{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T21:25:40Z","timestamp":1790198740940,"version":"4.1.0"},"posted":{"date-parts":[[2025,8,14]]},"group-title":"Molecular Biology","reference-count":127,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,2]]},"abstract":"<jats:p>Lupus nephritis (LN), a severe manifestation of Systemic Lupus Erythematosus (SLE), is a heterogeneous disease driven by diverse immune and tissue cell types. We obtained 538K single-cell and 140K single-nuclear profiles from kidney biopsies of 155 LN patients and 30 pre-implantation transplant biopsy controls, along with 325K single-cell blood profiles overlapping many of these patients. We identified key tissue cell types and cell states, and immune cell states; we were able to determine cell states that were tissue specific, and those that were present in the blood. We observed that LN pathological features are significantly associated with cell states using differential gene expression and Covarying Neighborhood Analysis (CNA). These analyses revealed broad changes in cell states associated with irreversible chronic tissue damage. After controlling for the effects of ongoing tissue damage, we observed that expansion of key glomerular and Scar Associated Macrophages (SAMs) populations tracked with increasing inflammatory disease activity. SAMs appear to drive LN fibrosis and, in active disease, infiltrate the glomeruli more than other myeloid cells. These observations strongly support that therapeutic targeting of myeloid populations may offer an as-of-yet unproven strategy to prevent renal inflammation and ongoing kidney damage in LN.<\/jats:p>","DOI":"10.1101\/2025.08.11.669754","type":"posted-content","created":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T03:55:11Z","timestamp":1755230111000},"source":"Crossref","is-referenced-by-count":7,"title":["A population-scale atlas of blood and tissue in lupus nephritis"],"prefix":"10.64898","author":[{"given":"Nicholas W.","family":"Sugiarto","sequence":"first","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddarth","family":"Gurajala","sequence":"additional","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Curtis","sequence":"additional","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas M.","family":"Eisenhaure","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnon","family":"Arazi","sequence":"additional","affiliation":[{"name":"Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Fava","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Johns Hopkins University, Baltimore, MD, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Xiao","sequence":"additional","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Mears","sequence":"additional","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brad","family":"Rovin","sequence":"additional","affiliation":[{"name":"Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Celine C.","family":"Berthier","sequence":"additional","affiliation":[{"name":"Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter M.","family":"Izmirly","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer L.","family":"Barnas","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul J.","family":"Hoover","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Peters","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raktima","family":"Raychowdhury","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Horisberger","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. 3Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saori","family":"Sakaue","sequence":"additional","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard A.","family":"Furie","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Northwell Health, Great Neck, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. Michael","family":"Belmont","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0421-8483","authenticated-orcid":false,"given":"David A.","family":"Hildeman","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. Steve","family":"Woodle","sequence":"additional","affiliation":[{"name":"Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Dall'Era","sequence":"additional","affiliation":[{"name":"Rheumatology Division, University of California San Francisco, San Francisco, CA, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaim","family":"Putterman","sequence":"additional","affiliation":[{"name":"Division of Rheumatology and Department of Microbiology and Immunology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diane