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A Unified Molecular Signature of Systemic Lupus Erythematosus Revealed by Integrated, Multi-Cohort Transcriptomic Analysis

https://doi.org/10.1101/834093
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A decrease in complement is associated with increased renal and hematologic activity in patients with systemic lupus erythematosus
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Updating the American college of rheumatology revised criteria for the classification of systemic lupus erythematosus
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Modular Transcriptional Repertoire Analyses of Adults With Systemic Lupus Erythematosus Reveal Distinct Type I and Type II Interferon Signatures
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Blockade of Interferon‐γ Normalizes Interferon‐Regulated Gene Expression and Serum CXCL10 Levels in Patients With Systemic Lupus Erythematosus
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Gene Expression and Pharmacodynamic Changes in 1,760 Systemic Lupus Erythematosus Patients From Two Phase III Trials of BAFF Blockade With Tabalumab
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Anifrolumab, an Anti–Interferon‐α Receptor Monoclonal Antibody, in Moderate‐to‐Severe Systemic Lupus Erythematosus
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Transgenic Mice That Overexpress Metallothionein-I Are Protected from Cadmium Lethality and Hepatotoxicity
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Leflunomide, a reversible inhibitor of pyrimidine biosynthesis?
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Diagnostic value of progranulin in patients with lupus nephritis and its correlation with disease activity
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Sex Differences in the Blood Concentration of Tacrolimus in Systemic Lupus Erythematosus and Rheumatoid Arthritis Patients with CYP3A5*3/*3
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[69] Overview of metallothionein
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Oxygen free radicals and metallothionein
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Bullous skin diseases
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Systemic Lupus Erythematosus
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Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients
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Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients
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CD161 Defines a Transcriptional and Functional Phenotype across Distinct Human T Cell Lineages
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A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus
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Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses
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Oxysterol Sensing through the Receptor GPR183 Promotes the Lymphoid-Tissue-Inducing Function of Innate Lymphoid Cells and Colonic Inflammation
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Human 6-sulfo LacNAc (slan) dendritic cells have molecular and functional features of an important pro-inflammatory cell type in lupus erythematosus
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Oxysterols regulate encephalitogenic CD4+ T cell trafficking during central nervous system autoimmunity
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Widely divergent transcriptional patterns between SLE patients of different ancestral backgrounds in sorted immune cell populations
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Metallothionein protection of cadmium toxicity
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The immunosuppressant leflunomide inhibits lymphocyte proliferation by inhibiting pyrimidine biosynthesis.
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Impaired Immunity and Enhanced Resistance to Endotoxin in the Absence of Neutrophil Elastase and Cathepsin G
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Peripheral blood gene expression profiling in Sjögren's syndrome
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Dominant Th1 and Minimal Th17 Skewing in Discoid Lupus Revealed by Transcriptomic Comparison with Psoriasis
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EBI2 mediates B cell segregation between the outer and centre follicle
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An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis
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Oxysterols direct B-cell migration through EBI2
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Oxysterols direct immune cell migration via EBI2
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SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer
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Amplification of IFN-α-induced STAT1 activation and inflammatory function by Syk and ITAM-containing adaptors
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A CD8+ T cell transcription signature predicts prognosis in autoimmune disease
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Mice lacking neutrophil elastase reveal impaired host defense against gram negative bacterial sepsis
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A guide to immunometabolism for immunologists
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Neutrophils in the pathogenesis and manifestations of SLE
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Immunometabolism in systemic lupus erythematosus
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Single-cell technologies — studying rheumatic diseases one cell at a time
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Novel risk genes for systemic lupus erythematosus predicted by random forest classification
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Ultraviolet light-induced DNA damage triggers apoptosis in nucleotide excision repair-deficient cells via Bcl-2 decline and caspase-3/-8 activation
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Transcriptional firing helps to drive NETosis
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Metallothionein protects DNA from oxidative damage
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Photosensitivity in lupus erythematosus, UV photoprovocation results compared with history of photosensitivity and clinical findings
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Interferon-γ–Stimulated Genes, but Not USP18, Are Expressed in Livers of Patients With Acute Hepatitis C
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Systemic Lupus Erythematosus
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Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus
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Expression and regulation of a human metallothionein gene carried on an autonomously replicating shuttle vector.
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Targeted disruption of metallothionein I and II genes increases sensitivity to cadmium.
