GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE334nnn/GSE334132/primaryOK200TranscriptomicsBos taurusExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE334132GEOGSEfalseTLR4 governs strain-specific transcriptional responses of bovine mammary epithelial cells challenged by Staphylococcus aureus and its small colony variantStaphylococcus aureus small colony variants (SCVs) are metabolically adapted, slow-growing subpopulations responsible for chronic, recurrent bovine mastitis through enhanced intracellular persistence and immune evasion. The role of Toll-like receptor 4 (TLR4) in regulating bovine mammary epithelial transcriptional responses to S. aureus SCV challenge remains poorly understood. Using CRISPR-Cas9-generated TLR4-knockout (TLR4-KO) MAC-T cells combined with RNA sequencing, global transcriptional responses of wild-type (WT) and TLR4-KO MAC-T cells infected with S. aureus SCV Heba3231 and its isogenic parental strain (PS) were compared. The WT cells mounted highly divergent S. aureus strain-specific responses, with only 0.5% overlap in differentially expressed genes between PS and SCV conditions. The PS infection induced apoptotic and HIF-1 signalling pathways, whereas SCV infection promoted lipid metabolic reprogramming, accompanied by suppression of epithelial barrier integrity genes. TLR4 disruption dramatically amplified transcriptional dysregulation, with a 192-fold increase for the PS (1,921 DEGs) and a 6.6-fold increase for SCV (2,279 DEGs) relative to WT infected controls. This revealed a large core set of TLR4-regulated genes with approximately 57% shared across S. aureus strains that govern innate immunity, structural homeostasis, and apoptotic coordination. WFDC2, ITGB3, SH3BGRL, and HKDC1 emerged as novel TLR4-dependent candidate genes. Collectively, these findings identify TLR4 as a key determinant of strain-specific transcriptional discrimination and epithelial homeostasis during S. aureus infection, with particular relevance to SCV-mediated persistence in bovine mastitis.2026/06/08GSE334132GSM9781691GSM9781692GSM9781690GSM9781695GSM9781696GSM9781693GSM9781694GSM9781699GSM9781688GSM9781689GSM9781700GSM9781697GSM9781698GSM9781701GSM978170235707334132Bos taurus