Altered expression and mutations in cell cycle genes CCND1, CDK4, CDKN2B and TP53 are associated with Pakistani breast cancer patients

Background: Breast cancer impacts nearly one-third of women globally during their lifetime, with the risk increasing in those exhibiting elevated gene expression linked to genetic polymorphisms. In Pakistan, breast cancer ranks among the top 20 leading causes of death, affecting one in every nine women. Methods and Results: Gene expression analysis was performed by quantifying mRNA levels of CCND1, CDK4 , and CDKN2B genes using TaqMan probe-based reverse transcription quantitative PCR (RT-qPCR). In parallel, genomic DNA was extracted from breast tissue samples, and specific regions of the CCND1, CDK4, CDKN2B , and TP53 genes were amplified to identify nucleotide variants. Relative to adjacent normal breast tissue, upregulation of CCND1 and CDK4 was observed in 77.78% and 66.67% of cases, respectively, whereas CDKN2B was downregulated in 88.89% of samples. Variant analysis of CCND1 revealed three previously reported polymorphisms (rs55911137, rs3862792, rs9344). In CDK4 , two novel missense mutations were identified at codons 97 (D97N) and 114 (A114T), in addition to two known intronic variants, rs78130877 and rs2069502, located in introns 3 and 4, respectively. Furthermore, a nonsense mutation was detected in TP53, involving a substitution at codon 169 that replaced methionine with a premature stop codon (AUG → UAG), potentially impairing protein structure and function. Conclusion: The observed upregulation of CCND1 and CDK4 , along with the downregulation of CDKN2B and the presence of genetic mutations in these genes and TP53 , may serve as significant biomarkers for breast cancer. These findings could aid in disease prognosis, inform treatment strategies, and support diagnostic efforts.