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Ligand Modulation of the Epstein-Barr Virus-induced Seven-transmembrane Receptor EBI2
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Induction of Lectin-like Transcript 1 (LLT1) Protein Cell Surface Expression by Pathogens and Interferon-γ Contributes to Modulate Immune Responses
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Human Neutrophils Secrete Bioactive Paucimannosidic Proteins from Azurophilic Granules into Pathogen-Infected Sputum
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Proteomic Analysis of Human Neutrophil Granules
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The problems and pitfalls in systemic lupus erythematosus drug discovery
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Mice lacking desmocollin 1 show epidermal fragility accompanied by barrier defects and abnormal differentiation
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Neutrophil elastase and myeloperoxidase regulate the formation of neutrophil extracellular traps
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CD161 (NKR-P1A) Costimulation of CD1d-dependent Activation of Human T Cells Expressing Invariant Vα24JαQ T Cell Receptor α Chains
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Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood
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Selective blockade of the inhibitory Fcγ receptor (FcγRIIB) in human dendritic cells and monocytes induces a type I interferon response program
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Blood leukocyte microarrays to diagnose systemic onset juvenile idiopathic arthritis and follow the response to IL-1 blockade
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A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation
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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
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PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
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Methods to increase reproducibility in differential gene expression via meta-analysis
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The role of neutrophils in the pathogenesis of systemic lupus erythematosus
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The potential of neutrophil elastase inhibitors as anti-inflammatory therapies
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Measurement of Prosocial Reasoning among Chinese Adolescents
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Levels of Heavy Metals in Popular Cigarette Brands and Exposure to These Metals via Smoking
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Leveraging heterogeneity across multiple data sets increases accuracy of cell-mixture deconvolution and reduces biological and technical biases
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Bacterial cell biology outside the streetlight
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Human Desmocollin 1 (Dsc1) Is an Autoantigen for the Subcorneal Pustular Dermatosis Type of IgA Pemphigus
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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Degradation of Outer Membrane Protein A in Escherichia coli Killing by Neutrophil Elastase
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Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses
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Netting Neutrophils Are Major Inducers of Type I IFN Production in Pediatric Systemic Lupus Erythematosus
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A comprehensive time-course–based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set
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Epstein-Barr virus-induced genes: first lymphocyte-specific G protein-coupled peptide receptors
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Assessment of Splice Variant-Specific Functions of Desmocollin 1 in the Skin
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Sifalimumab, an anti-interferon-α monoclonal antibody, in moderate to severe systemic lupus erythematosus: a randomised, double-blind, placebo-controlled study
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Safety and efficacy of leflunomide in the treatment of lupus nephritis refractory or intolerant to traditional immunosuppressive therapy: an open label trial
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Patients with systemic lupus erythematosus, myositis, rheumatoid arthritis and scleroderma share activation of a common type I interferon pathway
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Association of the interferon signature metric with serological disease manifestations but not global activity scores in multiple cohorts of patients with SLE
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EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY
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Clonal variation of cadmium response in human tumor cell lines
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Synthesis and Anticancer Properties of Water-Soluble Zinc Ionophores
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A Meta-analysis of Lung Cancer Gene Expression Identifies PTK7 as a Survival Gene in Lung Adenocarcinoma
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Fine Ambient Particles Induce Oxidative Stress and Metal Binding Genes in Human Alveolar Macrophages
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Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity
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Methotrexate in systemic lupus erythematosus: a systematic review of its efficacy
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Interleukin-27 inhibition of HIV-1 involves an intermediate induction of type I interferon
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IL-12 selectively programs effector pathways that are stably expressed in human CD8+ effector memory T cells in vivo
inferredcites →https://doi.org/10.1182/blood-2013-02-482893openalex-snapshot
Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation
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Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients
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Granules of the Human Neutrophilic Polymorphonuclear Leukocyte
inferredcites →https://doi.org/10.1186/1741-7015-9-65openalex-snapshot
Meta-analysis of microarray data using a pathway-based approach identifies a 37-gene expression signature for systemic lupus erythematosus in human peripheral blood mononuclear cells
inferredcites →https://doi.org/10.1186/1746-1596-8-88openalex-snapshot
Expression level of the growth factor progranulin is related with development of systemic lupus erythematosus
inferredcites →https://doi.org/10.1186/ar1015openalex-snapshot
Microarray analysis of gene expression in lupus.
