for a specific sample such that it is possible to follow the sample through a given process.

[00356] Cells are transferred to a container for use in administration to a patient. In some embodiments, once a therapeutically sufficient number of TILs are obtained using the expansion methods described above, they are transferred to a container for use in administration to a patient.

[00357] In an embodiment, TILs expanded using APCs of the present disclosure are administered to a patient as a pharmaceutical composition. In an embodiment, the pharmaceutical composition is a suspension of TILs in a sterile buffer. TILs expanded using PBMCs of the present disclosure may be administered by any suitable route as known in the art. In some embodiments, the T-cells are administered as a single intra-arterial or intravenous infusion, which preferably lasts approximately 30 to 60 minutes. Other suitable routes of administration include intraperitoneal, intrathecal, and intralymphatic.

[00358] In an embodiment, TILs expanded using the methods of the present disclosure are administered to a patient as a pharmaceutical composition. In an embodiment, the pharmaceutical composition is a suspension of TILs in a sterile buffer. TILs expanded using PBMCs of the present disclosure may be administered by any suitable route as known in the art. In some embodiments, the T-cells are administered as a single intra-arterial or intravenous infusion, which preferably lasts approximately 30 to 60 minutes. Other suitable routes of administration include intraperitoneal, intrathecal, and intralymphatic administration.

[00359] Any suitable dose of TILs can be administered. In some embodiments, from about 2.3xlO ¹⁰ to about 13.7xlO ¹⁰ TILs are administered, with an average of around 7.8xlO ¹⁰ TILs, particularly if the cancer is melanoma. In an embodiment, about 1.2xlO ¹⁰ to about 4.3xlO ¹⁰ of TILs are administered. In some embodiments, about 3xl0 ¹⁰ to about 12xlO ¹⁰ TILs are administered. In some embodiments, about 4xlO ¹⁰ to about 10xl0 ¹⁰ TILs are administered. In some embodiments, about 5xl0 ¹⁰ to about 8xl0 ¹⁰ TILs are administered. In some embodiments, about 6xlO ^llJ to about 8xl0 ^llJ TILs are administered. In some embodiments, about 7xlO ^llJ to about 8x10 ¹⁰ TILs are administered. In some embodiments, the therapeutically effective dosage is about 2.3xlO ¹⁰ to about 13.7xl0 ¹⁰ . In some embodiments, the therapeutically effective dosage is about 7.8xlO ¹⁰ TILs, particularly of the cancer is melanoma. In some embodiments, the therapeutically effective dosage is about 1.2xlO ¹⁰ to about 4.3xlO ¹⁰ of TILs. In some embodiments, the therapeutically effective dosage is about 3xl0 ¹⁰ to about 12xlO ¹⁰ TILs. In some embodiments, the therapeutically effective dosage is about 4xlO ¹⁰ to about 10xl0 ¹⁰ TILs. In some embodiments, the therapeutically effective dosage is about 5xl0 ¹⁰ to about 8xl0 ¹⁰ TILs. Tn some embodiments, the therapeutically effective dosage is about 6x10 ¹⁰ to about 8x10 ¹⁰ TTLs. In some embodiments, the therapeutically effective dosage is about 7xlO ¹⁰ to about 8xlO ¹⁰ TILs. [00360] In some embodiments, the number of the TILs provided in the pharmaceutical compositions of the invention is about IxlO ⁶ , 2xl0 ⁶ , 3xl0 ⁶ , 4xl0 ⁶ , 5xl0 ⁶ , 6xl0 ⁶ , 7xl0 ⁶ 8xl0 ⁶ , 9xl0 ⁶ , IxlO ⁷ , 2xl0 ⁷ , 3xl0 ⁷ , 4xl0 ⁷ , 5xl0 ⁷ , 6xl0 ⁷ , 7xl0 ⁷ , 8xl0 ⁷ , 9xl0 ⁷ , IxlO ⁸ , 2xl0 ⁸ , 3xl0 ⁸ , 4xl0 ⁸ , 5xl0 ⁸ , 6xl0 ⁸ , 7xl0 ⁸ , 8xl0 ⁸ , 9xl0 ⁸ , IxlO ⁹ , 2xl0 ⁹ , 3xl0 ⁹ , 4xl0 ⁹ , 5xl0 ⁹ , 6xl0 ⁹ , 7xl0 ⁹ , 8xl0 ⁹ , 9xl0 ⁹ , IxlO ¹⁰ , 2xlO ¹⁰ , 3xlO ¹⁰ , 4xlO ¹⁰ , 5xlO ¹⁰ , 6xlO ¹⁰ , 7xlO ¹⁰ , 8xlO ¹⁰ , 9xlO ¹⁰ , IxlO ¹¹ , 2xlO ⁿ , 3xlO ^u , 4xlO ⁿ , 5xlO ⁿ , 6xlO ^u , 7xlO ^xl , 8xlO ⁿ , 9xlO ^u , IxlO ¹² , 2xl0 ¹² , 3xl0 ¹² , 4xl0 ¹² , 5xl0 ¹² , 6xl0 ¹² , 7xl0 ¹² , 8xl0 ¹² , 9xl0 ¹² , IxlO ¹³ , 2xl0 ¹³ , 3x10°, 4xl0 ¹³ , 5xl0 ¹³ , 6xl0 ¹³ , 7xl0 ¹³ , 8xl0 ¹³ , and 9xl0 ¹³ . In an embodiment, the number of the TILs provided in the pharmaceutical compositions of the invention is in the range of IxlO ⁶ to 5xl0 ⁶ , 5xl0 ⁶ to IxlO ⁷ , IxlO ⁷ to 5xl0 ⁷ , 5xl0 ⁷ to IxlO ⁸ , IxlO ⁸ to 5xl0 ⁸ , 5xl0 ⁸ to IxlO ⁹ , IxlO ⁹ to 5xl0 ⁹ , 5xl0 ⁹ to IxlO ¹⁰ , IxlO ¹⁰ to 5xlO ¹⁰ , 5xlO ¹⁰ to IxlO ¹¹ , 5xlO ⁿ to IxlO ¹² , IxlO ¹² to 5xl0 ¹² , and 5xl0 ¹² to IxlO ¹³ .

[00361] In some embodiments, the concentration of the TILs provided in the pharmaceutical compositions of the invention is less than, for example, 100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%, 0.0005%, 0.0004%, 0.0003%, 0.0002% or 0.0001% w/w, w/v or v/v of the pharmaceutical composition.

[00362] In some embodiments, the concentration of the TILs provided in the pharmaceutical compositions of the invention is greater than 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19.75%, 19.50%, 19.25% 19%, 18.75%, 18.50%, 18.25% 18%, 17.75%, 17.50%, 17.25% 17%,

16.75%, 16.50%, 16.25% 16%, 15.75%, 15.50%, 15.25% 15%, 14.75%, 14.50%, 14.25% 14%,

13.75%, 13.50%, 13.25% 13%, 12.75%, 12.50%, 12.25% 12%, 11.75%, 11.50%, 11.25% 11%,

10.75%, 10.50%, 10.25% 10%, 9.75%, 9.50%, 9.25% 9%, 8.75%, 8.50%, 8.25% 8%, 7.75%,

7.50%, 7.25% 7%, 6.75%, 6.50%, 6.25% 6%, 5.75%, 5.50%, 5.25% 5%, 4.75%, 4.50%, 4.25%, 4%, 3.75%, 3.50%, 3.25%, 3%, 2.75%, 2.50%, 2.25%, 2%, 1.75%, 1.50%, 125%, 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%, 0.0005%, 0.0004%, 0.0003%, 0.0002% or 0.0001% w/w, w/v, or v/v of the pharmaceutical composition.

[00363] In some embodiments, the concentration of the TILs provided in the pharmaceutical compositions of the invention is in the range from about 0.0001% to about 50%, about 0.001% to about 40%, about 0.01% to about 30%, about 0.02% to about 29%, about 0.03% to about 28%, about 0.04% to about 27%, about 0.05% to about 26%, about 0.06% to about 25%, about 0.07% to about 24%, about 0.08% to about 23%, about 0.09% to about 22%, about 0.1% to about 21%, about 0.2% to about 20%, about 0.3% to about 19%, about 0.4% to about 18%, about 0.5% to about 17%, about 0.6% to about 16%, about 0.7% to about 15%, about 0.8% to about 14%, about 0.9% to about 12% or about 1% to about 10% w/w, w/v or v/v of the pharmaceutical composition.

