Integrated Analysis of Transcriptome and Epigenome Reveals ENSR00000272060 as a Potential Biomarker in Gastric Cancer

Abstract

Background: Enhancer RNAs (eRNAs) are involved in gene expression regulation. Although functional roles of eRNAs in the pathophysiology of neoplasms have been reported, their involvement in gastric cancer (GC) is less known. Materials & methods: A network-based integrative approach was utilized for analyzing transcriptome and epigenome alterations in GC, and an eRNA was selected for experimental validation. Survival analysis and clinicopathological associations were also performed. Results: A hub eRNA, ENSR00000272060, showed significantly increased expression in tumor versus nontumor tissues, as well as an association with clinicopathological features. A seven-gene prognostic model was also constructed. Conclusion: The constructed network provides a comprehensive understanding of the underlying processes implicated in the progression of GC, along with a starting point from which to derive potential diagnostic/prognostic biomarkers.

Plain language summary

What is this summary about?

We provide an overview of a study on genetic materials related to stomach cancer. This study could help identify factors that change the progress of this disease. We used genetic information from a specific disease database. One of the genetic materials that was assessed is eRNA. It was examined in some samples of gastric cancer. We analyzed gastric tissues to confirm our findings. The goal of this study was to find out whether we could identify a disease-related eRNA.

What were the results?

We found an eRNA that showed genetic differences between examined samples. It was also related to the stage of the disease.

What do the results mean?

The results show that there is a difference in the amount of examined eRNA between samples. It suggests that we may be able to use it to detect the disease earlier.

Tweetable abstract

ENSR00000272060, an enhancer RNA, could be a promising diagnostic biomarker for gastric cancer.

Keywords::

• biomarkers
• enhancer RNA
• epigenomics
• stomach neoplasms
• systems biology

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.futuremedicine.com/doi/suppl/10.2217/epi-2023-0213

Author contributions

P Nikpour designed the study and provided financial resources. B Bahrami performed all bioinformatics analyses with contributions from M Wolfien. B Bahrami did in vitro experiments with the supervision of P Nikpour. B Bahrami, M Wolfien and P Nikpour interpreted and discussed the results. B Bahrami and P Nikpour wrote the manuscript. All the authors critically reviewed and revised the paper.

Financial disclosure

This work was supported by a grant from Isfahan University of Medical Sciences, Isfahan, Iran (grant no. 398981). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Competing interests disclosure

The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Writing disclosure

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained approval ID from the Ethics Committee of Isfahan University of Medical Sciences (IR.MUI.MED.REC.1398.696) for the research described. In addition, all patients provided written informed consent to the Iran National Tumor Bank prior to participation.

Data sharing statement

The results published or shown here are in whole or part based upon data generated by the TCGA Research Network: www.cancer.gov/tcga. The data that support the findings of this study are available from the corresponding author, [PN], upon reasonable request.

Additional information

Funding

This work was supported by a grant from Isfahan University of Medical Sciences, Isfahan, Iran (grant no. 398981). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.