Homologous Recombination Deficiency Research Articles

Homologous recombination deficiency gene panel analysis results in synchronous endometrial and ovarian cancers.

The objective of this study was to analyze the genetic alterations of tumors within the scope of the homologous recombination deficiency gene panel in patients diagnosed with synchronous endometrial ovarian cancer who have been followed for over 5 years using next-generation sequencing. DNA was isolated from the patient's formalin-fixed, paraffin-embedded tissue blocks. Next-generation sequencing was performed using the Illumina capture-based sequencing method. Samples were sequenced using the Sophia HR Solution DNA Kit. Seven patients were included in this study. The ratios of likely pathogenic (LP)/pathogenic (P) somatic mutations in ATM (serine/threonine kinase or Ataxia-telangiectasia mutated gene), BRCA2 (breast cancer type 2 susceptibility gene), BARD1 (BRCA1 associated RING domain 1), TP53 (tumor protein p53), BIRP1 (BRCA1-interacting helicase 1 gene), PALB2 (partner and localizer of BRCA2), and CHECK2 were 21 (48.8%), 8 (18.6%), 5 (11.6%), 3 (6.9%), 2 (4.6%), 2 (4.6%), and 2 (4.6%), respectively, in endometrium, and the ratios of somatic mutations in ATM, BRCA2, TP53, BARD1, RAD54L (DNA repair/recombination protein like), BIRP1, and RAD51D (RAD51 recombinase paralog D) were 24 (60%), 6 (15%), 5 (12.5%), 2 (5%), 2 (5%), 1 (2.5%), and 1 (2.5%), respectively, in ovary. In endometrioid-synchronous endometrial ovarian cancer cases, P/LP mutations were observed in ATM and CHECK2 genes in endometrium and ATM, BRCA2, and TP53 genes in ovary. In two non-endometrioid-synchronous endometrial ovarian cancer cases, CHEK2 (checkpoint kinase 2) mutations were observed in endometrium and ATM and TP53 mutations in ovary, whereas in one case, P/LP mutations in ATM and TP53 genes were common in both tissues. Pathogenic variations confirming the diagnosis of synchronous endometrial ovarian cancer with genetic alterations were identified in all but one case. ATM gene mutation emerged as the most common alteration and has a potential association with a favorable prognosis.

Germline and somatic testing for homologous repair deficiency in patients with prostate cancer (part 1 of 2).

Unfortunately, not all metastatic castration resistant prostate cancer (mCRPC) patients receive available life-prolonging systemic therapies, emphasizing the need to optimize mCRPC treatment selections. Better guidelines are necessary to determine genetic testing in prostate cancer. In this two-part expert opinion-based guide, we provide an expert consensus opinion on the utilization of germline and somatic testing to detect HRR alterations in patients with mCRPC. This guide was developed by a multidisciplinary expert panel that convened in 2023-2024, including representatives from medical oncology, urology, radiation oncology, pathology, medical genomics, and basic science. We argue for the widespread adoption of germline testing in all patients with prostate cancer and for somatic mutations testing in patients at the time of recurrent/metastatic disease. In this first part, we review how genomic testing is performed. We also review how to overcome certain barriers to integrate genetic and biomarker testing into clinical practice.

A boost or a redundancy? on the value of combination of androgen receptor signal inhibitor and PARP inhibitor for advanced prostate cancer

AbstractPoly (ADP-ribose) polymerase (PARP) inhibitor (PARPi), as a novel endocrine therapy, has been investigated in patients with metastatic castration-resistant prostate cancer (mCRPC) in recent years. Multiple large-scale clinical trials have consistently demonstrated that various PARP inhibitors, including olaparib, rucaparib, niraparib, and talazoparib, confer longer radiographic progression-free survival (rPFS) compared to new hormonal agents (NHA) in mCRPC patients with homologous recombination deficiency (HRD). Moreover, the incidence of grade 3 and above adverse events did not significantly increase. Additionally, when combined with androgen receptor signaling inhibitors (ARSI), olaparib, niraparib, and talazoparib have shown significant extension of rPFS but also an increased occurrence of serious adverse events in HRD-positive patients. Only PROpel yielded positive results among the homologous recombination repair (HRR) mutation negative population. Therefore, it remains uncertain whether ARSI-PARPi combination therapy should be considered as first-line treatment for mCRPC patients without HRR mutations. In this review article, we aim to elucidate the necessity and feasibility of combination therapy versus monotherapy specifically within the HRR mutant population while exploring its potential applicability to other non-HRR mutant subtypes. Furthermore, we conducted a comprehensive search on registered clinical trials at present to summarize the research progress of PARP inhibitors in prostate cancer patients at different disease stages.

