Homologous Recombination Mutations Research Articles

Somatic mutations in four novel genes contribute to homologous recombination deficiency in breast cancer: a real-world clinical tumor sequencing study.

Breast cancers involving mutations in homologous recombination (HR) genes, most commonly BRCA1 and BRCA2 (BRCA1/2), respond well to PARP inhibitors and platinum-based chemotherapy. However, except for these specific HR genes, it is not clear which other mutations contribute to homologous recombination defects (HRD). Here, we performed next-generation sequencing of tumor tissues and matched blood samples from 119 breast cancer patients using the OncoScreen Plus panel. Genomic mutation characteristics and HRD scores were analyzed. In the HR genes, we found that BRCA1/2 and PLAB2 mutations were related to HRD. HRD was also detected in a subset of patients without germline or somatic mutations in BRCA1/2, PLAB2, or other HR-related genes. Notably, LRP1B, NOTCH3, GATA2, and CARD11 (abbreviated as LNGC) mutations were associated with high HRD scores in breast cancer patients. Furthermore, functional experiments demonstrated that silencing CARD11 and GATA2 impairs HR repair efficiency and enhances the sensitivity of tumor cells to olaparib treatment. In summary, in the absence of mutations in the HR genes, the sensitivity of tumor cells to PARP inhibitors and platinum-based chemotherapy may be enhanced in a subset of breast cancer patients with LNGC somatic mutations.

Abstract 1317 Characterization of cytoplasmic, mitochondrial, and peroxisomal malate dehydrogenase via missense single nucleotide mutations and homologous recombination mutations in the budding yeast Saccharomyces cerevisiae

Abstract 1317 Characterization of cytoplasmic, mitochondrial, and peroxisomal malate dehydrogenase via missense single nucleotide mutations and homologous recombination mutations in the budding yeast Saccharomyces cerevisiae

Abstract C064: Chronic platinum exposure induces cell-intrinsic type1 interferon/STING pathway activation in homologous recombination-deficient pancreatic cancer to drive sensitivity to checkpoint immunotherapy

Abstract Background: Although platinum-based chemotherapy is standard treatment for pancreatic ductal adenocarcinoma (PDAC) patients with germline/somatic mutations in homologous recombination (mutHRD), a subset become platinum-resistant. We have shown that patients with mutHRD PDAC progressing on platinum chemotherapy respond to dual immune checkpoint blockade (ICB) with anti-PD1+CTLA-4. We sought to model these clinical findings in preclinical models to interrogate mechanisms in platinum-resistant mutHRD PDAC that drive ICB sensitivity. Methods: We examined the association between objective disease response following anti-PD1+CTLA-4 ICB and duration of platinum chemotherapy exposure in platinum-resistant mutHRD PDAC patients. Cisplatin- resistant and sensitive Brca2-silenced (via shRNA knockdown) KPC cancer cells were generated and characterized in vitro and in vivo. Results: In 12 mutHRD PDAC patients treated with salvage dual ICB after progression on platinum-based chemotherapy, 7 (58%) demonstrated either partial response or stable disease. Notably, duration of prior platinum exposure was associated with post-ICB disease response. To model these findings preclinically, syngeneic mice implanted with cisplatin-sensitive or resistant shBrca2 or wildtype KPC tumor cells and subsequently treated with gemcitabine+cisplatin chemotherapy demonstrated expected rapid tumor growth of cisplatin-resistant shBrca2 tumors. However, we observed a profound reduction in tumor volumes when these chronically cisplatin-resistant KPC-shBrca2 tumors were subsequently treated with anti-PD-1+CTLA4 ICB, compared to wildtype-KPC or cisplatin-sensitive KPC-shBrca2 tumors (P<0.001). To understand mechanistic underpinnings of these observations, whole transcriptome sequencing revealed significant differential upregulation of type1 interferon and cGAS-STING pathways in cisplatin-resistant KPC-shBrca2 tumor cells compared to wildtype-KPC or cisplatin-sensitive KPC-shBrca2 controls (P-adj≤0.05). Confocal immunofluorescence imaging confirmed constitutively upregulated cGAS and STING expression in cisplatin-resistant KPC-shBrca2 compared to wildtype-KPC or cisplatin-sensitive KPC-shBrca2 tumor cells. Activation of type1 interferon/STING manifested in a secretome enriched for T-cell trafficking cytokines CXCL10, CXCL9, and CCL5 from cisplatin-resistant KPC-shBrca2 cells. Intriguingly, evaluable mutHRD patient tumors responsive to dual ICB also demonstrated baseline increase in CXCL9/10 and CCL5 expression compared with ICB-resistant mutHRD tumors (n=3 each) via Nanostring analysis. As such, we observed increased transwell (in vitro) and intratumoral (in vivo) CD8+ T-cell trafficking to cisplatin-resistant KPC-shBrca2 tumors compared with cisplatin-sensitive KPC-shBrca2 controls. Conclusions: Chronicity of platinum exposure in mutHRD PDAC potentiates ICB sensitivity via induction of cell-autonomous type-1 interferon/cGAS-STING signaling and ensuing T-cell trafficking to the PDAC tumor microenvironment. Citation Format: Ifeanyichukwu Ogobuiro, Anna Bianchi, Lucas Caeiro, Haleh Amirian, Luis Nivelo, Iago De Castro Silva, Karthik Rajkumar, Andrew Adams, Vanessa Garrido, Samara Singh, Nagaraj Nagathihalli, Nipun Merchant, Ramiro Verdun, Peter Hosein, Jashodeep Datta. Chronic platinum exposure induces cell-intrinsic type1 interferon/STING pathway activation in homologous recombination-deficient pancreatic cancer to drive sensitivity to checkpoint immunotherapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C064.

