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2. A cross-disease meta-GWAS identifies four new susceptibility loci shared between systemic sclerosis and Crohn’s disease

Author

González-Serna, D., Ochoa, E., López-Isac, E., Julià, A., Degenhardt, F., Ortego-Centeno, N., Radstake, T.R.D.J., Franke, A., Marsal, S., Mayes, M.D., Martín, J., Márquez, A., Assassi, S., Zhou, X., Tan, F.K., Arnett, F.C., Reveille, J.D., Gorlova, O., Chen, W.V., Ying, J., Gregersen, P.K., Lee, A.T., Voskuyl, A.E., de Vries-Bouwstra, J., Magro-Checa, C., Broen, J., Koeleman, B.P.C., Simeón, C.P., Fonollosa, V., Guillén, A., Carreira, P., Castellví, I., González-Gay, M.A., Ríos, R., Callejas-Rubio, J.L., Vargas-Hitos, J.A., García-Portales, R., Camps, M.T., Fernández-Nebro, A., González-Escribano, M.F., García-Hernández, F.J., Castillo, M.J., Aguirre, M.Á., Gómez-Gracia, I., Rodríguez-Rodríguez, L., Fernández-Gutiérrez, B., de la Peña, P.G., Vicente, E., Andreu, J.L., Fernández de Castro, M., López-Longo, F.J., Martínez, L., Espinosa, G., Tolosa, C., Pros, A., Rodríguez-Carballeira, M., Narváez, F.J., Rubio-Rivas, M., Ortiz-Santamaría, V., Madroñero, A.B., Díaz, B., Trapiella, L., Sousa, A., Egurbide, M.V., Fanlo-Mateo, P., Sáez-Comet, L., Díaz-González, F., Hernández, V., Beltrán, E., Román-Ivorra, J.A., Grau, E., Alegre-Sancho, J.J., Blanco-García, F.J., Oreiro, N., Freire, M., Balsa, A., Ortiz, A.M., Hunzelmann, N., Riemekasten, G., Distler, J.H.W., Witte, T., Airó, P., Beretta, L., Santaniello, A., Bellocchi, C., Lunardi, C., Moroncini, G., Gabrielli, A., and Scleroderma, Genetic, Consortium

Abstract

Genome-wide association studies (GWASs) have identified a number of genetic risk loci associated with systemic sclerosis (SSc) and Crohn’s disease (CD), some of which confer susceptibility to both diseases. In order to identify new risk loci shared between these two immune-mediated disorders, we performed a cross-disease meta-analysis including GWAS data from 5, 734 SSc patients, 4, 588 CD patients and 14, 568 controls of European origin. We identified 4 new loci shared between SSc and CD, IL12RB2, IRF1/SLC22A5, STAT3 and an intergenic locus at 6p21.31. Pleiotropic variants within these loci showed opposite allelic effects in the two analysed diseases and all of them showed a significant effect on gene expression. In addition, an enrichment in the IL-12 family and type I interferon signaling pathways was observed among the set of SSc-CD common genetic risk loci. In conclusion, through the first cross-disease meta-analysis of SSc and CD, we identified genetic variants with pleiotropic effects on two clinically distinct immune-mediated disorders. The fact that all these pleiotropic SNPs have opposite allelic effects in SSc and CD reveals the complexity of the molecular mechanisms by which polymorphisms affect diseases.