L.","family":"Kamen","sequence":"additional","affiliation":[{"name":"Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maureen A.","family":"McMahon","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Grossman","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth C.","family":"Kalunian","sequence":"additional","affiliation":[{"name":"School of Medicine, University of California San Diego, La Jolla, California, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey B.","family":"Hodgin","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Michigan, Ann Arbor, MI, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernanda","family":"Payan-Schober","sequence":"additional","affiliation":[{"name":"Department of Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Apruzzese","sequence":"additional","affiliation":[{"name":"Pfizer Inc., New York, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harris","family":"Perlman","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla M.","family":"Cuda","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Wofsy","sequence":"additional","affiliation":[{"name":"Rheumatology Division, University of California San Francisco, San Francisco, CA, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9308-237X","authenticated-orcid":false,"given":"Joel M.","family":"Guthridge","sequence":"additional","affiliation":[{"name":"Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1450-1549","authenticated-orcid":false,"given":"Jennifer H.","family":"Anolik","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judith A.","family":"James","sequence":"additional","affiliation":[{"name":"Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"Accelerating Medicines Partnerships Rheumatoid Arthritis\/Systemic Lupus Erythematosus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepak A.","family":"Rao","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Davidson","sequence":"additional","affiliation":[{"name":"Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle A.","family":"Petri","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Johns Hopkins University, Baltimore, MD, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jill P.","family":"Buyon","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nir","family":"Hacohen","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3250-3804","authenticated-orcid":false,"given":"Betty","family":"Diamond","sequence":"additional","affiliation":[{"name":"Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1901-8265","authenticated-orcid":false,"given":"Soumya","family":"Raychaudhuri","sequence":"additional","affiliation":[{"name":"Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026032622052681000_2025.08.11.669754v2.1","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1056\/NEJMe2208772","article-title":"Progress toward better treatment of lupus","volume":"387","year":"2022","journal-title":"N. Engl. J. Med"},{"key":"2026032622052681000_2025.08.11.669754v2.2","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1002\/art.41632","article-title":"Prevalence of systemic lupus erythematosus in the United States: Estimates from a meta-analysis of the Centers for Disease Control and Prevention national lupus registries","volume":"73","year":"2021","journal-title":"Arthritis Rheumatol"},{"key":"2026032622052681000_2025.08.11.669754v2.3","doi-asserted-by":"crossref","first-page":"2006","DOI":"10.1002\/art.40192","article-title":"The incidence and prevalence of systemic lupus erythematosus in New York County (Manhattan), New York: The Manhattan Lupus Surveillance Program","volume":"69","year":"2017","journal-title":"Arthritis Rheumatol"},{"key":"2026032622052681000_2025.08.11.669754v2.4","first-page":"1996","article-title":"The incidence and prevalence of systemic lupus erythematosus in San Francisco County","volume":"69","year":"2017","journal-title":"California: The California Lupus Surveillance Project. Arthritis Rheumatol"},{"key":"2026032622052681000_2025.08.11.669754v2.5","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(21)00578-x"},{"key":"2026032622052681000_2025.08.11.669754v2.6","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2001180"},{"key":"2026032622052681000_2025.08.11.669754v2.7","doi-asserted-by":"publisher","DOI":"10.2215\/CJN.00490109"},{"key":"2026032622052681000_2025.08.11.669754v2.8","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1002\/acr.22685","article-title":"Incidence of end-stage renal disease among newly diagnosed systemic lupus erythematosus patients: The Georgia lupus registry","volume":"68","year":"2016","journal-title":"Arthritis Care Res. (Hoboken"},{"key":"2026032622052681000_2025.08.11.669754v2.9","doi-asserted-by":"publisher","DOI":"10.1002\/art.38006"},{"key":"2026032622052681000_2025.08.11.669754v2.10","doi-asserted-by":"publisher","DOI":"10.1093\/ndt\/gfs073"},{"key":"2026032622052681000_2025.08.11.669754v2.11","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/s41572-019-0141-9","article-title":"Lupus nephritis","volume":"6","year":"2020","journal-title":"Nat. Rev. Dis. Primers"},{"key":"2026032622052681000_2025.08.11.669754v2.12","doi-asserted-by":"publisher","DOI":"10.15537\/smj.2018.10.22435"},{"key":"2026032622052681000_2025.08.11.669754v2.