BRCA1 Promoter Research Articles

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.

Mechanistic Insights into the Hypermethylation of BRCA1 Evinces a Novel Pathway to Breast Tumorigenesis

BackgroundBreast cancer is the most common and dreadful form of cancer globally. Inherited mutations in the breast cancer susceptibility gene, BRCA1, increases the cumulative risk of developing breast cancer by 70‐80%. However, hereditary mutations account for only 5‐10% of the breast cancer burden. At the same time, the rest of this menace is attributed to sporadic cases where patients rarely encounter a BRCA1 mutation. Instead, upto 60% of these patients manifest low BRCA1 expression associated with BRCA1 promoter hypermethylation—moreover, many hereditary cases with a mutated BRCA1 allele exhibit promoter hypermethylation in the second allele. Interestingly, most of these cases also develop into a hyper‐aggressive and drug‐resistant form, Triple Negative Breast Cancer (TNBC), where Estrogen Receptors (ER), Progesterone receptors (PR) and Human epidermal growth factor receptors (Her2) are absent or minimally expressed. But the molecular signaling governing this tumorigenesis has remained elusive with an unresolved question of whether promoter hypermethylation is the master controller of the process of tumorigenesis or is a mere consequence of tumor progression.Objective &amp; MethodologyTo unravel the truth behind this enigma, we induced site‐specific methylations in the CpG island of BRCA1 promoter on wildtype BRCA1 backgrounds using a modified version of CRISPR technology.ResultsInducing site‐specific methylation on the BRCA1 promoter effectuated its downregulation via alteration in the balance between its alternate transcripts ‘β’ and ‘α’. Methylation also attenuated the expression of a long noncoding RNA, NBR2 (Neighbor of BRCA1 gene 2), which is transcribed through the BRCA1 promoter in the reverse direction. It, in turn, activates a feedback loop leading to further downregulation of BRCA1 associated with impaired DNA damage repair and a shift in the balance between apoptosis and autophagy evident under glucose starvation conditions. Further, the β subunit of hCG (human chorionic gonadotrophin) hormone, which is often associated with aggressive forms of BRCA1 mutated breast cancers, was significantly overexpressed. With regards to TNBC progression, methylation also led to the downregulation of the hormone receptors except for ER‐ α, which was found to be overexpressed. This ER‐ α surge helps the cells survive the onslaught following DNA Damage under BRCA1 defective condition.ConclusionFor the first time, this study elucidates the molecular signaling behind breast tumorigenesis involving BRCA1 hypermethylation. Like BRCA1 mutation screening, our findings open up an outstanding opportunity for screening sporadic breast cancers in females using the combination of NBR2, β‐hCG, and BRCA1 hypermethylation as biomarkers from blood. Moreover, as therapeutic intervention, this study also provides scope for the use of BRCA1 hypermethylation reversing drugs like methotrexate, drugs like biguanides that show better action under NBR2 depleted conditions and development of β‐hCG inhibitors for a better prognosis.

PTEN Loss and BRCA1 Promoter Hypermethylation Negatively Predict for Immunogenicity in BRCA-Deficient Ovarian Cancer.

Ovarian cancers can exhibit a prominent immune infiltrate, but clinical trials have not demonstrated substantive response rates to immune checkpoint blockade monotherapy. We aimed to understand genomic features associated with immunogenicity in BRCA1/2 mutation-associated cancers. Using the Cancer Genome Atlas whole-exome sequencing, methylation, and expression data, we analyzed 66 ovarian cancers with either germline or somatic loss of BRCA1/2 and whole-exome sequencing, immunohistochemistry, and CyTOF in 20 ovarian cancers with germline BRCA1/2 pathogenic variants from Penn. We found two groups of BRCA1/2 ovarian cancers differing in their immunogenicity: (1) 37 tumors significantly enriched for PTEN loss (11, 30%) and BRCA1 promoter-hypermethylated (10, 27%; P = .0016) and (2) PTEN wild-type (28 of 29 tumors) cancers, with the latter group having longer overall survival (OS; P = .0186, median OS not reached v median OS = 66.1 months). BRCA1/2-mutant PTEN loss and BRCA1 promoter-hypermethylated cancers were characterized by the decreased composition of lymphocytes estimated by gene expression (P = .0030), cytolytic index (P = .034), and cytokine expression but higher homologous recombination deficiency scores (P = .00013). Large-scale state transitions were the primary discriminating feature (P = .001); neither mutational burden nor neoantigen burden could explain differences in immunogenicity. In Penn tumors, PTEN loss and high homologous recombination deficiency cancers exhibited fewer CD3+ (P = .05), CD8+ (P = .012), and FOXP3+ (P = .0087) T cells; decreased PRF1 expression (P = .041); and lower immune costimulatory and inhibitory molecule expression. Our study suggests that within ovarian cancers with genetic loss of BRCA1/2 are two subsets exhibiting differential immunogenicity, with lower levels associated with PTEN loss and BRCA hypermethylation. These genomic features of BRCA1/2-associated ovarian cancers may inform considerations around how to optimally deploy immune checkpoint inhibitors in the clinic.

