{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T23:27:29Z","timestamp":1792106849580,"version":"4.4.0"},"reference-count":30,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2024,7,27]],"date-time":"2024-07-27T00:00:00Z","timestamp":1722038400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","award":["K08AR082939"],"award-info":[{"award-number":["K08AR082939"]}],"id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["acrjournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["ACR Open Rheumatology"],"published-print":{"date-parts":[[2024,10]]},"abstract":"<jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>The pathogenesis of inflammatory myopathies is poorly understood and there is a need to dissect the transcriptome in more granular ways beyond gene expression.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We used a set of muscle RNA\u2010sequencing data from different myositis subtypes grouped by their specific autoantibodies (n = 152). We quantified annotated RNA transcripts for each myositis subtype and identified uniquely expressed RNA as well as transcriptional similarities among myositis types. In addition, we quantified event\u2010based alternative splicing with predicted protein changes. And finally, we searched for cryptic exons.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We saw considerable overlap in RNA expression among subtypes. In addition,\n                      <jats:italic>MADCAM1<\/jats:italic>\n                      was previously shown to be uniquely expressed in Mi\u20102 myositis; we discovered it was two noncanonical transcripts that predominantly contributed to the observed increased expression. At the transcriptional level, dermatomyositis subtypes were least similar to inclusion body myositis (IBM) or Jo1, followed by HMGCR, then SRP and other dermatomyositis subtype. Additionally, we discovered many alternative splicing events that were unique by myositis subgroup, including events in muscle dystrophy genes and one event in\n                      <jats:italic>SRP72<\/jats:italic>\n                      , which was seen uniquely in SRP myositis. Finally, we looked for previously reported cryptic exons in IBM and did not find them.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The large degree of transcriptional overlap among myositis subtypes reinforces the need to use disease (in addition to healthy) controls to find unique features of autoimmune disease. Unique alterations in the transcriptome that are seen in one myositis subtype and not others advance our understanding of distinct disease pathology.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/acr2.11724","type":"journal-article","created":{"date-parts":[[2024,7,27]],"date-time":"2024-07-27T23:39:25Z","timestamp":1722123565000},"page":"690-699","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Distinct Transcript\u2010Level Expression Profiles and Unique Alternative Splicing in Inflammatory Myopathies"],"prefix":"10.1002","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9214-521X","authenticated-orcid":false,"given":"Rayan","family":"Najjar","sequence":"first","affiliation":[{"name":"University of Washington  Seattle Washington"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hugh","family":"Alessi","sequence":"additional","affiliation":[{"name":"University of Washington  Seattle Washington"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6338-9218","authenticated-orcid":false,"given":"Iago","family":"Pinal\u2010Fernandez","sequence":"additional","affiliation":[{"name":"National Institute of Arthritis and Musculoskeletal and Skin Disease National Institutes of Health  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3732-3252","authenticated-orcid":false,"given":"Andrew L.","family":"Mammen","sequence":"additional","affiliation":[{"name":"National Institute of Arthritis and Musculoskeletal and Skin Disease National Institutes of Health  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5912-8840","authenticated-orcid":false,"given":"Tomas","family":"Mustelin","sequence":"additional","affiliation":[{"name":"University of Washington  Seattle Washington"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,7,27]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/joim.12451"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/art.41964"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.autrev.2018.10.004"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1136\/ard.60.2.116"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1097\/01.md.0000173991.74008.b0"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1136\/annrheumdis-2019-216599"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-021-02365-5"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1212\/WNL.0000000000008128"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.3892\/br.2014.407"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2407-11-418"},{"key":"e_1_2_6_12_1","first-page":"6","article-title":"Alternative splicing in Alzheimer's disease","volume":"2","author":"Love JE","year":"2015","journal-title":"J Parkinsons Dis Alzheimers Dis"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.713540"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1136\/annrheumdis-2021-220308"},{"key":"e_1_2_6_15_1","unstructured":"AndrewsS.FastQC: a quality control tool for high throughput sequence data. 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