Homologous Recombination DNA Repair Genes Research Articles

Gene fusions during the early evolution of mesothelioma correlate with impaired DNA repair and Hippo pathways.

Malignant pleural mesothelioma (MPM), a rare cancer a long latency period (up to 40 years) between asbestos exposure and disease presentation. The mechanisms coupling asbestos to recurrent somatic alterations are poorly defined. Gene fusions arising through genomic instability may create novel drivers during early MPM evolution. We explored the gene fusions that occurred early in the evolutionary history of the tumor. We conducted multiregional whole exome sequencing (WES) of 106 samples from 20 patients undergoing pleurectomy decortication and identified 24 clonal nonrecurrent gene fusions, three of which were novel (FMO9P-OR2W5, GBA3, and SP9). The number of early gene fusion events detected varied from zero to eight per tumor, and presence of gene fusions was associated with clonal losses involving the Hippo pathway genes and homologous recombination DNA repair genes. Fusions involved known tumor suppressors BAP1, MTAP, and LRP1B, and a clonal oncogenic fusion involving CACNA1D-ERC2, PARD3B-NT5DC2, and STAB2-NT5DC2 fusions were also identified as clonal fusions. Gene fusions events occur early during MPM evolution. Individual fusions are rare as no recurrent truncal fusions event were found. This suggests the importance of early disruption of these pathways in generating genomic rearrangements resulting in potentially oncogenic gene fusions.

TRIUMPH: Phase II trial of rucaparib monotherapy in patients with metastatic hormone-sensitive prostate cancer harboring germline DNA repair gene mutations.

190 Background: Androgen deprivation therapy (ADT) is the backbone of treatment for patients (pts) with metastatic prostate cancer (PCa), but many pts find this difficult to tolerate. Treatment with non-castrating regimens may avoid or delay the toxicities of hormonal therapy. The activity of PARP inhibitors (PARPi) in pts with homologous recombination DNA-repair (HRD) mutations (muts) and metastatic castration-resistant PCa has been established. We hypothesized here that the benefit of ARPi can be maintained in the absence of ADT in a biomarker-selected (HRD mutated) population with PCa. We designed a Phase 2 study in men with hormone-naïve, metastatic PCa who harbored a germline HRD mut treated with rucaparib monotherapy (without ADT). Methods: This was a multi-center, single arm Phase 2 study (NCT03413995) in men with asymptomatic hormone-sensitive metastatic PCa who received rucaparib 600mg by mouth daily. During consenting, pts were informed and had to opt out of ADT-based therapy. Pts must have had a germline mutation in an HRD gene on clinical-grade testing. The primary endpoint was confirmed PSA50 response rate. Key secondary endpoints included safety, objective response rate (ORR), and radiographic progression-free survival (rPFS). The trial was designed to detect a 25% absolute increase in PSA50 response from a null of 50%. Results: 12 pts were enrolled, 7 with BRCA1/2 and 5 with CHEK2 muts. The confirmed PSA50 response rate to rucaparib was 41.7% (N=5/12, 95% CI: 19.3-68.1%), which did not meet the pre-specified efficacy boundary to enroll additional patients to 2nd stage. In pts with measurable disease, the ORR was 60% (N=3/5, all with BRCA2). Median rPFS on rucaparib was 10.3 months (95% CI: 4.0 mo - NR). At the time of the interim analysis, 3 pts remained on study. The majority of adverse events (AE) were Grade ≤2 and expected. Translational studies are ongoing. Conclusions: Rucaparib can induce clinical responses in a biomarker-selected PCa population without concurrent ADT. However, the pre-specified threshold of PSA50 response was not met. Although durable responses were observed in a subset of pts, PARPi without ADT in metastatic hormone sensitive PCa will not be pursued. Clinical trial information: NCT03413995 . [Table: see text]

Pan-cancer analysis of the spectrum of homologous recombination DNA repair (HRR) pathway genes in the Indian population: A retrospective observational study

Background: Homologous recombinant repair (HRR) deficit and the associated sensitivity to poly (ADP-ribose) polymerase inhibitors (PARPi) has been well studied in breast, ovarian, prostate, and pancreatic cancers, but very little is known about it in other cancer types. Objectives: We sought to understand the spectrum of HRR mutations in various cancer types, with the goal of identifying therapeutic targets in lesser-explored cancers. Materials and Methods: In this retrospective study conducted between January 2021 and December 2022, we analyzed a cohort of 659 patients with various cancer types with mutations in 15 HRR genes using next generation sequencing, at 4baseCare Onco Solutions Pvt. Ltd., Bengaluru, Karnataka, India. Results: We identified a total of 825 gene variants, including 366 likely pathogenic/pathogenic mutations (44.4%), with BRCA1 (196 variants; 22.8%), BRCA2 (183 variants; 21.3%), and ATM (157 variants; 18.3%) being prevalent. Germline and somatic mutations were prevalent in BRCA1 (114 variants; 60.3%) and BRCA2 (46 variants; 24%), respectively. Recurrent mutations were identified in 8 genes, including BRCA1, BRCA2, BRIP1, BARD1, CDK12, CHEK2, PALB2 and RAD54L. BRCA1 and BRCA2 mutations were observed in breast, gynecologic, and musculoskeletal cancers; ATM and BRCA2 in gastrointestinal and biliary tract cancers, respiratory, and head-and-neck cancers; BRCA2 and CDK12 in genitourinary cancers. Additionally, co-occurring mutations (in genes such as BRCA1-BRIP1, ATM-BRCA2, ATM-BRIP1) and known therapeutically significant mutations were identified. Conclusions: The presence of therapeutically significant HRR mutations across a broad spectrum of cancer types in our study suggests that these mutations can possibly be targeted, especially in cancers where there is a paucity of therapeutic targets. Further, non-BRCA HRR genes, such as ATM and CDK12, could play a more prominent role than previously recognized.

