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WO 2019/068099 Al 04 April 2019 (04.04.2019) W 1P O PCT

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WO 2019/068099 Al 04 April 2019 (04.04.2019) W 1P O PCT (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2019/068099 Al 04 April 2019 (04.04.2019) W 1P O PCT (51) International Patent Classification: HOSPITAL, INC. [US/US]; 75 Francis Street, Boston, C07K 14/705 (2006.01) C12Q 1/68 (2018.01) Massachusetts 021 15 (US). C12N 5/06 (2006.01) (72) Inventors: ANDERSON, Ana Carrizosa; c/o 75 Francis (21) International Application Number: Street, Boston, Massachusetts 021 15 (US). KUCHROO, PCT/US2018/053791 Vijay; c/o 75 Francis Street, Boston, Massachusetts 021 15 (US). SINGER, Meromit; c/o 4 15 Main Street, Cambridge, (22) International Filing Date: Massachusetts 02142 (US). REGEV, Aviv; c/o 415 Main 0 1 October 2018 (01. 10.2018) Street, Cambridge, Massachusetts 02142 (US). (25) Filing Language: English (74) Agent: SCHER, Michael B. et al.; Johnson, Marcou & (26) Publication Language: English Isaacs, LLC, P.O. Bo 691, Hoschton, Georgia 30548 (US). (30) Priority Data: (81) Designated States (unless otherwise indicated, for every 62/565,862 29 September 2017 (29.09.2017) US kind of national protection available): AE, AG, AL, AM, 62/588,101 17 November 2017 (17. 11.2017) US AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, (71) Applicants: THE BROAD INSTITUTE, INC. [US/US]; DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, 415 Main Street, Cambridge, Massachusetts 02142 (US). HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, MASSACHUSETTS INSTITUTE OF TECHNOLOGY KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, [US/US]; 77 Massachusetts Avenue, Cambridge, Massa¬ MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, chusetts 02139 (US). THE BRIGHAM AND WOMEN'S (54) Title: METHODS AND COMPOSITIONS FOR MODULATING SUPPRESSION OF LYMPHOCYTE ACTIVITY FIG. 1 as ¾ (57) Abstract: The subject matter disclosed herein is generally directed to a novel CD8+ T cell subtype associated with suppressive or regulatory T cell functions. Moreover, the subject matter disclosed herein is generally directed to methods and compositions for use of the subtype. Also, disclosed herein are gene signatures and markers associated with the subtype and use of said signatures and markers. Further disclosed are therapeutic methods of using said gene signatures and immune cell subtype. Further disclosed are pharmaceutical compositions comprising populations of CD8+ TILs depleted for a specific subtype. Further disclosed are interactions with other T cell subtypes. o [Continued on nextpage] W O 2019/068099 A l I lllll II lllll lllll lllll llll I II III lllll lllll lllll lllll lllll llll llll llll llll OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available) : ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: — with international search report (Art. 21(3)) — with sequence listing part of description (Rule 5.2(a)) METHODS AND COMPOSITIONS FOR MODULATING SUPPRESSION OF LYMPHOCYTE ACTIVITY CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application Nos. 62/565,862, filed September 29, 2017 and 62/588,101, filed November 17, 2017. The entire contents of the above-identified applications are hereby fully incorporated herein by reference. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH [0002] This invention was made with government support under grant numbers MH1 05960, CA1 87975, AI073748 and NS045937 awarded by the National Institutes of Health. The government has certain rights in the invention. REFERENCE TO AN ELECTRONIC SEQUENCE LISTING [0003] The contents of the electronic sequence listing (BROD_2167WP_ST25.txt"; Size is 7 Kilobytes and it was created on September 24, 2018) is herein incorporated by reference in its entirety. TECHNICAL FIELD [0004] The subject matter disclosed herein is generally directed to CD4+ and CD8+ T lymphocyte subtypes and their interactions associated with immune responses in cancer. Moreover, the subject matter disclosed herein is generally directed to detecting, isolating and modulating said subtypes. BACKGROUND [0005] Characterizing different T cell subpopulations and their underlying driving mechanisms contributes to our understanding of protective immunity in successful pathogen clearance, T cell regulation during uncontrolled tumor growth and chronic infections, and T cell regulation during autoimmunity. Recent advances on this front have enabled the development of improved vaccines and novel immune-based therapies for various cancers. Applicants have previously shown that a CD8 T cell dysfunction gene signature can be decoupled from activation gene signature and