High Homologous Recombination Deficiency Research Articles

Luminal androgen receptor subtype and tumor-infiltrating lymphocytes groups based on triple-negative breast cancer molecular subclassification.

In our previous study, we developed a triple-negative breast cancer (TNBC) subtype classification that correlated with the TNBC molecular subclassification. In this study, we aimed to evaluate the predictor variables of this subtype classification on the whole slide and to validate the model's performance by using an external test set. We explored the characteristics of this subtype classification and investigated genomic alterations, including genomic scar signature scores. First, TNBC was classified into the luminal androgen receptor (LAR) and non-luminal androgen receptor (non-LAR) subtypes based on the AR Allred score (≥ 6 and < 6, respectively). Then, the non-LAR subtype was further classified into the lymphocyte-predominant (LP), lymphocyte-intermediate (LI), and lymphocyte-depleted (LD) groups based on stromal tumor-infiltrating lymphocytes (TILs) (< 20%, > 20% but < 60%, and ≥ 60%, respectively). This classification showed fair agreement with the molecular classification in the test set. The LAR subtype was characterized by a high rate of PIK3CA mutation, CD274 (encodes PD-L1) and PDCD1LG2 (encodes PD-L2) deletion, and a low homologous recombination deficiency (HRD) score. The non-LAR LD TIL group was characterized by a high frequency of NOTCH2 and MYC amplification and a high HRD score.

CK2-HTATSF1-TOPBP1 signaling axis modulates tumor chemotherapy response.

Homologous recombination (HR) plays a key role in maintaining genomic stability, and the efficiency of the HR system is closely associated with tumor response to chemotherapy. Our previous work reported that CK2 kinase phosphorylates HTATSF1 Ser748 (pS748) to facilitate HTATSF1 interaction with TOPBP1, which in turn, promotes RAD51 recruitment and HR repair. However, the clinical implication of the CK2-HTATSF1-TOPBP1 pathway in tumorigenesis and chemotherapeutic response remains to be elucidated. Here, we report that the CK2-HTATSF1-TOPBP1 axis is generally hyperactivated in multiple malignancies and renders breast tumors less responsive to chemotherapy. In contrast, deletion mutations of each gene in this axis, which also occur in breast and lung tumor samples, predict higher HR deficiency (HRD) scores, and tumor cells bearing a loss-of-function mutation of HTATSF1 are vulnerable to PARP inhibitors (PARPis) or platinum drugs. Taken together, our study suggests that the integrity of the CK2-HTATSF1-TOPBP1 axis is closely linked to tumorigenesis, and serves as an indicator of tumor HR status and modulates chemotherapy response.

Abstract PO3-15-10: Enhanced Cancer Cell Proliferation and Aggressive Phenotype Counterbalance in Breast Cancer with High BRCA1 Gene Expression

Abstract Introduction: It is estimated that 5–10% of all breast cancer cases have a hereditary component with BRCA1 mutation being one of the most frequently observed gene mutations in breast cancer patients. BRCA1 plays a crucial role in DNA repair, and its mutation has been extensively studied. However, the clinical significance of BRCA1 gene expression remains largely unexplored. Given that heightened DNA repair mechanisms can potentially increase cancer cell proliferation, we hypothesized that breast cancer with high BRCA1 gene expression might be associated with aggressive tumor biology and worse survival. Methods: The clinical, pathological and gene expression levels of a total of 6,245 breast cancer patients were analyzed from three large independent cohorts: METABRIC (n = 1,903), GSE96058 (n = 3,273), and The Cancer Genome Atlas (TCGA, n = 1,069). The data was retrieved through cBioPortal. The xCell algorithm was used to correlate the BRCA1 gene expression with the stromal and immune cell fractions infiltrating the tumor microenvironment (TME). Results: BRCA1 gene expression was higher in breast cancer patients without BRCA1 mutation, and it correlated with the DNA repair activity (p = 0.026 and p &amp;lt; 0.01 respectively), however, it did not correlate with BRCA2 gene expression (p = 0.38). Breast cancer with high BRCA1 gene expression was associated with cancer cell proliferation as evidenced by higher Nottingham histological grade (p &amp;lt; 0.001), Ki67 expression (p &amp;lt; 0.001), significant enrichment of cell proliferation-related gene sets such as E2F Targets, G2M Checkpoint, MYC Targets V1 and V2, Mitotic Spindle (all FDR &amp;lt; 0.25), and significantly less infiltration of stromal cells such as adipocytes, fibroblasts, microvascular and lymphatic endothelial cells, and pericytes (all p &amp;lt; 0.05). High BRCA1 gene expression was associated with higher homologous recombination deficiency, intratumor genomic heterogeneity, and fraction altered (all p &amp;lt; 0.001); however, there was no correlation observed with mutation rates or neoantigens. It was observed that breast cancer with high BRCA1 gene expression had less infiltration of CD8 T cells, dendritic cells, regulatory T cells, and B cells and had higher infiltration of Th1 cells (all p &amp;lt; 0.05). To our surprise, there was no significant difference in overall survival regardless of the subtypes (except for ER+/HER2- subtype in METABRIC cohort, p = 0.03). Breast cancer with low BRCA1 gene expression enriched cancer aggravating pathway gene sets such as Cancer Stem Cell-related signaling pathways (NOTCH and HEDGEHOG), Angiogenesis, Epithelial Mesenchymal Transition, Inflammatory Response, and TGF-beta signaling (all FDR &amp;lt; 0.25). Conclusion: Contrary to our initial hypothesis, we did not find any significant association between BRCA1 gene expression and survival outcomes in breast cancer patients. Based on the results of our study, we speculate that the interplay between enhanced cancer cell proliferation and aggressive tumor characteristics may counterbalance the effect of high BRCA1 expression in breast cancer. Citation Format: Kohei Chida, Masanori Oshi, Arya Mariam Roy, Itaru Endo, Kazuaki Takabe. Enhanced Cancer Cell Proliferation and Aggressive Phenotype Counterbalance in Breast Cancer with High BRCA1 Gene Expression [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-15-10.

