AMP RA/SLE Publications

Updated 04/14/22

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CELLULAR DECONSTRUCTION OF INFLAMMED SYNOVIUM DEFINES DIVERSE INFLAMMATORY PHENOTYPES IN REHUMATOID ARTHRTIS
Fan Zhang, Anna Helena Jonsson, Aparna Nathan, Kevin Wei, …Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network, …et al.
https://www.biorxiv.org/content/10.1101/2022.02.25.481990v1

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. 2021 Nov 16. doi: 10.1002/art.42023

DYNAMIC SPECTRUM OF ECTOPIC LYMPHOID B CELL ACTIVATION IN THE RA SYNOVIUM CHARACTERIZED BY NR4A NUCLEAR RECEPTOR EXPRESSION
Nida Meednu, Javier Rangel-Moreno, Fan Zhang, Katherine Escalera-Rivera, Elisa Corsiero, Edoardo Prediletto, Edward DiCarlo, Susan Goodman, Laura T Donlin, Soumya Raychaudhuri, Michele Bombardieri, Costantino Pitzalis, Dana E Orange, Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network, Andrew McDavid, Jennifer H Anolik
Cell Reports. http://dx.doi.org/10.2139/ssrn.3928095

PRECISION MEDICINE IN RHEUMATOID ARTHRITIS
Bhamidipati K and Wei K
Best Pract Res Clin Rheumatol. 2022 Mar;36(1):101742

SLAMF7 ENGAGEMENT SUPERACTIVATES MACROPHAGES IN ACUTE AND CHRONIC INFLAMMATION
Simmons D, Nguyen H, Gomez-Rivas E, Jeong Y, Jonsson AH, Chen A, Lange J, Dyer G, Blazar P, Earp B, Coblyn J, 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

THE CD6/ALCAM PATHWAY PROMOTES LUPUS NEPHRITIS VIA T CELL-MEDIATED RESPONSES
Chalmers SA, Ramachandra RA, Garcia SJ, Der E, Herlitz L, Ampudia J, Chu D, Jordan N, Zhang T, Parodis I, Gunnarsson I, Ding H, Shen N, Petri M, Mok CC, Saxena R, Polu K, Connelly S, Ng C, Mohan C, Putterman C.
J Clin Invest; 2022 Jan 4;132(1): e147334; doi: 10.1172/JCI147334

Urine Proteomics and Renal Single Cell Transcriptomics Implicate IL-16 in Lupus Nephritis
Fava A, Rao DA, Mohan C, Zhang T, Rosenberg A, Fenaroli P, Belmont HM, Izmirly P, Clancy R, Monroy-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 RA/SLE network, Buyon, J, Petri M
Arthritis Rheumatol. 2021 Nov 16. doi: 10.1002/art.42023

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, The Accelerating Medicines Partnership RA/SLE network, Petri MA, Buyon JP.
Lupus Sci Med: first published as 10.1136/lupus-2021-000522 on 13 August 2021

The Power of Systems Biology: Insights on Lupus Nephritis from the Accelerating Medicines Partnership
A Fava, S Raychaudhuri, DA Rao
Rheum Dis Clin North Am. 2021 Aug;47(3):335-350. doi: 10.1016/j.rdc.2021.04.003

IFN-g and TNF-a drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 and other 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
Genome Med. 2021 Apr 20;13(1):64. doi: 10.1186/s13073-021-00881-3

Maximizing statistical power to detect clinically associated cell states with scPOST
Nghia Millard, Ilya Korsunsky, Kathryn Weinand, Chamith Y. Fonseka, Aparna Nathan, Joyce B. Kang, Soumya Raychaudhuri
Cell Rep Methods. 2021 Nov 16;1(8):100120. doi: 10.1016/j.crmeth.2021.100120

