Bulk Sequencing of CD45- cells from HD and SSc patients
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ABSTRACT:
PROVIDER: PRJNA836881 | ENA |
REPOSITORIES: ENA
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Project description:Skin cells were depleted from CD45+ and dead cells using microBeads, purity 95%. CD45- cells were RNA sequenced (bulk) to find differentially regulated genes between healthy donors and scleroderma patients (SSc)
2022-05-13 | GSE202649 | GEO
Project description:Exploration of proteome differences between CD45+ and CD45- cell types in renal cell carcinoma tumors and normal adjacent tissue patient samples.
2020-10-14 | PXD014370 | Pride
Project description:Transcriptome analysis of CD14+ monocytes from SSc patients
| PRJNA662949 | ENA
Project description:In systemic sclerosis (SSc) evidence suggests abnormal keratinocyte-fibroblast interactions. We investigated the potential epidermal dysfunction in SSc and its effects on dermis homeostasis. Epidermal equivalents (EE) were generated from six healthy donor (HD) and four SSc keratinocytes. Skin and EE expression of proliferation, differentiation, and activation markers was evaluated by immunohistochemistry. The transcriptomic profile of SSc-EE and HD-EE was identified by RNAseq analysis. EE conditioned medium (CM) was used to stimulate fibroblasts, and their production of interleukin (IL)-6, IL-8, matrix metalloproteinase (MMP)-1, type-I collagen (col-I), and fibronectin was assessed by ELISA. Compared to HD, SSc-EE exhibited aberrant differentiation, enhanced expression of activation markers, and lower mitotic rate of basal keratinocytes, reproducing most of the abnormalities observed in SSc epidermis. RNAseq analysis revealed that, compared to HD-EE, SSc-EE were characterized by the downregulation of HOX gene family members and by the upregulation of metabolic and oxidative stress molecular pathways. EE-CM enhanced the fibroblast production of IL-6, IL-8, MMP-1, Col-I, and fibronectin (p<0.05). Except for Col-I and fibronectin, this effect was 2-fold higher in the presence of CM generated form SSc-EE. IL-1 was, at least in part, responsible for keratinocyte-dependent fibroblast activation. SSc-EE recapitulate the in vivo characteristic of SSc epidermis demonstrating that SSc keratinocytes have an intrinsically altered differentiation program possibly due to the downregulation of genes from the HOX family. The increased metabolic and oxidative stress associated with SSc epidermis may participate to dermis chronic inflammation and fibrosis
2021-08-13 | GSE156173 | GEO
Project description:To identifying new blood derived prognostic biomarkers of lung disease progression in systemic sclerosis patients, we performed RNA-seq on whole blood from progressing SSc-ILD patients and controls enrolled in the FaSScinate clinical trial or an independent cohort.
2023-07-26 | GSE231691 | GEO
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
Project description:Objective: MicroRNAs (miRNAs) control key elements of mRNA stability and likely contribute to the dysregulated lung gene expression observed in systemic sclerosis associated interstitial lung disease (SSc-ILD). We analyzed the miRNA gene expression of tissue and cells from SSc-ILD patients. A chronic lung fibrotic murine model was used. Methods: RNA was isolated from lung tissue of 12 SSc-ILD patients and 5 control lungs. High-resolution computed tomography (HRCT) was performed at baseline and 2-3 years after treatment. Lung fibroblasts and PBMCs were isolated from healthy controls and SSc-ILD patients. miRNA and mRNA were analyzed by microarray, quantitative polymerase chain reaction, and/or Nanostring; pathway analysis was performed by DIANA-miRPath v2.0 software. Wild-type and miR-155 deficient (miR-155ko) mice were exposed to bleomycin. Results: Lung miRNA microarray data distinguished patients with SSc-ILD from healthy controls with 185 miRNA differentially expressed (q<0.25). DIANA-miRPath revealed 57 KEGGs pathways related to the most dysregulated miRNAs. miR-155 and miR-143 were strongly correlated with progression of the HRCT score. Lung fibroblasts showed only mild expression of miR-155/miR-21 after several stimuli. miR-155 PBMC expression strongly correlated with lung function tests in SSc-ILD. miR-155ko mice developed milder lung fibrosis, survived longer, and showed a weaker lung induction of several genes after bleomycin exposure compared to wild-type mice. Conclusions: miRNAs are dysregulated in lungs and PBMCs of SSc-ILD patients. Based on mRNA-miRNA interaction analysis and pathway tools, miRNAs may play a role in the progression of the disease. Our findings suggest that targeting miR-155 might provide a novel therapeutic strategy for SSc-ILD. Lung biopsies taken from open lung biopsy from SSc-ILD patients (n=15 samples) and from cancer free control patients (n=5) during ressection of the lung tumor.
2016-08-01 | E-GEOD-81293 | biostudies-arrayexpress
Project description:Systemic sclerosis (SSc) is a rare and devastating connective tissue disorder that results in fibrosis and vascular abnormalities that affect the skin and visceral organs, and SSc-associated pulmonary fibrosis (SSc-PF) is the leading cause of death amongst SSc patients. Racial disparity is noticeable in SSc as African Americans (AA) have a higher frequency and severity of diseases than European Americans (EA). Using RNAseq, we determined differentially expressed genes (DEGs) in primary pulmonary fibroblasts (pFBs) outgrown from SSc-PF lungs (SScL) and normal lungs (NL) of AA and EA patients to characterize the unique transcriptomic signatures of AA-NL and AA-SScL pFBs by performing a systems level analysis. We identified 69 DEGs in “AA-NL vs. EA-NL” and 384 DEGs in “AA-SScL vs. EA-SScL” comparisons, and only 7.5% DEGs were commonly deregulated in the “SScL vs. NL in AA and EA” disease mechanisms comparison. Surprisingly, we also identified a disease-like signature in AA-NL pFBs. Our data highlight that the transcriptome of AA pFBs is unique and may hold the key to understanding racial disparity in SSc-PF, the first step in developing efficacious therapeutic strategies.
2023-03-01 | GSE215841 | GEO
Project description:Bulk RNA-seq characterization of human cortical organoids derived from two HD patients (CAG55 and 59) and one healthy (CAG19) sibling's induced pluripotent stemm cells (iPSCs) and human embryonic stemm cells H9 .
2023-12-11 | GSE220847 | GEO
Project description:We here used whole blood gene expression profiling to differentiate SSc patients from healthy controls (HC) and to identify a specific gene expression and predictive genes for SSc-overlap syndromes.
2020-02-12 | GSE145120 | GEO