Abstract PO2-08-11: The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours

Abstract Background: Identification of germline mutations in hereditary breast cancer (HBC) genes can have profound benefits in the treatment of breast cancer (BC) and manging risk for patient and the family. In addition, sequencing of the tumours can reveal clinically relevant somatic features, such as homologous recombination deficiency (HRD) and mutational signatures, that can guide treatment which are not discernible by germline sequencing alone. We hypothesised that current standard of care where women diagnosed with BC are not routinely offered tumour sequencing is suboptimal as fails to exploit all therapeutic vulnerabilities which can be exploited in the treatment of BC. The MAGIC study is the first prospective trial in Australia of unselected invasive BCs in general oncology practice combining both germline and tumour sequencing. Methods: The MAGIC study included a total of 651 consecutive consented patients presenting with non-metastatic BC between June 2020 to March 2023. It included invasive BC, high-grade DCIS and pleomorphic LCIS. The sequencing was conducted in two phases; for phase one, 157 cases underwent whole genome sequencing (WGS) on both germline and matched BC DNA while for phase two, 494 cases underwent only germline whole exome sequencing. Germline variants were interrogated for pathogenic variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, BARD1, BRIP1, RAD51B, RAD51C, RAD51D, MLH1, MSH2, MSH6, PMS2, CDH1, PTEN, STK11, TP53 and NTHL1. Tumour homologous recombination (HR) repair deficiency was calculated using HRDetect (Nat Med 2017;23:517). For BCs showing a high HRDetect score ( &amp;gt;0.75) all HBC gene promoter CpG islands were assessed for hypermethylation using the Twist NGS Methylation system. Mutational signatures were calculated from somatic mutations identified from whole genome sequenced BCs using the DeconstructSig package in R (Genome Biol. 2016;17:31) and referenced against the COSMIC v2 signature catalogue. Results: Actionable germline variants in any HBC gene were identified in 7.7% of cases (7.8% of invasive and 6.1% of in situ BC) with 5.2% having an actionable mutation in an HR pathway gene (BRCA1, BRCA2, PALB2 and RAD51C). Most cases with pathogenic variants showed bi-allelic inactivation in the tumour. All BRCA1, BRCA2 and PALB2 tumours showed high HRDetect and/or HRD scores consistent with loss of HR repair function, indicating them to be the underlying hereditary driver of the BC. One BC with a pathogenic PMS2 variant showed retention of the wild-type allele with no evidence of a mismatch repair mutational signature suggesting PMS2 was not the driver of this BC. Of the 157 BC in phase one that underwent WGS and did not have a germline pathogenic HBC gene variant, 16% (18/117 invasive and 3/13 DCIS) had an HRDetect score of &amp;gt;0.7 indicative of a homologous recombination repair defect and therefore biologically a “BRCA-like” tumour. Of these 21 BRCA-like cases, only 3 invasive BCs had clear somatic bi-allelic inactivation of an HBC gene that could explain the high HRDetect score (2 BRCA1 and 1 BRCA2). One of the 21 BRCA-like cases had a germline variant of unknown significance (VUS) in an HBC gene (a BRCA2 missense variant in an ER+ tumour. The tumour showed loss of the wild-type allele). Of the BRCA-like cases, 71% were ER positive which included 3 invasive lobular cancers. Conclusion: Tumour sequencing identified three times as many cases that might be eligible for HR repair defect targeted therapy than germline testing alone (16% versus 5.2%). Unlike a previous study (Ann Oncol., 2019 30:1071-1079), the majority of the BRCA-like BCs were ER+ with no evidence of a VUS in a known HBC gene suggesting these are driven by novel germline or somatic mutations in genes involved in DNA HR repair. Citation Format: Ian Campbell, Lisa Devereux, Kirsten Hogg, Luxi Lal, Michelle Sinclair, Lesley Stafford, Magnus Zethoven, Anita Skandarajah, Paul James, Geoffrey Lindeman, Bruce Mann, Dilanka De Silva. The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-08-11.

Abstract PO1-16-03: GDP-mannose enhances the efficacy of PARP inhibitors and immunotherapy in triple-negative breast cancer

Abstract Background: Triple-negative breast cancer (TNBC) patients with high HRD scores benefit from poly (ADP-ribose) polymerase (PARP) inhibitors, while those with low HRD scores still lack therapeutic options. Homologous recombination deficiency (HRD) induction is an effective strategy to broaden the indications of PARP inhibitors. Metabolic reprogramming is a critical feature of TNBC. In this study, we aimed to explore novel metabolic biomarkers for HRD and new strategy for sensitizing PARP inhibitors. Methods: We utilized TNBC metabolomics to systematically evaluate metabolites that were correlated with HRD. A crucial metabolite, GDP-mannose (GDP-M), that impedes homologous recombination repair (HR) and sensitizes PARP inhibitors was identified and functionally validated. We further explored the detailed mechanism and proposed a potential treatment strategy utilizing GDP-M for TNBC in preclinical models. Results: Systematic metabolomic analysis revealed that GDP-mannose (GDP-M) was significantly enriched in basal-like tumors with HRD. GDP-M promoted cisplatin-induced DNA double-strand breaks by inducing HRD. Mechanistically, the low expression of the upstream enzyme GMPPA led to the endogenous upregulation of GDP-M, which further promoted the ubiquitin-mediated degradation of BRCA2 to inhibit HR. GMPPA expression and GDP-M could serve as predictive biomarkers for HRD and the response to PARP inhibitors. Therapeutically, we validated that the combination of GDP-M and PARP inhibitors synergistically inhibit tumor growth in multiple preclinical models. Moreover, GDP-M supplementation plus PARP inhibition activated STING-dependent antitumor immunity and further augmented the efficacy of anti-PD-1 antibodies. Conclusions: GDP-M promotes the degradation of BRCA2 and thus enhances the sensitivity of PARP inhibitors in TNBC. The combination of GDP-M, PARP inhibitors and anti-PD-1 immunotherapy may be a potential treatment strategy for HRD-low TNBC. Citation Format: Yi Xiao, Jiahan Ding, Yi-Zhou Jiang, Zhi-Ming Shao, Genhong Di, Fan Yang, Xiaoqing Song. GDP-mannose enhances the efficacy of PARP inhibitors and immunotherapy in triple-negative breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-16-03.