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.kint.2017.11.023"},{"key":"2026032622052681000_2025.08.11.669754v2.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.kint.2023.09.002"},{"key":"2026032622052681000_2025.08.11.669754v2.15","doi-asserted-by":"publisher","DOI":"10.1136\/annrheumdis-2013-204620"},{"key":"2026032622052681000_2025.08.11.669754v2.16","doi-asserted-by":"publisher","DOI":"10.1186\/s13075-024-03275-z"},{"key":"2026032622052681000_2025.08.11.669754v2.17","doi-asserted-by":"publisher","DOI":"10.1136\/lupus-2018-000271"},{"key":"2026032622052681000_2025.08.11.669754v2.18","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1002\/art.39026","article-title":"Predictors of long-term renal outcome in lupus nephritis trials: lessons learned from the Euro-Lupus Nephritis cohort","volume":"67","year":"2015","journal-title":"Arthritis Rheumatol"},{"key":"2026032622052681000_2025.08.11.669754v2.19","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.kint.2019.07.018","article-title":"Kidney biopsy-based management of maintenance immunosuppression is safe and may ameliorate flare rate in lupus nephritis","volume":"97","year":"2020","journal-title":"Kidney Int"},{"key":"2026032622052681000_2025.08.11.669754v2.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.03.008"},{"key":"2026032622052681000_2025.08.11.669754v2.21","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf1970"},{"key":"2026032622052681000_2025.08.11.669754v2.22","unstructured":"M. Nakano , M. Kono , K. Asahara , T. Katsuyama , S. Kubo , E. Katsuyama , Y. Fujita , H. Inokuchi , T. Nishino , T. Arakawa , T. Kawashima , S. Noma , R. Bagherzadeh , Y. Matsumoto , J. Inamo , H. Takahashi , B. Natsumoto , X. Zhang , S.-C. Bae , A. Suzuki , H. Hatano , C. Terao , Y. Tanaka , Y. Matsumoto , K. Yamamoto , K. Ishigaki , Cellular and molecular fine mapping pinpoints new immunopathology of lupus, bioRxiv (2025)p. 2025.12.08.693110."},{"key":"2026032622052681000_2025.08.11.669754v2.23","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-019-0398-x"},{"key":"2026032622052681000_2025.08.11.669754v2.24","doi-asserted-by":"publisher","DOI":"10.1136\/lupus-2023-000932"},{"key":"2026032622052681000_2025.08.11.669754v2.25","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.adl1666"},{"key":"2026032622052681000_2025.08.11.669754v2.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-025-02291-8"},{"key":"2026032622052681000_2025.08.11.669754v2.27","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1002\/acr.24066","article-title":"Accelerating Medicines Partnership: Organizational structure and preliminary data from the phase 1 studies of lupus nephritis","volume":"72","year":"2020","journal-title":"Arthritis Care Res. (Hoboken"},{"key":"2026032622052681000_2025.08.11.669754v2.28","first-page":"481","article-title":"Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases","volume":"3","year":"2022","journal-title":"Med (N. Y"},{"key":"2026032622052681000_2025.08.11.669754v2.29","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0"},{"key":"2026032622052681000_2025.08.11.669754v2.30","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01066-4"},{"key":"2026032622052681000_2025.08.11.669754v2.31","doi-asserted-by":"publisher","DOI":"10.1038\/s12276-022-00892-z"},{"key":"2026032622052681000_2025.08.11.669754v2.32","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2018090912"},{"key":"2026032622052681000_2025.08.11.669754v2.33","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-019-0378-1"},{"key":"2026032622052681000_2025.08.11.669754v2.34","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2005477117"},{"key":"2026032622052681000_2025.08.11.669754v2.35","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2026684118"},{"key":"2026032622052681000_2025.08.11.669754v2.36","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05769-3"},{"key":"2026032622052681000_2025.08.11.669754v2.