Novel protein-based prognostic signature linked to immunotherapeutic efficiency in ovarian cancer

BackgroundPersonalized medicine remains an unmet need in ovarian cancer due to its heterogeneous nature and complex immune microenvironments, which has gained increasing attention in the era of immunotherapy. A key obstacle is the lack of reliable biomarkers to identify patients who would benefit significantly from the therapy. While conventional clinicopathological factors have exhibited limited efficacy as prognostic indicators in ovarian cancer, multi-omics profiling presents a promising avenue for comprehending the interplay between the tumor and immune components. Here we aimed to leverage the individual proteomic and transcriptomic profiles of ovarian cancer patients to develop an effective protein-based signature capable of prognostication and distinguishing responses to immunotherapy.MethodsThe workflow was demonstrated based on the Reverse Phase Protein Array (RPPA) and RNA-sequencing profiles of ovarian cancer patients from The Cancer Genome Atlas (TCGA). The algorithm began by clustering patients using immune-related gene sets, which allowed us to identify immune-related proteins of interest. Next, a multi-stage process involving LASSO and Cox regression was employed to distill a prognostic signature encompassing five immune-related proteins. Based on the signature, we subsequently calculated the risk score for each patient and evaluated its prognostic performance by comparing this model with conventional clinicopathological characteristics.ResultsWe developed and validated a protein-based prognostic signature in a cohort of 377 ovarian cancer patients. The risk signature outperformed conventional clinicopathological factors, such as age, grade, stage, microsatellite instability (MSI), and homologous recombination deficiency (HRD) status, in terms of prognoses. Patients in the high-risk group had significantly unfavorable overall survival (p < 0.001). Moreover, our signature effectively stratified patients into subgroups with distinct immune landscapes. The high-risk group exhibited higher levels of CD8 T-cell infiltration and a potentially greater proportion of immunotherapy responders. The co-activation of the TGF-β pathway and cancer-associated fibroblasts could impair the ability of cytotoxic T cells to eliminate cancer cells, leading to poor outcomes in the high-risk group.ConclusionsThe protein-based signature not only aids in evaluating the prognosis but also provides valuable insights into the tumor immune microenvironments in ovarian cancer. Together our findings highlight the importance of a thorough understanding of the immunosuppressive tumor microenvironment in ovarian cancer to guide the development of more effective immunotherapies.

Exploring Molecular Drivers of PARPi Resistance in BRCA1-Deficient Ovarian Cancer: The Role of LY6E and Immunomodulation.

Approximately 50% of patients diagnosed with ovarian cancer harbor tumors with mutations in BRCA1, BRCA2, or other genes involved in homologous recombination repair (HR). The presence of homologous recombination deficiency (HRD) is an approved biomarker for poly-ADP-ribose polymerase inhibitors (PARPis) as a maintenance treatment following a positive response to initial platinum-based chemotherapy. Despite this treatment option, the development of resistance to PARPis is common among recurrent disease patients, leading to a poor prognosis. In this study, we conducted a comprehensive analysis using publicly available datasets to elucidate the molecular mechanisms driving PARPi resistance in BRCA1-deficient ovarian cancer. Our findings reveal a central role for the interferon (IFN) pathway in mediating resistance in the context of BRCA1 deficiency. Through integrative bioinformatics approaches, we identified LY6E, an interferon-stimulated gene, as a key mediator of PARPi resistance, with its expression linked to an immunosuppressive tumor microenvironment (TME) encouraging tumor progression and invasion. LY6E amplification correlates with poor prognosis and increased expression of immune-related gene signatures, which is predictive of immunotherapy response. Interestingly, LY6E expression upon PARPi treatment resistance was found to be dependent on BRCA1 status. Gene expression analysis in the Orien/cBioPortal database revealed an association between LY6E and genes involved in DNA repair, such as Rad21 and PUF60, emphasizing the interplay between DNA repair pathways and immune modulation. Moreover, PUF60, Rad21, and LY6E are located on chromosome 8q24, a locus often amplified and associated with the progression of ovarian cancer. Overall, our study provides novel insights into the molecular determinants of PARPi resistance and highlights LY6E as a promising prognostic biomarker in the management of HRD ovarian cancer. Future studies are needed to fully elucidate the molecular mechanisms underlying the role of LY6E in PARPi resistance.

Therapeutic implications of homologous repair deficiency testing in patients with prostate cancer (Part 2 of 2).

Unfortunately, not all metastatic castration-resistant prostate cancer (mCRPC) patients receive available life-prolonging systemic therapies, emphasizing the need to optimize mCRPC treatment selections. Better guidelines are necessary to determine genetic testing for prostate cancer. In this two-part expert opinion-based guide, we provide an expert consensus opinion on the utilization of germline and somatic testing to detect HRR alterations in patients with mCRPC. This guide was developed by a multidisciplinary expert panel that convened in 2023-2024, including representatives from medical oncology, urology, radiation oncology, pathology, medical genomics, and basic science. In this second part, we highlight how genetic testing can lead to improved, life-prolonging mCRPC therapeutic strategies based on a review of the recent phase III trials and subsequent regulatory approvals for PARP inhibitors in mCRPC.

Real-world genome profiling in Japanese patients with pancreatic ductal adenocarcinoma focusing on HRD implications.

