Differential RNA expression profiles and competing endogenous RNA-associated regulatory networks during the progression of atherosclerosis

Abstract

Aim: To identify differential mRNA and ncRNA expression profiles and competing endogenous RNA-associated regulatory networks during the progression of atherosclerosis (AS). Materials & methods: We systematically analyzed whole-transcriptome sequencing of samples from different stages of AS to evaluate their long noncoding RNA (lncRNA), circular RNA (circRNA), miRNA and mRNA profiles. Results: We constructed three AS-related competing endogenous RNA regulatory networks of differentially expressed circRNAs, lncRNAs, miRNAs and mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that the circRNAs in the network were enriched in lipid metabolic processes and participated in the PPAR signaling pathway. Furthermore, lncRNAs were related to receptor activity, myofibrils and cardiovascular system development. Conclusion: The current findings further clarified the regulatory mechanisms at different stages of AS and may provide new ideas and targets for AS.

Keywords::

• atherosclerosis
• ceRNA network
• competing endogenous RNAs
• ncRNAs
• whole-transcriptome sequencing

Supplementary Data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2020-0252

Author contributions

Y Fu and C Sun performed animal experiments and wrote the paper. Q Li and X Xi designed the primers and conducted qRT-PCR assays. F Qian, C Li and D Shang provided technical assistance and performed bioinformatics analyses. C Wang, X Peng and M Piao raised animals and collected tissues. W Qu, J Tian and B Yu analyzed the data. X Gu and J Tian conceived of, designed and supervised the study. All authors read and approved the final manuscript.

Acknowledgments

We would like to give our sincere appreciation to the reviewers for their helpful comments on this article.

Financial & competing interests disclosure

This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 91739113, 81971715 to J.W.T. and 81827806 to B.Y.), the National Key R&D Program of China (Grant No. 2016YFC1301100 to B.Y.), the Fok Ying-Tong Education Foundation for Young Teachers (171032 to J.W.T), the Foundation of Guangxi Key Laboratory of Diabetic Systems Medicine (GKLCDSM-20200101-01 to J.W.T), the Natural Science Foundation of Heilongjiang Province of China (H2018022 to J.T.T) and the Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education (KF201820 to Y.H.F.). 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.

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

Ethical conduct of research

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

We have uploaded the sequencing data in NCBI databases (BioProject- PRJNA608817: www.ncbi.nlm.nih.gov/sra/PRJNA608817; PRJNA609051: www.ncbi.nlm.nih.gov/sra/PRJNA609051).

Additional information

Funding

This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 91739113, 81971715 to J.W.T. and 81827806 to B.Y.), the National Key R&D Program of China (Grant No. 2016YFC1301100 to B.Y.), the Fok Ying-Tong Education Foundation for Young Teachers (171032 to J.W.T), the Foundation of Guangxi Key Laboratory of Diabetic Systems Medicine (GKLCDSM-20200101-01 to J.W.T), the Natural Science Foundation of Heilongjiang Province of China (H2018022 to J.T.T) and the Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education (KF201820 to Y.H.F.). 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. No writing assistance was utilized in the production of this manuscript.