Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis: Horisberger A, Griffith A, Keegan J, Arazi A, Pulford J, Murzin E, Howard K, Hancock B, Fava A, Sasaki T, Ghosh T, Inamo J, Beuschel R, Cao Y, Preisinger K, Gutierrez-Arcelus M, Eisenhaure TM, Guthridge J, Hoover PJ, Dall’Era M, Wofsy D, Kamen DL, Kalunian KC, Furie R, Belmont M, Izmirly P, Clancy R, Hildeman D, Woodle ES, Apruzzese W, McMahon MA, Grossman J, Barnas JL, Payan-Schober F, Ishimori M, Weisman M, Kretzler M, Berthier CC, Hodgin JB, Demeke DS, Putterman C; Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network; Brenner MB, Anolik JH, Raychaudhuri S, Hacohen N, James JA, Davidson A, Petri MA, Buyon JP, Diamond B, Zhang F, Lederer JA, Rao DA. J Clin Invest. 2025 Jun 19;135(16):e181034. doi: 10.1172/JCI181034. PMID: 40536813; PMCID: PMC12352894.
Analysis of human factor H-related gene and protein expressed in rheumatoid arthritis synovium identifies a novel mechanism promoting dysregulated complement pathway activation: Banda NK, Moreland LW, Deane KD, Simberg D, Scheinman RI, Frank RM, Seifert JA; Accelerating Medicines Partnership (AMP) RA/SLE Network; Lau R, Pitzalis C, Lewis MJ, Holers VM. Sci Rep. 2025 Jun 4;15(1):19633. doi: 10.1038/s41598-025-03589-1. PMID: 40467630; PMCID: PMC12137822.
Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis: Inamo J, Keegan J, Griffith A, Ghosh T, Horisberger A, Howard K, Pulford JF, Murzin E, Hancock B, Dominguez ST, Gurra MG, Gurajala S, Jonsson AH, Seifert JA, Feser ML, Norris JM, Cao Y, Apruzzese W, Bridges SL, Bykerk VP, Goodman S, Donlin LT, Firestein GS, Bathon JM, Hughes LB, Filer A, Pitzalis C, Anolik JH, Moreland L, Hacohen N, Guthridge JM, James JA, Cuda CM, Perlman H, Brenner MB, Raychaudhuri S, Sparks JA; Accelerating Medicines Partnership RA/SLE Network; Holers VM, Deane KD, Lederer J, Rao DA, Zhang F. J Clin Invest. 2025 Mar 17;135(6):e185217. doi: 10.1172/JCI185217. PMID: 40091833; PMCID: PMC11910230.
Extrarenal symptoms associate with worse quality of life in patients enrolled in the AMP RA/SLE Lupus Nephritis Network: Philip M Carlucci, Katherine Preisinger, Kristina K Deonaraine, Devyn Zaminski, Maria Dall’Era, Heather T Gold, Kenneth Kalunian, Andrea Fava, H Michael Belmont, Ming Wu, Chaim Putterman, Jennifer Anolik, Jennifer L Barnas, Richard Furie, Betty Diamond, Anne Davidson, David Wofsy, Diane Kamen, Judith A James, Joel M Guthridge, William Apruzzese, Deepak Rao, Michael H Weisman, Peter M Izmirly, Jill Buyon, Michelle Petri, The Accelerating Medicines Partnership in RA/SLE Network , The Accelerating Medicines Partnership in RA/SLE Network, Extrarenal symptoms associate with worse quality of life in patients enrolled in the AMP RA/SLE Lupus Nephritis Network, Rheumatology, Volume 64, Issue 3, March 2025, Pages 1193–1200, https://doi.org/10.1093/rheumatology/keae189
Granzyme K activates the entire complement cascade: Donado CA, Theisen E, Zhang F, Nathan A, Fairfield ML, Rupani KV, Jones D, Johannes KP; Accelerating Medicines Partnership RA/SLE Network; Raychaudhuri S, Dwyer DF, Jonsson AH, Brenner MB. Nature. 2025 Feb 6. doi: 10.1038/s41586-025-08713-9. Epub ahead of print. PMID: 39914456.
Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis: Faust HJ, Cheng TY, Korsunsky I, Watts GFM, Gal-Oz ST, Trim WV, Kongthong S, Jonsson AH, Simmons DP, Zhang F, Padera R, Chubinskaya S; Accelerating Medicines Partnership: RA/SLE Network; Wei K, Raychaudhuri S, Lynch L, Moody DB, Brenner MB. Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis. Nat Commun. 2024 Nov 14;15(1):9859. doi: 10.1038/s41467-024-52586-x. PMID: 39543086; PMCID: PMC11564742.
