Journal of Isfahan Medical School

Journal of Isfahan Medical School

Comprehensive Analysis of eRNAs and Genes Involved in Gastric Cancer and Constructing a Prognostic Model Predicting the Overall Survival of Patients

Document Type : Original Article(s)

Authors
Basireh Bahrami 1
Parvaneh Nikpour 2
1 MSc, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
2 Associate Professor, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
10.48305/jims.v41.i724.0488
Abstract
Background: Gastric cancer (GC) is one of the most prevalent cancers and the first cause of cancer-related deaths in Iran. These patients are diagnosed at advanced stages, which leads to poor prognosis because there is inadequate knowledge of molecular factors to provide diagnostic/prognostic biomarkers. The aim of the current study was the comprehensive analysis of enhancer RNAs (eRNAs) to determine their molecular interactions with other genes and propose a survival-related model for patients.
Methods: RNA-sequencing raw data of GC patients were downloaded from The Cancer Genome Atlas (TCGA), and differentially-expressed eRNAs and genes in tumors compared to non-tumor samples were extracted. The target genes of each eRNA were then identified based on physical distance, correlation, and a regulatory network was constructed with these elements. A prognostic model for predicting the overall survival of patients was eventually established by performing univariate and multivariate Cox regression analyses, and the performance of the model was surveyed.
Findings: By performing differential expression analysis, 69 and 2606 differentially-expressed eRNAs and genes were extracted, respectively, and by identifying the relationships between these elements, a regulatory network consisting of 84 nodes and 119 edges was constructed. A three-components survival-related model subsequently was established which could predict patients' outcomes.
Conclusion: Based on the results, the 3-component constructed model, including an eRNA and two other genes, can be considered as a possible prognostic tool; however, further research is needed to clinically implement it.
Keywords
Enhancer
RNA
Stomach neoplasms
Survival analysis
Systems biology
RNA-Seq

Subjects

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Journal of Isfahan Medical School
Volume 41, Issue 724
4th Week, August
July and August 2023
Pages 488-495

  • Receive Date 28 May 2023
  • Accept Date 11 June 2023