DESIGN AND APPLICATION OF SINGLE-CELL RNA SEQUENCING TO STUDY KIDNEY IMMUNE CELLS IN LUPUS NEPHRITIS
Deepak A. Rao, Arnon Arazi, David Wofsy, and Betty Diamond
Nat Rev Nephrol. 2020 Apr;16(4):238-250. doi: 10.1038/s41581-019-0232-6

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):e138345. doi: 10.1172/jci.insight.138345

Notch signaling drives synovial fibroblast identity and arthritis pathology
Wei K, Korsunsky I, Marshall JL, Gao A, Watts GFM, Major T, Croft AP, Watts J, Blazar PE, Lange JK, Thornhill TS, Filer A, Raza K, Donlin LT; Accelerating Medicines Partnership Rheumatoid Arthritis & Systemic Lupus Erythematosus (AMP RA/SLE) Consortium, Siebel CW, Buckley CD, Raychaudhuri S, Brenner MB
Nature. 2020 Jun;582(7811):259-264. doi: 10.1038/s41586-020-2222-z

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares
Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB
N Engl J Med. 2020 Jul 16;383(3):218-228. doi: 10.1056/NEJMoa2004114

PRIME Time in Rheumatoid Arthritis
Ellen M Gravallese, William H Robinson
N Engl J Med. 2020 Jul 16;383(3):278-279. doi: 10.1056/NEJMe2018218

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares
Dana E. Orange, Vicky Yao, Kirsty Sawicka, John Fak, Mayu O. Frank, Salina Parveen, Nathalie E. Blachere, Caryn Hale, Fan Zhang, Soumya Raychaudhuri, Olga G. Troyanskaya, and Robert B. Darnell
N Engl J Med 2020; 383:218-228, DOI: 10.1056/NEJMoa2004114

SAFETY OF RESEARCH CORES OBTAINED FROM CLINICALLY INDICATED BIOPSIES IN THE ACCELERATING MEDICINES PARTNERSHIP NETWORK
Jill Buyon, Michael Belmont, Peter Izmirly, Nicole Bornkamp, Catherine Trad, Rohit Bhan, Kimberly Robins, Robert Clancy, Chaim Putterman, Ming Wu, AMP Network
Lupus Sci Med. 2021 Aug;8(1): e000522. doi: 10.1136/lupus-2021-000522

The Accelerating Medicines Partnership – Organizational Structure and Preliminary Data from the Phase 1 Studies of Lupus Nephritis
Paul Hoover, Evan Der, Celine C. Berthier, Arnon Arazi, James A. Lederer, Judith A. James, Jill Buyon, Michelle Petri, H. Michael Belmont, Peter Izmirly, David Wofsy, Nir Hacohen, Betty Diamond, Chaim Putterman, Ann Davidson
Arthritis Care Res (Hoboken). 2020 Feb;72(2):233-242. doi: 10.1002/acr.24066. Epub 2020 Jan 13

PD-1hiCXCR5– T peripheral helper cells promote B cell responses in lupus via MAF and IL-21
Alexandra V. Bocharnikov, Joshua Keegan, Vanessa S. Wacleche, Ye Cao, Chamith Y. Fonseka, Guoxing Wang, Eric S. Muise, Kelvin X. Zhang, Arnon Arazi, Gregory Keras, Zhihan J. Li, Yujie Qu, Michael F. Gurish, Accelerating Medicines Partnership (AMP) RA/SLE Network, Michelle Petri, Jill P. Buyon, Chaim Putterman, David Wofsy, Judith A. James, Joel M. Guthridge, Betty Diamond, Jennifer H. Anolik, Matthew F. Mackey, Stephen E. Alves, Peter A. Nigrovic, Karen H. Costenbader, Michael B. Brenner, James A. Lederer, and Deepak A. Rao
JCI Insight. 2019 Oct 17;4(20): e130062. doi: 10.1172/jci.insight.130062