[00364] In some embodiments, the concentration of the TILs provided in the pharmaceutical compositions of the invention is in the range from about 0.001% to about 10%, about 0.01% to about 5%, about 0.02% to about 4.5%, about 0.03% to about 4%, about 0.04% to about 3.5%, about 0.05% to about 3%, about 0.06% to about 2.5%, about 0.07% to about 2%, about 0.08% to about 1.5%, about 0.09% to about 1%, about 0.1% to about 0.9% w/w, w/v or v/v of the pharmaceutical composition.

[00365] In some embodiments, the amount of the TILs provided in the pharmaceutical compositions of the invention is equal to or less than 10 g, 9.5 g, 9.0 g, 8.5 g, 8.0 g, 7.5 g, 7.0 g, 6.5 g, 6.0 g, 5.5 g, 5.0 g, 4.5 g, 4.0 g, 3.5 g, 3.0 g, 2.5 g, 2.0 g, 1.5 g, 1.0 g, 0.95 g, 0.9 g, 0.85 g,

0.8 g, 0.75 g, 0.7 g, 0.65 g, 0.6 g, 0.55 g, 0.5 g, 0.45 g, 0.4 g, 0.35 g, 0.3 g, 0.25 g, 0.2 g, 0.15 g,

0.1 g, 0.09 g, 0.08 g, 0.07 g, 0.06 g, 0.05 g, 0.04 g, 0.03 g, 0.02 g, 0.01 g, 0.009 g, 0.008 g, 0.007 g, 0.006 g, 0.005 g, 0.004 g, 0.003 g, 0.002 g, 0.001 g, 0.0009 g, 0.0008 g, 0.0007 g, 0.0006 g, 0.0005 g, 0.0004 g, 0.0003 g, 0.0002 g, or 0.0001 g.

[00366] In some embodiments, the amount of the TILs provided in the pharmaceutical compositions of the invention is more than 0.0001 g, 0.0002 g, 0.0003 g, 0.0004 g, 0.0005 g, 0.0006 g, 0.0007 g, 0.0008 g, 0.0009 g, 0.001 g, 0.0015 g, 0.002 g, 0.0025 g, 0.003 g, 0.0035 g,

0.004 g, 0.0045 g, 0.005 g, 0.0055 g, 0.006 g, 0.0065 g, 0.007 g, 0.0075 g, 0.008 g, 0.0085 g,

0.009 g, 0.0095 g, 0.01 g, 0.015 g, 0.02 g, 0.025 g, 0.03 g, 0.035 g, 0.04 g, 0.045 g, 0.05 g, 0.055 g, 0.06 g, 0.065 g, 0.07 g, 0.075 g, 0.08 g, 0.085 g, 0.09 g, 0.095 g, 0.1 g, 0.15 g, 0.2 g, 0.25 g,

0.3 g, 0.35 g, 0.4 g, 0.45 g, 0.5 g, 0.55 g, 0.6 g, 0.65 g, 0.7 g, 0.75 g, 0.8 g, 0.85 g, 0.9 g, 0.95 g, 1 g, 1 .5 g, 2 g, 2.5, 3 g, 3.5, 4 g, 4.5 g, 5 g, 5.5 g, 6 g, 6.5 g, 7 g, 7.5 g, 8 g, 8.5 g, 9 g, 9.5 g, or 10 g-

[00367] The TILs provided in the pharmaceutical compositions of the invention are effective over a wide dosage range. The exact dosage will depend upon the route of administration, the form in which the compound is administered, the gender and age of the subject to be treated, the body weight of the subject to be treated, and the preference and experience of the attending physician. The clinically-established dosages of the TILs may also be used if appropriate. The amounts of the pharmaceutical compositions administered using the methods herein, such as the dosages of TILs, will be dependent on the human or mammal being treated, the severity of the disorder or condition, the rate of administration, the disposition of the active pharmaceutical ingredients and the discretion of the prescribing physician.

[00368] In some embodiments, TILs may be administered in a single dose. Such administration may be by injection, e.g., intravenous injection. In some embodiments, TILs may be administered in multiple doses. Dosing may be once, twice, three times, four times, five times, six times, or more than six times per year. Dosing may be once a month, once every two weeks, once a week, or once every other day. Administration of TILs may continue as long as necessary.

[00369] In some embodiments, an effective dosage of TILs is about IxlO ⁶ , 2xl0 ⁶ , 3xl0 ⁶ , 4xl0 ⁶ , 5xl0 ⁶ , 6xl0 ⁶ , 7xl0 ⁶ , 8xl0 ⁶ , 9xl0 ⁶ , IxlO ⁷ , 2xl0 ⁷ , 3xl0 ⁷ , 4xl0 ⁷ , 5xl0 ⁷ , 6xl0 ⁷ , 7xl0 ⁷ , 8xl0 ⁷ , 9xl0 ⁷ , IxlO ⁸ , 2xl0 ⁸ , 3xl0 ⁸ , 4xl0 ⁸ , 5xl0 ⁸ , 6xl0 ⁸ , 7xl0 ⁸ , 8xl0 ⁸ , 9xl0 ⁸ , IxlO ⁹ , 2xl0 ⁹ , 3xl0 ⁹ , 4xl0 ⁹ , 5xl0 ⁹ , 6xl0 ⁹ , 7xl0 ⁹ , 8xl0 ⁹ , 9xl0 ⁹ , IxlO ¹⁰ , 2xlO ¹⁰ , 3xl0 ¹⁰ , 4xlO ¹⁰ , 5xl0 ¹⁰ , 6xlO ¹⁰ , 7xlO ^lo 8xlO ¹⁰ , 9xlO ¹⁰ , IxlO ¹¹ , 2xlO ⁿ , 3xl0 ^u , 4xlO ^u , 5xl0 ⁿ , 6xlO ^u , 7xlO ^u , 8xl0 ^lx , 9xlO ⁿ , IxlO ¹² , 2xl0 ¹² , 3xl0 ¹² , 4xl0 ¹² , 5xl0 ¹² , 6xl0 ¹² , 7xl0 ¹² , 8xl0 ¹² , 9xl0 ¹² , IxlO ¹³ , 2xl0 ¹³ , 3xl0 ¹³ , 4xl0 ¹³ , 5xl0 ¹³ , 6xl0 ¹³ , 7xl0 ¹³ , 8xl0 ¹³ , and 9xl0 ¹³ . In some embodiments, an effective dosage of TILs is in the range of IxlO ⁶ to 5xl0 ⁶ , 5xI0 ⁶ to IxlO ⁷ , IxlO ⁷ to 5xI0 ⁷ , 5xI0 ⁷ to IxlO ⁸ , IxlO ⁸ to 5xl0 ⁸ , 5xl0 ⁸ to IxlO ⁹ , IxlO ⁹ to 5xl0 ⁹ , 5xl0 ⁹ to IxlO ¹⁰ , IxlO ¹⁰ to 5xl0 ¹⁰ , 5xl0 ¹⁰ to IxlO ¹¹ , SxlO ¹¹ to IxlO ¹² , IxlO ¹² to 5xl0 ¹² , and 5xl0 ¹² to IxlO ¹³ .

