BRAF mutations and the association of V600E with CD133 and CDX2 expression in a Pakistani colorectal carcinoma cohort

• Published in: BMC cancer 2024-09, Vol.24 (1), p.1162-13, Article 1162
• Main Authors: Hassan, Sobia, Mirza, Talat, Khatoon, Ambrina, Bukhari, Uzma, Shaikh, Fouzia, Karim, Asad
• Format: Article
• Language: English
• Subjects: AC133 Antigen - genetics; AC133 Antigen - metabolism; Adult; Aged; Aged, 80 and over; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Cancer stem cells; Cancer therapies; CDX2 protein; CDX2 Transcription Factor - genetics; CDX2 Transcription Factor - metabolism; Cell differentiation; Clinical decision making; Cohort Studies; Colon cancer; Colorectal cancer; Colorectal carcinoma; Colorectal Neoplasms - genetics; Colorectal Neoplasms - metabolism; Colorectal Neoplasms - pathology; Development and progression; Drug resistance; Drug therapy; Ethanol; Female; Genetic; Genetic aspects; Genetic testing; Health aspects; Homology; Humans; Immunohistochemistry; Informed consent; Kinases; Male; Medical prognosis; Membrane proteins; Metastasis; Middle Aged; Mortality; Multivariate analysis; Mutation; Pakistan - epidemiology; Physiological aspects; Polymorphism; Population genetics; Population studies; Prominin-1; Proteins; Proto-Oncogene Proteins B-raf - genetics; Stem cells; Transcription factors; Vemurafenib
• ISSN: 1471-2407; 1471-2407
• DOI: 10.1186/s12885-024-12925-z

Despite a high incidence of colorectal carcinoma, data regarding genetic aberrations in colorectal carcinoma (CRC) patients in Pakistan is scarce. This study aimed to determine the frequency of BRAFV600E mutations in colorectal carcinoma tissue in the Pakistani population and to associate BRAFV600E expression with CD133, a marker of colorectal stem cells, and CDX2 marker of differentiation. Sanger Sequencing of exon 15 (426 bp) including the hotspot V600E was performed on formalin-fixed-paraffin-embedded (FFPE) CRC tissue samples of 115 patients. The samples were subjected to immunohistochemistry (IHC) to assess the expression of BRAFV600E, CDX2, and CD133. Additionally, homology modelling and docking were performed to investigate novel deletions revealed in sequencing. Twenty-four (20.8%) BRAF variants were identified in the coding region, with V600E mutations detected in 14 (12.2% )cases (GenBank: PP003258.1; Pop Set: 2678087296). Moreover, a wide spectrum of novel non-V600E mutations (8.6%) were identified, including deletions and missense variations. In-silico analysis revealed that due to large deletions in the coding region of three samples, the affinity of the anti-BRAF drugs (Encorafenib and Vemurafenib) for the active site decreased in comparison to the wild type. The IHC analysis showed that BRAFV600E expression was significantly associated with CD133 expression (χ  = 26.351; p =