WO2023131894A1

WO2023131894A1 - Genomic loss of heterozygosity as a predictive biomarker for treatment with talazoparib and methods of treatment thereof

Info

Publication number: WO2023131894A1
Application number: PCT/IB2023/050085
Authority: WO
Inventors: Alan Douglas LAIRD
Original assignee: Pfizer Inc.
Priority date: 2022-01-08
Filing date: 2023-01-05
Publication date: 2023-07-13
Also published as: TW202339754A

Abstract

The present invention relates to a method of selecting a subject having a cancer with a deficiency in homologous recombination repair, for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, and methods of treatment thereof, including: a) determining a gLOH score from a biopsy of the cancer; b) selecting the subject for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score; and c) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, to the selected subject.

Description

GENOMIC LOSS OF HETEROZYGOSITY AS A PREDICTIVE BIOMARKER FOR TREATMENT WITH TALAZOPARIB AND METHODS OF TREATMENT THEREOF

Field of the Invention

The present invention relates to methods of selecting patients for treatment with talazoparib and methods of treatment thereof.

Background

Poly (ADP-ribose) polymerase (PARP) engages in the naturally occurring process of deoxyribonucleic acid (DNA) repair in a cell. PARP inhibition has been shown to be an effective therapeutic strategy against tumors associated with mutations in double-strand DNA repair genes by inducing synthetic lethality (Sonnenblick, A., et al., Nat. Rev. Clin. Oncol, 2015, 12(1 ), 27-4). PARP inhibition is synthetically lethal in cells with homozygous deletions or deleterious alterations, or both, in DNA damage response (DDR) genes involved either directly or indirectly in homologous recombination repair (HRR) (Lord, CJ, et al., Science, 2017; 355: 1152-1158).

DDR is a network of pathways which have evolved to repair damaged DNA. These include mismatch repair, base excision repair, and homologous recombination repair (HRR) among others. HRR is particularly important in maintaining genomic integrity given its high fidelity in repairing double-strand DNA breaks. Inhibition of PARP results in accumulation of single-strand DNA breaks and in DNA stress due to PARP trapping, which ultimately culminates in double-strand DNA breaks. Hence, PARP inhibitors are selectively lethal to cancer cells deficient in HRR - this is an example of synthetic lethality, a mechanism whereby deficiency in function of one gene or gene product has little effect alone but is toxic in combination with deficiency in function of a second gene or gene product.

Talazoparib is a potent, orally available small molecule PARP inhibitor, which is cytotoxic to human cancer cell lines harboring gene mutations that compromise DNA repair, an effect referred to as synthetic lethality, and by trapping PARP protein on DNA thereby preventing DNA repair, replication, and transcription.

The compound, talazoparib, which is “(8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1 - methyl-1 H-1 ,2,4-triazol-5-yl)-8,9-dihydro-2/-/-pyrido[4,3,2-cte]phthalazin-3(7/-/)-one”, also known as “(8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1 -methyl-1 /-/-1 ,2,4-triazol-5-yl)-2,7,8,9- tetrahydro-3/-/-pyrido[4,3,2-c/e]phthalazin-3-one” (also referred to as “PF-06944076”, “MDV3800”, and “BMN673”) is a PARP inhibitor, having the structure,

Talazoparib

Talazoparib, and pharmaceutically acceptable salts thereof, including the tosylate salt, are disclosed in International Publication Nos. WO 2010/017055 and WO 2012/054698. Additional methods of preparing talazoparib, and pharmaceutically acceptable salts thereof, including the tosylate salt, are described in International Publication Nos. WO 2011/097602, WO 2015/069851 , and WO 2016/019125. Additional methods of treating cancer using talazoparib, and pharmaceutically acceptable salts thereof, including the tosylate salt, are disclosed in International Publication Nos. WO 2011/097334 and WO 2017/075091.

TALZENNA® (talazoparib) (0.25 mg and 1 mg capsules) has been approved in several countries, including the United States, and in the European Union, and is approved or under review with anticipated approvals in other countries for the treatment of adult patients with deleterious or suspected deleterious gBRCAm HER2-negative locally advanced or metastatic breast cancer. Additional capsule strengths, 0.5 mg and 0.75 mg, have been approved in the United States. Talazoparib has shown activity in metastatic castration-resistant prostate cancers with alterations in genes either directly or indirectly associated with HRR (de Bono et al., Lancet Oncol. 2021 Sep;22(9):1250- 1264). Talazoparib is under development for a variety of human cancers both as a single agent and in combination with other agents.

Most cancer drugs are effective in some patients, but not in others. This can be due to genetic variation among tumors, and can be observed even among tumors within the same patient. Variable patient response is particularly pronounced with respect to targeted therapeutics. Therefore, the full potential of targeted therapies may not be realized without suitable tests for determining which patients will benefit from which drugs. According to the National Institutes of Health (NIH), the term "biomarker" is defined as "a characteristic that is objectively measured and evaluated as an indicator of normal biologic or pathogenic processes or pharmacological response to a therapeutic intervention."

There are three distinct types of cancer biomarkers: (1 ) prognostic biomarkers, (2) predictive biomarkers, and (3) pharmacodynamic biomarkers. A prognostic biomarker is used to classify a cancer, e.g., a solid tumor, according to aggressiveness, i.e. , rate of growth and/or metastasis, and refractiveness to treatment. This is sometimes called distinguishing "good outcome" tumors from "poor outcome" tumors. A predictive biomarker is used to assess the probability that a particular patient will benefit from treatment with a particular drug. For example, patients with breast cancer in which the ERBB2 (HER2 or NEU) gene is amplified are likely to benefit from treatment with trastuzumab (HERCEPTIN®), whereas patients without ERBB2 gene amplification are unlikely to benefit from treatment with trastuzumab. A pharmacodynamic biomarker is an indication of the effect(s) of a drug on a patient while the patient is taking the drug. Accordingly, pharmacodynamic biomarkers often are used to guide dosage level and dosing frequency, during the early stages of clinical development of a new drug. For a discussion of cancer biomarkers, see, e.g., Sawyers, 2008, Nature 452:548-552.

Talazoparib is active in metastatic castration-resistant prostate cancer with DNA repair gene mutations and in gBRCA-mutant HER2-negative locally advanced or metastatic breast cancer; however, the utility of talazoparib for cancer patients may go beyond these indications. Furthermore, for indications in which talazoparib has shown activity, not all patients benefit from talazoparib treatment. As such, there is a need to select which patients bearing tumors with DNA repair gene mutations might respond to talazoparib and to identify cancer patients who may respond to talazoparib treatment beyond patients having DNA repair gene mutated cancers. Therefore, there is a need for diagnostic methods based on predictive biomarkers that can be used to identify cancer patients that are likely (or unlikely) to respond to treatment with talazoparib. Summary

The present invention provides, in part, methods of selecting patients and identifying cancers for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, and methods of treatment thereof. This summary is provided to introduce a selection of concepts in a simplified form that are further described below in the detailed description. This summary is not intended to identify key features or essential features of the claimed subject matter, nor is it intended to be used in isolation as an aid in determining the scope of the claimed subject matter.