Pancreatic ductal adenocarcinoma (PDAC) poses significant challenges due to its high mortality, making it a critical area of research. This retrospective observational study aimed to analyze real-world data from comprehensive genome profiling (CGP) of Japanese patients with PDAC, mainly focusing on differences in gene detection rates among panels and the implications for homologous recombination deficiency (HRD) status. This study enrolled 2568 patients with PDAC who had undergone CGP between June 2019 and December 2021 using data from the nationwide Center for Cancer Genomics and Advanced Therapeutics database. Two types of CGP assays (tissue and liquid biopsies) were compared and a higher detection rate of genetic abnormalities in tissue specimens was revealed. HRD-related gene alterations were detected in 23% of patients, with BRCA1/2 mutations accounting for 0.9% and 2.9% of patients, respectively. Treatment outcome analysis indicated that patients with BRCA1/2 mutations had a longer time to treatment discontinuation with FOLFIRINOX than gemcitabine plus nab-paclitaxel as first-line therapy (9.3 vs. 5.6 months, p = 0.028). However, no significant differences were observed in the treatment response among the other HRD-related genes. Logistic regression analysis identified younger age and family history of breast, prostate, and ovarian cancers as predictive factors for HRD-related gene alterations. Despite the lack of progression-free survival data and the inability to discriminate between germline and somatic mutations, this study provides valuable insights into the clinical implications of CGP in Japanese patients with PDAC. Further research is warranted to optimize panel selection and elucidate the efficacy of platinum-based therapies depending on the HRD status.

Predictive value of homologous recombination deficiency status for survival outcomes in primary tubo-ovarian high-grade serous carcinoma.

This is a protocol for a Cochrane Review (prognosis). The objectives are as follows: To evaluate the predictive value of the prognostic factor HRD status, as determined by various clinically validated HRD assays at the time of staging laparotomy, compared to BRCA1/2 mutation status for progression-free survival and overall survival in patients with tubo-ovarian high-grade serous carcinoma treated in the first-line setting with a combination of surgery and platinum-based chemotherapy and/or maintenance with PARP inhibitors.

Abstract C095: Molecular characterization of gastric adenocarcinoma from Latinos shows homologous recombination deficiency

Abstract Latinos have a higher risk of developing gastric cancer (GC) than non-Latino Whites (NLW). Multiple studies have shown increased treatment resistance in diffuse-type cancers, which are more prevalent in Latino patients and dominated by the genomically stable (GS) genomic subtype. However, there is little genomic data from Latino gastric tumors due to the few studies targeting this minority population. Here, we attempt to rectify the disparity of genomic data by performing whole exome and/or low-coverage whole genome sequencing on tumors from 195 Latino gastric adenocarcinoma patients, from Colombia and Mexico. We also analyze 42 Latino patients from the US from a previous study. In total, we analyze tumors from 237 patients, the largest cohort of Latino gastric cancer tumors comprehensively sequenced thus far. Molecular subtyping of our cohort shows a higher proportion of tumors with a genomically stable (GS) subtype, 59%, and less with chromosomal instability (CIN), 24%, than reported in non-Latino patients from the Cancer Genome Atlas (20% and 50% respectively). Our earlier study of germline variants from Latinos, indicated a potential enrichment of variant related to homologous recombination deficiency (HRD), an important DNA repair mechanism. Focusing on this pathway, we performed HRD scoring and show that CIN tumors had the highest HRD score compared to all other subtypes. An alternative method analyzing somatic mutational patterns identified an indel mutational signature (ID6), also related to HRD, was enriched in GS tumors. Overall, these data provide a broader picture of the genomic landscape of Hispanic tumors, highlighting HRD targeting drugs as a potential treatment for both GS diffuse-types cancers particularly seen in Latinos and CIN tumors found more generally in gastric cancer. Citation Format: Dennis J Montoya, Ana Estrada-Florez, Paul Lott, Katherine Chiu, John Suarez-Olaya, Fabian Castro, Magdalena Echeverry de Polanco, Javier Torres, Mabel Bohorquez, Luis Carvajal-Carmona. Molecular characterization of gastric adenocarcinoma from Latinos shows homologous recombination deficiency [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C095.

Abstract C010: Integrating germline and somatic data to resolve variants of uncertain significance (VUS) in colorectal cancer (CRC) patients who self-identified as Hispanic/Latino

