Transcriptome analysis of CD4+ T cells in coeliac disease highlighting BACH2 as a key regulatory gene.
Ciara Coleman*, Emma M Quinn*, Ben Molloy, Patricia Dominguez Castro, Paul Cormican, Valerie Trimble, Nasir Mahmud, Ross McManus
Department of Clinical Medicine, Trinity College Dublin
Genetic studies have to date identified 43 genome wide significant coeliac disease susceptibility (CD) loci comprising over 70 candidate genes. However, how altered regulation of such disease associated genes contributes to CD pathogenesis remains to be elucidated. Recently there has been considerable emphasis on characterising cell type specific and stimulus dependent genetic variants.
To assay the transcriptome of CD4+ T cells in individuals with CD and those without CD, using various stimuli to determine characteristic gene expression patterns. To use pathway and network analysis to identify key pathways involved in CD and to group genes into biologically related expression modules composed of potentially functionally related genes.
Use RNA sequencing to profile over 70 transcriptomes of CD4+ T cells. To identify key CD biological pathways using Goseq and KEGG pathway annotations. To use WGCNA to group genes into biologically related expression modules.
We identified extensive transcriptional changes across all conditions, with the previously established CD gene IFNy the most strongly up-regulated gene (log2 fold change 4.6; Padjusted=2.40x10-11). We show a significant correlation of differentially expressed genes with genetic studies of the disease to date (Padjusted=0.002), and 21 CD candidate susceptibility genes are differentially expressed under one or more of the conditions used in this study. Pathway analysis revealed significant enrichment of immune related processes. Network analysis identified several modules of coordinately expressed CD genes and highlighted IFNy and the transcription factor BACH2 as key regulatory genes in CD. We show for the first time significant differential expression of BACH2 regulated genes in CD (P
We characterised over 70 transcriptomes from coeliac patients and controls in both resting and stimulated cells and identified large transcriptional changes that significantly mirror previous genetic studies of the disease. Differential expression is strongly associated with genes of immunological function and is associated with several co-expression networks, the most strongly of which feature IFNy and BACH2. BACH2 is genetically associated with CD and down regulated under all conditions tested. We identify a strong association of CD with a network of BACH2 regulated genes, supporting emerging evidence of an important role of BACH2 in the regulation of T-cell differentiation and prevention of autoimmune disease.Dd