Mutations In Homologous Recombination Genes Research Articles

Mutations in homologous recombination genes and response to treatment in GOG 218: An NRG Oncology study

Mutations in homologous recombination genes and response to treatment in GOG 218: An NRG Oncology study

Germline and somatic homologous recombination gene mutations in high-grade serous ovarian cancer and clinical outcome.

5579Background: Mutations in homologous recombination (HR) genes other than BRCA1/2 genes have been reported to cause a BRCA-like phenotype in up to 50% of HGSOC. PARP inhibitors (PARPi) are effect...

Abstract A12: Mutations in homologous recombination genes and response to treatment in GOG 218: An NRG Oncology Study.

Abstract Objective: Bevacizumab is an anti-vascular endothelial growth factor monoclonal antibody with activity in ovarian cancer. GOG 218 was a phase III, randomized trial in advanced primary ovarian, fallopian tube, and peritoneal carcinoma (collectively, OC), examining the role of adding bevacizumab to a regimen of q21 day carboplatin and paclitaxel. Our objective was to examine whether mutations in homologous recombination (HR) genes affect response to treatment. Methods: We sequenced germline (from blood) and/or somatic (from neoplastic tissue) DNA from 1195 women enrolled in GOG 218 using the targeted capture and multiplex sequencing assay BROCA-HR, focusing on 16 DNA repair genes. Defects in HR were defined as germline or somatic mutations in genes predicted to affect HR, including BRCA1, BRCA2, and others. Proportional hazards models were used to provide estimates of relative hazards for progression free survival (PFS) and overall survival (OS) adjusted for clinical characteristics. Results: Of 1195 women with OC, germline or somatic mutations were identified in 147 (12.3%) in BRCA1, 78 (6.5%) in BRCA2, and 81 (6.8%) in other, non-BRCA HR genes. Total mutation frequency (all genes combined) in those with high-grade serous histology was 26.9% (261/971), but this was not significantly higher than the mutation frequency in endometrioid histology (10/42, 23.8%), clear cell histology (6/28, 21.4%), or unspecified carcinoma (20/90, 22.2%). Mutation frequency also did not differ by disease site. Median PFS and OS by group were as follows: BRCA1: 15.6 and 53.7 months, BRCA2: 21.6 and 75.2 months, non-BRCA HR: 16 and 56 months, and no mutation: 12.6 and 42 months. Adjusting for study treatment, stage, residual disease, and initial performance status, hazards for progression and death compared to those without mutations were significantly lower for those with mutations, specifically with BRCA1 mutations (hazard ratio (HR) 0.80, 95% CI 0.66 – 0.97, p=0.02 for PFS; HR 0.75, 95% CI 0.60 – 0.95, p=0.02 for OS), with BRCA2 mutations (HR 0.52, 95% CI 0.40 – 0.67, p<0.0001 for PFS; HR 0.37, 95% CI 0.25 – 0.53, p<0.0001 for OS), and with non-BRCA HR mutations (HR 0.73, 95% CI 0.57 – 0.94, p=0.01 for PFS; HR 0.67, 95% CI 0.50 – 0.90, p=0.007 for OS). The analysis of PFS and OS by mutation status and treatment arm is underway. Conclusions: Women with OC with either germline or somatic mutations affecting HR have significantly longer PFS and OS than those without mutations. Disease site and histology were not predictive of mutation status. The effect of mutation status on response by treatment arm will be reported at presentation. Citation Format: Barbara M. Norquist, Mark F. Brady, Maria I. Harrell, Tom D. Walsh, Ming K. Lee, Suleyman Gulsuner, Sarah S. Bernards, Silvia Casadei, Robert A. Burger, Susan A. Davidson, Robert S. Mannel, Paul A. DiSilvestro, Heather A. Lankes, Nilsa C. Ramirez, Mary Claire King, Michael J. Birrer, Elizabeth M. Swisher. Mutations in homologous recombination genes and response to treatment in GOG 218: An NRG Oncology Study. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A12.