Homologous recombination DNA repair gene RAD51, XRCC2 & XRCC3 polymorphisms and breast cancer risk in South Indian women.

BackgroundHomologous recombination repair (HRR) accurately repairs the DNA double-strand breaks (DSBs) and is crucial for genome stability. Genetic polymorphisms in crucial HRR pathway genes might affect genome stability and promote tumorigenesis. Up to our knowledge, the present study is the first to investigate the impact of HRR gene polymorphisms on BC development in South Indian women. The present population-based case-control study investigated the association of polymorphisms in three key HRR genes (XRCC2-Arg188His, XRCC3-Thr241Met and RAD51-G135C) with BC risk.Materials and methodsPolymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for genotyping the HRR variants in 491 BC cases and 493 healthy women.ResultsWe observed that the XRCC3 Met allele was significantly associated with BC risk [OR:1.27 (95% CI: 1.02–1.60); p = 0.035]. In addition, the homozygous mutant (C/C) genotype of RAD51 G135C variant conferred 2.19 fold elevated risk of BC [OR: 2.19 (95% CI: 1.06–4.54); p = 0.034]. Stratified analysis of HRR variants and BC clinicopathological features revealed that the XRCC3-Thr241Met and RAD51-G135C variants are associated with BC progression. Combined SNP analysis revealed that the individuals with RAD51-C/C, XRCC2-Arg/Arg, and XRCC3-Thr/Thr genotype combination have three-fold increased BC risk.ConclusionThe present study imparts additional evidence that genetic variants in crucial HRR pathway genes might play a pivotal role in modulating BC risk in South Indian women.

Analysis of homologous recombination DNA repair gene mutation status in patients with metastatic small cell lung cancer treated with cediranib and olaparib on NCI 9881 study.

8563 Background: Cediranib, a pan-vascular endothelial growth factor receptor tyrosine kinase inhibitor, suppresses expression of homologous recombination DNA repair (HRR) genes and increases sensitivity of tumors to a poly-(ADP-ribose) polymerase (PARP) inhibitor in vitro and in vivo models of breast and ovarian cancer. Olaparib, a PARP inhibitor, demonstrated clinical efficacy in patients with advanced solid tumor with a deleterious mutation in HRR genes. We hypothesized that cediranib induces HRR deficient phenotype by suppressing expression of HRR genes and cediranib and olaparib combination (C+O) results in an objectives response in patients with HRR proficient (HRP) advanced solid tumors. Herein, we report the biomarker data from analyses of targeted sequencing of 84 DNA repair (DR) genes with BROCA-HR assay in patients with metastatic small cell lung cancer (mSCLC). Methods: This multi-institutional phase 2 trial enrolled patients with mSCLC previously treated with a platinum-based chemotherapy. Patients received cediranib 30mg orally (po) daily plus olaparib 200mg po twice daily until disease progression or unacceptable toxicity. The primary endpoint was objective response rate (ORR) by RECIST v1.1. A tumor biopsy was obtained from the patients with safely accessible metastatic tumor. HRR deficiency (HRD) was defined as presence of a deleterious mutation in any of the 10 key HRR-related genes per BROCA-HR assay including: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12 (somatic mutations only), NBN, PALB2, RAD51C, or RAD51D. Otherwise, the tumors were defined as HRR proficiency (HRP). Results: A total of 25 patients with SCLC received the study treatment. Fourteen patients had available tumor biopsy samples and/or germline available for BROCA-HR. One patient (7%) was determined to have a HRD tumor by a presence of PALB2 mutation. This patient had stable disease as a best overall response but came off study due to unequivocal clinical progression. Thirteen patients (93%) had a HRP tumor. Six of these (46%) patients had PR. Median PFS in patients with HPR tumors was 122 days. The most common gene alterations detected by BROCA-HR assay was TP53 (93%) and RB1 (79%). Other DR gene alterations noted from our study samples were MRE11, CKD12 PALB2, ERCC4, FANCB, and BAP1. Conclusions: HRD was infrequent in our mSCLC samples. C+O resulted in objective responses in 46% of mSCLC patients with HRP tumors. Mutations in TP53 and RB1 were the most common gene alterations. Further investigation in warranted to confirm this observation. Clinical trial information: NCT02498613.

Abstract PS11-10: A Phase 1b/2 Study of the BET inhibitor ZEN003694 in combination with talazoparib for treatment of patients with TNBC without gBRCA1/2 mutations

