The development of Bovine Respiratory Disease (BRD ) in beef cattle is associated with stressful events, including auction and transport. To characterize immunity at the primary site of pathogen colonization in BRD, we evaluated stress responses in lung cells from beef stocker cattle to understand mucosal immune changes. Stocker calves were sampled via bronchoalveolar lavage fluid collection within 24 hours of auction and transport to a new facility (Stressed, n=12), or allowed to acclimate for 2 months at the new facility before sampling (Acclimated, n=7). Lavage cellular RNA was extracted and sequenced for bulk RNA-seq gene expression. The resulting fastq files are included in this repository and named based on the calf’s unique identifier at sampling. The metadata file provides the key to which experimental group each calf belongs, as well as pertinent sequencing metadata values and MD5 sums to ensure file quality. Raw data counts are included in the counts.txt file, and are organized with genes as the row names and calf unique identifiers as the column names. Code files for DESeq2 and CIBERSORTx analysis are included as final analysis code.R and Cibersortx analysis.R. Differential gene expression analysis of RNA sequencing data demonstrated a profound upregulation of inflammatory genes in Stressed calves compared to Acclimated calves, including expression of CXCL8, CSF3R, IL1B, and CCL22. The top pathway upregulation in Stressed calves involved neutrophil migration and chemotaxis, and cytokine signaling. To predict cellular population proportions from the data, CIBERSORTx was used to deconvolute bulk RNA-seq gene counts. This analysis showed that Stressed calves had significantly increased BALF neutrophils compared to Acclimated calves (p =0.003). Neutrophilic infiltration occurred in the absence of pathogen colonization of the lungs in most calves, as demonstrated by a multi-pathogen respiratory qPCR screen. As such, the stress induced an inflammatory response in the lungs not explained by pathogen exposure. This study provides strong evidence that shipping stress in beef stocker calves can paradoxically trigger increased rather than suppressed inflammatory pulmonary mucosal immune responses, which have important implications for the pathogenesis of BRD. All animals were sampled under institutional IACUC approval.
Transport stress induces paradoxical increases in airway inflammatory responses in beef stocker cattle
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