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Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [RNA-seq]

ABSTRACT: Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [RNA-seq]

PROVIDER: PRJNA1049831 | ENA |

REPOSITORIES: ENA

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Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus

Project description:Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus

| PRJNA1049862 | ENA

Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [methylation]

Project description:Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [methylation]

| PRJNA1049861 | ENA

Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [methylation]

Project description:Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by systemic inflammation that involves various immune cell types. Monocytes are central players in promoting and regulating inflammation. Different monocyte subsets exist and change their proportions during physiological immune responses and under pathological conditions, including SLE, supporting different roles in inflammatory responses. In this study, we obtained the epigenetic and transcriptomic profiles of the three monocyte subsets, classical, intermediate and non-classical monocytes in an SLE cohort. We found different common and subset-specific alterations. While SLE classical monocytes had a stronger proinflammatory profile with an important interferon influence priming them towards macrophage differentiation, non-classical monocytes had a phenotype related to T cell differentiation regulation, with several indications pointing towards a Th17 promoting behavior. Integration of these bulk datasets with single-cell RNA-seq data of an SLE cohort shed light on the heterogeneity of our monocytes, confirming the interferon signature profile of classical monocytes and pointing towards intermediate and non-classical populations associated with exacerbated complement activation pathways, among others. With this analysis, we confirm the differential role of monocyte subsets in the pathogenesis of SLE and give insight into their regulatory mechanisms.

2024-10-30 | GSE249639 | GEO

Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [RNA-seq]

Project description:Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by systemic inflammation that involves various immune cell types. Monocytes play a central role in promoting and regulating inflammation. Peripheral blood classical monocytes subsequently differentiate into intermediate monocytes and then non-classical monocytes, assuming diverse roles and undergoing changes in their proportions during physiological immune responses and pathological conditions, including SLE. In this study, we obtained the epigenetic and transcriptomic profiles of these three monocyte subsets in an SLE cohort. We found different common and subset-specific alterations. While SLE classical monocytes had a stronger proinflammatory profile with an important interferon influence priming them towards macrophage differentiation, non-classical monocytes had a phenotype related to T cell differentiation regulation, with several indications pointing towards a Th17 promoting behavior. Integration of these bulk datasets with single-cell RNA-seq data of an SLE cohort shed light on the heterogeneity of our monocytes, confirming the interferon signature profile of classical monocytes and pointing towards intermediate and non-classical populations associated with exacerbated complement activation pathways, among others. Our results indicate a subversion of the epigenome and transcriptome in monocyte differentiation toward non-classical subsets in SLE, involving the STAT1 pathway and impacting function in relation to disease activity.

2024-10-30 | GSE249619 | GEO

Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-30 | GSE249641 | GEO

Systemic lupus erythematosus

Project description:Systemic lupus erythematosus

| PRJNA203032 | ENA

Spatial transcriptomics of Cutaneous and Systemic Lupus Erythematosus skin

Project description:We performed spatial transcriptomics on a case series of different clinical subtypes of cutaneous lupus erythematosus including acute cutaneous lupus erythematosus (malar rash, systemic lupus erythematosus). Our goals were to (1) determine which differentially expressed genes (DEGs) could be attributed to specific cell populations in specific locations within the tissue, (2) determine if spatial transcriptomics could better distinguish between CLE clinical subtypes than bulk RNA approaches and (3) examine potential cell-cell communication pathways within the skin lesions.

2021-10-01 | GSE182825 | GEO

Gene expression analysis in canine discoid/chronic lupus erythematosus, mucocutaneous lupus erythematosus and pyoderma

Project description:We performed a comparative immunology case study of client-owned dogs to determine if immune and skin gene expression profiles in spontaneous canine cutaneous lupus erythematosus mirror those observed in human cutaneous lupus.

2022-03-23 | GSE160260 | GEO

Transcription profiling of BXSB mice to study lupus erythematosus

Project description:Genetic basis of systemic lupus erythematosus in BXSB mice.

2013-01-30 | E-MIMR-7 | biostudies-arrayexpress

Gene expression in cutaneous lupus erythematosus

Project description:Lesional skin biopsies were taken from patients with active, untreated lupus skin disease (chronic discoid lupus erythematosus, CDLE, n=6; subacute cutaneous lupus erythematosus, SCLE, n=5). Healthy control specimens (HC) were obtained from healthy skin of 5 patients undergoing plastic surgery. In every case, two 4mm punch biopsies were taken. One was flash-frozen in liquid nitrogen and afterwards processed for mRNA isolation. The second biopsy was fixed in 5% formalin solution overnight, and was proceeded for histological investigation.The one-color Agilent 60-mer oligo microarray (Agilent, Santa Clara, CA) was used for gene expression analyses. Statistical analyses were performed using the Agilent Feature Extraction Softwareâ¢ and the Rosetta Resolverâ¢ gene expression data analysis system. The presented gene list (Table S1) includes normalized sample/ control log10-ratios (expression > 2-fold enhanced, p<0.01).

2017-02-24 | E-MTAB-5542 | biostudies-arrayexpress

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