[00370] In some embodiments, an effective dosage of TILs is in the range of about 0.01 mg/kg to about 4.3 mg/kg, about 0.15 mg/kg to about 3.6 mg/kg, about 0.3 mg/kg to about 3.2 mg/kg, about 0.35 mg/kg to about 2.85 mg/kg, about 0.15 mg/kg to about 2.85 mg/kg, about 0.3 mg to about 2.15 mg/kg, about 0.45 mg/kg to about 1.7 mg/kg, about 0.15 mg/kg to about 1.3 mg/kg, about 0.3 mg/kg to about 1.15 mg/kg, about 0.45 mg/kg to about 1 mg/kg, about 0.55 mg/kg to about 0.85 mg/kg, about 0.65 mg/kg to about 0.8 mg/kg, about 0.7 mg/kg to about 0.75 mg/kg, about 0.7 mg/kg to about 2.15 mg/kg, about 0.85 mg/kg to about 2 mg/kg, about 1 mg/kg to about 1.85 mg/kg, about 1.15 mg/kg to about 1.7 mg/kg, about 1.3 mg/kg mg to about 1.6 mg/kg, about 1.35 mg/kg to about 1.5 mg/kg, about 2.15 mg/kg to about 3.6 mg/kg, about 2.3 mg/kg to about 3.4 mg/kg, about 2.4 mg/kg to about 3.3 mg/kg, about 2.6 mg/kg to about 3.15 mg/kg, about 2.7 mg/kg to about 3 mg/kg, about 2.8 mg/kg to about 3 mg/kg, or about 2.85 mg/kg to about 2.95 mg/kg.

[00371] In some embodiments, an effective dosage of TTLs is in the range of about 1 mg to about 500 mg, about 10 mg to about 300 mg, about 20 mg to about 250 mg, about 25 mg to about 200 mg, about 1 mg to about 50 mg, about 5 mg to about 45 mg, about 10 mg to about 40 mg, about 15 mg to about 35 mg, about 20 mg to about 30 mg, about 23 mg to about 28 mg, about 50 mg to about 150 mg, about 60 mg to about 140 mg, about 70 mg to about 130 mg, about 80 mg to about 120 mg, about 90 mg to about 110 mg, or about 95 mg to about 105 mg, about 98 mg to about 102 mg, about 150 mg to about 250 mg, about 160 mg to about 240 mg, about 170 mg to about 230 mg, about 180 mg to about 220 mg, about 190 mg to about 210 mg, about 195 mg to about 205 mg, or about 198 to about 207 mg.

[00372] An effective amount of the TILs may be administered in either single or multiple doses by any of the accepted modes of administration of agents having similar utilities, including intranasal and transdermal routes, by intra-arterial injection, intravenously, intraperitoneally, parenterally, intramuscularly, subcutaneously, topically, by transplantation, or by inhalation.

[00373] Additional exemplary and non-limiting procedures for collection of tumor material, cryopreservation, and TIL manufacture are provided below.

[00374] The starting material for TIL manufacturing is a disaggregated and cryopreserved cell suspension containing autologous TIL and tumor cells from an eligible patient. An exemplary flow diagram is provided for collection and processing of the tumor starting material.

[00375] The tumor is surgically resected and then trimmed to remove visibly necrotic tissue, visibly healthy (non-cancerous) tissue, fat tissue, and excess blood. The trimmed tumor weight should be greater than or equal to 2 grams (> 2 grams). Tumors weighing over 7 g may be divided into smaller portions and individually disaggregated. [00376] Each tumor fragment is placed into an individual sterile bag containing media, collagenase and DNAse. Exemplary reagents are shown in the following table:

[00377] The bag is then heat sealed and its contents are disaggregated to generate a homogeneous cell suspension containing tumor and TIL. Disaggregation is performed by a device, such as the Tiss-U-Stor device described herein, which runs a program to deliver a defined number of repeated physical compression events, with a defined compression pressure over a defined duration to ensure enzyme access into the tumor tissue thereby accelerating enzymatic digestion. The number of cycles, pressure, temperature, and duration are recorded for each individual tumor.

[00378] The homogenized cell suspension is then aseptically filtered using a 200 pm filter (Baxter, RMC2159) and the filtrate passed aseptically into the cryopreservation bag. BloodStor 55-5 (Biolife Solutions, Bothell, WA) is aseptically added to achieve 5% DMSO. The cell suspension is then cryopreserved using the Tiss-U-Stor device with a defined cooling program, and the measured temperature profile is recorded for each individual cell suspension derived from each tumor portion. The cryopreserved cell suspension is stored in vapor-phase of liquid nitrogen.

[00379] The cryopreserved cell suspension recommended storage condition is < -130°C. [00380] The cell suspension is transported from the clinical site to the GMP cell therapy manufacturing site by a qualified courier service packaged in a container validated to ensure the cryopreserved cell suspension is maintained at < -130°C.

[00381] Tiss-u-Stor. Resected tumors are evaluated for weight and condition. For each tumor fragment, extraneous material is removed and the fragment weighed. A CS50N bag is opened, up to about 7g of tumor is added and the bag is then sealed. 15 ml of EDM digest medium is added to the bag with 2pl gentamicin/amphotericin per ml EDM by syringe via needleless port followed by removal of air from the from the bag into the syringe.

[00382] The tumor tissue and disaggregation media in the disaggregation bag is placed in the temperature controlled tissue disaggregator. The temperature is increased from ambient temperature to 35°C at a rate of 1.5°C/min and maintained at 35°C for a total of about 45 minutes during which time the disaggregator is active at 240 cycles per minute.

[00383] Once disaggregated the tumor material is filtered through an inline filter into a secondary freezing bag. 1.5 ml of Blood stor (DMSO) is injected via a needleless port and air removed.

[00384] 2 ml. of the suspension is withdrawn for testing.

[00385] For optional cry opreservation, the cryobag is loaded into a freezing cassette and the freezing cassette placed in the Via freeze. The Via freeze is then cooled to -80°C, preferably directly from 35°C to -80°C at a rate of -2°C/min.

[00386] The frozen cryobag is then transferred to liquid nitrogen storage.

[00387] Autologous tissue used for culturing in the United Kingdom (UK) should conform to HTA-GD-20, Guide to Quality and Safety Assurance for Human Tissue and Cells for Patient Treatment, established by the UK’s Human Tissue Authority with suitable consent, Chain of Identity, Chain of Custody and screening to confirm donors are negative for Hepatitis B virus, Hepatitis C virus, HIV-1 & 2, HTLV-1 & 2, and Syphilis.

[00388] Manufacturing involves outgrowth and expansion from a cryopreserved cell suspension containing TILs and tumor cells derived from a resected tumor. If the tumor is greater than about 7 g, the resection process generates multiple cryopreserved cell suspensions, where each cell suspension derives from a 2 - 7 g tumor fragment. Typically, only one cell suspension is needed to be thawed for 1 TIL outgrowth while the remaining cryopreserved cell suspensions remain in GMP control and held at the recommended storage condition (vapor phase of liquid nitrogen). [00389] In certain embodiments the cell suspension has been filtered after disaggregation, prior to cry opreservation. Exemplary Manufacturing Raw Materials are provided in the following table:

[00390] T cell medium (TCM) contains Albumin (human), human Holo Transferrin, and animal origin cholesterol. The source plasma used to manufacture Albumin and Transferrin are sourced from the USA and the donors are tested for adventitious agents.

[00391] Cholesterol is sourced from sheep wool grease originating in Australia/New Zealand, which complies with USDA regulations prohibiting ruminant original material from countries with reported cases of transmission spongiform encephalopathy (TSE).

[00392] Fetal Bovine Serum (FBS) is sourced from Australia / New Zealand in compliance with the USDA regulations prohibiting ruminant original material from countries with reported cases of transmission spongiform encephalopathy (TSE). The FBS is tested in compliance with 21 CFR part 113.47, specifically including: bluetongue virus, bovine adenovirus, bovine parvovirus, bovine respiratory syncytial virus, bovine viral diarrhea virus, rabies virus, reovirus, cytopathic agents, haemadsorbing agents. The FBS is heat inactivated at 56°C for 30 minutes and triple 0.1 pm filtered to provide two orthogonal viral removal steps.

[00393] Human AB Serum is sourced from Valley Biomedical, an FDA registered establishment (1121958). Each donor unit is tested for Hepatitis B surface Antigen (HBsAg), Hepatitis B Virus (HBV) Nucleic acid Amplification Test (NAT), anti-Human Immunodeficiency Virus (HIV) type 1 and 2, HIV-1 NAT, anti-Hepatitis C Virus (HCV), HCV NAT, and a test for syphilis by FDA approved methods. The serum is heat inactivated at 56°C for 30 minutes and 0.1 pm filtered.

