BRCA1 Promoter Methylation Research Articles

Methylation of BRCA1 promoter in sporadic breast cancer.

Methylation of BRCA1 promoter in sporadic breast cancer.

Clinicopathological features, genetic alterations, and BRCA1 promoter methylation in Japanese male patients with breast cancer

PurposeMale breast cancer (MBC) is a rare cancer accounting for only 1% of all male cancers and is, therefore, poorly studied. We aimed to characterize the subtypes of MBC in Japanese patients based on genetic profiling, the presence of tumor-infiltrating cells, and the expression of immunohistochemical markers.MethodsThis retrospective study included 103 patients with MBC diagnosed between January 2009 and December 2019 at various hospitals in Japan. Clinicopathological patient characteristics were obtained from medical records, and formalin-fixed paraffin-embedded tissue specimens were analyzed for histological markers, mutations of 126 genes, BRCA1 methylation, and stromal tumor-infiltrating lymphocytes.ResultsThe median patient age was 71 (range 31–92) years. T1-stage tumors were the most frequent (47.6%), and most were node negative (77.7%). The majority of tumors were positive for estrogen receptor (98.1%), progesterone receptor (95.1%), and androgen receptor (96.1%), and BRCA2 was the most frequently mutated gene (12.6%). The most common treatment was surgery (99.0%), either total mastectomy (91.1%) or partial mastectomy (7.0%). Survival analysis showed a 5-year recurrence-free survival rate of 64.4% (95% confidence interval [CI] 46.7–88.8) and a 5-year overall survival rate of 54.3% (95% CI 24.1–100.0).ConclusionJapanese MBC is characterized by a high rate of hormonal receptor positivity and BRCA2 somatic mutation. Due to the observed clinicopathological differences in MBC between the Western countries and Japan, further prospective studies are needed to evaluate the most suitable treatment strategies.

Clinical and molecular characteristics of ARIEL3 patients who derived exceptional benefit from rucaparib maintenance treatment for high-grade ovarian carcinoma

ObjectiveARIEL3 (NCT01968213) is a placebo-controlled randomized trial of the poly(ADP-ribose) polymerase inhibitor rucaparib as maintenance treatment in patients with recurrent high-grade ovarian carcinoma who responded to their latest line of platinum therapy. Rucaparib improved progression-free survival across all predefined subgroups. Here, we present an exploratory analysis of clinical and molecular characteristics associated with exceptional benefit from rucaparib. MethodsPatients were randomized 2:1 to receive rucaparib 600 mg twice daily or placebo. Molecular features (genomic alterations, BRCA1 promoter methylation) and baseline clinical characteristics were evaluated for association with exceptional benefit (progression-free survival ≥2 years) versus progression on first scan (short-term subgroup) and other efficacy outcomes. ResultsRucaparib treatment was significantly associated with exceptional benefit compared with placebo: 79/375 (21.1%) vs 4/189 (2.1%), respectively (p < 0.0001). Exceptional benefit was more frequent among patients with favorable baseline clinical characteristics and with carcinomas harboring molecular evidence of homologous recombination deficiency (HRD). A comparison between patients who derived exceptional benefit from rucaparib and those in the short-term subgroup revealed both clinical markers (no measurable disease at baseline, complete response to latest platinum, longer penultimate platinum-free interval) and molecular markers (BRCA1, BRCA2, RAD51C, and RAD51D alterations and genome-wide loss of heterozygosity) significantly associated with exceptional benefit. ConclusionsExceptional benefit in ARIEL3 was more common in, but not exclusive to, patients with favorable clinical characteristics or molecular features associated with HRD. Our results suggest that rucaparib can deliver exceptional benefit to a diverse set of patients with recurrent high-grade ovarian carcinoma.

Alterations in Homologous Recombination-Related Genes and Distinct Platinum Response in Metastatic Triple-Negative Breast Cancers: A Subgroup Analysis of the ProfiLER-01 Trial.

