Analysis of TP53 gene in breast cancer and comparison with the canine counterparts

Abstract

Cancer is marked by uncontrolled cell division with the potential to invade and spread to other tissues. Tumor suppressor genes (TSGs) like Tumor Protein p53 (TP53) are critical for cellular homeostasis, regulating processes such as the cell cycle, DNA repair, and apoptosis. Mutations in TP53 are common in cancers, including breast cancer, disrupting its tumor-suppressing function. This study investigated TP53 nucleotide variants in breast cancer patients from Punjab, Pakistan, to evaluate their impact on protein function and gene regulation. Blood samples were collected from ten breast cancer patients, and DNA was extracted using a standard organic method. DNA quality was assessed using a nanodrop spectrophotometer, and TP53 regions were amplified with specific primers for sequencing. Sequencing results were analyzed using bioinformatics tools: Chromas and bioedit for sequence visualization and editing, basic local alignment search tool (BLAST) for alignment with reference sequences, and Mutation Tester for identifying novel and known single nucleotide polymorphisms (SNPs). Express protein analysis system (EXPASY) compared normal and mutated codon and amino acid sequences, while protter and trrosetta modelled primary and 3D protein structures, respectively, to assess functional changes. The study identified several genetic variations. A cytosine deletion in exon 4 (NM_000546.6:c.528delC) caused a frameshift, producing a truncated protein (NP_000537.3:p.H178Tfs*69) in sample 4. Intron variants included an SNP (NM_000546.6:c.672+62A>G, Rs1625895) in samples 2, 3, 4, and 5, a cytosine deletion (NM_000546.6:c.783-56delC) in samples 2, 4, 5, 6, 7, and 10, and an adenine deletion (NM_000546.6:c.920-32delA, Rs1266367430) in sample 2. While the exon 4 mutation directly impacts protein structure, intronic mutations may influence splicing or gene regulation. Further studies with larger cohorts and transcriptomic or proteomic analyses are required to explore the functional implications of these mutations and their role in breast cancer pathogenesis, potentially revealing new therapeutic targets.