Abstract Background: Metastatic triple-negative breast cancer (TNBC) is an aggressive and heterogeneous cancer with limited therapeutic options. PARP inhibitors (PARPi) are approved to treat breast cancer harboring germline BRCA1/2 (gBRCA1/2) mutations and have not shown efficacy in homologous recombination DNA repair (HRR) proficient tumors. In pre-clinical models, the BET inhibitor (BETi) ZEN003694 sensitizes wild-type BRCA1/2 tumors to PARPi through downregulation of HRR gene expression, providing a rationale for combination therapy. We report initial results from a Ph 1b/2 trial evaluating the combination of ZEN003694 and the PARPi, talazoparib, in TNBC patients without gBRCA1/2 mutations. Methods: A Ph 1b dose-finding segment will be followed by a single-arm Ph 2 Simon 2-stage segment. Ph 1b evaluated several dose combinations of ZEN003694 and talazoparib, with safety and recommended Ph 2 dose (RP2D) as primary endpoints and pharmacokinetics (PK), pharmacodynamics (PD), and clinical benefit rate (CBR = Objective response rate (ORR) + stable disease > 4 months) as secondary endpoints. The Ph 2 segment has CBR as the primary endpoint and progression free survival (PFS) and duration of response as secondary endpoints. Eligibility criteria included TNBC (ER/PR < 10% and not a candidate for endocrine therapy), HER2-, wild-type gBRCA1/2, and > 1 prior chemotherapy regimen for metastatic disease. Patients were dosed daily in continuous 28-day cycles until disease progression or unacceptable toxicity. Dose limiting toxicity (DLT) period was one cycle. Adverse events (AE), PK, and PD in whole blood and tissue biopsies were assessed. Response endpoints were assessed per RECIST 1.1 every 2 cycles. Results: Findings of the Ph 1b are reported. 15 patients with a median 3 lines of prior therapy in the metastatic setting were enrolled in 3 dose-finding cohorts. RP2D was determined to be 48mg ZEN003694 plus 0.75mg talazoparib. Across the cohorts, the most common AE was thrombocytopenia (TCP) (73%) with 53% G3/4 (Table 1). G4 TCP was the DLT and 1 DLT patient required a platelet transfusion. TCP could be managed to G1/2 levels with intermittent dose holds and reductions. Other G1/2 AEs included fatigue, anorexia, neutropenia, nausea, dysgeusia, and photophobia. Dose intensity analysis showed average daily doses of ZEN003694 and talazoparib could be maintained above 40mg and 0.5mg, respectively, over 4 cycles. Exposures of ZEN003694 and talazoparib were dose proportional with no drug-drug PK interactions. At RP2D, PD assessment by a whole blood mRNA assay for BET-dependent genes demonstrated robust down-regulation of CCR1, IL1RN, and IL8 to < 50% of baseline for > 8 h. Expression of HRR genes, RAD51 and BRCA1, in whole blood also decreased for > 8 h. Analysis of an on-treatment biopsy showed robust and durable BET target modulation assessed by comparing RNA sequence data with a reference BET dependent signature. Across the 3 cohorts, ORR by Investigator was 38% (5/13), including 1 CR and 4 PRs, and CBR was 57% (8/14). 6 of the 15 patients are ongoing as of data analysis date (2-9 cycles), with 1 patient responding for > 6 months. Conclusions: Combination of ZEN003694 and talazoparib demonstrated anti-cancer activity in pretreated metastatic TNBC patients without gBRCA1/2 mutations. TCP is frequent but manageable with dose adjustments. PK is predictable, and PD data show meaningful target engagement. The Ph 2 part of the trial is currently ongoing. Grade 3/4 Adverse EventsCohort 1(1mg talazoparib + 48mg ZEN003694)N=6Cohort 2(0.75 mg talazoparib + 48mg ZEN003694)N=6Cohort 3(1mg talazoparib + 36mg ZEN003694)N=3Thrombocytopenia3 (G3), 2 (G4, DLT)1 (G3), 1 (G4, DLT)1 (G3)Diarrhea1 (G3)00Neutropenia01 (G3)0 Citation Format: Philippe Aftimos, Mafalda Oliveira, Kevin Punie, Valentina Boni, Erika Hamilton, Ayca Gucalp, Payal Shah, Lida Mina, Priyanka Sharma, Lisa Bauman, Eric Campeau, Sarah Attwell, Margo Snyder, Karen Norek, Akos Czibere, Yanke Yu, Michael H Silverman, Sanjay Lakhotia, Susan Domchek, Jennifer Litton, Mark Robson. A Phase 1b/2 Study of the BET inhibitor ZEN003694 in combination with talazoparib for treatment of patients with TNBC without gBRCA1/2 mutations [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS11-10.

Abstract IA19: Genetic risk for subsequent breast cancer among female survivors of childhood cancer

Abstract Due to advancement in cancer therapy, greater than 80% of children diagnosed with cancer will survivor five or more years. It is estimated there are half a million childhood cancer survivors currently living in the US. Survivors are at increased risk of subsequent neoplasms, mostly considered therapy related. Breast cancer is one of the most common subsequent neoplasms among female survivors. It is known that radiation dose and volume to the breast is a major risk factor, leading to 20-fold increased risk with rate of cumulative incidence reaching 30% by age of 50 years. For non-irradiated survivors, literature also reported the risk of chemotherapy agents including anthracyclines. However, the genetic contribution was largely unknown before the groundbreaking genomic project was launched for the St. Jude Lifetime Cohort (SJLIFE) a few years ago. We analyzed the whole-genome sequencing data for 4402 survivors (2090 females, median age at follow up = 30 years, and median length of follow up = 22 years) from SJLIFE study. Pathogenic/likely (P/LP) variants were identified for 156 cancer predisposition genes and 127 DNA repair genes, respectively, with a small number of genes overlapped between the two gene sets. We also constructed a polygenic risk score based on 172 SNPs established from de novo breast cancer genetic association studies using the general population. Based on the multivariate piecewise exponential models, rate of subsequent breast cancer was significantly increased for female survivors who carried a P/LP variant in cancer predisposition genes and with or without chest irradiation. In addition, rate of subsequent breast cancer was significantly increased among all female survivors, especially survivors who carried a P/LP variant in homologous recombination DNA repair genes in conjunction with treatment exposures of chest irradiation (≥20Gy) and/or anthracyclines (doses in the second and third tertiles). Finally, we found survivors with high polygenic risk score had increased risk of developing subsequent breast cancer over and beyond the monogenic risk conferred by rare P/LP variants in breast cancer predisposition genes. Interestingly, African Americans seem to have the lowest prevalence of subsequent breast cancer among three different race groups: 1.3% for African Americans, 4.1% for European Americans and 5.9% for Asian/Native-Indian Americans. On the other hand, African Americans seem to have higher risk in developing subsequent breast cancer among carriers of P/LP variants compared to European Americans. We anticipate utilizing common susceptibility loci in combination with rare high-risk P/LP variants and other risk factors may inform a better strategy for breast cancer risk stratification among survivors of childhood cancer. Citation Format: Zhaoming Wang. Genetic risk for subsequent breast cancer among female survivors of childhood cancer [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr IA19.

