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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
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Comprehensive transcriptomic profiling and mutational landscape of primary gastric linitis plastica
Zhu Liu1, Lian-Lian Hong1, Jin-Sen Zheng1
1Zhejiang Cancer Institute, Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, People's Republic of China.
Summary
Gastric linitis plastica (GLP) has unique genomic and transcriptomic features. Hippo pathway dysfunction is key, with specific gene mutations and pathway alterations identified, aiding diagnosis and treatment.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Primary gastric linitis plastica (GLP) is a rare gastric cancer subtype with poor prognosis.
- Comprehensive molecular characterization and therapeutic targets for GLP are largely unknown.
Purpose of the Study:
- To elucidate the distinct genomic and transcriptomic profiles of primary gastric linitis plastica.
- To identify potential therapeutic targets and understand the molecular mechanisms driving GLP development.
Main Methods:
- Whole exome sequencing (WES) and whole transcriptome sequencing (WTS) were performed on 10 primary GLP tumor-normal tissue pairs.
- TCGA data were utilized for comparative analysis of mutated and overexpressed genes.
- Immunohistochemistry (IHC) was employed to validate specific protein expressions.
Main Results:
- GLP exhibits unique genomic and transcriptomic signatures, with Hippo pathway dysfunction implicated in its development.
- Six highly mutated genes (AOX1, ANKRD36C, CPXM1, PTPN14, RPAP1, DCDC1) and MUC6 (20% mutation rate) were identified.
- GLP shows high immunodeficiency, low AMPK activity, and significant upregulation of PI3K-AKT pathway genes (PIK3R2, AKT3, IGF1). IGF2BP3 and MUC16 were identified as potential therapeutic targets.
Conclusions:
- This study provides the first integrated genomic and transcriptomic profiles of primary gastric linitis plastica.
- The findings offer insights into GLP pathogenesis and identify potential biomarkers for diagnosis, prognosis, and targeted therapy.
