{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T18:09:45Z","timestamp":1778695785146,"version":"3.51.4"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T00:00:00Z","timestamp":1660089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["PID2020-119032RB-I00"],"award-info":[{"award-number":["PID2020-119032RB-I00"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["MCIN\/AEI\/10.13039\/501100011033"],"award-info":[{"award-number":["MCIN\/AEI\/10.13039\/501100011033"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["831434"],"award-info":[{"award-number":["831434"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"name":"FEDER\/Junta de Andaluc\u00eda-Consejer\u2019a de Transformaci\u00f3n Econ\u00f3mica, Industria, Conocimiento y Universidades","award":["P20_00335"],"award-info":[{"award-number":["P20_00335"]}]},{"name":"FEDER\/Junta de Andaluc\u00eda-Consejer\u2019a de Transformaci\u00f3n Econ\u00f3mica, Industria, Conocimiento y Universidades","award":["B-CTS-40-UGR20"],"award-info":[{"award-number":["B-CTS-40-UGR20"]}]},{"name":"Ministerio de Universidades"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>Systemic Lupus Erythematosus is a complex autoimmune disease that leads to significant worsening of quality of life and mortality. Flares appear unpredictably during the disease course and therapies used are often only partially effective. These challenges are mainly due to the molecular heterogeneity of the disease, and in this context, personalized medicine-based approaches offer major promise. With this work we intended to advance in that direction by developing MyPROSLE, an omic-based analytical workflow for measuring the molecular portrait of individual patients to support clinicians in their therapeutic decisions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Immunological gene-modules were used to represent the transcriptome of the patients. A dysregulation score for each gene-module was calculated at the patient level based on averaged z-scores. Almost 6100 Lupus and 750 healthy samples were used to analyze the association among dysregulation scores, clinical manifestations, prognosis, flare and remission events and response to Tabalumab. Machine learning-based classification models were built to predict around 100 different clinical parameters based on personalized dysregulation scores.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>MyPROSLE allows to molecularly summarize patients in 206 gene-modules, clustered into nine main lupus signatures. The combination of these modules revealed highly differentiated pathological mechanisms. We found that the dysregulation of certain gene-modules is strongly associated with specific clinical manifestations, the occurrence of relapses or the presence of long-term remission and drug response. Therefore, MyPROSLE may be used to accurately predict these clinical outcomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>MyPROSLE (https:\/\/myprosle.genyo.es) allows molecular characterization of individual Lupus patients and it extracts key molecular information to support more precise therapeutic decisions.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbac332","type":"journal-article","created":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T22:25:17Z","timestamp":1660170317000},"source":"Crossref","is-referenced-by-count":36,"title":["Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8440-312X","authenticated-orcid":false,"given":"Daniel","family":"Toro-Dom\u00ednguez","sequence":"first","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5186-0735","authenticated-orcid":false,"given":"Jordi","family":"Martorell-Marug\u00e1n","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"},{"name":"Department of Statistics. University of Granada , 18071, Granada, Spain"},{"name":"Data Science for Health Research Unit. Fondazione Bruno Kessler , 38123, Trento, Italy"}]},{"given":"Manuel","family":"Martinez-Bueno","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"}]},{"given":"Ra\u00fal","family":"L\u00f3pez-Dom\u00ednguez","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"},{"name":"Department of Statistics. University of Granada , 18071, Granada, Spain"}]},{"given":"Elena","family":"Carnero-Montoro","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"}]},{"given":"Guillermo","family":"Barturen","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"}]},{"given":"Daniel","family":"Goldman","sequence":"additional","affiliation":[{"name":"Johns Hopkins University School of Medicine , Baltimore, Maryland"}]},{"given":"Michelle","family":"Petri","sequence":"additional","affiliation":[{"name":"Johns Hopkins University School of Medicine , Baltimore, Maryland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6173-7255","authenticated-orcid":false,"given":"Pedro","family":"Carmona-S\u00e1ez","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"},{"name":"Department of Statistics. University of Granada , 18071, Granada, Spain"}]},{"given":"Marta E","family":"Alarc\u00f3n-Riquelme","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government , PTS Granada, Avenida de la Ilustraci\u00f3n 114, 18016, Granada, Spain"},{"name":"Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute , 171 67, Solna, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2022,8,10]]},"reference":[{"key":"2022092013231930600_ref1","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1016\/S0140-6736(13)61499-3","article-title":"Clinical aspects of autoimmune rheumatic diseases","volume":"382","author":"Goldblatt","year":"2013","journal-title":"Lancet Lond Engl"},{"key":"2022092013231930600_ref2","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nrd.2017.227","article-title":"Next generation antibody drugs: pursuit of the \u2018high-hanging fruit\u2019","volume":"17","author":"Carter","year":"2018","journal-title":"Nat Rev Drug Discov"},{"key":"2022092013231930600_ref3","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1002\/art.41518","article-title":"Modulation of Cardiometabolic Disease Markers by Type I Interferon Inhibition in Systemic Lupus Erythematosus","volume":"73","author":"Casey","year":"2021","journal-title":"Arthritis Rheumatol"},{"key":"2022092013231930600_ref4","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.molmed.2020.09.009","article-title":"Leveraging Heterogeneity in Systemic Lupus Erythematosus for New Therapies","volume":"27","author":"Allen","year":"2021","journal-title":"Trends Mol Med"},{"key":"2022092013231930600_ref5","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.autrev.2017.11.009","article-title":"Targeting interferons and their pathways in systemic lupus erythematosus","volume":"17","author":"Chasset","year":"2018","journal-title":"Autoimmun Rev"},{"key":"2022092013231930600_ref6","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1002\/art.1780350606","article-title":"Derivation of the SLEDAI. A disease activity index for lupus patients. The Committee on Prognosis Studies in SLE","volume":"35","author":"Bombardier","year":"1992","journal-title":"Arthritis Rheum"},{"issue":"Suppl 11","key":"2022092013231930600_ref7","doi-asserted-by":"crossref","first-page":"S37","DOI":"10.1002\/acr.20572","article-title":"Measures of adult systemic lupus erythematosus: updated version of British Isles Lupus Assessment Group (BILAG 2004), European Consensus Lupus Activity Measurements (ECLAM), Systemic Lupus Activity Measure, Revised (SLAM-R), Systemic Lupus Activity Questionnaire for Population Studies (SLAQ), Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K), and Systemic Lupus International Collaborating Clinics\/American College of Rheumatology Damage Index (SDI)","volume":"63","author":"Romero-Diaz","year":"2011","journal-title":"Arthritis Care Res"},{"key":"2022092013231930600_ref8","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/s41591-019-0407-5","article-title":"Molecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study","volume":"25","author":"Sicklick","year":"2019","journal-title":"Nat Med"},{"key":"2022092013231930600_ref9","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2020.01016","article-title":"Pathway-Based Drug Response Prediction Using Similarity Identification in Gene Expression","volume":"11","author":"Madani Tonekaboni","year":"2020","journal-title":"Front Genet"},{"key":"2022092013231930600_ref10","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.1038\/s41598-019-39019-2","article-title":"Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data","volume":"9","author":"Franco","year":"2019","journal-title":"Sci Rep"},{"key":"2022092013231930600_ref11","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.imlet.2017.08.002","article-title":"Towards personalized medicine for patients with autoimmune diseases: Opportunities and 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