Identification of differentially expressed lncRNAs and candidate ceRNA networks across Mastitis stages in Sahiwal cattle

Along with being a significant disease in dairy cattle which incurs economic loss, mastitis also affects a wide range of parameters that involve milk yield and quality. However, the role of long non-coding RNAs (lncRNAs) in the regulation of mastitis in distinct stages of the disease in Sahiwal cows is yet to be understood. This study characterised lncRNA expression profiles and competing endogenous RNA (ceRNA) networks across healthy, subclinical, and clinical mastitis stages using RNA-Seq data from milk somatic cells. Five biologically relevant ceRNA modules were identified: Five ceRNA modules were identified that are biologically relevant: MSTRG.21615.2, is predicted to sponge bta-miR-760-3p and bta-miR-212, and involved in co-regulation of OAT and SIRT2, leading to dysregulation of urea-cycle and NAD ⁺ -metabolism; MSTRG.19791.1-bta-miR-2382-5p, which activates an extracellular antioxidant network (SOD3, CAT, GPX family, PARK7); MSTRG.1150.15-bta-miR-92b, which regulates the PTEN/PI3K-AKT signalling axis; MSTRG.19363.1-bta-miR-1296, involved in the nuclear import machinery (KPNA7, RCC1, RANBP1, NUP50), with reduced expression in clinical versus subclinical mastitis; and MSTRG.25768.1-bta-miR-2425-5p, linked to extracellular matrix remodelling via the ADAMTS. The binding prediction of all six lncRNA-miRNA pairs were favourable, with the highest predicted affinity observed for MSTRG.1150.15-bta-miR-92b (−15.4 ± 6.9 kcal/mol) and moderate but biologically relevant binding for MSTRG.19363.1-bta-miR-1296 (−7.8 ± 4.2 kcal/mol). Molecular dynamics over 50 ns revealed that the MSTRG.19363.1-bta-miR-1296 complex was the most stable, exhibiting lowest RMSD and radius of gyration values, suggesting that it may be a viable regulator of nuclear transport during the progression of mastitis. These results shed light on the underlying mechanisms of lncRNA-regulated networks associated with dairy cattle mastitis.