Abstract A015: 53BP1 loss mediated PARP inhibitor resistance in BRCA1-deficient pancreatic cancer is overcome with immune checkpoint blockade

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer characterized by the presence of mutations in homologous recombination (HR) repair genes, including BRCA1 and BRCA2, in approximately 20% of diagnosed cases. 53BP1 (tumor protein p53 binding protein 1) nucleates the anti-end resection machinery at DNA double strand break (DSB)s thereby countering BRCA1 activity. Importantly, BRCA1-deficient PDACs that are typically sensitive to poly-ADP ribose polymerase inhibitors (PARPi) become resistant in the absence of 53BP1. Here, we demonstrate that loss of 53BP1 results in enhanced DNA end-resection, increased micronuclei, and cytoplasmic dsDNA, leading to activation of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, activating pro-inflammatory signaling. This not only enhances CD8+ T cell infiltration but also activates macrophages and natural killer (NK) cells culminating in tumor growth inhibition. Loss of 53BP1 correlates with response to immune checkpoint blockade (ICB) and improved overall survival. Finally, BRCA1-deficient tumors that develop resistance to PARPi due to the loss of 53BP1 are susceptible to ICB. Taken together, our findings provide a rationale for combining PARPi with ICB to overcome PARPi-resistance in BRCA1-deficient pancreatic cancers. Citation Format: Jeffrey Patterson-Fortin, Yajie Sun, Sen Han, Zhe Li, Zuzanna Nowicka, Yuna Hirohashi, Susan Kilgas, Jae Kyo Yi, Alexander Spektor, Wojciech Fendler, Panagiotis Konstantinopoulos, Alan D. D'Andrea, Dipanjan Chowdhury. 53BP1 loss mediated PARP inhibitor resistance in BRCA1-deficient pancreatic cancer is overcome with immune checkpoint blockade [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A015.

Abstract B147: The relationship between germline variants and clinicopathological characteristics in triple negative breast cancer patients from Colombia

Abstract Introduction: Triple-negative breast cancer (TNBC) is the molecular subtype with the worst prognosis among breast tumors. It has been shown that the presence of germline variants can influence disease onset, progression, tumor biology, and other outcomes, however, to this date, the differences in clinical-pathological features according to germline variants in an admixed population like Colombian women, have not been yet explored. Therefore, the aim of this study was to explore the relationship between clinical-pathological characteristics and germline mutations in TNBC patients from Colombia. Methodology: This is a descriptive analysis that included 47 Colombian women with confirmed diagnosis of hereditary TNBC treated at the National Cancer Institute of Colombia, from 2008 to 2022. Germline mutations in 105 genes were assessed using the TruSigth multi-gene panel, and patients were divided according to the identified mutation into the following groups: BRCA1 carriers (n=18), BRCA2 carriers (n=13), homologous recombination (HR) gene carriers (n=13), and carriers of mutations in other genes (n=3). Fisher’s and Pearson’s chi-squared tests were used for categorical variables, and differences were considered statistically significant if p<0.05. Results: Among our cohort, the identified mutation with the highest prevalence was the c.5123C>A p. (Ala1708Glu) in the BRCA1 gene (36,9%). Regarding clinical-pathological features, we observed statistically significant differences in the distribution of germline mutations by age at diagnosis (p=0.042), body mass index (BMI) (p=0.04), and tumor differentiation (p=0.01). Women younger than 50 years at diagnosis had the highest frequency of BRCA1 (23,9%) mutations. Overweight (BMI: 25-30) and obese (BMI>30) patients presented a higher proportion of mutations in the BRCA1 (15,2%) and BRCA2 (13,0%) genes, compared to patients with mutations in HR repair pathways (8,6%) and mutations in other genes (2,2%). This is interesting as previous reports have shown an association between BRCA1/2 mutations with BMI and chronic inflammation, which could influence the development and progression of breast cancer. Poorly differentiated tumors (Bloom-Richardson: III) were more frequently observed in patients with BRCA1 mutations (32,6%), followed by patients with mutations in the HR genes (17,4%). It is possible that this is related to the genetic changes that germline mutations induce within the tumor, which ultimately lead to a less differentiated disease. Conclusion: Our study confirms the greater proportion of mutations in BRCA1/2 genes in TNBCs among the Colombian population. The characterization of clinical-pathological characteristics of germline mutation-related tumors may help improve diagnosis, prognosis assessment, and targeted therapeutic approaches. Further studies with larger patient cohorts are needed to confirm our findings. Additionally, large-scale studies are also warranted to elucidate the landscape of germline mutations relevant to the Colombian population, along with its clinical implications. Citation Format: Yina Tatiana Zambrano Ordonez, Laura Rey Vargas, Paula Daniela Morales, Silvia Juliana Serrano. The relationship between germline variants and clinicopathological characteristics in triple negative breast cancer patients from Colombia [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr B147.