BRCA2 promoter hypermethylation as a biomarker for the leukemic transformation of myeloproliferative neoplasms.

Aim: To characterize the actionable biomarker for leukemic transformation (LT) of myeloproliferative neoplasms (MPNs) at the DNA damage repair promoter methylation level. Materials & methods: Bioinformatic analysis and experimental validation were performed to identify the MPNs-LT specific biomarker out of the promoter methylation of 236 DNA damage repair genes with GSE42042 dataset and an in-house cohort of 80 MPNs. Results: Hypermethylation of BRCA2 promoter was characterized as the JAK2 mutation-independent epigenetic marker for MPNs-LT and repressed mRNA and protein expression, leading to olaparib hypersensitivity in the leukemic cells from MPNs-LT. Conclusion: Expressional silence of BRCA2 by promoter methylation compels the homologous recombination deficiency and vulnerability to PARP inhibition and serves as an actionable marker for targeted therapy for MPNs-LT.

Abstract P5-13-09: Identifying homologous recombination deficiency in breast cancer: Genomic instability score thresholds differ in breast cancer subtypes

Abstract Background: Patients with homologous recombin ation (HR) deficient tumors may benefit from treatment with DNA damaging agents. Markers of genomic instability can be used to identify HR deficiency, including a 3-biomarker Genomic Instability Score (GIS). For patients with ovarian cancer (OC), the FDA-approved GIS threshold for identifying HR deficiency is 42, set as the 5th percentile for BRCA deficient tumors. Recently, a lower 1st percentile cutoff of 33 was explored in OC; this threshold was significantly associated with improved outcome after platinum-based treatment.1,2 Determining an optimal GIS threshold for different types of tumors is crucial, as the GIS distribution may vary between different cancers and even between different cancer subtypes. We propose GIS thresholds for breast cancer separately for triple-negative breast cancer (TNBC) and estrogen receptor-positive (ER+) breast cancer, using the exploratory threshold of 33 for OC as a comparator. Methods: GISs in BRCA deficient tumors were determined for patients newly diagnosed with varying stages of OC, TNBC, or ER+ breast cancer across 5 cohorts (Timms et al,3 TCGA,4 Abkevich et al,5 TBCRC008,6 the OlympiaD trial7). GIS was determined as a combination of loss of heterozygosity, telomeric-allelic imbalance, and large-scale state transitions. BRCA deficiency was defined by loss of function resulting from a pathogenic variant in BRCA1 or BRCA2 or by methylation of the BRCA1 promoter region, with loss of heterozygosity in the affected gene. GIS distributions in different cancer types and subtypes were compared using the Kolmogorov-Smirnov test. A normal distribution was fit to GISs in BRCA deficient ER+ breast tumors. The 1st percentile of the fitted distribution was chosen as the threshold. Results: A total of 561 OC tumors (190 BRCA deficient), 99 TNBC tumors (44 BRCA deficient), and 406 ER+ breast tumors (76 BRCA deficient) were included across the 5 cohorts. When score distributions were evaluated for BRCA deficient tumors, the GIS distribution within ER+ breast cancer was significantly different than for OC (p=9.6x10-5) and TNBC (p=3.2x10-4). This indicates that different GIS thresholds are appropriate for breast cancer subtypes and that the GIS threshold developed for OC is not appropriate for ER+ breast cancer. The 1st percentile of a normal distribution fit in BRCA deficient ER+ breast cancer tumors yields a threshold of 24. Using this threshold, 45.1% (183/406; 75 BRCA deficient, 108 BRCA intact) of ER+ breast tumors were HR deficient. In contrast, the GIS distribution for TNBC was not significantly different than for OC (p=0.77). Using the exploratory threshold of 33, 63.6% (63/99; 44 BRCA deficient, 19 BRCA intact) of TNBC tumors were HR deficient. Conclusions: When compared to OC, the distribution of GIS in BRCA deficient tumors was different for ER+ breast cancer, but not for TNBC. These findings are consistent with the fact that OC and TNBC are known to have similar molecular signatures.8 Exploratory thresholds of 24 for ER+ breast cancer, and 33 for TNBC and OC could be examined to determine if these cutoffs are associated with a benefit from treatment with DNA targeting agents. Clinical validity and utility of these more inclusive 1% thresholds would require demonstration of correlation with clinical outcomes. The threshold difference observed between these cancer subtypes also suggests that cancer or cancer subtype specific thresholds may be needed as evaluations of HR deficiency expands beyond OC to identify candidates for PARP inhibitors.

