Comprehensive functional genomic analyses link APC somatic mutation and mRNA-miRNA networks to the clinical outcome of stage-III colorectal cancer patients

Biomedical Journal

Jeng-Fu You¹  Po-Jung Huang¹  En Chin²  Jiarong Lin³  Yu-Hao Liu⁴  Hsuan Liu⁵  Heng-Hsuan Huang⁶  Jy-Ming Chiang⁷  Jau-Song Yu⁸  Ian Yi-Feng Chang⁹  Bertrand Chin-Ming Tan^1,10  Sum-Fu Chiang^1,10  Wen-Sy Tsai^1,11  Hsin-Yuan Hung^1,11  Chia-Yu Yang^1,11  Pei-Shan Lu^1,11 

[1] Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan;Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan;Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan;;Department of Otolaryngology-Head &Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan;Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan;Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan;Neck Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan;Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan;Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan;

关键词: Colorectal cancer;    Next-generation sequencing;    Adenomatous polyposis coli;    Transcriptome;    Exome;   

DOI  :  

来源: DOAJ

【 摘 要 】

Background: Colorectal cancer (CRC) is a major health concern globally, but exhibits regional and/or environmental distinctions in terms of outcome especially for patients with stage III CRC. Methods: From 2014 to 2016, matched pairs of tumor and adjacent normal tissue samples from 60 patients with stage I–IV CRC from Chang Gung Memorial Hospital in Taiwan were analyzed using next-generation sequencing. The DNA, mRNA, and miRNA sequences of paired tumor tissues were profiled. An observational study with survival analysis was done. Online datasets of The Cancer Genome Atlas (TCGA) and The International Cancer Genome Consortium (ICGC) were also integrated and compared. Results: The gene that exhibited the highest mutation rate was adenomatous polyposis coli (APC) (75.0%), followed by TP53 (70.0%), KRAS (56.6%), and TTN (48.3%). APC was also the most frequently mutated gene in TCGA and ICGC datasets. Surprisingly, for non-metastatic cases (stages I-III), CRC patients with mutated APC had better outcome in terms of overall survival (p = 0.041) and recurrence free survival (p = 0.0048). Particularly for stage III CRC, the overall survival rate was 94.4% and 67.7%, respectively (p = 0.018), and the recurrence free survival rate was 94.4% and 16.7%, respectively (p = 0.00044). Further clinical and gene expression analyses revealed that the APC wt specimens to a greater extent exhibit poor differentiation state as well as EGFR upregulation, providing molecular basis for the poor prognosis of these patients. Finally, based on integrated transcriptome analysis, we constructed the mRNA-miRNA networks underlying disease recurrence of the stage III CRC and uncovered potential therapeutic targets for this clinical condition. Conclusion: For stage III CRC, patients with mutated APC had better overall and recurrence free survival.

【 授权许可】

Unknown