Published
2020

3. GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways

Author

López-Isac, E., Acosta-Herrera, M., Kerick, M., Assassi, S., Satpathy, A.T., Granja, J., Mumbach, M.R., Beretta, L., Simeón, C.P., Carreira, P., Ortego-Centeno, N., Castellvi, I., Bossini-Castillo, L., Carmona, F.D., Orozco, G., Hunzelmann, N., Distler, J.H.W., Franke, A., Lunardi, C., Moroncini, G., Gabrielli, A., de Vries-Bouwstra, J., Wijmenga, C., Koeleman, B.P.C., Nordin, A., Padyukov, L., Hoffmann-Vold, A.-M., Lie, B., Ríos, R., Callejas, J.L., Vargas-Hitos, J.A., García-Portales, R., Camps, M.T., Fernández-Nebro, A., González-Escribano, M.F., García-Hernández, F.J., Castillo, M.J., Aguirre, M.A., Gómez-Gracia, I., Fernández-Gutiérrez, B., Rodríguez-Rodríguez, L., García de la Peña, P., Vicente, E., Andreu, J.L., Fernández de Castro, M., López-Longo, F.J., Martínez, L., Fonollosa, V., Guillén, A., Espinosa, G., Tolosa, C., Pros, A., Rodríguez-Carballeira, M., Narváez, F.J., Rubio-Rivas, M., Ortiz-Santamaría, V, Madroñero, A.B., González-Gay, M.A., Díaz, B., Trapiella, L., Sousa, A., Egurbide, M.V., Fanlo-Mateo, P., Sáez-Comet, L., Díaz, F., Hernández, V, Beltrán, E., Román-Ivorra, J.A., Grau E., Alegre-Sancho, J.J., Freire, M., Blanco-García, F.J., Oreiro, N., Witte, T., Kreuter, A., Riemekasten, G., Airó P., Magro, C., Voskuyl, A.E., Vonk, M.C., Hesselstrand, R., Proudman S., Stevens, W., Nikpour, M., Zochling, J., Sahhar, J., Roddy, J., Nash, P., Tymms, K., Rischmueller, M., Lester, S., Vyse, T., Herrick, A.L., Worthington, J., Denton C.P., Allanore, Y., Brown, M.A., Radstake, T.R.D.J., Fonseca, C., Chang H.Y., Mayes, M.D., Martin, J., European Scleroderma Group, Australian Scleroderma Interest Group (ASIG), Universidad de Salamanca, Ministerio de Economía y Competitividad (España), Junta de Andalucía, Ministerio de Educación, Cultura y Deporte (España), Instituto de Salud Carlos III, Howard Hughes Medical Institute, Federal Ministry of Education and Research (Germany), Universidad de Cantabria, [López-Isac E, Acosta-Herrera M, Kerick M] Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain. [Assassi S] The University of Texas Health Science Center-Houston, Houston, USA. [Satpathy AT, Granja J] Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, USA. Howard Hughes Medical Institute, Stanford University, Stanford, USA. [Simeón CP] Servei de Medicina Interna, Vall d'Hebron Hospital Universitari, Barcelona, Spain, Vall d'Hebron Barcelona Hospital Campus, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Rheumatology, and AII - Inflammatory diseases

Subjects
0301 basic medicine, Chemistry(all), AUTOIMMUNITY, Àcids nucleics, General Physics and Astronomy, Genome-wide association study, Disease, VARIANTS, Biochemistry, ANNOTATION, 0302 clinical medicine, Phosphopantothenoylcysteine decarboxylase, Single nucleotide, Non-U.S. Gov't, lcsh:Science, skin and connective tissue diseases, características del estudio::metaanálisis [CARACTERÍSTICAS DE PUBLICACIONES], Multidisciplinary, Nucleid acid conformation, integumentary system, Research Support, Non-U.S. Gov't, High-Throughput Nucleotide Sequencing, Genètica - Tècnica, 3. Good health, Nucleic acids, Sequence analysis DNA, Medical genetics, medicine.medical_specialty, Chromatin Immunoprecipitation, GENES, Investigative Techniques::Epidemiologic Methods::Epidemiologic Research Design::Genome-Wide Association Study [ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT], Science, Non-P.H.S, Single-nucleotide polymorphism, Scleroderma systemic, Computational biology, Physics and Astronomy(all), Biology, Research Support, Study Characteristics::Meta-Analysis [PUBLICATION CHARACTERISTICS], Genetic polymorphisms, enfermedades de la piel y tejido conjuntivo::enfermedades del tejido conjuntivo::esclerodermia sistémica [ENFERMEDADES], Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Functional genomics, Genome-wide association studies, Systemic sclerosis, Rheumatic diseases, CLASSIFICATION, N.I.H, 03 medical and health sciences, Research Support, N.I.H., Extramural, Diacylglycerol kinase theta, Molecular genetics, REVEALS, Journal Article, medicine, Humans, Vascular Diseases, Risk factor, Polymorphism, Genomes, GENOME-WIDE ASSOCIATION, METAANALYSIS, 030203 arthritis & rheumatology, Scleroderma, Systemic, Biochemistry, Genetics and Molecular Biology(all), Polimorfisme genètic, HUMAN-CELLS, Extramural, Bayes Theorem, General Chemistry, Sequence Analysis, DNA, Fibrosis, 030104 developmental biology, Scleroderma (Disease), Skin and Connective Tissue Diseases::Connective Tissue Diseases::Scleroderma, Systemic [DISEASES], técnicas de investigación::métodos epidemiológicos::diseño de la investigación epidemiológica::estudio de asociación genómica completa [TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS], Nucleic Acid Conformation, VISUALIZATION, lcsh:Q, U.S. Gov't, Esclerodèrmia, Research Support, U.S. Gov't, Non-P.H.S, Metaanàlisi, Genetics and Molecular Biology(all), Genome-Wide Association Study
Abstract