Somatic mutations that affect early genetic progression and immune microenvironment in gastric carcinoma

Gastric carcinoma (GC) is a high heterogeneity and malignant tumor with a poor prognosis. The current implementation of immunotherapy in GC is limited due to the insufficient exploration of immune-related mutations and speculated early mutation events. Therefore, we performed whole-exome sequencing on 40 patients with GC to explore their genetic characteristics, shedding light on the order of genetic events, somatic mutations impacting the immune microenvironment, and potential biomarkers for immunotherapy. Regarding genetic events, TP53 disruptions were identified as frequent and early events in GC progression, often occurring alongside other gene mutations. The mutations occurring in GANS, SMAD4, and POLE were early independent events. Patients harboring CSMD3, FAT4, FLG, KMT2C, LRP1B, MUC5B, MUC16, PLEC, RNF43, SYNE1, TP53, TTN, XIRP2, and ZFHX4 mutations tended to have decreased B cells, T cells, macrophage, neutrophil, and dendritic cells infiltration, except for the ARID1A gene mutations. We also found patients with microsatellite instability-high tumors had higher homologous recombination deficiency (HRD) scores. HRD showed a positive correlation with tumor mutational burden, which might serve as indirect evidence supporting the potential of HRD as a biomarker for GC. These findings highlighted GC's high heterogeneity and complexity and provided valuable insights into the somatic mutations that affect early genetic progression and immune microenvironment.

Association between Homologous Recombination Repair Defect Status and Long-Term Prognosis of Early HER2-Low Breast Cancer: A Retrospective Cohort Study.

As a newly identified subtype of HER2-negative tumors associated with a less favorable prognosis, it remains crucial to evaluate potential prognostic and predictive factors, particularly non-invasive biomarkers, for individuals with human epidermal growth factor 2 (HER2) low early-stage breast cancer (EBC). Multiple investigations have highlighted that HER2-negative patients with EBC exhibiting high homologous recombination deficiency (HRD) scores display lower rates of pathological complete response (PCR) to neoadjuvant chemotherapy (NAC). Nevertheless, no study to date has explored the correlation between HRD and the long-term prognosis in HER2-low patients with EBC. This retrospective observational study focuses on primary EBC sourced from The Cancer Genome Atlas dataset (TCGA). It reveals the gene mutation landscape in EBC with low HER2 expression and elucidates the tumor immune landscape across different HRD states. Utilizing bioinformatics analysis and Cox proportional models, along with the Kaplan-Meier method, the study assesses the correlation between HRD status and disease-specific survival (DSS), disease-free interval (DFI), and progression-free interval (PFI). Subgroup analyses were conducted to identify potential variations in the association between HRD and prognosis. In the patients with HER2-low breast cancer, patients with homologous recombination related genes (HRRGs) defects had an HRD score about twice that of those without related genes mutations, and were at higher risk of acquiring ARID1A, ATM, and BRCA2 mutations. We also found that most immune cell abundances were significantly higher in EBC tumors with high HRD than in EBC tumors with low HRD or HRD-medium, particularly plasma B-cell abundance, CD8 T-cell abundance, and M1 macrophages. In addition, these tumors with HRD-high also appear to have significantly higher tumor immune scores and lower interstitial scores. Then, we analyzed the relationship between different HRD status and prognosis. There was statistical significance (P = .036 and P = .046, respectively) in DSS and PFI between the HRD-low and HRD-high groups, and patients with HRD-high EBC showed relatively poor survival outcomes. A medium HRD score (hazard ratio, HR = 2.15, 95% CI: 1.04-4.41, P = .038) was a significant risk factor for PFI. Hormone receptor positivity is an important factor in obtaining medium-high HRD score and poor prognosis. Higher HRD scores were associated with poorer PFI outcomes, particularly in people with HR+/HER2-low. Varied HRD states exhibited distinctions in HRRGs and the tumor immune landscape. These insights have the potential to assist clinicians in promptly identifying high-risk groups and tailoring personalized treatments for patients with HER2-low EBC, aiming to enhance long-term outcomes.

Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets

The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly because of its low incidence rate, accounting for only 0.5% to 1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of 10 MaBC cases (n = 10) were delineated and correlated with clinical and histopathologic characteristics. Using fluorescence in situ hybridization, an additional cohort of 18 patients was interrogated to supplement WGS findings. The genomic landscape of MaBC uncovered significant genetic alterations that could influence diagnosis and treatment. We found common somatic mutations in key driver genes, such as FAT1, GATA3, SMARCA4, and ARID2. Our study also mapped out structural variants that impact cancer-associated genes, such as ARID1A, ESR1, GATA3, NTRK1, and NF1. Using a WGS-based classifier, homologous recombination deficiency (HRD) was identified in 2 cases, both presenting with deleterious variants in BRCA2. Noteworthy was the observation of FGFR1 amplification in 21% of cases. Altogether, we identified at least 1 potential therapeutic target in 8 of the 10 cases, including high tumor mutational burden, FGFR1 amplification, and HRD. Our study is the first WGS characterization of MaBC, which uncovered potentially relevant variants, including structural events in cancer genes, HRD signatures, and germline pathogenic mutations. Our results demonstrate unique genetic markers and potential treatment targets in MaBC, thereby underlining the necessity of tailoring treatment strategies for this understudied patient population. These WGS-based findings add to the growing knowledge of MaBC genomics and highlight the need to expand research on this type of cancer.

Guanosine diphosphate-mannose suppresses homologous recombination repair and potentiates antitumor immunity in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with poor prognosis. TNBCs with high homologous recombination deficiency (HRD) scores benefit from DNA-damaging agents, including platinum drugs and poly(ADP-ribose) polymerase (PARP) inhibitors, whereas those with low HRD scores still lack therapeutic options. Therefore, we sought to exploit metabolic alterations to induce HRD and sensitize DNA-damaging agents in TNBCs with low HRD scores. We systematically analyzed TNBC metabolomics and identified a metabolite, guanosine diphosphate (GDP)-mannose (GDP-M), that impeded homologous recombination repair (HRR). Mechanistically, the low expression of the upstream enzyme GDP-mannose-pyrophosphorylase-A (GMPPA) led to the endogenous up-regulation of GDP-M in TNBC. The accumulation of GDP-M in tumor cells further reduced the interaction between breast cancer susceptibility gene 2 (BRCA2) and ubiquitin-specific peptidase 21 (USP21), which promoted the ubiquitin-mediated degradation of BRCA2 to inhibit HRR. Therapeutically, we illustrated that the supplementation of GDP-M sensitized DNA-damaging agents to impair tumor growth in both in vitro (cancer cell line and patient-derived organoid) and in vivo (xenograft in immunodeficient mouse) models. Moreover, the combination of GDP-M with DNA-damaging agents activated STING-dependent antitumor immunity in immunocompetent syngeneic mouse models. Therefore, GDP-M supplementation combined with PARP inhibition augmented the efficacy of anti-PD-1 antibodies. Together, these findings suggest that GDP-M is a crucial HRD-related metabolite and propose a promising therapeutic strategy for TNBCs with low HRD scores using the combination of GDP-M, PARP inhibitors, and anti-PD-1 immunotherapy.

Clinical outcome and molecular landscape of patients with ARID1A-loss gastric cancer.

Chromatin remodelers are commonly altered in human cancer. The mutation of AT-rich interactive domain 1A (ARID1A) in gastric cancer (GC), a component of the SWI/SNF chromatin remodeling complex, was proven associated with treatment response in our previous study. However, ARID1A loss of function was caused not only by mutations but also copy number deletions. The clinicopathologic, genomic, and immunophenotypic correlates of ARID1A loss is largely uncharacterized in GC. Here, 819 patients with clinicopathological information and sequencing data or formalin-fixed paraffin-embedded tissues from four cohorts, Zhongshan Hospital (ZSHS) cohort (n = 375), The Cancer Genome Atlas (TCGA) cohort (n = 371), Samsung Medical Center (SMC) cohort (n = 53), and ZSHS immunotherapy cohort (n = 20), were enrolled. ARID1A loss was defined by genome sequencing or deficient ARID1A expression by immunohistochemistry. We found that ARID1A mutation and copy number deletion were enriched in GC with microsatellite instability (MSI) and chromosomal-instability (CIN), respectively. In the TCGA and ZSHS cohorts, only CIN GC with ARID1A loss could benefit from fluorouracil-based adjuvant chemotherapy. In the SMC and ZSHS immunotherapy cohorts, ARID1A loss exhibited a tendency of superior responsiveness and indicated favorable overall survival after anti-PD-1 immunotherapy. ARID1A-loss tumors demonstrated elevated mutation burden, neoantigen load, and interferon gamma pathway activation. Moreover, in CIN GC, ARID1A loss was correlated with higher homologous recombination deficiency. ARID1A loss defines a distinct subtype of GC characterized by high levels of genome instability, neoantigen formation, and immune activation. These tumors show sensitivity to both chemotherapy and anti-PD-1 immunotherapy. This study provides valuable insights for precision treatment strategies in GC.

Inhibition of neuroactive ligand–receptor interaction pathway can enhance immunotherapy response in colon cancer: an in silico study

ABSTRACT Background The potential mechanism underlying the association between Homologous recombination deficiency (HRD) and immunotherapy in colon cancer has not been investigated. Methods The exon sequencing data and transcriptome data of 456 colon adenocarcinoma (COAD) patients were obtained from the TCGA database. Pathway activity score was calculated by GSVA methods and engaged in further survival analysis. The prognostic value of the candidate pathways was validated in an external GEO cohort and an immunotherapy cohort. Results Patients with high HRD were associated with poor prognosis, lower tumor mutation burden and microsatellite instability, higher fraction genome alteration, and less sensitivity to immunotherapy in COAD. And then, the neuroactive ligand–receptor interaction pathway was over-activated in high-HRD tumors and associated with immunosuppression in colon cancer with high HRD. Besides, the pathway was associated with prognosis and immunotherapy response in COAD. Moreover, genes in this pathway such as LTB4R2 can be used as a novel target for therapy development in colon cancer. Conclusion Our study not only revealed the potential mechanism of HRD and the function of the neuroactive ligand–receptor interaction pathway in colon cancer but also provided new clues for the improvement of immunotherapy response in colon cancer.