Phase II study of niraparib in patients with advanced melanoma with genetic homologous recombination (HR) mutation/alteration.

TPS9596 Background: There are a limited number of therapeutic options available for metastatic melanoma patients progressing on the checkpoint inhibitor(s) and BRAF-targeting drugs. PARP inhibitors have been approved in the setting of BRCA1/2 germline mutations, and have demonstrated activity in the setting of HR deficiency in other cancers. Documentation of PARP inhibitors in melanoma would have clear clinical impact. We have previously shown that 21-34% of metastatic melanomas harbor at least 1 molecular aberration in the HR pathway, considered pathogenic, and likely leading to HR deficiency. Previously, we demonstrated dramatic regression of tumors harboring HR mutation(s) with PARP inhibitor treatment in a PDX model. These findings provide a strong rationale to evaluate the clinical efficacy of a PARP inhibitor in patients with advanced melanoma with HR deficiency. Methods: This is a single arm, open-label, multi-center phase II trial. The primary objective of the study is: To evaluate the clinical efficacy of niraparib in advanced melanoma patients with HR deficiency. The secondary objectives is to evaluate PFS, OS, and safety profile of niraparib. The key eligibility criteria: Advanced melanoma patients with mutation in any of the following: ARID1A/B, ARID2, ATM, ATR, ATRX, BARD1, BRCA1/2, BAP1, BRIP1, CHEK2, FANCD2, MRN11A, RAD50, RAD51, RAD54B, PALB2 (requires a genetic analysis result performed at any CLIA-certified laboratory) disease progression on PD1-antibody therapy and if BRAF mutant, BRAF/MEK inhibitors ≥ 18 years of age; ECOG PS ≤ 1; prior systemic cytotoxic therapy ≤1 regimen; no limit on number of prior immunotherapy or targeted therapy regimens. No symptomatic brain metastasis; active brain lesions ≥6 mm size, or requiring steroid treatment Patients will be treated with oral niraparib once daily (28-day cycle); the dose will be 300 mg (if weight ≥77 kg and platelet counts of ≥150,000 µL); otherwise 200 mg RECIST 1.1 will be used to evaluate clinical response every 8 weeks. Adverse events will be recorded according to CTCAE version 4.03. The primary study endpoint is overall response rate. Simon’s optimal 2-stage design is proposed. With significance level of5% and 80% power, our null hypothesis that the true response rate is 0.10 will be tested against a one-sided alternative: H0: p ≤ 10%, a response rate of no real interest VS H1: p ≥ 30%, a response rate that would be of considerable interest 10 patients will be analyzed for a response evaluation in the first stage of the study, and 19 in the second stage, for a total of 29 patients. If the response rate is 10% (1/10) or less at the end of the first stage, further accrual will be terminated. With 2 or more responses in the first stage, accrual will continue to a total of 29 patients for this cohort. The null hypothesis will be rejected if ≥6 responses are observed in a cohort of 29 subjects. Clinical trial information: NCT03925350 .

Correlation of homologous recombination deficiency (HRD) score with response to the first-line treatment of immune checkpoint inhibitors plus chemotherapy in non-small cell lung cancer.

e21121 Background: Homologous recombination (HR) gene mutations were reported to be associated with efficiency of immune checkpoint inhibitors (ICIs). However, up to date, no recognized standard has been set up for definition of HR mutation (+), which limited its clinical application. Homologous recombination deficiency (HRD) score reflects genomic scar induced by HR genes alteration and disfunction. Thus, it may be worth to explore whether HRD score could predict the efficacy of ICIs-based therapy. Methods: We collected tumor tissues from metastatic non-small cell lung cancer (NSCLC) patients who received first-line treatment of ICIs combined with platinum-based chemotherapy. HRD score testing were carried by BGI genomic scar analysis kit, which calculates the sum of loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), large-scale state transitions (LST) scores, and corrected by ploidy of tumor samples, through next generation sequencing(NGS) data. The association of HRD score and response to ICIs plus chemotherapy were analyzed. Results: 22 EGFR/ALK wild-type metastatic NSCLC patients were included. The average HRD score was 24.57, varying from -26.37 to 92.34. Threshold traversal was performed based on analysis of the progression free survival (PFS) data from the included NSCLC patients. HRD score 31 or more were define as HRD (+). Kaplan-Meier PFS Survival analysis showed prolonged median PFS (mPFS) in HRD (+) versus HRD (-) NSCLC patients (N/A vs. 7.0 ms, Log-rank P = 0.029; HR 0.20, 95%CI 0.04-0.96, likelihood-ratio P = 0.03). The objective response rate (ORR) was 45.5% (5/11) in HRD(+) versus 27.2% (3/11) in HRD(-) patients. In patients with PD-L1 TPS≥1% (22C3), the mPFS was N/A vs. N/A, and the ORR was 75.0% (3/4) vs. 37.5% (3/8), in HRD (+) vs. HRD(-) patients. In patients with PD-L1 TPS < 1% (22C3), the mPFS was 8.5 ms vs.2.0 ms (Log-rank P = 0.0085; HR 0.08, 95%CI 0.01-0.82, likelihood-ratio P = 0.02), and the ORR were 28.6% (2/7) vs. 0%(0/3), in HRD (+) vs. HRD(-) patients. Conclusions: In addition to PD-L1 expression level, HRD score would be a potential promising biomarker for predicting the efficiency of ICIs plus platinum-based chemotherapy in NSCLC patients.

