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This has made it challenging to understand drivers of long-term SLE outcomes. Our objective was to identify whether changes in DNA methylation over time, in an actively flaring SLE cohort, were associated with remission and whether these changes meaningfully subtype SLE patients.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Fifty-nine multi-ethnic SLE patients had clinical visits and DNA methylation profiles at a flare and approximately 3\u00a0months later. Methylation was measured using the Illumina EPIC array. We identified sites where methylation change between visits was associated with remission at the follow-up visit using\n                      <jats:italic>limma<\/jats:italic>\n                      package and a\n                      <jats:italic>time x remission<\/jats:italic>\n                      interaction term. Models adjusted for batch, age at diagnosis, time between visits, age at flare, sex, medications, and cell-type proportions. Separately, a paired T-test identified Bonferroni significant methylation sites with\u2009\u2265\u20093% change between visits (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009546). Methylation changes at these sites were used for unsupervised consensus hierarchical clustering. Associations between clusters and patient features were assessed.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Nineteen patients fully remitted at the follow-up visit. For 1,953 CpG sites, methylation changed differently for remitters vs. non-remitters (Bonferroni\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.05). Nearly half were within genes regulated by interferon. The largest effect was at cg22873177; on average, remitters had 23% decreased methylation between visits while non-remitters had no change. Three SLE patient clusters were identified using methylation differences agnostic of clinical outcomes. All Cluster 1 subjects (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200912) experienced complete flare remission, despite similar baseline disease activity scores, medications, and demographics as other clusters. Methylation changes at six CpG sites, including within immune-related\n                      <jats:italic>CD45<\/jats:italic>\n                      and\n                      <jats:italic>IFI<\/jats:italic>\n                      genes, were particularly distinct for each cluster, suggesting these may be good candidates for stratifying patients in the future.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Changes in DNA methylation during active SLE were associated with remission status and identified subgroups of SLE patients with several distinct clinical and biological characteristics. DNA methylation patterns might help inform SLE subtypes, leading to targeted therapies based on relevant underlying biological pathways.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13148-024-01792-x","type":"journal-article","created":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T13:59:10Z","timestamp":1734530350000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Changes in DNA methylation are associated with systemic lupus erythematosus flare remission and clinical subtypes"],"prefix":"10.1186","volume":"16","author":[{"given":"Mary K.","family":"Horton","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne","family":"Nititham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly E.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Katz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chun Jimmie","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinoos","family":"Yazdany","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Dall\u2019Era","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte","family":"Hurabielle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa F.","family":"Barcellos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindsey A.","family":"Criswell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina M.","family":"Lanata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,12,18]]},"reference":[{"issue":"22","key":"1792_CR1","doi-asserted-by":"publisher","first-page":"e143654","DOI":"10.1172\/jci.insight.143654","volume":"5","author":"P Coit","year":"2020","unstructured":"Coit P, Ortiz-Fernandez L, Lewis EE, McCune WJ, Maksimowicz-McKinnon K, Sawalha AH. 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All participants signed a written informed consent to participate.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"NA.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The author(s) declared the following potential conflicts of interest with respect to the research, authorship, and\/or publication of this article: M.K.H., J.N., K.E.T., P.K., M.D., C.H., L.F.B., L.A.C., and C.L. declare no conflict of interest. C.J.Y. has received consulting fees from Maze Therapeutics, HiBio, Santa Ana, TRex Bio, ImYoo, and DeciBio; received payment for honoraria at Renji Hospital School of Medicine, American College of Medic al Genetics and Genomics, St Jude\u2019s Children\u2019s Research Hospital, Yonsei University College of Medicine, and the Lupus Research Alliance; received support for attending meetings from Icahn School of Medicine at Mount Sinai, Parker Institute for Cancer Immunotherapy, Renji Hospital School of Medicine, Northwestern University Feinberg School of Medicine, and St Jude\u2019s Children\u2019s Research Hospital; participated on advisory\/data safety monitoring board for DropPrint Genomics and Related Sciences; leadership role in other boards\/societies\/groups including Survey Genomics, Arc Institute, and DropPrint Genomics; has stock in Survey Genomics, Related Sciences, Maze Therapeutics, and DropPrint Genomics; has received equipment or gifts\/service from Illumina; and has other financial or non-financial interests at Chan Zuckerberg Initiative, Genentech, ScaleBio, Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, BioLegend, and Illumina. J.Y. has grant\/contracts from Gilead, Astra Zeneca, and BMS Foundation; has received consulting fees from Astra Zeneca, Aurinia, Pfizer, Immpact Bio, and Adelphi Values; and is the research lead for the ACR RISE registry.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"181"}}