inferredcites →https://doi.org/10.1186/ar2450openalex-snapshot
The renal metallothionein expression profile is altered in human lupus nephritis
inferredcites →https://doi.org/10.1186/ar2584openalex-snapshot
Interactions among type I and type II interferon, tumor necrosis factor, and β-estradiol in the regulation of immune response-related gene expressions in systemic lupus erythematosus
inferredcites →https://doi.org/10.1186/ar2780openalex-snapshot
B cells in autoimmunity
inferredcites →https://doi.org/10.1186/ar3271openalex-snapshot
Risk factors for ANA positivity in healthy persons
inferredcites →https://doi.org/10.1186/ar3317openalex-snapshot
Underexpression of mitochondrial-DNA encoded ATP synthesis-related genes and DNA repair genes in systemic lupus erythematosus
inferredcites →https://doi.org/10.1186/ar3330openalex-snapshot
Gene expression profiles from discordant monozygotic twins suggest that molecular pathways are shared among multiple systemic autoimmune diseases
inferredcites →https://doi.org/10.1186/ar3433openalex-snapshot
Mechanisms of B cell autoimmunity in SLE
inferredcites →https://doi.org/10.1186/ar4060openalex-snapshot
Restoration of regulatory and effector T cell balance and B cell homeostasis in systemic lupus erythematosus patients through vitamin D supplementation
inferredcites →https://doi.org/10.1186/ar4087openalex-snapshot
Serum progranulin levels are elevated in patients with systemic lupus erythematosus, reflecting disease activity
inferredcites →https://doi.org/10.1186/ar4256openalex-snapshot
Update on differences between childhood-onset and adult-onset systemic lupus erythematosus
inferredcites →https://doi.org/10.1186/s12920-017-0293-yopenalex-snapshot
Differential gene expression in disease: a comparison between high-throughput studies and the literature
inferredcites →https://doi.org/10.1186/s13000-016-0579-yopenalex-snapshot
Potential molecular characteristics in situ in response to repetitive UVB irradiation
inferredcites →https://doi.org/10.1186/s13075-014-0489-xopenalex-snapshot
Shared signatures between rheumatoid arthritis, systemic lupus erythematosus and Sjögren’s syndrome uncovered through gene expression meta-analysis
inferredcites →https://doi.org/10.1186/s40478-014-0093-yopenalex-snapshot
Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases
inferredcites →https://doi.org/10.1191/0961203304lu1067sropenalex-snapshot
Double-blind, randomized, placebo-controlled pilot study of leflunomide in systemic lupus erythematosus
inferredcites →https://doi.org/10.1191/096120399680411281openalex-snapshot
Classification and definition of major flares in SLE clinical trials
inferredcites →https://doi.org/10.1371/annotation/58cf4d21-f9b0-4292-94dd-3177f393a284openalex-snapshot
Correction: Differential Expression Analysis for Pathways
inferredcites →https://doi.org/10.1371/journal.pcbi.1002967openalex-snapshot
Differential Expression Analysis for Pathways
inferredcites →https://doi.org/10.1371/journal.pone.0023900openalex-snapshot
B Cell Signature during Inactive Systemic Lupus Is Heterogeneous: Toward a Biological Dissection of Lupus
inferredcites →https://doi.org/10.1371/journal.pone.0028125openalex-snapshot
TRAF6 and IRF7 Control HIV Replication in Macrophages
inferredcites →https://doi.org/10.1371/journal.pone.0034594openalex-snapshot
Heterogeneity of Inflammatory and Cytokine Networks in Chronic Plaque Psoriasis
inferredcites →https://doi.org/10.1371/journal.pone.0062366openalex-snapshot
Interferon-Beta Induces Distinct Gene Expression Response Patterns in Human Monocytes versus T cells
inferredcites →https://doi.org/10.1371/journal.pone.0065542openalex-snapshot
Granulin Exacerbates Lupus Nephritis via Enhancing Macrophage M2b Polarization
inferredcites →https://doi.org/10.1371/journal.pone.0067003openalex-snapshot
SLE Peripheral Blood B Cell, T Cell and Myeloid Cell Transcriptomes Display Unique Profiles and Each Subset Contributes to the Interferon Signature
inferredcites →https://doi.org/10.1371/journal.pone.0074893openalex-snapshot
Interferon Signature in the Blood in Inflammatory Common Variable Immune Deficiency
inferredcites →https://doi.org/10.1371/journal.pone.0083457openalex-snapshot
EBI2 Is a Negative Regulator of Type I Interferons in Plasmacytoid and Myeloid Dendritic Cells
inferredcites →https://doi.org/10.1371/journal.pone.0083776openalex-snapshot
Cell-Specific Type I IFN Signatures in Autoimmunity and Viral Infection: What Makes the Difference?