Abstract Germline and somatic genetic testing have become cornerstones for assessing patient risk and tailoring cancer treatment, respectively, relying on the ability to distinguish pathogenic from benign variants. Typically, clinical reporting from these tests is conducted independently, serving distinct clinical objectives and audiences. However, integrating the underlying genomic data from both germline and somatic tests can enhance interpretative clarity, particularly in resolving variants of unknown significance (VUS) that lack sufficient evidence to determine pathogenicity. This ambiguity is especially problematic for non-White populations and those of non-European ancestry, where VUSs are disproportionately found, thereby limiting the scope of precision medicine and perpetuating health disparities. To assess the potential utility of an integrated model, we examined a prospective cohort of 88 self-identified Hispanic patients with colorectal cancer (CRC), performing both germline and somatic genomic analyses. We found that at least one germline VUS was identified in 44% (39/88) of participants, compared to a frequently reported rate of below 15%. By integrating tumor transcriptome data, mutational signatures, and copy number variations with traditional germline testing, we aimed to clarify VUSs and identify driver mutations. Integrating data modalities of the tumor transcriptome, mutational signatures, and copy number variations alongside traditional germline testing can help clarify VUSs and identify driver mutations. We constructed a model whereby the assessment of VUSs was based on the putative functional impact on either the DNA mutational patterns or allelic expression observed in tumor RNA. Using our integrated model, we deemed the oncogene AXIN2 VUS of one participant was likely biologically significant due to mutant-allele specific expression observed in the tumor RNA. Furthermore, we showed that 26% (10/39) of participants harbored a VUS that was very likely benign based on the tumor mutational profile and RNA expression. These included variants associated with homologous recombination in PALB2 and BRCA2 as well as genes associated with DNA repair like MLH1, PMS2, POLE and POLD1. Among patients with VUSs in genes associated with homologous recombination deficiency (HRD), none exhibited HRD via copy number analyses. Conversely, of the six patients that did exhibit HRD, only one had a pathogenic variant in a gene associated with HRD (ATM). Additionally, we identified tumors with a DNA mismatch repair deficiency phenotype (high tumor mutational burden, high microsatellite instability, DNA mismatch repair deficiency mutational signature) but without a pathogenic variant in a Lynch syndrome-associated gene. Methylation analysis revealed hypermethylation of the MLH1 promoter in these cases, explaining the tumor phenotype. This finding indicates that our integrative method can accurately predict DNA mismatch repair deficiency even without a genetic alteration in a DNA mismatch repair gene. Citation Format: Jonathan Amzaleg, Julie O. Culve, Charité N. Ricker, Natalia Gutierrez, Yuxin Jin, Brigette Waldrup, Carmen Chaves, Lucia Enriquez, Joel Sanchez-Mendez, Daisy Hernandez, Bodour Salhia, Lourdes Baezconde-Garbanati, Mariana C. Stern, Enrique Velazquez Villarreal, John D. Carpten, Heinz-Joseph Lenz, David W. Craig. Integrating germline and somatic data to resolve variants of uncertain significance (VUS) in colorectal cancer (CRC) patients who self-identified as Hispanic/Latino [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C010.

Frequent CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression

We analyzed genomic data from the prostate cancer of African- and European American men to identify differences contributing to racial disparity of outcome. We also performed FISH-based studies of Chromodomain helicase DNA-binding protein 1 (CHD1) loss on prostate cancer tissue microarrays. We created CHD1-deficient prostate cancer cell lines for genomic, drug sensitivity and functional homologous recombination (HR) activity analysis. Subclonal deletion of CHD1 was nearly three times as frequent in prostate tumors of African American than in European American men and it associates with rapid disease progression. CHD1 deletion was not associated with HR deficiency associated mutational signatures or HR deficiency as detected by RAD51 foci formation. This was consistent with the moderate increase of olaparib and talazoparib sensitivity with several CHD1 deficient cell lines showing talazoparib sensitivity in the clinically relevant concentration range. CHD1 loss may contribute to worse disease outcome in African American men.

Abstract A031: Identification of therapeutic vulnerabilities in the subset of pancreatic ductal adenocarcinoma (PDAC) with homologous recombination deficiency

Abstract The genetic landscape of pancreatic ductal adenocarcinoma (PDAC) is characterized by mutations in the KRAS, TP53, CDKN2A and SMAD4 genes alongside multiple low-frequency mutations, which may offer opportunities for precision medicine. The success of poly-ADP-ribose polymerase (PARP) inhibitors in metastatic PDAC characterized by germline mutations in the Breast Cancer (BRCA) genes has led to the hypothesis that mutations in other BRCAness genes may sensitize PDAC to PARP inhibitors. To test this hypothesis, we used KPC mice as a backbone (Pdx1-Cre; LSL-KrasG12D/+; LSL-Trp53R172H/+) to generate models of PDAC driven by the loss of Ataxia Telangiectasia mutated (Atm, KPCA) or Brca1 (KPCB). Loss of Atm or Brca1 resulted in homologous recombination deficiency and genomic instability in vivo. In vitro cultures of KPCA and KPCB PDAC cells had higher numbers of micronuclei and were more radiosensitive than KPC cells. Next, we performed bulk and single-cell RNA sequencing to identify therapeutic vulnerabilities associated with Atm or Brca1 loss. We found that loss of Atm upregulated ATR signaling, suggesting ATR as a therapeutic target in KPCA mice. In agreement, ATR inhibition improved the survival of KPCA mice, with evidence of tumor growth delay. However, though PARP inhibition significantly improved the survival of KPCB mice, with delayed tumor growth, it was ineffective in KPCA mice. In addition, transcriptomic analysis showed an enrichment of immune cells in KPCB PDAC compared to KPC and KPCA PDAC. Notably, we found greater levels of STING signaling, a more diverse and abundant cytokine profile and more CD8 T cells in KPCB PDAC, suggesting sensitivity to immune checkpoint blockade (ICB). However, ICB was ineffective in KPCB mice as a single agent or in combination with PARP inhibition. Based on our transcriptomic data, we hypothesized that boosting antigen priming using a CD40 agonist (CD40a) in combination with FLT3-L may improve ICB efficacy in our mouse models of BRCAness. Immunotherapy consisting of combined ICB, CD40a and FLT-3L had little efficacy in either KPCA or KPCB mice. However, ATR inhibition improved the efficacy of combined ICB, CD40a and FLT-3L in KPCA mice, as indicated by increased CD8 T cell infiltration in the tumor, delayed tumor growth and longer survival. In contrast, we found that PARP inhibition combined with ICB, CD40a and FLT-3L was ineffective in KPCB mice. In summary, we present evidence to suggest that PDAC characterized by BRCAness is not a homogeneous group with respect to sensitivity to PARP inhibition, composition of the tumor microenvironment and response to immunotherapy. We highlight ATM loss as a potential predictive biomarker of ATR inhibitor efficacy and immunotherapy in PDAC. Future directions include the evaluation of inflammation as a therapeutic vulnerability in murine PDAC with loss of Brca1. Ultimately, we aim to inform clinical trials to refine precision medicine of PDAC characterized by BRCAness. Citation Format: Mathias Tesson, Kay Kong, Peter Repsicak, Aldo Bader, Ya-Ching Hsieh, Craig Nourse, Kristina Kirschner, Crispin Miller, Ed Roberts, David Chang, Jen Morton. Identification of therapeutic vulnerabilities in the subset of pancreatic ductal adenocarcinoma (PDAC) with homologous recombination deficiency [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A031.