[00394] Irradiated Buffy Coat sourcing, preparation, shipment and storage: The Scottish National Blood Transfusion Service (SNBTS) screens donors, collects the blood component, prepares and irradiates buffy coats. The SNBTS is licensed by the United Kingdom’s Human Tissue Authority (license number 11018) in accordance with the Blood, Safety and Quality Regulations (2005) to procure, process, test, store and distribute blood, blood components and tissues.

[00395] Healthy donor screening meets or exceeds the requirements described in the United States Code of Federal Regulations (CFR) Title 21 Part 1271.75 with the exception that donors live in the United Kingdom. While this presents a theoretical risk of sporadic Creutzfeldt-Jakob Disease (sCJD) or variant Creutzfeldt- Jakob Disease (vCJD), the United Kingdom has a robust national surveillance program. The most recent annual report, covering May 1990 to December 31st 2018 (National CJD Research & Surveillance Unit, 2018), confirms the incidence of sCJD in the UK is comparable to those observed elsewhere in the world, including countries that are free of bovine spongiform encephalopathy (BSE). There have been no reported cases of vCJD in 2017 through April 5th 2020, and only two cases identified nationally since January 1st 2012 (NCJDRSU Monthly Report, 2020). This rigorous surveillance network has eliminated transfusion transmitted vCJD infections with none reported since 2007 (National CJD Research & Surveillance Unit, 2018). Exemplary eligible donor testing meets 21 CFR Part 1271.85 requirements and adds Hepatitis E testing which is not required. [00396] The licensed blood establishment prepares clinical grade irradiated buffy coats which are suitable to treat patients with severe neutropenia. To prepare the buffy coats, blood is centrifuged to form three layers: the red blood cell layer, the buffy coat layer and the plasma layer. Buffy coats from 10 donors are irradiated with 25 to 50 Gy irradiation to arrest cell growth. The clinical grade irradiated buffy coats are prepared and shipped to the GMP manufacturing facility by overnight courier using a controlled temperature shipper including a temperature monitor. The shipment occurs one day before use in the manufacturing process. [00397] Upon receipt, the buffy coats are held at 15 - 30°C until use in manufacturing. [00398] Irradiated Feeder Cell Preparation. Buffy coats from up to ten unique donors are pooled, then centrifuged by Ficoll gradient density centrifugation to harvest peripheral blood mononuclear cells (PBMCs). Approximately 4 x 10 ⁹ viable white blood cells are resuspended in TCM supplemented with approximately 8% human AB serum, 3000 lU/mL IL-2 and 30 ng OKT-3 in a closed static cell culture bag. The PBMC are released per specification.

[00399] The PBMC are also tested for sterility and mycoplasma. Immediately prior to starting step 3, a sample of the formulated feeder cell, including media, IL-2 and OKT3, is removed. This sample is incubated and analyzed on days 13, 17 and 18 to confirm that the feeder cells do not expand.

[00400] Albumin (human), also known as Human Serum Albumin (HSA), is sourced from US donors. All plasma donations are individually tested and non-reactive to HBsAg, anti -HIV 1, anti-HIV 2, and anti-HCV antibodies. Each plasma pool is tested and found negative for HBsAg, anti -HIV 1, anti-HIV 2, and HCV-RNA by NAT. The HSA product is manufactured according to GMP regulations fulfilling the production and testing criteria of US and European Pharmacopoeia.

[00401] TIL Outgrowth. The cell suspension is seeded at approximately 0.25 x 10 ⁶ to 0.75 x 10 ⁶ viable cells/mL into TCM supplemented with 10% FBS, 0.25 pg/mL Amphotericin B with 10 pg/mL Gentamicin (Life Technologies, Grand Island, NY), and interleukin-2 (IL-2; aldesluekin) 3000 TU/mL (Clinigen, Ntirnberg, Germany) and cultured in standard cell culture conditions (37°C, 5% CO2).

[00402] On day 5, half of the media is removed and replaced with TCM supplemented with 10% FBS, 0.50 pg/mL Amphotericin B, 20 pg/mL Gentamicin and 6000 ZU/mL IL-2.

[00403] On day 7, if the cell concentration is > 1.5 x 10 ⁶ viable cells/mL, the TIL outgrowth culture is diluted with three times the volume to maintain approximately 0.1 x 10 ⁶ to 2.0 x 10 ⁵ viable cells/mL. If the cell concentration is < 1.5 x 10 ⁶ viable cells/mL, half of the media is replaced. In either option, the media is TCM supplemented with 10% FBS, 0.50 pg/mL Amphotericin B, 20 pg/mL Gentamicin and 6000 lU/mL IL-2.

[00404] On day 10, if the cell concentration is > 1.5 x 10 ⁶ viable cells/mL, the TIL outgrowth culture is diluted with three times the volume to maintain approximately 0.1 x 10 ⁶ to 2.0 x 10 ⁵ viable cells/mL. If the cell concentration is < 1.5 x 10 ⁶ viable cells/mL, half of the media is replaced. In either option, the media added is TCM supplemented with 10% FBS, 0.50 pg/mL Amphotericin B, 20 pg/mL Gentamicin and 6000 lU/mL IL-2.

[00405] TILs are activated using an anti-CD3 antibody (OKT3) to provide a CD3 specific stimulation when bound to the FC receptor of irradiated feeder cells from allogeneic peripheral blood mononuclear cells (PBMCs). The feeders provide a natural source of additional costimulation to support the added anti-CD3 (OKT-3).

[00406] On day 12, 1 to 20 x 10 ⁶ viable T cells from the TIL outgrowth Step 2 are added to 2.0 to 4.0 x 10 ⁹ viable irradiated feeder cells (Section 8.1.4.4) using approximately 30 ± 10 ng/mL OKT3, approximately 8% Human AB Serum and 3000 ± 1000 lU/mL IL-2. The TIL activation culture is incubated for 6 days at standard cell culture conditions.

[00407] On day 18, the activated TILs continue expansion by aseptically adding the activated TIL cell suspension into a bioreactor containing T cell media supplemented with approximately 8% Human AB Serum and 3000 lU/mL IL-2.

[00408] On day 19, the TIL expansion is provided a continuous feed of T cell media supplemented with 3000 lU/mL IL-2 until harvest.

[00409] TILs are harvested by washing the cells using SEFIATM. The cells are concentrated by centrifugation then washed 2-4 times using phosphate buffered saline (PBS) supplemented with 1% human serum albumin (HSA). The cells are then resuspended in PBS + 1% HSA to approximately 50-60 mL. [00410] The washed and concentrated cells are aseptically transferred into a cryobag and a portion removed for lot release testing and retained samples. To formulate drug product (DP) the TILs are then cooled to 2-8°C and formulated, e.g. 1 :1 with cryoprotectant containing 16% HSA and 20% DMSO, to achieve a formulated product of > 5 x 10 ⁹ viable cells suspended in approximately 10% DMSO and 8.5% HSA in PBS. A portion is removed for lot release testing and retained samples. The cryobag is cooled to -80°C.

[00411] The following table shows examples of TIL manufacture process variations.

[00412] The following table shows Drug Product Data

[00413] Comparing cryopreserved and fresh cell suspensions, representative yields were consistent as demonstrated by similar drug substance yield, viability, and percent T cells.

[00414] Optimization of Cry opreservation - As a surrogate to tumor material, isolated PBMCs were digested using the Tiss-U-Stor process and materials. Commercial cryopreservation agents (CPAs) were evaluated across a range of conditions to determine which reagent maximized postthaw viability. The post-thaw viabilities of two CPAs, CryostorlO and Stem Cell Banker DMSO free, were similar. CryoStor based DMSO was then compared with Bloodstor 55-5, a DMSO based cryopreservative, and the higher concentration BloodStor product was selected since it was more concentrated thus allowing for a smaller cryobag. Cryopreservation was then compared following a protocol that either held the material at 4°C for 10 minutes, then decreased the temperature at a rate of -l°C/min or decreased from 35°C to -80°C directly at a rate of -2°C/min. Post-thaw viability was similar between the two cry opreservation protocols used. [00415] During cooling, ice nucleation releases heat. Undercooling, a phenomenon where the released heat appears to warm the solution, is associated with lower post-thaw recoveries. Temperature data was recorded from test articles during cry opreservation using both protocols. Undercooling was observed in both independent runs using the -l°C/min protocol, whereas the - 2°C/min cooling protocol recorded no undercooling event once, and in the second independent run, an undercooling event was observed to release less heat relative to the alternative protocol. [00416] The cryopreserved DP is transferred to vapor phase LN2 for storage and transport at < -130°C.