According to Embodiment 1 of the invention, there is provided a method of selecting a subject having a cancer with a deficiency in homologous recombination repair for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; and b) selecting the subject for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

According to Embodiment 2 of the invention, there is provided a method of treating a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; b) selecting the subject for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score; and c) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

According to Embodiment 3 of the invention, there is provided a method of identifying a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; and b) selecting the cancer for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

According to Embodiment 4 of the invention, there is provided a method of treating a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; b) selecting the cancer for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score; and c) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

Described below are embodiments of the invention, where for convenience Embodiments 1 , 2, 3 and 4 (E1 , E2, E3 and E4) are identical to the embodiments provided above.

It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention, as claimed.

Brief Description of the Drawing

The Figure shows a bar chart of the best overall response (confirmed) of gLOH score based on Blinded Independent Central Review. The bar chart is annotated by best response, mutation group, mutation type, and mutation zygosity. Abbreviations include: CR, Complete Response; PR, Partial Response; SD, Stable Disease; Non- CR/Non-PD, Non-Complete Response/Non-Progressive Disease; PD, Progressive Disease; NE, Non-Evaluable; gLOH (genomic loss of heterozygosity), and alt (alteration or mutation). Other DDR11 genes include, but are not limited to, ATR, CHEK2, FANCA, MLH1 , MRE11A, NBN, and RAD51 C. Tumor variant type is based on the corresponding DDR11 mutation group. Definitions in regard to zygosity include: Homozygous, patient has >1 homozygous DDR11 mutation; Heterozygous, patient has no homozygous DDR11 mutation, but has >1 heterozygous DDR11 mutation; Unknown, patient has no homozygous or heterozygous DDR11 mutation, but has >1 DDR1 1 mutation of unknown zygosity; Not evaluable, patient has no adequate DDR11 mutation.

Detailed Description

The present invention may be understood more readily by reference to the following detailed description of the embodiments and preferred embodiments of the invention. It is to be understood that the terminology used herein is for the purpose of describing specific embodiments only and is not intended to be limiting. It is further to be understood that unless specifically defined herein, the terminology used herein is to be given its traditional meaning as known in the relevant art. E1 A method of selecting a subject having a cancer with a deficiency in homologous recombination repair, as defined above.

E2 A method of treating a cancer having a deficiency in homologous recombination repair, in a subject, as defined above.

E3 A method of identifying a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, as defined above.

E4 A method of treating a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, as defined above.

E5 A method of embodiment 1 or 2, wherein the cancer is sensitive to treatment with talazoparib.

E6 A method of any one of embodiments 1 to 4, wherein the cancer is prostate cancer.

E7 A method of embodiment 6, wherein the prostate cancer is metastatic prostate cancer.

E8 A method of embodiment 6, wherein the prostate cancer is castration-resistant prostate cancer.

E9 A method of embodiment 8, wherein the castration-resistant prostate cancer is metastatic castration-resistant prostate cancer.

E10 A method of embodiment 1 or 3, wherein the deficiency in homologous recombination repair of the cancer is determined by next generation sequencing. E11 A method of embodiment 1 or 3, wherein step a) is performed by next generation sequencing.

E12 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least about 8.0%.

E13 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least about 8.3%.

E14 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least about 8.8%.

E15 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least about 9%; at least about 9.2%; at least about 10%; at least about 11 %; at least about 12%; at least about 13%; at least about 14%; at least about 15%; at least about 16%; at least about 17%; at least about 18%; at least about 19%; at least about 20%; at least about 21 %; at least about 22%; at least about 23%; at least about 24%; or at least about 25%.

E16 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least 8.0%.

E17 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least 8.3%.

E18 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least 8.8%.

E19 A method of any one of embodiments 1 to 11 , wherein the gLOH score is at least 9%; at least 9.2%; at least 10%; at least 11 %; at least 12%; at least 13%; at least 14%; at least 15%; at least 16%; at least 17%; at least 18%; at least 19%; at least 20%; at least 21 %; at least 22%; at least 23%; at least 24%; or at least 25%. E20 A method of embodiment 1 or 2, wherein the subject is human.

Each of the embodiments of the present invention described herein may be combined with one or more other embodiments of the present invention described herein which is not inconsistent with the embodiment(s) with which it is combined. In addition, each of the embodiments below describing the invention envisions within its scope the pharmaceutically acceptable salts of the compound of the invention.

As used herein, the singular form "a", "an", and "the" include plural references unless indicated otherwise.

As used herein, the term “about” when used to modify a numerically defined parameter (e.g., an amount of talazoparib) means that the parameter may vary by as much as 10% below or above the stated numerical value for that parameter. For example, a dose of about 1 mg may vary between 0.9 mg and 1.1 mg.

“Abnormal cell growth”, as used herein, unless otherwise indicated, refers to cell growth that is independent of normal regulatory mechanisms (e.g., loss of contact inhibition). Abnormal cell growth may be benign (not cancerous), or malignant (cancerous).

For purposes of the present invention, “DDR mutation(s)”, “DDR alteration(s)”, ‘”HRR mutation(s)” and “HRR alteration(s)” refer to alterations/mutations in genes involved directly or indirectly in homologous recombination repair (HRR). Though not as scientifically robust as the phrase “DNA damage response”, it is commonly understood that “DDR” may also be referred to as “DNA damage repair” or “DNA repair”.

The terms “cancer”, “cancerous”, and “malignant” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. As used herein “cancer” refers to any malignant and/or invasive growth or tumor caused by abnormal cell growth. As used herein “cancer” refers to solid tumors named for the type of cells that form them, cancer of blood, bone marrow, or the lymphatic system. Examples of solid tumors include, but are not limited to, sarcomas and carcinomas. Examples of cancers of the blood include, but are not limited to, leukemias, lymphomas and myeloma. The term “cancer” includes but is not limited to a primary cancer that originates at a specific site in the body, a metastatic cancer that has spread from the place in which it started to other parts of the body, a recurrence from the original primary cancer after remission, and a second primary cancer that is a new primary cancer in a person with a history of previous cancer of different type from latter one. Examples of cancer include, but are not limited to, carcinoma, lymphoma, leukaemia, blastoma, and sarcoma. More particular examples of such cancers include squamous cell carcinoma, myeloma, lung cancer, small-cell lung cancer, small cell prostate cancer, non-small cell lung cancer, glioma, hodgkin’s lymphoma, non-hogkin’s lymphoma, follicular lymphoma (FL), diffuse large B-cell lymphoma (DLCBCL), acute myeloid leukaemia (AML), multiple myeloma, gastrointestinal (tract) cancer, renal cancer, ovarian cancer, uterine cancer, endometrial cancer, liver cancer, kidney cancer, renal cell carcinoma, prostate cancer, castration-sensitive prostate cancer (CSPC), castration-resistant prostate cancer (CRPC), thyroid cancer, melanoma, chondrosarcoma, neuroblastoma, pancreatic cancer, glioblasoma, multiformer, cervical cancer, rectal cancer, brain cancer, stomach cancer, bladder cancer, hepatoma, hepatocellular carcinoma, breast cancer, colon cancer, head and neck cancer, and salivary gland cancer.

