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Comprehensive lncRNAs expression profiling reveals the potential role of lncRNAs in systemic lupus erythematosus [Human LncRNA Array v3.0]

ABSTRACT: long non-coding RNAs (lncRNAs) are novel non-coding RNAs which play an important part in regulating gene transcription and translation, modulating protein function, and acting as competing endogeneous RNA. Moveover, there is increasing evidence showing that aberrant expressions of lncRNAs are implicated in various cancers. Yet, their roles in systemic lupus erythematosus (SLE), a prototypical autoimmune disease, remain unknown. To reveal the implications of LncRNAs in SLE, we used Human LncRNA Array v3.0 microarrays to measure the expression profiles of lncRNAs in T cells of patients with SLE and healthy controls. we found 869 upregulated lncRNAs and 1066 downregulated lncRNAs in SLE patients compared with controls. Coding-non-coding gene coexpression (CNC) network was constructed based on the correlation analysis between the differentially expressed lncRNA and mRNA. Downregulation of two lncRNAs, uc001ykl.1 and ENST00000448942 was established using Real-time quantitative PCR. These results showed abrrant expression profiles of lncRNAs in T cells of SLE patients and revealed their potential role in SLE.

ORGANISM(S): Homo sapiens

PROVIDER: GSE84654 | GEO | 2018/03/08

REPOSITORIES: GEO

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Project description:Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn’s disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD. In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in inflamed and non-inflamed colon pinch biopsies from the IBD patients using expression microarrays platform. In this study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC compared to the healthy controls. In case of inflamed CD and UC (iCD and iUC), we identified 438 and 745 differentially expressed lncRNAs, respectively, while in case of the non-inflamed CD and UC (niCD and niUC), we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (p-value < 0.001, Pearson’s Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed that they are involved in immune response, pro-inflammatory cytokine activity and MHC protein complex. The lncRNA expression profiling in both inflamed and non-inflamed CD and UC, successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggests their potential as biomarkers in IBD. A total of 96 biopsy samples (including 6 samples used as technical replicates) extracted from different colonic locations from 45 patients (CD=13, UC=20, Controls=12) were profiled using Agilent Custom 8x60K format lncRNA expression microarray. In Gencode v15 lncRNA microarray design, each lncRNA transcript is targeted by two probes covering 22,001 lncRNA transcripts corresponding to 12,963 lncRNA genes. In addition, each array contains 17,535 randomly-selected protein-coding targets, of which 15,182 (unique 12,787) correspond to protein-coding genes.

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Comprehensive lncRNAs expression profiling reveals the potential role of lncRNAs in systemic lupus erythematosus [Human LncRNA Array v3.0]

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