Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis

Abstract

Background Psoriasis is a chronic immune-mediated inflammatory dermatosis. Long noncoding RNAs (lncRNAs) play an important role in immune-related diseases. This study aimed to identify potential immune-related lncRNA biomarkers for psoriasis. Methods We screened differentially expressed immune-related lncRNAs biomarkers using GSE13355 (skin biopsy samples of 180 cases) from Gene Expression Omnibus (GEO). Moreover, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA) were performed to explore biological mechanisms in psoriasis. In addition, we performed LASSO logistic regression to identify potential diagnostic lncRNAs and further verify the diagnostic value and relationship with drug response using two validation sets: GSE30999 (skin biopsy samples of 170 cases) and GSE106992 (skin biopsy samples of 192 cases). Furthermore, we estimated the degree of infiltrated immune cells and investigated the correlation between infiltrated immune cells and diagnostic lncRNA biomarkers. Results A total of 394 differentially expressed genes (DEGs) were extracted from gene expression profile. GO and KEGG analysis of target genes found that immune-related lncRNAs were primarily associated with epidermis development, skin development, collagen-containing extracellular matrix, and glycosaminoglycan binding and mainly enriched in cytokine-cytokine receptor interaction and influenza A and chemokine signaling pathway. We found that LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1, CARMN, CCDC18-AS1, EPB41L4A-AS, and LINC01214 exhibited well diagnostic efficacy. The ROC and ROC CI were 0.944 (0.907–0.982), 0.953 (0.919–0.987), 0.822 (0.758–0.887), 0.854 (0.797–0.911), 0.957(0.929–0.985), 0.894 (0.846–0.942), and 0.964 (0.937–0.991) for LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1,CARMN, CCDC18-AS1, EPB41L4A-AS1, and LINC01214. LINC01137, LINC01215, and LINC01214 were correlated with drug response. LINC01137, CCDC18-AS1, and CARMN were positively correlated with activated memory CD4 T cell, activated myeloid dendritic cell (DC), neutrophils, macrophage M1, and T follicular helper (Tfh) cells, while negatively correlated with T regulatory cell (Treg). LINC01215, MAPKAPK5-AS1, TPT1-AS1, EPB41L4A-AS, and LINC01214 were negatively correlated with activated memory CD4 T cell, activated myeloid DC, neutrophils, macrophage M1, and Tfh, while positively correlated with Treg. Conclusions These findings indicated that these immune-related lncRNAs may be used as potential diagnostic and predictive biomarkers for psoriasis.

A Prognostic Pyroptosis-Related lncRNAs Risk Model Correlates With the Immune Microenvironment in Colon Adenocarcinoma

“…POC1B-AS1 is also a risk factor in the prognostic model of endometrial carcinoma ( Liu J. et al, 2021 ). In psoriasis, CCDC18-AS1, regarded as immune-related lncRNA, can be a potential diagnostic biomarker ( Fan et al, 2021 ). THUMPD3-AS1 can regulate self-renewal by ceRNA network of miR-543 and ONECUT2 associated with non-small cell lung cancer ( Hu et al, 2019 ).…”

A Five Autophagy-Related Long Non-Coding RNA Prognostic Model for Patients with Lung Adenocarcinoma

“…30 Taken together, we believe that the GADPH-LINC01116 axis plays a positive role in lung cancer and more biochemistry experiments are needed to test this idea. LINC01137 was previously found to be an immunerelated biomarker in the diagnosis of psoriasis and also an indicator for chemical stress response 31,32 and the upregulation of it may result in poor overall survival. MLST8 (MTOR Associated Protein, LST8 Homolog) is an essential part of the mTORC1 pathway and has the ability to enhance the mTOR kinase activity.…”

Analysis of Long Noncoding RNAs-Related Regulatory Mechanisms in Duchenne Muscular Dystrophy Using a Disease-Related lncRNA-mRNA Pathway Network

“…In DMD, the immune system is activated and several types of immune cells, such as CD4+ and CD8+ T cells, Tregs, and NK cells, invade the skeletal muscles [16]. A recent study showed that lncRNA CCDC18-AS1 is positively correlated with activated myeloid dendritic cells and neutrophils [52], in concordance with our results that showed that the expression of lncRNA CCDC18-AS1 was positively correlated with the proportion of activated NK cells, neutrophils, and Tregs but negatively correlated with resting myeloid dendritic cells and M2 macrophages. Our study also showed that the proportions of Tregs, activated NK cells, neutrophils, M2 macrophages, and resting myeloid dendritic cells were signifcantly diferent between patients with DMD and normal control individuals.…”