Abstract C006: LODESTAR: A Single Arm Phase II Study of Rucaparib in Solid Tumors with Pathogenic Germline or Somatic Variants in Homologous Recombination Repair (HRR) Genes

Abstract Purpose: Poly (ADP-ribose) polymerase inhibitors (PARPi) have proven clinical utility in platinum-sensitive breast, ovary, pancreas, and prostate cancers with homologous recombination deficiency (HRD). We explored whether PARPi might be efficacious in other solid tumors and for a broader range of genomic variants. Patients and Methods: This single-arm phase II study assessed rucaparib monotherapy in patients with advanced, platinum-sensitive or -resistant solid tumors and pathogenic variants (PVs) in BRCA1, BRCA2, PALB2, RAD51C, RAD51D (Cohort A) or BARD1, BRIP1, FANCA, NBN, RAD51B (Cohort B). The primary endpoint was overall response rate (ORR) in cohort A. Secondary endpoints included disease control rate (DCR), progression free survival (PFS), overall survival (OS) and safety[SS3] [SA4] in the entire study population. Available tumors were analyzed for pre-specified exploratory objective of allele specific loss of heterozygosity (LOH). [SA7] HRD signature (HRDsig) and platinum sensitivity status were explored as biomarkers for rucaparib activity in post hoc exploratory analyses. The study was terminated early by the sponsor due to feasibility concerns. Results: Eighty-three patients were enrolled (Cohort A: 63; Cohort B: 20). Fifty-seven patients in Cohort A and 16 in Cohort B were evaluable for efficacy analysis. The[LM8] [SA9] ORR of cohort A was 16% (95% CI 9-27%) and DCR was 61% (95% CI 48-73%). LOH and HRDsig were available for 48% of Cohort A and 71% of Cohort B. Of 11 patients who had a response to treatment, 6 tumors were HRDsig+, 1 HRDsig-and 4 were unknown. The ORR and DCR were significantly greater in patients with HRDsig+ vs HRDsig-tumors (ORR: HRDsig+ 32% [95% CI 15-54%] vs HRDsig-3% [95% CI 0-15%], p &amp;lt; 0.01; DCR: HRDsig+ 74% [95% CI 51-88%] vs HRDsig-38% [95% CI 24-55%], p = 0.02). mPFS was numerically longer for HRDsig+ vs HRDsig-: 7.0 mos (95% CI, 4.3 – inf), vs. 3.0 mos (95% CI 2.3-5.6), HR 0.57, p = 0.14. mPFS was greater for platinum sensitive vs resistant tumors (7.82 mos [95% CI 5.5-inf] vs. 2.9 mos [95% CI 1.8-inf], HR 0.28, p = 0.02); Neither tumor tissue of origin nor specific mutation was independently predictive of outcome. The HR for progression in tumors that were both HRDsig+ and platinum sensitive versus those that were HRDsig-and platinum resistant was 0.09 (95% CI 0.01-0.55, p = 0.047). The Rucaparib safety profile was consistent with prior studies. Conclusion: Rucaparib has activity across solid tumors with PVs in HRR genes, regardless of tissue of origin. Patients with platinum resistant or HRDsig-tumors had limited clinical benefit from rucaparib. The combined use of HRDsig and platinum sensitivity to predict sensitivity to PARPi is encouraging as a biomarker strategy and warrants prospective study. Citation Format: Sriram Anbil, Nicholas J Seewald, Kevin Lin, Marcia Craib, Christy Connor, Heidi Giordano, Karen McLachlan, Tanya Kwan, Lara Maloney, Hanna Tukachinsky, Alexa Schrock, Shuoguo Wang, Ethan Sokol, Brennan Decker, Katherine Nathanson, Susan Domchek, Kim Reiss. LODESTAR: A Single Arm Phase II Study of Rucaparib in Solid Tumors with Pathogenic Germline or Somatic Variants in Homologous Recombination Repair (HRR) Genes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C006.

