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Homo sapiens

ABSTRACT: Joint-specific DNA transcriptome signatures in rheumatoid arthritis [RNA-seq]

PROVIDER: PRJNA317757 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3350550_1.fastq.gz	Fastqsanger.gz
	SRR3350550_2.fastq.gz	Fastqsanger.gz
	SRR3350570_1.fastq.gz	Fastqsanger.gz
	SRR3350570_2.fastq.gz	Fastqsanger.gz
	SRR3350580_1.fastq.gz	Fastqsanger.gz

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Homo sapiens

Project description:Joint-specific DNA methylation signatures in rheumatoid arthritis [methylation array]

| PRJNA317756 | ENA

Joint-specific DNA transcriptome signatures in rheumatoid arthritis [RNA-seq]

Project description:Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. Using genome-wide methods, we show differences between RA knee and hip FLS in the methylation of genes encoding biological pathways, such as IL-6 signaling via JAK-STAT pathway. Furthermore, differentially expressed genes are identified between knee and hip FLS using RNA-seq. Double-evidenced genes that are both differentially methylated and expressed include multiple HOX genes. Joint-specific DNA signatures suggest that RA disease mechanisms might vary from joint to joint, thus potentially explaining some of the diversity of drug responses in RA patients.

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Bisulfite-seq of synovial biopsies from rheumatoid arthritis patients

Project description:Synovial biopsies from rheumatoid arthritis patients were obtained and profiled using bisulfite-seq for whole-genome DNA methylation. Patients were stratified according to the number of swollen joints they had (SJC, swollen joint count) and divided in three groups for the differential expression analysis: None (SJC = 0), Low (1<= SJC <= 8), High (SJC > 8).

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Project description:Differential DNA methylation in Rheumatoid arthritis

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Project description:DNA methylome signature in rheumatoid arthritis

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RNA-seq of synovial biopsies from rheumatoid arthritis patients

Project description:Synovial biopsies from rheumatoid arthritis patients were obtained and profiled using RNA-seq. Patients were stratified according to the number of swollen joints they had (SJC, swollen joint count) and divided in three groups for the differential expression analysis: None (SJC = 0), Low (1<= SJC <= 8), High (SJC > 8).

2021-04-26 | E-MTAB-6684 | biostudies-arrayexpress

Dissecting the molecular control of immune cell accumulation in the inflamed joint

Project description:Mechanisms governing entry and exit of immune cells into, and out of, inflamed joints, remain poorly understood. We sought herein to identify the key molecular pathways regulating such migration. Using murine models of inflammation in conjunction with mice expressing a photoconvertible fluorescent protein we characterized the migration of cells from joints to draining lymph nodes (LN) and performed RNA-seq analysis on isolated cells, identifying genes associated with migration and retention. We further refined the gene list to those specific for joint inflammation. RNA-seq data revealed pathways and genes previously highlighted as characteristic of Rheumatoid arthritis (RA) in patient studies, validating the methodology. Focusing on pathways associated with cell migration, adhesion and movement, we identified genes involved in the retention of immune cells in the inflamed joint, namely JAM-A, and identified a role for such molecules in T cell differentiation in vivo. Thus, using a combination of novel cell tracking approaches and murine models of inflammatory arthritis we have identified genes, pathways and anatomically specific tissue signatures regulating cell migration in a variety of inflamed sites. This unique skin and joint specific dataset will be an invaluable resource for the identification of novel therapeutic targets for arthritis and other inflammatory disorders.

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Expression data from Rheumatoid Arthritis synovial tissue samples

Project description:Rheumatoid arthritis (RA) is a complex and clinically heterogeneous autoimmune disease. Microarray analysis of 83 synovial samples provides insight into the expression-level differences between patients at the site of disease activity. Synovial samples from Rheumatoid Arthritis patients were obtained during joint resection and profiled using microarrays.

2014-04-22 | E-GEOD-48780 | biostudies-arrayexpress

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