GSE161396
Multipopulational transcriptome analysis of beef cattle at arrival to identify and further validate candidate biomarkers for predicting clinical bovine respiratory disease
Objective: Classify and further validate BRD-associated genes and mechanisms found to be differentially expressed at facility arrival in post-weaned beef cattle from multiple independent populations. Our approach was to profile and compare at-arrival whole blood transcriptomes of post-weaned beef cattle that failed to develop symptoms associated with clinical BRD and cattle that ultimately were diagnosed and treated for clinical BRD within the first 28 days of facility arrival, further stratifying diseased animals into severity cohorts. Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina Novaseq 6000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR with likelihood-ratio testing. Genes were considered differentially expressed with an FDR cutoff of 0.05. Downstream analysis involved PCA, gene ontology term enrichment, pathway analysis, protein-protein interaction networking, and IPA. Results: 132 differentially expressed genes were identified between all three cohorts. Biological processes and pathways primarily involved neutrophilic activity, antimicrobial killing, cell cornification, and inflammatory signaling/regulation. Conlusions: This study corroborated genes and pathways identified in our previous work, while providing novel genes and pathways for future analysis. Overall design: 48 whole blood mRNA samples of stocker cattle at facility arrival were sequenced with an Illumina Novaseq 6000. Disease severity cohorts: "Healthy" animals never showed clinical signs throughout the course of that year's study. "Treated_1" showed clinical signs after arrival and were only treated with injectable antimicrobials. "Treated_2+" showed clinical signs after arrival and were treated more than one time with injectable antimicrobials and/or were euthanized due to clinical decline. The antimicrobials used to treat clinical respiratory disease were florfenicol, ceftiofur, and enrofloxacin.