Abstract 6003: 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.

Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases

Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.

Comprehensive Genomic Profile of Heterogeneous Long Follow-Up Triple-Negative Breast Cancer and Its Clinical Characteristics Shows DNA Repair Deficiency Has Better Prognostic

Triple-negative breast cancer (TNBC) presents a marked diversity at the molecular level, which promotes a clinical heterogeneity that further complicates treatment. We performed a detailed whole exome sequencing profile of 29 Mexican patients with long follow-up TNBC to identify genomic alterations associated with overall survival (OS), disease-free survival (DFS), and pathologic complete response (PCR), with the aim to define their role as molecular predictive factors of treatment response and prognosis. We detected 31 driver genes with pathogenic mutations in TP53 (53%), BRCA1/2 (27%), CDKN1B (9%), PIK3CA (9%), and PTEN (9%), and 16 operative mutational signatures. Moreover, tumors with mutations in BRCA1/2 showed a trend of sensitivity to platinum salts. We found an association between deficiency in DNA repair and surveillance genes and DFS. Across all analyzed tumors we consistently found a heterogeneous molecular complexity in terms of allelic composition and operative mutational processes, which hampered the definition of molecular traits with clinical utility. This work contributes to the elucidation of the global molecular alterations of TNBC by providing accurate genomic data that may help forthcoming studies to improve treatment and survival. This is the first study that integrates genomic alterations with a long follow-up of clinical variables in a Latin American population that is an underrepresented ethnicity in most of the genomic studies.

Comprehensive Analysis of Germline Variants in Mexican Patients with Hereditary Breast and Ovarian Cancer Susceptibility

Hereditary breast and ovarian cancer syndrome (HBOC) represents 5⁻10% of all patients with breast cancer and is associated with high-risk pathogenic alleles in BRCA1/2 genes, but only for 25% of cases. We aimed to find new pathogenic alleles in a panel of 143 cancer-predisposing genes in 300 Mexican cancer patients with suspicion of HBOC and 27 high-risk patients with a severe family history of cancer, using massive parallel sequencing. We found pathogenic variants in 23 genes, including BRCA1/2. In the group of cancer patients 15% (46/300) had a pathogenic variant; 11% (33/300) harbored variants with unknown clinical significance (VUS) and 74% (221/300) were negative. The high-risk group had 22% (6/27) of patients with pathogenic variants, 4% (1/27) had VUS and 74% (20/27) were negative. The most recurrent mutations were the Mexican founder deletion of exons 9-12 and the variant p.G228fs in BRCA1, each found in 5 of 17 patients with alterations in this gene. Rare VUS with potential impact at the protein level were found in 21 genes. Our results show for the first time in the Mexican population a higher contribution of pathogenic alleles in other susceptibility cancer genes (54%) than in BRCA1/2 (46%), highlighting the high locus heterogeneity of HBOC and the necessity of expanding genetic tests for this disease to include broader gene panels.