1693: Blood Immunophenotyping Distinguishes Three Subgroups of Lupus Nephritis Patients with Distinct Kidney Infiltrates and Interferon Signatures

Alice Horisberger¹, Alec Griffith¹, Arnon Arazi², Joshua Keegan¹, Kaitlyn Howard¹, Takanori Sasaki¹, Tusharkanti Ghosh³, Andrea Fava⁴, Jun Inamo⁵, John Pulford¹, Ekaterina Murzin¹, Brandon Hancock¹, Katie Preisinger⁶, Maria Gutierrez-Arcelus⁷, Thomas Eisenhaure⁸, Joel Guthridge⁹, Paul Hoover¹⁰, Maria Dall'Era¹¹, David Wofsy¹¹, Diane L. Kamen¹², Kenneth Kalunian¹³, Richard Furie¹⁴, H Michael Belmont¹⁵, Peter Izmirly⁶, Robert Clancy¹⁶, David Hildeman¹⁷, steve Woodle¹⁷, William Apruzzese¹⁸, Maureen McMahon¹⁹, Jennifer Grossman²⁰, Jennifer Barnas²¹, Fernanda Payan-Schober²², Mariko Ishimori²³, Accelerating Medicines Partnership Program RA SLE Network²³, Matthias Kretzler²⁴, Celine Berthier²⁴, Jeff Hodgin²⁴, Dawit Demeke²⁴, Chaim Putterman²⁵, Nir Hacohen⁸, Michael Brenner¹, Jennifer Anolik²¹, Anne Davidson²⁶, Judith James⁹, Soumya Raychaudhuri¹⁰, Michelle Petri²⁷, Jill Buyon¹⁶, Betty Diamond²⁶, The Accelerating Medicines Partnership In RA/SLE²⁸, Fan Zhang²⁹, James Lederer¹ and Deepak Rao¹⁰, ¹Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ²Broad Institute of MIT and Harvard, Melrose, MA, ³School of Public Health, University of Colorado, Anschutz Medical Campus, Aurora, CO, ⁴Johns Hopkins University, Baltimore, MD, ⁵University of Colorado School of Medicine, Aurora, CO, ⁶New York University School of Medicine, New York, NY, ⁷Boston Children's Hospital, Boston, MA, ⁸Broad Institute of MIT and Harvard, Cambridge, MA, ⁹Oklahoma Medical Research Foundation, Oklahoma City, OK, ¹⁰Brigham and Women's Hospital, Boston, MA, ¹¹University of California San Francisco, San Francisco, CA, ¹²Medical University of South Carolina, Charleston, SC, ¹³University of California San Diego, La Jolla, CA, ¹⁴Northwell Health, Manhasset, NY, ¹⁵NYU School of Medicine, New York, NY, ¹⁶NYU Grossman School of Medicine, New York, NY, ¹⁷University of Cincinnati College of Medicine, Cincinnati, OH, ¹⁸Accelerating Medicines Partnership® Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP® RA/SLE) Network, Boston, MA, ¹⁹UCLA David Geffen School of Medicine, Los Angeles, CA, ²⁰University of California Los Angeles, Los Angeles, CA, ²¹University of Rochester Medical Center, Rochester, NY, ²²Texas Tech University Health Sciences Center, El Paso, TX, ²³Cedars-Sinai Medical Center, Los Angeles, CA, ²⁴University of Michigan, Ann Arbor, MI, ²⁵Albert Einstein College of Medicine, Bronx, NY, ²⁶Feinstein Institutes for Medical Research, Manhasset, NY, ²⁷Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Timonium, MD, ²⁸multisites, multisites, ²⁹University of Colorado, Aurora, CO

Background/Purpose: Patients with lupus nephritis (LN) have variable responses to standard-of-care therapy, and a third of patients with class III, IV, or V show a progressive decline in kidney function. Identifying distinct inflammatory processes associated with LN using non-invasive tools may improve treatment targeting. Here, we aimed to identify subgroups of LN patients that differ in systemic immune activity and to evaluate their relationship to kidney pathology.

Methods: Mass cytometry using four 48-marker panels was applied to characterize peripheral blood mononuclear cells from 140 patients with active, biopsy-proven proliferative (class III or IV +/- V, n=98) or membranous (class V, n=42) nephritis and 40 healthy controls in the Accelerated Medicine Partnership RA/SLE Network Phase II study. K-means clustering was used to stratify patients based on the proportions of 55 immune cell subsets defined using B cell-, T cell-, myeloid cell-, and NK cell-focused panels.

Results: Unsupervised analysis of all samples identified 3 patient subgroups based on blood immunophenotypes (Figure 1A). The first group (G0) included all controls and 20% LN patients; the two others (G1, G2) included only LN patients. A cytometric IFN-I score, based on MX1, siglec1 and ISG15 expression, was significantly different between the three groups; G0-LN patients had comparable scores to controls and G1 displayed the highest values (Figure 1B). G2 membership was driven by an increased proportion of GZMB⁺ GZMK^+/- CD8 T cells, plus increased CD86^dim monocytes and activated B cells including CD11c^hi cells (Figure 1C). G2 was associated with higher histologic activity scores, whereas G0 had higher chronicity scores, even after controlling for race, corticoid dose, immunosuppressant use, and previous history of renal biopsy (Figure 2). Complete renal response (CR), determined at 1 year in patients with baseline urine protein-creatinine ratio > 1, was more frequent in G2 than in G0/G1 LN patients, independently of history of previous renal biopsy (CR in G2 = 15 [41%] vs others = 9 [18%]; OR [95%CI] = 3.9 [1.3,12.5]; p.adj = 0.02). Finally, we asked whether the composition of immune cell infiltrates in the kidney, evaluated by scRNA-seq of kidney biopsies, differed between the 3 blood-defined subgroups. G2 patients had kidney T cell infiltrates enriched in GZMB⁺/GZMK⁺ CD8 T cell subsets and in myeloid cells with an activated and phagocytic profile compared to G0/G1 patients. In contrast, G1 patients showed the highest expression of IFN-I gene signature across the groups, consistent with the pattern seen in blood (Figure 3).