Background: a specific subset of metastatic triple-negative breast cancers (mTNBC) is characterized by homologous recombination deficiency (HRD), leading to enhanced sensitivity to platinum-based chemotherapy. Apart from mutations in BRCA1/2 genes, the evaluation of other HRD-related alterations has been limited to date. As such, we analyzed data from mTNBC patients enrolled in the ProfiLER-01 study to determine the prevalence of alterations in homologous recombination-related (HRR) genes and their association with platinum sensitivity. Methods: next-generation sequencing and promoter methylation of BRCA1 and RAD51C were performed on tumors from patients with mTNBC, using a panel of 19 HRR genes. Tumors were separated into three groups based on their molecular status: mutations in BRCA1/2, mutations in other HRR genes (BRCA1/2 excluded) or BRCA1/RAD51C promoter methylation and the absence of molecular alterations in HRR genes (groups A, B and C, respectively). Sensitivity to platinum-based chemotherapy was evaluated through the radiological response. Results: mutations in BRCA1/2 were detected in seven (13.5%) patients, while alterations in other HRR genes or hypermethylation in BRCA1 or RAD51C were reported in 16 (30.7%) patients; furthermore, no alteration was found in the majority of patients (n = 29; 55.8%). Among 27 patients who received platinum-based chemotherapy, the disease control rate was 80%, 55% and 18% (groups A, B and C, respectively; p = 0.049). Regarding group B, patients with disease control exhibited mutations in FANCL, FANCA and the RAD51D genes or RAD51C methylation; Conclusion: mutations in HRR genes and epimutations in RAD51C were associated with disease control through platinum-based chemotherapy. As such, apart from well-characterized alterations in BRCA1/2, a more comprehensive evaluation of HRD should be considered in order to enlarge the selection of patients with mTNBC that could benefit from platinum-based chemotherapy.

Highlights from Recent Cancer Literature

Breaking Insights| September 16 2022 Highlights from Recent Cancer Literature Author & Article Information Online ISSN: 1538-7445 Print ISSN: 0008-5472 ©2022 American Association for Cancer Research2022American Association for Cancer Research Cancer Res (2022) 82 (18): 3189–3190. https://doi.org/10.1158/0008-5472.CAN-82-18-BI Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record September 16 2022 Citation Highlights from Recent Cancer Literature. Cancer Res 15 September 2022; 82 (18): 3189–3190. https://doi.org/10.1158/0008-5472.CAN-82-18-BI Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search Although BRCA1/2 alterations have been reported to predict platinum sensitivity, BRCA1 alterations have not consistently correlated with platinum sensitivity in clinical trials. Menghi and colleagues have now identified an explanation for these discordant results. They found that in contrast to BRCA1/2 mutations, BRCA1 promoter methylation (BRCA1meth) was not correlated with response to platinum agents in triple-negative breast and ovarian cancer patients. In vivo studies revealed that BRCA1meth is lost during chemotherapy treatment, leading to BRCA1 reactivation and acquired platinum resistance. Expert Commentary: This study suggests that the reversibility of BRCA1meth may explain the inconsistent platinum efficacy observed in BRCA1-deficient tumors. Menghi F, Banda K, Kumar P, Straub R, Dobrolecki L, Rodriguez IV, et al. Genomic and epigenomic BRCA alterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas. Science Translational Medicine 2022;14:eabn1926. doi: 10.1126/scitranslmed.abn1926. Promoter methylation of the... You do not currently have access to this content.

Constitutional BRCA1 Methylation and Risk of Incident Triple-Negative Breast Cancer and High-grade Serous Ovarian Cancer

