Project description:Purpose: To compare transcriptome profile of CD14+ blood monocytes from systemic sclerosis (SSc) patients and healthy controls. Methods: CD14+ monocytes were isolated from peripheral blood of lcSSc (n=5, age=54.4±6.7), dcSSc patients (n=5, age=51.8±7.2) and age- and sex-matched healthy controls (HC) (n=5, age=50.8±9.7). Total RNA was isolated and polyA libraries were prepared using TruSeq Stranded mRNA kit. Next Generation Sequencing was performed using Illumina HiSeq 4000 platform. Differentially expressed genes were computed using DESeq2 algorithm. Results: We detected 1440 differentially expressed genes between dcSSc vs HC and 225 between lcSSc and HC respectively (p≤0.01; log2 ratio≥0.5, Fig 1). Among those, in dcSSc 1076 were upregulated (e.g. MMP9, IL1R2, FLT3, MIF, TLR9) and 364 were downregulated (e.g. TGFBR1, CD44, CD244, HLA-DRA, HLA-G). In lcSSc 160 transcripts were upregulated (e.g. CCL2, WNT5B, MMP17) and 65 were downregulated (e.g. KLF11, IRAK2). We identified 123 commonly deregulated genes between SSc subgroups (e.g. CCL3, CD14, IL27, MMP17). Principal component analysis showed close clustering within SSc subgroups and clear separation from healthy controls. Pathway analysis revealed alterations in several biological processes important in fibrogenesis including antigen presentation, MIF-induced immune responses, TGF-β, NOTCH and WNT signalling pathways. qPCR analysis further confirmed differences in gene expression on mRNA level (n HC=8, n SSc=25, p≤0.05). Conclusions: To our knowledge, this is the first global transcriptome analysis of peripheral blood CD14+ monocytes in SSc. Our results suggest a primary activation of monocytes in peripheral blood, which might be further translated into novel cellular biomarker of the disease and potentially used for distinguishing between responders and non-responders to a novel treatment in future clinical trials.

2021-09-10 | GSE157840 | GEO

Transcriptomic Analysis of Classical Monocytes from African American Patients with Systemic Sclerosis

Project description:Systemic sclerosis is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects African Americans (AA). Additionally, monocytes show heightened activation in SSc, and in AA relative to European ancestry (EA) individuals. Monocytes are thus a good target tissue for elucidating disease mechanisms. In this study, we sought to identify differentially expressed genes in classical monocytes from AA SSc patients relative to unaffected AA controls. We performed RNAseq to profile the transcriptome on FACS-isolated classical monocytes (CD14++CD16-) from 16 female AA SSc cases and 18 female AA controls. We observed modest gene expression differences between cases and controls. The genes harboring the top differentially methylated cytosines are enriched for metabolic processes. The relatively modest differences in gene expression observed between patients and controls is consistent with prior evidence of stronger inflammatory signatures in AA.

2022-02-07 | GSE196070 | GEO

Histone modifications underlie monocyte dysregulation in Systemic Sclerosis patients, underlining the treatment potential of epigenetic targeting [RNA-seq]

Project description:Systemic sclerosis (SSc) is a chronic autoimmune disease that mainly affects the connective tissue. Monocytes have been shown to be an important cell type involved in the pathogenesis of SSc. By performing RNA-sequencing analysis on whole RNA isolated from peripheral blood CD14+ monocytes obtained from SSc patients, together with healthy controls matched for sex and age, obtained from the University Medical Center Utrecht (definite SSc cohort), and the University of Milan (non-fibrotic SSc cohort), we aimed to characterize the transcriptomic landscape of monocytes of patients with (pre-clinical) systemic sclerosis. Moreover, ChIPseq data was available for a part of the subjects included in the RNA-seq analysis and the correlation between the histone marks and gene expression was studied. The samples used in this study are part of the SYSCLASS cohort.

2019-03-06 | GSE124073 | GEO

Expression data from intermediate monocytes from healthy donors and autoimmune uveitis patients

Project description:Human peripheral monocytes have been categorized into three subsets based on differential expression levels of CD14 and CD16. However, the factors that influence the distribution of monocyte subsets and the roles which each subset plays in autoimmunity are not well studied. To compare the gene expression profiling 1) on intermediate monocytes CD14++CD16+ monocytes between healthy donors and autoimmune uveitis patients and 2) among 3 monocyte subsets in health donors, here we purified circulating intermediate CD14++CD16+ monocytes from 5 patients with autoimmune uveitis (labeled as P1-5) and 4 healthy donors (labeled as HD1-4) by flow cytometry and isolated total RNA to proceed microarray assay. In addition, we also purified CD14+CD16++ (non-classical monocytes) and CD14++CD16- (classical monocytes) from 4 healthy donors to do microarray. We demonstrate that CD14++CD16+ monocytes from patients and healthy control donors share a similar gene expression profile. The CD14+CD16++ cells (non-classical monocytes) display the most distinctive gene expression profiling when compared to intermediate CD14++CD16+ monocytes and classical CD14++CD16- monocytes.

2015-03-17 | GSE66936 | GEO

DNA Methylation Analysis in Classical Monocytes from African American Patients with Systemic Sclerosis

Project description:Systemic sclerosis is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects African Americans (AA). Additionally, monocytes show heightened activation in SSc, and in AA relative to European ancestry (EA) individuals. Monocytes are thus a good target tissue for elucidating disease mechanisms. In this study, we sought to investigate differentially methylated loci in classical monocytes from AA SSc patients and unaffected AA controls. We used Illumina’s MethylationEPIC BeadChip to profile DNA methylation patterns on FACS-isolated classical monocytes (CD14++CD16-) from 12 female AA SSc cases and 12 female AA controls. We observed modest DNA methylation differences between cases and controls. The genes harboring the top differentially methylated cytosines are enriched for immune pathways and metabolic processes. The relatively modest differences in DNA methylation observed between patients and controls is consistent with prior evidence of stronger inflammatory signatures in AA.

2022-02-07 | GSE196007 | GEO

Differentially expressed transcripts in SLE blood monocytes

Project description:To better characterize the molecules that could potentially confer antigen presenting capacity to SLE monocytes, we assessed their gene expression profile. Blood monocytes from five healthy controls and five pediatric SLE patients were isolated using CD14+ selection. Because drugs used to treat SLE could induce considerable transcriptional changes, we selected active, newly diagnosed patients who had never received oral or intravenous (IV) medications.

2014-06-03 | E-GEOD-46907 | biostudies-arrayexpress

Transcriptome analysis of CD14+ monocytes from SSc patients

Project description:Transcriptome analysis of CD14+ monocytes from SSc patients

| PRJNA662949 | ENA