Homologous Recombination DNA Repair Gene Aberrations—Are We More Alike Than Different?

Homologous Recombination DNA Repair Gene Aberrations—Are We More Alike Than Different?

Mthfd2 Modulates Mitochondrial Function and DNA Repair to Maintain the Pluripotency of Mouse Stem Cells.

SummaryThe pluripotency of stem cells determines their developmental potential. While the pluripotency states of pluripotent stem cells are variable and interconvertible, the mechanisms underlying the acquisition and maintenance of pluripotency remain largely elusive. Here, we identified that methylenetetrahydrofolate dehydrogenase (NAD+-dependent), methenyltetrahydrofolate cyclohydrolase (Mthfd2) plays an essential role in maintaining embryonic stem cell pluripotency and promoting complete reprogramming of induced pluripotent stem cells. Mechanistically, in mitochondria, Mthfd2 maintains the integrity of the mitochondrial respiratory chain and prevents mitochondrial dysfunction. In the nucleus, Mthfd2 stabilizes the phosphorylation of EXO1 to support DNA end resection and promote homologous recombination repair. Our results revealed that Mthfd2 is a dual-function factor in determining the pluripotency of pluripotent stem cells through both mitochondrial and nuclear pathways, ultimately ensuring safe application of pluripotent stem cells.

Preliminary efficacy data of platinum-pretreated small cell lung cancer (SCLC) cohort of NCI 9881 study: A phase II study of cediranib in combination with olaparib in advanced solid tumors.

9065 Background: Cediranib, a pan-vascular endothelial growth factor receptor tyrosine kinase inhibitor, suppresses expression of BRCA1, BRCA2, and RAD51 and increases sensitivity of tumors to poly-(ADP-ribose) polymerase (PARP) inhibitors in vitro. Olaparib, a PARP inhibitor, demonstrated clinical efficacy in patients with advanced solid tumors carrying a germline BRCA mutation. We therefore tested the anti-tumor activity of cediranib and olaparib combination in patients (pts) with advanced solid tumors. Here, we report the data from the SCLC cohort. Methods: This multi-institutional, two-stage, phase 2 study enrolled pts with metastatic SCLC previously treated with a minimum of one prior line of platinum-based chemotherapy in advanced setting. Patients were treated with cediranib 30mg po daily plus olaparib 200mg po BID until disease progression or unacceptable toxicity. The primary endpoint was objective response rate (ORR) by RECIST v1.1. Baseline tumor biopsies were obtained for biomarker analyses. Results: Baseline characteristics of the 25 pts enrolled are summarized below. The overall ORR rate was 28% (95% CI: 0.104,0.456). Median duration of response was 3.8 months (mos). Six of 8 pts had an objective response lasting longer than 3 mos up to 10.3 months. Disease control rate (# of pts with CR, PR or SD / # evaluable pts) was 88% (95% CI: 0.75,1.01). Median progression free survival was 4.1 mos (95% CI: 2.3, 6.2). Median OS was 5.5 mos (95% CI: 3.4, NA). Grade 3/4 adverse events (G3/4 AEs), irrespective of attribution, occurred in 14 of 25 (56%). G3/4 AEs occurring in > 10% of pts were hypertension (21%), fatigue (17%) and weight loss (13%). Conclusions: The cediranib/olaparib combination resulted in promising clinical activity with ORR of 28% in biomarker-unselected pts with platinum-pretreated SCLC. The regimen required prompt initiation of antihypertensives, but AEs were overall manageable. Analyses of mutation status in homologous recombination DNA repair genes are going and will be correlated with clinical activity. Clinical trial information: NCT02498613. [Table: see text]

Preliminary efficacy data of triple-negative breast cancer cohort of NCI 9881 study: A phase II study of cediranib in combination with olaparib in advanced solid tumors.

