Absence of the proprotein convertase FURIN in naive CD8+ T cells modifies the transcriptome of the cells

ABSTRACT: Purpose: FURIN is a member of the proprotein convertase subtilisin/kexin (PCSK) family of serine endoproteases important in converting immature proproteins into their functional form. While FURIN is important in various aspects of the immune response such as in CD4+ T cells, FURIN´s role in CD8+ T cells is unclear. Here, we isolated naive CD8+ T cells from conditional T cell specific Furin KO (Cd4-Cre-Furinflox/flox) and WT (Furinflox/flox) mice and studied the genome-wide gene expression pattern using RNA sequencing. Methods: Total RNA was isolated from the naive CD8+ T cells and the RNA-sequencing data was produced by the Finnish Functional Genomics Centre of Turku Bioscience (University of Turku, Turku, Finland) using Illumina HiSeq 2000. Data processing pipeline was built on Snakemake wrappers, and used STAR to quantify features from quality and adapter trimmed reads in gene level. Prior the normalisation and differential gene expression analysis with DESeq2, the matrix of raw gene counts was prefiltered to keep only rows that have at least 10 reads total. Result tables were annotated with biomaRt. Results: Snakemake preprocessing pipeline measured 55573 genes against GRCm38, ENSEMBL release 97. 15843 of them was used for statistical testing. Full result tables for each treatment were ranked by p-value and the normalized DESeq2 abundances in samples were included. The genes with BH-adjusted p-value <0.05 was considered differentially expressed. Conclusions: Our study revealed that the abscence of FURIN from the naive CD8+ T cells causes an effector-like phenotype in comparison to the WT cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE186812 | GEO | 2023/04/28

REPOSITORIES: GEO