Study of Secondary Epimutations in Cis of the Promoter in Germline Tumor Suppressor Genes As a Cause of Hereditary Breast and Ovarian Cancer

Cancer is a multifactorial and highly heterogeneous disease. Breast cancer (BC) is the main malignant neoplasm in women and has the highest incidence and mortality rates worldwide. About 10% of all BC cases are hereditary and its most common form is Hereditary Breast and Ovarian Cancer Syndrome (HBOC).In a study conducted by our research group in a cohort of 300 Mexican women with HBOC using a panel of 143 genes of susceptibility to different types of cancer (Quezada-Urban et al., 2018), we found that 74% of patients were negative for variants in the coding regions and only 15% of patients had at least one pathogenic variant in 18 different genes. In several types of hereditary cancer syndromes, it has been shown that germline genetic alterations such as single nucleotide variations, and indels in cis of the promoter region of tumor suppressor genes modify the methylation pattern and cause epigenetic silencing and the concomitant somatic loss of heterozygosity. These events are known as secondary cis epimutations and represent an alternative mechanism of molecular pathogenesis in patients with hereditary cancer syndromes. In this work we are investigating in germline gDNA the methylation profile in the promoter region of 18 tumor suppressor genes in 231 patients negative for pathogenic variants and 156 matched controls by using direct bisulfite massive parallel sequencing. So far, we have extracted gDNA and treated with sodium bisulfite from all patient and control samples. From the converted gDNA, we amplified the promoter region of the 18 study genes by PCR (9,675 endpoint PCR products). We have prepared a total of 387 genomic libraries from which we perform massive sequencing and bioinformatic analysis of 229 patients, 74 controls and 2 positive controls. Currently, we have found 4 patients with promoter hypermethylation in the RAD51C, POLH, EPCAM, and BRCA1 genes that can be generated by a secondary cis epimutation. We have found statistically significant differences in the methylation levels of the promoter regions of the BRCA1/2, PMS2, FANCI, MLH1, PALB2, POLH, ERCC3, ATM, MSH2, BRIP1, and EPCAM genes in patients compared with controls. This result suggests that low level basal methylation marks could be potential biomarkers of HBOC pathogenesis. Interestingly, our studies indicate that hypermethylation at the promoter of MSH2, PALB2, BRIP1, and EPCAM are associated with HBOC risk, and that specific hypermethylation at the CpG sites of MSH2 and PALB2 (cg47630224 and cg23652916, respectively), could be potential biomarkers in HBOC risk. Lastly, according to preliminary in silico results, the co-occurrence of site-specific hypermethylation in MSH2 and PALB2 is possibly due to the absence of interaction of the common transcription factor SP4 in a GC-box site. These findings expand our vision of the genetic and epigenetic mechanisms of susceptibility to this disease. Citation Format: Miguel Ruiz De La Cruz, Héctor Martínez Gregorio, Clara Estela Díaz Velásquez, Aldo Hugo De La Cruz Montoya, Fidel de la Cruz Hernández-Hernández, Felipe Vaca Paniagua. Study of secondary epimutations in cis of the promoter in germline tumor suppressor genes as a cause of hereditary breast and ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6003.