Mutations in Homologous Recombination Genes and Loss of Heterozygosity Status in Advanced-Stage Breast Carcinoma.

Poly (adenosine diphosphate-ribose) polymerase inhibitors (PARPis) have demonstrated antitumor activity in cancers with a homologous recombination deficiency (HRD) and have recently been approved by the FDA for the treatment of germline BRCA1/2-mutation-associated breast cancer. PARPis have also been found to be efficacious in BRCA wild-type (BRCAwt) lesions with high genomic loss of heterozygosity (LOH-high). The goal of this study was to retrospectively investigate the tumor mutations in homologous recombination (HRR) genes and the LOH score in advanced-stage breast carcinomas (BCs). Sixty-three patients were included in our study, 25% of whom had HRR gene mutations in their tumors, including 6% BRCA1/2 and 19% non-BRCA-containing gene mutations. An HRR gene mutation was associated with a triple-negative phenotype. Twenty-eight percent of the patients had an LOH-high score, which, in turn, was associated with a high histological grade, a triple-negative phenotype, and a high tumor mutational burden (TMB). Among the six patients who received PARPi therapy, one had a tumor with a PALB2 mutation other than BRCA and had a clinical partial response. Twenty-two percent of the LOH-low tumors had BRCAwt-HRR gene mutations, compared with 11% of the LOH-high tumors. Comprehensive genomic profiling revealed a subset of breast cancer patients with a BRCAwt-HRR gene mutation that would be missed by an LOH test. The necessity of next-generation sequencing coupled with HRR gene analysis for PARPi therapy requires further investigation in clinical trials.

Abstract P5-02-45: An HRD scoring system based on long-focal copy number alterations predictive of PARP inhibitor response

Abstract Homologous recombination deficiency (HRD) is characterized by a defective double-stranded DNA repair mechanism due to alterations in the homologous recombination (HR) pathway. Deleterious mutations in HR pathway genes can help identify potential responders to platinum-based chemotherapies and PARP inhibitors (PARPi), which promote apoptosis in HRD cells. Until recently, the use of PARPi in breast cancer (BC) was limited to advanced or metastatic disease with pathogenic or likely pathogenic germline BRCA (gBRCA) mutations. However, the use of PARPi has expanded to treat early-stage HER2-negative BC with a high risk of recurrence and gBRCA mutations, HER2-negative BC with somatic BRCA mutations, and triple-negative BC. To date, no universal method for HRD scoring is accepted; therefore, biomarkers are needed to stratify patients into PARPi responders and nonresponders more effectively. Because PARPi are used to treat HRD-driven cancers, we aimed to identify genomic consequences of HRD. For HRD-specific features, we calculated the proportion of long-focal total copy number alterations (LF-tCNA), which estimates amplification events for long-focal segments. Aneuploidy is especially prevalent in medullary, metaplastic, and invasive micropapillary BCs. These copy number variations are not necessarily consequences of HRD but can influence HRD scores. Genome-wide loss of heterozygosity (gwLOH) can be a result of HRD and used as a biomarker for HRD. We developed several scoring methods based on LF-tCNA, gwLOH, and aneuploidy scores. These scores were tested as predictors of HRD, defined as known loss-of-function germline mutations in BRCA1, BRCA2, PALB2, or BARD1 (TCGA-BRCA cohort, n = 1,032). To calculate the optimal HRD score, we used multivariate logistic regression analysis with HRD as an outcome and LF-tCNA, LOH, and ploidy as predictors. Based on the results of logistic regression, LF-tCNA and ploidy were selected to calculate HRD status. The positive and negative predictive values (PPV, NPV) were used to set the upper and lower thresholds, respectively. Samples with HRD scores above 7 (PPV) have the greatest potential for PARPi and platinum-based therapy response, while scores below -1 (NPV) were considered HRD wild type (WT). To validate the developed HRD score, we tested the score by combining BC cohorts (MSK_NCI and MET500 cohorts, n = 164) and used gBRCA1/2 pathogenic mutations as an outcome. Our HRD scoring system distinguished HRD WT from HRD-positive samples (AUC = 0.81) more effectively than a previously reported score based on LOH, telomeric-allelic imbalance (TAI), and large-scale state transitions (LST) (AUC = 0.72). We tested our HRD scoring system across tumor microenvironment molecular subtypes. The median HRD score in the basal-like subtype was increased compared to other subtypes, supporting the prevalence of gBRCA1/2 pathogenic mutations in this subtype. Moreover, the number of HRD-positive patients and the percent positive agreement, defined as the proportion of positive test results from our HRD also positive for HR mutations, were calculated for each BC subtype. Only 22% of basal-like HRD-positive samples also carried germline HR pathway mutations, which indicates 78% of HRD-positive patients who might benefit from PARPi or platinum treatment would have been missed by germline HR gene panels. This BC HRD scoring method is a promising tool for identifying HRD patients who may respond to PAPRi and platinum-based therapies, but additional studies are required for clinical validation. Citation Format: Maria Gurileva, Nikita Kotlov, Anna Love, Alexandra Melnikova, Krystle Nomie, Nathan Fowler, Alexander Bagaev. An HRD scoring system based on long-focal copy number alterations predictive of PARP inhibitor response [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-45.

