4.8 Article

Distinct transcriptome architectures underlying lupus establishment and exacerbation

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Discovering dominant tumor immune archetypes in a pan-cancer census

Alexis J. Combes et al.

Summary: This study identifies common patterns of the immune system in different types of cancer and proposes strategies to modulate tumor immunity for improved therapy. The findings provide new insights into cancer immunity and offer a rational approach to enhance treatment.
Article Rheumatology

Immune cell multiomics analysis reveals contribution of oxidative phosphorylation to B-cell functions and organ damage of lupus

Yusuke Takeshima et al.

Summary: This study revealed the importance of oxidative phosphorylation/mitochondrial dysfunction in SLE memory B cells through transcriptomic, epigenomic, and genomic analysis. The PRDX6 gene was identified as a key driver in SLE B cells. Furthermore, the OXPHOS signature was associated with type I IFN signaling-related genes and correlated with SLE organ damage and specific clinical phenotypes.

ANNALS OF THE RHEUMATIC DISEASES (2022)

Article Biotechnology & Applied Microbiology

Exaggerated false positives by popular differential expression methods when analyzing human population samples

Yumei Li et al.

Summary: During population-level RNA-seq studies, the actual false discovery rates of DESeq2 and edgeR sometimes exceed 20%, recommending the use of the Wilcoxon rank-sum test.

GENOME BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics

Maya Ghoussaini et al.

Summary: Open Targets Genetics is an open-access integrative resource that aggregates human GWAS and functional genomics data to make connections between GWAS-associated loci and likely causal genes. Users can search, prioritize, and explore GWAS signals through data visualizations provided by the portal.

NUCLEIC ACIDS RESEARCH (2021)

Review Biochemistry & Molecular Biology

Leveraging Heterogeneity in Systemic Lupus Erythematosus for New Therapies

Marilyn E. Allen et al.

Summary: SLE, a multisystem, chronic autoimmune disease, has diverse treatment options with varied efficacy. Despite many failed attempts in the past, the approval of belimumab in 2011 marked a successful milestone in SLE drug development. Insights from transcriptomics studies provide a deeper understanding of the molecular and clinical heterogeneity of SLE, offering valuable insights for future drug development and clinical practices.

TRENDS IN MOLECULAR MEDICINE (2021)

Article Rheumatology

Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus

Xianyong Yin et al.

Summary: This study conducted the largest genome-wide meta-analysis for SLE in East Asian populations, identifying 46 novel loci and prioritizing putative causal variants using Bayesian statistical approach. The findings highlight the power of large-scale genetic discovery in shedding light on the genetic and biological understandings of SLE.

ANNALS OF THE RHEUMATIC DISEASES (2021)

Article Biochemistry & Molecular Biology

GTRD: an integrated view of transcription regulation

Semyon Kolmykov et al.

Summary: The Gene Transcription Regulation Database (GTRD) contains uniformly annotated NGS data related to gene transcription regulation and provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts

Aaron Graubert et al.

Summary: Post-sequencing quality control is crucial for RNA-seq data analysis, and RNA-SeQC 2 provides an efficient way to assess sample quality across a wide range of RNA-seq protocols.

BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

Multi?cell type gene coexpression network analysis reveals coordinated interferon response and cross?cell type correlations in systemic lupus erythematosus

Bharat Panwar et al.

Summary: Systemic lupus erythematosus (SLE) is an incurable autoimmune disease that predominantly affects women. Research has shown that the presence of interferon response signature stratifies SLE patients into two distinct groups, and identified certain genes associated with disease severity.

GENOME RESEARCH (2021)

Article Genetics & Heredity

An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

Edward Mountjoy et al.

Summary: In this study, an open resource was introduced to systematically fine map and prioritize genes across published GWAS loci, aiming at identifying causal genes associated with complex traits. By training a machine learning model using genetics and functional genomics data, the authors were able to distinguish causal genes from neighboring genes, outperforming distance-based models. The prioritized genes were found to be enriched for known approved drug targets, suggesting their potential in drug development.

NATURE GENETICS (2021)

Article Biochemistry & Molecular Biology

Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases

Mineto Ota et al.

Summary: Genetic studies have identified variant loci associated with immune-mediated diseases, with eQTL analysis revealing dynamic variations of eQTL effects in the context of immunological conditions and cell types. These cell-type-specific eQTLs showed significant enrichment in immune disease-associated genetic variants, providing insights into the immunogenetic functions of disease-associated variants under in vivo disease conditions.
Article Biology

Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures

Gaia Andreoletti et al.

Summary: Gaia Andreoletti et al. leverage cell-sorted RNA-seq data and machine learning to investigate gene expression patterns in immune cell subtypes purified from Asian and White patients with a medical diagnosis of systemic lupus erythematosus (SLE). They report distinct clinical subtypes of SLE and identify ethnicity- and disease-specific gene clusters, potentially contributing toward the future development of personalized therapeutic strategies for patients with SLE.

COMMUNICATIONS BIOLOGY (2021)

Review Immunology

BAFF signaling in B cell metabolism

Ellen McAllister et al.

Summary: BAFF is a crucial cytokine that not only maintains B cell homeostasis but also drives a metabolic program in B cells, increasing their capacity to divide. Components of the signaling cascades initiated by BAFF have roles in metabolic reprogramming, and further exploration of BAFF signaling in B cell metabolism could help identify metabolic vulnerabilities in hyperactive B cells in autoimmunity.

CURRENT OPINION IN IMMUNOLOGY (2021)

Article Biochemical Research Methods

NicheNet: modeling intercellular communication by linking ligands to target genes

Robin Browaeys et al.