The term “patient” or “subject” refers to any single subject for which therapy is desired or that is participating in a clinical trial, epidemiological study or used as a control, including humans and mammalian veterinary patients such as cattle, horses, dogs and cats. In certain preferred embodiments, the patient or subject is a human.

The term “treat” or “treating” a cancer, as used herein, means to administer a therapy according to the present invention to a subject having cancer, or diagnosed with cancer, to achieve at least one positive therapeutic effect, such as, for example, reduced number of cancer cells, reduced tumor size, reduced rate of cancer cell infiltration into peripheral organs, or reduced rate of tumor metastases or tumor growth, reversing, alleviating, inhibiting the progress of, or preventing the recurrence of the disorder or condition to which such term applies, or one or more symptoms of such disorder or condition. The term "treatment", as used herein, unless otherwise indicated, refers to the act of treating as "treating" is defined immediately above. The term “treating” also includes adjuvant and neo-adjuvant treatment of a subject. For the purposes of this invention, beneficial or desired clinical results include, but are not limited to, one or more of the following: reducing the proliferation of (or destroying) neoplastic or cancerous cells; inhibiting metastasis or neoplastic cells; shrinking or decreasing the size of tumor; remission of the cancer; decreasing symptoms resulting from the cancer; increasing the quality of life of those suffering from the cancer; decreasing the dose of other medications required to treat the cancer; delaying the progression the cancer; curing the cancer; overcoming one or more resistance mechanisms of the cancer; and prolonging survival of patients suffering from the cancer. Positive therapeutic effects in cancer can be measured in a number of ways (see, for example, W. A. Weber, J. Nucl. Med. 50:1 S-10S (200)). In some embodiments, the treatment achieved by a method of the invention is any of partial response (PR), complete response (CR), stable disease (SD), progressive disease (PD), overall response (OR), objective response rate (ORR), progression free survival (PFS), radiographic PFS, disease free survival (DFS) and overall survival (OS). PFS, also referred to as “Time to Tumor Progression” indicates the length of time during and after treatment that the cancer does not grow, and includes the amount of time patients have experienced a CR or PR, as well as the amount of time patients have experienced stable disease (SD). DFS refers to the length of time during and after treatment that the patient remains free of disease. OS refers to a prolongation in life expectancy as compared to naive or untreated subjects or patients. In some embodiments, response to a method of the invention is any of PR, CR, SD, PD, PFS, DFS, ORR, OR or OS. Response to a method of the invention, including duration of soft tissue response, is assessed using Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST 1.1 ) response criteria. In some embodiments, the treatment achieved by a method of the invention is measured by the time to PSA progression, the time to initiation of cytotoxic chemotherapy and the proportion of patients with PSA response greater than or equal to 50%. The treatment regimen for a method of the invention that is effective to treat a cancer patient may vary according to factors such as the disease state, age, and weight of the patient, and the ability of the therapy to elicit an anti-cancer response in the subject. While an embodiment of any of the aspects of the invention may not be effective in achieving a positive therapeutic effect in every subject, it should do so in a statistically significant number of subjects as determined by any statistical test known in the art such as, but not limited to, the Cox log-rank test, the Cochran-Mantel-Haenszel log-rank test, the Student’s t-test, the chi2-test, the ll-test according to Mann and Whitney, the Kruskal-Wallis test (H-test), Jonckheere-Terpstrat-test and the Wilcon on- test. The term “treatment” also encompasses in vitro and ex vivo treatment, e.g., of a cell, by a reagent, diagnostic, binding compound, or by another cell.

As used herein, a “dosage”, an “amount”, an “effective dosage” or “effective amount” of drug, compound or pharmaceutical formulation is an amount sufficient to have a beneficial or desired effect on any one or more symptoms (biochemical, histological and I or behavioral) of the disease, its complications and intermediate pathological phenotypes presenting during development of the disease. For therapeutic use, a “therapeutically effective amount” refers to that amount of a compound being administered which will relieve to some extent one or more of the symptoms of the disorder being treated. In reference to the treatment of cancer, a therapeutically effective amount refers to that amount which has the effect of (1) reducing the size of the tumor, (2) inhibiting (that is, slowing to some extent, preferably stopping) tumor metastasis, (3) inhibiting to some extent (that is, slowing to some extent, preferably stopping) tumor growth or tumor invasiveness, (4) relieving to some extent (or, preferably, eliminating) one or more signs or symptoms associated with the cancer, (5) decreasing the dose of other medications required to treat the disease, (6) enhancing the effect of another medication, and I or (7) delaying the progression of the disease of patients. An effective dosage can be administered in one or more administrations. For the purposes of this invention, an effective dosage of drug, compound, or pharmaceutical formulation is an amount sufficient to accomplish prophylactic or therapeutic treatment either directly or indirectly. As is understood in the clinical context, an effective dosage of drug, compound or pharmaceutical formulation may or may not be achieved in conjunction with another drug, compound or pharmaceutical formulation.

In an embodiment, an amount of talazoparib, or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of from about 0.1 mg to about 2 mg once a day, preferably from about 0.25 mg to about 1 .5 mg once a day, and more preferably from about 0.5 mg to about 1 .0 mg once a day. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.1 mg, about 0.25 mg, about 0.35 mg, about 0.5 mg, about 0.75 mg or about 1 .0 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.1 mg, about 0.25 mg, about 0.35 mg, or about 0.5 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.25 mg, about 0.35 mg, or about 0.5 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof and preferably a tosylate salt thereof, is administered at a daily dosage of about about 0.5 mg, about 0.75 mg or about 1.0 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.1 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.25 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.35 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.5 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 0.75 mg once daily. In an embodiment, talazoparib or a pharmaceutically acceptable salt thereof, and preferably a tosylate salt thereof, is administered at a daily dosage of about 1 .0 mg once daily. Dosage amounts provided herein refer to the dose of the free base form of talazoparib or are calculated as the free base equivalent of an administered talazoparib salt form. For example, a dosage or amount of talazoparib, such as 0.5, 0.75 mg or 1 .0 mg refers to the free base equivalent. This dosage regimen may be adjusted to provide the optimal therapeutic response. For example, the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation.

The term “pharmaceutically acceptable salt”, as used herein, unless otherwise indicated, refers to a formulation of a compound that does not cause significant irritation to an organism to which it is administered and does not abrogate the biological activity and properties of the compound. In certain instances, pharmaceutically acceptable salts are obtained by reacting a compound described herein, with acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like. In some instances, pharmaceutically acceptable salts are obtained by reacting a compound having acidic group described herein with a base to form a salt such as an ammonium salt, an alkali metal salt, such as a sodium or a potassium salt, an alkaline earth metal salt, such as a calcium or a magnesium salt, a salt of organic bases such as dicyclohexylamine, /V-methyl-D-glucamine, tris(hydroxymethyl)methylamine, and salts with amino acids such as arginine, lysine, and the like, or by other methods previously determined.