Analysis of multiple genomic-factors affecting the homologous recombination deficiency (HRD) in Chinese ovarian cancer.

88 Background: A large proportion of (but not all) ovarian cancers with high homologous recombination deficiency (HRD) scores are sensitive to Poly (ADP-ribose) polymerase inhibitors (PARPi). This study aimed to identify multiple genomic factors that could increase HRD scores, helped us understand the potential causes for high HRD scores, and thus make therapy decisions. Methods: A total of 370 Chinese ovarian cancer patients were retrospectively obtained from ovarian patients for HRD status and HRR gene alterations from October, 2021 to January, 2023. Patient information including age, gender, pathology type was collected. All specimens were detected by OncoDrug-SeqTM603-gene panel assay through next-generation sequencing (NGS) using Illumina NovaSeq 6000. The interaction between genomic alternation and its overall instability was analyzed to look for multi-factors affecting HRD. Results: Of 370 patients, there were 296 (80.08%) patients with over 50 years, 225(76.01%) with positive HRD, and 48 (16.2%) patients with BRCA1/2 mutations. The top ten commonly mutated genes were TP53 (54.05%), BRCA1 (8.1%), BRCA2 (8.11%), KRAS (8.11%), PDE1C (8.11%), ARID1A (5.41%), BRAF (5.41%), CDK12 (5.41%), CHEK2 (5.41%), and MSH2 (5.41%).Among of them, there were 24.32% of patients with both HRR and TP53 mutations, and 13.51% of patients had both BRCA1/2 and TP53 mutations. Furthermore, in the trio negative of BRCA1/2, TP53, and HRD groups, KRAS mutations were found in 30 (50%)patients. The mutations in TP53, BRAC1/2, and other HRR genes had positive correlations with HRD scores. Importantly, BRCA1/2-negative patients with mutant TP53 other than wild type had a significantly high HRD score (p&lt;0.05). Although it did not hold true for other HRR gene (excluding BRCA) negative patients (p&gt;0.05), an increasing trend in HRD score was still observed. Conclusions: Alterations of multiple genes including TP53, BRAC1/2, and other HRR genes are correlated with higher HRD scores. In this Chinese cohort, a large number of BRCA1/2-negative patients with TP53 mutations tend to have higher HRD scores. Whether this specific subgroup of Chinese ovarian cancers can benefit from PARPi is in question, although they present high HRD scores.

Biallelic BRCA Loss and Homologous Recombination Deficiency in Nonbreast/Ovarian Tumors in Germline BRCA1/2 Carriers.

Breast and ovarian tumors in germline BRCA1/2 carriers undergo allele-specific loss of heterozygosity, resulting in homologous recombination deficiency (HRD) and sensitivity to poly-ADP-ribose polymerase (PARP) inhibitors. This study investigated whether biallelic loss and HRD also occur in primary nonbreast/ovarian tumors that arise in germline BRCA1/2 carriers. A clinically ascertained cohort of BRCA1/2 carriers with a primary nonbreast/ovarian cancer was identified, including canonical (prostate and pancreatic cancers) and noncanonical (all other) tumor types. Whole-exome sequencing or clinical sequencing results (n = 45) were analyzed. A pan-cancer analysis of nonbreast/ovarian primary tumors from germline BRCA1/2 carriers from The Cancer Genome Atlas (TCGA, n = 73) was used as a validation cohort. Ages of nonbreast/ovarian cancer diagnosis in germline BRCA1/2 carriers were similar to controls for the majority of cancer types. Nine of 45 (20%) primary nonbreast/ovarian tumors from germline BRCA1/2 carriers had biallelic loss of BRCA1/2 in the clinical cohort, and 23 of 73 (32%) in the TCGA cohort. In the combined cohort, 35% and 27% of primary canonical and noncanonical BRCA tumor types, respectively, had biallelic loss. High HRD scores (HRDex > 42) were detected in 81% of tumors with biallelic BRCA loss compared with 22% (P < .001) of tumors without biallelic BRCA loss. No differences in genomic profile, including mutational signatures, mutation spectrum, tumor mutational burden, or microsatellite instability, were found in primary nonbreast/ovarian tumors with or without biallelic BRCA1/2 loss. A proportion of noncanonical primary tumors have biallelic loss and evidence of HRD. Our data suggest that assessment of biallelic loss and HRD could supplement identification of germline BRCA1/2 mutations in selection of patients for platinum or PARP inhibitor therapy.

The clinical value of homologous recombination deficiency score in prostate cancer.