1077 Background: Cediranib, a pan-vascular endothelial growth factor receptor tyrosine kinase inhibitor, suppresses expression of BRCA1, BRCA2, and RAD51 and increases sensitivity of tumors to poly-(ADP-ribose) polymerase (PARP) inhibitors in vitro. Olaparib, a PARP inhibitor, demonstrates clinical efficacy in patients with germline BRCA1/2 mutations and HER2-negative metastatic breast cancer. We therefore tested the anti-tumor activity of the combination of cediranib and olaparib in patients (pts) with metastatic triple-negative breast cancer (TNBC). Methods: This multi-institutional, two-stage, phase II study enrolled patients with metastatic TNBC previously treated with a minimum of one prior line of systemic therapy in the advanced setting. Patients were treated with cediranib 30mg po daily plus olaparib 200mg po BID until disease progression or unacceptable toxicity. The primary endpoint was objective response rate by RECIST v1.1. Baseline tumor biopsies were obtained for biomarker analyses. Results: Baseline characteristics of the 37pts enrolled are summarized below. The overall objective response rate was 14% (95% CI: 0.025, 0.2453). Median duration of response was 2.0 months (mos) with a range of 1.8 to 6.3 mos. Disease control rate ((# of pts with CR, PR or SD)/(# of evaluable pts)) was 81% (95% CI: 0.6846, 0.937). Median PFS was 3.7 mos (95% CI: 2.1, 4.3). Grade 3/4 adverse events (G3/4 AEs), irrespective of attribution, occurred in 25 of 38 (66%).G3/4 AEs occurring in > 5% of pts were hypertension (24%) and dyspnea (11%), diarrhea (8%) vomiting (8%). Conclusions: The cediranib/olaparib combination resulted in promising objective responses in 14% of biomarker-unselected patients with heavily pre-treated, metastatic TNBC. The regimen required prompt initiation of antihypertensives, but AEs were overall manageable. Analyses of mutation status in homologous recombination DNA repair genes are ongoing and will be correlated with clinical outcome. Clinical trial information: NCT02498613 . [Table: see text]

Analysis of Epigenetic Alterations in Homologous Recombination DNA Repair Genes in Male Breast Cancer.

Background: Male breast cancer (BC) is a distinct neoplasm with low but rising incidence, frequently diagnosed as advanced stage disease. Considering the relevance of altered homologous recombination repair (HRR) in male BC, we aimed to explore the biomarker potential of aberrant promoter methylation of ATM, BRCA1, PALB2, RAD51B, and XRCC3. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples from 128 male BC patients, paired adjacent normal tissue and 19 gynecomastia cases were collected and assessed by quantitative methylation-specific PCR (qMSP). Non-parametric tests were used to compare methylation levels between tumor and non-tumor samples and to seek for associations with clinicopathological variables. Results: Only RAD51B and XRCC3 disclosed significant differences between tumor and gynecomastia (p < 0.0001 and p = 0.020, respectively). Assembled in a panel, RAD51B and XRCC3 promoter methylation discriminated male BC from gynecomastia with 91.5% sensitivity, 89.5% specificity, and 91.2% accuracy. Moreover, promoter methylation levels were lower in paired non-tumor tissues, comparing to tumor samples. No associations were found between epigenetic alterations and clinicopathological features, as well as with RAD51 and XRCC3 immunoexpression and methylation levels. Conclusion: Quantitative promoter methylation of RAD51B and XRCC3 constitutes a promising and accurate biomarker for male BC. Validation in larger series and in liquid biopsies is warranted to confirm its usefulness in detection and monitoring settings.

Randomized phase II study of olaparib with or without cediranib in men with metastatic castration-resistant prostate cancer (mCRPC).

111 Background: Cediranib, a vascular endothelial growth factor receptor tyrosine kinase inhibitor, suppresses expression of BRCA1, BRCA2, and RAD51 and increases sensitivity of tumors to poly (ADP-ribose) polymerase (PARP) inhibitors in vitro. Olaparib, a PARP inhibitor, demonstrates clinical efficacy in men with DNA repair deficient, mCRPC. We therefore performed a randomized phase 2 trial comparing olaparib with or without cediranib in men with mCRPC. Methods: Men with a minimum of one prior line of systemic therapy for mCRPC were randomized 1:1 to receive cediranib 30mg po daily plus olaparib 200mg po BID (Arm A) or olaparib 300mg BID alone (Arm B). At radiographic progression, patients (pts) in Arm B could crossover to Arm A. The primary endpoint was radiographic progression-free survival (rPFS). Secondary endpoints were objective response rate (ORR) and PSA50 decline rate (PSA50). Tumor biopsy specimens were obtained for biomarker analyses pre- and on-treatment. Results: Baseline characteristics of the 90 pts enrolled are summarized below. The median rPFS was 11.1 versus 4.0 months in Arm A and Arm B, respectively (Hazard Ratio 0.54, 95% CI 0.317, 0.928, p=0.026). Trends toward a higher ORR (19% and 12%), Disease Control Rate (Stable Disease + Partial Response) (77% and 64%,) and PSA50 (29% and 17%) were observed in Arm A compared to Arm B, respectively. Thirteen pts in Arm B crossed over to Arm A. One pt had a PR after crossover. Grade 3/4 adverse events (G3/4 AEs), irrespective of attribution, occurred in 77% and 58% of Arm A and Arm B pts, respectively. G3/4 AEs occurring in &gt;10% of pts were hypertension (32%), fatigue (23%) and diarrhea (11%) in Arm A, and anemia (16%) and lymphopenia (11%) in Arm B. Conclusions: The cediranib/olaparib combination significantly improves rPFS in unselected, mCRPC pts. AEs were manageable. Analyses of mutation status in homologous recombination DNA repair genes are pending and will be key in interpreting the data. Clinical trial information: NCT02893917. [Table: see text]

Extreme responses to immune checkpoint blockade following bipolar androgen therapy and enzalutamide in patients with metastatic castration resistant prostate cancer.