Systemic sclerosis (SSc) is an autoimmune disease that shows one of the highest mortality rates among rheumatic diseases. We perform a large genome-wide association study (GWAS), and meta-analysis with previous GWASs, in 26,679 individuals and identify 27 independent genome-wide associated signals, including 13 new risk loci. The novel associations nearly double the number of genome-wide hits reported for SSc thus far. We define 95% credible sets of less than 5 likely causal variants in 12 loci. Additionally, we identify specific SSc subtype-associated signals. Functional analysis of high-priority variants shows the potential function of SSc signals, with the identification of 43 robust target genes through HiChIP. Our results point towards molecular pathways potentially involved in vasculopathy and fibrosis, two main hallmarks in SSc, and highlight the spectrum of critical cell types for the disease. This work supports a better understanding of the genetic basis of SSc and provides directions for future functional experiments., We thank Sofia Vargas, Sonia García, and Gema Robledo for their excellent technical assistance and all the patients and control donors for their essential collaboration. We thank National DNA Bank Carlos III (University of Salamanca, Spain) that supplied part of the control DNA samples from Spain, WTCCC and EIRA Consortiums, and PopGen 2.0 network. This work was supported by Spanish Ministry of Economy and Competitiveness (grant ref. SAF2015-66761-P), Consejeria de Innovacion, Ciencia y Tecnologia, Junta de Andalucía (P12-BIO-1395), Ministerio de Educación, Cultura y Deporte through the program FPU, Juan de la Cierva fellowship (FJCI-2015-24028), Red de Investigación en Inflamación y Enfermadades Reumaticas (RIER) from Instituto de Salud Carlos III (RD16/0012/0013), and Scleroderma Research Foundation and NIH P50- HG007735 (to H.Y.C.). H.Y.C. is an Investigator of the Howard Hughes Medical Institute. PopGen 2.0 is supported by a grant from the German Ministry for Education and Research (01EY1103). M.D.M and S.A. are supported by grant DoD W81XWH-18-1- 0423 and DoD W81XWH-16-1-0296, respectively

Published
2019
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7. Influence of the STAT3 genetic variants in the susceptibility to psoriatic arthritis and Behcet’s disease

Author

Cénit, María Carmen, Ortego-Centeno, Norberto, Raya, Enrique, Callejas, José L., García-Hernandez, Francisco J., Castillo-Palma, María Jesús, Fernandez-Sueiro, J.L., Magro, Cesar, Solans, Roser, Castañeda, Santos, Camps, Maite, Hidalgo, Ana, Espinosa, Gerard, González-Gay, Miguel A., González-Escribano, M.F., and Martín, Javier

Published
2013
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9. AB0009 The HLA Class I Region in Behçet's Disease: Identifying the Most Relevant Amino Acid Positions

Author

Ortiz-Fernández, L., primary, Carmona, F.D., additional, Montes-Cano, M.-A., additional, García-Lozano, J.-R., additional, Conde-Jaldόn, M., additional, Ortego-Centeno, N., additional, Castillo-Palma, M.-J., additional, Espinosa, G., additional, Graña-Gil, G., additional, Sánchez-Bursόn, J., additional, Juliá, M.R., additional, Solans, R., additional, Blanco, R., additional, Barnosi-Marín, A.-C., additional, Fanlo, P., additional, Rodriguéz-Carballeira, M., additional, Camps, T., additional, Castañeda, S., additional, Martín, J., additional, and González-Escribano, M.F., additional