About 25% of all triple-negative breast cancers (TNBCs) and 10% to 20% of high-grade serous ovarian cancers (HGSOCs) harbor BRCA1 promoter methylation. While constitutional BRCA1 promoter methylation has been observed in normal tissues of some individuals, the potential role of normal tissue methylation as a risk factor for incident TNBC or HGSOC is unknown. To assess the potential association between white blood cell BRCA1 promoter methylation and subsequent risk of incident TNBC and HGSOC. This case-control study included women who were participating in the Women's Health Initiative study who had not received a diagnosis of either breast or ovarian cancer before study entrance. A total of 637 women developing incident TNBC and 511 women developing incident HGSOC were matched with cancer-free controls (1841 and 2982, respectively) in a nested case-control design. Cancers were confirmed after central medical record review. Blood samples, which were collected at entry, were analyzed for BRCA1 promoter methylation by massive parallel sequencing. The study was performed in the Mohn Cancer Research Laboratory (Bergen, Norway) between 2019 and 2022. Associations between BRCA1 methylation and incident TNBC and incident HGSOC were analyzed by Cox proportional hazards regression. Of 2478 cases and controls in the TNBC group and 3493 cases and controls in the HGSOC group, respectively, 7 (0.3%) and 3 (0.1%) were American Indian or Alaska Native, 46 (1.9%) and 30 (0.9%) were Asian, 1 (0.04%) and 1 (0.03%) was Native Hawaiian or Pacific Islander, 326 (13.2%) and 125 (3.6%) were Black or African, 56 (2.3%) and 116 (3.3%) were Hispanic, 2046 (82.6%) and 3257 (93.2%) were White, and 35 (1.4%) and 35 (1.0%) were multiracial. Median (range) age at entry was 62 (50-79) years, with a median interval to diagnosis of 9 (TNBC) and 10 (HGSOC) years. Methylated BRCA1 alleles were present in 194 controls (5.5%). Methylation was associated with risk of incident TNBC (12.4% methylated; HR, 2.35; 95% CI, 1.70-3.23; P < .001) and incident HGSOC (9.4% methylated; HR, 1.93; 95% CI, 1.36-2.73; P < .001). Restricting analyses to individuals with more than 5 years between sampling and cancer diagnosis yielded similar results (TNBC: HR, 2.52; 95% CI, 1.75-3.63; P < .001; HGSOC: HR, 1.82; 95% CI, 1.22-2.72; P = .003). Across individuals, methylation was not haplotype-specific, arguing against an underlying cis-acting factor. Within individuals, BRCA1 methylation was observed on the same allele, indicating clonal expansion from a single methylation event. There was no association found between BRCA1 methylation and germline pathogenic variant status. The results of this case-control suggest that constitutional normal tissue BRCA1 promoter methylation is significantly associated with risk of incident TNBC and HGSOC, with potential implications for prediction of these cancers. These findings warrant further research to determine if constitutional methylation of tumor suppressor genes are pancancer risk factors.

587P Sequential approach to determine the HRD status with BRCA1 promotor methylation status and shallow whole genome sequencing (sWGS)

High-grade serous ovarian cancer (HGSOC) is now characterized by the status deficient (HRD) or proficient (HRP) of homologous recombination repair (HR). This status is currently determined by the screening of tumoral BRCA1/2 mutation and the Genomic Instability score (GIS) first developed by Myriad. Our goal is to test and develop other simpler and less expensive approach to determine the HR status with BRCA1 promoter methylation status and shallow whole genome sequencing (sWGS) profile.

MicroRNA-126 expression in the peripheral white blood cells of patients with breast and ovarian cancer is a potential biomarker for the early prediction of cancer risk in the carriers of methylated BRCA1.

Constitutive breast cancer type 1 gene (BRCA1) promoter methylation is associated with increased cancer risk, but its role in cancer-free (CF) female carriers is incompletely understood. MicroRNA (miR) is modulated during early tumorigenesis. The present study assessed the modulation of miR-126 expression in the peripheral white blood cells (WBC) of patients with breast cancer (BC) and ovarian cancer (OC) as a biomarker of cancer risk in BRCA1 methylation carriers. A total of 1,114 female subjects [502 patients with BC, 187 patients with OC and 425 CF volunteers] were involved. Screening for BRCA1 promoter methylation in WBC was performed using the methylation–specific polymerase chain reaction (PCR) assay, BRCA1 mRNA was analyzed using a reverse transcription-quantitative PCR assay and miR-126 expression was analyzed using a stem-loop RT-qPCR assay. WBC BRCA1 promoter methylation status was significantly associated with OC (P=0.0266), early-onset BC (P=0.0003) and triple-negative BC (P=0.0066). Notably, 9.4% of the CF group exhibited WBC BRCA1 promoter methylation. In addition, high levels of miR-126 in WBCs were detected in all three groups. The increased level of miR-126 was significantly associated with a lower risk of distant metastasis (P=0.045) in BC, but a higher risk of disease progression and death (P=0.0029) in OC. There was a positive correlation between BRCA1 mRNA and miR-126 levels in the WBCs of all three groups, regardless of BRCA1 promoter methylation status. Notably, circulating miR-126 level was decreased in the BC and OC groups, but not in the CF group. Together, these results suggest the likely involvement of miR-126 in the constitutional methylation of BRCA1 promoter-related malignancies. Therefore, miR-126 may be a candidate biomarker for the early prediction of BC and OC risk in CF BRCA1 methylation carriers.