Immune checkpoint inhibition has been shown to have limited efficacy in patients with metastatic prostate cancer. Prostate cancers that harbor certain homologous recombination (HR) DNA repair gene mutations, inactivating CDK12 mutations or have underlying mismatch repair deficiency may be effectively treated with immunotherapy. Combination therapy may improve clinical response rates to immune checkpoint blockade. We observed profound prostate-specific antigen (PSA) and/or objective responses to immune checkpoint blockade following prior treatment with bipolar androgen therapy (BAT) and enzalutamide. We report three cases of patients with metastatic castration resistant prostate cancer (mCRPC) undergoing therapy with anti-PD-1 inhibitors. All patients underwent both somatic molecular testing and germline genetic testing. Two of the three patients with mCRPC harbored an inactivating mutation in an HR DNA repair gene (BRCA2, ATM). No patient demonstrated mismatch repair deficiency, nor were CDK12 alterations present. All three patients had been treated with BAT and enzalutamide before immune checkpoint blockade, a paradoxical approach for the treatment of mCRPC developed by our group. These cases of mCRPC suggest that immune checkpoint blockade may have therapeutic potential in patients with prostate cancer, especially following immune activation ("priming") using BAT and enzalutamide.

Adaptive mutability of colorectal cancers in response to targeted therapies.

The emergence of drug resistance limits the efficacy of targeted therapies in human tumors. The prevalent view is that resistance is a fait accompli: when treatment is initiated, cancers already contain drug-resistant mutant cells. Bacteria exposed to antibiotics transiently increase their mutation rates (adaptive mutability), thus improving the likelihood of survival. We investigated whether human colorectal cancer (CRC) cells likewise exploit adaptive mutability to evade therapeutic pressure. We found that epidermal growth factor receptor (EGFR)/BRAF inhibition down-regulates mismatch repair (MMR) and homologous recombination DNA-repair genes and concomitantly up-regulates error-prone polymerases in drug-tolerant (persister) cells. MMR proteins were also down-regulated in patient-derived xenografts and tumor specimens during therapy. EGFR/BRAF inhibition induced DNA damage, increased mutability, and triggered microsatellite instability. Thus, like unicellular organisms, tumor cells evade therapeutic pressures by enhancing mutability.

845PD - CDK12-altered prostate cancer: Clinical features and therapeutic outcomes to standard systemic therapies, PARP inhibitors, and PD1 inhibitors

BackgroundAlthough once considered a homologous recombination DNA repair gene, CDK12 is now thought to have a distinct role in maintaining genomic stability. In prostate cancer, inactivating CDK12 mutations lead to gene fusion-induced neoantigens and possibly sensitivity to PD1 inhibitors. MethodsWe conducted a retrospective multicenter study to identify advanced prostate cancer patients with loss-of-function CDK12 mutations. We characterized their clinical features and therapeutic outcomes, including sensitivity to PARP and PD1 inhibitors. Results58 men with at least monoallelic CDK12 alterations were identified from 9 academic centers; 28 (48%) had biallelic inactivation. Tissue for genomics was from primary tumors in 45 cases (77%) and from metastatic sites in 13 cases (23%). All CDK12 mutations were somatic-only. Median age at diagnosis was 60 y (41–78 y), 71%/29% were white/nonwhite, 79% had Gleason sum 9-10, 10% had ductal/intraductal histology, 76% had stage T3/T4 disease, 47% had metastases at diagnosis, and the median PSA was 24ng/mL. Of those undergoing primary ADT (± Abi, ± Doce) for advanced disease (n=54), only 85% had a PSA50 response, with median PFS of 11.8 (95% CI 8.3–15.4) mo; OS from ADT initiation was 40.8 (95% CI 18.7–53) mo. Of those receiving first-line Abi/Enza for mCRPC (n=34), only 47% had a PSA50 response, with median PFS of 4.3 (95% CI 2.6–6.0) mo. Of those receiving a first Taxane agent for mCRPC (n=20), only 35% had a PSA50 response, with median PFS of 4.0 (95% CI 2.6–5.3) mo. Eleven men received a PARP inhibitor (10 Olaparib, 1 Rucaparib): none had a PSA50 response, and median PFS was 3.6 (95% CI 3.0–4.2) mo. Eight men received a PD1 inhibitor as 4th to 6th-line mCRPC therapy (5 Pembro, 3 Nivo): 38% had a PSA50 response, and median PFS was 6.6 (95% CI 2.3–10.8) mo. ConclusionsCDK12-altered prostate cancer is an aggressive subtype presenting at young age, with high Gleason grade, and often with de novo M1 disease at diagnosis. Outcomes to hormonal and taxane therapies are poor, and PARP inhibitors are also ineffective. A proportion of these patients respond favorably to PD1 inhibitors, implicating CDK12 deficiency in immunotherapy responsiveness. Legal entity responsible for the studyEmmanuel S. Antonarakis. FundingHas not received any funding. DisclosureE.S. Antonarakis: Advisory / Consultancy, Research grant / Funding (institution): Janssen; Advisory / Consultancy, Research grant / Funding (institution): Astellas; Advisory / Consultancy, Research grant / Funding (institution): Sanofi; Advisory / Consultancy, Research grant / Funding (institution): Dendreon; Advisory / Consultancy, Research grant / Funding (institution): Medivation; Advisory / Consultancy: ESSA; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Advisory / Consultancy, Research grant / Funding (institution): Clovis; Advisory / Consultancy, Research grant / Funding (institution): Merck; Research grant / Funding (institution): Johnson & Johnson; Research grant / Funding (institution): Genentech; Research grant / Funding (institution): Novartis; Advisory / Consultancy, Research grant / Funding (institution): Bristol-Myers Squibb; Advisory / Consultancy: Eli Lilly; Licensing / Royalties: Qiagen. N. Agarwal: Advisory / Consultancy: Astellas; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Advisory / Consultancy: Argos; Advisory / Consultancy, Research grant / Funding (institution): Bristol-Myers Squibb; Advisory / Consultancy, Research grant / Funding (institution): Clovis; Advisory / Consultancy, Research grant / Funding (institution): Eisai; Advisory / Consultancy, Research grant / Funding (institution): Exelixis; Advisory / Consultancy, Research grant / Funding (institution): EMD Serono; Advisory / Consultancy, Research grant / Funding (institution): Eli Lilly; Advisory / Consultancy: Foundation One; Advisory / Consultancy, Research grant / Funding (institution): Genentech; Advisory / Consultancy, Research grant / Funding (institution): Janssen; Advisory / Consultancy, Research grant / Funding (institution): Merck; Advisory / Consultancy, Research grant / Funding (institution): Medivation; Advisory / Consultancy, Research grant / Funding (institution): Novartis; Advisory / Consultancy, Research grant / Funding (institution): Nektar; Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Research grant / Funding (institution): Bavarian Nordic; Research grant / Funding (institution): Calithera; Research grant / Funding (institution): Celldex. B.L. Maughan: Advisory / Consultancy: Peloton Therapeutics; Advisory / Consultancy: Bristol-Myers Squibb; Advisory / Consultancy: Tempus; Advisory / Consultancy: Bayer; Advisory / Consultancy: Exelixis; Advisory / Consultancy: Janssen; Advisory / Consultancy: Astellas. M. Hussain: Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Advisory / Consultancy, Research grant / Funding (institution): Bayer; Honoraria (self), Research grant / Funding (institution): Genentech; Honoraria (self): Sanofi Genzyme; Honoraria (self): Research To Practice; Honoraria (self): Aptitude Health; Honoraria (self): Epics. All other authors have declared no conflicts of interest.