[00417] Sample sterility is tested and retained samples are frozen using a Cool cell® (Biocision, Larkspur, CA) at -80°C then transferred to vapor phase LN2 for storage purposes. [00418] In an aspect, the invention provides methods for evaluating TIL compositions. TIL potency analysis comprises evaluation of analytes characteristic of TIL activation, including but not limited to indicators of mechanism of action. Exemplary non-limiting mechanisms of action include tumor cell killing, cytokine secretion, proliferation, persistence, and properties indicative of the mechanisms. Analysis can comprise enumeration of T cells and target cells, for example by flow cytometry, percent killing which can be observed by fluorescence or luminescence in plate-based or flow cytometry or other methods such as cartridge-based methods, characterization of individual cells to determine expression of markers including but not limited to expression of cytokines, cell surface markers, expression levels of genes that are induced in activated T-cells, including and not limited to reporter molecules engineered to be expressed under activating conditions, or other hallmarks of T cell activation.

[00419] Measures of TIL potency include TIL cellular composition and phenotype, such as but not limited to numbers and proportions of CD8 ⁺ cells, memory phenotype including without limitation effector memory and central memory, measures of cytotoxicity using various cell lines, cytotoxicity using patient specific tumor, expression of cytokines or a panels of cytokines, and cell proliferation and persistence.

[00420] In certain embodiments, there is provided a bioassay for quantification of TIL potency. In certain embodiments, the bioassay comprises multiparameter or polychromatic intracellular flow cytometry. Intracellular flow cytometry is particularly advantageous for assessment of T cell specific parameters on an individual cell basis and ensures accurate determination even in heterogeneous cell populations. Multiparameter flow cytometry permits simultaneous detection or two or more components, which can include two or more cytokines, combined with high throughput. Cartridge-based analytical technologies are also contemplated, such as but not limited to the cartridges manufactured by Chemometec chemometec.com/products/nucleocounter-nc-200-automated-cell- counter/ or Accellixaccellix.com/technology/).

[00421] Unlike ELIS As and similar methods used on bulk supernatant, intracellular assays described herein are cell and cell type specific. Advantageously, individual cytokine producing cells can be identified and enriched if desired. In certain embodiments, the intracellular methods avoid cytotoxicity and effects of the methods on the assayed cells are reversible.

[00422] In certain embodiments, a TIL population is cocultured with cells engineered to activate T cells via CD3, the signaling component of the T-cell receptor (TCR). In certain embodiments, a modified TIL population is cocultured with cells engineered to activate T cells as well as engage and activate a costimulatory receptor. A convenient example of activating cells comprises K562 cells engineered to express a binding protein or antibody or antigen binding fragment thereof that binds to and activates the TCR. In certain embodiments, the antibody comprises 0KT3. In certain embodiments, the antigen binding fragment comprises a singlechain variable fragment (scFv) from OKT3. Co-culture of ITIL-168 DP with stimulatory K562- 0KT3 cells allows for T cell activation via TCR. In certain embodiments, there is provided a negative control, for example, without limitation, nontransduced clonal K562 cells, K562-NT. The ratio of TILs to activating cells can be adjusted as needed. In certain embodiments, the ration of TILs to activating cells is from 10: 1 to 1 : 10. Non-limiting examples include coculture of TILs with stimulatory K562-OKT3 cells in ratios such as 10: 1, 9: 1, 8: 1, 7:1, 6: 1, 5:1, 4: 1, 3: 1, 2: 1, 1 : 1, 1 :2, 1 :3, 1 :4, 1 :5, 1:6, 1 :7, 1:8, 1 :9, or 1 :10.

[00423] In certain embodiments, the potency analysis method is used to determine potency of a TIL population cocultured with a “standard” cell type. A non-limiting example is a K562 cell engineered to express a ligand, such as but not limited to an antibody or antigen binding fragment thereof, such as an 0KT3 antibody or antigen binding fragment thereof that binds to and activates a T-cell receptor on the TIL. In certain embodiments, the potency analysis method is used to determine potency of a TIL population cocultured with tumor cells or cells engineered to express a tumor associated antigen. In certain embodiments, the potency analysis method is used to determine potency of a TIL population cocultured with tumor cells from the same patient as the source of the TILs.

[00424] Potency can be reported as:

[00425] % Potency Reportable = AVG _{K 62scFvOKT3} ~ AVG _K562NT

[00426] A l 'G indicates the average potency determined by assay in triplicate.

[00427] Potency may be calculated as the frequency of all viable CD2+ cells that are positive for one or more of CD137, CD107a, TNF-a and IFN-y, preferably CD107a and IFN-y.

[00428] The potency analysis method can be applied at any stage of TIL manufacture. In certain embodiments, TIL manufacture comprises monitoring potency of the TIL manufacture from one culture step to the next. In certain embodiments, TIL manufacture comprising monitoring TIL potency throughout the TIL manufacture. In some embodiments, TIL manufacture may comprise measuring TIL potency to confirm or adjust the number of cells from a culture step used to seed a subsequent culture step. TIL quality attributes include potency, viability, cell count and purity. In certain embodiments, TIL manufacture comprises measuring the potency of TILs processed from a tumor. In certain embodiments, TIL manufacture comprises measuring the potency of TILs from a pre-REP expansion culture. In certain embodiments, TIL manufacture comprises measuring the potency of TILs during a preexpansion REP. In certain embodiments, TIL manufacture comprises measuring the potency of TILs at the end of a REP. In certain embodiments, TIL manufacture comprises measuring the potency of TILs at the end of a second REP. In certain embodiments, TIL manufacture comprises measuring TIL potency during REP, for example mid-REP. In certain embodiments, TIL manufacture comprises measuring TIL potency prior to cry opreservation and/or after thawing of a cryopreserved cells. In certain embodiments, TIL manufacture comprises measuring the potency of TIL drug product (TIL DP). The potency testing at any stage of TIL manufacture may further comprise enrichment or isolation of more potent TILs, for example the top 40%, or the top 50%, or the top 60%, or the top 70%, or the top 80%, or the top 90% of the TILs. In certain embodiments, the enrichment or isolation comprises separation of TILs from inhibitory cells.

[00429] Non-limiting examples of analytes indicative of TIL activation and potency include IFN-y, CD107a, CD137 (4-1BB). Other markers indicative or TIL activation or beneficial anti- tumor characteristics include, but are not limited to, TL-lbeta, IL-2, TL-4, TL-6, TL-8, TL-10, TL- 12p70, granzyme A/B, perforin, caspase 3 and other chemokine markers.

[00430] CD107a (aka lysosomal-associated membrane protein-1 or LAMP-1) is a marker of degranulation of NK cells and CD8+ T-cells. IFN-y is a pleiotropic cytokine with antiviral, antitumor, and immunomodulatory functions. IFN-y has been shown to increase the motility of antigen-specific CD8+ T-cells to the antigen-expressing (target) cells and enhance the killing of target cells. IFN-y concentration in the tumor microenvironments has been linked to better immune checkpoint blockade efficacy, comprises an indicator of T-cell activation. In an embodiment, there is an analysis of IFN-y and CD107a. CD137 (4-1BB) is a member of the TNFR family and functions as a costimulatory molecule to promote proliferation and survival of activated T cells. Expression of CD137 on T cells is found in T cells that have recently been activated by TCR engagement. TNF is a proinflammatory cytokine produced by activated T cells and indicative of robust antitumor activity.

[00431] Potency due to autocrine stimulation of TIL by cytokines or potency due to paracrine stimulation of anti-tumor effects mediated by other cells in the tumor microenvironment is detectable in Applicant’s method, although if there is high background in the T cell +K562 parenteral, Applicants have not yet observed it. Potency markers indicating persistence may be detected in a cell proliferation assay.