e17011 Background: Aberrations in homologous recombination repair (HRR) genes serve as biomarkers for guiding the treatment decision of PARP inhibitors in prostate cancer (PCa). Homologous recombination deficiency (HRD) score which directly shows the consequence of the loss of HRR function (genomic scars) may be a more reliable biomarker for identifying patients who are sensitive to PARP inhibitors. Methods: This study involved 50 patients with PCa, including mHSPC (n = 37), mCRPC (n = 11), and locally advanced PCa (n = 2). Tumor tissue specimens were collected for targeted next-generation sequencing for 406 cancer-related genes and HRD detection. HRD score was calculated based on over 50,000 single-nucleotide polymorphisms (SNP) distributed across the human genome, incorporating three SNP-based assays: loss of heterozygosity, telomeric allelic imbalance, and large-scale state transition. All the experiments were performed in OrigiMed, a College of American Pathologists accredited and Clinical Laboratory Improvement Amendments certified laboratory. Results: The median HRD score was 34.5 (ranged from 14 to 64). With the median value as cutoff, the mutation rates of HRR were 32% (8/25) and 12% (3/25) in the high and low HRD score groups, respectively. BRCA2 mutations (P = 0.011), AR mutations (P = 0.032), RB1 mutations (P = 0.035) and altered HRR pathway (P = 0.017) were associated with high HRD scores. The mutation frequencies of AR and TP53 were significantly higher in mCRPC compared to mHSPC ( AR: 45.5% [5/11] vs 2.7% [1/37], P &lt; 0.001; TP53: 63.6% [7/11] vs 24.3% [9/37], P = 0.027). A total of 9 patients carried HRR germline mutations (5 BRCA2, 1 BRIP1, 1 RAD50, 1 RAD51D, and 1 ATM). It was found that patients with BRCA2 germline mutations had a higher HRD score (median = 37) than those with other germline mutations ( BRIP1: 25, RAD50: 19, RAD51D: 35, ATM: 36). In the 6 patients who received HRD-related treatments (including cisplatin based chemotherapy or olaparib), 1 of the 2 patients with low HRD score had PSA progression after 251 days (the other one was lost to follow up), while no PSA progression was observed in the 4 patients with high HRD score with a median follow-up of 107 days (range: 40-274 days). A mCRPC case with high HRD score (37) and HRR wild-type who received second line docetaxel+cisplatin even achieved undetectable PSA. Another mHSPC patient with a high HRD score (37) and a BRCA2 germline mutation also had no detectable PSA after first-line docetaxel+cisplatin therapy. Conclusions: To our knowledge, this is the first study in China reporting the association of HRD score and platinum-based treatments in PCa. Our results supported the possibility that HRD score could be predictive for the efficacy of platinum-based chemotherapy.

A multicenter phase I/II trial of induction chemotherapy followed by camrelizumab, apatinib, plus chemotherapy as first-line treatment for extensive-stage small-cell lung cancer.

8590 Background: Extensive-stage small-cell lung cancer (ES-SCLC) is a highly aggressive tumor with poor prognosis and limited treatment options. It is necessary to explore new first-line therapeutic strategies to improve patients’ outcomes. This study aimed to assess the safety and efficacy of induction chemotherapy followed by camrelizumab, apatinib plus chemotherapy as first-line treatment in patients with ES-SCLC. Methods: Patients (pts) aged 18-75 years with histopathologically confirmed ES-SCLC and ECOG performance score of 0-1 who did not receive systemic treatment were prospectively enrolled to this study. After two 21-day cycles of induction chemotherapy (etoposide 100 mg/m2 on days 1-3 and carboplatin AUC 5 mg/mL/min on day 1 [EC]), pts received camrelizumab (200 mg, q3w) plus apatinib (250 mg, qd) and EC for 2-4 cycles, then followed by camrelizumab and apatinib as maintenance treatment until disease progression/unacceptable toxicity/up to two years. The primary endpoint was safety. Secondary endpoints were objective response rate (ORR), PFS and OS. Targeted sequencing and whole transcriptome sequencing (WTS) were performed for pts who had sufficient tissue samples. Results: From Jan 28, 2021 to Aug 20, 2022, 40 eligible pts were enrolled. At the data cut-off (Jan 21, 2023), the median follow-up time was 13.6 months. Grade 3/4 treatment-related adverse events (TRAEs) were reported in 72.5% (29/40) of pts. The most common grade 3/4 TRAEs were decreased neutrophil count (35.0%, 14/40), anemia (15.0%, 6/40), decreased platelet count (12.5%, 5/40), increased serum alanine aminotransferase (12.5%, 5/40), and hyponatremia (12.5%, 5/40). Hemoptysis was observed in 15.0% of (6/40) pts, all of whom were grade 1-2. No treatment-related deaths occurred. Efficacy was evaluated in 36 pts who received two cycles of induction therapy and had at least one post-treatment efficacy evaluation. The ORR after two cycles of induction chemotherapy was 66.7% (24/36). The overall ORR and disease control rate reached 88.9% (32/36) and 97.2% (35/36), respectively. The median PFS was 7.4 months (95% CI: 6.5-8.3). The 1-year OS rate was 63.4%. Thirty and 20 pts underwent targeted sequencing and WTS, respectively. Pts with high tumor mutational burden level (TMB ≥ 7.0, p &lt; 0.001), high homologous recombination deficiency score (HRD ≥ 34.0, p = 0.012), and altered RB1 (p &lt; 0.001) presented a longer PFS, respectively. WTS suggested that high expression of cancer-associated fibroblast signature was associated with a shorter PFS (p = 0.001). Conclusions: Induction chemotherapy followed by camrelizumab, apatinib plus EC and then maintenance therapy showed acceptable safety and encouraging efficacy, and might be a promising regimen as first-line treatment in ES-SCLC. TMB, HRD and RB1 might be predictive biomarkers of response to the regimen. Clinical trial information: NCT05001412 .

Genomic and transcriptomic characterization of ovarian cancer under neoadjuvant and adjuvant chemotherapy.