Abstract A07: Homologous recombination mutations and overall survival in high-grade serous, endometrioid, and clear cell ovarian carcinomas.

Abstract Background: Defects in homologous recombination (HR) DNA repair are common in high grade serous ovarian, peritoneal and fallopian tube carcinoma (HGSOC). Other than mutations in BRCA1 and BRCA2 (BRCA1/2), the molecular causes of HR deficiency have not been well delineated. The frequency of HR deficiency in non-serous ovarian carcinoma is not known. We previously identified that germline and somatic HR mutations in 13 genes in OC was associated with improved survival. We sought to replicate these data in an independent tumor set, while sequencing a larger number of DNA repair genes. Methods: We used BROCA-HR to sequence 65 DNA repair genes in germline (blood) and tumor DNA from 363 women with ovarian (262), peritoneal (91), or fallopian tube (10) carcinoma from an institutional tissue bank. Cox proportional hazards models, adjusted for stage and residual tumor after cytoreduction, were used to assess associations between mutations in DNA repair genes in HR or related pathways and overall survival from diagnosis. Results: In total, 96/363 (25%) patients had 59 germline and 45 somatic deleterious mutations in HR genes, including 34 germline and 22 somatic BRCA1/2 mutations. Damaging mutations found in other HR genes included 25 germline and 23 somatic in the following genes: 5 ATM, 6 ATR, 1 BAP1, 2 BARD1, 6 BLM, 2 BRIP1, 2 BRE, 1 BRCC3, 2 CHEK2, 1 ERCC1, 1 FANCG, 1 FANCI, 2 FANCL, 8 FANCM, 1 NBN, 2 PALB2, 1 RAD51D, 1 RBBP8, 1 SLX4, 1 UIMC1 and 1 XRCC2. Of 322 HGSOC, HR mutations occurred in 86 patients (26.7%) including 54 (16.8%) germline and 32 somatic (9.9%). HR mutation rates were similar across the different non-serous histologies. Of 13 clear cell OC, 2 (15.3%) had germline mutations in non-BRCA1/2 HR genes and 3 (23.1%) had PTEN/PIK3CA mutations. Of 27 endometrioid OC, 3 (11.1%) had HR mutations (1 germline BRCA1, and 2 non-BRCA1/2 somatic HR mutations). PTEN/PIK3CA mutations were identified in 9 (2.8%) HGSOC, 3 (23.1%) clear cell and 2 (7.5%) endometrioid. HR mutations demonstrated a trend towards improved long-term overall survival (hazard ratio = 0.78, 96% CI 0.57-1.05) after accounting for stage and debulking status. Conclusions: These data not only indicate that damaging HR mutations, both germline and somatic, are found in endometrioid and clear cell as well as HGSOC, but also confirm our previous results showing an association between HR mutations and improved overall survival in OC. We are now sequencing 163 additional non-serous OC to augment the current analysis and these data will be available at presentation. Citation Format: Maria I. Harrell, Matthew J. Maurer, Ethan P. Heinzen, Ming K. Lee, Kimberly R. Kalli, Kathy J. Agnew, Ann L. Oberg, Tom Walsh, Barbara M. Norquist, Lynn C. Hartmann, Scott H. Kaufmann, Elizabeth M. Swisher. Homologous recombination mutations and overall survival in high-grade serous, endometrioid, and clear cell ovarian carcinomas. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A07.

Abstract 4251: Paclitaxel is necessary for improved survival in epithelial ovarian cancers with somatic homologous recombination gene mutations