Soluble urine activated leukocyte cell adhesion molecule is a strong predictor of lupus nephritis: Chu D, Schwartz N, Ampudia J, Guthridge J, James J, Buyon JP, Connelly S, Fung M, Ng CT; Accelerating Medicines Partnership: RA/SLE Network; Fava A, Petri M, Mohan C, Putterman C. Rheumatology (Oxford). 2024 Oct 15:keae559. doi: 10.1093/rheumatology/keae559. Epub ahead of print. PMID: 39404817.
Association of Autoantibody Concentrations and Trajectories With Lupus Nephritis Histologic Features and Treatment Response: Fava A, Wagner CA, Guthridge CJ, Kheir J, Macwana S, DeJager W, Gross T, Izmirly P, Belmont HM, Diamond B, Davidson A, Utz PJ, Weisman MH, Magder LS; Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network; Guthridge JM, Petri M, Buyon J, James JA. Arthritis Rheumatol. 2024 Nov;76(11):1611-1622. doi: 10.1002/art.42941. Epub 2024 Aug 9. PMID: 38962936; PMCID: PMC11521769.
Automated multi-scale computational pathotyping (AMSCP) of inflamed synovial tissue
Bell RD, Brendel M, Konnaris MA, Xiang J, Otero M, Fontana MA, Bai Z; Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium; Krenitsky DM, Meednu N, Rangel-Moreno J, Scheel-Toellner D, Carr H, Nayar S, McMurray J, DiCarlo E, Anolik JH, Donlin LT, Orange DE, Kenney HM, Schwarz EM, Filer A, Ivashkiv LB, Wang F. Nat Commun. 2024 Aug 29;15(1):7503. doi: 10.1038/s41467-024-51012-6. PMID: 39209814; PMCID: PMC11362542.
Interferon subverts an AHR–JUN axis to promote CXCL13+ T cells in lupus: Law C, Wacleche VS, Cao Y, Pillai A, Sowerby J, Hancock B, Horisberger A, Bracero S, Skidanova V, Li Z, Adejoorin I, Dillon E, Benque IJ, Nunez DP, Simmons DP, Keegan J, Chen L, Baker T, Brohawn PZ, Al-Mossawi H, Hao LY, Jones B, Rao N, Qu Y, Alves SE; Accelerating Medicines Partnership: RA/SLE Network; Jonsson AH, Shaw KS, Vleugels RA, Massarotti E, Costenbader KH, Brenner MB, Lederer JA, Hultquist JF, Choi J, Rao DA. Nature. 2024 Jul;631(8022):857-866. doi: 10.1038/s41586-024-07627-2. Epub 2024 Jul 10.
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis
Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, Zhu Z; Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network; Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S.
Nature Communications. 2024 May 31. doi: 10.1038/s41467-024-48620-7. PMID: 38821936; PMCID: PMC11143375.
Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis: Bai Z, Bartelo N, Aslam M, Murphy EA, Hale CR, Blachere NE, Parveen S, Spolaore E, DiCarlo E, Gravallese EM, Smith MH; Accelerating Medicines Partnership RA/SLE Network; Frank MO, Jiang CS, Zhang H, Pyrgaki C, Lewis MJ, Sikandar S, Pitzalis C, Lesnak JB, Mazhar K, Price TJ, Malfait AM, Miller RE, Zhang F, Goodman S, Darnell RB, Wang F, Orange DE. Sci Transl Med. 2024 Apr 10;16(742):eadk3506. doi: 10.1126/scitranslmed.adk3506. Epub 2024 Apr 10. PMID: 38598614; PMCID: PMC11931728.
Longitudinal patterns and predictors of response to standard-of-care therapy in lupus nephritis: data from the Accelerating Medicines Partnership Lupus Network: Izmirly PM, Kim MY, Carlucci PM, Preisinger K, Cohen BZ, Deonaraine K, Zaminski D, Dall’Era M, Kalunian K, Fava A, Belmont HM, Wu M, Putterman C, Anolik J, Barnas JL, Diamond B, Davidson A, Wofsy D, Kamen D, James JA, Guthridge JM, Apruzzese W, Rao DA, Weisman MH; Accelerating Medicines Partnership in RA/SLE Network; Petri M, Buyon J, Furie R. Arthritis Res Ther. 2024 Feb 20;26(1):54. doi: 10.1186/s13075-024-03275-z. PMID: 38378664; PMCID: PMC10877793.