Conclusion: Blood immunophenotyping identified 3 groups of LN patients with different patterns of immune cell infiltration and likelihood of response to treatment. Cytometric profiles distinguished patients with a signature involving activated CD8 T cells, CD11c^hi B cells and activated myeloid cells (G2) from those with the highest IFN scores (G1). Patients with increased blood and kidney CD8 GZMB⁺GZMK^+/- cells (G2) had increased renal activity scores at baseline and a higher likelihood of response at 1 year.








A. Horisberger: None; A. Griffith: None; A. Arazi: None; J. Keegan: None; K. Howard: None; T. Sasaki: None; T. Ghosh: None; A. Fava: Annexon Biosciences, 2, Sanofi, 1; J. Inamo: None; J. Pulford: None; E. Murzin: None; B. Hancock: None; K. Preisinger: None; M. Gutierrez-Arcelus: None; T. Eisenhaure: None; J. Guthridge: None; P. Hoover: None; M. Dall'Era: Annexon Biosciences, 2, 5, AstraZeneca, 2, Aurinia, 2, Biogen, 2, GlaxoSmithKlein, 2, 5, Pfizer, 2; D. Wofsy: Amgen, 7, Novartis, 7; D. Kamen: None; K. Kalunian: AbbVie/Abbott, 2, Amgen, 5, AstraZeneca, 2, Aurinia, 2, Bristol-Myers Squibb(BMS), 2, Eli Lilly, 2, EquilliumBio, 2, Genentech, 2, Gilead, 2, Janssen, 2, KezarBio, 1, Merck/MSD, 2, Novartis, 2, Pfizer, 2, Remegene, 2, Roche, 2, UCB, 5; R. Furie: Biogen, 2, 5; H. Belmont: Alexion, 6, Aurinia, 6; P. Izmirly: None; R. Clancy: None; D. Hildeman: None; s. Woodle: None; W. Apruzzese: Pfizer, 3; M. McMahon: None; J. Grossman: None; J. Barnas: None; F. Payan-Schober: None; M. Ishimori: None; A. RA SLE Network: None; M. Kretzler: amfAR, 5, Angion, 5, Astellas, 2, AstraZeneca, 5, Boehringer-Ingelheim, 5, Certa, 5, Chinook, 5, Eli Lilly, 5, Gilead, 5, Goldfinch Bio, 5, IONIS, 5, Janssen, 2, 5, Maze Therapeutics, 5, Moderna, 5, NovoNordisk, 5, Poxel, 2, Regeneron, 5, RenalytixAI, 5, Travere, 5, UCB, 2; C. Berthier: None; J. Hodgin: AstraZeneca, 5, 6, Eli Lilly, 5, Gilead, 5, Janssen, 5, Moderna, 5, Novo Nordisk, 5, Regeneron, 5; D. Demeke: None; C. Putterman: Equillium, 2, KidneyCure, 1, Progentec, 2; N. Hacohen: None; M. Brenner: 4FO Ventures, 2, GlaxoSmithKlein(GSK), 2, Mestag Therapeutics, 2, 11, Third Rock Ventures, 2; J. Anolik: None; A. Davidson: None; J. James: Bristol-Myers Squibb(BMS), 5, GlaxoSmithKlein(GSK), 2, Novartis, 2, Progentec Biosciences, 5; S. Raychaudhuri: AbbVie, 6, Janssen, 1, Mestag, Inc, 2, 8, Pfizer, 1, Sanofi, 1, Sonoma, 1, 8; M. Petri: Alexion, 1, Amgen, 1, AnaptysBio, 1, Annexon Bio, 1, Argenx, 1, Arhros-Focus Med/Ed, 6, AstraZeneca, 1, 5, Aurinia, 1, 5, 6, Axdev, 1, Biogen, 1, Boxer Capital, 2, Cabaletto Bio, 2, Caribou Biosciences, 2, CVS Health, 1, Eli Lilly, 1, 5, Emergent Biosolutions, 1, Exagen, 5, Exo Therapeutics, 2, Gilead Biosciences, 2, GlaxoSmithKlein(GSK), 1, 5, 6, Horizon Therapeutics, 2, Idorsia Pharmaceuticals, 2, IQVIA, 1, Janssen, 1, 5, Kira Pharmaceuticals, 2, MedShr, 6, Merck/EMD Serono, 1, Momenta Pharmaceuticals, 2, Nexstone Immunology, 2, Nimbus Lakshmi, 2, Proviant, 2, Sanofi, 2, Sinomab Biosciences, 2, Thermofisher, 5, UCB, 2; J. Buyon: Bristol-Myers Squibb(BMS), 2, GlaxoSmithKlein(GSK), 2, Related Sciences, 1; B. Diamond: Alpine, 12, DSMB, DBV, 2, 2, IMT, 2, Kyverna, 2, Nighthawk, 2, ONO, 2; T. In RA/SLE: None; F. Zhang: None; J. Lederer: None; D. Rao: AstraZeneca, 2, Bristol-Myers Squibb, 2, 5, GlaxoSmithKlein(GSK), 2, Hifibio, 2, Janssen, 5, Merck, 5, Scipher Medicine, 2.