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PLoS One. 2019 Jun 25;14(6):e0218116. doi: 10.1371/journal.pone.0218116. eCollection 2019.

Integrated analysis of microRNA regulation and its interaction with mechanisms of epigenetic regulation in the etiology of systemic lupus erythematosus.

Author information

1
Universidad Simon Bolivar, Basic and Biomedical Faculty, Barranquilla, Colombia.
2
CMCC- Centro de Matemática, Computação e Cognição, Laboratório do Biologia Computacional e Bioinformática-LBCB, Universidade Federal do ABC, Sao Paulo, Brazil.
3
Clínica de la Costa, Department of Nephrology, Barranquilla, Colombia.
4
Universidad de Cadiz, Department of Biomedicine, Biotechnology and Public Health, Cadiz, Spain.
5
Universidad del Norte, School of Medicine, Barranquilla, Colombia.
6
Universidad Libre, School of Medicine, Barranquilla, Colombia.
7
Infectious Diseases Department, J. Craig Venter Institute, Rockville, Maryland, United States of America.
8
Universidad Popular del Cesar, Basic and Biomedical Faculty, Valledupar, Colombia.
9
ACCONP, Barranquilla, Colombia.
10
ColNalPinillos, Mompós, Colombia.
11
Procaps S.A., Research and Development, Barranquilla, Colombia.

Abstract

The aim of this study was to identity in silico the relationships among microRNAs (miRNAs) and genes encoding transcription factors, ubiquitylation, DNA methylation, and histone modifications in systemic lupus erythematosus (SLE). To identify miRNA dysregulation in SLE, we used miR2Disease and PhenomiR for information about miRNAs exhibiting differential regulation in disease and other biological processes, and HMDD for information about experimentally supported human miRNA-disease association data from genetics, epigenetics, circulating miRNAs, and miRNA-target interactions. This information was incorporated into the miRNA analysis. High-throughput sequencing revealed circulating miRNAs associated with kidney damage in patients with SLE. As the main finding of our in silico analysis of miRNAs differentially expressed in SLE and their interactions with disease-susceptibility genes, post-translational modifications, and transcription factors; we highlight 226 miRNAs associated with genes and processes. Moreover, we highlight that alterations of miRNAs such as hsa-miR-30a-5p, hsa-miR-16-5p, hsa-miR-142-5p, and hsa-miR-324-3p are most commonly associated with post-translational modifications. In addition, altered miRNAs that are most frequently associated with susceptibility-related genes are hsa-miR-16-5p, hsa-miR-374a-5p, hsa-miR-34a-5p, hsa-miR-31-5p, and hsa-miR-1-3p.

Conflict of interest statement

The authors have declared that no competing interests exist.

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