ArticleScience (New York, N.Y.)2022
Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus.
Erratum issuedOpen access · greenAbstract read
In one paragraph
Article in Science (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 312 papers, 5 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
312citing papers in PubMed, 5 pooled it
84.9field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
312 citing papers in PubMed, 5 syntheses or guidelines pooled it, 508 citations in OpenAlex.
- Comparative transcriptomic meta-analysis reveals elevated TCL1A expression in human circulating immune cells across chronic pain conditions.British journal of anaesthesia · 2026Pooled it
- Application of multi-omics in systemic autoimmune rheumatic diseases: a bibliometric and visualization analysis.Frontiers in immunology · 2026Pooled it
- Insights into the pathogenesis of rheumatic and immune diseases from single-cell omics.Frontiers in immunology · 2026Pooled it
- Optimized summary-statistic-based single-cell eQTL meta-analysis.Scientific reports · 2025Pooled it
- Organ-based characterization of B cells in patients with systemic lupus erythematosus.Frontiers in immunology · 2025Pooled it
- Interferon regulatory factors orchestrate CD8International journal of molecular medicine · 2026Review
- Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis.Clinical reviews in allergy & immunology · 2026Review
- Phosphoproteomic dysregulation promotes tumor proliferation in Cushing's disease.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Protein biomarkers of inflammation in women with SLE and their newborn children.Lupus science & medicine · 2026Article
- A statistical framework for disease classification with scRNA-Seq Data.bioRxiv : the preprint server for biology · 2026Article
- Scalable context-dependent single-cell eQTL mapping reveals disease-relevant regulatory variation beyond static models.medRxiv : the preprint server for health sciences · 2026Article
- From Genome-Wide Association Study Signal to Mechanism in Rheumatoid Arthritis: Lessons From a Single Risk Locus.Arthritis & rheumatology (Hoboken, N.J.) · 2026Article
- DeOPUS: cellular deconvolution via optimized power-transformed unmixing with shrinkage.Briefings in bioinformatics · 2026Article
- Epigenetic regulation of B cell tolerance and dysfunction in autoimmune disease.Nature reviews. Immunology · 2026Review
- Article
- Sex-specific trajectories of nonlinear immune aging at single-cell level.Nature communications · 2026Article
- IDEAL-Age: an interpretable deep learning framework for single-cell resolution profiling of immunological aging.Genome biology · 2026Article
- Deep interpretable learning of sample representations for characterizing disease states in single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Expression of VISTA on peripheral blood mononuclear cells in Systemic lupus erythematosus: association with disease activity and treatment status.Clinical and experimental medicine · 2026Article
- Autoreactive B cells in systemic lupus erythematosus: insights from integrative multi-omics analyses.Inflammation and regeneration · 2026Review
252 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Commented on by
- Erratum issued
Authors and funding
30 authors at 6 institutions in 2 countries.
Richard K Perez *School of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-8230-1832
M Grace Gordon *Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA.ORCID 0000-0003-4321-9187
Meena Subramaniam *Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA.ORCID 0000-0003-1534-567X
Min Cheol KimSchool of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-9005-590X
George C HartoularosBiological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA.ORCID 0000-0001-6980-2368
Sasha TargSchool of Medicine, University of California, San Francisco, CA, USA.
Yang SunDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0002-9344-8060
Anton OgorodnikovDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.
Raymund BuenoDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-8534-9399
Andrew LuUCLA-Caltech Medical Scientist Training Program, Los Angeles, CA, USA.ORCID 0000-0002-7594-6445
Mike ThompsonDepartment of Computer Science, University of California, Los Angeles, CA, USA.ORCID 0000-0003-1546-0512
Nadav RappoportDepartment of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Be'er Sheva, Israel.ORCID 0000-0002-7218-2558
Andrew DahlSection of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.ORCID 0000-0001-6520-4766
Cristina M LanataDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0002-6017-4921
Mehrdad MatloubianDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-6233-985X
Lenka MaliskovaInstitute for Human Genetics, University of California, San Francisco, CA, USA.ORCID 0000-0001-7677-3833
Serena S KwekDivision of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-5097-2711
Tony LiDivision of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-7432-0646
Michal SlyperKlarman Cell Observatory, Broad Institute, Cambridge, MA, USA.ORCID 0000-0002-3002-0366
Julia WaldmanKlarman Cell Observatory, Broad Institute, Cambridge, MA, USA.ORCID 0000-0002-0584-5833
Danielle DionneKlarman Cell Observatory, Broad Institute, Cambridge, MA, USA.ORCID 0000-0002-8338-4323
Orit Rozenblatt-RosenKlarman Cell Observatory, Broad Institute, Cambridge, MA, USA.ORCID 0000-0001-6313-3570
Lawrence FongDivision of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0002-6428-428X
Maria Dall'EraSchool of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-7439-2316
Brunilda BalliuDepartment of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.ORCID 0000-0001-8953-804X
Aviv RegevKlarman Cell Observatory, Broad Institute, Cambridge, MA, USA.ORCID 0000-0003-3293-3158
Jinoos YazdanyDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0002-3508-4094
Lindsey A CriswellDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.