Real-World Efficacy and Safety of PARP Inhibitors in Recurrent Ovarian Cancer Patients With Somatic BRCA and Other Homologous Recombination Gene Mutations.

Real-world data regarding the use of poly (ADP-ribose) polymerase (PARP) inhibitors in recurrent ovarian cancer patients with non-BRCA homologous recombination (HR) mutations or somatic BRCA mutations are lacking. The purpose of our study is to evaluate the response rate, duration of treatment, time to progression (TTP), and toxicities of olaparib, niraparib, and rucaparib in somatic BRCAm and non-BRCA HR-mutated patients. This was a retrospective study using the electronic medical record to identify patients across our health system who were initiated on a PARP inhibitor for ovarian cancer between December 2014 and December 2019. Patients were screened for the presence of a somatic BRCA1/2 mutation or a mutation in non-BRCA HR genes. Data were collected via chart review. For the efficacy analysis, 8 patients had somatic BRCA mutations and 12 patients had HR mutations. The overall response rate (ORR) was 50% for BRCA-mutated (BRCAm) patients and 9.1% for non-BRCA HR-mutated (non-BRCA HRm) patients. 72.7% of patients with non-BRCA HR mutations had stable disease. The duration of therapy ranged from 2 to 66 months. The median TTP was 9.5 months. Overall, 66.7% of patients in the entire cohort started on a reduced dose of PARP inhibitor. Dose reductions due to AEs were observed in 52.4% of patients, while AEs requiring treatment interruption occurred in 61.9%. We found that PARP inhibitors provided stable disease in a high proportion of recurrent ovarian cancer patients who had pathogenic HR mutations, with toxicities comparable to major trials. Patients with non-BRCA HR and somatic BRCA mutations could benefit from PARP inhibitors.

Efficacy of chemotherapy according to BRCA status in patients with high-grade serous ovarian carcinoma at first platinum-sensitive relapse

ObjectiveChemotherapy for high-grade serous ovarian cancers in platinum-sensitive relapse includes carboplatin/paclitaxel, carboplatin/gemcitabine, and carboplatin/pegylated liposomal doxorubicin. According to in vitro data, BRCA mutated patients are sensitive to replicative stress agents...

Abstract B065: Polymerase theta inhibition activates the cGAS-STING signaling pathway and elicits an immune response in homologous recombination-deficient pancreatic adenocarcinoma

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy that harbors mutations in homologous recombination (HR) repair genes in up to 25% of cases. Defects in HR impart to tumor cells a specific vulnerability to poly-ADP ribose polymerase inhibitors and platinum-based chemotherapy. However, not all patients respond, and some who initially respond develop resistance and progress. Thus, new therapies that are effective against HR-deficient PDAC are needed. Here, we show that inactivation of the HR pathway in PDAC is associated with overexpression of polymerase theta (Polθ, or POLQ), a key enzyme that regulates the alternative non-homologous end-joining (alt-NHEJ) pathway of double-strand break (DSB) DNA repair. Using both human and murine HR-deficient PDAC models, we find that POLQ knockdown is synthetically lethal with mutations in HR genes (BRCA1, BRCA2, and PALB2) as well as the DNA damage repair gene ATM. Further, we present the first findings that POLQ knockdown enhances cytosolic micronucleus formation and activates cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling. In an in vivo murine model, POLQ inhibition also leads to STING-dependent recruitment of immune cells and enhanced CD8+ T cell infiltration in the BRCA2-deficient tumor microenvironment (TME). Through its role in the alt-NHEJ pathway, we thus find that POLQ is critical for DSB repair in HR-deficient PDAC, and its inhibition presents a novel synthetic lethal approach to suppress tumor growth while simultaneously stimulating an immune response in the PDAC TME. Citation Format: Grace Oh, Annie Wang, Lidong Wang, Jiufeng Li, Gregor Werba, Daniel Weissinger, Ende Zhao, Surajit Dhara, Rosmel Hernandez, Amanda Ackermann, Despoina Kalfakakou, Emily A. Kawaler, Talia Golan, Theodore H. Welling, Agnel Sfeir, Diane M. Simeone. Polymerase theta inhibition activates the cGAS-STING signaling pathway and elicits an immune response in homologous recombination-deficient pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B065.

Clinicogenomic characteristics and synthetic lethal implications of germline homologous recombination-deficient hepatocellular carcinoma.