e17571 Background: Neoadjuvant chemotherapy (NACT) has become a routine selection for late-staged ovarian cancer patients to reduce the tumor load before debulking surgery; and chemotherapy remains as the mainstream therapy for ovarian cancer. However, the effects of NACT on the cancer genome and the molecular determinates of tumor response to chemotherapy in ovarian cancer have not been characterized systematically. Methods: We obtained 121 clinical samples from 44 ovarian cancer patients (19 underwent NACT and 25 did not) and collected the key clinical features for these samples such as age, tumor stage, platinum-free interval, and platinum response. We then performed whole-exome sequencing for all the 121 samples and RNA-sequencing for 54 samples. We conducted a systematic comparative analysis between samples collected from the patients with and without NACT to characterize the effects of NACT on the cancer genome and transcriptomes. Focusing on the genomic and transcriptomic differences of treatment-naive samples between platinum sensitive and resistant patients, we also did a comparative analysis to identify molecular features that can predict the response to platinum. Results: We observed significantly elevated mutational signatures associated with platinum chemotherapy in the samples from patients who have undergone NACT. We also found increased microsatellite instability (MSI) in the post-NACT primary samples compared to treatment-naive ones. Interestingly, the prevalence of CCNE1 amplification significantly decreased in the post-NACT metastatic samples of patients. Consistently, the mRNA expression of CCNE1 appeared to down-regulated in such samples. Furthermore, the expression signature of cancer hallmarks related to this gene decreased in post-NACT metastatic samples, such as E2F targets, G2M checkpoint, and mitotic spindle. Remarkably, we found that homologous recombination deficiency (HRD) is a strong indicator for platinum sensitivity, which was also supported by HRD-associated mutational signatures. The expression signature of immune-related hallmarks was significantly upregulated in sensitive primary samples, including interferon alpha response, interferon gamma response, and IL6 JAK STAT3 signaling. Conclusions: Based on comprehensive profiling for genomic and transcriptomic characterization of a large cohort of ovarian cancer patients, we found that (i) NACT likely increased MSI and decreased prevalence of CCNE1 amplification; and (ii) a high HRD score and elevated immune-related expression signatures can strongly predict the sensitivity to platinum-based chemotherapy. These results lays a key foundation for develop novel, effective therapies for ovarian cancer.

Unveiling the interplay between mutational signatures and tumor microenvironment: a pan-cancer analysis.

While recent studies have separately explored mutational signatures and the tumor microenvironment (TME), there is limited research on the associations of both factors in a pan-cancer context. We performed a pan-cancer analysis of over 8,000 tumor samples from The Cancer Genome Atlas (TCGA) project. Machine learning methods were employed to systematically explore the relationship between mutational signatures and TME and develop a risk score based on TME-associated mutational signatures to predict patient survival outcomes. We also constructed an interaction model to explore how mutational signatures and TME interact and influence cancer prognosis. Our analysis revealed a varied association between mutational signatures and TME, with the Clock-like signature showing the most widespread influence. Risk scores based on mutational signatures mainly induced by Clock-like and AID/APOBEC activity exhibited strong pan-cancer survival stratification ability. We also propose a novel approach to predict transcriptome decomposed infiltration levels using genome-derived mutational signatures as an alternative approach for exploring TME cell types when transcriptome data are unavailable. Our comprehensive analysis revealed that certain mutational signatures and their interaction with immune cells significantly impact clinical outcomes in particular cancer types. For instance, T cell infiltration levels only served as a prognostic biomarker in melanoma patients with high ultraviolet radiation exposure, breast cancer patients with high homologous recombination deficiency signature, and lung adenocarcinoma patients with high tobacco-associated mutational signature. Our study comprehensively explains the complex interplay between mutational signatures and immune infiltration in cancer. The results highlight the importance of considering both mutational signatures and immune phenotypes in cancer research and their significant implications for developing personalized cancer treatments and more effective immunotherapy.

Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration

There is emerging evidence about the predictive role of homologous recombination deficiency (HRD), but this is less defined in gastrointestinal (GI) and thoracic malignancies. We reviewed whole genome (WGS) and transcriptomic (RNA-Seq) data from advanced GI and thoracic cancers in the Personalized OncoGenomics trial (NCT02155621) to evaluate HRD scores and single base substitution (SBS)3, which is associated with BRCA1/2 mutations and potentially predictive of defective HRD. HRD scores were calculated by sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. Regression analyses examined the association between HRD and time to progression on platinum (TTPp). We included 223 patients with GI (n = 154) or thoracic (n = 69) malignancies. TTPp was associated with SBS3 (p < 0.01) but not HRD score in patients with GI malignancies, whereas neither was associated with TTPp in thoracic malignancies. Tumors with gBRCA1/2 mutations and a somatic second alteration exhibited high SBS3 and HRD scores, but these signatures were also present in several tumors with germline but no somatic second alterations, suggesting silencing of the wild-type allele or BRCA1/2 haploinsufficiency. Biallelic inactivation of an HR gene, including loss of XRCC2 and BARD1, was identified in BRCA1/2 wild-type HRD tumors and these patients had prolonged response to platinum. Thoracic cases with high HRD score were associated with high RECQL5 expression (p ≤ 0.025), indicating another potential mechanism of HRD. SBS3 was more strongly associated with TTPp in patients with GI malignancies and may be complementary to using HRD and BRCA status in identifying patients who benefit from platinum therapy.

Tumor immune contexture predicts recurrence after prostatectomy and efficacy of androgen deprivation and immunotherapy in prostate cancer