“Tumor” as it applies to a subject diagnosed with, or suspected of having, a cancer refers to a malignant or potentially malignant neoplasm or tissue mass of any size, and includes primary tumors and secondary neoplasms. A solid tumor is an abnormal growth or mass of tissue that usually does not contain cysts or liquid areas. Examples of solid tumors are sarcomas, carcinomas, and lymphomas. Leukemias (cancers of the blood) generally do not form solid tumors (National Cancer Institute, Dictionary of Cancer Terms).

“Tumor burden” also referred to as a “tumor load’, refers to the total amount of tumor material distributed throughout the body. Tumor burden refers to the total number of cancer cells or the total size of tumor(s), throughout the body, including lymph nodes and bone marrow. Tumor burden may be determined by a variety of methods known in the art, such as, e.g., using callipers, or while in the body using imaging techniques, e.g., ultrasound, bone scan, computed tomography (CT), or magnetic resonance imaging (MRI) scans.

The term “tumor size” refers to the total size of the tumor which can be measured as the length and width of a tumor. Tumor size may be determined by a variety of methods known in the art, such as, e.g., by measuring the dimensions of tumor(s) upon removal from the subject, e.g., using callipers, or while in the body using imaging techniques, e.g., bone scan, ultrasound, CR or MRI scans.

The present invention relates to a method of selecting a subject having a cancer with a deficiency in homologous recombination repair for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) selecting the subject for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score. The method further comprises administering talazoparib, or a pharmaceutically acceptable salt thereof, to the selected subject. The present invention relates to a method of selecting a subject having a cancer with a deficiency in homologous recombination repair for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) selecting the subject for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score; and further comprising administering talazoparib, or a pharmaceutically acceptable salt thereof, to the selected subject.

The methods of the present invention are useful for selecting a subject for treatment with talazoparib. In particular, the methods of the present invention are useful for selecting a subject having a cancer with a deficiency in homologous recombination repair for treatment with talazoparib, or a pharmaceutically acceptable salt thereof.

The present invention relates to a method of treating a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

In an aspect, this invention relates to a use of talazoparib, or a pharmaceutically acceptable salt thereof, in the treatment of a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

In an aspect, this invention relates to a use of talazoparib, or a pharmaceutically acceptable salt thereof, as a medicament for the treatment of a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

The methods of the present invention are useful for treating cancer. In particular, the methods of the present invention are useful for treating a cancer having a deficiency in homologous recombination repair. Additionally, the methods of the present invention are useful for identifying a cancer having a deficiency in homologous recombination repair, that is sensitive to cancer treatment, such as treatment with talazoparib. In some embodiments, the methods provided result in one or more of the following effects: (1) inhibiting cancer cell proliferation; (2) inhibiting cancer cell invasiveness; (3) inducing apoptosis of cancer cells; (4) inhibiting cancer cell metastasis; (5) inhibiting angiogenesis; or (6) overcoming one or more resistance mechanisms relating to a cancer treatment.

In an embodiment, the present invention relates to a method of identifying a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

“Genomic loss of heterozygosity” or “gLOH” is caused by defects in homologous recombination repair (HRR) and results in regions of the genome where genes are present in homozygous or hemizygous states. According to the methods of the present invention, a subject having a cancer with a deficiency in homologous recombination repair is selected for treatment with talazoparib based on a gLOH score. The gLOH score may be determined according to Sokol et al, JCO Precis Oncol. 2020;4:442-465, which provides a detailed description of gLOH measurement and performance, as follows: Method: LOH segments are inferred across the 22 autosomal chromosomes using the genome-wide aneuploidy/copy number profile and minor allele frequency (AF) of the >3,500 polymorphic single nucleotide polymorphisms (SNPs) sequenced in the FoundationOne®CDx (Foundation Medicine, Inc.) assay. Using a comparative genomic hybridization-like method, a log-ratio profile of the sample was obtained by normalizing the sequence coverage obtained at all exons and genome-wide SNPs against a process-matched normal control (Frampton GM, et al: Nat. Biotechnol 31 : 1023-1031 , 2013). This profile was segmented and interpreted using AFs of sequenced SNPs to estimate copy number (Ci) and minor allele count (Mi) at each segment (i). A segment was determined to have LOH if Ci + 0 and Mi = 0. Low tumor content or low aneuploidy were the most common reasons for failure to pass the quality control to perform gLOH inference. Two types of LOH segments were excluded from the calculation of percent gLOH: LOH segments that spanned > 90% of a whole chromosome or chromosome arm because these LOH events usually arise through non-HRD mechanisms (eg, mitotic nondisjunction) and regions in which LOH inference was ambiguous. For each tumor, the percent gLOH was computed as 100* the total length of nonexcluded LOH regions (xi) divided by the total length of nonexcluded regions of the genome.

In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 8.8%; at least about 9%; at least about 9.2%; at least about 10%; at least about 11 %; at least about 12%; at least about 13%; at least about 14%; at least about 15%; at least about 16%; at least about 17%; at least about 18%; at least about 19%; at least about 20%; at least about 21 %; at least about 22%; at least about 23%; at least about 24%; or at least about 25%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 24%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 23%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 22%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 21 %. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 20%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 19%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 18%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 17%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 16%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 15%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 14%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 13%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 12%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 11%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 10%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 9%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 8.8%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 8.3%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least about 8.0%.

In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 8.8%; at least 9%; at least 9.2%; at least 10%; at least 11 %; at least 12%; at least 13%; at least 14%; at least 15%; at least 16%; at least 17%; at least 18%; at least 19%; at least 20%; at least 21 %; at least 22%; at least 23%; at least 24%; or at least 25%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 24%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 23%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 22%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 21 %. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 20%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 19%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 18%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 17%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 16%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 15%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 14%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 13%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 12%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 11 %. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 10%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 9%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 8.8%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 8.3%. In an embodiment of the present invention, the gLOH score or the percent gLOH is at least 8.0%.

Next generation sequencing (NGS) is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing. While there are a number of different NGS platforms using different sequencing technologies, all NGS platforms perform sequencing of millions of small fragments of DNA in parallel. One of skill in the art is familiar with next generation sequencing.

According to the methods of the present invention, the deficiency in homologous recombination repair in a cancer or tumor may be determined using next generation sequencing. According to the methods of the present invention, a gLOH score from a biopsy of a cancer may be determined using next generation sequencing. For example, a panel-based sequencing assay capable of assessing gLOH, such as FoundationOne®CDx (Foundation Medicine, Inc.) may be utilized. gLOH is available as part of the FoundationOne®CDx test in select gynecological diseases. Biallelic alterations in DDR/HRR genes have been reported to be associated with increased gLOH across a range of tumor types, including those that may benefit from PARP inhibitors, such as breast, ovarian, prostate, and pancreatic cancers (Westphalen B, et al. Clin Cancer Res. 2021 ). However, in general, gLOH scores are relatively low in prostate cancer and do not exhibit the dynamic range seen in breast and ovarian cancers (Sokol ES, et al. JCO Precis Oncol. 2020;4:442-465.)

A method of selecting a subject having a cancer with a deficiency in homologous recombination repair for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; and b) selecting the subject for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, if the gLOH score is at least 8.8%

A method of identifying a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, if the gLOH score is at least 8.8%

In an embodiment, this invention relates to a method of treating a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, if the gLOH is at least 8.8%.

