Gwas gene hautagaien inplikazio funtzionala eritasun zeliakoaren patogenesian

123 p.(eng):129 p.(eusk)La enfermedad celíaca (EC) es una enfermedad autoinmune que se desarrolla en personas con susceptibilidad genética. En los últimos años se han realizado diversos estudios de asociación genómica, en los que se han identificado nuevas regiones asociadas a EC y se han propuesto una larga lista de genes candidato.Los objetivos de esta tesis han sido, por un lado repetir los estudios de asociación en población española y por otro lado hacer un estudio funcional de los genes candidato propuestos.Debido a las diferencias genéticas entre poblaciones, no todas las regiones genéticas aparecen asociadas en cada una de las poblaciones a estudio. En el caso de la población española, hemos obtenido resultados variados. Algunas de las regiones aparecen asociadas y otras no, y además hemos sido capaces de identificar nuevas regiones asociadas en nuestra población.Para el estudio funcional de los genes candidato, hemos analizado la expresión de dichos genes en varios tipos de muestras. Por un lado biopsias intestinales de pacientes celiacos al diagnóstico y tras el tratamiento, y controles no celíacos; y por otro lado poblaciones celulares extraídas de las biopsias de dichos pacientes, con el objetivo de analizar con mayor precisión lo que ocurre en cada uno de los tipos celulares.Los resultados obtenidos demuestran una vez más la complejidad de la EC, ya que la relación entre los genes alterados y los SNPs asociados no es direct

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

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.The authors thank the technical and human support provided by SGIker of the UPV/EHU. The work was funded by ISCIII Research Project Grants PI13/01201 and PI16/00258, cofunded by the European Union ERDF/ESF "A way to make Europe" and by Basque Department of Health project 2011/111034 to JRB and Basque Department of Health project 2015/111068 to I.S., N.F.-J. was supported by an IARC Postodctoral Fellowship (FP7 Marie Curie Actions-People-COFUND) and a Postdoctoral Fellowship from the Basque Department of Education. I.R.-G. and A.J.-M. are supported by predoctoral fellowship grants from the UPV/EHU and the Basque Department of Education, respectively

Accuracy in Copy Number Calling by qPCR and PRT: A Matter of DNA

The possible implication of copy number variation (CNV) in the genetic susceptibility to human disease needs to be assessed using robust methods that can be applied at a population scale. In this report, we analyze the performance of the two major techniques, quantitative PCR (qPCR) and paralog ratio test (PRT), and investigate the influence of input DNA amount and template integrity on the reliability of both methods. Analysis of three genes (PRELID1, SYNPO and DEFB4) in a large sample set showed that both methods are prone to false copy number assignments if sufficient attention is not paid to DNA concentration and quality. Accurate normalization of samples is essential for reproducible qPCR because it avoids the effect of differential amplification efficiencies between target and control assays, whereas PRT is generally more sensitive to template degradation due to the fact that longer amplicons are usually needed to optimize sensitivity and specificity of paralog sequence PCR. The use of normalized, high quality genomic DNA yields comparable results with both methods

Gwas gene hautagaien inplikazio funtzionala eritasun zeliakoaren patogenesian

123 p.(eng):129 p.(eusk)La enfermedad celíaca (EC) es una enfermedad autoinmune que se desarrolla en personas con susceptibilidad genética. En los últimos años se han realizado diversos estudios de asociación genómica, en los que se han identificado nuevas regiones asociadas a EC y se han propuesto una larga lista de genes candidato.Los objetivos de esta tesis han sido, por un lado repetir los estudios de asociación en población española y por otro lado hacer un estudio funcional de los genes candidato propuestos.Debido a las diferencias genéticas entre poblaciones, no todas las regiones genéticas aparecen asociadas en cada una de las poblaciones a estudio. En el caso de la población española, hemos obtenido resultados variados. Algunas de las regiones aparecen asociadas y otras no, y además hemos sido capaces de identificar nuevas regiones asociadas en nuestra población.Para el estudio funcional de los genes candidato, hemos analizado la expresión de dichos genes en varios tipos de muestras. Por un lado biopsias intestinales de pacientes celiacos al diagnóstico y tras el tratamiento, y controles no celíacos; y por otro lado poblaciones celulares extraídas de las biopsias de dichos pacientes, con el objetivo de analizar con mayor precisión lo que ocurre en cada uno de los tipos celulares.Los resultados obtenidos demuestran una vez más la complejidad de la EC, ya que la relación entre los genes alterados y los SNPs asociados no es direct