THE IMMUNE CELL LANDSCAPE IN KIDNEYS OF LUPUS NEPHRITIS PATIENTS
Arnon Arazi, Deepak A. Rao, Celine C. Berthier, Anne Davidson, Yanyan Liu, Paul J. Hoover, Adam Chicoine, Thomas M. Eisenhaure, A. Helena Jonsson, Shuqiang Li, David J. Lieb, Edward P. Browne, Akiko Noma, Danielle Sutherby, Scott Steelman, Dawn E. Smilek, Patti Tosta, William Apruzzese, Elena Massarotti, Maria Dall’Era, Meyeon Park, Diane L. Kamen, Richard A. Furie, Fernanda Payan-Schober, Jill P. Buyon, Michelle A. Petri, Chaim Putterman, Kenneth C. Kalunian, E. Steve Woodle, James A. Lederer, David A. Hildeman, Chad Nusbaum, Matthias Kretzler, Jennifer H. Anolik, Michael B. Brenner, David Wofsy, Nir Hacohen, Betty Diamond, Accelerating Medicines Partnership
Nat Immunol. 2019 Jul;20(7):902-914. doi: 10.1038/s41590-019-0398-x

Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways
Evan Der, Hemant Suryawanshi, Pavel Morozov, Manjunath Kustagi, Beatrice Goilav, Saritha Ranabathou, Peter Izmirly, Robert Clancy, H. Michael Belmont, Mordecai Koenigsberg, Michelle Mokrzycki, Helen Rominieki, Jay Graham, Juan Rocca, Nicole Bornkamp, Nicole Jordan, Emma Schulte, Ming Wu, James Pullman, Kamil Slowikowski, Soumya Raychaudhuri, Joel Guthridge, Judith James, Accelerating Medicine Partnership (AMP), Jill Buyon, Thomas Tuschl, Chaim Putterman
Nat Immunol. 2019 Jul;20(7):915-927. doi: 10.1038/s41590-019-0386-1. Epub 2019 May 20

Elucidating the molecular circuitry of autoimmunity
Navin Varadarajan & Chandra Mohan
Nat Immunol. 2019 Jul;20(7):777-778. doi: 10.1038/s41590-019-0436-8

Single-cell RNA sequencing for the study of lupus nephritis
Der E, Suryawanshi H, Buyon J, Tuschl T, Putterman C
Lupus Sci Med. 2019 Jun 4;6(1): e000329. doi: 10.1136/lupus-2019-000329

Histologic and transcriptional evidence of subclinical synovial inflammation in rheumatoid arthritis patients in clinical remission
Dana E. Orange, Phaedra Agius, Edward F. DiCarlo, Serene Mirza, Tania Pannellini, Jackie Szymonifka, Caroline S. Jiang, Mark P. Figgie, Mayu O. Frank, William H. Robinson, Laura T. Donlin, Cristina Rozo, Ellen M. Gravallese, Vivian P. Bykerk, and Susan M. Goodman
Arthritis Rheumatol. 2019 Jul; 71(7): 1034–1041

Distinct fibroblast subsets drive inflammation and damage in arthritis
Adam P. Croft, Joana Campos, Kathrin Jansen, Jason D. Turner, Jennifer Marshall, Moustafa Attar, Loriane Savary, Corinna Wehmeyer, Amy J. Naylor, Samuel Kemble, Jenefa Begum, Kerstin Dürholz, Harris Perlman, Francesca Barone, Helen M. McGettrick, Douglas T. Fearon, Kevin Wei, Soumya Raychaudhuri, Ilya Korsunsky, Michael B. Brenner, Mark Coles, Stephen N. Sansom, Andrew Filer, Christopher D. Buckley
Nature. 2019 Jun;570(7760):246-251. doi: 10.1038/s41586-019-1263-7