We performed an in-depth examination of pathogenic germline variants (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts. We used a merged whole-exome or RNA sequencing data set derived from in-house ( n = 230) and The Cancer Genome Atlas ( n = 362) databases of multiethnic HCC samples. We also evaluated synthetic lethal approaches targeting mutations in homologous recombination (HR) genes using HCC cells selected from five genomic databases of cancer cell lines. A total of 110 PGVs in DDR pathways in 96 patients were selected. Of the PGV carriers, 44 were HR-altered and found to be independently associated with poorer disease-free survival after hepatectomy. The most frequently altered HR gene in both germline and somatic tissues was POLQ , and this variant was detected in 22.7% (10/44) and 23.8% (5/21) of all the corresponding carriers, respectively. PGVs in HR were significantly associated with upregulation of proliferation and replication-related genes and familial risk of HCC. Samples harboring PGVs in HR with loss of heterozygosity were most strongly correlated with the genomic footprints of deficient HR, such as mutation burden and denovoSig2 (analogous to Catalogue of Somatic Mutations in Cancer [COSMIC] 3), and poor outcome. Pharmacologic experiments with HCC cells defective in BRCA2 or POLQ suggested that tumors with this phenotype are synthetic lethal with poly(ADP-ribose) polymerase inhibitors. Our findings suggest that germline HR defects in HCC tend to confer a poor prognosis and result in distinctive genomic scarring. Tests of the clinical benefits of HR-directed treatments in the affected patients are needed.

A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes

Talazoparib, a PARP inhibitor, is active in germline BRCA1 and BRCA2 (gBRCA1/2)-mutant advanced breast cancer, but its activity beyond gBRCA1/2 is poorly understood. We conducted Talazoparib Beyond BRCA (NCT02401347), an open-label phase II trial, to evaluate talazoparib in patients with pretreated advanced HER2-negative breast cancer (n = 13) or other solid tumors (n = 7) with mutations in homologous recombination (HR) pathway genes other than BRCA1 and BRCA2. In patients with breast cancer, four patients had a Response Evaluation Criteria in Solid Tumors (RECIST) partial response (overall response rate, 31%), and three additional patients had stable disease of ≥6 months (clinical benefit rate, 54%). All patients with germline mutations in PALB2(gPALB2; encoding partner and localizer of BRCA2) had treatment-associated tumor regression. Tumor or plasma circulating tumor DNA (ctDNA) HR deficiency (HRD) scores were correlated with treatment outcomes and were increased in all gPALB2 tumors. In addition, a gPALB2-associated mutational signature was associated with tumor response. Thus, talazoparib has been demonstrated to have efficacy in patients with advanced breast cancer who have gPALB2 mutations, showing activity in the context of HR pathway gene mutations beyond gBRCA1/2.

MCL-319 LP-284 - A Highly Potent Small Molecule Targeting Mantle Cell Lymphoma.

Mantle cell lymphoma (MCL) is a rare and aggressive form of B-cell non-Hodgkin lymphoma (NHL). Approximately 40%-50% of MCL patients carry inactivating mutations in the gene ataxia telangiectasia mutated (ATM), a core component of the cell's DNA damage response system. MCL cells with mutations in ATM are known to have increased chromosomal imbalance, copy number loss, and hypersensitivity to DNA-damaging agents. LP-184, a small-molecule DNA-damaging agent, is known to be synthetically lethal in tumors with DNA-repair deficiencies, including tumors with ATM mutations. However, DNA damage by LP-184 is dependent on activation by the oxidoreductase prostaglandin reductase 1 (PTGR1), which is expressed at low levels in many hematological cancers. We synthesized LP-284, an enantiomer of LP-184, which retains synthetic lethality in cancers with impaired DNA damage repair pathway genes (e.g., ERCC1, ERCC2, ERCC3, ERCC6), but LP-284's activity is independent of PTGR1 expression. We demonstrated that LP-284 has enhanced tumoricidal activity in multiple hematological cancer cell lines using a B-cell NHL panel. The IC50 values for all 6 MCL cell lines treated with LP-284 were among the lowest for all hematological cell lines tested with LP-284. These MCL cell lines included cell lines resistant to ibrutinib, zanubrutinib, venetoclax, and bortezomib. Additionally, among the 6 MCL cell lines tested, the 3 cell lines with mutations in the nucleotide excision repair (NER) or homologous recombination (HR) DNA damage repair pathways had lower LP-284 IC50 values than the 3 cell lines without NER or HR mutations. Because ATM orchestrates the activities of the NER and HR pathways, MCL patients with ATM deficiencies are likely to have better responses to LP-284 treatment. Collectively, these data indicate that LP-284 is a promising preclinical DNA-damaging agent that possesses nanomolar-range anti-tumor activities in multiple and diverse MCL cell lines, with the potential to treat MCL patients who are resistant to other therapies.

