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Cell-intrinsic Innate Immune Responses against Chikungunya Virus in a Human Ex Vivo Synovial Fibroblast Model [scRNA-seq]

ABSTRACT: Single-cell RNAseq dataset on CHIKV-infected fibroblasts. Overall conclusions: Strong induction of innate immune responses, depending on the amount of viral RNA in the cells we found an antagonism against transcription factors such as STAT1 and JAK1.

ORGANISM(S): Homo sapiens

PROVIDER: GSE176361 | GEO | 2021/06/09

REPOSITORIES: GEO

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Cell-intrinsic Innate Immune Responses against Chikungunya Virus in a Human Ex Vivo Synovial Fibroblast Model

Project description:Purpose: Human primary synovial fibroblasts extracted from the knee were established as an ex vivo infection model for Chikungunya Virus. The cell-intrinsic immune response was determined using RNA-seq of infected and uninfected fibroblasts from healthy donors and donors with an osteoarthritic background. Methods: Fibroblasts of four osteoarthritic and two healthy donors were infected with CHIKV strain LR2006-OPY at an MOI of 10 in the presence or absence of the CHIKV neutralizing antibody C9 and total RNA was extracted at 24 hours post infection. Deep sequencing with paired-end reads was performed using an Illumina platform and data was analyzed with CLC Genomics Workbench 12 (QIAGEN) by mapping the human reads onto the hg19 reference genome scaffold (GCA_000001405.28). Unmapped reads not matching the human genome were subsequently mapped onto the CHIKV genome LR2006_OPY (DQ443544.2). Results: For osteoartritic fibroblasts ~25-35 Mio reads per sample, for healthy donor fibroblasts ~50-60 Mio reads per sample were achieved. Analysis revealed no major differences in the resting or infection-induced transcriptome (R2 = 0.9085 and 0.9086, respectively), yet some non-inflammation related pathways were significantly different regulated as determined by Gene Ontology analysis. Conclusion: Osteoarthritic fibroblasts were found to be an accessible source of primary cells suitable for studying CHIKV infection and pathophysiology. The cells did not majorly differ from the rarely avaiblabe healthy donor fibroblasts on the transcriptomic level, and did not show signs of pre-activation or inflammation in the absence of infection.

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