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. 2018 May 10;9(5):245.
doi: 10.3390/genes9050245.

Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease

Irati Romero-Garmendia  1 , Koldo Garcia-Etxebarria  2 , Hector Hernandez-Vargas  3 , Izortze Santin  4   5 , Amaia Jauregi-Miguel  6 , Leticia Plaza-Izurieta  7 , Marie-Pierre Cros  8 , Maria Legarda  9 , Iñaki Irastorza  10 , Zdenko Herceg  11 , Nora Fernandez-Jimenez  12   13 , Jose Ramon Bilbao  14   15
Affiliations

Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease

Irati Romero-Garmendia et al. Genes (Basel). .

Abstract

The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted _targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.

Keywords: celiac disease; co-expression; complex disease; gene regulation; transcription factor.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Co-expressed gene modules and differentially co-expressed genes in response to gliadin; (a) Representation of co-expression modules of acute (purple arrow) and chronic (golden arrow) response to gliadin. Each square represents a gene, while genes forming a co-expression module share a color. The number of genes used for the construction of modules is indicated for each experiment, and the numbers in bold represent the amount of modules identified in each experiment and condition; (b) Representation of differentially co-expressed genes (DCGs; black squares) and enrichment analysis for transcription factor binding sites (TFBS). Three transcription factors (TFs) were identified in the acute experiment (purple) and 8 TFs in the chronic experiment (gold).
Figure 2
Figure 2
Co-expression and Gene Ontology (GO) annotation studies in DCGs. Co-expression pattern changes of DCGs with enrichment for CAMP Responsive Element Binding Protein 1 (CREB1), ETS domain-containing protein (ELK1) and homeobox protein Hox-A5 (HOXA5) binding sites, from treated celiac disease (CD) to active CD (chronic experiment). Each small square represents the P-value of the correlation between the expression levels of a specific gene pair (red-blue scale represents positive to negative Spearman correlation). Below, the top 10 GO annotations for those DCGs compared to the whole-genome. GO terms are indicated in the Y axis. The X axis shows the log10 fold-enrichment (ratio between the percentage of genes annotated with the GO term in the test set and the number of genes annotated with such term in the whole-genome (*** p < 0.001, ** p < 0.01 and * p < 0.05)).
Figure 3
Figure 3
Gene expression analysis. Gene expression analysis of TFs identified by WGCNA (active CD n = 30, control n = 18) and their _target genes (active CD n = 16, control n = 14) in duodenal biopsies. Data are expressed as mean ± SD (standard deviation) (*** p < 0.001, ** p < 0.01 and * p < 0.05).
Figure 4
Figure 4
In vitro characterization of selected TFs. (A) The translocation of IFN regulatory factor-1 (IRF1) and CREB1 to the nucleus was analyzed by Western blot in 3 independent experiments upon stimulation with pepsin-trypsin digested gliadin (PT-G) or pepsin-trypsin digested BSA (PT-BSA) as control; (B) Band intensity was quantified and normalized to the intensity of the band corresponding to HDAC1. Mean values were compared with a t-test. Data are expressed as mean ± SEM.
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References

    1. Green P.H.R., Cellier C. Celiac disease. N. Engl. J. Med. 2007;357:1731–1743. doi: 10.1056/NEJMra071600. - DOI - PubMed
    1. Greco L., Romino R., Coto I., Di Cosmo N., Percopo S., Maglio M., Paparo F., Gasperi V., Limongelli M.G., Cotichini R., et al. The first large population based twin study of coeliac disease. Gut. 2002;50:624–628. doi: 10.1136/gut.50.5.624. - DOI - PMC - PubMed
    1. Van Heel D.A., Franke L., Hunt K.A., Gwilliam R., Zhernakova A., Inouye M., Wapenaar M.C., Barnardo M.C., Bethel G., Holmes G.K., et al. A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat. Genet. 2007;39:827–829. doi: 10.1038/ng2058. - DOI - PMC - PubMed
    1. Dubois P., Trynka G., Franke L., Hunt K.A., Romanos J., Curtotti A., Zhernakova A., Heap G.A., Ádány R., Aromaa A., et al. Multiple common variants for celiac disease influencing immune gene expression. Nat. Genet. 2010;42:295–302. doi: 10.1038/ng.543. - DOI - PMC - PubMed
    1. Trynka G., Hunt K.A., Bockett N.A., Romanos J., Mistry V., Szperl A., Bakker S.F., Bardella M.T., Bhaw-Rosun L., Castillejo G., et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat. Genet. 2011;43:1193–1201. doi: 10.1038/ng.998. - DOI - PMC - PubMed

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