Published
2015
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10. IFNL4 ss469415590 polymorphism is associated with unfavourable clinical and immunological status in HIV-infected individuals

Author

Machmach, K., primary, Abad-Molina, C., additional, Romero-Sánchez, M.C., additional, Dominguez-Molina, B., additional, Moyano, M., additional, Rodriguez, M.M., additional, Rafii-El-Idrissi Benhnia, M., additional, Jimenez-Mejias, M.E., additional, Vidal, F., additional, Muñoz-Fernández, M.A., additional, Genebat, M., additional, Viciana, P., additional, González-Escribano, M.F., additional, Leal, M., additional, and Ruiz-Mateos, E., additional

Published
2015
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11. Kallikrein genes are associated with lupus and glomerular basement membrane-specific antibody-induced nephritis in mice and humans

Author

Liu, Kui, Li, Quan-Zhen, Delgado-Vega, Angelica M., Abelson, Anna-Karin, Sánchez, Elena, Kelly, Jennifer A., Li, Li, Liu, Yang, Zhou, Jinchun, Yan, Mei, Ye, Qiu, Liu, Shenxi, Xie, Chun, Zhou, Xin J., Chung, Sharon A., Pons-Estel, Bernardo, Witte, Torsten, de Ramón, Enrique, Bae, Sang-Cheol, Barizzone, Nadia, Sebastiani, Gian Domenico, Merrill, Joan T., Gregersen, Peter K., Gilkeson, Gary G., Kimberly, Robert P., Vyse, Timothy J., Kim, Il, D'Alfonso, Sandra, Martin, Javier, Harley, John B., Criswell, Lindsey A., Wakeland, Edward K., Alarcón-Riquelme, Marta E., Mohan, Chandra, Danieli, M.G., Galeazzi, M., Querini, P.R., Migliaresi, S., Scherbarth, H.R., Lopez, J.A., Motta, E.L., Gamron, S., Drenkard, C., Menso, E., Allievi, A., Tate, G.A., Presas, J.L., Palatnik, S.A., Abdala, M., Bearzotti, M., Alvarellos, A., Caeiro, F., Bertoli, A., Paira, S., Roverano, S., Graf, C.E., Bertero, E., Caprarulo, C., Buchanan, G., Guillerón, C., Grimaudo, S., Manni, J., Catoggio, L.J., Soriano, E.R., Santos, C.D., Prigione, C., Ramos, F.A., Navarro, S.M., Berbotto, G.A., Jorfen, M., Romero, E.J., Garcia, M.A., Marcos, J.C., Marcos, A.I., Perandones, C.E., Eimon, A., Battagliotti, C.G., Armadi-Simab, K., Gross, W.L., Gromica-Ihle, E., Peter, H.H., Manger, K., Schnarr, S., Zeidler, H., Schmidt, R.E., Ortego, N., Callejas, J.L., Jiménez-Alonso, J., Sabio, M., Sánchez-Román, J., Garcia-Hernandez, F.J., Camps, M., López-Nevot, M.A., González-Escribano, M.F., Harley, J.H., Riquelme, M.A., Kimberly, R., Criswell, L., Langefeld, C., Tsao, B., Jacob, C., Liu, Kui, Li, Quan-Zhen, Delgado-Vega, Angelica M., Abelson, Anna-Karin, Sánchez, Elena, Kelly, Jennifer A., Li, Li, Liu, Yang, Zhou, Jinchun, Yan, Mei, Ye, Qiu, Liu, Shenxi, Xie, Chun, Zhou, Xin J., Chung, Sharon A., Pons-Estel, Bernardo, Witte, Torsten, de Ramón, Enrique, Bae, Sang-Cheol, Barizzone, Nadia, Sebastiani, Gian Domenico, Merrill, Joan T., Gregersen, Peter K., Gilkeson, Gary G., Kimberly, Robert P., Vyse, Timothy J., Kim, Il, D'Alfonso, Sandra, Martin, Javier, Harley, John B., Criswell, Lindsey A., Wakeland, Edward K., Alarcón-Riquelme, Marta E., Mohan, Chandra, Danieli, M.G., Galeazzi, M., Querini, P.R., Migliaresi, S., Scherbarth, H.R., Lopez, J.A., Motta, E.L., Gamron, S., Drenkard, C., Menso, E., Allievi, A., Tate, G.A., Presas, J.L., Palatnik, S.A., Abdala, M., Bearzotti, M., Alvarellos, A., Caeiro, F., Bertoli, A., Paira, S., Roverano, S., Graf, C.E., Bertero, E., Caprarulo, C., Buchanan, G., Guillerón, C., Grimaudo, S., Manni, J., Catoggio, L.J., Soriano, E.R., Santos, C.D., Prigione, C., Ramos, F.A., Navarro, S.M., Berbotto, G.A., Jorfen, M., Romero, E.J., Garcia, M.A., Marcos, J.C., Marcos, A.I., Perandones, C.E., Eimon, A., Battagliotti, C.G., Armadi-Simab, K., Gross, W.L., Gromica-Ihle, E., Peter, H.H., Manger, K., Schnarr, S., Zeidler, H., Schmidt, R.E., Ortego, N., Callejas, J.L., Jiménez-Alonso, J., Sabio, M., Sánchez-Román, J., Garcia-Hernandez, F.J., Camps, M., López-Nevot, M.A., González-Escribano, M.F., Harley, J.H., Riquelme, M.A., Kimberly, R., Criswell, L., Langefeld, C., Tsao, B., and Jacob, C.