have shown that the signatures for each CD8 T cell state is present in distinct single cell populations (see, e.g., WO2017075451A1, WO201 7075478 A2, WO2017075465A1 and US provisional application number 62/384,557, filed September 7, 2016). Previous studies have characterized subsets of regulatory T cells (Treg) that selectively suppress development of autoantibody formation by inhibiting function of follicular T-helper cells (see, e.g., US20130302276A1; and WO2016196912A1). It is believed that the breadth of the functional potential of CD4+ and CD8+ T cells is far from understood, and that gaining a deeper understanding will lead to further advancements. [0006] Consequently, there exists a continuous need to provide additional and preferably improved markers, products and methods allowing to determine the functional state of immune cells. Likewise, there exists a continuous need to provide additional and preferably improved molecular targets involved in immune responses, as well as therapeutically useful substances and compositions impinging on such molecular targets to modulate immune responses. [0007] Citation or identification of any document in this application is not an admission that such document is available as prior art to the present invention. SUMMARY [0008] It is an objective of the present invention to identify CD8+ TIL subtypes present in tumor infiltrating lymphocytes (TIL) during tumor growth. It is another objective of the present invention to detect gene signatures and biomarkers specific to the CD8+ TIL subtypes, whereby cells may be detected and isolated. It is another objective of the present invention to provide for adoptive cell transfer methods for treatment of a cancer by transferring more functional CD8+ TIL populations. It is another objective of the present invention to provide for treatment of a cancer by modulating CD8+ T cell populations to be more functional. It is another objective of the present invention to improve immunotherapy treatment. [0009] In one aspect, the present invention provides for an isolated T cell characterized in that the T cell comprises expression of one or more genes selected from the group consisting of: T RSF9, PRF1, BHLHE40 (DEC1), IRF8, GLDC, STAT3, CST7, IL1R2, EEF2, SLC2A3, SQSTM1, RBPJ, NABPl, ACTN1, T RSF4, SERPINB9, FOSL2, CAPG, KLRC1, IL18R1, JTJ B , EEF1A1, TNFRSF18, RGS2, FKB2, RPL5, PEX16, LAT2, KDM5B, HILPDA, GEM, DEN 4A, BCL2L1 1, ADAM8, PGLYRP1, IKZF2 (Helios), MT1, KIT, SERPINE2, CCRL2, CSF1, EPASl, RUNX2, SPRY2 and XCRl; or genes in Table 6 . In another example embodiment, the isolated T cell is characterized in that the T cell does not comprise expression of HMMR and comprises expression of one or more genes selected from T RSF9, PRF1, BHLHE40 (DEC1), IRF8, GLDC, STAT3, CST7, IL1R2, EEF2, SLC2A3, SQSTM1, RBPJ, NABPl, ACTN1, TNFRSF4, SERPINB9, FOSL2, CAPG, KLRC1, IL18R1, JU B, EEF1A1, T FRSF 18, RGS2, FKB2, RPL5, PEX16, LAT2, KDM5B, HILPDA, GEM, DEN 4A, BCL2L1 1, ADAM8, PGLYRP1, IKZF2, MT1, KIT, SERPINE2, CCRL2, CSF1, EPASl, RUNX2, SPRY2 and XCRl. In another example embodiment, the isolated T cell is characterized by expression of one or more CD8, TIM3, PD1, MT1, and IKZF2, as well as expression of one or more genes selected from the group consisting of TNFRSF 9, PRF1, BHLHE40 (DEC1), IRF8, GLDC, STAT3, CST7, IL1R2, EEF2, SLC2A3, SQSTM1, RBPJ, NABPl, ACTN1, TNFRSF4, SERPINB9, FOSL2, CAPG, KLRC1, IL18R1, JUNB, EEF1A1, TNFRSF 18, RGS2, NFKB2, RPL5, PEX16, LAT2, KDM5B, HILPDA, GEM, DENND4A, BCL2L1 1, ADAM8, PGLYRP1, KIT, SERPINE2, CCRL2, CSF1, EPASl, RUNX2, SPRY2 and XCRl. In another example embodiment, the isolated T cell may be characterized by expression of one or more CD8, TIM3, PD1, MT1, and IKZF2, as well as expression of one or more genes selected from the group consisting of TNFRSF9, PRFl, BHLHE40 (DEC1), IRF8, GLDC, STAT3, CST7, IL1R2, EEF2, SLC2A3, SQSTM1, RBPJ, NABPl, ACTN1, TNFRSF4, SERPINB9, FOSL2, CAPG, KLRC1, IL18R1, JUNB, EEF1A1, TNFRSF 18, RGS2, NFKB2, RPL5, PEX16, LAT2, KDM5B, HILPDA, GEM, DENND4A, BCL2L1 1, ADAM8, PGLYRP1, KIT, SERPINE2, CCRL2, CSF1, EPASl, RUNX2, SPRY2 and XCRl, and does not comprise expression of HMMR. The isolated T cell may be further characterized in that the T cell comprises upregulation of one or more genes selected from the group consisting of TNFRSF9, PRFl, BHLHE40, IRF8, GLDC, STAT3, CST7, IL1R2, EEF2, SLC2A3, SQSTM1, RBPJ, NABPl, ACTN1, TNFRSF4, SERPINB9, FOSL2, CAPG, KLRC1, IL18R1, JUNB, EEF1A1, TNFRSF 18, RGS2, NFKB2, RPL5, PEX16, LAT2, KDM5B, HILPDA, GEM, DENND4A, BCL2L1 1, ADAM8, PGLYRP1, IKZF2, KIT, SERPINE2, CCRL2, CSF1, EPASl, RUNX2, SPRY2 and XCRl as compared to all CD8+ TIM3+ PD1+ T cells.
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