Differential Response to Olaparib Treatment Among Men with Metastatic Castration-resistant Prostate Cancer Harboring BRCA1 or BRCA2 Versus ATM Mutations

BackgroundPoly ADP-ribose polymerase (PARP) inhibitors, such as olaparib, are being explored as a treatment option for metastatic castration-resistant prostate cancer (mCRPC) in men harboring mutations in homologous recombination DNA-repair genes. Whether responses to PARP inhibitors differ according to the affected gene is currently unknown. ObjectiveTo determine whether responses to PARP inhibitors differ between men with BRCA1/2 and those with ATM mutations. Design, setting, and participantsThis was a multicenter retrospective review of 23 consecutive men with mCRPC and pathogenic germline and/or somatic BRCA1/2 or ATM mutations treated with olaparib at three academic sites in the USA. Outcome measurements and statistical analysisThe proportion of patients achieving a ≥50% decline in prostate-specific antigen (PSA50 response) was compared using Fisher's exact test. Clinical and radiographic progression-free survival (PFS) and overall survival were estimated using Kaplan-Meier analyses and compared using the log-rank test. Results and limitationsThe study included two men with BRCA1 mutations, 15 with BRCA2 mutations, and six with ATM mutations. PSA50 responses to olaparib were achieved in 76% (13/17) of men with BRCA1/2 versus 0% (0/6) of men with ATM mutations (Fisher's exact test; p=0.002). Patients with BRCA1/2 mutations had median PFS of 12.3mo versus 2.4mo for those with ATM mutations (hazard ratio 0.17, 95% confidence interval 0.05–0.57; p=0.004). Limitations include the retrospective design and relatively small sample size. ConclusionsMen with mCRPC harboring ATM mutations experienced inferior outcomes to PARP inhibitor therapy compared to those harboring BRCA1/2 mutations. Alternative therapies should be explored for patients with ATM mutations. Patient summaryMutations in BRCA1/2 and ATM genes are common in metastatic prostate cancer. In this study we compared outcomes for men with BRCA1/2 mutations to those for men with ATM mutations being treated with olaparib. We found that men with ATM mutations do not respond as well as men with BRCA1/2 mutations.

DNA Repair Gene Alterations and PARP Inhibitor Response in Patients With Metastatic Castration-Resistant Prostate Cancer.

Background: PARP inhibition is a promising therapeutic strategy for the treatment of men with metastatic castration-resistant prostate cancer whose tumors harbor homologous recombination DNA repair gene alterations. However, questions remain for many practicing clinicians about which patients are ideally suited for PARP inhibitor treatment. This report details our institutional experience using PARP inhibitor therapy in patients whose tumors harbored specific DNA repair gene alterations. Patients and Methods: We performed a retrospective chart review to identify patients at Oregon Health & Science University who were treated with PARP inhibition. We identified 8 patients and determined the impact of the specific DNA repair gene alterations on tumor response and time on treatment with PARP inhibition. Results: A number of DNA repair gene alterations were identified. Three patients had pathogenic BRCA2 mutations and one had a BRCA2 mutation of uncertain significance. Conversely, the 4 other patients' tumors harbored alterations in other DNA repair genes, none of which were clearly pathogenic. A statistically significant difference in benefit was seen between patients whose tumors harbored BRCA2 gene alterations and those whose tumors did not, as measured by >50% decline in prostate-specific antigen levels (100% vs 0%; P=.03) and duration on therapy (31.4 vs 6.4 weeks; P=.03). Conclusions: Our results demonstrate that not all DNA repair alterations are equally predictive of PARP inhibitor response. Importantly, all responding patients had tumors harboring BRCA2 DNA repair alterations, including one without a known pathogenic mutation. Conversely, among the 4 nonresponders, several DNA repair alterations in genes other than BRCA2 were identified that were not clearly pathogenic. This demonstrates the need to carefully examine the functional relevance of the DNA repair alterations identified, especially in genes other than BRCA2, when considering patients for PARP inhibitor treatment.

