Identification of Prognostic Biomarkers of Hepatocellular Carcinoma Via Long Noncoding RNA Expression and Copy Number Alterations

Abstract

Aim: This study aimed to identify long noncoding RNAs (lncRNAs) with potential to be prognostic biomarkers of hepatocellular carcinoma (HCC) by analyzing copy number alterations (CNAs). Methods: RNA Sequencing data of 369 HCC patients was downloaded from The Cancer Genome Atlas database and analyzed with a series of systematic bioinformatics methods. Results: LncRNA-CNA association analysis revealed that many lncRNAs were located in sites frequently amplified or deleted. Three upregulated lncRNAs (LINC00689, SNHG20 and MAFG-AS1) with copy amplification and one downregulated lncRNA TMEM220-AS1 with copy deletion were associated with poor prognosis of HCC. Conclusion: This study reveals that differentially expressed lncRNAs correlate with CNAs in HCC. Moreover, the differentially expressed lncRNAs and their copy amplification/deletions could be promising prognostic biomarkers of HCC.

Keywords::

• copy number variation
• hepatocellular carcinoma
• lncRNA
• prognostic

Supplementary data

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Financial & competing interests disclosure

This work was supported by the major national S&T projects for infectious diseases (no. 2018ZX10301401), Key Research & Developement Plan of Zhejiang Province (no. 2019C04005), the National Key Research and Development Program of China (no. 2018YFC2000500), the National Natural Science Foundation of China (no. 81571953) and National key Research and development program (no. 2019YFC0840600). The authors have no 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.

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

Ethical conduct of research

This study was approved by the Clinical Research Ethics Committee of Shenzhen people’s Hospital and the First Affiliated Hospital of Zhejiang University. The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Data sharing statement

The authors certify that all the original data in this research could be obtained from public database.

Additional information

Funding

This work was supported by the major national S&T projects for infectious diseases (no. 2018ZX10301401), Key Research & Developement Plan of Zhejiang Province (no. 2019C04005), the National Key Research and Development Program of China (no. 2018YFC2000500), the National Natural Science Foundation of China (no. 81571953) and National key Research and development program (no. 2019YFC0840600). The authors have no 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. No writing assistance was utilized in the production of this manuscript.