Genome-wide expression profiling of long non-coding RNAs and competing endogenous RNA networks in alopecia areata

Sisi Qi; Youyu Sheng; Ruiming Hu; Feng Xu; Ying Miao; Jun Zhao; Qinping Yang; Sisi Qi; Youyu Sheng; Ruiming Hu; Feng Xu; Ying Miao; Jun Zhao; Qinping Yang

doi:10.3934/mbe.2021037

Mathematical Biosciences and Engineering

2021, Volume 18, Issue 1: 696-711. doi: 10.3934/mbe.2021037

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Research article

Genome-wide expression profiling of long non-coding RNAs and competing endogenous RNA networks in alopecia areata

Department of Dermatology, Huashan Hospital, Fudan University, 12 Cent Urumqi Rd, Shanghai 200040, China

Received: 14 July 2020 Accepted: 14 October 2020 Published: 18 December 2020

Background Long non-coding RNAs (lncRNAs) regulate gene expression in concert with microRNAs (miRNAs) and mRNAs. This study was designed to explore the potential roles of lncRNAs and their related competing endogenous RNA (ceRNA) networks in alopecia areata (AA).

Methods This study comprised six participants (three AA patients and three healthy individuals) whose serum lncRNA profiles were evaluated by lncRNA sequencing. Following differential expression analysis, and function enrichment analysis, a lncRNA-miRNA-mRNA network was then constructed using various bioinformatics tools and validated using quantitative reverse-transcription PCR (qRT-PCR).

Results We identified 220 mRNAs and 166 lncRNAs that were differentially expressed in AA patients. The differentially expressed mRNAs were predominantly associated with cytokine-cytokine receptor interactions, MAPK signaling and Ras signaling pathways. The differentially expressed lncRNAs were primarily associated with cytokine-cytokine receptor interactions, chemokine signaling pathways, axon guidance, and legionellosis. In addition, qRT-PCR analyses verified the upregulation of AC005562.1, AF131217.1, and RP11-251G23.5 and downregulation of RP11-231E19.1 in AA patients.

Conclusion We constructed a complex ceRNA network for AA and discovered that various RP11 lncRNAs including RP11-251G23.5 and RP11-231E19 may play a crucial role in the pathogenesis of AA via the regulation of the cytokine-cytokine receptor interaction pathway, which could serve as a therapeutic target for alopecia areata in clinical interventions.
- sequencing,
- long non-coding RNAs,
- competing endogenous RNAs,
- differential expression analysis,
- alopecia areata
Citation: Sisi Qi, Youyu Sheng, Ruiming Hu, Feng Xu, Ying Miao, Jun Zhao, Qinping Yang. Genome-wide expression profiling of long non-coding RNAs and competing endogenous RNA networks in alopecia areata[J]. Mathematical Biosciences and Engineering, 2021, 18(1): 696-711. doi: 10.3934/mbe.2021037

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Abstract

Background Long non-coding RNAs (lncRNAs) regulate gene expression in concert with microRNAs (miRNAs) and mRNAs. This study was designed to explore the potential roles of lncRNAs and their related competing endogenous RNA (ceRNA) networks in alopecia areata (AA).

Methods This study comprised six participants (three AA patients and three healthy individuals) whose serum lncRNA profiles were evaluated by lncRNA sequencing. Following differential expression analysis, and function enrichment analysis, a lncRNA-miRNA-mRNA network was then constructed using various bioinformatics tools and validated using quantitative reverse-transcription PCR (qRT-PCR).

Results We identified 220 mRNAs and 166 lncRNAs that were differentially expressed in AA patients. The differentially expressed mRNAs were predominantly associated with cytokine-cytokine receptor interactions, MAPK signaling and Ras signaling pathways. The differentially expressed lncRNAs were primarily associated with cytokine-cytokine receptor interactions, chemokine signaling pathways, axon guidance, and legionellosis. In addition, qRT-PCR analyses verified the upregulation of AC005562.1, AF131217.1, and RP11-251G23.5 and downregulation of RP11-231E19.1 in AA patients.

Conclusion We constructed a complex ceRNA network for AA and discovered that various RP11 lncRNAs including RP11-251G23.5 and RP11-231E19 may play a crucial role in the pathogenesis of AA via the regulation of the cytokine-cytokine receptor interaction pathway, which could serve as a therapeutic target for alopecia areata in clinical interventions.

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