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ORIGINAL RESEARCH article

Front. Bioinform.
Sec. Integrative Bioinformatics
Volume 4 - 2024 | doi: 10.3389/fbinf.2024.1494717

Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development

Provisionally accepted
Wenlun Wang Wenlun Wang 1,2*Yan HUANG Yan HUANG 1Qing YUAN Qing YUAN 1Chaohang YU Chaohang YU 1Wenbin LI Wenbin LI 1Nanqing Zhou Nanqing Zhou 1Qianmin HU Qianmin HU 1Shengcai WU Shengcai WU 1Shirui YU Shirui YU 1Feng Zhang Feng Zhang 1Lingyun Zhu Lingyun Zhu 2
  • 1 Department of Food Science and Engineering, Moutai College, Renhuai, Guizhou, China
  • 2 College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China

The final, formatted version of the article will be published soon.

    The precise role of lncRNAs in skeletal muscle development and atrophy remain elusive. We conducted a bioinformatic analysis of 26 GEO datasets from mouse studies, encompassing embryonic development, postnatal growth, regeneration, cell proliferation, and differentiation, using R and relevant packages (limma et al.). LncRNA-miRNA relationships were predicted using miRcode and lncBaseV2, with miRNA-mRNA pairs identified via miRcode, miRDB, and Targetscan7. Based on the ceRNA theory, we constructed and visualized the lncRNA-miRNA-mRNA regulatory network using ggalluvial among other R packages. GO, Reactome, KEGG, and GSEA explored interactions in muscle development and regeneration. We identified five candidate lncRNAs (Xist, Gas5, Pvt1, Airn, and Meg3) as potential mediators in these processes and microgravity-induced muscle wasting. Additionally, we created a detailed lncRNA-miRNA-mRNA regulatory network, including interactions such as lncRNA Xist/miR-126/IRS1, lncRNA Xist/miR-486-5p/GAB2, lncRNA Pvt1/miR-148/RAB34, and lncRNA Gas5/miR-455-5p/SOCS3. Significant signaling pathway changes (PI3K/Akt, MAPK, NF-κB, cell cycle, AMPK, Hippo, and cAMP) were observed during muscle development, regeneration, and atrophy. Despite bioinformatics challenges, our research underscores the significant roles of lncRNAs in muscle protein synthesis, degradation, cell proliferation, differentiation, function, and metabolism under both normal and microgravity conditions. This study offers new insights into the molecular mechanisms governing skeletal muscle development and regeneration.

    Keywords: lncRNA, muscle development and regeneration, Cell proliferation and differentiation, muscle atrophy, ceRNA network, signaling pathway

    Received: 11 Sep 2024; Accepted: 23 Dec 2024.

    Copyright: © 2024 Wang, HUANG, YUAN, YU, LI, Zhou, HU, WU, YU, Zhang and Zhu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Wenlun Wang, Department of Food Science and Engineering, Moutai College, Renhuai, Guizhou, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.