In another aspect, this invention relates to a use of talazoparib, or a pharmaceutically acceptable salt thereof, in the treatment of a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, if the gLOH score is at least 8.8%.

In another aspect, this invention relates to a use of talazoparib, or a pharmaceutically acceptable salt thereof, as a medicament for the treatment of a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) determining a gLOH score from a biopsy of the cancer; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, if the gLOH score is at least 8.8%.

In an embodiment of the invention, the subject is a mammal.

In an embodiment of the invention, the subject is a human.

In embodiments the methods of the present invention may be useful for the treatment of cancers including but not limited to cancers of the: circulatory system, for example, heart (sarcoma [angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma], myxoma, rhabdomyoma, fibroma, lipoma and teratoma), mediastinum and pleura, and other intrathoracic organs, vascular tumors and tumor-associated vascular tissue; respiratory tract, for example, nasal cavity and middle ear, accessory sinuses, larynx, trachea, bronchus and lung such as small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), bronchogenic carcinoma (squamous cell, undifferentiated small cell, undifferentiated large cell, adenocarcinoma), alveolar (bronchiolar) carcinoma, bronchial adenoma, sarcoma, lymphoma, chondromatous hamartoma, mesothelioma; gastrointestinal system, for example, esophagus (squamous cell carcinoma, adenocarcinoma, leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), gastric, pancreas (ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel (adenocarcinoma, lymphoma, carcinoid tumors, Karposi's sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), large bowel (adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma); genitourinary tract, for example, kidney (adenocarcinoma, Wilm's tumor [nephroblastoma], lymphoma, leukemia), bladder and/or urethra (squamous cell carcinoma, transitional cell or urothelial carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma), testis (seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma); liver (for example, hepatoma, hepatocellular carcinoma), cholangiocarcinoma, hepatoblastoma, angiosarcoma, hepatocellular adenoma, hemangioma, pancreatic endocrine tumors (such as pheochromocytoma, insulinoma, vasoactive intestinal peptide tumor, islet cell tumor and glucagonoma); bone, for example, osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticulum cell sarcoma), multiple myeloma, malignant giant cell tumor chordoma, osteochronfroma (osteocartilaginous exostoses), benign chondroma, chondroblastoma, chondromyxofibroma, osteoid osteoma and giant cell tumors; nervous system, for example, neoplasms of the central nervous system (CNS), primary CNS lymphoma, skull cancer (osteoma, hemangioma, granuloma, xanthoma, osteitis deformans), meninges (meningioma, meningiosarcoma, gliomatosis), brain cancer (astrocytoma, medulloblastoma, glioma, ependymoma, germinoma [pinealoma], glioblastoma multiform, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors), spinal cord neurofibroma, meningioma, glioma, sarcoma); reproductive system, for example, gynecological, uterus (endometrial carcinoma), cervix (cervical carcinoma, pre-tumor cervical dysplasia), ovaries (ovarian carcinoma [serous cystadenocarcinoma, mucinous cystadenocarcinoma, unclassified carcinoma], granulosa-thecal cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma, intraepithelial carcinoma, adenocarcinoma, fibrosarcoma, melanoma), vagina (clear cell carcinoma, squamous cell carcinoma, botryoid sarcoma (embryonal rhabdomyosarcoma), fallopian tubes (carcinoma) and other sites associated with female genital organs; placenta, penis, prostate, testis, and other sites associated with male genital organs; hematologic system, for example, blood (myeloid leukemia [acute and chronic], acute lymphoblastic leukemia, chronic lymphocytic leukemia, myeloproliferative diseases, multiple myeloma, myelodysplastic syndrome), Hodgkin's disease, nonHodgkin's lymphoma [malignant lymphoma]; oral cavity, for example, lip, tongue, gum, floor of mouth, palate, and other parts of mouth, parotid gland, and other parts of the salivary glands, tonsil, oropharynx, nasopharynx, pyriform sinus, hypopharynx, and other sites in the lip, oral cavity and pharynx; skin, for example, malignant melanoma, cutaneous melanoma, basal cell carcinoma, squamous cell carcinoma, Karposi's sarcoma, moles dysplastic nevi, lipoma, angioma, dermatofibroma, and keloids; adrenal glands: neuroblastoma; and other tissues including connective and soft tissue, retroperitoneum and peritoneum, eye, intraocular melanoma, and adnexa, breast, head or/and neck, anal region, thyroid, parathyroid, adrenal gland and other endocrine glands and related structures, secondary and unspecified malignant neoplasm of lymph nodes, secondary malignant neoplasm of respiratory and digestive systems and secondary malignant neoplasm of other sites.

Examples of “cancer” when used herein in connection with the present invention include cancer selected from lung cancer (NSCLC and SCLC), breast cancer (including triple negative breast cancer, hormone positive breast cancer, HER2 negative breast cancer, HER2 positive breast cancer and triple positive breast cancer), ovarian cancer, colon cancer, rectal cancer, cancer of the anal region, prostate cancer (including castration-sensitive or hormone sensitive prostate cancer and hormone-refractory prostate cancer, also known as castration-resistant prostate cancer), hepatocellular carcinoma, diffuse large B-cell lymphoma, follicular lymphoma, melanoma and salivary gland tumor or a combination of one or more of the foregoing cancers.

Examples of “cancer” when used herein in connection with the present invention include cancer selected from lung cancer (NSCLC and SCLC), breast cancer (including triple negative breast cancer, hormone positive breast cancer, and HER2 negative breast cancer), ovarian cancer, prostate cancer (including castration-sensitive or hormone sensitive prostate cancer and hormone-refractory prostate cancer, also known as castration-resistant prostate cancer), or a combination of one or more of the foregoing cancers.

Examples of “cancer” when used herein in connection with the present invention include cancer selected from prostate cancer, androgen receptor positive breast cancer, hepatocellular carcinoma, and salivary gland tumor, or a combination of one or more of the foregoing cancers. Examples of “cancer” when used herein in connection with the present invention include cancer selected from androgen receptor positive breast cancer, hepatocellular carcinoma, and salivary gland tumor, or a combination of one or more of the foregoing cancers.

Examples of “cancer” when used herein in connection with the present invention include cancer selected from triple negative breast cancer, hormone positive breast cancer, HER2 negative breast cancer, triple positive breast cancer, castration-sensitive prostate cancer, castration-resistant prostate cancer, hepatocellular carcinoma, and salivary gland tumor or a combination of one or more of the foregoing cancers.

Examples of “cancer” when used herein in connection with the present invention include cancer selected from triple negative breast cancer, hormone positive breast cancer, and HER2 negative breast cancer, or a combination of one or more of the foregoing cancers.

Examples of “cancer” when used herein in connection with the present invention include cancer selected from castration-sensitive prostate cancer and castration- resistant prostate cancer, or a combination of one or more of the foregoing cancers.

In one embodiment of the invention, the cancer is a solid tumor.

In one embodiment of the invention, the cancer is a solid tumor which solid tumor is androgen-dependent.