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31772-9"},{"key":"2026032622052681000_2025.08.11.669754v2.38","doi-asserted-by":"publisher","DOI":"10.1038\/sj.bdj.2010.981"},{"key":"2026032622052681000_2025.08.11.669754v2.39","doi-asserted-by":"crossref","unstructured":"K. Jeong , J. Je , T. Dusabimana , H. Kim , S. W. Park , Early growth response 1 contributes to renal IR injury by inducing proximal tubular cell apoptosis. Int. J. Mol. Sci. 24 (2023).","DOI":"10.3390\/ijms241814295"},{"key":"2026032622052681000_2025.08.11.669754v2.40","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1136\/ard-2022-222605","article-title":"Age-associated B cells contribute to the pathogenesis of rheumatoid arthritis by inducing activation of fibroblast-like synoviocytes via TNF-\u03b1-mediated ERK1\/2 and JAK-STAT1 pathways","volume":"81","year":"2022","journal-title":"Ann. Rheum. Dis"},{"key":"2026032622052681000_2025.08.11.669754v2.41","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv715"},{"key":"2026032622052681000_2025.08.11.669754v2.42","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4772-0"},{"key":"2026032622052681000_2025.08.11.669754v2.43","doi-asserted-by":"publisher","DOI":"10.1038\/mi.2017.8"},{"key":"2026032622052681000_2025.08.11.669754v2.44","doi-asserted-by":"publisher","DOI":"10.1126\/science.284.5421.1835"},{"key":"2026032622052681000_2025.08.11.669754v2.45","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abo0686"},{"key":"2026032622052681000_2025.08.11.669754v2.46","doi-asserted-by":"publisher","DOI":"10.1038\/nature20810"},{"key":"2026032622052681000_2025.08.11.669754v2.47","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-023-01577-7"},{"key":"2026032622052681000_2025.08.11.669754v2.48","doi-asserted-by":"publisher","DOI":"10.1177\/1759720X13485503"},{"key":"2026032622052681000_2025.08.11.669754v2.49","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11013-2"},{"key":"2026032622052681000_2025.08.11.669754v2.50","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1002\/ar.24260","article-title":"What makes the kidney susceptible to hypoxia?","volume":"303","year":"2020","journal-title":"Anat. Rec. (Hoboken"},{"key":"2026032622052681000_2025.08.11.669754v2.51","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-022-10485-8"},{"key":"2026032622052681000_2025.08.11.669754v2.52","doi-asserted-by":"publisher","DOI":"10.1126\/science.ade2292"},{"key":"2026032622052681000_2025.08.11.669754v2.53","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-00882-0"},{"key":"2026032622052681000_2025.08.11.669754v2.54","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2006.08.010"},{"key":"2026032622052681000_2025.08.11.669754v2.55","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/s00296-025-05910-7","article-title":"Sex- and gender-related differences in systemic lupus erythematosus: a scoping review","volume":"45","year":"2025","journal-title":"Rheumatol. Int"},{"key":"2026032622052681000_2025.08.11.669754v2.56","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1007\/s11255-022-03112-9","article-title":"Prognostic value of modified National Institute of Health activity and chronicity scoring in determining complete renal response in newly diagnosed lupus nephritis: a retrospective single centre study","volume":"54","year":"2022","journal-title":"Int. Urol. Nephrol"},{"key":"2026032622052681000_2025.08.11.669754v2.57","doi-asserted-by":"crossref","first-page":"108952","DOI":"10.1016\/j.jdiacomp.2025.108952","article-title":"Nicotinamide n-methyltransferase inhibitor synergizes with sodium-glucose cotransporter 2 inhibitor to protect renal tubular epithelium in experimental models of type 2 diabetes mellitus","volume":"39","year":"2025","journal-title":"J. Diabetes Complications"},{"key":"2026032622052681000_2025.08.11.669754v2.58","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1007\/s10157-024-02545-z","article-title":"Knockdown of nicotinamide N-methyltransferase ameliorates renal fibrosis caused by ischemia-reperfusion injury and remodels sphingosine