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Series GSE267173 Query DataSets for GSE267173
Status Public on May 20, 2024
Title Short-chain fatty acids abrogate Japanese encephalitis virus-induced inflammation in microglial cells via miR200a-3p/ZBTB20/Ikβα axis
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Japanese encephalitis virus (JEV), a member of the Flaviviridae family, is a leading cause of viral encephalitis in humans. Survivors of this infection often develop life-long neurological sequelae. Short-chain fatty acids (SCFAs) produced in the gut are vital mediators of the gut-brain axis. We aimed to study microRNA-based mechanisms of SCFAs in an in vitro model of JEV infection. N9 microglial cells were pre-treated with SCFA cocktail before JEV infection. Cytokine bead analysis (CBA), immunoblotting and PCR were performed to analyse relevant inflammatory markers. microRNA sequencing was performed using Illumina Hiseq and Bioinformatical tools were used for differentially expressed (DE) miRNAs and Weighted gene co-expression network analysis (WGCNA). microRNA mimic/inhibitor experiments and luciferase assay were performed to study miRNA-target interaction. A significant reduction in MCP1 and TNFα along with reduced expression of phospho-NF-κB was observed in SCFA conditions. Significant attenuation of HDAC activity and protein expression was recorded. miRNA sequencing revealed 160 DE miRNAs in SCFA+JEV treated cells at 6 hours post infection (HPI). WGCNA revealed miR-200a-3p, a hub miRNA significantly upregulated in SCFA conditions. Transcription factor ZBTB20 was bioinformatically predicted and validated as a gene target for miR200a-3p. Further miRNA mimic/inhibitor assay demonstrated that miR-200-3p regulated ZBTB20 along with Iκβα that possibly dampened NF-κB signal activation downstream.
Overall design N9 microglial cells were pre-treated with SCFA for 12 hours followed by JEV infection for 6hours and 24 hours. There were 4 groups in both the infection timeline namely, Control, SCFAControl, JEVcontrol, SCFAJEV. Total RNA extraction was performed using phenol chloroform method. Differential expression analysis in all 24 conditions was performed by small RNA sequencing (Illumina) according to the manufacturer's instructions.
Contributor(s) Basu A, Majumdar A, Priya Siva Venkatesh I
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Submission date May 10, 2024
Last update date May 20, 2024
Contact name Anirban Basu
Organization name National Brain Research Centre
Department Cellular and molecular neuroscience
Street address Nainwal Mor, Manesar
City Gurugram
State/province Haryana
ZIP/Postal code 122052
Country India
Platforms (1)
GPL15103 Illumina HiSeq 1000 (Mus musculus)
Samples (24)
GSM8261816 3-1Control6hpi_R1
GSM8261817 3-2-SCFACONTROL6hpi_R1
GSM8261818 3-3JEVControl6hpi_R1
BioProject PRJNA1110163

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE267173_01_Expression_Counts.xlsx 206.2 Kb (ftp)(http) XLSX
GSE267173_02_Normalized_Expression_Counts.xlsx 236.0 Kb (ftp)(http) XLSX
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