The Great Majority of Homologous Recombination Repair-Deficient Tumors Are Accounted for by Established Causes.

Background: Gene-agnostic genomic biomarkers were recently developed to identify homologous recombination deficiency (HRD) tumors that are likely to respond to treatment with PARP inhibitors. Two machine-learning algorithms that predict HRD status, CHORD, and HRDetect, utilize various HRD-associated features extracted from whole-genome sequencing (WGS) data and show high sensitivity in detecting patients with BRCA1/2 bi-allelic inactivation in all cancer types. When using only DNA mutation data for the detection of potential causes of HRD, both HRDetect and CHORD find that 30–40% of cases that have been classified as HRD are due to unknown causes. Here, we examined the impact of tumor-specific thresholds and measurement of promoter methylation of BRCA1 and RAD51C on unexplained proportions of HRD cases across various tumor types. Methods: We gathered published CHORD and HRDetect probability scores for 828 samples from breast, ovarian, and pancreatic cancer from previous studies, as well as evidence of their biallelic inactivation (by either DNA alterations or promoter methylation) in HR-related genes. ROC curve analysis evaluated the performance of each classifier in specific cancer. Tenfold nested cross-validation was used to find the optimal threshold values of HRDetect and CHORD for classifying HR-deficient samples within each cancer type. Results: With the universal threshold, HRDetect has higher sensitivity in the detection of biallelic inactivation in BRCA1/2 than CHORD and resulted in a higher proportion of unexplained cases. When promoter methylation was excluded, in ovarian carcinoma, the proportion of unexplained cases increased from 26.8 to 48.8% for HRDetect and from 14.7 to 41.2% for CHORD. A similar increase was observed in breast cancer. Applying cancer-type-specific thresholds led to similar sensitivity and specificity for both methods. The cancer-type-specific thresholds for HRDetect reduced the number of unexplained cases from 21 to 12.3% without reducing the 96% sensitivity to known events. For CHORD, unexplained cases were reduced from 10 to 9% while sensitivity increased from 85.3 to 93.9%. Conclusion: These results suggest that WGS-based HRD classifiers should be adjusted for tumor types. When applied, only ∼10% of breast, ovarian, and pancreas cancer cases are not explained by known events in our dataset.

Constitutional BRCA1 methylation and risk of incident triple-negative breast cancer and high-grade serous ovarian cancer.

10509 Background: About 25% of all triple-negative breast cancer (TNBC) and 10–20% of high-grade serous ovarian cancers (HGSOC) harbor BRCA1 promoter methylation. While constitutional BRCA1 promoter methylation has been observed in normal tissues of some individuals, the potential role of normal tissue methylation as a risk factor for incident TNBC or HGSOC risk is unknown. Methods: The objective of this study was to assess potential correlation between white blood cell (WBC) BRCA1 promoter methylation and subsequent risk of incident TNBC and HGSOC. To do so, we analyzed samples from women participating in the Women’s Health Initiative (WHI) study who had not been diagnosed with either breast or ovarian cancer prior to study entrance. A total of n = 636 women developing incident TNBC and 509 women developing incident HGSOC were matched with cancer-free controls (n = 1838 and 2979) in a nested case-control design. Cancers were confirmed after central medical record review. Blood samples, collected at entry, were analyzed for BRCA1 promoter methylation by massive parallel sequencing. Associations between BRCA1 methylation and incident TNBC and incident HGSOC were analyzed by unconditional logistic regression. Results: Age at entry was 62 (median; range 50 to 79) years, with median interval to diagnosis of 9 (TNBC) and 10 (HGSOC) years. The presence of methylated BRCA1 alleles was significantly associated with higher risk of incident TNBC (OR 2.44, 95% CI 1.79–3.33; P &lt;.001) and incident HGSOC (OR 1.87, 95% CI 1.32–2.61; P &lt;.001). Restricting analyses to individuals with &gt; 5 years between sampling and cancer diagnosis yielded similar results (&gt; 5 years; TNBC: OR 2.53, 95% CI 1.81–3.54; P &lt;.001; HGSOC: OR 1.81, 95% CI 1.21–2.63; P =.003). Across individuals, methylation was not haplotype-specific, arguing against an underlying cis-acting factor. Within individuals, BRCA1 methylation was observed on the same allele, indicating clonal expansion from a single methylation event. Conclusions: Constitutional normal tissue BRCA1 promoter methylation is significantly associated with risk of incident TNBC and HGSOC with implications for prediction of these cancers not associated with germline mutations. These findings warrant further research to determine if constitutional methylation of tumor suppressor genes are pan-cancer risk factors.

