{"id":521,"date":"2023-03-18T12:25:53","date_gmt":"2023-03-18T12:25:53","guid":{"rendered":"https:\/\/arcaid-h2020.eu\/?page_id=521"},"modified":"2023-03-18T12:25:54","modified_gmt":"2023-03-18T12:25:54","slug":"genyo","status":"publish","type":"page","link":"https:\/\/arcaid-h2020.eu\/?page_id=521","title":{"rendered":"GENyO"},"content":{"rendered":"<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Research Areas to select<\/strong><\/span><\/p>\n<ul>\n<li><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Studies on the molecular stratification of systemic autoimmune diseases (PRECISESADS): <\/strong>this study aims at the use of integrated gene expression and methylation data from blood and specific cell populations to define the molecular pathways for each patient\u00b4s disease. This will lead us to a new molecular diagnosis and to personalized medicine possibilities. The aim is also to identify classifiers that can be used to determine if a patient may become active or fall into remission, whether long-term or short term. Here the candidate will be involved in the analysis of longitudinal transcriptome data to determine the best molecular pattern to define the evolution of the disease. In addition we are investigating major functional differences between the clusters identified.<\/span><\/li>\n<li><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Molecular Phenotyping of Disease States and the genetics behind each disease state:<\/strong>During period of flare, not all lupus patients fall within the same molecular pattern of disease. We have identified 3 possible molecular patterns: inflammatory, lymphoid and interferon. Each disease state may have a different genetic basis. We have identified a new locus strongly associated in the inflammatory cluster and analyzing the genes involved, while attempting to dissect their function and role in the pathogenesis of the disease. Here the person will be involved in the analysis of single-cell transcriptome data from blood and tissues, according to the patient\u00b4s disease state, or exome sequencing of the individuals of interest.<\/span><\/li>\n<li><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Studies on mouse models of SLE: <\/strong>Mouse models of SLE help us understand the mechanisms of disease. We have been working on the role of the BANK1 gene and the appearance of various subsets of B cells, including pro-inflammatory B cells and regulatory B cells. In addition, the role of the microbiome in the development and differentiation of B cell subsets in the spleen but also kidney and intestine, including single-cell RNASeq.<\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Relevant publications:<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Kozyrev, S.V*., Abelson, A.K*., Wojcik, J., Zaghlool, A., Linga Reddy, P.M.V., Sanchez, E., Yin, H., Gunnarsson, I., Svenungsson, E., Sturfelt, G., J\u00f6nsen, A., Truedsson, L., Pons-Estel, B., Witte, T., D\u2019Alfonso, S., Momigliano-Richiardi, P., Danieli, M.G., Gutierrez, C., Su\u00e1rez, A., Junker, P., Laustrup, H., Gonz\u00e1lez-Escribano, M.F., Martin, J., Abderrahim, H., and <strong>Alarc\u00f3n-Riquelme, M.E<\/strong>. The B Cell Gene BANK1 is Associated with Systemic Lupus Erythematosus Through the Effect of Several Functional Variants <em>Nat Genet<\/em> 40(2):211-6, 2008<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Bentham, J., Morris, D.L., Cunninghame-Graham, D.S., Pinder, C.L., Tombleson, P., Behrens, T.W., Criswell, L.A., Gaffney, P., Martin, J., Fairfax, B., Knight, J., Syvannen, AC., Ronnblom, L., Graham, R.R., Wither, J.E., Rioux, J.D., <strong>Alarc\u00f3n-Riquelme, M.E<\/strong>., and Vyse, T.J. Genetic Association Analyses Implicate aberrant gene regulation of the innate and adaptive immunity genes in the pathogenesis of SLE implicated by genetics. <em>Nat Genet<\/em> 47: 1457\u20131464, 2015.