[00432] In certain embodiments, analytes that distinguish cell subsets are examined. Non limiting examples are CD62L and CD45RO which in different combination can distinguish among effector cells (CD62L-, CD45RO-), effector memory cells (CD62L-, CD45RO+), central memory cells (CD62L+, CD45RO+) and stem cell memory cells (CD62L+, CD45RO-).

[00433] Other examples indicative of desirable subsets, activated subsets, cells preferred to be discarded include clearance subsets, such as B cells, monocytes, granulocytes, NK cells, Melanoma tumor cells and other subsets include, but are not limited to, CD3, CD4, CD8, CD95, CCR7 and CD45RO, to distinguish between naive, T memory stem cells (SCM), effector, effector memory, and central memory subsets.

[00434] An assay overview is provided for cryopreserved cells. As described above, the assay is suitable to determine TIL potency at any stage of manufacture, and includes TIL from any process, culture, or expansion step, and TIL fresh or cryopreserved. Cryopreserved cells are thawed typically provided a recovery period before potency testing of about 1-2 hr, 2-4 hr, 4-6 hr., 6-8 hr., 8-10 hr., 10-12 hr, or overnight (up to 24 hr), before testing. After the recovery period, or on day 2 (day 1 for fresh TIL), thawed TIL are then mixed with a population of stimulatory cells (e.g. K562 or other non T cell line engineered with OKT3 scFv fragment) capable of engaging and stimulating the TILs via the TCR. The number of cells post recovery going into the assay, for example transduced and untransduced cells, seeded in the assay may be from about 1 x 10 ⁵ , 2 x 10 ⁵ , 3 x 10 ⁵ , 4 x 10 ⁵ , 5 x 10 ⁵ , 6 x 10 ⁵ , 7 x 10 ⁵ , 8 x 10 ⁵ , 9 x 10 ⁵ , 1 x 10 ⁶ , 2 x 10 ⁶ , 3 x 10 ⁶ , 4 x 10 ⁶ , 5 x 10 ⁶ , 6 x 10 ⁶ , 7 x 10 ⁶ , 8 x 10 ⁶ , 9 x 10 ⁷ , 1 x 10 ⁷ , 2 x 10 ⁷ , 3 x 10 ⁷ , 4 x 10 ⁷ , 5 x 10 ⁷ , 6 x 10 ⁷ , 7 x 10 ⁷ , 8 x 10 ⁷ , 9 x 10 ⁷ , 1 x 10 ⁸ , 2 x 10 ⁸ , 3 x 10 ⁸ , 4 x 10 ⁸ , 5 x 10 ⁸ , 6 x 10 ⁸ , 7 x 10 ⁸ , 8 x 10 ⁸ , 9 x 10 ⁸ , 1 x 10 ⁹ cells. The mixed cell composition may be incubated for about 8-10 hr., 10-12 hr, 12-14 hr., 14-16 hr., 16-18 hr., 18-20 hr., 20-22 hr., 22-24 hr., 24-26 hr., 26-28 hr., 28-30 hr., 30-32 hr., 32-34 hr. or 34-36 hr. with an inhibitor of protein transport inhibitors (e.g. Brefeldin A and Monensin which may be at a concentration from about 10X, 20X, 30X, 40X, 50X, 60X, 70X, 80X, 90X, 100X, 200X, 300X, 400X, 500X, 600X, 700X, 800X, 900X, 1000X, 200X, 3000X, 4000X, 5000X, 6000X, 7000X, 8000X, 9000X or 10,000X) and optionally one or more reagents to monitor pertinent markers that identify degranulating cells post activation (e.g., anti-CD107a). CD107a may be added to mark T cell degranulation prior to analyzing cell count, viability and/or cell purity, which may be determined by flow cytometry or a cartridge based method. The incubation period may be about 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12, 12.5, 13, 13.5, 14, 14.5, 15, 15.5, 16, 16.5, 17, 17.5, 18, 18.5, 19, 19.5, 20, 20.5, 21, 21.5, 22, 22.5, 23, 23.5, 24, 24.5, 25, 25.5, 26, 26.2, 27, 27.5, 28, 28.5, 29, 29.5, 30, 30.5, 31, 31.5, 32, 32.5, 33, 33.5, 34, 34.5, 35, 35.5, or 36 hours After an effective incubation period, the cell culture is treated to distinguish live and dead cells and the cells are permeabilized and fixed. The concentration of the fixative and the time of fixing may be optimized and is within the purview of one of skill in the art. The treatment may be for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 30, 31, 32, 33, 34 or 35 minutes. Permeabilized cells are stained for intracellular and extracellular markers and the markers measured by flow cytometry or a cartridge based method. The antibody cocktail used to stain the cells of potency markers (e.g., CD2, TNFa, IFNg, CD137) can vary across different fluorophores (e.g. PE, PCP-eF710, APC, APC-Cy7, BV711, eFLOUR506, GFP etc.) concentration volume (0.5, 1.0, 1.2, 1.25, 1.3,

I l l 1.5, 1 .75, 1.8, 1 .9, 2.0, 2.5, 3, 3.5, 4 etc.) and incubation time (5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60 mins, etc.). A stain may be utilized to distinguish between live and dead cells.

[00435] All patent filings, websites, other publications, accession numbers and the like cited above or below are incorporated by reference in their entirety for all purposes to the same extent as if each individual item were specifically and individually indicated to be so incorporated by reference. If different versions of a sequence are associated with an accession number at different times, the version associated with the accession number at the effective filing date of this application is meant. The effective filing date means the earlier of the actual filing date or filing date of a priority application referring to the accession number if applicable. Likewise, if different versions of a publication, website or the like are published at different times, the version most recently published at the effective filing date of the application is meant unless otherwise indicated. Any feature, step, element, embodiment, or aspect of the invention can be used in combination with any other unless specifically indicated otherwise. Although the present invention has been described in some detail by way of illustration and example for purposes of clarity and understanding, it will be apparent that certain changes and modifications may be practiced within the scope of the appended claims.

EXAMPLES

Example 1. Characterization of the Transcriptomic and T-cell Receptor (TCR) Clonal Heterogeneity of Tumor-Infiltrating Lymphocyte (TIL) Therapy Infusion Products by Single-Cell Sequencing and Correlative Analyses With Clinical Efficacy in Patients With Advanced Cutaneous Melanoma

[00436] Introduction: TIL products made from tumor digests produced high clinical response rates (67% overall response rate; 19% complete responses) and a safety profile consistent with lymphodepletion and high-dose interleukin (IL)-2 in a retrospective analysis of a single-center compassionate use clinical series of 21 patients with advanced cutaneous melanoma (Hawkins, et al. Cancer Res. 2021 ;81 [13 suppl] :LB 150). Using single-cell and bulk sequencing techniques, this translational subanalysis is the first to characterize TIL therapy infusion product composition, cell-cell interactions, TCR repertoire, and correlate findings with clinical efficacy. [00437] Methods: Suitable patients underwent resection of >1 cm ³ of tumor tissue for TIL production. Quantitative disease assessments were conducted and analyzed retrospectively per Response Evaluation Criteria in Solid Tumors version 1.1 when feasible. TIL products were characterized using RNA-based bulk TCR sequencing and paired single-cell RNA and TCR sequencing techniques. TCR repertoire clonality was assessed using multiple metrics, including Gini coefficient. Descriptive statistical testing was performed using Wilcoxon test; P values were not adjusted for multiplicity.

