Identification of driving genes of familial adenomatous polyposis by differential gene expression analysis and weighted gene co-expression network analysis

• Published in: Technology and health care Vol. 32; no. 3; pp. 1675 - 1696
• Main Authors: Lin, Wan-Rong, Liu, Wei-Qing, Meng, Xuan-Yu, Liu, Xiao-Ting, Kou, Zhi-Yong, Li, Wen-Liang, Yang, Jun
• Format: Journal Article
• Language: English
• Published: London, England SAGE Publications 01.01.2024; Sage Publications Ltd; IOS Press
• Subjects: Adenoma; Adenomatous Polyposis Coli - genetics; Biomarkers; Biomarkers, Tumor - genetics; Cancer; Colorectal cancer; Familial adenomatous polyposis; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Genes; Genetic disorders; Humans; Krueppel-like factor; Metastases; Modules; Network analysis; Pathogenesis; Polymerase chain reaction; Polyps; Real-Time Polymerase Chain Reaction; TLR3 protein; Toll-like receptors; Tumors; DEGs; driver gene; WGCNA; Familial adenomatous polyposis; bioinformatics
• ISSN: 0928-7329; 1878-7401; 1878-7401
• DOI: 10.3233/THC-230719

BACKGROUND: Despite the advancement of new screening strategies and the advances in pharmacological therapies, the cancerization rates of familial adenomatous polyposis (FAP) are stable and even increased in the last years. Therefore, it necessitates additional research to characterize and understand the underlying mechanisms of FAP. OBJECTIVE: To determine the genes that drive the pathogenesis of familial adenomatous polyposis (FAP). METHODS: We performed on a cohort (GSE111156) gene profile, which consist of four group of gene expressions (the gene expressions of cancer, adenoma and normal tissue of duodenal cancer from patients with FAP were defined as Case N, Case A and Case C respectively, while that of adenoma tissue from patients with FAP who did not have duodenal cancer was Ctrl A). Tracking Tumor Immunophenotype (TIP) website was applied to reveal immune infiltration profile and signature genes of FAP. We merged the genes of key module (pink and midnight module) with signature genes to obtained the biomarkers related with FAP pathogenesis. The expression of these five biomarkers in FAP intratumoral region (IT) and tumor rim (TR) was detected with Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). RESULTS: In total, 220, 23 and 63 DEGs were determined in Cases C, A and N, in comparison to Ctrl A. In total, 196 and 10 DEGs were determined in Cases C and A, separately, as compared to Case N. A total of four biomarkers including CCL5, CD3G, CD2 and TLR3 were finally identified associated with pink module, while only one biomarker (KLF2) associated with midnight module was identified. All biomarkers were evidently raised in FAP IT tissues utilizing qRT-PCR. CONCLUSION: We identified five potential biomarkers for pathogenesis of FAP to understand the fundamental mechanisms of FAP progression and revealed some probable targets for the diagnosis or treatment of FAP.