Comprehensive genomic profiling of male breast cancer patients with multiple primary tumors through matched germline and somatic whole exome sequencing

Male breast cancer (MBC) is a rare disease with strong genetic associations. Germline pathogenic variants (PVs) in the BRCA1/2 genes account for approximately 15% of MBC cases, while recent studies have identified an additional 5% of cases harboring PVs in non-BRCA1/2 genes. The personal and family history of non-BRCA1/2 MBC patients suggests an unexplained genetic predisposition that requires further investigation. In this study, we selected MBC cases with multiple primary tumors and applied whole exome sequencing (WES) to matched germline and somatic samples, aiming to uncover previously unknown genetic susceptibility factors for MBC and provide a comprehensive overview of somatic driver mutations in both breast and other cancer types in male patients. Thirteen MBC cases with multiple primary tumors, including prostate, stomach, colon, kidney, lung, skin, tongue, and urinary bladder cancers, were included. WES was performed on matched germline and tumor DNA, comprising 35 samples in total. The sequencing data were processed using the DRAGEN Enrichment pipeline (Illumina) and subsequently analyzed with a customized bioinformatics pipeline to identify candidate germline PVs, driver somatic variants, and shared molecular pathways across the different tumors in each MBC patient. We identified eight germline PVs in 5 out of 13 (38.5%) MBC cases, which were found in established or candidate cancer-associated genes, including ATM, BRCA2, E2F4, ERCC3, FH, NTHL1, TGM4, and ZFHX3. Utilizing the available tumor samples, we also investigated loss of heterozygosity (LOH) in somatic samples, but no LOH was detected for the identified germline PVs. In the somatic analysis, NOTCH1 emerged as one of the most frequently mutated genes in breast tumor samples. Among the other tumor types, a colon cancer sample showed the highest number of somatic mutations and exhibited microsatellite stability (MSS) and POLE mutations, consistent with the MSS ultra-mutated phenotype observed in POLE-mutated colon cancers. Additionally, 26 actionable somatic alterations were identified, with TP53 and PIK3CA being the most frequently altered genes. Consistent with previous findings, PIK3CA was the most commonly mutated gene in breast tumor samples specifically. Notably, an actionable alteration in TSC2 was detected in a kidney cancer sample. By comparing tumor-normal data across the breast and other primary tumors in the same patient, we identified shared driver somatic mutations and pathways. In some cases, tumors shared a single driver mutation, while in others, they shared mutations within cancer-relevant pathways. These findings underscore the importance of analyzing global somatic mutation patterns to identify key pathways and genes involved in cancer. Overall, this matched germline and somatic analysis providing a comprehensive genomic profiling of MBC patients add new insights into the genetic susceptibility of MBC and identifies potential actionable somatic alterations, with significant implications for cancer prevention and personalized therapeutic strategies.