Stochasticity in threshold of homologous recombination deficiency (HRD) score.

e17561 Background: HRD test from Myriad Inc. was approved by FDA as a biomarker for niraparib in ovarian cancer. Its threshold (as 42) was initially established by capturing 95% of tumors with BRCA1/2 mutation and BRCA1 promoter methylation in the training cohort. Here, we explored the stochasticity of such threshold, when the test noises themselves were concerned. Methods: We simulated HRD scores from figure 1 of Telli et al., 2016 by assigning the median from each histogram bin to the associated samples. The threshold was calculated, as described in the original paper, and the standard error (SE) and confidence interval (CI) for such threshold were estimated from bootstrapping the cohort. Furthermore, the entire cohort was down-sampled to determine the effect of sample size on the threshold. Results: The threshold of 42.5 was calculated from our simulated dataset, close to the original one, with SE of 1.62 and 95% CI of 40.75 - 47.5 for the bootstrap. As expected, SE steadily increased to 2.21, 2.84, 2.97 when the sample sizes decreased to 250, 230, and 210 respectively. When the dataset was further down-sampled to include only 200 BRCA deficient samples, SE increased to 3.76, and drastically, CI ranged between 36.5 and 51.2. Conclusions: We have showed there exists manifest stochasticity in the original threshold of 42 for the Myriad HRD test, which is likely close to platform noise in magnitude. The minimum size of BRCA deficient patients to obtain a stable threshold is 200, as shown in our study.

Investigation of BRCA1 methylation and FAT3 mutation as a potential biomarker in ovarian cancer samples

Ovarian cancer is one of the most dangerous and leading gynecological cancer with significant cancer related mortality among women. As the cancer detection is the key to increased survival, we aimed to test molecular markers in Ovarian Cancer (OC) Figo stage I, II and III tumor samples in order to identify genetic/epigenetic events having biomarker potential. Seven genes (BRCA1, IGFBP-3, DAPK1, RASSF1, CDKN2A, MLH1, and ANO5) were studied for their methylation status and three genes (FAT1, FAT3 and NF1) were tested for their mutation status on 24 ovarian cancer tumor samples and 10 normal ovarian tissue samples. The methylation frequency for BRCA1 and DAPK1 was found to be 83.3% and 8.3% respectively while no hypermethylation was observed for IGFBP-3, RASSF1, CDKN2A, ANO5 and MLH1 genes for selected CpG sites in all samples. BRCA1 hypermethylation was frequently found in serous (88.7%) than mucinous (66.6%) histotype (p < 0.035). Statistically, BRCA1 methylation was found commonly in older females (>45 year) (88%, n = 18), however, data was not significant (p < 0.25). BRCA1 methylation was also found to be associated with Figo stage III (78.5%) patients (p < 0.04), suggesting that this could be a late event in progression of ovarian cancers. Out of 24 OC samples, FAT1 (4.16%), FAT3(16.6%), and NF1 (8.3%) were found to be mutated for selected alleles. FAT3 mutation was recurrent in mucinous histology but did not display any significant correlation with clinic-pathological characteristics of tumor samples. Our study reports, frequent BRCA1 promoter methylation in serous and mucinous OC samples and therefore, it may serve as potential biomarker in therapeutic settings in future. FAT3 is an emerging diagnostic biomarker however, its clinical utility is required to be validated in a large cohort of ovarian cancer samples.

