Unveiling a ceRNA Network Involving IL-8 and TNF-α in Active Generalized Vitiligo by Multi-Omics Integration.

Abstract

Background: Active generalised vitiligo (AGV) is an autoimmune disorder characterised by progressive melanocyte loss. However, the molecular mechanisms underlying AGV, particularly the roles of non-coding RNAs and their interaction with proteomic changes, remain poorly understood. The aim of this study was to systematically identify key regulatory networks and molecular changes in AGV by integrating proteomic and whole-transcriptome data.

Methods: Data-independent acquisition mass spectrometry (DIA-MS) and whole transcriptome sequencing (WTS) were performed on whole blood samples from three AGV patients and three healthy individuals (HIs). Bioinformatic analyses were then used to identify differentially expressed proteins (DEPs), messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs). Co-expression and competing endogenous RNA (ceRNA) networks were constructed and visualised using Cytoscape. Key hub genes and cytokine levels were then validated using quantitative reverse transcription PCR (qRT-PCR) and immunoassays in an independent cohort.

Results: We identified 15 DEPs and 669 differentially expressed mRNAs (DEmRNAs), as well as significant alterations in 258 lncRNAs, 29 miRNAs and 44 circRNAs in AGV. Functional enrichment analysis revealed their involvement in chemokine signaling and lysosomal pathways. Protein-protein interaction network analysis revealed ten hub genes, including CXCL8, CXCR1, CXCR2 and IL1R2. We established a core ceRNA regulatory network featuring long non-coding RNAs (eg NUTM2B-AS1, LINC00894), circular RNAs (eg ASAP1, CDR2) and microRNAs (eg hsa-mir-3613-3p, hsa-mir-511-5p) that potentially modulate inflammatory responses. Experimental validation confirmed significantly elevated levels of the pro-inflammatory cytokines IL-8 and TNF-α in AGV patients, and qRT-PCR results for nine of the ten hub genes were consistent with the sequencing data.

Conclusion: Our integrated multi-omics analysis uncovers a novel ceRNA network and highlights the significant upregulation of IL-8 and TNF-α in AGV. These findings provide new insights into the post-transcriptional regulatory mechanisms and inflammatory pathways driving AGV and offer potential therapeutic targets.