inferredcites →https://doi.org/10.1371/journal.pone.0135682openalex-snapshot
The c.503T>C Polymorphism in the Human KLRB1 Gene Alters Ligand Binding and Inhibitory Potential of CD161 Molecules
inferredcites →https://doi.org/10.1371/journal.pone.0166312openalex-snapshot
RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities
inferredcites →https://doi.org/10.1371/journal.ppat.1003681openalex-snapshot
MAIT Cells Detect and Efficiently Lyse Bacterially-Infected Epithelial Cells
inferredcites →https://doi.org/10.1590/s0100-879x2008000900005openalex-snapshot
ABCB1 C1236T, G2677T/A and C3435T polymorphisms in systemic lupus erythematosus patients
inferredcites →https://doi.org/10.2119/2006-00085.baechleropenalex-snapshot
An Interferon Signature in the Peripheral Blood of Dermatomyositis Patients is Associated with Disease Activity
inferredcites →https://doi.org/10.2337/db14-1208openalex-snapshot
The Streetlight Effect in Type 1 Diabetes
inferredcites →https://doi.org/10.3389/fimmu.2013.00362openalex-snapshot
Modulation of NK Cell Function by Genetically Coupled C-Type Lectin-Like Receptor/Ligand Pairs Encoded in the Human Natural Killer Gene Complex
inferredcites →https://doi.org/10.3390/ijms14036044openalex-snapshot
The Role of Metallothionein in Oxidative Stress
inferredcites →https://doi.org/10.4049/jimmunol.0802226openalex-snapshot
IFN-β1a Inhibits the Secretion of Th17-Polarizing Cytokines in Human Dendritic Cells via TLR7 Up-Regulation
inferredcites →https://doi.org/10.4049/jimmunol.0803600openalex-snapshot
Activation of Mammalian Target of Rapamycin Controls the Loss of TCRζ in Lupus T Cells through HRES-1/Rab4-Regulated Lysosomal Degradation
inferredcites →https://doi.org/10.4049/jimmunol.0902314openalex-snapshot
Major Differences in the Responses of Primary Human Leukocyte Subsets to IFN-β
inferredcites →https://doi.org/10.4049/jimmunol.1100450openalex-snapshot
Netting Neutrophils Induce Endothelial Damage, Infiltrate Tissues, and Expose Immunostimulatory Molecules in Systemic Lupus Erythematosus
inferredcites →https://doi.org/10.4049/jimmunol.1101284openalex-snapshot
Inflammasome Activation of IL-18 Results in Endothelial Progenitor Cell Dysfunction in Systemic Lupus Erythematosus
inferredcites →https://doi.org/10.4049/jimmunol.1103031openalex-snapshot
Cross-Species Transcriptional Network Analysis Defines Shared Inflammatory Responses in Murine and Human Lupus Nephritis
inferredcites →https://doi.org/10.4049/jimmunol.1300376openalex-snapshot
A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling
inferredcites →https://doi.org/10.4049/jimmunol.1301319openalex-snapshot
IFN Priming Is Necessary but Not Sufficient To Turn on a Migratory Dendritic Cell Program in Lupus Monocytes
inferredcites →https://doi.org/10.4049/jimmunol.1303296openalex-snapshot
Leukocyte Protease Binding to Nucleic Acids Promotes Nuclear Localization and Cleavage of Nucleic Acid Binding Proteins
inferredcites →https://doi.org/10.4049/jimmunol.153.6.2417openalex-snapshot
Human NKR-P1A. A disulfide-linked homodimer of the C-type lectin superfamily expressed by a subset of NK and T lymphocytes.
inferredcites →https://doi.org/10.4049/jimmunol.165.9.5338openalex-snapshot
Human Double-Negative T Cells in Systemic Lupus Erythematosus Provide Help for IgG and Are Restricted by CD1c
inferredcites →https://doi.org/10.4049/jimmunol.168.12.6071openalex-snapshot
Transendothelial Migratory Pathways of Vδ1+TCRγδ+ and Vδ2+TCRγδ+ T Lymphocytes from Healthy Donors and Multiple Sclerosis Patients: Involvement of Phosphatidylinositol 3 Kinase and Calcium Calmodulin-Dependent Kinase II
inferredcites →https://doi.org/10.4049/jimmunol.175.12.7791openalex-snapshot
Cutting Edge: Lectin-Like Transcript 1 Is a Ligand for the CD161 Receptor
inferredcites →https://doi.org/10.4049/jimmunol.175.12.7796openalex-snapshot
Cutting Edge: Lectin-Like Transcript-1 Is a Ligand for the Inhibitory Human NKR-P1A Receptor
inferredcites →https://doi.org/10.4049/jimmunol.178.2.1122openalex-snapshot
Identification of Genes Selectively Regulated by IFNs in Endothelial Cells
inferredcites →https://doi.org/10.4049/jimmunol.179.9.6352openalex-snapshot
Demethylation of CD40LG on the Inactive X in T Cells from Women with Lupus
inferredcites →https://doi.org/10.4049/jimmunol.180.10.6508openalex-snapshot
Functional Consequences of Interactions between Human NKR-P1A and Its Ligand LLT1 Expressed on Activated Dendritic Cells and B Cells
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