Systematic search for new predictors associated with IBD.

<p>Predictors were built using the tool Prophet and the 54,675 probes contained in the chip, using the leave-one-out cross-validation strategy, to identify classifiers genes for inflammatory bowel disease, IBD (A), Crohn’s disease, CD (B), ulcerative colitis, UC (C), CD <i>vs.</i> UC (D), low inflammation subtypes of CD and UC (E), and high inflammation subtypes of CD <i>vs.</i> UC (F). Data are represented as box and whiskers plots, where the error bars designate the smallest and largest observations and dots designate the outliers. Data was analyzed by two-way ANOVA followed by Bonferroni post test, <i>p</i> values higher than 0.05 were considered not significant (ns), *<i>p</i><0.01, **<i>p</i><0.001.</p

Systematic search for new predictors associated with clinical variables.

<p>Predictors were built using the tool Prophet and the 54,675 probes contained in the microarray, using the leave-one-out cross-validation strategy, to identify classifiers genes for glucocorticoid sensitivity (A), glucocorticoid dependency (B) or need for surgery (C). Data are represented as box and whiskers plots, where the error bars designate the smallest and largest observations and dots designate the outliers. Data was analyzed by two-way ANOVA followed by Bonferroni post test, <i>p</i> values higher than 0.05 were considered not significant (ns), *<i>p</i><0.01, **<i>p</i><0.001.</p

Discovery of Crohn’s disease (CD) and ulcerative colitis (UC) inflammatory subtypes by gene expression profiling.

<p>(A) Unsupervised hierarchical clustering of UC (blue), CD (red) and healthy controls (green) cases using the 54,675 probes contained in the chip. Up-regulated genes are shown in red and down-regulated genes in green. (B) Supervised hierarchical clustering of CD cases or UC cases using differentially expressed genes between CD and healthy (261 probes) and UC and healthy (1255 probes) respectively. This process defined two subgroups for both CD and UC cases. Functional analyses were performed using PANTHER Classification System. Examples of genes of each category are shown. (C) Clustering of samples using principal component analysis: CD1 (pink), CD2 (red), UC1 (light blue), UC2 (dark blue), healthy controls (green). (D) Association between clinical characteristics and CD and UC subtypes. Data represents the proportion of patients of each disease subtype included in different clinical variables, *<i>p</i><0.05, Fisher exact test, CD1 <i>vs.</i> CD2 or UC1 <i>vs.</i> UC2. Complete clinical data is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076235#pone.0076235.s002" target="_blank">Table S1</a>. (E) Number of differentially expressed genes (<i>p</i><0.05, t-test) in different comparisons among groups and with a fold change >1 or <−1.</p

DataSheet_2_Experimental and genetic evidence for the impact of CD5 and CD6 expression and variation in inflammatory bowel disease.csv

Crohn’s disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) resulting from the interaction of multiple environmental, genetic and immunological factors. CD5 and CD6 are paralogs encoding lymphocyte co-receptors involved in fine-tuning intracellular signals delivered upon antigen-specific recognition, microbial pattern recognition and cell adhesion. While CD5 and CD6 expression and variation is known to influence some immune-mediated inflammatory disorders, their role in IBD remains unclear. To this end, Cd5- and Cd6-deficient mice were subjected to dextran sulfate sodium (DSS)-induced colitis, the most widely used experimental animal model of IBD. The two mouse lines showed opposite results regarding body weight loss and disease activity index (DAI) changes following DSS-induced colitis, thus supporting Cd5 and Cd6 expression involvement in the pathophysiology of this experimental IBD model. Furthermore, DNA samples from IBD patients of the ENEIDA registry were used to test association of CD5 (rs2241002 and rs2229177) and CD6 (rs17824933, rs11230563, and rs12360861) single nucleotide polymorphisms with susceptibility and clinical parameters of CD (n=1352) and UC (n=1013). Generalized linear regression analyses showed association of CD5 variation with CD ileal location (rs2241002CC) and requirement of biological therapies (rs2241002C-rs2229177T haplotype), and with poor UC prognosis (rs2241002T-rs2229177T haplotype). Regarding CD6, association was observed with CD ileal location (rs17824933G) and poor prognosis (rs12360861G), and with left-sided or extensive UC, and absence of ankylosing spondylitis in IBD (rs17824933G). The present experimental and genetic evidence support a role for CD5 and CD6 expression and variation in IBD’s clinical manifestations and therapeutic requirements, providing insight into its pathophysiology and broadening the relevance of both immunomodulatory receptors in immune-mediated disorders.</p

DataSheet_1_Experimental and genetic evidence for the impact of CD5 and CD6 expression and variation in inflammatory bowel disease.pdf

Crohn’s disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) resulting from the interaction of multiple environmental, genetic and immunological factors. CD5 and CD6 are paralogs encoding lymphocyte co-receptors involved in fine-tuning intracellular signals delivered upon antigen-specific recognition, microbial pattern recognition and cell adhesion. While CD5 and CD6 expression and variation is known to influence some immune-mediated inflammatory disorders, their role in IBD remains unclear. To this end, Cd5- and Cd6-deficient mice were subjected to dextran sulfate sodium (DSS)-induced colitis, the most widely used experimental animal model of IBD. The two mouse lines showed opposite results regarding body weight loss and disease activity index (DAI) changes following DSS-induced colitis, thus supporting Cd5 and Cd6 expression involvement in the pathophysiology of this experimental IBD model. Furthermore, DNA samples from IBD patients of the ENEIDA registry were used to test association of CD5 (rs2241002 and rs2229177) and CD6 (rs17824933, rs11230563, and rs12360861) single nucleotide polymorphisms with susceptibility and clinical parameters of CD (n=1352) and UC (n=1013). Generalized linear regression analyses showed association of CD5 variation with CD ileal location (rs2241002CC) and requirement of biological therapies (rs2241002C-rs2229177T haplotype), and with poor UC prognosis (rs2241002T-rs2229177T haplotype). Regarding CD6, association was observed with CD ileal location (rs17824933G) and poor prognosis (rs12360861G), and with left-sided or extensive UC, and absence of ankylosing spondylitis in IBD (rs17824933G). The present experimental and genetic evidence support a role for CD5 and CD6 expression and variation in IBD’s clinical manifestations and therapeutic requirements, providing insight into its pathophysiology and broadening the relevance of both immunomodulatory receptors in immune-mediated disorders.</p

Genetic variants showing heterogeneous genetic effects on CVD risk across autoimmune diseases.

<p>For each associated SNP (<b>A:</b> rs17465637. <b>B:</b> rs11924705. <b>C:</b> rs2895811. <b>D:</b> rs6789378) the Odds Ratio (OR, black dots) and 95% confidence intervals (horizontal lines) are shown for each of the 6 autoimmune diseases and the combined autoimmune cohort (AID). The SNPs showing a significant association with CVD risk in an autoimmune disease are highlighted in red. For each of the three genotypes of each SNP (risk allele homozygous, heterozygous, non-risk allele homozygous), the incidence of CVD is described in the accompanying table.</p

Established CVD risk variants associated with CVD risk in the six autoimmune diseases.

<p>Established CVD risk variants associated with CVD risk in the six autoimmune diseases.</p

Established autoimmune susceptibility variants also associated with CVD risk.

<p>Established autoimmune susceptibility variants also associated with CVD risk.</p

Functional characterization of the genetic clusters associated with CVD risk across autoimmune diseases.

<p>Functional characterization of the genetic clusters associated with CVD risk across autoimmune diseases.</p