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Toro, D., Martorell-Marug\u00e1n, J., Goldman, D., Petri, M., Carmona-S\u00e1ez, P., and <strong>Alarc\u00f3n-Riquelme, M.E<\/strong>. Longitudinal Stratification of Gene Expression Reveals Three SLE Groups of Disease Activity Progression <em>Arthritis Rheum<\/em> 70(12):2025-2035, 2018.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Barturen, G., Beretta, L., Cervera, R., Van Vollenhoven, R., and <strong>Alarc\u00f3n-Riquelme, M.E<\/strong>. Moving Towards a Molecular Taxonomy of Autoimmune Rheumatic Diseases. <em>Nat Rev Rheumatol<\/em> 14(2):75-93, 2018.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Toro-Dom\u00ednguez, D., Dom\u00ednguez-L\u00f3pez, R., Garc\u00eda Moreno, A., Villatoro-Garc\u00eda, J.A., Martorell-Marug\u00e1n, J., Goldman, D., Petri, M., Wojdyla, D., Pons-Estel, B.A., Isenberg, D., Morales-Montes de Oca, G., Trejo-Zambrano, M.I., Garc\u00eda Gonz\u00e1lez, B., G\u00f3mez-Mart\u00edn, D., Romero-D\u00edaz, J., Carmona-Saez, P., and <strong>Alarc\u00f3n-Riquelme, M.E<\/strong>. Differential Treatments and Risk for Severe Nephritis Based on a Longitudinal Systemic Lupus Erythematosus Stratification. <em>Sci Rep<\/em> 9(1): 15502, 2019.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Barturen G, Babaei S, Catal\u00e0-Moll F, Mart\u00ednez-Bueno M, Makowska Z, Martorell-Marug\u00e1n J, Carmona-S\u00e1ez P, Toro-Dom\u00ednguez D, Carnero-Montoro E, Teruel M, Kerick M, Acosta-Herrera M, Le Lann L, Jamin C, Rodr\u00edguez-Ubreva J, Garc\u00eda-G\u00f3mez A, Kageyama J, Buttgereit A, Hayat S, Mueller J, Lesche R, Hernandez-Fuentes M, Juarez M, Rowley T, White I, Mara\u00f1\u00f3n C, Gomes Anjos T, Varela N, Aguilar-Quesada R, Garrancho FJ, L\u00f3pez-Berrio A, Rodriguez Maresca M, Navarro-Linares H, Almeida I, Azevedo N, Brand\u00e3o M, Campar A, Faria R, Farinha F, Marinho A, Neves E, Tavares A, Vasconcelos C, Trombetta E, Montanelli G, Vigone B, Alvarez-Errico D, Li T, Thiagaran D, Blanco Alonso R, Corrales Mart\u00ednez A, Genre F, L\u00f3pez Mej\u00edas R, Gonzalez-Gay MA, Remuzgo S, Ubilla Garcia B, Cervera R, Espinosa G, Rodr\u00edguez-Pint\u00f3 I, De Langhe E, Cremer J, Lories R, Belz D, Hunzelmann N, Baerlecken N, Kniesch K, Witte T, Lehner M, Stummvoll G, Zauner M, Aguirre-Zamorano MA, Barbarroja N, Castro-Villegas MC, Collantes-Estevez E, de Ramon E, D\u00edaz Quintero I, Escudero-Contreras A, Fern\u00e1ndez Rold\u00e1n MC, Jim\u00e9nez G\u00f3mez Y, Jim\u00e9nez Mole\u00f3n I, Lopez-Pedrera R, Ortega-Castro R, Ortego N, Raya E, Artusi C, Gerosa M, Meroni PL, Schioppo T, De Groof A, Ducreux J, Lauwerys B, Maudoux AL, Cornec D, Devauchelle-Pensec V, Jousse-Joulin S, Jouve PE, Rouvi\u00e8re B, Saraux A, Simon Q, Alvarez M, Chizzolini C, Dufour A, Wynar D, Balog A, Bocskai M, De\u00e1k M, Dulic S, K\u00e1d\u00e1r G, Kov\u00e1cs L, Cheng Q, Gerl V, Hiepe F, Khodadadi L, Thiel S, de Rinaldis E, Rao S, Benschop RJ, Chamberlain C, Dow ER, Ioannou Y, Laigle L, Marovac J, Wojcik J, Renaudineau Y, Borghi MO, Frosteg\u00e5rd J, Mart\u00edn J, Beretta L, Ballestar E, McDonald F, Pers JO, <strong>Alarc\u00f3n-Riquelme ME.<\/strong> Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases. <em>Arthritis Rheumatol<\/em> 73(6):1073-1085, 2021.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Morell, M., Varela, N., Coppard, C., Castillejo-L\u00f3pez, C., Wu, Y.Y., Luque, M.J., Garc\u00eda, M.A., <strong>Alarc\u00f3n-Riquelme, M.E<\/strong>., and Mara\u00f1\u00f3n, C. SIDT1 is a Key Player in Interferon Responses to TLR7 and TLR9. <em>eBIOMedicine<\/em> 76:103808. doi: 10.1016\/j.ebiom.2021.103808.