[00438] Results: As of December 31, 2019, 21 patients underwent treatment; data are reported for patients with assessable products (n=20 for RNA-based bulk TCR sequencing, and 18 for paired single-cell RNA and TCR sequencing). Analysis of the single-cell RNA sequencing data identified several cell subpopulations with distinct transcriptional signatures previously undescribed in TIL products, including MX1+0AS1+ T cells, 2 subsets of mixed gamma/delta CD8+ T cells, and CD8+ regulatory T cells. The combined frequency of MX1+0AS1+ T cells and apoptotic CD8+ T cells was significantly lower among responders versus non-responders ( =.OO 12). Transcriptional state of the MX1+0AS1+ TIL subpopulation may be maintained by the IRF7 transcription factor, as suggested by gene regulatory network analysis. Among all patients, cell-cell interaction analyses identified potentially detrimental signaling interactions, including the TGFp, galectin, Fas ligand, and MIF pathways, among different TIL product subpopulations. Analysis of the bulk TCR sequencing data suggested that higher clonality of TIL product TCR repertoire (a, P, y, 5) was associated with response (all F’< 02). Low TCR repertoire similarity was observed among TIL products from different patients. The majority of TCRs were previously undescribed. Joint analysis of the single-cell RNA and TCR sequencing data suggested that higher clonality was observed among EOMES+ TIL product subpopulations and that higher clonality among CD62L+ TIL product subpopulations was associated with response (P=.OO12).

[00439] Conclusions: This subanalysis characterized TIL therapy infusion products using single-cell and bulk sequencing techniques, and is the first of its kind aimed at identifying actionable TIL therapy improvements to improve outcomes for patients with advanced cutaneous melanoma. Collectively, these findings suggest that a significant fraction of the clonotypes contained in TIL infusion products are unique to each patient, highlighting a potential benefit of TIL therapy versus more targeted T-cell therapies. These hypothesis-generating data identified potential TIL improvement opportunities and putative response biomarkers that warrant further study. Materials and Methods

[00440] Bulk TCR Sequencing of TIL Product. RNA of TIL product samples was extracted using the RNeasy mini kit (Qiagen, cat. 74104). The extracted RNA samples were then sent over to IRepertoire ¹ for bulk TCR sequencing using their Repseq+ technology. Alpha chain, beta chain, delta chain, and gamma chain RNA molecules were amplified and enriched in separate reactions and sequenced separately.

[00441] Analysis of Bulk TCR Sequencing Data. Raw FASTQ files were processed using IRepertoire’ s standard bioinformatic pipeline to obtain clonotype-level counts data as well as overall repertoire clonality and diversity metrics. The Immunarch R package ² was used to analyze the clonotype-level counts data and calculate additional repertoire clonality, diversity, and similarity metrics. The clonotype-level counts data of each sample were down sampled to the same level of total clone counts across all samples before clonality and diversity metrics were calculated.

[00442] Putative antigen specific TCR clonotype groups were identified using the GLIPH2 algorithm ³ . Three public immune receptor databases, including the VDJDB database ⁴ , the McPAS-TCR database ⁵ , and the TBAdb database ⁶ , were used to identify the associated antigens for each clonotype group.

[00443] Paired Single Cell RNA and TCR Sequencing of TIL Product. Cryopreserved TIL product samples were thawed and rested overnight in RPMI culture media supplemented with 10% FBS, 50 pM beta-Mercaptoethanol, 100 units/mL penicillin, 100 ug/mL streptomycin, and 1000 lU/mL IL-2, followed by a Percoll purification step to remove debris and dead cells. The purified cells were then loaded to the Chromium controller ⁷ for single-cell sequencing library preparation. Vendor provided reagents and standard protocols were used to generate paired single-cell RNA and TCR sequencing libraries for each TIL product sample. Final libraries were sequenced using Illumina’s NovaSeq sequencer at Genewiz ⁸ .

[00444] Analysis of Paired Single Cell RNA and TCR Sequencing data. Raw FASTQ files were processed using the Cell Ranger software ⁷ with default parameters. The resulting counts matrix were then analyzed using the Seurat ⁹ R package. The counts matrix was first filtered based on the total number of genes and the fraction of mitochondria genes detected in each cell. Cells with a fraction of mitochondria gene detected being greater than 10% or with a total number of genes detected being less than 800 were excluded from further analysis The top 2000 highly variable genes in each TIL product sample were then identified and used as the anchor genes for sample integration to remove any technical batch effect. Cell cycle scores of each cell were calculated and regressed out from the integrated counts matrix, followed by unsupervised clustering which partitions all cells into several cell subpopulations with distinct transcriptional signatures.

[00445] Differential gene expression analyses were performed between each cell subpopulation and the rest of cells to identify a list of upregulated and downregulated genes associated with each cell subpopulation. Gene set overrepresentation analysis was performed using the clusterProfiler ¹⁰ R package on the up- and down- regulated gene lists respectively to identify biological processes associated with each cell subpopulation. Within each cell subpopulation, differential gene expression analysis and gene set overrepresentation analysis were performed between cells from responders and cells from non-responders. The fractional abundance of each cell subpopulation in each TIL product sample was calculated and correlated to clinical response.

[00446] Gene regulatory network analysis was performed using the SCENIC ¹¹ R package on each single-cell gene expression profde to score the activity level of each transcription factor in each cell. The activity score of each transcription factor is averaged within each cell subpopulation and standardized across cell subpopulations. The top 20 most active transcription factors of each cell subpopulation were identified as the list of key transcription factors responsible for maintaining the transcriptional signature of that cell subpopulation.

[00447] The CellChat ¹² R package was used to identify the significant expression of any known ligand-receptor pairs among each cell subpopulations.

[00448] To identify genes associated with clonal expansion, each detected gene was used to define a subpopulation of cells from each TIL product sample where only cells that express that gene is included. TCR repertoire clonality metrics, including Gini Coefficient, of the cell subpopulations from each TIL product sample is calculated. The top 100 cell subpopulations with the highest population size-adjusted Gini Coefficient are identified for each TIL product sample. The 100 genes that defined these cell subpopulations were identified as the genes being associated with higher clonal expansion in each TIL product sample. The most common higher clonal expansion-associated genes across all TIL product samples were identified as the genes being associated with higher overall clonal expansion across all TIL product samples. The same above-mentioned process is used to obtain the genes being associated with lower clonal expansion in each TIL product sample, and the genes being associated with lower overall clonal expansion across all TIL product samples. The Gini coefficient of each gene-defined cell subpopulation were correlated to patient response to identify cell subpopulations whose TCR repertoire clonality was significantly correlated with response.

References

[00449] 1. irepertoire.com/; note: IRepertoire is the vendor that performed bulk TCR-Seq and processed the raw sequencing data

[00450] 2. immunarch.com/index.html; note: Immunarch is the R package that was used to calculating various clonality metrics

[00451] 3. Huang et al, Nature Biotechnology 38, 1194-1202 (2020)

[00452] 4. Shugay et al, Nucleic Acids Research 46, D419-D427 (2018)

[00453] 5. Tickotsky et al, Bioinformatics 33, 2924-2929 (2017)

[00454] 6. Zhang et al, Bioinformatics 36, 897-903 (2020)

[00455] 7. 1 Oxgenomics. com;/ note: The Chromium machine and reagents from 10X genomics was used to perform the library preparation step of paired single-cell RNA and TCR sequencing. The Cell Ranger software from 10X genomics was used to process raw FASTQ files.

[00456] 8.genewiz.com/en; note: Genewiz is the vendor that performed the sequencing of paired single-cell RNA and TCR sequencing library

[00457] 9. satijalab.org/seurat/; note: Seurat is the R package that was used to perform the unsupervised clustering of single cell RNA sequencing data and the differential gene expression analysis between cell populations

[00458] 10. bioconductor.org/packages/release/bioc/html/clusterProfiler. html; note: clusterProfiler is the R package that was used to perform gene set over-representation analysis [00459] 11. Aibar et al, Nature Methods 14, 1083-1086 (2017)

[00460] 12. Jin et al, Nature Communications 12, 1088 (2021) Example 2. Analysis of Bulk TCR-Seq and Paired Single-Cell RNA and TCR-Seq Data of TIL Product Samples

[00461] Solid tumors are characterized by marked clonal heterogeneity with a variety of antigens, including neoantigens, which often differ between patients and cancer types. ¹ Melanoma has a high mutational burden and marked clonal heterogeneity both within individual patients and between patients. ^1,2 Despite treatment advances with targeted therapies and checkpoint inhibitors, most patients with advanced melanoma ultimately relapse and have limited treatment options, ³ highlighting an unmet medical need. Autologous tumor-infdtrating lymphocyte (TIL) products are comprised of an unrestricted T-cell receptor (TCR) repertoire and can recognize a broad set of tumor-associated antigens, including neoantigens specific to each patient’s tumor. ⁴ A retrospective analysis of a single-center, compassionate use clinical series of TILs for the treatment of advanced cutaneous melanoma in 21 patients demonstrated high clinical response rates, with a 67% overall response rate and 19% complete response rate, and a safety profile consistent with lymphodepletion and high-dose interleukin (IL)-2. ⁵ There are 10 ⁶ expected TCR-P clonotypes, (most of which are not well characterized by function or previously annotated) and of these, a small subset of clones from TILs will demonstrate anti-tumor activity. ^6,7 Furthermore, predictive models for anti-tumor reactivity have limited positive and negative predictive power. ⁸ For these reasons, an unselected approach maximizes the potential for the limited number of clones with anti-tumor activity to reach the final TIL product.