Association of the IL-15 and IL-15Rα genes with celiac disease

Celiac disease is a chronic autoimmune condition triggered by dietary gluten in genetically predisposed individuals and the treatment is a strict gluten-free diet. The major predisposing genes are HLA-DQA1 and HLA-DQB1, but these are not sufficient for disease development. One of the candidate genes worth studying is interleukin (IL)-15 gene, together with its specific receptor, IL-15Rα, as they participate in promoting lymphocyte signaling and survival, and the establishment of appropriate conditions for villous atrophy, then acting as key players in the immunopathogenesis of CD. Here we analyze IL-15 and IL-15Rα genes in samples from the Spanish Consortium for Genetics of Celiac Disease (CEGEC) collection, identifying two regulatory single-nucleotide polymorphisms (SNP) that might be associated with celiac disease: rs4956400 (p-value 0.0112, OR 1.21, 95% CI 1.04–1.40) and rs11100722 (p-value 0.0087, OR 1.24, 95% CI 1.06–1.45), both located upstream the IL15 gene. When the expression of both genes was assessed, these two SNPs were found to be correlated with IL-15 higher protein expression. Besides, rs8177655 from IL15RA was also associated to mRNA IL-15 expression in CD patients. Finally, three SNPs from IL15RA intronic regions, rs2296141, rs3136614 and rs3181148, and another from its 3’UTR region, rs2229135, could be related to the age of diagnosis of celiac disease patients.This study was performed thanks to the grants from the Junta de Castilla y León (VA016A10-2), Instituto de Salud Carlos III FEDER (PI10/01647 and PI13/01201), Basque Dpt. of Health (2011/111034) and FPI-University of Valladolid.Peer Reviewe

<i>THEMIS</i> and <i>PTPRK</i> in celiac intestinal mucosa: coexpression in disease and after <i>in vitro</i> gliadin challenge

Celiac disease (CD) is an immune mediated, polygenic disorder, where HLA-DQ2/DQ8 alleles contribute around 35% to genetic risk, but several other genes are also involved. Genome-wide association studies (GWASs) and the more recent immunochip genotyping projects have fine-mapped 39 regions of genetic susceptibility to the disease, most of which harbor candidate genes that could participate in this disease process. We focused our attention to the GWAS peak on chr6: 127.99–128.38 Mb, a region including two genes, thymocyte-expressed molecule involved in selection (THEMIS) and protein tyrosine phosphatase, receptor type, kappa (PTPRK), both of which have immune-related functions. The aim of this work was to evaluate the expression levels of these two genes in duodenal mucosa of active and treated CD patients and in controls, and to determine whether SNPs (rs802734, rs55743914, rs72975916, rs10484718 and rs9491896) associated with CD have any influence on gene expression. THEMIS showed higher expression in active CD compared with treated patients and controls, whereas PTPRK showed lower expression. Our study confirmed the association of this region with CD in our population, but only the genotype of rs802734 showed some influence in the expression of THEMIS. On the other hand, we found a significant positive correlation between THEMIS and PTPRK mRNA levels in CD patients but not in controls. Our results suggest a possible role for both candidate genes in CD pathogenesis and the existence of complex, regulatory relationships that reside in the vast non-coding, functional intergenic regions of the genome. Further investigation is needed to clarify the impact of the disease-associated SNPs on gene function.Facultad de Ciencias ExactasLaboratorio de Investigaciones del Sistema Inmun

THEMIS and PTPRK in celiac intestinal mucosa: Coexpression in disease and after in vitro gliadin challenge

Celiac disease (CD) is an immune mediated, polygenic disorder, where HLA-DQ2/DQ8 alleles contribute around 35% to genetic risk, but several other genes are also involved. Genome-wide association studies (GWASs) and the more recent immunochip genotyping projects have fine-mapped 39 regions of genetic susceptibility to the disease, most of which harbor candidate genes that could participate in this disease process. We focused our attention to the GWAS peak on chr6: 127.99–128.38 Mb, a region including two genes, thymocyte-expressed molecule involved in selection (THEMIS) and protein tyrosine phosphatase, receptor type, kappa (PTPRK), both of which have immune-related functions. The aim of this work was to evaluate the expression levels of these two genes in duodenal mucosa of active and treated CD patients and in controls, and to determine whether SNPs (rs802734, rs55743914, rs72975916, rs10484718 and rs9491896) associated with CD have any influence on gene expression. THEMIS showed higher expression in active CD compared with treated patients and controls, whereas PTPRK showed lower expression. Our study confirmed the association of this region with CD in our population, but only the genotype of rs802734 showed some influence in the expression of THEMIS. On the other hand, we found a significant positive correlation between THEMIS and PTPRK mRNA levels in CD patients but not in controls. Our results suggest a possible role for both candidate genes in CD pathogenesis and the existence of complex, regulatory relationships that reside in the vast non-coding, functional intergenic regions of the genome. Further investigation is needed to clarify the impact of the disease-associated SNPs on gene function.Fil: Bondar, Constanza María. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas. Laboratorio de Investigaciones del Sistema Inmune; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Plaza Izurieta, Leticia. Universidad del País Vasco; EspañaFil: Fernandez Jimenez, Nora. Universidad del País Vasco; EspañaFil: Irastorza, Iñaki. Hospital Universitario Cruces; EspañaFil: Withoff, Sebo. University of Groningen; Países BajosFil: Grupo CEGEC. No especifica;Fil: Wijmenga, Cisca. University of Groningen; Países BajosFil: Chirdo, Fernando Gabriel. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas. Laboratorio de Investigaciones del Sistema Inmune; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Bilbao, Jose Ramon. Universidad del País Vasco; Españ

Growth time dependence of mean void volume in human colonic adenocarcinoma T84 3D cell cultures.

<p>The blue curve represents control cultures and the red curve represents cultures treated with TGF-β.</p