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.

Value of the loss of heterozygosity to BRCA1 variant classification

At least 10% of the BRCA1/2 tests identify variants of uncertain significance (VUS) while the distinction between pathogenic variants (PV) and benign variants (BV) remains particularly challenging. As a typical tumor suppressor gene, the inactivation of the second wild-type (WT) BRCA1 allele is expected to trigger cancer initiation. Loss of heterozygosity (LOH) of the WT allele is the most frequent mechanism for the BRCA1 biallelic inactivation. To evaluate if LOH can be an effective predictor of BRCA1 variant pathogenicity, we carried out LOH analysis on DNA extracted from 90 breast and seven ovary tumors diagnosed in 27 benign and 55 pathogenic variant carriers. Further analyses were conducted in tumors with PVs yet without loss of the WT allele: BRCA1 promoter hypermethylation, next-generation sequencing (NGS) of BRCA1/2, and BRCAness score. Ninety-seven tumor samples were analyzed from 26 different BRCA1 variants. A relatively stable pattern of LOH (65.4%) of WT allele for PV tumors was observed, while the allelic balance (63%) or loss of variant allele (15%) was generally seen for carriers of BV. LOH data is a useful complementary argument for BRCA1 variant classification.

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.

BRCA1 promoter hypermethylation on circulating tumor DNA correlates with improved survival of patients with ovarian cancer.

Methylation of the BRCA1 promoter is an epigenetic gene expression regulator and is frequently observed in ovarian cancer; however, conversion of methylation status is thought to drive disease recurrence. Therefore, longitudinal monitoring of methylation status by liquid biopsy in cell‐free DNA may be a predictive marker. In total, 135 plasma samples were collected from 69 ovarian cancer patients before and during systemic treatment. Our liquid biopsy assay could detect down to a single molecule of methylated DNA in a high background of normal DNA (0.03%) with perfect specificity in control samples. We found that 60% of the cancer patients exhibited BRCA1 promoter hypermethylation at one point, although 24% lost hypermethylation during treatment. Multivariate survival analyses indicate that relapses are independent events and that hypermethylation and methylation conversion are independently correlated to longer relapse‐free survival. We present a highly sensitive and specific methylation‐specific quantitative PCR‐based liquid biopsy assay. BRCA1 promoter hypermethylation is frequently found in ovarian cancer and is often reversed upon recurrence, indicating the selection of therapy‐resistant clones and unfavorable clinical outcome.

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]

Molecular and clinical determinants of response and resistance to rucaparib for recurrent ovarian cancer treatment in ARIEL2 (Parts 1 and 2)

ARIEL2 (NCT01891344) is a single-arm, open-label phase 2 study of the PARP inhibitor (PARPi) rucaparib in relapsed high-grade ovarian carcinoma. In this post hoc exploratory biomarker analysis of pre- and post-platinum ARIEL2 samples, RAD51C and RAD51D mutations and high-level BRCA1 promoter methylation predict response to rucaparib, similar to BRCA1/BRCA2 mutations. BRCA1 methylation loss may be a major cross-resistance mechanism to platinum and PARPi. Genomic scars associated with homologous recombination deficiency are irreversible, persisting even as platinum resistance develops, and therefore are predictive of rucaparib response only in platinum-sensitive disease. The RAS, AKT, and cell cycle pathways may be additional modulators of PARPi sensitivity.