NATURE METHODS (2020)

Article Medicine, General & Internal

Trial of Anifrolumab in Active Systemic Lupus Erythematosus

Eric F. Morand et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Immunology

Mapping systemic lupus erythematosus heterogeneity at the single-cell level

Djamel Nehar-Belaid et al.

NATURE IMMUNOLOGY (2020)

Review Rheumatology

2019 update of the EULAR recommendations for the management of systemic lupus erythematosus

Antonis Fanouriakis et al.

ANNALS OF THE RHEUMATIC DISEASES (2019)

Article Medicine, Research & Experimental

Patrolling monocytes promote the pathogenesis of early lupus-like glomerulonephritis

Jeeba Kuriakose et al.

JOURNAL OF CLINICAL INVESTIGATION (2019)

Article Immunology

The immune cell landscape in kidneys of patients with lupus nephritis

Arnon Arazi et al.

NATURE IMMUNOLOGY (2019)

Article Immunology

CD8+ T Lymphocyte and NK Cell Network: Circuitry in the Cytotoxic Domain of Immunity

Roman Uzhachenko et al.

FRONTIERS IN IMMUNOLOGY (2019)

Review Immunology

Human Monocyte Subsets and Phenotypes in Major Chronic Inflammatory Diseases

Theodore S. Kapellos et al.

FRONTIERS IN IMMUNOLOGY (2019)

Article Biochemistry & Molecular Biology

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

Annalisa Buniello et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Differential control of human Treg and effector T cells in tumor immunity by Fc-engineered anti-CTLA-4 antibody

Danbee Ha et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Review Immunology

T Cells That Help B Cells in Chronically Inflamed Tissues

Deepak A. Rao

FRONTIERS IN IMMUNOLOGY (2018)

Article Genetics & Heredity

Identification of context-dependent expression quantitative trait loci in whole blood

Dania V. Zhernakova et al.

NATURE GENETICS (2017)

Article Genetics & Heredity

Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease

Urko M. Marigorta et al.

NATURE GENETICS (2017)

Article Multidisciplinary Sciences

Transancestral mapping and genetic load in systemic lupus erythematosus

Carl D. Langefeld et al.

NATURE COMMUNICATIONS (2017)

Review Immunology

The non-canonical NF-κB pathway in immunity and inflammation

Shao-Cong Sun

NATURE REVIEWS IMMUNOLOGY (2017)

Article Rheumatology

Definition and initial validation of a Lupus Low Disease Activity State (LLDAS)

Kate Franklyn et al.

ANNALS OF THE RHEUMATIC DISEASES (2016)

Review Rheumatology

Activation of mTOR (mechanistic target of rapamycin) in rheumatic diseases

Andras Perl

NATURE REVIEWS RHEUMATOLOGY (2016)

Article Biochemical Research Methods

variancePartition: interpreting drivers of variation in complex gene expression studies

Gabriel E. Hoffman et al.

BMC BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

Romain Banchereau et al.

Review Urology & Nephrology

The role of neutrophils and NETosis in autoimmune and renal diseases

Sarthak Gupta et al.

NATURE REVIEWS NEPHROLOGY (2016)

Review Rheumatology

New insights into the immunopathogenesis of systemic lupus erythematosus

George C. Tsokos et al.

NATURE REVIEWS RHEUMATOLOGY (2016)

Article Medicine, General & Internal

Multitarget Therapy for Induction Treatment of Lupus Nephritis A Randomized Trial

Zhihong Liu et al.

ANNALS OF INTERNAL MEDICINE (2015)

Article Rheumatology

The evolution of drug discovery in systemic lupus erythematosus

Daniel J. Wallace

NATURE REVIEWS RHEUMATOLOGY (2015)

Article Biochemistry & Molecular Biology

The Molecular Signatures Database Hallmark Gene Set Collection

Arthur Liberzon et al.

CELL SYSTEMS (2015)

Article Biochemical Research Methods

HTSeq-a Python framework to work with high-throughput sequencing data

Simon Anders et al.

BIOINFORMATICS (2015)

Article Multidisciplinary Sciences

Genetic and epigenetic fine mapping of causal autoimmune disease variants

Kyle Kai-How Farh et al.

NATURE (2015)

Review Rheumatology

The complement system in systemic lupus erythematosus: an update

Jonatan Leffler et al.

ANNALS OF THE RHEUMATIC DISEASES (2014)

Review Immunology

Type I Interferon in the Pathogenesis of Lupus

Mary K. Crow

JOURNAL OF IMMUNOLOGY (2014)

Review Rheumatology

The BAFF/APRIL system in SLE pathogenesis

Fabien B. Vincent et al.

NATURE REVIEWS RHEUMATOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Genetics & Heredity

Systematic identification of trans eQTLs as putative drivers of known disease associations

Harm-Jan Westra et al.

NATURE GENETICS (2013)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Review Immunology

Standardizing immunophenotyping for the Human Immunology Project

Holden T. Maecker et al.

NATURE REVIEWS IMMUNOLOGY (2012)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Review Immunology

Phenotypic and functional heterogeneity of human memory B cells

Inaki Sanz et al.

SEMINARS IN IMMUNOLOGY (2008)

Article Mathematical & Computational Biology

Adjusting batch effects in microarray expression data using empirical Bayes methods

W. Evan Johnson et al.

BIOSTATISTICS (2007)

Article Immunology

Interferon and granulopoiesis signatures in systemic lupus erythematosus blood

L Bennett et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2003)

Review Rheumatology

Cytokines and systemic lupus erythematosus

GS Dean et al.

ANNALS OF THE RHEUMATIC DISEASES (2000)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)