BRCA1 and RAD51C promotor methylation in human resectable pancreatic adenocarcinoma

BackgroundHomozygous Recombination Deficiency (HRD) is associated with sensitivity to PARP-inhibitors (PARPi) in different cancer types. In pancreatic adenocarcinoma (PA) the main cause of HRD is BRCA1/2 germline mutation and patients with mutations in BRCA1/2 may benefit from PARPi. Recently other mechanisms leading to HRD were described in different cancer types, including gene mutations and epigenetic changes such as promoter hypermethylation. In PA, BRCA1 promoter hypermethylation, a known mechanism of gene silencing, was recently described. However, results are discordant between North American studies (0.7% of PA) and Asian ones (up to 60% of PA) and the association with HRD is not clear. MethodsHere, we developed 2 quantifications methods to explore BRCA1 and RAD51C promoter methylation in a series of 121 Formalin Fixed-Paraffin-Embedded (FFPE) specimens from resected PA without neoadjuvant treatment. The methylation-specific PCR was done with 2 different methods after DNA bisulfite conversion: a digital droplet PCR, and a PCR followed by capillary electrophoresis, to score the methylated / non methylated ratios in tumor samples. Methods were validated for specificity and sensibility using 100, 20, 10, 5 and 0% methylated commercial DNA for fragment analysis with a detection cutoff of 5–10%. Limit of blank was defined as 5 dropplets/20µL for RAD51C and 1 dropplet/20µL for BRCA1 for ddPCR. Samples were reviewed by a pathologist, macrodissected before DNA extraction to obtain 50–60% of tumoral cells. DNAs were treated for bisulfite conversion and analyzed using both methods in parallel to known positive and negative controls in each run. Results and conclusionNo methylation at BRCA1 or RAD51C was found in this series of PA suggesting that HRD gene promoter methylation is a rare event in European patients.

Development and validation of a novel quantitative BRCA1 promoter methylation assay in ovarian carcinoma

BRCA1 methylation may confer homologous recombination deficiency (HRD) in ovarian carcinomas and loss of methylation can be a mechanism of therapeutic resistance. We sought to develop and validate a clinical grade, quantitative assay for BRCA1 promoter methylation and characterize the impact of BRCA1 methylation in ovarian carcinoma.

Unveiling Novel Therapeutic Drug Targets and Prognostic Markers of Triple Negative Breast Cancer.

Triple negative breast cancer represents multiple genomic and transcriptomic heterogeneities. Genetic and epigenetic changes emerging in TNBC help it in acquiring resistance against immunological response. Distant metastasis, lack of clinically targeted therapies and prognostic markers make it the most aggressive form of breast cancer. In this review, we showed that driver alterations in targeted genes AR, ERR, TIL, TAM, miRNA, mTOR and immunosuppressive cytokines are predominantly involved in complicating TNBC by inducing cell proliferation, invasion and metastasis, and by inhibiting apoptosis. The role of node status, cathepsin-D, Ki-67 index, CD3+TIL, BRCA1 promoter methylation value and p53 as an efficient prognostic factor have also been studied to predict the disease free and overall survival rate in TNBC patients. The present review article is an attempt to gain an insight with a new vision on the etiology of TNBC, its treatment strategies and prognostic marker to identify the outcome of standard therapies and to re-design future treatment strategies to provide maximum benefit to patients.

Basal expression of RAD51 foci predicts olaparib response in patient-derived ovarian cancer xenografts.