Noah ZaitlenCenter for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA.ORCID 0000-0002-3553-3670
Chun Jimmie YeDivision of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-6560-3783
University of California, San Francisco · USBroad Institute · USUniversity of California, Los Angeles · USBen-Gurion University of the Negev · ILCalifornia Institute of Technology · USUniversity of Chicago · US
Funding
Training Grant in Genomic Analysis and InterpretationT32HG002536 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Valerie A Arboleda, Harold Pimentel · 2002 to 2026
$8.6MRESOURCE-BASED CENTER FOR THE ADVANCEMENT OF PRECISION MEDICINE IN RHEUMATOLOGYP30AR070155 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Mary C Nakamura · 2016 to 2026
$8.2MLeveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotencyU01HG012079 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Chongyuan Luo, Kathrin Plath · 2021 to 2026
$6.9MMethods for Genome-wide Association Studies in Admixed PopulationsR01HG006399 · NHGRI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L · 2011 to 2024
$6.3MDeterminants of response to cancer immunotherapyR35CA253175 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Lawrence Fong · 2021 to 2026
$5.8MOptimizing imputation for diverse populations in a distributed frameworkU01HG009080 · NHGRI · STANFORD UNIVERSITY · PI KENNY, EIMEAR ELIZABETH · 2016 to 2020
$5.2MRacial/ethnic and socioeconomic disparities in biologic and clinical SLE outcomesU01DP005120 · DP · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI DALL'ERA, MARIA, YAZDANY, JINOOS · 2014 to 2018
$4.8MSINGLE-CELL MULTI-OMIC APPROACHES TO MECHANISTICALLY CHARACTERIZE PSYCHIATRIC DISORDER RISK LOCI IN THE HUMAN BRAINR01MH125252 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LUO, CHONGYUAN · 2021 to 2025
$3.7M(PQ3) A functional genomic approach to identification and interpretation of germline-tumor genetic interactionsR01CA227237 · NCI · DANA-FARBER CANCER INST · PI GUSEV, ALEXANDER, ZAITLEN, NOAH A · 2018 to 2022
$3.5MGenomic Approaches to Population Health in Multi-Ethnic Hospital SystemsR01HG011345 · NHGRI · UNIVERSITY OF COLORADO DENVER · PI ARBOLEDA, VALERIE A, GIGNOUX, CHRISTOPHER R · 2020 to 2023
$3.1MRarely Common: Uncovering the dominant role of rare variants in the genetic architecture of complex human traits.R01GM142112 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HERNANDEZ, RYAN D. · 2021 to 2024
$2.2MImmunotherapy of human bladder cancerR01CA194511 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FONG, LAWRENCE · 2015 to 2019
$2.1MACL HHS U01DP005120Howard Hughes Medical InstituteNCCDPHP CDC HHS U01 DP005120NCI NIH HHS R01 CA194511NCI NIH HHS R01 CA223484NCI NIH HHS R01 CA227237NCI NIH HHS R35 CA253175NHGRI NIH HHS F31 HG011007NHGRI NIH HHS R01 HG006399NHGRI NIH HHS R01 HG011345NHGRI NIH HHS T32 HG002536NHGRI NIH HHS U01 HG009080NHGRI NIH HHS U01 HG012079NHGRI NIH HHS U01 HG012192NHLBI NIH HHS K25 HL121295NIAID NIH HHS R21 AI133337NIAMS NIH HHS K24 AR074534NIAMS NIH HHS P30 AR070155NIAMS NIH HHS R01 AR071522NIDCR NIH HHS R03 DE025665NIGMS NIH HHS R01 GM142112NIMH NIH HHS R01 MH125252
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
Indexed as
Interferon Type ILupus Erythematosus, SystemicCase-Control StudiesCD8-Positive T-LymphocytesHumansLeukocytes, MononuclearRNA-SeqTranscription, GeneticInterferon Type I
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.