Physical Activity Moderates Inflammatory Gene Expression in Rheumatoid Arthritis
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ABSTRACT:
PROVIDER: PRJNA743095 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15017353_1.fastq.gz | Fastqsanger.gz | |||
| SRR15017353_2.fastq.gz | Fastqsanger.gz | |||
| SRR15017354_1.fastq.gz | Fastqsanger.gz | |||
| SRR15017354_2.fastq.gz | Fastqsanger.gz | |||
| SRR15017355_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Background/Purpose: Prior studies show an independent association between greater physical activity and lower inflammatory markers among adults in the general population, but the impact of physical activity on systemic inflammation in people with rheumatoid arthritis (RA) hasn’t been thoroughly investigated. We therefore aimed to determine whether physical activity behavior associates with differential expression of inflammatory genes in RA. Methods: Data derive from baseline assessments for a prospective observational cohort of patients with RA. At each study visit, we obtained detailed clinical information, collected peripheral whole blood for subsequent RNA sequencing (RNA-seq), and provided participants with actigraphs (GT9X ActiGraph Link device) to objectively measure physical activity by wearing the device at home for 7 consecutive 24-hour periods. Participants were categorized into three physical activity groups based on the highest (“active”), middle (“intermediate”), and lowest (“inactive”) tertiles for percentage of time spent in moderate/vigorous physical activity (metabolic equivalent (MET) level ≥2.00) across the sample. Results: There were 35 patients with complete clinical, actigraphy, and transcriptomic data available for analysis. The participants had a mean age of 56 years, were 90% female, and self-reported the following racial/ethnic identities: 32% white, 11% African American, 8% Asian, 40% Hispanic. Participants spent 48%, 41%, and 12% of time awake in sedentary, light, and moderate physical activity, respectively. None of the participants achieved vigorous activity. The patients in the most active group were younger but did not otherwise significantly differ by clinical and demographic characteristics compared to the other physical activity groups. However, in the differential gene expression analysis comparing the highest versus lowest physical activity tertiles, there were 365 up- and 402 down-regulated genes at an adjusted P value < 0.1. Gene set enrichment analysis revealed that the most physically active patients exhibited downregulation of diverse innate and adaptive immune signaling pathways. Assessment of upstream cytokine activation states demonstrated inhibition of type I, II and III interferons and activation of EPO in the highest physical activity tertile patients. Conclusion: Among a racially and ethnically diverse RA cohort, participants who spent more time in moderately intense physical activity had down-regulation of genes involved in both innate and adaptive immune signaling compared to those who were more sedentary. These findings provide mechanistic evidence to support a disease-modifying effect of physical activity in RA.
2021-09-01 | GSE179302 | GEO
Project description:Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced inter-patient heterogeneity. To characterize RA at the molecular level and to uncover key pathomechanisms, we performed whole-genome gene expression analyses. Synovial tissues from rheumatoid arthritis patients were compared to those from osteoarthritis patients and to normal donors. Keywords: disease state analysis
2004-11-04 | GSE1919 | GEO
Project description:Genome wide DNA methylation profiling of monocytes from healthy donors and rheumatoid arthritis patients. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in CD11b+CD33+CD15neg monocytes isolated from PBMCs of 17 healthy donors and 47 rheumatoid arthritis patients with different disease activity scores (DAS28).
2019-12-31 | GSE134429 | GEO
Project description:Baker2013 - Cytokine Mediated Inflammation in
Rheumatoid Arthritis
This model by Baker M. 2013, describes
the interaction between pro and anti-inflammatory cytokine
signalling in rheumatoid arthritis.
Using two ordinary differential equations, the first model
[BIOMD0000000550]
analyses bifurcation and describes different pathological states by
altering inflammatory regulation parameters.
The second model
[BIOMD0000000549]
includes the effect that ageing has on pro-inflammatory signalling,
allowing for time-dependant properties and disease progression to
be observed. The author also describes potential dosing for
reversal of the disease state.
This model is described in the article:
Mathematical modelling of
cytokine-mediated inflammation in rheumatoid arthritis.
Baker M, Denman-Johnson S, Brook BS,
Gaywood I, Owen MR.
