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Patients were stratified based on immunophenotyping data. Subsequently, we examined clinical and transcriptomic differences among these stratified clusters.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Patients with IMDs were stratified into two clusters based on their immunophenotypes. Cluster 1 was enriched with differentiated B cells, including unswitched memory B cells (USM B), switched memory B cells, double-negative B cells and plasmablasts, while cluster 2 was enriched with na\u00efve B cells. Higher disease activity in rheumatoid arthritis and decreased respiratory functions in systemic sclerosis were observed in cluster 1, whereas the disease activity of systemic lupus erythematosus was higher in cluster 2. Numerous differentially expressed genes were detected in USM B. Cluster 1 was associated with glycosylation processes in USM B and elevated B cell-activating factor signalling from myeloid cells in B cells, while cluster 2 exhibited higher B-cell receptor signalling in USM B. Patients in cluster 2, which had an elevated age-associated B-cell signature, exhibited more frequent flares, suggesting that an increased proportion of na\u00efve B cells with this signature is associated with poor prognosis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Immunophenotyping-based clusters and transcriptome-based states revealed quantitative and qualitative differences in B cells. To predict IMD prognosis, assessing both the quantity and quality of na\u00efve B cells may be crucial.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1136\/rmdopen-2024-005310","type":"journal-article","created":{"date-parts":[[2025,4,10]],"date-time":"2025-04-10T01:45:12Z","timestamp":1744249512000},"page":"e005310","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":1,"title":["Integration of transcriptome and immunophenotyping data highlights differences in the pathogenetic kinetics of B cells across immune-mediated disease"],"prefix":"10.1136","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9724-4911","authenticated-orcid":false,"given":"Shinji","family":"Izuka","sequence":"first","affiliation":[{"name":"Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 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