The search for biomarkers to evaluate ovarian cancer (OC) homologous recombination (HR) function and predict the response to therapy is an urgent clinical need to improve the selection of patients who could benefit from platinum- and olaparib (poly-ADP ribose polymerase inhibitors, PARPi)-based therapies. We used a large collection of OC patient-derived xenografts (PDXs) (n = 47) and evaluated their HR status based on BRCA1/2 mutations, BRCA1 promoter methylation and the HRDetect score. RAD51 foci were quantified in formalin-fixed, paraffin-embedded untreated tumour specimens by immunofluorescence and the messenger RNA expression of 21 DNA repair genes by real-time PCR. Tumour HR deficiency predicted both platinum and olaparib responses. The basal level of RAD51 foci evaluated in geminin-positive/replicating cells strongly inversely correlated with olaparib response (p = 0.011); in particular, the lower the foci score, the greater the sensitivity to olaparib, while low RAD51 foci score seems to associate with platinum activity. The basal RAD51 foci score is a candidate predictive biomarker of olaparib response in OC patients as it can be easily translatable in a clinical setting. Moreover, the findings corroborate the importance of OC-PDXs as a reliable tool to identify and validate biomarkers of response to therapy.

Examining the Prevalence of Homologous Recombination Repair Defects in ER+ Breast Cancers

Cancers with defects in the homologous recombination repair (HRD) pathway exhibit increased sensitivity to platinum agents and PARP inhibitors (PARPi). HRD can occur secondary to germline or somatic acquired genetic alterations in HR genes or BRCA1 promoter methylation, but a plurality of HRD cancers do not have known explanatory mechanisms. HRD is known to be most frequent in triple negative breast cancers. We sought to determine the frequency of HRD, defined by genomic signatures, in ER+/Her2- breast cancers, the largest segment of the overall breast cancer population.The Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) has made the whole-genomes of 2,658 cases available for analysis. We used the available breast cancer cases in this dataset as our study substrate and further categorized them as ER+/Her2-, TNBC, or unlabeled. Large-scale state transitions (LST) are well-described ultra-structural "genomic scars" that can be assessed and scored using computational techniques, and serve as an inference for HRD. LST has been associated with responsiveness to PARPi, consistent with its use as a surrogate for HRD. We dichotomized LST scores > = 15 as HRD. We further examined the prevalence of the single base substitution signature 3 (SBS3) and indel signature 6 (ID6) previously associated with BRCA1/2 cases by the PCAWG project as additional surrogates for HRD. The Mann-Whitney test was used to assess differences across groups.There were 73 breast cancer genomes contributed to PCAWG by the EU breast cancer cohort, all of which were labeled ER+/Her2-. There were 44 breast cancer genomes contributed by UK ("UK cohort") labeled TNBC. As expected, we observed statistically significant differences in mean LST scores and SBS3 between the ER+ and TNBC cohorts. Within the ER+/Her2- cohort, 11 of 73 cases (15%) had HRD as defined by high LST. The HRD status of these 11 cases is supported by elevated ID6 and SBS3 compared to the 62 cases with low LST.Our work suggests that HRD may be as prevalent as 15% in ER+Her2- breast cancer. Given the preponderance of ER+ breast cancer, women with ER+ breast cancer with HRD may outnumber the 40% of women with TNBC with HRD. In a future with rapid, clinical grade assays for HRD, many more breast cancer patients may be eligible for synthetically lethal combination therapies than previously anticipated.

Abstract 2044: Genomic scar score: a robust model to predict recombination repair deficient based on genomic instability

Abstract Background: Clinical benefit of PARP inhibitors or Platinum-based chemotherapy has been observed and well proved in BRCA mutation patients. However, there are other mechanisms to induce recombination repair deficient (HRD), such as BRCA methylation, ATM expression loss; HRR gene mutation in addition to BRCA mutation. Whether these complicated HRD events or phenotype could be measured by a unified model to accurately identify HRD positive patients is important. Methods: In this study, we use support vector machine method to build genomic scar (GS) model to predict HRD events, which takes different types of chromosomal copy number into consideration to evaluate genomic instability. The accuracy of GS model was tested by different NGS platform from WGS to two captured SNP Panel. GS status association with Cisplatin-based chemotherapy was also preliminarily validated. Results: GS model displayed more than 95% accuracy to detect BRCA-ness events and is also able to enrich different types of HRR dysfunction, such as HRR-related mutation or BRCA1 promoter methylation. Moreover, GS model can identify patient benefits from Cisplatin-based chemotherapy, and GS score (GSS) high group had longer progression free survival (PFS) than GSS low group (11 vs 8.5 months, HR=0.5, P=0.05). Meanwhile, GSS showed the high concordance among different NGS platform including WGS; two captured SNP Panels, which implied the high robustness of GS model. Conclusion: GS was a robust model to predict HRD and had the clinical potential to enrich patients who will response to PARP inhibitors and/or Platinum-based chemotherapy. Citation Format: Hao Wen, Shuang Yang, Xuejun Chen, Ying Weng, Changbin Zhu, Li Ruan, Hua Dong, Xiaohua Wu. Genomic scar score: a robust model to predict recombination repair deficient based on genomic instability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2044.