Abstract C046: Targeting wild-type IDH1 sensitizes homologous recombination proficient pancreatic cancer to PARP inhibition

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related mortality in the United States. While Poly (ADP-ribose) polymerase (PARP) inhibitors show promise for PDAC with Homologous Recombination Deficiency (HRD), this mutation is present in less than 10% of cases. Our research focuses on exploiting a vulnerability in the remaining 90% of HR proficient (HRP) tumors. We identified that wild-type isocitrate dehydrogenase 1 (IDH1) plays a critical role in HR repair. By inhibiting IDH1, we discovered suppression of the homologous recombination (HR) pathway, leading to compromised genomic integrity. This renders cancer cells more susceptible to PARP inhibitor therapy, offering a novel therapeutic approach for HRP PDAC. Methods:We assessed the impact of IDH1 inhibition on HR pathway activity using Western blotting to measure HR repair protein levels and HR reporter assays. The effect of IDH1 inhibition (Ivosidenib) combined with PARP inhibition (Olaparib) on in vitro growth inhibition was assessed through drug combination assays. Additionally, we investigated the molecular mechanisms underlying the synergistic effects of the drug combination. To further evaluate the therapeutic potential of IDH1 inhibition in combination with PARP inhibitors, we examined tumor growth in xenograft models of PDAC in athymic nude mice and survival studies were performed in C57BL/6J mice transplanted with orthotopic murine pancreatic cancer. Results:Wild-type IDH1 blockade induces a BRCA-like phenotype by decreasing α-ketoglutarate (αKG) levels and causing histone hypermethylation. This leads to decreased HR repair efficiency in HRP pancreatic cancer cells (MiaPaCa-2 and Panc-1), resulting in a strong synergistic effect when combined with the DNA-damaging agent Olaparib. The combination treatment significantly reduced cell survival in both short and long-term assays. Furthermore, we discovered that these compounds complemented each other in the DNA damage response, leading to increased γ-H2AX (DNA damage marker) and apoptosis. In vivo studies using murine PDAC models demonstrated that the combination of ivosidenib and olaparib synergistically enhanced anti-tumor activity compared to either single agent alone. Conclusion:These data provide novel insight into the mechanisms underlying in the context of HRP cancer susceptibility to a dual treatment approach involving an IDH1 inhibitor and a PARP inhibitor. This approach holds promise for precision medicine in pancreatic cancer treatment, although further pre- clinical studies are needed for validation and refinement. Citation Format: Mehrdad Zarei, Omid Hajihassani, Hallie J. Graor, Soubhi Tahhan, Alexander W. Loftus, Faith Nakazzi, Semmer A. Ali, Parnian Naji, Luke D. Rothermel, Jonothan R. Brody, Jordan M. Winter. Targeting wild-type IDH1 sensitizes homologous recombination proficient pancreatic cancer to PARP inhibition [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C046.

Abstract A055: Multiomics profiling reveals druggable tumor-stroma interactions in ATM-deficient pancreatic cancer

Abstract The complex biology of pancreatic ductal adenocarcinoma (PDAC) remains a significant challenge and limits overcoming its dismal prognosis. The tumor microenvironment (TME), shaped by dynamic interactions between cancer-associated fibroblasts (CAFs), immune and tumor cells, plays a crucial role in PDAC pathogenesis. Uncharted field lies in the impact of specific gene mutations within the tumor epithelium on orchestrating distinct oncogenic TME patterns. Our investigation into homologous recombination deficiency (HRD), caused by mutations in genes like ATM, reveals its role in promoting PDAC aggressiveness and triggering a pronounced desmoplastic reaction, suggesting a unique TME programing. Through single-cell-resolved and multiomics analyses of murine ATM and/or P53-depleted PDACs, and validation in human cases, we unveil transcriptional, translational, and secretory regulatory events, shed light on the intricate interplay between tumor genetics and PDAC microenvironment and pave the way for the elaboration of novel personalized therapies. Murine tumor analysis using single-nucleus multiomics RNA and ATAC sequencing, alongside histological validation in human tissues, revealed specific enrichment of myCAFs in ATM-deficient tumors and reduced populations of T cells and macrophages. Molecular signatures and cell-cell communication inference uncovered ATM-specific interactions within the TME, highlighting TGF-β signaling as pivotal in mediating dialog between CAFs and an aggressive EMT-like tumor cell subset prevalent in ATM-depleted tumors. Additionally, distinct communication patterns were observed between CAFs and immune cells, associated with specific epigenetic and molecular profiles. Mechanistically, transcriptomics, secretomics and proteomics investigations confirmed increased TGFβ release by ATM-deficient PDAC cells and identified a reactive oxygen species (ROS)-mediated mechanism affecting tumor cell behavior and interactions with CAFs. Consistently, a combinatorial therapy targeting TGF-β-mediated tumor-stroma dialog reversed cancer-promoting TME remodeling and exacerbated FOLFIRINOX cytotoxic effects, in vivo, exclusively in ATM-deficient HRD PDACs. Dissecting the biology of ATM-deficient HRD malignant cells, our study unveils their pivotal role in orchestrating oncogenic communication networks with CAFs and immune cells, along with specific tumor promoting stromal reprogramming. Our findings paint a comprehensive picture of how distinct tumor-stroma interactions reshape the TME, steering it towards a cancer-promoting outcome and shed light on the potential to exploit genotype-specific vulnerabilities via tailored tumor-stroma interference strategies. Citation Format: Elodie Roger, Hannah M. Mummey, Eleni Zimmer, Julia Ragg, Yuna Lee, Kyle J. Gaulton, Alica K. Beutel, Christopher J. Halbrook, Lukas Perkhofer, Johann Gout, Alexander Kleger. Multiomics profiling reveals druggable tumor-stroma interactions in ATM-deficient pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A055.

