Skin transcriptome revealed key cellular functions affected by digital dermatitis in lactating dairy cows

Bovine digital dermatitis (DD) is a complex multibacterial disease that is a major cause of lameness in cattle. In this study, skin tissue biopsies from the center of active (M2/M4.1) DD lesions or non-active (M0/ M4/M1) skin of multiparous Holstein dairy cows (n = 7/group) were performed to assess the impact of DD on the skin transcriptome via RNA-seq analysis. The skin biopsies were performed using a sterile biopsy punch, and the RNA samples were sequenced using Illumina, NovaSeq S4 at the University of Minnesota Genomics Center. Principal component analysis (PCA) and the differentially expressed (DE) genes based on the comparison of DD over non-active cows (NA) were cal- culated using the DESeq2 package in R. The final DE were 4,769 and 4,463 genes upregulated and downregulated, respectively. To further investigate the biological function of the DE genes (FDR \u3c0.05) with at least ± 2-fold change were retained for an enrichment pathway analysis using gene ontology (GO) terms and the enrichGO function in the Clus- terprofiler package in R. The FDR cut-off value was set to \u3c0.01. The PCA analysis clearly discriminated the skin transcriptome between DD cows and NA. Genes coding for several keratins-associated proteins, including KRT34, KRTAP21–1, and KRTAP4–9 were downregulated in DD cows. The GO terms associated with downregulated genes in the Cellular Component category were mainly correlated with collagen- containing extracellular matrix and keratin filament, while GO terms in the Biological Process category were related to humoral immune response and biomineral tissue development. Upregulated genes were highly enriched in the Molecular Function GO terms of cell adhesion and skin development as well as intermediate filament cytoskeleton in the Cellular Component category. Overall, this skin transcriptome evalu- ation comparing NA and DD cows identified key biological pathways in which there was a dysregulation in the skin extracellular matrix, encompassing the keratinization process, collagen binding, and immune response caused by DD lesions. This transcriptomic data set captures the molecular adaptations in the development of bovine DD, which can be further utilized to target suitable management and nutritional strategies to reduce this infectious disease