Homologous recombination–deficient mutation cluster in tumor suppressor RAD51C identified by comprehensive analysis of cancer variants

Mutations in homologous recombination (HR) genes, including BRCA1, BRCA2, and the RAD51 paralog RAD51C, predispose to tumorigenesis and sensitize cancers to DNA-damaging agents and poly(ADP ribose) polymerase inhibitors. However, ∼800 missense variants of unknown significance have been identified for RAD51C alone, impairing cancer risk assessment and therapeutic strategies. Here, we interrogated >50 RAD51C missense variants, finding that mutations in residues conserved with RAD51 strongly predicted HR deficiency and disrupted interactions with other RAD51 paralogs. A cluster of mutations was identified in and around the Walker A box that led to impairments in HR, interactions with three other RAD51 paralogs, binding to single-stranded DNA, and ATP hydrolysis. We generated structural models of the two RAD51 paralog complexes containing RAD51C, RAD51B-RAD51C-RAD51D-XRCC2 and RAD51C-XRCC3. Together with our functional and biochemical analyses, the structural models predict ATP binding at the interface of RAD51C interactions with other RAD51 paralogs, similar to interactions between monomers in RAD51 filaments, and explain the failure of RAD51C variants in binding multiple paralogs. Ovarian cancer patients with variants in this cluster showed exceptionally long survival, which may be relevant to the reversion potential of the variants. This comprehensive analysis provides a framework for RAD51C variant classification. Importantly, it also provides insight into the functioning of the RAD51 paralog complexes.

Abstract 798: Comprehensive genomic profiling of tissue and liquid biopsies reveals the landscape of reversion mutations

Abstract Loss of function mutations in homologous recombination (HR) repair genes predispose individuals to cancer due to the genomic instability brought about by the inability to properly repair DNA. These alterations may also identify patients eligible for treatment with poly (ADP-ribose) polymerase (PARP) inhibitors and platinum drugs that exploit synthetic lethality; however, resistance eventually occurs. This resistance is largely the result of reversion mutations, which restore the DNA repair function of mutated HR genes. We employed a computational approach to identify patients with breast, ovarian, pancreas, or prostate cancer who underwent comprehensive genomic profiling (CGP; Foundation Medicine, Inc.) and had reversion mutations in the BRCA1, BRCA2, PALB2, RAD51C, or RAD51D genes. Reversion mutations were identified in six different categories: 1) missense mutations that occur at the same amino acid position as a deleterious alteration, 2) non-frameshift deletion mutations that encompass a deleterious alteration, 3) frameshift mutations that restore the open reading frame of another frameshift mutation, 4) splice-site mutations that occur at the same exon as a deleterious alteration, 5) copy number losses that remove a deleterious alteration, and 6) intragenic deletions that lead to loss of deleterious mutation. Using our computational approach, we identified 483 patients who 1,112 reversion mutation pairs in both solid tissue- and liquid biopsy-derived samples. The most frequently observed category was a non-frameshift deletion of a deleterious mutation. Overall, a greater number of reversion mutations were found in liquid biopsy samples. BRCA2 was the most frequently reverted gene followed by BRCA1, PALB2, RAD51D, and RAD51C. BRCA1-mutated samples had up to six reversion mutations, and for BRCA2, we observed as many as 228 putative reversion pairs in one sample. PALB2, RAD51C, and RAD51D had no more than two reversion mutations. We further examined co-occurring alterations and found correlations with genes in multiple signaling pathways including the MYC signaling pathway, which contained more mutations in reversion-positive samples. Lastly, we explored real-world longitudinal data from reversion-positive samples and found that the presence of a reversion mutation was significantly associated with lower overall survival for breast, ovarian, and prostate cancer patients. In summary, we characterized the landscape of reversion mutations in patients who underwent tissue or liquid biopsy-based CGP during clinical cancer treatment. Our data provide a better perspective for the identification and treatment of cancers involving a reversion mechanism. Citation Format: Shannon T. Bailey, Meijuan Li, James Thornton, Lei Yang, Chenming Cui, Mark Hartman, Garrett Frampton, Brennan Decker, Christine Vietz. Comprehensive genomic profiling of tissue and liquid biopsies reveals the landscape of reversion mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 798.

Homologous recombination pathway alternations in relation to prognosis of MSS/pMMR colorectal cancer patients treated with immune checkpoint inhibitors (ICIs).

e15517 Background: Colorectal cancer is a common malignant tumor in the gastrointestinal tract and represents the third deadliest cancer worldwide. Recently, the advent of immune checkpoint inhibitors (ICIs) has provided significant survival benefit for colorectal cancer(CRC) patients with MSI-H/dMMR. However, the majority of MSS/pMMR CRC patients show poorly durable responses of immunotherapy, and more proper predictive biomarker is required to guiding immunotherapy treatment for these CRC cancer patients. The purpose of the present study was to explore the role of Homologous recombination (HR) pathway alternations in predicting the prognosis of MSS/pMMR CRC patients treated with ICIs. Methods: All data of patients undergoing immunotherapy were obtained from the cBioPortal database (https://www. cbioportal.org), which include genomic sequencing datasets and clinical data for eight diverse cancers from MSKCC, and RNAseq data and clincial data for CRC from International Cancer Genome Consortium (TCGA). Results: In the MSKCC cohort, HR mutation was analyzed by univariate Cox regression in nine different cancers, the analysis performed revealed HR mutation were associated with a better prognosis of colcrectal cancer (p = 0.003; HR, 0.24; 95%Cl, 0.09-0.62) and melanoma (p = 0.042; HR,0.66; 95% Cl, 0.09-0.62), with no significant correlations in other cancers. By doing survival analysis of the CRC patients without MSI-H/dMMR status by Kaplan–Meier (KM) method. The results showed that the OS of the patients with HR-MT was signifcantly longer than that of patients with HR-WT (P = 0.0029), and no significance association has been identified between Tumor Mutational Burden (TMB) and overall prognosis of patients without MSI-H/dMMR. Notably, in TCGA CRC dataset, we found TMB and Neoantigens were significantly higher in HR-MT patients than that of HR-WT patients(p < 0.0001), and a higher-level expression of CD8 T cell were also observed in the HR-MT patients patients in TCGA dataset (p = 0.036). Conclusions: Our study results showed that HR-mutation is a favorable prognostic factor in these CRC patients with MSS/pMMR, which can be used as a potential biomarker for predicting the immunotherapy efficacy of these patients.