Urine proteomic signatures of histological class, activity, chronicity, and treatment response in lupus nephritis: Fava A, Buyon J, Magder L, Hodgin J, Rosenberg A, Demeke DS, Rao DA, Arazi A, Celia AI, Putterman C, Anolik JH, Barnas J, Dall’Era M, Wofsy D, Furie R, Kamen D, Kalunian K, James JA, Guthridge J, Atta MG, Monroy Trujillo J, Fine D, Clancy R, Belmont HM, Izmirly P, Apruzzese W, Goldman D, Berthier CC, Hoover P, Hacohen N, Raychaudhuri S, Davidson A, Diamond B; Accelerating Medicines Partnership in RA/SLE network; Petri M. Urine proteomic signatures of histological class, activity, chronicity, and treatment response in lupus nephritis. JCI Insight. 2024 Jan 23;9(2):e172569. doi: 10.1172/jci.insight.172569. PMID: 38258904; PMCID: PMC10906224.
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution
Kang JB, Shen AZ, Sakaue S, Luo Y, Gurajala S, Nathan A, Rumker L, Aguiar VRC, Valencia C, Lagattuta K, Zhang F, Jonsson AH, Yazar S, Alquicira-Hernandez J, Khalili H, Ananthakrishnan AN, Jagadeesh K, Dey K; Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network; Daly MJ, Xavier RJ, Donlin LT, Anolik JH, Powell JE, Rao DA, Brenner MB, Gutierrez-Arcelus M, Raychaudhuri S.
Nature Genetics . 2023 Dec 20:2023. doi: 10.1038/s41588-023-01586-6. Epub 2023 Nov 30. PMID: 38036787; PMCID: PMC10787945.
Deconstruction of rheumatoid arthritis synovium defines inflammatory phenotypes
Zhang F, Jonsson A, Nathan A, Wei K, Millard N, Xiao Q, Gutierrez-Arcelus M, Apruzzese W, Watts G, Weisenfeld D, Kang J, Rumker L, Mears J, Slowikowski K, Weinand K, Orange D, Rangel-Moreno J, Geraldino-Pardilla L, Deane K, Tabechian D, Ceponis A, Firestein G, Maybury M, Sahbudin I, Ben-Artzi A, Mandelin A, Nerviani A, Rivellese F, Pitzalis C, Hughes L, Horowitz D, DiCarlo E, Gravallese E, Boyce B, Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network, Moreland L, Goodman S, Perlman H, Holers V, Liao K, Filer A, Bykerk V, Rao D, Donlin L, Anolik J, Brenner M, Raychaudhuri S, Albrecht J, Barnas J, Bathon J, Boyle D, Bridges Jr. S, Campbell D, Carr H, Chicoine A, Cordle A, Curtis M, Dunn P, Forbess L, Gregersen P, Guthridge J, Ivashkiv L, Ishigaki K, James J, Keras G, Korsunsky I, Lakhanpal A, Lederer J, Li Z, Li Y, McDavid A, Meednu N, Mantel I, McGeachy M, Raza K, Reshef Y, Ritchlin C, Robinson W, Sakaue S, Seifert J, Smith M, Scheel-Toellner D, Utz P, Weisman M, Zhu Z
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Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium
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Dynamic regulatory elements in single-cell multimodal data capture autoimmune disease heritability and implicate key immune cell states
Gupta, A., Weinand, K., Nathan, A. et al. Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability. Nat Genet 55, 2200–2210 (2023). https://doi.org/10.1038/s41588-023-01577-7
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles
Sakaue S, Weinand K, Isaac S, Dey KK, Jagadeesh K, Kanai M, Watts GFM, Zhu Z; Accelerating Medicines Partnership® RA/SLE Program and Network; Brenner MB, McDavid A, Donlin LT, Wei K, Price AL, Raychaudhuri S. Nat Genet. 2024 Apr;56(4):615-626. doi: 10.1038/s41588-024-01682-1. Epub 2024 Apr 9. PMID: 38594305; PMCID: PMC11456345.
Associations Between Rheumatoid Arthritis Clinical Factors and Synovial Cell Types and States: Weisenfeld D, Zhang F, Donlin L, Jonsson AH, Apruzzese W, Campbell D; Accelerating Medicines Partnership Program: RA/SLE Network; Rao DA, Wei K, Holers VM, Gravallese E, Moreland L, Goodman S, Brenner M, Raychaudhuri S, Filer A, Anolik J, Bykerk V, Liao KP. Associations Between Rheumatoid Arthritis Clinical Factors and Synovial Cell Types and States. Arthritis Rheumatol. 2024 Mar;76(3):356-362. doi: 10.1002/art.42726. Epub 2024 Jan 19. PMID: 37791989; PMCID: PMC10922423.
