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Series GSE189136 Query DataSets for GSE189136
Status Public on Nov 30, 2021
Title Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: We analyzed RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients and healthy subjects. Our goal was to evaluate the transcriptional profiles of ST2825-treated PBMC to identify its therapeutic potential.
Methods: We analyzed bulk RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients after stimulation with LPS and IL-1β, PBMC were treated with the MyD88 chemical inhibitor, ST2825. Collection of RNA was performed after 24 h of treatment and samples were sequenced to determine transcriptional changes and regulated processes in treated PBMC.
Results: paired-end reads were mapped to the hg19 human genome assembly. RNA levels were normalized using DESeq. We identified 796 differentially expressed (DE) genes by 2-fold change (p<0.05) between RA patients and healthy subjects. Our analysis revealed 631 DE genes between DMARDs-naïve RA patients before and after ST2825 treatment. We identified 471 DE genes between LPS-stimulated RA PBMC and LPS-stimulated RA PBMC treated with ST2825.
Conclusion: Our study provides comprehensive evidence supporting the potential application of the MyD88 inhibitor, ST2825, as a modulator of gene expression signtaures involved in pathogenic processes in PBMC from DMARDs-naïve RA patients. Our indepth analysis of RNA-seq data will serve as a valuable resource containing the inflammatory gene expression signatures by MyD88.
 
Overall design Identification of the potential effect of ST2825 as an inhibitor of MyD88-dependent gene expression signatures to modulate inflammatory processes in RA patients.
 
Contributor(s) Ramirez-Perez S, Bhattaram P
Citation(s) 35002734
Submission date Nov 18, 2021
Last update date Jan 12, 2022
Contact name Sergio Ramirez-Perez
E-mail(s) ser.ramirez_iq@hotmail.com
Organization name Emory University
Department Orthopaedics
Lab Bhattaram Lab
Street address 615 Michael St NE
City Atlanta
State/province Georgia
ZIP/Postal code 30322
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (19)
GSM5694892 PBMC_CS1_UTx
GSM5694893 PBMC_CS4_UTx
GSM5694894 PBMC_RA3_UTx
Relations
BioProject PRJNA781616
SRA SRP346782

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE189136_Normalized_DESeq_matrix.txt.gz 3.2 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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