In one embodiment of the invention, the cancer is a solid tumor which solid tumor expresses androgen receptors.

In one embodiment, the cancer is prostate cancer.

In one embodiment, the cancer is high-risk prostate cancer.

In one embodiment, the cancer is locally advanced prostate cancer.

In one embodiment, the cancer is high-risk locally advanced prostate cancer.

In one embodiment, the cancer is metastatic prostate cancer.

In one embodiment, the cancer is hormone sensitive prostate cancer, also known as castration-sensitive prostate cancer. Hormone sensitive prostate cancer is usually characterized by histologically or cytologically confirmed adenocarcinoma of the prostate which is still responsive to androgen deprivation therapy.

In one embodiment, the cancer is non-metastatic hormone sensitive prostate cancer. In one embodiment, the cancer is high risk, non-metastatic hormone sensitive prostate cancer.

In one embodiment, the cancer is metastatic hormone sensitive prostate cancer.

In one embodiment, the cancer is castration-sensitive prostate cancer.

In one embodiment, the cancer is non-metastatic castration-sensitive prostate cancer.

In one embodiment, the cancer is metastatic castration-sensitive prostate cancer.

In one embodiment, the cancer is castration-sensitive prostate cancer with DDR mutations. In one embodiment, the cancer is non-metastatic castration-sensitive prostate cancer with DDR mutations. In one embodiment, the cancer is metastatic castration-sensitive prostate cancer with DDR mutations. The DDR genes mutated include, but are not limited to, ATM, ATR, BRCA1 , BRCA2, CDK12, CHEK2, FANCA, MLH1 , MRE11A, NBN, PALB2, and RAD51 C.

In one embodiment, the cancer is castration-resistant prostate cancer, also known as hormone-refractory prostate cancer or androgen-independent prostate cancer. Castration resistant prostate cancer is usually characterised by histologically or cytologically confirmed adenocarcinoma of the prostate which is castration resistant (for example defined as 2 or more consecutive rises of PSA, >1 week between each assessment, optionally resulting in 2 or more 50% or greater increases over the nadir, with PSA level >2 ng/mL), in a setting of castrate levels of testosterone (for example < 1.7 nmol/L level of testosterone or <50 ng/dL level of testosterone), which castrate levels of testosterone are achieved by androgen deprivation therapy and I or post orchiectomy.

In one embodiment, the cancer is castration-resistant prostate cancer.

In one embodiment, the cancer is non-metastatic castration-resistant prostate cancer.

In one embodiment, the cancer is metastatic castration-resistant prostate cancer.

In one embodiment, the cancer is castration-resistent prostate cancer with mutations. In one embodiment, the cancer is non-metastatic castration- resistent prostate cancer with DDR mutations. In one embodiment, the cancer is metastatic castration-resistant prostate cancer with DDR mutations. The DDR genes mutated include, but are not limited to, ATM, ATR, BRCA1 , BRCA2, CDK12, CHEK2, FANCA, MLH1 , MRE11A, NBN, PALB2, and RAD51C.

In one embodiment, the cancer is breast cancer.

In one embodiment, the cancer is locally advanced or metastatic breast cancer.

In one embodiment, the cancer is triple negative breast cancer.

In one embodiment, the cancer is hormone positive breast cancer, including estrogen positive and I or progesterone positive breast cancer.

In one embodiment, the cancer is HER2 negative breast cancer.

In one embodiment, the cancer is germline BRCA-mutated HER2-negative breast cancer.

In one embodiment, the cancer is HER2 positive breast cancer.

In one embodiment, the cancer is triple positive breast cancer.

In one embodiment, the cancer is ovarian cancer.

In one embodiment, the cancer is small cell lung cancer.

In one embodiment, the cancer is Ewing’s sarcoma.

In one embodiment, the cancer is hepatocellular carcinoma.

In one embodiment, the cancer is salivary gland tumor.

In one embodiment, the cancer is locally advanced.

In one embodiment, the cancer is non-metastatic.

In one embodiment, the cancer is metastatic.

In one embodiment, the cancer is refractory.

In one embodiment, the cancer is relapsed.

In one embodiment, the cancer is intolerable of standard treatment.

In one embodiment of the present invention, the method is administered to a subject diagnosed with cancer, which cancer has developed resistance to treatment.

In a further aspect, the methods of the present invention may additionally comprise administering further anti-cancer agents, such as anti-tumor agents, antiangiogenesis agents, signal transduction inhibitors and antiproliferative agents, which amounts are together effective in treating said cancer. In some such embodiments, the anti-tumor agent is selected from the group consisting of mitotic inhibitors, alkylating agents, anti-metabolites, intercalating antibiotics, growth factor inhibitors, radiation, cell cycle inhibitors, enzymes, topoisomerase inhibitors, biological response modifiers, antibodies, cytotoxics, anti-hormones, androgen deprivation therapy and anti- androgens. In an embodiment of the present invention, the further anti-cancer agent is an anti-androgen. In an embodiment of the present invention, the anti-androgen is enzalutamide or apalutamide. is from an Open-Label, Phase 2 Trial of

Castration-Resistant Prostate Cancer with DNA

Scores and Associated

Correlative

METHODS

Clinical trial

An open-label phase II clinical trial of the PARP inhibitor talazoparib in patients with metastatic castration-resistant prostate cancer with DNA repair alterations (de Bono et al., Lancet Oncol. 2021 Sep;22(9): 1250-1264) was conducted.

Eligibility criteria:

Eligible patients were men aged 18 years or older with progressive metastatic castration-resistant prostate cancers of adenocarcinoma histology. Progressive disease was defined as a minimum of three increasing prostate-specific antigen (PSA) values with an interval of at least 1 week between readings, soft-tissue disease progression as defined by Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST 1.1 ), or bone disease progression defined by Prostate Cancer Working Group 3 (PCWG3) criteria with two or more new metastatic lesions on bone scan. The screening central laboratory PSA value needed to be 2 pg/L or higher if the candidate was qualifying solely by PSA progression. Clinical trial inclusion criteria were amended after initiation. The original clinical trial design allowed the enrollment of patients with measurable and non-measurable disease in two overlapping cohorts: cohort A, which included patients with DDR alterations in genes involved directly or indirectly in HRR likely to sensitize to PARP inhibition, and cohort B, which included patients with DNA defects in an expanded panel of genes that are likely to, or might, sensitize to PARP inhibition. With the approval of protocol amendment three on Feb 15, 2018, enrollment was restricted to patients with measurable disease and with DNA alterations likely to sensitize to PARP inhibition, which originally comprised a panel of 13 genes. FANCD2 and FANCI did not pass subsequent validation requirements, leaving the following panel of 11 HRR genes that were used in the analyses: ATM, ATR, BRCA1 , BRCA2, CHEK2, FANCA, MLH1 , MRE11A, NBN, PALB2, and RAD51 C (referred to as “DDR11”). Other inclusion criteria were an Eastern Cooperative Oncology Group (ECOG) performance status of 0-2; bilateral orchiectomy or ongoing androgen deprivation therapy with a gonadotropin-releasing hormone agonist or antagonist, with serum testosterone of 50 ng/dL or less (<1 .73 nmol/L) at screening; stable bisphosphonate or denosumab dose for at least 4 weeks for patients receiving these therapies; estimated life expectancy of at least 6 months (as assessed by investigator); and previous treatment with one or two chemotherapy regimens (>1 taxane-based) in the metastatic setting (castrationsensitive or castration-resistant prostate cancer; patients could have received radium- 233 or cabazitaxel, or both) and progressed on at least one novel hormone therapy (enzalutamide, abiraterone, or both) given for metastatic castration-resistant prostate cancers.