9P BRCA1 promoter methylation confers a more favorable prognosis to systemically untreated young triple-negative breast cancer patients than tumour BRCA1 mutation

The prognoses of systemically treated, triple-negative breast cancer (TNBC) patients with a pathogenic tumor BRCA1 mutation (tBRCA1m) or BRCA1 promoter methylation (BRCA1 PM) have been widely studied. However, the prognosis for systemically untreated women remains unknown. This study investigates the prognosis of systemically untreated young N0 TNBC patients according to tumor BRCA1 status.

Examination of ATM, BRCA1, and BRCA2 promoter methylation in patients with pancreatic cancer

BackgroundPancreatic cancer is a lethal disease with a poor 5-year survival rate. Pathogenic germline variants in the coding regions of ATM, BRCA1, and BRCA2 are found in up to 4.8% of pancreatic cancer patients. Germline promoter methylation and gene silencing arising from a germline variant or through other mechanisms have been described as a cause of tumor suppressor gene inactivation. MethodsWe measured the level of promoter methylation of the ATM, BRCA1, and BRCA2 genes in peripheral blood lymphocytes from 655 patients with pancreatic cancer using real-time PCR. ResultsNo evidence of germline promoter methylation of any of these genes was found. Promoter methylation levels were minimal with no patient having promoter methylation greater than 3.4%, 3.3%, and 7.6% for ATM, BRCA1 and BRCA2, respectively, well below levels found in patients who have inherited promoter methylation (∼50%). ConclusionsWe found no evidence of germline promoter methylation for the pancreatic susceptibility genes ATM, BRCA1 and BRCA2 in patients with pancreatic cancer. This study reveals that constitutive germline methylation of promoter CpG islands is rare in pancreatic cancer.

Prevalence of BRCA1 and BRCA2 genes promoter hypermethylation in breast cancer tissue.

Recent advances in the treatment of breast cancer (BC) have been related to the personalization of therapy. The methylation status of the promoter regions of tumor suppressor genes such as BRCA1and BRCA2is supposed to be useful as a prognostic factor in BC patients. To investigate the frequency of hypermethylation in the promoter regions of BRCA1and BRCA2genes in tumor tissue of BC patients, and the relation of hypermethylation to the clinical course of the disease. Molecular genetic studies were performed on 50BC tissue samples in order to determine the methylation status of the promoter regions of the BRCA1and BRCA2genes. Hypermethylation of the BRCA1promoter region was detected in 34% of BC cases, hypermethylation of the BRCA2promoter region- in 50% of cases, and hypermethylation of the promoter region of both genes- in 20% of cases. A significant increase in the incidence of hypermethylation of the BRCA2promoter region was found in the group of patients older than 56years, mainly in patients with triple-negative breast cancer and without family history of BC. The high frequency of hypermethylation in the promoter regions of BRCA1and BRCA2genes, as well as their co-methylation in tumor tissue of BC patients has been detected.

Loss of BRCA1 expression and morphological features associated with BRCA1 promoter methylation status in triple-negative breast cancer.

Aberrant DNA methylation in the BRCA1 promoter region causes epigenetic silencing of BRCA1 gene expression, which is critical for breast cancer development. However, how BRCA1 promoter methylation status alters histological features remains poorly understood. Here, we investigated the possibility to predict BRCA1 promoter methylation status based on the morphological and immunohistochemical features of triple-negative breast cancers (TNBCs). The morphological features of 53 TNBCs were evaluated with hematoxylin-eosin staining, with immunohistochemical staining of BRCA1, androgen receptor, p53, cytokeratin 5/6, and epidermal growth factor receptor. BRCA1 promoter methylation status was used to distinguish BRCA1 promoter-methylated tumors (BPMTs) from BRCA1 promoter-unmethylated tumors (BPUTs) dependent on pathological characteristics. BPMTs comprised approximately 26% of the TNBCs. Immunohistochemical analysis found that BRCA1 protein expression was significantly lower in BPMT compared with BPUT (p = 0.016). Morphologically, BPMTs were associated with high mitotic index (p = 0.017), pushing margin (p = 0.017), a circumscribed growth pattern (p = 0.014), and a syncytial growth pattern (p = 0.034) compared with BPUTs. We then assessed the potential of predicting BRCA1 promoter methylation status by using published score systems based on these morphological characteristics. A receiver operating characteristic analysis showed an area under the curve of 0.80. This study found that BRCA1 promoter methylation status could be derived from morphological features and lower BRCA1 expression of TNBCs, which may help identify suitable cases for target treatment with PARP inhibitors.