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry
Fan Zhang, Kevin Wei, Kamil Slowikowski, Chamith Y. Fonseka, Deepak A. Rao, Stephen Kelly, Susan M. Goodman, Darren Tabechian, Laura B. Hughes, Karen Salomon-Escoto, Gerald F. M. Watts, William Apruzzese, David J. Lieb, David L. Boyle, Arthur M. Mandelin II, Accelerating Medicines Partnership: RA Phase 1, AMP RA/SLE, Brendan F. Boyce, Edward DiCarlo, Ellen M. Gravallese, Peter K. Gregersen, Larry Moreland, Gary S. Firestein, Nir Hacohen, Chad Nusbaum, James A. Lederer, Harris Perlman, Costantino Pitzalis, Andrew Filer, V. Michael Holers, Vivian P. Bykerk, Laura T. Donlin, Jennifer H. Anolik, Michael B. Brenner, Soumya Raychaudhuri
Nat Immunol. 2019 Jul;20(7):928-942. doi: 10.1038/s41590-019-0378-1. Epub 2019 May 6

Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis
Evan Der, Saritha Ranabothu, Hemant Suryawanshi, Kemal M. Akat, Robert Clancy, Pavel Morozov, Manjunath Kustagi, Mareike Czuppa, Peter Izmirly, H. Michael Belmont, Tao Wang, Nicole Jordan, Nicole Bornkamp,4 Janet Nwaukoni, July Martinez, Beatrice Goilav, Jill P. Buyon, Thomas Tuschl, and Chaim Putterman
JCI Insight. 2017 May 4;2(9):e93009. doi: 10.1172/jci.insight.93009

Massive NIH–industry project opens portals to target validation
Elie Dolgen
Nat Rev Drug Discov. 2019 Feb 27. doi: 10.1038/d41573-019-00033-8

HBEGF+ macrophages identified in rheumatoid arthritis promote joint tissue invasiveness and are reshaped differentially by medications
Kuo D, Ding J, Cohn I, Zhang F, Wei K, Rao D, Rozo C, Sokhi U, Accelerating Medicines Partnership RA/SLE Network, DiCarlo E, Brenner MB, Bykerk VP, Goodman S, Raychaudhuri S, Rätsch G, Ivashkiv LB, Donlin LT
Sci Transl Med. 2019 May 8;11(491): eaau8587. doi: 10.1126/scitranslmed.aau8587

METHODS FOR HIGH-DIMENSONAL ANALYSIS OF CELLS DISSOCIATED FROM CYROPRESERVED SYNOVIAL TISSUE
Donlin LT, Rao DA, Wei K, Slowikowski K, McGeachy MJ, Turner JD, Meednu N, Mizoguchi F, Gutierrez-Arcelus M,, Lieb DJ, Keegan J, Muskat K, Hillman J, Rozo C, Ricker E,, Eisenhaure TM, Li S, Browne EP, Chicoine A, Sutherby D, Noma A; Accelerating Medicines Partnership RA/SLE Network, Nusbaum C, Kelly S, Pernis AB,, Ivashkiv LB, Goodman SM,, Robinson WH, Utz PJ, Lederer JA, Gravallese EM, Boyce BF, Hacohen N,, Pitzalis C, Gregersen PK, Firestein GS, Raychaudhuri S, Moreland LW, Holers VM, Bykerk VP, Filer A, Boyle DL, Brenner MB, Anolik JH
Arthritis Res Ther. 2018 Jul 11;20(1):139. doi: 10.1186/s13075-018-1631-y

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data
Orange DE, Agius P, DiCarlo EF, Robine N, Geiger H, Szymonifka J, McNamara M, Cummings R, Andersen KM, Mirza S, Figgie M, Ivashkiv L, Pernis AB, Jiang C, Frank M, Darnell R, Lingampali N, William R, Gravallese E, Bykerk VP, Goodman SM, Donlin LT; Accelerating Medicine Partnership: RA/SLE Network
Arthritis Rheumatol. 2018 May;70(5):690-701. doi: 10.1002/art.40428. Epub 2018 Apr 2