Abstract 4336: Integrative genomic and transcriptomic analysis of leiomyosarcoma

Abstract Leiomyosarcomas (LMS) are malignant tumors of smooth-muscle origin that occur across age groups. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown, and few therapeutic options exist for LMS patients. To detect somatic mutations, copy number alterations, and structural rearrangements, we performed whole-exome and transcriptome sequencing of 49 and 37 LMS tumors, respectively, and performed integrative analysis. Recurrence analysis identified TP53, RB1, and ATRX as significantly mutated genes and various other cancer-associated genes mutated at low frequency, indicating substantial mutational heterogeneity. Copy number analysis revealed widespread chromosomal gains and losses and highly rearranged genomes in all tumors. Additionally, chromothripsis and whole-genome duplication were detected in 35% and 51% of cases, respectively. Principle component analysis and unsupervised hierarchical clustering of transcriptome data revealed three distinct subgroups of patients. Furthermore, we detected multiple non-recurrent fusion transcripts resulting from chromosomal rearrangements, many of which were predicted to result in loss of TP53 and RB1 function. In-depth analysis of these loci revealed protein-damaging microdeletions, intragenic or distal inversions, and exon skipping events as additional, previously unrecognized mechanisms of TP53 and RB1 disruption. Integration of whole-exome and transcriptome data demonstrated biallelic disruption of TP53 and RB1 in 92% and 94% of cases, respectively, and tumors with wildtype RB1 displayed loss of CDKN2A expression, overexpression of CCND1, or mutation of MAX resulting in CDK4 and CCND2 overexpression as alternative mechanisms of RB1 suppression. We also detected alternative lengthening of telomeres (ALT) in 78% of cases, and identified recurrent alterations in telomere maintenance genes such as ATRX, RBL2, and SP100, providing novel insight into the genetic basis of this mechanism. Finally, most tumors displayed hallmarks of “BRCAness”, including alterations in homologous recombination DNA repair genes and enrichment of specific mutational signatures, and cultured LMS cells were sensitive towards olaparib and cisplatin. This comprehensive genomic and transcriptomic analysis has unveiled that LMS is characterized by mutational heterogeneity, genomic instability, near-universal inactivation of TP53 and RB1, and frequent whole-genome duplication. Furthermore, we have established that most LMS tumors rely on ALT to escape replicative senescence, and identified recurrent alterations in a broad spectrum of telomere maintenance genes. Finally, our findings uncover “BRCAness” as potentially actionable feature of LMS tumors, and provide a rich resource for guiding future investigations into the mechanisms underlying LMS development and the design of novel therapeutic strategies. Citation Format: Priya Chudasama, Sadaf Mughal, Mathijs Sanders, Daniel Hübschmann, Inn Chung, Aurélie Ernst, Bernd Kasper, Hans-Georg Kopp, Sebastian Bauer, Karsten Rippe, Benedikt Brors, Marcus Renner, Peter Hohenberger, Claudia Scholl, Stefan Fröhling. Integrative genomic and transcriptomic analysis of leiomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4336.

TRITON2: An international, multicenter, open-label, phase II study of the PARP inhibitor rucaparib in patients with metastatic castration-resistant prostate cancer (mCRPC) associated with homologous recombination deficiency (HRD).

TPS388 Background: Up to 25% of patients with advanced prostate cancer, including mCRPC, have a deleterious germline or somatic mutation in BRCA1, BRCA2, ATM or another homologous recombination (HR) DNA repair gene that can serve as a molecular marker to select those who may respond to poly(ADP-ribose) polymerase inhibitors (PARPis). PARPis are lethal to cells with HRD, and PARPi treatment has shown preliminary evidence of an antitumor effect in patients with mCRPC who harbor a mutation in an HR DNA repair gene (Mateo et al. N Engl J Med. 2015;373:1697-708). These data provide a compelling rationale for evaluating rucaparib, a potent PARP1, PARP2 and PARP3 inhibitor, in patients with mCRPC associated with HRD. Methods: TRITON2 (NCT02952534) is a phase 2 study evaluating rucaparib 600 mg BID in patients with mCRPC. Patients with a deleterious germline or somatic BRCA1, BRCA2 or ATM mutation (per prior local test or central test during screening) will be enrolled into 1 of 2 cohorts based on the presence or absence of measurable visceral and/or nodal disease. An exploratory cohort will enroll patients with an alteration in any of 12 other prespecified HR genes (eg, RAD51C, RAD51D and PALB2), with or without measurable visceral and/or nodal disease. Patients must have progressed on androgen receptor signaling–directed therapy and 1 prior taxane-based chemotherapy for mCRPC. Patients who received prior treatment with a PARPi, mitoxantrone, cyclophosphamide or platinum-based chemotherapy are excluded. The primary endpoint is objective response rate measured using modified RECIST v1.1/PCWG3 for patients with soft-tissue disease and prostate-specific antigen response for patients with nonmeasurable disease. Secondary endpoints include duration of response, radiographic progression-free survival, overall survival, clinical benefit rate and safety. Pretreatment blood samples collected from all patients will enable development of a plasma-based companion diagnostic to select patients who may benefit from rucaparib treatment. Patients (≈160) will be enrolled at &gt; 100 sites worldwide. Clinical trial information: NCT02952534.