Abstract B088: Epigenetic reprograming in ATM-deficient pancreatic cancer: targeting EZH2- mediated oncogenic traits

Abstract Despite extensive research, the complex biology of pancreatic ductal adenocarcinoma (PDAC) continues to impede progress in improving its prognosis. Its resistance to conventional therapies, along with diverse mutations, necessitate improved molecular stratification to develop tailored approaches and to improve survival of PDAC patients. Our previous studies on ATM- deficient models revealed that serine/threonine kinase ATM loss induces homologous recombination deficiency (HRD), promoting invasiveness and desmoplastic reactions, while also sensitizing tumors to platinum-based therapies and PARP1 inhibition. Interestingly, our data also identified the histone-methyltransferase EZH2 as a direct ATM substrate to operate as a crucial regulator of ATM-specific oncogenic traits. In detail, murine and human ATM-deficient tumors accumulated EZH2, suggesting that ATM status contributes to rewiring the epigenetic landscape of pancreatic tumors, subsequently supporting oncogenic features. To investigate how EZH2 impacts ATM-deficient PDAC pathogenesis, we generated conditional double ATM and EZH2-knockout in the Kras G12D/+ ; Ptf1a Cre/+ mice (AKC, Atm fl/fl ; LSL-Kras G12D/+ ; Ptf1a Cre/+ , and EAKC, Ezh2 fl/fl ; Atm fl/fl ; LSL-Kras G12D/+ ; Ptf1a Cre/+ ). EZH2 depletion in AKC mice prolonged overall survival and reinstated a differentiated phenotype. Furthermore, PDAC patients with negative ATM and EZH2 expression from the TCGA-PAAD cohort (PanCancer Atlas) also showed significantly extended progression-free survival compared to ATM neg EZH2 pos patients. In line, CRISPR/Cas9-mediated EZH2 depletion in ATM-deficient pancreatic cancer cells affected their epigenetic landscape and significantly upregulated transcriptomic programs associated with cell differentiation, thereby restoring differentiated tumor features ex vivo. We showed that ATM status significantly impacts EZH2 activity through a post-translational pathway, promoting tumor supportive EZH2 activity in pancreatic cancer. ATM kinase facilitates EZH2 ubiquitination and degradation by recruiting the Cullin1 E3-ubiquitin ligase complex. Additionally, combining an EZH2 inhibitor with PARP inhibition enhances cytotoxicity in ATM- deficient HRD PDAC. Overall, our findings demonstrate that ATM deficiency drives a pro- oncogenic mesenchymal differentiation program via the histone-methyltransferase EZH2. We emphasize the importance of stratifying patients based on ATM status before considering pharmacological interference with EZH2, offering a promising approach for targeting ATM- deficient HRD tumors. Citation Format: Elodie Roger, Anna Härle, Lukas Perkhofer, Elisabeth Hessmann, Alexander Kleger, Johann Gout. Epigenetic reprograming in ATM-deficient pancreatic cancer: targeting EZH2- mediated oncogenic traits [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B088.

Abstract B029: Repurposing Digital PCR to Diagnose and Create a Novel Genomic Signature for Homologous Recombination Deficiency in Pancreatic Adenocarcinoma

Abstract Introduction: Germline mutations in DNA repair genes are often associated with increased risk of cancer. Mutations that affect the homologous recombination (HR) DNA repair pathway ( e.g., BRCA 1 and BRCA2) are known drivers of pancreatic adenocarcinoma. Early detection relies on identification of pathogenic mutations in patients with a family history of cancer. Next generation sequencing panels often use a select set of pathogenic variants for diagnosis, meaning that individuals with variants of uncertain significance may be missed, limiting testing of other family members for the potentially disease-causing variant. Here we describe a digital PCR assay developed to detect BRCA1 and BRCA2 variant that may eventually serve as a rapid, cost-effective alternative to sequencing that costs less than $5.00 per sample with results in 24 hours. This study highlights the need for better diagnostic tools, which will become critically important as we begin to study pathogenic mutations in more diverse populations. Methods: We have collected blood from 4 BRCA1 mutants and 5 BRCA2 mutants who have already undergone germline sequencing from commercially available assays. Clinicopathologic data has been collected as well. We designed two fluorescently labelled TaqMan probes, one that recognizes the wild-type BRCA alleles and one specific for mutant BRCA alleles. Briefly, 1 ng of genomic DNA is mixed with amplicon primers and fluorescent Taq-Man probes, then partitioned into 20,000 separate 517 picoliter wells. Quantification and detection are achieved based upon the fluorescent signal measured from each well. Results: We have successfully confirmed pathologic BRCA1 and BRCA2 mutations previously identified with next generation sequencing in 100% of samples analyzed. All three BRCA2 mutations generate a premature stop codon leading to a truncated protein and are known to be pathogenic. Two related patients have the same BRCA1 frameshift mutation that results in a premature stop codon, and one patient has a duplicated cytosine that leads to a frameshift mutation that is one of three characterized Ashkenazi Jewish founder mutations that increases cancer risk in this population . Conclusions: Here we report an innovative assay using digital PCR (dPCR) that provides a cost-effective, time-efficient method to identify MMR mutants and characterize VUS in patients and their families. Citation Format: Jennifer Brooke Valerin, Sophie Hasson, Valeria Rangel, Nicholas Pannunzio. Repurposing Digital PCR to Diagnose and Create a Novel Genomic Signature for Homologous Recombination Deficiency in Pancreatic Adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B029.

