Bulk Sequencing of CD45- cells from HD and SSc patients
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ABSTRACT:
PROVIDER: PRJNA836881 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19158452.fastq.gz | Fastqsanger.gz | |||
| SRR19158453.fastq.gz | Fastqsanger.gz |
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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.
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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.
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