metabolism","volume":"28","year":"2024","journal-title":"Clin. Exp. Nephrol"},{"key":"2026032622052681000_2025.08.11.669754v2.59","doi-asserted-by":"publisher","DOI":"10.1016\/j.matbio.2018.02.006"},{"key":"2026032622052681000_2025.08.11.669754v2.60","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11049-4"},{"key":"2026032622052681000_2025.08.11.669754v2.61","doi-asserted-by":"publisher","DOI":"10.1136\/annrheumdis-2013-205139"},{"key":"2026032622052681000_2025.08.11.669754v2.62","doi-asserted-by":"publisher","DOI":"10.1093\/ndt\/gfr517"},{"key":"2026032622052681000_2025.08.11.669754v2.63","doi-asserted-by":"publisher","DOI":"10.1096\/fj.202000651"},{"key":"2026032622052681000_2025.08.11.669754v2.64","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1631-3"},{"key":"2026032622052681000_2025.08.11.669754v2.65","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.add8945"},{"key":"2026032622052681000_2025.08.11.669754v2.66","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a005017"},{"key":"2026032622052681000_2025.08.11.669754v2.67","doi-asserted-by":"publisher","DOI":"10.1038\/S41580-020-0237-9"},{"key":"2026032622052681000_2025.08.11.669754v2.68","first-page":"688060","article-title":"Role of macrophages and related cytokines in kidney disease","volume":"8","year":"2021","journal-title":"Front. Med. (Lausanne"},{"key":"2026032622052681000_2025.08.11.669754v2.69","doi-asserted-by":"publisher","DOI":"10.1002\/dvg.23529"},{"key":"2026032622052681000_2025.08.11.669754v2.70","doi-asserted-by":"publisher","DOI":"10.1002\/path.1415"},{"key":"2026032622052681000_2025.08.11.669754v2.71","doi-asserted-by":"crossref","unstructured":"A. Fava , J. Buyon , L. Magder , J. Hodgin , A. Rosenberg , D. S. Demeke , D. A. Rao , A. Arazi , A. I. Celia , C. Putterman , J. H. Anolik , J. Barnas , M. Dall\u2019Era , D. Wofsy , R. Furie , D. Kamen , K. Kalunian , J. A. James , J. Guthridge , M. G. Atta , J. Monroy Trujillo , D. Fine , R. Clancy , H. M. Belmont , P. Izmirly , W. Apruzzese , D. Goldman , C. C. Berthier , P. Hoover , N. Hacohen , S. Raychaudhuri , A. Davidson , B. Diamond , Accelerating Medicines Partnership in RA\/SLE network, M. Petri , Urine proteomic signatures of histological class, activity, chronicity, and treatment response in lupus nephritis. JCI Insight 9 (2024).","DOI":"10.1172\/jci.insight.172569"},{"key":"2026032622052681000_2025.08.11.669754v2.72","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1177\/0961203320967761","article-title":"Milk fat globule epidermal growth factor 8 (MFG-E8) on monocytes is a novel biomarker of disease activity in systemic lupus erythematosus","volume":"30","year":"2021","journal-title":"Lupus"},{"key":"2026032622052681000_2025.08.11.669754v2.73","doi-asserted-by":"crossref","first-page":"18565","DOI":"10.1038\/s41598-019-55061-6","article-title":"Polymorphisms of MFGE8 are associated with susceptibility and clinical manifestations through gene expression modulation in Koreans with systemic lupus erythematosus","volume":"9","year":"2019","journal-title":"Sci. Rep"},{"key":"2026032622052681000_2025.08.11.669754v2.74","doi-asserted-by":"publisher","DOI":"10.1095\/biolreprod.109.078600"},{"key":"2026032622052681000_2025.08.11.669754v2.75","doi-asserted-by":"publisher","DOI":"10.1016\/j.matbio.2010.04.001"},{"key":"2026032622052681000_2025.08.11.669754v2.76","doi-asserted-by":"publisher","DOI":"10.1038\/oncsis.2013.27"},{"key":"2026032622052681000_2025.08.11.669754v2.77","doi-asserted-by":"publisher","DOI":"10.1080\/19336918.2015.1008332"},{"key":"2026032622052681000_2025.08.11.669754v2.78","doi-asserted-by":"publisher","DOI":"10.1038\/nm.3902"},{"key":"2026032622052681000_2025.08.11.669754v2.79","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1016\/j.ekir.2025.02.009","article-title":"The evolution of crescents in lupus nephritis","volume":"10","year":"2025","journal-title":"Kidney Int. Rep"},{"key":"2026032622052681000_2025.08.11.669754v2.80","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0337679100"},{"key":"2026032622052681000_2025.08.11.669754v2.81","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2249.2005.02897.x"},{"key":"2026032622052681000_2025.08.11.669754v2.82","doi-asserted-by":"publisher","DOI":"10.1002\/art.11225"},{"key":"2026032622052681000_2025.08.11.669754v2.83","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1901340116"},{"key":"2026032622052681000_2025.08.11.669754v2.84","doi-asserted-by":"publisher","DOI":"10.1172\/JCI181034"},{"key":"2026032622052681000_2025.08.11.669754v2.85","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-022-04433-9"},{"key":"2026032622052681000_2025.08.11.669754v2.86","doi-asserted-by":"crossref","unstructured":"J. Hunnicutt , M. E. Georgiou , A. Richards , H. Quasny , L. Magder , D. Goldman , M. A. Petri , Patients achieving low lupus disease activity state, systemic lupus erythematosus disease control or remission showed lower rates of organ damage during longitudinal follow-up: analysis of the Hopkins Lupus Cohort. Lupus Sci. Med. 11 (2024).","DOI":"10.1136\/lupus-2024-001206"},{"key":"2026032622052681000_2025.08.11.669754v2.87","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2024.114253"},{"key":"2026032622052681000_2025.08.11.669754v2.88","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1016\/j.tem.2024.04.009","article-title":"Lipid-associated macrophages between aggravation and alleviation of metabolic diseases","volume":"35","year":"2024","journal-title":"Trends Endocrinol. Metab"},{"key":"2026032622052681000_2025.08.11.669754v2.89","doi-asserted-by":"crossref","first-page":"e70448","DOI":"10.1096\/fj.202403227R","article-title":"SPP1 macrophages across diseases: A call for reclassification?","volume":"39","year":"2025","journal-title":"FASEB J"},{"key":"2026032622052681000_2025.08.11.669754v2.90","doi-asserted-by":"crossref","first-page":"9575","DOI":"10.1038\/s41467-024-53700-9","article-title":"Induction of a distinct macrophage population and protection from lung injury and fibrosis by Notch2 blockade","volume":"15","year":"2024","journal-title":"Nat. Commun"},{"key":"2026032622052681000_2025.08.11.669754v2.91","doi-asserted-by":"crossref","unstructured":"E. M. King , Y. Zhao , C. M. Moore , B. Steinhart , K. C. Anderson , B. Vestal , P. K. Moore , S. A. McManus , C. M. Evans , K. J. Mould , E. F. Redente , A. L. McCubbrey , W. J. Janssen , Gpnmb and Spp1 mark a conserved macrophage injury response masking fibrosis-specific programming in the lung. JCI Insight 9 (2024).","DOI":"10.1172\/jci.insight.182700"},{"key":"2026032622052681000_2025.08.11.669754v2.92","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1038\/s41586-024-07907-x","article-title":"Amplification of autoimmune organ damage by NKp46-activated ILC1s","volume":"634","year":"2024","journal-title":"Nature"},{"key":"2026032622052681000_2025.08.11.669754v2.93","doi-asserted-by":"publisher","DOI":"10.1111\/imm.13952"},{"key":"2026032622052681000_2025.08.11.669754v2.94","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2025.01.002"},{"key":"2026032622052681000_2025.08.11.669754v2.95","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2022.07.004"},{"key":"2026032622052681000_2025.08.11.669754v2.96","doi-asserted-by":"crossref","first-page":"e20241873","DOI":"10.1084\/jem.20241873","article-title":"Accelerating Medicines Partnership in RA\/SLE network, N. Hacohen, A. Davidson, A human-mouse atlas of intrarenal myeloid cells identifies conserved disease-associated macrophages in lupus nephritis","volume":"222","year":"2025","journal-title":"J. Exp. Med"},{"key":"2026032622052681000_2025.08.11.669754v2.97","doi-asserted-by":"publisher","DOI":"10.1002\/art.30613"},{"key":"2026032622052681000_2025.08.11.669754v2.98","unstructured":"RePORT \u27e9 RePORTER. https:\/\/reporter.nih.gov\/search\/n17gcxvd0EiSaYry0_ayxg\/project-details\/10452169."},{"key":"2026032622052681000_2025.08.11.669754v2.99","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.ajpath.2024.09.006","article-title":"Kidney Precision Medicine Project, M. T. Eadon, The Kidney Precision Medicine Project and single-cell biology of the injured proximal tubule","volume":"195","year":"2025","journal-title":"Am. J. Pathol"},{"key":"2026032622052681000_2025.08.11.669754v2.100","doi-asserted-by":"crossref","first-page":"F77","DOI":"10.1152\/ajprenal.00427.2018","article-title":"Renal proximal tubular epithelial cells exert immunomodulatory function by driving inflammatory CD4+ T cell responses","volume":"317","year":"2019","journal-title":"Am. J. Physiol. Renal Physiol"},{"key":"2026032622052681000_2025.08.11.669754v2.101","doi-asserted-by":"crossref","unstructured":"S. Liu , Y. Zhao , S. Lu , T. Zhang , M. T. Lindenmeyer , V. Nair , S. E. Gies , G. Wu , R. G. Nelson , J. Czogalla , H. Aypek , S. Zielinski , Z. Liao , M. Schaper , D. Fermin , C. D. Cohen , D. Delic , C. F. Krebs , F. Grahammer , T. Wiech , M. Kretzler , C. Meyer-Schwesinger , S. Bonn , T. B. Huber , Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy. Genome Med. 15, 2 (2023).","DOI":"10.1186\/s13073-022-01145-4"},{"key":"2026032622052681000_2025.08.11.669754v2.102","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2021.04.048"},{"key":"2026032622052681000_2025.08.11.669754v2.103","doi-asserted-by":"crossref","first-page":"4335","DOI":"10.1093\/rheumatology\/keac067","article-title":"High incidence of proliferative and membranous nephritis in SLE patients with low proteinuria in the Accelerating Medicines Partnership","volume":"61","author":"Accelerating Medicines Partnership (AMP) RA\/SLE Network","year":"2022","journal-title":"Rheumatology (Oxford"},{"key":"2026032622052681000_2025.08.11.669754v2.104","doi-asserted-by":"publisher","DOI":"10.1136\/lupus-2021-000522"},{"key":"2026032622052681000_2025.08.11.669754v2.105","doi-asserted-by":"publisher","DOI":"10.1002\/art.1780400928"},{"key":"2026032622052681000_2025.08.11.669754v2.106","doi-asserted-by":"publisher","DOI":"10.1002\/art.34473"},{"key":"2026032622052681000_2025.08.11.669754v2.107","doi-asserted-by":"publisher","DOI":"10.1111\/j.1523-1755.2004.00443.x"},{"key":"2026032622052681000_2025.08.11.669754v2.108","doi-asserted-by":"crossref","unstructured":"I. Korsunsky , A. Nathan , N. Millard , S. Raychaudhuri , Presto scales Wilcoxon and auROC analyses to millions of observations, Bioinformatics (2019). https:\/\/www.biorxiv.org\/content\/10.1101\/653253v1.abstract.","DOI":"10.1101\/653253"},{"key":"2026032622052681000_2025.08.11.669754v2.109","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-021-00933-1"},{"key":"2026032622052681000_2025.08.11.669754v2.110","doi-asserted-by":"publisher","DOI":"10.1016\/j.clim.2022.109213"},{"key":"2026032622052681000_2025.08.11.669754v2.111","doi-asserted-by":"crossref","unstructured":"A.-C. Villani , R. Satija , G. Reynolds , S. Sarkizova , K. Shekhar , J. Fletcher , M. Griesbeck , A. Butler , S. Zheng , S. Lazo , L. Jardine , D. Dixon , E. Stephenson , E. Nilsson , I. Grundberg , D. McDonald , A. Filby , W. Li , P. L. De Jager , O. Rozenblatt-Rosen , A. A. Lane , M. Haniffa , A. Regev , N. Hacohen , Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356 (2017).","DOI":"10.1126\/science.aah4573"},{"key":"2026032622052681000_2025.08.11.669754v2.112","doi-asserted-by":"crossref","first-page":"1964","DOI":"10.1038\/s41592-025-02793-1","article-title":"Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions","volume":"22","year":"2025","journal-title":"Nat. Methods"},{"key":"2026032622052681000_2025.08.11.669754v2.113","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25960-2"},{"key":"2026032622052681000_2025.08.11.669754v2.114","doi-asserted-by":"crossref","first-page":"3096","DOI":"10.1002\/art.38790","article-title":"Treatment of lupus nephritis with abatacept: the Abatacept and Cyclophosphamide Combination Efficacy and Safety Study","volume":"66","author":"ACCESS Trial Group","year":"2014","journal-title":"Arthritis Rheumatol"},{"key":"2026032622052681000_2025.08.11.669754v2.115","doi-asserted-by":"publisher","DOI":"10.1016\/j.apmr.2016.02.009"},{"key":"2026032622052681000_2025.08.11.669754v2.116","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3437"},{"key":"2026032622052681000_2025.08.11.669754v2.117","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07901-8"},{"key":"2026032622052681000_2025.08.11.669754v2.118","doi-asserted-by":"crossref","first-page":"e84","DOI":"10.1093\/nar\/gkz425","article-title":"CRISPR\/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries","volume":"47","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026032622052681000_2025.08.11.669754v2.119","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10861-2"},{"key":"2026032622052681000_2025.08.11.669754v2.120","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4042"},{"key":"2026032622052681000_2025.08.11.669754v2.121","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-021-00881-3"},{"key":"2026032622052681000_2025.08.11.669754v2.122","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4314"},{"key":"2026032622052681000_2025.08.11.669754v2.123","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: Computational identification of cell Doublets in Single-cell transcriptomic data","volume":"8","year":"2019","journal-title":"Cell Syst"},{"key":"2026032622052681000_2025.08.11.669754v2.124","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06708-y"},{"key":"2026032622052681000_2025.08.11.669754v2.125","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad0501"},{"key":"2026032622052681000_2025.08.11.669754v2.126","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3192"},{"key":"2026032622052681000_2025.08.11.669754v2.127","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21246-9"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.08.11.669754","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T21:25:17Z","timestamp":1775165117000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.08.11.669754"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,14]]},"references-count":127,"URL":"https:\/\/doi.org\/10.1101\/2025.08.11.669754","relation":{},"subject":[],"published":{"date-parts":[[2025,8,14]]},"subtype":"preprint"}}