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Published on: March 24, 2015
Computational identification and experimental validation of shared diagnostic biomarkers and gene signatures across
Xinyue Zhu1, Chunyu Liang1, Zhihua Xu2
1Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, P.R. China.
Background:
HLA-B27 is strongly associated with a spectrum of immune-mediated diseases, including axial spondyloarthritis (axSpA), psoriatic arthritis (PsA), inflammatory bowel disease (IBD), and acute anterior uveitis (AAU). However, the shared molecular mechanisms and cross-disease diagnostic biomarkers remain poorly defined. This study aimed to identify common gene signatures and potential diagnostic biomarkers across HLA-B27-related diseases using bioinformatics analysis and experimental validation.
Methods:
Gene expression datasets for axSpA, PsA, ulcerative colitis (UC), Crohn's disease (CD), and AAU were retrieved from the Gene Expression Omnibus (GEO) database. Disease-specific diagnostic genes were identified via differential expression analysis, least absolute shrinkage and selection operator (LASSO) regression, and receiver operating characteristic (ROC) curve analysis (AUC > 0.9). Shared biomarkers were determined by intersecting differentially expressed genes (DEGs) across all five diseases. Protein-protein interaction (PPI) networks, functional enrichment analyses, and single-sample gene set enrichment analysis (ssGSEA) were performed to explore biological pathways and immune infiltration patterns. Competing endogenous RNA (ceRNA)-transcription factor (TF) regulatory networks were constructed, and potential therapeutic agents were predicted using the Drug-Gene Interaction Database (DGIdb). Finally, the expression of candidate genes was validated by RT-qPCR and Western blot in peripheral blood mononuclear cells (PBMCs) from patients with ankylosing spondylitis (AS) and UC.
Results:
A total of 2485, 380, 2682, 2232, and 481 DEGs were identified for axSpA, PsA, UC, CD, and AAU, respectively, with ABCD2 being the only shared biomarker across all five diseases. Disease-specific diagnostic gene panels were established (3 genes for axSpA, 6 for PsA, 15 for UC, 9 for CD, and 4 for AAU). Two major gene clusters were uncovered: an arthritis-related cluster (LAG3, IL15, PRF1, TBX21, IL2RB) and an extra-articular disease-related cluster (IL6, FN1, F2R, HIF1A, ANGPT2). Immune infiltration profiles varied significantly across diseases. Regulatory network analysis revealed complex ceRNA-TF interactions and identified several candidate drugs. In PBMCs, ABCD2 was upregulated in AS and UC, PRF1 in AS, and FN1, IL-6, and F2R in UC.
Conclusion:
This study identifies ABCD2 as a potential cross-disease biomarker and two context-dependent key gene clusters for HLA-B27-associated immune-mediated diseases, providing exploratory candidates for future research.
