81) Designated States (Unless Otherwise Indicated, for Every a 61K 31/4 709 (2006.01) a 61K 45/06 (2006.01) Kind of National Protection Av Ailable
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) ( (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A 61K 31/4 709 (2006.01) A 61K 45/06 (2006.01) kind of national protection av ailable) . AE, AG, AL, AM, A61P35/00 (2006.01) 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, (21) International Application Number: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, PCT/US2020/024810 HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (22) International Filing Date: KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY,MA, MD, ME, 26 March 2020 (26.03.2020) MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (25) Filing Language: English SC, SD, SE, SG, SK, SL, ST, SV, SY, TH, TJ, TM, TN, TR, (26) Publication Language: English TT, TZ, UA, UG, US, UZ, VC, VN, WS, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 62/827,616 0 1 April 2019 (01.04.2019) US kind of regional protection available) . ARIPO (BW, GH, 62/860,694 12 June 2019 (12.06.2019) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (71) Applicant: KURA ONCOLOGY, INC. [US/US]; 3033 TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, Science Park Road, Suite 220, San Diego, CA 92121 (US). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, (72) Inventor: GUALBERTO, Antonio; 77 Chaudler Street, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, Boston, MA 02 116 (US). TR), OAPI (BF, BJ, CF, CG, Cl, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). (74) Agent: KASSAB, Darren J. et al.; Jones Day, 250 Vesey Street, New York, NY 10281-1047 (US). (54) Title: METHODS OF TREATING CANCER WITH FARNESYLTRANSFERASE INHIBITORS □ D [ SD i PR □ PD SD PR FIGURE 1A FIGURE IB (57) Abstract: The present invention relates to the field of cancer therapy. Specifically, provided are methods of treating cancer, for example, Diffuse Large B Cell Lymphoma ("DLBCL") and/or Mycosis Fungoides ("MF"), with a farnesyltransferase inhibitor (FTI) that include determining whether the subject is likely to be responsive to the FTI treatment based on gene expression characteristics. [Continued on next page] Published: METHODS OF TREATING CANCER WITH FARNESYLTRANSFERASE INHIBITORS CROSS REFERENCE [0001] This application claims the benefit of priority from U.S. Provisional Application No. 62/860,694, filed on June 12, 2019, and further claims the benefit of priority from U.S. Provisional Application No. 62/827,616, filed on April 1, 2019. Each of the foregoing related applications, in its entirety, is incorporated herein by reference. FIELD [0002] The present invention relates to the field of cancer therapy. In particular, provided are methods of treating cancer with farnesyltransferase inhibitors. BACKGROUND [0003] Stratification of patient populations to improve therapeutic response rate is increasingly valuable in the clinical management of cancer patients. Farnesyltransferase inhibitors (FTI) are therapeutic agents that have utility in the treatment of cancers, such as Diffuse Large B Cell Lymphoma (“DLBCL”) and/or Mycosis Fungoides (“MF”). However, patients respond differently to an FTI treatment. Therefore, methods to predict the responsiveness of a subject having cancer to an FTI treatment, or methods to select cancer patients for an FTI treatment, represent unmet needs. The methods and compositions provided herein meet these needs and provide other related advantages. SUMMARY [0004] Provided herein are methods to treat CXCL12-expressing cancer in a subject including administering a therapeutically effective amount of an FTI to the subject having a CXCL12-expressing cancer. Provided herein are also methods to predict the responsiveness of a subject having cancer for an FTI treatment, methods to select a cancer patient for an FTI treatment, methods to stratify cancer patients for an FTI treatment, and methods to increase the responsiveness of a cancer patient population for an FTI treatment. In some embodiments, the methods include analyzing a sample from the subject having cancer to determining that the subject has CXCL 12-expressing cancer prior to administering the FTI to the subject. In some embodiments, the FTI is tipifarnib. In specific embodiments, the cancer is Diffuse Large B Cell Lymphoma (DLBCL). In specific embodiments, the cancer is Mycosis Fungoides (MF). [0005] Provided herein are methods to treat CXCL 12-expressing Diffuse Large B Cell Lymphoma (DLBCL) in a subject including administering a therapeutically effective amount of an FTI to the subject having a CXCL 12-expressing DLBCL. Provided herein are also methods to predict the responsiveness of a subject having DLBCL for an FTI treatment, methods to select a DLBCLpatient for an FTI treatment, methods to stratify DLBCL patients for an FTI treatment, and methods to