Carlucci PM, Li J, Fava A, Deonaraine KK, Wofsy D, James JA, Putterman C, Diamond B, Davidson A, Fine DM, Monroy-Trujillo J, Atta MG, DeJager W, Guthridge JM, Haag K, Rao DA, Brenner MB, Lederer JA, Apruzzese W, Belmont HM, Izmirly PM, Zaminski D, Wu M, Connery S, Payan-Schober F, Furie R, Dall’Era M, Cho K, Kamen D, Kalunian K, Anolik J, Barnas J, Ishimori M, Weisman MH; Accelerating Medicines Partnership (AMP) RA/SLE Network; Buyon JP, Petri M. Rheumatology (Oxford). 2022 Nov 2;61(11):4335-4343. doi: 10.1093/rheumatology/keac067. PMID: 35212719; PMCID: PMC9629353.
Short- and Long-Term Progression of Kidney Involvement in Systemic Lupus Erythematosus Patients with Low-Grade Proteinuria
Wang S, Spielman A, Ginsberg M, Petri M, Rovin BH, Buyon J, Broder A.
Clin J Am Soc Nephrol. 2022 Aug;17(8):1150-1158. doi: 10.2215/CJN.01280122. Epub 2022 Jul 26.
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Granzyme K+ CD8 T cells form a core population in inflamed human tissue.
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Sci Transl Med. 2022 Jun 15;14(649):eabo0686. doi: 10.1126/scitranslmed.abo0686. Epub 2022 Jun 15.
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Analysis of Complement Gene Expression, Clinical Associations, and Biodistribution of Complement Proteins in the Synovium of Early Rheumatoid Arthritis Patients Reveals Unique Pathophysiologic Features.
Banda NK, Deane KD, Bemis EA, Strickland C, Seifert J, Jordan K, Goldman K, Morgan BP, Moreland LW, Lewis MJ, Pitzalis C, Holers VM.
J Immunol. 2022 Jun 1;208(11):2482-2496. doi: 10.4049/jimmunol.2101170. Epub 2022 May 2.
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Dynamic spectrum of ectopic lymphoid B cell activation and hypermutation in the RA synovium characterized by NR4A nuclear receptor expression
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Cell Rep. 2022 May 3;39(5):110766. doi: 10.1016/j.celrep.2022.110766.
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Urine Proteomics and Renal Single-Cell Transcriptomics Implicate Interleukin-16 in Lupus Nephritis
Fava A, Rao DA, Mohan C, Zhang T, Rosenberg A, Fenaroli P, Belmont HM, Izmirly P, Clancy R, Trujillo JM, Fine D, Arazi A, Berthier CC, Davidson A, James JA, Diamond B, Hacohen N, Wofsy D, Raychaudhuri S, Apruzzese W, Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus Network; Buyon J, Petri M.
Arthritis Rheumatol. 2022 May;74(5):829-839. doi: 10.1002/art.42023. Epub 2022 Apr 16.
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SLAMF7 engagement superactivates macrophages in acute and chronic inflammation.
Simmons DP, Nguyen HN, Gomez-Rivas E, Jeong Y, Jonsson AH, Chen AF, Lange JK, Dyer GS, Blazar P, Earp BE, Coblyn JS, Massarotti EM, Sparks JA, Todd DJ; Accelerating Medicines Partnership (AMP) RA/SLE Network, Rao DA, Kim EY, Brenner MB.
Sci Immunol. 2022 Feb 11;7(68):eabf2846. doi: 10.1126/sciimmunol.abf2846. PMID: 35148199
High incidence of proliferative and membranous nephritis in SLE patients with low proteinuria in the Accelerating Medicines Partnership
Carlucci PM, Li J, Fava A, Deonaraine KK, Wofsy D, James JA, Putterman C, Diamond B, Davidson A, Fine DM, Monroy-Trujillo J, Atta MG, DeJager W, Guthridge JM, Haag K, Rao DA, Brenner MB, Lederer JA, Apruzzese W, Belmont HM, Izmirly PM, Zaminski D, Wu M, Connery S, Payan-Schober F, Furie R, Dall’Era M, Cho K, Kamen D, Kalunian K, Anolik J, Barnas J, Ishimori M, Weisman MH, Accelerating Medicines Partnership (AMP) RA/SLE Network; Buyon JP, Petri M.