[00462] TIL therapy infusion product composition, TCR repertoire, and mediators of cell-cell interaction were characterized in a translational subanalysis of the compassionate use clinical series. Patients with histologically confirmed malignant melanoma and no standard-of-care treatment options underwent resection of >1 cm ³ of tumor tissue for TIL production. ⁵ Patients received lymphodepleting chemotherapy (cyclophosphamide 60 mg/kg/d ^x 2 days, fludarabine 25 mg/m ² /d ^x 5 days) followed by TIL infusion and post- TIL short course of high-dose IL-2 (600,000-720,000 lU/kg) on a compassionate use basis. ⁵ Efficacy was assessed locally through standard disease assessment imaging and retrospectively analyzed per Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1 when feasible? TCR repertoire clonality and diversity of TIL products were assessed using multiple metrics, including Gini coefficient, using the Immunarch package. ⁹ TIL products were assessed using RNA-based bulk TCR sequencing and paired single-cell RNA and TCR sequencing techniques. Putative antigen/tumor-reactive clones were inferred using GLTPH2 (grouping of lymphocyte interactions by paratope hotspots 2) algorithm ¹⁰ and publicly available TCR annotation databases including VDJdb public database. ¹¹ Unsupervised clustering of cells and differential gene expression analysis was performed using the Seurat package. ¹² Gene set over-representation analysis was performed using the clusterProfiler package. ¹³ Gene regulatory network analysis was performed using the SCENIC package. ¹⁴ Cell-cell interaction analysis was performed using the CellChat package. ¹⁵ Descriptive statistical testing was performed using Wilcoxon test; P values were not adjusted for multiplicity.

[00463] As of December 31, 2019, 21 patients with advanced cutaneous melanoma underwent treatment. Of 21 patients, 20 had assessable products for RNA-based bulk TCR sequencing, and 18 had assessable products for paired single-cell RNA and TCR sequencing. Technical replicates showed a high Morisita index, demonstrating the reproducibility of the TCR testing method. ¹⁶ A low Morisita index was observed across patients, suggesting a minimal overlap in TCR repertoire and distinct TCR P-chain repertoires between TIL samples. ¹⁶

[00464] Recipients of TIL products with higher TCR P-chain repertoire clonality were more frequently observed to develop a response to therapy. Bulk TCR sequencing indicated that TIL products with higher TCR P-chain repertoire clonality were more frequently given to responders than non-responders. See Figure 1A. Similarly, TIL products with higher TCR a-chain, TCR-8 chain, and TCR y-chain repertoire clonality were more frequently given to responders than non- responders. Clonality was measured by Gini coefficient on a scale of 0 (even distribution) to 1 (uneven distribution). ¹⁷ Statistical significance was assessed by Wilcoxon test. Higher TCR P- chain repertoire clonality was correlated with a higher fraction of in silico predicted antigenreactive T cells based on GLIPH2 (grouping of lymphocyte interactions by paratope hotspots 2). See Figure IB. Antigen-reactive T-cells were inferred by the GLIPH2 algorithm. ¹⁰

[00465] Single-cell RNA sequencing analysis of TIL product samples identified several T-cell subpopulations with distinct gene expression profiles. See Figures 2A-2B. Multiple subpopulations were previously undescribed in TIL product samples. Certain T-cell populations were found at frequencies that differed between products administered to patients who developed responses compared to those who did not achieve a response. See Figures 3A-3C. The frequency of C7 (MX1+0AS1+; Figure 3A), C9 (BBC3+CHAC1+; Figure 3B), or C7 and C9 (Figure 3C) T-cell subpopulations in TIL product samples differed between responders and non- responder. Low abundance of C7 TIL or C9 TIL subpopulations was associated with response (Figures 3A and 3B). Low abundance of the combined C7 and C9 TIL subpopulations was also associated with response (Figure 3C).

[00466] Differential gene expression analyses were performed between each cell subpopulation and the rest of cells as described above to identify a list of upregulated and downregulated genes associated with each cell subpopulation. Gene set overrepresentation analysis (gene ontology analysis) was performed as described above on the up- and down- regulated gene lists respectively to identify biological processes associated with each cell subpopulation. See Figure 3D. Within each cell subpopulation, differential gene expression analysis and gene set overrepresentation analysis were performed between cells from responders and cells from non-responders. The fractional abundance of each cell subpopulation in each TIL product sample was calculated and correlated to clinical response.

[00467] Gene regulatory network analysis (to identify predicted master regulators associated with each cell cluster) was performed as described above on each single-cell gene expression profde to score the activity level of each transcription factor in each cell. The activity score of each transcription factor is averaged within each cell subpopulation and standardized across cell subpopulations. The top 20 most active transcription factors of each cell subpopulation were identified as the list of key transcription factors responsible for maintaining the transcriptional signature of that cell subpopulation. See Figure 3D.

[00468] TCR repertoire clonality assessed by bulk and single-cell TCR sequencing demonstrated concordance (A=0.85). See Figure 4A. The difference in Gini coefficient of TIL product samples assessed by single-cell TCR sequencing was increased when TCR clonality was combined with expression of CD62L (SELL; L-selectin). See Figures 4B-4C. Clonality was measured by Gini coefficient on a scale of 0 (even distribution) to 1 (uneven distribution). ¹ ' Statistical significance was assessed by Wilcoxon test.

[00469] Significant expression of any known ligand-receptor pairs among each cell subpopulations was identified as described above. See Figures 6A-6C. Figure 6B shows three of such pairs, where LGALS is the gene encodes the ligand, and CD45, CD44, HAVCR2 are the receptors that can interact with LGALS. Figure 6A shows the relative expression level of the ligand (or source or sender) in each cell cluster on the y axis, and the relative expression level of the receptors (or sinks, receiver) in each cell cluster on the x axis. Cluster 7 is the main cell type that secretes the ligand and all cell clusters express at least one of the receptors, which is also visualized in Figure 6C. The C7 T-cell subpopulation expresses high levels of GALECTIN9 (LGALS9) ligand, which may have an immunosuppressive function by interacting with its binding partners including TIM-3 (HAVCR2) and CD44, both of which are expressed in TIL product.

[00470] To identify genes associated with clonal expansion, each detected gene was used to define a subpopulation of cells from each TIL product sample where only cells that express that gene were included. TCR repertoire clonality metrics, including Gini Coefficient, of the cell subpopulations from each TIL product sample was calculated. The top 100 cell subpopulations with the highest population size-adjusted Gini Coefficient were identified for each TIL product sample. The 100 genes that defined these cell subpopulations were identified as the genes being associated with higher clonal expansion in each TIL product sample. The most common higher clonal expansion-associated genes across all TIL product samples were identified as the genes being associated with higher overall clonal expansion across all TIL product samples. See Figure 1C. Higher clonality was more frequently observed in more differentiated (EOMES+) T-cell subpopulations. The same above-mentioned process was used to obtain the genes being associated with lower clonal expansion in each TIL product sample, and the genes being associated with lower overall clonal expansion across all TIL product samples. The Gini coefficient of each gene-defined cell subpopulation were correlated to patient response to identify cell subpopulations whose TCR repertoire clonality was significantly correlated with response. See Figure 4B.

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