A DNA methylation-based liquid biopsy for triple-negative breast cancer

Here, we present a next-generation sequencing (NGS) methylation-based blood test called methylation DETEction of Circulating Tumour DNA (mDETECT) designed for the optimal detection and monitoring of metastatic triple-negative breast cancer (TNBC). Based on a highly multiplexed targeted sequencing approach, this assay incorporates features that offer superior performance and included 53 amplicons from 47 regions. Analysis of a previously characterised cohort of women with metastatic TNBC with limited quantities of plasma (<2 ml) produced an AUC of 0.92 for detection of a tumour with a sensitivity of 76% for a specificity of 100%. mDETECTTNBC was quantitative and showed superior performance to an NGS TP53 mutation-based test carried out on the same patients and to the conventional CA15-3 biomarker. mDETECT also functioned well in serum samples from metastatic TNBC patients where it produced an AUC of 0.97 for detection of a tumour with a sensitivity of 93% for a specificity of 100%. An assay for BRCA1 promoter methylation was also incorporated into the mDETECT assay and functioned well but its clinical significance is currently unclear. Clonal Hematopoiesis of Indeterminate Potential was investigated as a source of background in control subjects but was not seen to be significant, though a link to adiposity may be relevant. The mDETECTTNBC assay is a liquid biopsy able to quantitatively detect all TNBC cancers and has the potential to improve the management of patients with this disease.

Clinical and molecular characteristics of ARIEL3 patients who derived exceptional benefit from rucaparib maintenance treatment for high-grade ovarian cancer (HGOC).

5537 Background: ARIEL3 is a placebo-controlled randomized trial of the PARP inhibitor (PARPi) rucaparib as maintenance treatment in HGOC patients (pts) who responded to the latest line of platinum therapy (NCT01968213). Rucaparib improved progression-free survival (PFS) across all predefined subgroups. Here, we present an exploratory analysis of clinical and molecular characteristics associated with exceptional benefit from rucaparib. Methods: Pts were randomized 2:1 to receive rucaparib 600 mg BID or placebo. At the data cutoff of Dec 31, 2019, 33/375 (9%) and 1/189 (0.5%) pts were still ongoing and receiving rucaparib or placebo, respectively. Molecular features (genomic alterations, BRCA1 promoter methylation) and baseline clinical characteristics were compared between pts who derived exceptional benefit (PFS ≥2 yrs), and those with disease progression on first scan (≈12 wks; the short-term [ST] subgroup) within each treatment arm. Results: Of 564 pts, 83 (15%) showed exceptional benefit: 79/375 (21%) in the rucaparib arm and 4/189 (2%) in the placebo arm. Within the rucaparib arm, exceptional benefit pts had more favorable clinical prognostic factors at baseline compared with the ST subgroup (Table). While BRCA mutations were enriched in the rucaparib exceptional benefit subgroup, 34/79 (43%) of these pts were BRCA wild type. Among other biomarkers, RAD51C/D mutations were associated with exceptional benefit; low genome-wide loss of heterozygosity was enriched within the ST subgroup; and high BRCA1 methylation was present at similar fractions. Trends were similar in the placebo arm (Table). Conclusions: Exceptional benefit in ARIEL3 was more common in, but not exclusive to, pts with favorable clinical characteristics and known mechanisms of PARPi sensitivity. Our results suggest that rucaparib can deliver exceptional benefit to a diverse set of HGOC pts. Clinical trial information: NCT01968213. [Table: see text]