Abstract The impact of somatic mutations and genomic alterations in determining the clinical outcome of sporadic epithelial ovarian cancer (EOC) remains uncertain. Our goal was to identify molecular markers of optimal cytoreduction, chemotherapeutic response, and survival. We focused on genes in the homologous recombination (HR) DNA repair pathway, as germline mutations in these genes confer improved survival, and data suggest that somatic mutations may similarly predict improved survival and chemosensitivity. One hundred fifty-eight patients were included with diagnoses of serous, endometrioid, or clear cell EOC and underwent primary cytoreduction followed by platinum-based chemotherapy. We performed targeted massively parallel sequencing of 53 genes in known genes from pathways such as HR and checkpoint inhibition in primary surgical samples. Patients were treated with platinum and cyclophosphamide (n = 24) or platinum and paclitaxel (n = 67). We detected 226 deleterious variants in 35 distinct genes. TP53 mutations were found in tumors from 90 subjects (56%) and deleterious mutations in HR genes in 45 (28%). Twenty-three patient tumors (15%) were found to have homozygous copy number loss of genes in the HR pathway. We did not detect an overall survival (OS) benefit in advanced stage patients treated with platinum whose tumors had HR mutations/loss as compared to those without HR defects. However, OS was significantly different between patients (p = 0.0028) whose tumors had HR mutations/loss if they received cyclophosphamide (median 24.1 months) as compared to paclitaxel (median 50.4 months). Furthermore, in patients with both TP53 and HR gene mutations or deletions, median OS improved to 76.6 months in the platinum and paclitaxel treated cohort (p = 0.0001). In this analysis by chemotherapy regimen and mutation status, the patients with TP53 and HR mutation/loss demonstrated worse median OS than those without such defects when treated with platinum and cyclophosphamide (24.1 months vs. 32.7 months respectively), but improved survival over patients without TP53 and HR defects when treated with platinum and paclitaxel (76.6 months vs. 44.4 months respectively, p = 0.0100). We also found that a somatic HR mutation was significantly associated with suboptimal debulking status (p = 0.012). Chances for optimal debulking and early stage were significantly increased in patients with PTEN mutations (p = 0.042), leading to OS benefit. The survival benefit attributed to platinum agents in HR deficient ovarian cancers may depend upon the use of paclitaxel in addition to platinum. This merits elucidation of the mechanism, and may be due to the mitosis cell cycle specificity of paclitaxel, and ensuing inhibition of HR deficient genomically unstable tumor subclones. Citation Format: Stephanie Jean, Bradley Wubbenhorst, Jiaqi Li, Kara N. Maxwell, Lauren Fishbein, Michael W. McLane, Nandita Mitra, Lin Zhang, Katherine L. Nathanson, Janos L. Tanyi. Paclitaxel is necessary for improved survival in epithelial ovarian cancers with somatic homologous recombination gene mutations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4251. doi:10.1158/1538-7445.AM2015-4251

Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins.

Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks in mammalian cells, the defining step of which is homologous strand exchange directed by the RAD51 protein. The physiological importance of HR is underscored by the observation of genomic instability in HR-deficient cells and, importantly, the association of cancer predisposition and developmental defects with mutations in HR genes. The tumor suppressors BRCA1 and BRCA2, key players at different stages of HR, are frequently mutated in familial breast and ovarian cancers. Other HR proteins, including PALB2 and RAD51 paralogs, have also been identified as tumor suppressors. This review summarizes recent findings on BRCA1, BRCA2, and associated proteins involved in human disease with an emphasis on their molecular roles and interactions.

BRCA2 and RAD51 promote double-strand break formation and cell death in response to gemcitabine.

Replication inhibitors cause replication fork stalling and double-strand breaks (DSB) that result from processing of stalled forks. During recovery from replication blocks, the homologous recombination (HR) factor RAD51 mediates fork restart and DSB repair. HR defects therefore sensitize cells to replication inhibitors, with clear implications for cancer therapy. Gemcitabine is a potent replication inhibitor used to treat cancers with mutations in HR genes such as BRCA2. Here, we investigate why, paradoxically, mutations in HR genes protect cells from killing by gemcitabine. Using DNA replication and DNA damage assays in mammalian cells, we show that even short gemcitabine treatments cause persistent replication inhibition. BRCA2 and RAD51 are recruited to chromatin early after removal of the drug, actively inhibit replication fork progression, and promote the formation of MUS81- and XPF-dependent DSBs that remain unrepaired. Our data suggest that HR intermediates formed at gemcitabine-stalled forks are converted into DSBs and thus contribute to gemcitabine-induced cell death, which could have implications for the treatment response of HR-deficient tumors.