Rheumatology (Oxford). 2022 Feb 25;keac067. doi: 10.1093/rheumatology/keac067. PMID: 35212719
Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures
Latt KZ, Heymann J, Jessee JH, Rosenberg AZ, Berthier CC, Arazi A, Eddy S, Yoshida T, Zhao Y, Chen V, Nelson GW, Cam M ,Kumar P, Mehta M, Kelly MC, Kretzler M, Nephrotic Syndrome Study Network (NEPTUNE); Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium; Ray PE, Moxey-Mims M, Gorman GH, Lechner BL, Regunathan-Shenk R, Raj DS, Susztak K, Winkler CA, Kopp JB.
Kidney Int Rep. 2021 Nov 25;7(2):289-304. doi: 10.1016/j.ekir.2021.11.005. eCollection 2022 Feb.
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Rheumatoid Arthritis Synovial Inflammation Quantification Using Computer Vision.
Guan S, Mehta B, Slater D, Thompson JR, DiCarlo E, Pannellini T, Pearce-Fisher D, Zhang F, Raychaudhuri S, Hale C, Jiang CS, Goodman S, Orange DE.
ACR Open Rheumatol. 2022 Apr;4(4):322-331. doi: 10.1002/acr2.11381. Epub 2022 Jan 10.
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The Power of Systems Biology: Insights on Lupus Nephritis from the Accelerating Medicines Partnership
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Rheum Dis Clin North Am. 2021 Aug;47(3):335-350. doi: 10.1016/j.rdc.2021.04.003.
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Safety of procuring research tissue during a clinically indicated kidney biopsy from patients with lupus: data from the Accelerating Medicines Partnership RA/SLE Network
Deonaraine KK, Carlucci PM, Fava A, Li J, Wofsy D, James JA, Putterman C, Diamond B, Davidson A, Fine DM, Monroy-Trujillo J, Atta MG, Haag K, Rao DA, Apruzzese W, Belmont HM, Izmirly PM, Wu M, Connery S, Payan-Schober F , Furie RA, Berthier CC, Dall’Era M, Cho K, Kamen DL, Kalunian K, Anolik J, Ishimori M, Weisman MH, Accelerating Medicines Partnership RA/SLE network; Petri MA, Buyon JP.
Lus Sci Med . 2021 Aug;8(1):e000522. doi: 10.1136/lupus-2021-000522.
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IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation
Fan Zhang, Joseph R. Mears, Lorien Shakib, Jessica I. Beynor, Sara Shanaj, Ilya Korsunsky, Aparna Nathan, Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium, Laura T. Donlin & Soumya Raychaudhuri
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RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares.
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Integrated urine proteomics and renal single-cell genomics identify an IFN-γ response gradient in lupus nephritis.
Fava A, Buyon J, Mohan C, Zhang T, Belmont HM, Izmirly P, Clancy R, Trujillo JM, Fine D, Zhang Y, Magder L, Rao DA, Arazi A, Berthier CC, Davidson A, Diamond B, Hacohen N, Wofsy D, Apruzzese W; Accelerating Medicines Partnership in SLE network, Raychaudhuri S, Petri M.
JCI Insight. 2020 Jun 18;5(12):138345. doi: 10.1172/jci.insight.138345.
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Notch signalling drives synovial fibroblast identity and arthritis pathology
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Nature. 2020 Jun;582(7811):259-264. doi: 10.1038/s41586-020-2222-z. Epub 2020 Apr 22.
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The basic and translational science year in review: Confucius in the era of Big Data
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Semin Arthritis Rheum. 2020 Jun;50(3):373-379. doi: 10.1016/j.semarthrit.2020.02.010. Epub 2020 Mar 5.
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Accelerating Medicines Partnership: Organizational Structure and Preliminary Data From the Phase 1 Studies of Lupus Nephritis.
Hoover P, Der E, Berthier CC, Arazi A, Lederer JA, James JA, Buyon J, Petri M, Belmont HM, Izmirly P, Wofsy D, Hacohen N, Diamond B, Putterman C, Davidson A.
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PD-1hiCXCR5- T peripheral helper cells promote B cell responses in lupus via MAF and IL-21.
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The immune cell landscape in kidneys of patients with lupus nephritis.
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Nat Immunol. 2019 Jul;20(7):902-914. doi: 10.1038/s41590-019-0398-x. Epub 2019 Jun 17.
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Distinct fibroblast subsets drive inflammation and damage in arthritis.
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Nature. 2019 Jun;570(7760):246-251. doi: 10.1038/s41586-019-1263-7. Epub 2019 May 29.
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Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways.
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Nat Immunol. 2019 Jul;20(7):915-927. doi: 10.1038/s41590-019-0386-1. Epub 2019 May 20.
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