Treatment:

Patients were given oral talazoparib 1 mg per day (or 0.75 mg per day for patients with moderate renal impairment, defined as an estimated glomerular filtration rate of 30-59 mL/min per 1 .73 m²), with dose modification or appropriate supportive care, or both, given for recovery from grade 3 or 4 adverse events. Talazoparib was continued until progression, as determined on radiographic imaging, unacceptable toxicity, investigator decision, withdrawal of consent, or death. Increased PSA or circulating tumor cell counts alone were not a reason for discontinuing talazoparib.

Evaluation of tumor responses:

Radiographic assessments (CT [preferred] or MRI of the abdomen and pelvis, CT of chest, and whole-body radionuclide bone scan) were done every 8 weeks during the first 24 weeks, then every 12 weeks thereafter. Soft tissue responses were confirmed at least 4 weeks after the response was identified with CT or MRI, per RECIST 1.1 with no evidence of confirmed bone progression per Prostate Cancer Working Group 3 criteria on repeat bone scan at least 6 weeks later, per independent central review. Tumor oenomics:

DDR1 1 mutations were assessed in Formalin-Fixed Paraffin-Embedded (FFPE) tumor tissues using FoundationOne®CDx (Foundation Medicine, Inc.). gLOH scores were determined as an advanced genomic analytic of the FoundationOne®CDx analyses (method detailed in Sokol et al, JCO Precision Oncology 2020;4:442-465).

Statistical analysis:

The population of patients evaluable for antitumor activity (N=104) was defined as all enrolled patients who had measurable soft-tissue disease at screening per investigator assessment, had alterations in a gene within the 11 predefined DDR-HRR genes (ATM, ATR, BRCA1 , BRCA2, CHEK2, FANCA, MLH1 , MRE11A, NBN, PALB2, and RAD51C), and had received at least one dose of talazoparib. Patients with measurable disease at baseline and at least one valid assessment after baseline, per blinded independent central review, were assessed for best change from baseline in the sum of the diameter of the target lesions (as part of the objective response rate outcome). Tumor responses were categorized as complete response (CR), partial response (PR), stable disease (SD), or progressive disease (PD) by RECIST version 1.1. The primary endpoint was confirmed objective response rate (ORR), defined as best overall soft-tissue response of complete or partial response per RECIST 1.1 , by blinded independent central review. Secondary endpoints included time to objective response, duration of objective response, proportion of patients with a decrease in PSA of 50% or more from baseline, time to PSA progression, proportion of patients with conversion of circulating tumor cell count (proportion with a decrease from baseline of >5 to <5 cells per 7.5 mL blood or a decrease from >1 to 0 cells per 7.5 mL blood at any time, or any increase from <5 cells per 7.5 mL blood), radiographic progression-free survival (time from the first dose of talazoparib to progression in soft tissue as determined by radiography per RECIST 1.1 , per blinded independent central review and investigator assessment, in bone as per Prostate Cancer Working Group 3 criteria and independent central review, or death due to any cause, whichever occurred first), overall survival, safety, patient-reported outcomes, and pharmacokinetics.

Post hoc, antitumor activity endpoints were analyzed by HRR gene alteration group (BRCA1 , BRCA2, PALB2, ATM, and the other genes in the predefined panel of 11 DDR-HRR genes), in which patients were separated by HRR gene alteration using a hierarchical strategy, with BRCA1 or BRCA2 ranked above PALB2, PALB2 ranked above ATM, and ATM ranked above all other alterations.

RESULTS

Patient Characteristics of Antitumor

9 (9%) patients were Gleason group 1 , 31 (30%) patients were Gleason group 2, 63 (61 %) patients were Gleason group 3, and the Gleason group for 1 (1 %) patient was not reported [Gleason grades and associated grade groupings (1 to 5) refer to how the cancer cells look when compared to normal prostate cells. The higher the Gleason grade group, the more likely the cancer will grow and spread], 36 (35%) patients had visceral disease and 68 (65%) patients had non-visceral disease. The initial M stage of the patients at primary diagnosis was MO 39 (38%), M1 48 (46%), MX 13 (13%), and 4 (4%) patients were not reported [M category captures whether the cancer has metastasized to other parts of the body. MO: Cancer has not spread to other parts of the body. M1 : Cancer has spread to other parts of the body. MX: Metastasis cannot be measured]. The previous taxane use of the patients was as follows: 54 (52%) patients used docetaxel only, 49 (47%) patients used docetaxel and cabazitaxel, and the previous taxane use of 1 (1 %) patient was not reported. The use of prior hormone therapy by the patients was as follows: 37 (36%) patients used abiraterone only (, 37 (36%) patients used enzalutamide only, 28 (27%) patients used abiraterone and enzalutamide, and the prior hormone therapy use of 2 (2%) patients was not reported.

55 patients (53%) were evaluable for gLOH, 45 were non-evaluable for gLOH, and four lacked central lab gLOH results (non-evaluability for gLOH reflects inadequate tissue purity and/or quality).

After a median follow-up of 16.4 months, the objective response rate was 29.8% (31 of 104 patients; 95% Confidence Interval (Cl) 21.2-39.6).

Evaluation of Tumor qLOH Score as a Predictive Biomarker for Talazoparib Response

A potential association of gLOH high/low status with talazoparib response was explored and results are presented in Tables 1 and 2 below. Two gLOH high/low thresholds were explored. 8.8% was selected based on a publication demonstrating that this threshold distinguished prostate cancers bearing BRCA biallelic mutations from BRCA-wildtype prostate cancers with optimal sensitivity and specificity (Sokol et al, JCO Precision Oncology 2020;4:442-465)(results in Table 1). In addition, an agnostic threshold based on the median gLOH score (9.2%) in the efficacy population was explored (results in Table 2). Based on the 8.8% threshold, the ORR was significantly higher for gLOH-high [16/30 (53.3%), 95% Cl per Clopper-Pearson method of 34.3, 71.7%)] versus gLOH-low [3/25 (12.0%), 95% Cl 2.5, 31.2%; Odds ratio 8.381 , 2-sided p-value 0.0017, based on Fisher’s exact test]. Based on the 9.2% gLOH threshold, the ORR was also significantly higher for gLOH-high [15/28 (53.6%), 95% Cl 33.9, 72.5%] versus gLOH-low [4/27 (14.8%); 95% Cl 4.2, 33.7; Odds ratio 6.635, p-value 0.0041], The 8.8% threshold was selected for the additional gLOH high/low analyses detailed below.