Math Med Biol 2013 Dec; 30(4):
311-337
Abstract:
Rheumatoid arthritis (RA) is a chronic inflammatory disease
preferentially affecting the joints and leading, if untreated,
to progressive joint damage and disability. Cytokines, a group
of small inducible proteins, which act as intercellular
messengers, are key regulators of the inflammation that
characterizes RA. They can be classified into pro-inflammatory
and anti-inflammatory groups. Numerous cytokines have been
implicated in the regulation of RA with complex up and down
regulatory interactions. This paper considers a two-variable
model for the interactions between pro-inflammatory and
anti-inflammatory cytokines, and demonstrates that mathematical
modelling may be used to investigate the involvement of
cytokines in the disease process. The model displays a range of
possible behaviours, such as bistability and oscillations,
which are strongly reminiscent of the behaviour of RA e.g.
genetic susceptibility and remitting-relapsing disease. We also
show that the dose regimen as well as the dose level are
important factors in RA treatments.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000550.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000550 | BioModels
Project description:To investigate the pro-inflammatory and metabolic function of Rheumatoid Arthritis monocyte derived macrophages RNA sequencing was perfomed on polarised healthy and Rheumatoid Arthritis monocyte-derived macrophages
2023-01-20 | GSE223325 | GEO
Project description:Baker2013 - Cytokine Mediated Inflammation in
Rheumatoid Arthritis - Age Dependant
This model by Baker M. 2013, describes
the interaction between pro and anti-inflammatory cytokine
signalling in rheumatoid arthritis.
Using two ordinary differential equations, the first model
[BIOMD0000000550]
analyses bifurcation and describes different pathological states by
altering inflammatory regulation parameters.
The second model
[BIOMD0000000549]
includes the effect that ageing has on pro-inflammatory signalling,
allowing for time-dependant properties and disease progression to
be observed. The author also describes potential dosing for
reversal of the disease state.
This model is described in the article:
Mathematical modelling of
cytokine-mediated inflammation in rheumatoid arthritis.
Baker M, Denman-Johnson S, Brook BS,
Gaywood I, Owen MR.
Math Med Biol 2013 Dec; 30(4):
311-337
Abstract:
Rheumatoid arthritis (RA) is a chronic inflammatory disease
preferentially affecting the joints and leading, if untreated,
to progressive joint damage and disability. Cytokines, a group
of small inducible proteins, which act as intercellular
messengers, are key regulators of the inflammation that
characterizes RA. They can be classified into pro-inflammatory
and anti-inflammatory groups. Numerous cytokines have been
implicated in the regulation of RA with complex up and down
regulatory interactions. This paper considers a two-variable
model for the interactions between pro-inflammatory and
anti-inflammatory cytokines, and demonstrates that mathematical
modelling may be used to investigate the involvement of
cytokines in the disease process. The model displays a range of
possible behaviours, such as bistability and oscillations,
which are strongly reminiscent of the behaviour of RA e.g.
genetic susceptibility and remitting-relapsing disease. We also
show that the dose regimen as well as the dose level are
important factors in RA treatments.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000549.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000549 | BioModels
Project description:Rheumatoid arthritis is an autoimmune inflammatory joint condition which primarily affects the synovium of joints, characterised by synovial inflammation as well as articular cartilage and underlying bone destruction. Within this study, the proteomes of serum obtained from rheumatoid arthritis patients, and appropriate human controls, were analysed using liquid chromatography-tandem mass spectrometry. ProteoMiner™ equalisation columns were used to deplete high abundant proteins and reduce the protein concentration dynamic range.
2022-04-04 | PXD020235 | Pride
Project description:Genome-wide DNA methylation level was studied to determine whether Rheumatoid arthritis patients (cases) has methylation differences comparing to normal controls in PBLs. We used Illumina HumanMethylation450 BeadChip array to determine the genome-wide DNA methylation difference in PBLs from Rheumatoid arthritis patients (cases) and normal controls Bisulphite converted DNA from the Rheumatoid arthritis patients (cases) and normal controls were hybridized to the Illumina Illumina HumanMethylation450 BeadChip arrays
2013-01-21 | E-GEOD-42861 | biostudies-arrayexpress
Project description:The transcriptome of PBMC from rheumatoid arthritis patient hasn't been compenhensively profiled, and heterogeneous characteristics of blood monocytes in RA patients are much unknown. We performed the single cell transcriptomic analysis of PBMC from rheumatoid arthritis (RA) patient, and monocyte populations were extracted during the analysis. CD127 expression associated expression pattern of inflammatory genes was identified in RA patient's blood monocytes.
2020-11-10 | GSE159117 | GEO
Project description:Rheumatoid arthritis: aortic biopsies
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