increase the responsiveness of a DLBCL patient population for an FTI treatment. In some embodiments, the methods include analyzing a sample from the subject having DLBCL to determine that the subject has CXCL 12-expressing DLBCL prior to administering the FTI to the subject. In some embodiments, the FTI is tipifarnib. In specific embodiments, the DLBCL is primary mediastinal B-cell lymphoma (PMBCL). In specific embodiments, the DLBCL is primary DLBCL of the central nervous system (primary DLBCL-CNS). In specific embodiments, the DLBCL is primary cutaneous DLBCL, leg type. In specific embodiments, the DLBCL is T-cell/histiocyte-rich large B-cell lymphoma (T-cell/histiocyte-rich DLBCL). In specific embodiments, the DLBCL is Epstein-Barr virus (EBV)-positive DLBCL (EBV-positive DLBCL). In specific embodiments, the DLBCL is intravascular large B-cell lymphoma (intravascular DLBCL). In specific embodiments, the DLBCL is anaplastic large-cell kinase (ALK)-positive large B-cell lymphoma (ALK-positive DLBCL). In specific embodiments, the DLBCL is DLBCL, Not Otherwise Specified (DLBCL-NOS). In specific embodiments, the DLBCL is germinal-center B-cell-like DLBCL (GCB-DLBCL). In specific embodiments, the DLBCL is activated B-cell-like DLBCL (ABC-DLBCL). In specific embodiments, the DLBCL is double hit DLBCL. In specific embodiments, the DLBCL is a relapsed or refractory DLBCL. [0006] Provided herein are methods to treat CXCL 12-expressing Mycosis Fungoides (MF) in a subject including administering a therapeutically effective amount of an FTI to the subject having a CXCL 12-expressing MF. Provided herein are also methods to predict the responsiveness of a subject having MF for an FTI treatment, methods to select an MF patient for an FTI treatment, methods to stratify MF patients for an FTI treatment, and methods to increase the responsiveness of an MF patient population for an FTI treatment. In some embodiments, the methods include analyzing a sample from the subject having MF to determine that the subject has CXCL 12-expressing MF prior to administering the FTI to the subject. In some embodiments, the FTI is tipifarnib. In specific embodiments, the MF is Folliculotropic Mycosis Fungoides (FMF). In specific embodiments, the MF is Pagetoid Reticulosis. In specific embodiments, the MF is Granulomatous Slack Skin. In specific embodiments, the MF is a relapsed or refractory MF. [0007] Provided herein are methods to treat PRICKLE2-expressing Diffuse Large B Cell Lymphoma (DLBCL) in a subject including administering a therapeutically effective amount of an FTI to the subject having a PRICKLE2-expressing DLBCL. Provided herein are also methods to predict the responsiveness of a subject having DLBCL for an FTI treatment, methods to select a DLBCLpatient for an FTI treatment, methods to stratify DLBCL patients for an FTI treatment, and methods to increase the responsiveness of a DLBCL patient population for an FTI treatment. In some embodiments, the methods include analyzing a sample from the subject having DLBCL to determine that the subject has PRICKLE2-expressing DLBCL prior to administering the FTI to the subject. In some embodiments, the FTI is tipifarnib. In specific embodiments, the DLBCL is primary mediastinal B-cell lymphoma (PMBCL). In specific embodiments, the DLBCL is primary DLBCL of the central nervous system (primary DLBCL- CNS). In specific embodiments, the DLBCL is primary cutaneous DLBCL, leg type. In specific embodiments, the DLBCL is T-cell/histiocyte-rich large B-cell lymphoma (T-cell/histiocyte-rich DLBCL). In specific embodiments, the DLBCL is Epstein-Barr virus (EBV)-positive DLBCL (EBV-positive DLBCL). In specific embodiments, the DLBCL is intravascular large B-cell lymphoma (intravascular DLBCL). In specific embodiments, the DLBCL is anaplastic large-cell kinase (ALK)-positive large B-cell lymphoma (ALK-positive DLBCL). In specific embodiments, the DLBCL is DLBCL, Not Otherwise Specified (DLBCL-NOS). In specific embodiments, the DLBCL is germinal-center B-cell-like DLBCL (GCB-DLBCL). In specific embodiments, the DLBCL is activated B-cell-like DLBCL (ABC-DLBCL). In specific embodiments, the DLBCL is double hit DLBCL. In specific embodiments, the DLBCL is a relapsed or refractory DLBCL. [0008] In some embodiments, the sample from the subject can be a tumor biopsy or a body fluid sample. In some embodiments, the sample can be a whole blood sample, a partially purified blood sample, a peripheral blood sample, a serum sample, a cell sample or a lymph node sample. In some embodiments, the sample can be peripheral blood mononuclear cells (PBMC). [0009] In some embodiments, the methods provided herein include determining the expression level of the CXCL12 gene in a sample from a subject having DLBCL, wherein the subject is determined to have CXCL 12-expressing DLBCL if the expression level in the sample is greater than a reference level of the CXCL12.