The coexistence of a BRCA2 germline and a DICER1 somatic variant in two first-degree cousins suggests their potential synergic effect

Cancer predisposition syndromes are recognized in about 10% of pediatric malignancies with several genes specifically involved in a subset of pediatric tumors such as DICER1, in pleuropulmonary blastoma, cystic nephroma, and brain sarcomas. By contrast, the role of BRCA1/2 in pediatric cancer predisposition is still under investigation. We present two cases of young first-degree cousins, both carrying a germline BRCA2 variant and developing tumors characterized by somatic DICER1 mutations. Patient 1 presented with a cystic nephroma harboring a somatic DICER1 variant (p.Asp1810Tyr), while patient 2 had a primary intracranial DICER1-mutated sarcoma showing a distinct somatic DICER1 variant (p.Asp1709Glu) as well as biallelic inactivation of TP53 (p.Val173Leu, VAF 91%) and APC (p.Ile1307Lys, VAF 95%) and a pathogenic variant in KRAS (p.Gln61His). Both patients carried the same germline BRCA2 variant (p.Arg2842Cys) of unknown significance. The same variant was found in the mother of patient 2 and in the father of patient 1, who are siblings. A homologous recombination deficiency signature was not identified in any of the two tumors, possibly suggesting a reduction of BRCA2 activity. The association of BRCA2 and DICER1 variants in our cases hints at a potential cooperative role in cancer pathogenesis. Further studies are warranted to elucidate the interplay between BRCA1/2 and DICER1 variants and their implications for cancer predisposition and treatment in pediatric patients.

Characterization of DNA damage repair pathway utilization in high-grade serous ovarian cancers yields rational therapeutic approaches

While poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) have improved the prognosis of ovarian high-grade serous carcinoma (HGSC) tumors that are homologous recombination (HR) deficient (HRD), new therapeutic strategies are needed for tumors that are HR proficient (HRP) because they demonstrate greater resistance to current treatments and thus have poorer clinical outcomes. Additionally, clinical precautionary statements regarding potential risks associated with PARPi, such as myelodysplastic syndrome, highlight the need for combinatorial approaches that can lessen the dose and duration of PARPi treatment to reduce toxicities. Here, we evaluated DNA double-strand damage repair pathways in HRD and HRP ovarian cancer cell lines and found that in HRD cell lines, PARPi therapy reduced non-homologous end joining (NHEJ)-mediated repair, specifically due to decreased theta-mediated end-joining. The combination of PARPi with ATM serine/threonine kinase inhibitor (ATMi) suppressed both NHEJ and HR pathways in HRD and HRP cell lines, with synergistic increases in apoptosis and decreases in cell viability and colony formation. Interestingly, PARPi plus ATMi also decreased NF-κB p65 phosphorylation, which was not observed when PARPi was combined with inhibition of the ATR kinase (ATRi). These findings indicate that PARPi plus ATMi is a promising strategy for HGSC independent of underlying tumor HR status.

CYP1B1 promotes PARPi-resistance via histone H1.4 interaction and increased chromatin accessibility in ovarian cancer

IntroductionOvarian cancer is the most lethal gynecological cancer and presents significant therapeutic challenges. The discovery of synthetic lethality between PARP inhibitors (PARPi) and homologous recombination deficiency marked a new era in treating BRCA1/2-mutated tumors. However, PARPi resistance remains a major clinical challenge. MethodsRNA sequencing was used to identify genes altered by PARPi treatment and LC-MS was used to detect proteins interacting with CYP1B1. Resistance mechanisms were explored through ATAC-seq and gene expression manipulation. Additional techniques, including micrococcal nuclease digestion assays, DAPI staining, and fluorescence microscopy, were used to assess changes in nuclear morphology and chromatin accessibility. ResultsThe gradual exposure of Olaparib has developed a PARPi-resistant cell line, A2780-OlaR, which exhibits significant upregulation of CYP1B1 at both RNA and protein levels. Down-regulating CYP1B1 expression or using specific inhibitors decreased the cellular response to Olaparib. Linker histone H1.4 was identified as associated with CYP1B1. ATAC-seq showed differential chromatin accessibility between A2780-OlaR and parental cells, indicating that the downregulation of H1.4 was associated with increased chromatin accessibility and higher cell viability after Olaparib treatment. ConclusionOur findings reveal a novel role for CYP1B1 in driving PARPi resistance through distinct molecular mechanisms in A2780-OlaR. This study highlights the importance of chromatin accessibility in PARPi efficacy and suggests the CYP1B1/H1.4 axis as a promising therapeutic target for overcoming drug resistance in ovarian cancer, offering potentially therapeutic benefits.