Abstract

Immune-mediated nephritis contributes to disease in systemic lupus erythematosus, Goodpasture syndrome (caused by antibodies specific for glomerular basement membrane [anti-GBM antibodies]), and spontaneous lupus nephritis. Inbred mouse strains differ in susceptibility to anti-GBM antibody-induced and spontaneous lupus nephritis. This study sought to clarify the genetic and molecular factors that maybe responsible for enhanced immune-mediated renal disease in these models. When the kidneys of 3 mouse strains sensitive to anti-GBM antibody-induced nephritis were compared with those of 2 control strains using microarray analysis, one-fifth of the underexpressed genes belonged to the kallikrein gene family,which encodes serine esterases. Mouse strains that upregulated renal and urinary kallikreins exhibited less evidence of disease. Antagonizing the kallikrein pathway augmented disease, while agonists dampened the severity of anti-GBM antibody-induced nephritis. In addition, nephritis-sensitive mouse strains had kallikrein haplotypes that were distinct from those of control strains, including several regulatory polymorphisms,some of which were associated with functional consequences. Indeed, increased susceptibility to anti-GBM antibody-induced nephritis and spontaneous lupus nephritis was achieved by breeding mice with a genetic interval harboring the kallikrein genes onto a disease-resistant background. Finally, both human SLE and spontaneous lupus nephritis were found to be associated with kallikrein genes, particularly KLK1 and the KLK3 promoter, when DNA SNPs from independent cohorts of SLE patients and controls were compared. Collectively, these studies suggest that kallikreins are protective disease-associated genes in anti-GBM antibody-induced nephritis and lupus.

Published
2009
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19. 924 A GENOME-WIDE ASSOCIATION STUDY IDENTIFIED A NOVEL SUSCEPTIBILITY LOCUS GENE PBK (RS 17388536)FOR SUSTAINED VIROLOGICAL RESPONSE IN PATIENTS BEARING IL28B GENOTYPE CC

Author

Rojas, L., Maraver, M., Ortiz-Fernandez, L., Rojas, A., Conde, M., García-Valdecasas, M., García-Lozano, R., Del Campo, J.A., Sola, R., Forns, X., Moreno-Otero, R., Andrade, R., Diago, M., Salmeron, J., Rodrigo, L., Pons, J.A., Navarro, J.M., Calleja, J.L., Garcia-Samaniego, J., Butti, M., Cano, C., Millen, M., Millan, R., Gonzalez-Escribano, M.F., and Romero-Gomez, M.

Published
2012
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