Germline and Somatic Mutations in Homologous Recombination Genes Predict Platinum Response and Survival in Ovarian, Fallopian Tube, and Peritoneal Carcinomas

Hallmarks of germline BRCA1/2-associated ovarian carcinomas include chemosensitivity and improved survival. The therapeutic impact of somatic BRCA1/2 mutations and mutations in other homologous recombination DNA repair genes is uncertain. Using targeted capture and massively parallel genomic sequencing, we assessed 390 ovarian carcinomas for germline and somatic loss-of-function mutations in 30 genes, including BRCA1, BRCA2, and 11 other genes in the homologous recombination pathway. Thirty-one percent of ovarian carcinomas had a deleterious germline (24%) and/or somatic (9%) mutation in one or more of the 13 homologous recombination genes: BRCA1, BRCA2, ATM, BARD1, BRIP1, CHEK1, CHEK2, FAM175A, MRE11A, NBN, PALB2, RAD51C, and RAD51D. Nonserous ovarian carcinomas had similar rates of homologous recombination mutations to serous carcinomas (28% vs. 31%, P = 0.6), including clear cell, endometrioid, and carcinosarcoma. The presence of germline and somatic homologous recombination mutations was highly predictive of primary platinum sensitivity (P = 0.0002) and improved overall survival (P = 0.0006), with a median overall survival of 66 months in germline homologous recombination mutation carriers, 59 months in cases with a somatic homologous recombination mutation, and 41 months for cases without a homologous recombination mutation. Germline or somatic mutations in homologous recombination genes are present in almost one third of ovarian carcinomas, including both serous and nonserous histologies. Somatic BRCA1/2 mutations and mutations in other homologous recombination genes have a similar positive impact on overall survival and platinum responsiveness as germline BRCA1/2 mutations. The similar rate of homologous recombination mutations in nonserous carcinomas supports their inclusion in PARP inhibitor clinical trials.

Germline and somatic mutations in homologous recombination genes predict platinum response and improved overall survival in ovarian, fallopian tube, and peritoneal carcinomas

Germline and somatic mutations in homologous recombination genes predict platinum response and improved overall survival in ovarian, fallopian tube, and peritoneal carcinomas

Germline and somatic mutations in homologous recombination genes predict platinum response in ovarian, fallopian tube, and peritoneal carcinomas

Germline and somatic mutations in homologous recombination genes predict platinum response in ovarian, fallopian tube, and peritoneal carcinomas

A Genetic Screen for top3 Suppressors in Saccharomyces cerevisiae Identifies SHU1, SHU2, PSY3 and CSM2

Helicases of the RecQ family and topoisomerase III are evolutionarily conserved proteins important for maintenance of genome stability. In Saccharomyces cerevisiae, loss of the TOP3 gene, encoding topoisomerase III, results in a phenotype of slow growth, DNA damage sensitivity, meiotic defects, and hyperrecombination. The sole RecQ helicase in budding yeast, Sgs1, interacts with Top3 both physically and genetically, and the two proteins are thought to act in concert in vivo. Much recent genetic and biochemical evidence points to the role of RecQ helicases and topoisomerase III in regulating homologous recombination (HR) during DNA replication. Previously, we found that mutations in HR genes partially suppress top3 slow growth. Here, we describe the analysis of four additional mutational suppressors of top3 defects: shu1, shu2, psy3, and csm2. These genes belong to one epistasis group and their protein products interact with each other, strongly suggesting that they function as a complex in vivo. Their mutant phenotype indicates that they are important for error-free repair of spontaneous and induced DNA lesions, protecting the genome from mutation. These mutants exhibit an epistatic relationship with rad52 and show altered dynamics of Rad52-YFP foci, suggesting a role for these proteins in recombinational repair.