In summary, the ORR was significantly higher for gLOH-high versus gLOH-low using either threshold, although there were responses in gLOH-low patients for both cut-offs.

Table 1: Response Based on BICR Assessment (RECIST 1.1; PCWG3) by gLOH high/low status based on the 8.8% Threshold (efficacy population evaluable for gLOH, N=55).

^aClopper-Pearson method used^; ^bOdds Ratio > 1 indicates better outcome for High compared to Low; exact Cl is calculated. ^cP-value based on Fisher’s exact test.

Table 2: Response Based on BICR Assessment (RECIST 1.1; PCWG3) by gLOH high/low status based on the 9.2% Threshold (efficacy population evaluable for gLOH, N=55).

Next, potential associations of gLOH score with response within the gene mutation groups were explored using a bar chart of gLOH annotated by best response, mutation group, mutation type, and mutation zygosity (The Figure).

Selected results from this analysis are tabulated in Table 3. Table 3: Best Overall Response by RECIST v.1.1 by Gene Mutation Group and gLOH high/low status (efficacy population evaluable for gLOH, N=55).

As shown in Table 4, within the BRCA2 mutation group, ORR was robust regardless of gLOH status, but the ORR for gLOH-high was significantly higher for gLOH-high (12/17, 70.6%) than gLOH-low (3/13, 23.1%) [p=0.0253 by Fisher’s exact test].

Table 4: Associations of gLOH Status with Response for Tumors Bearing BRCA2 Alterations Based on the 8.8% Threshold.

^aClopper-Pearson method used^; ^bOdds Ratio > 1 indicates better outcome for high compared to low; exact Cl is calculated; ^cP-value based on Fisher’s exact test

As shown in Table 5, within the ATM mutation subgroup, the ORR for gLOH-high was numerically higher for gLOH-high (2/4, 50%) than gLOH-low (0/6, 0%), but not significantly (P=0.1333). Table 5: Associations of gLOH Status with Response for Tumors Bearing ATM Alterations Based on the 8.8% Threshold.

Radiographic progression-free survival (RECIST 1.1 ; BICR) in the gLOH- evaluable efficacy population was numerically superior for gLOH-high versus gLOH-low using either threshold (hazard ratio 0.68), but not significantly. Results based on the 8.8% threshold are tabulated in Table 6. The signs of early separation for gLOH-high from gLOH-low shown in Table 6 were subsequently lost. The hazard ratio (95% Cl^b) for 9.2% threshold was 0.68 (0.317,1.448); 2-sided P-value=0.3131 (detailed results not shown).

Table 6: Radiographic Progression-Free Survival (RECIST 1.1; BICR) by gLOH high/low status based on the 8.8% Threshold (efficacy population evaluable for gLOH, N=55).

^aBased on the Brookmeyer and Crowley method; ^bHazard ratio based on Cox proportional hazards model; under proportional hazards, hazard ratio < 1 indicates a reduction in hazard rate in favor of gLOH-High compared to gLOH-low; ^cP-value based on log-rank test;

Hence, gLOH-high status was associated with response within the efficacy population and was also associated with response within the BRCA2 gene mutation group. Next, potential associations of gLOH score with response within gene zygosity and mutation type subgroups were explored using the same annotated bar chart (The Figure). Based on this visualization, no obvious relationship between zygosity and gLOH was evident. With respect to mutation type, DDR11 short variants (ie, singlenucleotide variants, short insertion/deletions) were broadly distributed across the gLOH range. In contrast, copy number loss (which was confined to the BRCA2 gene alteration subgroup; n = 13 pts) was numerically associated with high gLOH scores and response: 3/25 gLOH-low have BRCA2 copy number loss (2 SD, 1 NE) whereas 10/30 gLOH-high have BRCA2 copy number loss (8 CR/PR, 1 SD, 1 non-CR/PD). This suggests that the statistically superior overall efficacy in DDR11 m-gLOH-high versus DDR1 1 m-gLOH-low (53% versus 12%, p = 0.0017) and superior efficacy in BRCA2m- gLOH-high versus BRCA2m-gLOH-low (71 % versus 23%, p=0.0253) in part reflects the relatively high fraction of BRCA2 copy number loss in the gLOH-high group.

Based on these retrospective ad hoc exploratory analyses in this heavily pretreated mCRPC population, gLOH-high status was associated with enhanced response to talazoparib within the gLOH-evaluable efficacy population and within the gLOH-evaluable BRCA2 alteration subgroup. These results demonstrated predictive potential for gLOH-high status in DDR11 m prostate cancer, and also within some of the 11 predefined DDR-HRR gene alteration subgroups.

In conclusion, these retrospective exploratory analyses in TALAPRO-1 demonstrated that gLOH high status was associated with response to talazoparib in metastatic castration-resistant prostate cancer with DNA repair gene mutations.

All publications and patent applications cited in the specification are herein incorporated by reference in their entirety. Although the foregoing invention has been described in some detail by way of illustration and example, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

Claims

- 35 - What is claimed is:

1 . A method of selecting a subject having a cancer with a deficiency in homologous recombination repair for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; and b) selecting the subject for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

2. A method of treating a cancer having a deficiency in homologous recombination repair, in a subject, comprising: a) selecting the subject according to the method of claim 1 ; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

3. A method of identifying a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) determining a genomic loss of heterozygosity (gLOH) score from a biopsy of the cancer; and b) selecting the cancer for treatment with talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

4. A method of treating a cancer having a deficiency in homologous recombination repair, that is sensitive to treatment with talazoparib, or a pharmaceutically acceptable salt thereof, comprising: a) selecting the cancer according to the method of claim 3; and b) administering a therapeutically effective amount of talazoparib, or a pharmaceutically acceptable salt thereof, based on the gLOH score.

5. The method of claim 1 or claim 2, wherein the cancer is sensitive to treatment with talazoparib.

6. The method of any one of claims 1-4, wherein the cancer is prostate cancer. - 36 -

7. The method of claim 6, wherein the prostate cancer is metastatic prostate cancer.

8. The method of claim 6, wherein the prostate cancer is castration-resistant prostate cancer.

9. The method of claim 8, wherein the castration-resistant prostate cancer is metastatic castration-resistant prostate cancer.

10. The method of claim 1 or claim 3, wherein the deficiency in homologous recombination repair of the cancer is determined by next generation sequencing.

11. The method of claim 1 or claim 3, wherein step a) is performed by next generation sequencing.

12. The method of any one of claims 1-11 , wherein the gLOH score is at least about 8.0%.

13. The method of any one of claims 1-11 , wherein the gLOH score is at least about 8.3%.

14. The method of any one of claims 1-11 , wherein the gLOH score is at least about 8.8%.

15. The method of any one of claims 1-11 , wherein the gLOH score is at least about 9%; at least about 9.2%; at least about 10%; at least about 11 %; at least about 12%; at least about 13%; at least about 14%; at least about 15%; at least about 16%; at least about 17%; at least about 18%; at least about 19%; at least about 20%; at least about 21 %; at least about 22%; at least about 23%; at least about 24%; or at least about 25%.

16. The method of claim 1 or 2, wherein the subject is human.