Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus

Creators: Perez, Richard K.; Gordon, M. Grace; Subramaniam, Meena; Kim, Min Cheol; Hartoularos, George C.; Targ, Sasha; Sun, Yang; Ogorodnikov, Anton; Bueno, Raymund; Lu, Andrew; Thompson, Mike; Rappoport, Nadav; Dahl, Andrew; Lanata, Cristina M.; Matloubian, Mehrdad; Maliskova, Lenka; Kwek, Serena S.; Li, Tony; Slyper, Michal; Waldman, Julia; Dionne, Danielle; Rozenblatt-Rosen, Orit; Fong, Lawrence; Dall'Era, Maria; Balliu, Brunilda; Regev, Aviv; Yazdany, Jinoos; Criswell, Lindsey A.; Zaitlen, Noah; Ye, Chun Jimmie

Abstract

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). Cases exhibited elevated expression of type 1 interferon–stimulated genes (ISGs) in monocytes, reduction of naïve CD4 + T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH + CD8 + T cells. Cell type–specific expression features predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data to map cell type–specific cis–expression quantitative trait loci and to link SLE-associated variants to cell type–specific expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE.

Additional Information

© 2022 American Association for the Advancement of Science. Received 16 October 2020; accepted 8 November 2021. We thank all members of the Ye lab for discussions. Funding: Supported by NIH grant P30AR070155 (C.J.Y., L.A.C., and J.Y.); NIH grants R01AR071522, U01HG012192, R21AI133337, and CZI P0535277 (C.J.Y.); CDC grant U01DP005120 (L.A.C. and J.Y.); the Lupus Research Alliance (L.A.C.); NIH grants K25HL121295, U01HG009080, R01HG006399, R01CA227237, and R03DE025665 and DoD grant W81XWH-16-2-0018 (N.Z.); NIH grants R01CA194511 and R01CA223484 (L.F.); the Manton Foundation, Klarman Cell Observatory, and Howard Hughes Medical Institute (A.R.); NIH grant 1F31HG011007 (M.G.G.); NSF grant GRFP 1650113 (G.C.H.); and NIH grant T32HG002536 (M.T.). Author contributions: M.Su., G.C.H., S.T., Y.S., and L.M. performed all experiments. R.K.P., M.G.G., M.Su., and C.J.Y. wrote the manuscript. R.K.P., M.G.G., and C.J.Y. revised the manuscript. R.K.P. and C.J.Y. performed all preprocessing, cell type annotations, single-cell analysis, pseudobulk, DE analysis, and clinical predictions. M.C.K. performed the trajectory analysis and RNA velocity. N.R. performed the UCSF EHR database queries. M.G.G. performed the Mendelian randomization analysis and eQTL analysis. S.S.K. and T.L. performed the TCR sequencing experiments. R.K.P. performed the TCR analysis. M.M., M.C., L.T., C.L., M.D., J.Y., and L.A.C. provided access to CLUES samples and all patient information. M.G.G., B.B., A.L., M.T., and N.Z. developed and implemented the decomposition and modified TWAS methods. A.D. aided heritability and subtype analyses. M.Sl., J.W., D.D., and O.R. performed the Immvar sequencing experiments. M.G.G., A.O., and R.B. organized and disseminated data into appropriate repositories. M.D., L.F., A.R., J.Y., L.A.C., and N.Z. provided critical edits and feedback to the manuscript. Competing interests: A.R. is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas, and was an SAB member of ThermoFisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics, and Asimov until 31 July 2020. From 1 August 2020, A.R. is an employee of Genentech. O.R.R. is a co-inventor on patent applications filed at the Broad related to single-cell genomics. O.R.R. has given numerous lectures about single-cell genomics to a wide variety of audiences and, in some cases, has received remuneration to cover time and costs. C.J.Y. is a SAB member for and holds equity in Related Sciences and ImmunAI, is a consultant for and holds equity in Maze Therapeutics, and is a consultant for Trex Bio. C.J.Y. has received research support from Chan Zuckerberg Initiative, Chan Zuckerberg Biohub, and Genentech. Data and materials availability: All data are available in the Human Cell Atlas Data Coordination Platform and at GEO accession number GSE137029. Genotypes are available at dbGap accession number phs002812.v1.p1. Code is available at 10.5281/zenodo.4724043 (62).

Attached Files

Supplemental Material - science.abf1970_sm.pdf

Supplemental Material - science.abf1970_tables_s1_to_s12.zip

Files

science.abf1970_sm.pdf

Files (27.2 MB)

Name	Size	Download all
science.abf1970_sm.pdf md5:c78e49e69cb6bd7b48a4b2dfe3c77229	9.6 MB	Preview Download
science.abf1970_tables_s1_to_s12.zip md5:50a8344ad234adf4ba19a769c9906532	17.6 MB	Preview Download

Additional details

	All versions	This version
Views	0	0
Downloads	0	0
Data volume	0 Bytes	0 Bytes