Introduction: Vitiligo is an autoimmune and chronically acquired skin disorder characterized by white macule and pigmented patches due to the dysfunctional melanocytes attacked by immune cells, which leads to the destruction of melanocytes. It approximated a prevalence of 0.5% to 2% worldwide. The pathogenesis of vitiligo is explained by the interplay of intrinsic melanocyte defects, autoimmune responses, and genetic and environmental influences. Most recent advancements in the treatment of vitiligo include novel treatments utilizing JAK inhibitors and regenerative therapies, topical corticosteroids and calcineurin inhibitors, and improvements in phototherapy techniques. Biologics, topical vitamin D analogues, and Microneedling. A recent meta-analysis revealed vitiligo to be associated with an increased risk of autoimmune thyroid diseases, alopecia errata, connective tissue diseases, pernicious anemia, and type 1 diabetes, as well as cardiovascular risks and metabolic diseases. Some genes impact this disease, and we analysed UPF2 gene using Bioinformatic.
Methods: Dataset collection
Search the disease on the NCBI website. (https://www.ncbi.nlm.nih.gov) and then evaluate the skin and blood samples in Homo Sapiens species. Analysised the desired sample on Geo2R and receive the result.
Data processing and differential expression analysis
The GSE dataset we used to download the normalized expression matrix of the microarray data. Choose two GSEs (GSE75819 and GSE90880). Next, the “limma R” packages were applied to identify DEGs in the dataset. Likewise, “GEOquery R’’ and ‘’Biobase R” and “ggplot 2” packages were used (Log FC>, P.value< 0.05), and a Venny diagram was drawn between DEGs.
Pathways & Ontology
We analysised “Reactome”,” KEGG” and “Wiki Pathway” on the Enrichr website in the Pathways section. (https://maayanlab.cloud/Enrichr) Likewise, analysised “GO Biological Process”, “GO Cellular Component,” and “GO Molecular Function” in the ontologies section. And selected P.value<0.05.
MiRNA-miRNA network construction and functional insights into correlated miRNA
Search the UPF2 gene on mirDB website and selected miRNA name with >90 Target Score. Check the gene+miRNA and next time check the Vitiligo disease +miRNA name. We work on a topic without any previous review.
lncRNA & miRNA connection
Search the UPF2 gene on the RNAinter website and changed miRNA in cat1 column to lncRNA by Run the Filter section in Excell app.
Finally, Molecular docking was done.
Results: Data preprocessing
We had 8 non-segmental Vitiligo and 6 Control in GSE90880, and it related to the blood sample, and we found 15 Normal Skin and 15 Lesional Vitiligo Skin in GSE75819, and it related to Skin sample. We found a common gene on the Venny Diagram website and worked on this gene on different websites. Gene expression was higher in Skin sample.
GO and KEGG enrichment analysis of autophagy-related DEG
Scrutinized pathways and Ontologies in this gene and analysised this information. And choose the P value<0.05. Using R software, we performed GO and KEGG enrichment analyses to analyse the underlying biological roles of these differentially expressed ARGs. Enrichment of various functions was initially demonstrated through GO enrichment analysis. Subsequently, GO and KEGG enrichment analyses elucidated the expression of associated genes in distinct functional enrichment sets while also highlighting potentially associated genes in several functions exhibiting significant enrichment. The results demonstrated that the most significant GO-enriched terms were involved in processes utilizing autophagy mechanisms, autophagy, cellular response to external stimulus and macroautophagy (biological processes); vascular membrane, autophagosome , autophagosome membrane and phagophore assembly site (cellular component); GTP binding, phosphatase binding, protein phosphatase binding and CARD domain binding (molecular function). In KEGG enrichment analysis, the differentially expressed ARGs were mainly involved in the processes of autophagy, influenza A, protein processing in the endoplasmic reticulum, and apoptosis
Conclusion: This disease occured more often in skin samples than in blood samples.
Keywords: Vitiligo disease, Vitiligo treatment, Vitiligo skin, White patches in skin .