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Technology platforms<\/strong><\/span><\/p>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">The NExtSeq 500: Next-Generation Sequencing from Illumina<\/span><\/li>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">The iScan System from Illumina<\/span><\/li>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Mass cytometry (Cytof\/Helios) from Fluidigm<\/span><\/li>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Flow cytometry: sorting, flow and imaging<\/span><\/li>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Bioinformatics analyses, enough capacity, servers<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Confocal microscopy<\/span><\/li>\n<li><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Animal models of SLE<\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Funding<\/strong><\/span><\/p>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Ministerio de Econom\u00eda y Competitividad, Plan Estatal de fomento de la Investigaci\u00f3n Cient\u00edfica de Excelencia 2020, Spain (2021-2023)<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Innovative Medicines Initiative Program of the European Uni\u00f3n (2014-2018): special funding of the project PRECISESADS<\/span><\/li>\n<li><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Innovative Medicines Initiative Program of the European Union (2019-2026): special funding of the project 3TR (PI)<\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>\u00a0<\/strong><strong>Additional information<\/strong><\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">International Collaborations: Dr Alarc\u00f3n-Riquelme heads the Managing Entity of the IMI funded project PRECISESADS, on the \u201cMolecular Re-classification of Systemic Autoimmune Diseases\u201d which joins 21 European academic groups, 2 SMEs and 5 Big Pharma. She is also the coordinator of 3TR: Taxonomy, Treatment, Targets, and Remission: <em>Identification of the Molecular Mechanisms of non-response to Treatments, Relapses and Remission in Autoimmune, Inflammatory, and Allergic Conditions. <\/em>The project joins 58 European academic groups, 3 biotechnology companies and 8 pharmaceutical companies.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\">Dr. Alarc\u00f3n-Riquelme is also a member of the Spanish Society of Rheumatology, The Spanish Society of Immunology, part of the Executive Board of SLEuro, Associate Editor of Arthritis &amp; Rheumatology, member of the Board of Rheumatology.<\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Links:<\/strong><\/span><\/p>\n<ul>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><a href=\"http:\/\/www.precisesads.eu\/\">http:\/\/www.precisesads.eu\/<\/a><\/span><\/li>\n<li data-mce-word-list=\"1\"><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><a href=\"http:\/\/3tr-imi.eu\/\">http:\/\/3tr-imi.eu\/<\/a><\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Whom to contact<\/strong>: Prof Marta E. Alarc\u00f3n-Riquelme at <a href=\"mailto:marta.alarcon@genyo.es\">marta.alarcon@genyo.es<\/a><\/span><\/p>\n<p><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 12pt;\"><strong>Requirements for secondment<\/strong>: The usual languages are Spanish and English. The student will need to have an insurance to cover any possible accidents within the Center, separate from the insurance during the stay in Spain.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Research Areas to select Studies on the molecular stratification of systemic autoimmune diseases (PRECISESADS): this study aims at the use<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-521","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=\/wp\/v2\/pages\/521","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=521"}],"version-history":[{"count":1,"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=\/wp\/v2\/pages\/521\/revisions"}],"predecessor-version":[{"id":522,"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=\/wp\/v2\/pages\/521\/revisions\/522"}],"wp:attachment":[{"href":"https:\/\/arcaid-h2020.eu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=521"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}