RNA-sequencing of butyrate-treated human lymphoblastoid cell lines shows dysregulated genes of multiple disease-related pathways

Abstract

Abstract Butyrate, a 4-carbon fatty acid produced from insoluble starch by the gut microbiome, plays key roles in mitochondrial respiration, activation of cell-surface G-protein-coupled receptors, and protein acetylation by inhibiting histone deacetylases (HDACs). Butyrate (as sodium salt) added to drinking water was shown to improve pathological symptoms in numerous model mouse disorders, including models for cancer metastasis, neuroinflammation, autism spectrum disorders, dementia, insulin resistance, and colorectal cancer. Over 5000 PubMed-listed studies feature butyrate in their title, yet its genome-wide transcriptomic effects have not been reported in human cell lines from multiple healthy donors. Here, we report the genome-wide transcriptomic effects of 1 mM sodium butyrate on human lymphoblastoid cell lines (LCLs) generated from blood samples of eight unrelated healthy donors. Paired bioinformatics analysis comparing the butyrate-treated LCLs to the same untreated cell line identified thousands of differentially expressed gene (DEG) transcripts with padj<0.05, of which over half were upregulated by butyrate. Pathway analysis showed that butyrate exposure of LCLs upregulated extracellular matrix, cell adhesion, junction organization, Wnt signaling, axonogenesis, and neurodevelopment pathways. Downregulated pathways included cell cycle, G2/M checkpoint, E2F/MYC targets, DNA replication and repair, mitotic spindle integrity, mTOR signaling, oxidative phosphorylation, unfolded-protein response, and translation/ribosome-related pathways. Our RNA-seq study, utilizing LCLs from healthy donors and paired bioinformatic analysis, opens venues for assessing butyrate effects on cellular pathways and potential therapeutics for cancer, metabolic, immune, and CNS-related disorders.