BackgroundProstate cancer is one of the most common cancers in men with notable interpatient heterogeneity. Implications of the immune microenvironment in predicting the biochemical recurrence-free survival (BCRFS) after radical prostatectomy and the efficacy of systemic therapies in prostate cancer remain ambiguous.MethodsThe tumor immune contexture score (TICS) involving eight immune contexture-related signatures was developed using seven cohorts of 1120 patients treated with radical prostatectomy (training: GSE46602, GSE54460, GSE70769, and GSE94767; validation: GSE70768, DKFZ2018, and TCGA). The association between the TICS and treatment efficacy was investigated in GSE111177 (androgen deprivation therapy [ADT]) and EGAS00001004050 (ipilimumab).ResultsA high TICS was associated with prolonged BCRFS after radical prostatectomy in the training (HR = 0.32, 95% CI 0.24–0.45, P < 0.001) and the validation cohorts (HR = 0.45, 95% CI 0.32–0.62, P < 0.001). The TICS showed stable prognostic power independent of tumor stage, surgical margin, pre-treatment prostatic specific antigen (PSA), and Gleason score (multivariable HR = 0.50, 95% CI 0.39–0.63, P < 0.001). Adding the TICS into the prognostic model constructed using clinicopathological features significantly improved its 1/2/3/4/5-year area under curve (P < 0.05). A low TICS was associated with high homologous recombination deficiency scores, abnormally activated pathways concerning DNA replication, cell cycle, steroid hormone biosynthesis, and drug metabolism, and fewer tumor-infiltrating immune cells (P < 0.05). The patients with a high TICS had favorable BCRFS with ADT (HR = 0.25, 95% CI 0.06–0.99, P = 0.034) or ipilimumab monotherapy (HR = 0.23, 95% CI 0.06–0.81, P = 0.012).ConclusionsOur study delineates the associations of tumor immune contexture with molecular features, recurrence after radical prostatectomy, and the efficacy of ADT and immunotherapy. The TICS may improve the existing risk stratification systems and serve as a patient-selection tool for ADT and immunotherapy in prostate cancer.

Abstract GS5-02: Neoadjuvant paclitaxel/olaparib in comparison to paclitaxel/carboplatinum in patients with HER2-negative breast cancer and homologous recombination deficiency – long-term survival of the GeparOLA study

Abstract Background: The GeparOLA study was designed to evaluate the efficacy and safety of the combination of paclitaxel (P) plus olaparib (O) as part of neoadjuvant chemotherapy (NACT) in patients with human epidermal growth factor receptor 2 (HER2)-negative, either hormone receptor (HR)-positive or HR-negative and homologous recombination deficiency (HRD) defined as having a g/tBRCA mutation and/or a high HRD score. Primary analysis showed a pCR rate of 55.1% (90% CI 44.5%-65.3%) with PO and 48.6% (90% CI 34.3%-63.2%) with P plus carboplatinum (Cb). The PO combination could not exclude a pCR rate of ≤55% in the PO arm but was significantly better tolerated. Analysis on the stratified subgroups showed higher pCR rates with PO in the cohorts of patients &amp;lt; 40 years and HR-positive tumors (Fasching Ann Oncol 2020). Here, we report long-term data. Methods: GeparOLA (NCT02789332) was a non-comparative, multicenter, prospective, randomized, open-label, phase II trial. Patients with primary HER2-negative breast cancer, HRD and indication for chemotherapy (cT2-cT4a-d or cT1c and cN+ or cT1c and pNSLN+ or cT1c and TNBC or cT1c and Ki-67 &amp;gt;20%) were randomly assigned to receive either P 80 mg/m2 weekly plus O 100 mg twice daily for 12 weeks or P plus Cb area under the curve 2 (AUC2) weekly for 12 weeks, both followed by four cycles of either 2-weekly or 3-weekly epirubicin 90 mg/m2 plus cyclophosphamide 600 mg/m2. Primary endpoint was pCR (ypT0/is ypN0) rate after NACT with PO followed by EC. Long-term efficacy endpoints included invasive disease-free survival (iDFS), distant disease-free survival (DDFS) and overall survival (OS). The time-to-event endpoints analysis is planned with median follow-up of at least 4 years and a follow-up completeness of at least 80%. Results: Between September 2016 and July 2018, 274 patients were screened, of whom 107 were randomized and 106 (PO N=69; PCb N=37) started treatment. The median age was 47.0 years (range 25.0-71.0); 32 patients were aged &amp;lt; 40 years; 36.2% of patients had cT1 tumors and 31.8% were cN-positive; the majority (86.8%) had grade 3 tumors and a Ki-67&amp;gt;20% (89.6%). Seventy-seven patients (72.6%) had TNBC. After a median follow-up of 49.8 months (range 0.1-69.1), 18 (15 in PO; 3 in PCb) iDFS events and 7 (6 in PO; 1 in PCb) deaths were reported. The 4-year survival rates are shown in the table below. iDFS (HR PO to PCb=2.86 [95%CI 0.83-9.9], log-rank p=0.081), DDFS (HR =3.03 [95%CI 0.67-13.67], log-rank p=0.129), and OS (HR=3.27 [95%CI 0.39-27.2], log-rank p=0.244) tended to be inferior with olaparib. Patients without g/tBRCA mutation seem to benefit from the use of carboplatinum (7/30 iDFS/DDFS events in PO; 0/16 in PCb, log-rank p=0.037, HR n.a.). Conclusions: In patients with HER2-negative and HRD breast cancer the use of olaparib instead of carboplatinum although showing comparable pCR rates, tended to result in an overall inferior outcome. This was mainly driven by the patients without a g/tBRCA mutation. In patients with a g/t BRCA mutation no difference between olaparib and carboplatinum was seen. Key words: Olaparib, HER2-negative breast cancer, HRD, survival Funding: The study was financially supported by AstraZeneca Citation Format: Peter A. Fasching, Sabine Schmatloch, Jan Hauke, Julia Rey, Christian Jackisch, Peter Klare, Theresa Link, Claus Hanusch, Jens Huober, Andrea Stefek, Sabine Seiler, Wolfgang D. Schmitt, Christoph Uleer, Gabriele Doering, Kerstin Rhiem, Andreas Schneeweiss, Carsten Denkert, Rita K. Schmutzler, Eric Hahnen, Michael Untch, Valentina Nekljudova, Jens-Uwe Blohmer, Sibylle Loibl. Neoadjuvant paclitaxel/olaparib in comparison to paclitaxel/carboplatinum in patients with HER2-negative breast cancer and homologous recombination deficiency – long-term survival of the GeparOLA study [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 GS5-02.