Gene expression profiling of indigenous Tharparkar and crossbred Vrindavani cattle affected with lameness using PBMC model.

Lameness is an economically significant, production-limiting syndrome that adversely affects the (re)production performance of animals besides deteriorating the quantity and quality aspects of milk in dairy cattle. The present study aimed to explore the potential biomarkers for painful foot lesions in indigenous Tharparkar and crossbred Vrindavani cattle affected with lameness. The differentially expressed genes in lame versus healthy animals were elucidated using microarray analysis and validated them by qRT-PCR. On microarray analysis, 504 genes were differentially expressed in lame crossbred cattle as compared to healthy counterparts. Similarly, 991 genes were differentially expressed in lame crossbred cattle as compared to the healthy Tharparkar animals. Various genes such as BOLA-DQA3, BOLA-DQA1, CCL4, CCR1, CCRL2, CXCL2, CXCL3, CXCL8, IL1A, IL1B, MMP-9 and SLC11A1 were common between both the comparisons (crossbred lame vs. crossbred normal cattle; and crossbred lame vs. normal Tharparkar cattle). The results revealed downregulation of multiple pro-inflammatory cytokines. Validation using qRT-PCR showed high correlation with the microarray results, except for the IRAK1 gene. The functional annotation and gene network analysis revealed involvement of various processes including inflammation, immunology, apoptosis, cell proliferation and cytoskeleton organization. The Ingenuity pathway analysis revealed three inhibited pathways in the comparison between lame and normal (healthy) crossbred cattle i.e., HMGB1-signalling pathway, Aryl hydrocarbon receptor signalling pathway, and Mitotic roles of pol-like kinase. Whereas, on comparison of lame crossbred with healthy Tharparkar cattle, the Situin signalling pathway was inhibited; the LxR/RxR activation pathway was activated. The results from microarray analysis, identifying differential expressed genes provides valuable insights into the development of molecular biomarkers for early detection of lameness-affected animals.