Exploration of BRCA1 and BRCA2 mutations in gastric cancer patients through next generation sequencing: implications for diagnosis and therapy

Abstract

Objectives: The study aims to characterize BRCA1/2 mutations in Pakistani gastric cancer (GC) patients, identifying unique pathogenic variants and evaluating their potential as diagnostic biomarkers, while also exploring therapeutic avenues for personalized treatment strategies.

Methodology: In this study, we investigated the role of Breast Cancer gene 1 (BRCA1) and Breast Cancer gene 2 (BRCA2) mutations in Pakistani GC patients and their functional implications using Next-Generation Sequencing (NGS).

Results: Through NGS, we identified a total of 19 mutations in BRCA1 and 11 mutations in BRCA2, all with high mutation quality scores. In silico analysis revealed one pathogenic mutation in BRCA1 and one in BRCA2, indicating a potential link to disease development. Notably, two pathogenic mutations (BRCA1 p.Ala1823Ser and BRCA2 p.Gln92fs) were exclusively observed in the Pakistani GC population, suggesting unique genetic markers. Further examination utilizing The Cancer Genome Atlas (TCGA) data confirmed the absence of these mutations in non-Pakistani GC samples, emphasizing their specificity. Sanger sequencing validated these findings. Real Time Quantitative PCR (RT-qPCR) analysis indicated significantly decreased BRCA1/2 gene expression in samples harboring pathogenic mutations, suggesting their potential as biomarkers for GC diagnosis. Immunohistochemistry corroborated this by showing reduced protein expression levels in mutated samples. Enrichment analysis highlighted associations of BRCA1/2 genes with DNA damage response pathways and cancer-related processes. DrugBank exploration revealed potential therapeutic agents targeting mutated BRCA1/2, such as Cisplatin and Estradiol, offering new avenues for treatment.

Conclusion: Our study identifies novel BRCA1/2 mutations specific to Pakistani GC patients, suggesting a distinct genetic susceptibility profile. These findings not only contribute to understanding GC pathogenesis but also hold implications for personalized treatment strategies in this population.

Keywords: BRCA genes; diagnosis; next generation sequencing; treatment.

Figure 1

This figure illustrates a comprehensive summary of mutations identified in both the overall and pathogenic categories within the BRCA1/2 genes among gastric cancer (GC) patients utilizing Whole Exome Sequencing (WES). A. Provides an overview of the total count of detected mutations in BRCA1/2 genes among GC patients. B. Specifically highlights the count of pathogenic mutations in BRCA1/2 genes among GC patients.

Figure 2

This figure displays visual representations employing oncoplots and lollipop plots to illustrate the observed BRCA1/2 mutations within The Cancer Genome Atlas (TCGA) gastric cancer (GC) patient cohort. The two rows depict the percentage of samples featuring BRCA1/2 mutations, and the accompanying lollipop plots emphasize the protein-level amino acid alterations resulting from these mutations.

Figure 3

This figure showcases a representative DNA sequencing chromatogram capturing the BRCA1/2 pathogenic mutations observed in gastric cancer (GC) samples.

Figure 4

This figure presents an evaluation of relative expression and receiver operating characteristics (ROC) curve analyses for BRCA1/2 genes, comparing groups of gastric cancer (GC) samples with pathogenic mutations and those without. (A) Illustrates the analysis of relative expression for BRCA1/2 genes using RT-qPCR, while (B) displays ROC curves derived from RT-qPCR expression data for BRCA1/2 genes. The classification threshold was set at a significance level of P<0.05.

Figure 5

This figure presents the proteomic expression analysis of BRCA1/2 proteins, conducted through immunohistochemistry (IHC), to compare gastric cancer (GC) samples with pathogenic mutations against those without. (A) Presents IHC images of the BRCA1 protein in GC tissues samples, and (B) presents IHC images of the BRCA2 protein in GC tissues samples. Variations in expression were evaluated by examining staining intensities.

Figure 6

This figure illustrates the outcomes of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses conducted on BRCA1/2 genes via Metascape. (A) Displays Cellular Component (CC) terms related to BRCA1/2 genes, (B) Highlights Molecular Function (MF) terms, (C) Showcases Biological Process (BP) terms, and (D) Outlines Kyoto Encyclopedia of Genes and Genomes (KEGG) terms associated with BRCA1/2 genes. A significance level of P<0.05 served as the cutoff criterion.