Core Homologous Recombination Mutations and Improved Survival in Nonpancreatic GI Cancers.

Homologous recombination mutations (HRM) have led to increased responses to platinum chemotherapy in pancreatic cancer. However, HRMs' role in nonpancreatic gastrointestinal (GI) cancers remains to be determined. Our objective was to evaluate the prognostic and predictive role of core (BRCA1, BRCA2, PALB2) and noncore HRM in nonpancreatic GI cancers receiving platinum therapy. This study performed at Moffitt Cancer Center included metastatic nonpancreatic GI cancer patients treated with platinum therapy. All patients had either a core or noncore HRM, determined by next generation sequencing. Response rates, median progression-free survival (PFS), and median overall survival (OS) were determined and compared between core versus noncore HRM patients. In the study, 69 patients with one or more HRM were included: 63.8% were male, 87.0% were Caucasian, and 47.9% had colorectal cancer. Twenty-one (30.4%) patients had a core HRM and 48 (69.6%) had a noncore HRM. Among evaluable patients (n=64), there was no significant difference in objective response: 20.0% with core HRM versus 22.7% with noncore HRM responded to platinum therapy (P=0.53). Median PFS was 10.4 months versus 7.1 months for core HRM versus noncore HRM, respectively (P=0.039). Median OS was 68.9 months versus 24.3 months (P=0.026) for core HRM versus noncore HRM, respectively. Our study demonstrated response of core and noncore HRM to platinum therapy in metastatic nonpancreatic GI malignancies, suggesting benefit in both groups. Core HRM patients had significantly increased median OS and median PFS compared with those with noncore HRM, suggesting potential prognostic and predictive significance. Larger prospective studies are needed to confirm our findings.

BrUOG360: A phase Ib/II study of copanlisib combined with rucaparib in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC).

128 Background: mCRPC with alterations in genes associated with homologous recombination (HR) DNA repair (e.g., BRCA1/2) is sensitive to poly ADP-ribose polymerase inhibitors (PARPi). Preclinical studies showed that PI3K inhibitors (PI3Ki) impairs HR and sensitize cancer cells to PARPi even in the absence of HR gene mutations. These results support our hypothesis that dual PI3K and PARP inhibition may improve clinical outcomes in progressive mCRPC. We describe preliminary results of a phase Ib/II study investigating safety of the combination of copanlisib (pan-class I PI3Ki) and rucaparib (PARP-1, -2 and -3 inhibitor). Methods: Enrollment criteria included progressive mCRPC, prior androgen inhibitors (abiraterone, enzalutamide, and/or apalutamide); prior taxane chemotherapy was allowed. HR-deficiency was not required for the phase Ib. The phase I followed a standard 3+3 escalation design. Dose schema: rucaparib (continuous oral administration twice daily) 400mg (dose level [DL] -1, 1), 500mg (DL 2) or 600mg (DL 3,4) and intravenous copanlisib (45mg D1, D15 (DL -1, -2); 45mg, D1, D8, D15 (DL 1, 2, 3); 60mg, D1, D8, D15 (DL 4); 28-day cycle). Adverse events (AE) were graded by CTCAE v5.0. The primary aim of the phase I was to establish the MTD and the recommended phase II dose (RP2D) of copanlisib in combination with rucaparib. Results: Eleven pts were enrolled with a median age of 63 (55-78) and median PSA of 12 ng/mL (0.018–2,101). Seven pts (63%) received prior chemotherapy (docetaxel [7], cabazitaxel [3]). Pathogenic HR mutations included BRCA1 (1), BRCA2 (3), CDK12 (1), and FANCA (1). Treatment-related AE included grade 2 (G2) leukopenia (30%), G2 anemia (20%), G2 rash (20%). Two dose-limiting toxicities (DLTs) were observed in DL 1: G3 rash and G3 AST/ALT elevation attributed to both drugs. Six pts were treated at DL -1 without DLTs. The RP2D was rucaparib 400mg BID with copanlisib 45mg (D1, D15; 28-day cycle). There were 2 confirmed PSA50 responses among 7 evaluable pts (28%). One pt had BRCA2 loss and 1 had PALB2 VUS (ongoing PSA response for 14 mo). Three stable disease and 1 partial response were observed among 6 pts evaluable by RECIST 1.1. Conclusions: The combination of rucaparib and copanlisib is well tolerated. The RP2D was rucaparib 400mg BID with copanlisib 45mg (D1, D15; 28-day cycle) with signal of efficacy. Enrollment in a phase 2 expansion cohort in HR-mutated mCRPC is ongoing. Clinical trial information: NCT04253262.