Use of nCounter mRNA profiling to identify at-arrival gene expression patterns for predicting bovine respiratory disease in beef cattle

Abstract

Background Transcriptomics has identified at-arrival differentially expressed genes associated with bovine respiratory disease (BRD) development; however, their use as prediction molecules necessitates further evaluation. Therefore, we aimed to selectively analyze and corroborate at-arrival mRNA expression from multiple independent populations of beef cattle. In a nested case-control study, we evaluated the expression of 56 mRNA molecules from at-arrival blood samples of 234 cattle across seven populations via NanoString nCounter gene expression profiling. Analysis of mRNA was performed with nSolver Advanced Analysis software (p < 0.05), comparing cattle groups based on the diagnosis of clinical BRD within 28 days of facility arrival (n = 115 Healthy; n = 119 BRD); BRD was further stratified for severity based on frequency of treatment and/or mortality (Treated_1, n = 89; Treated_2+, n = 30). Gene expression homogeneity of variance, receiver operator characteristic (ROC) curve, and decision tree analyses were performed between severity cohorts. Results Increased expression of mRNAs involved in specialized pro-resolving mediator synthesis (ALOX15, HPGD), leukocyte differentiation (LOC100297044, GCSAML, KLF17), and antimicrobial peptide production (CATHL3, GZMB, LTF) were identified in Healthy cattle. BRD cattle possessed increased expression of CFB, and mRNA related to granulocytic processes (DSG1, LRG1, MCF2L) and type-I interferon activity (HERC6, IFI6, ISG15, MX1). Healthy and Treated_1 cattle were similar in terms of gene expression, while Treated_2+ cattle were the most distinct. ROC cutoffs were used to generate an at-arrival treatment decision tree, which classified 90% of Treated_2+ individuals. Conclusions Increased expression of complement factor B, pro-inflammatory, and type I interferon-associated mRNA hallmark the at-arrival expression patterns of cattle that develop severe clinical BRD. Here, we corroborate at-arrival mRNA markers identified in previous transcriptome studies and generate a prediction model to be evaluated in future studies. Further research is necessary to evaluate these expression patterns in a prospective manner.

Influence of the At-Arrival Host Transcriptome on Bovine Respiratory Disease Incidence during Backgrounding

“…Furthermore, approximately 40% (32/81) of cattle entering this 45-day backgrounding period were subsequently diagnosed with BRD. While this relatively high rate of BRD is not uncommon in commercial beef production systems, the overall frequency of BRD treatment for this population is higher than cattle populations, especially those of the relatively same age and weight, as shown in our previous work [ 38 , 41 , 64 ]. Potentially, these cattle, having been maintained and transported from a single-source, relatively low-risk environment, were exposed to pathological and environmental features novel to them, and/or our detection of clinical BRD was more rigorous compared to large commercial operations.…”

“…While a limitation of this study is the lack of respiratory metagenomic or viral identity information, our findings suggest that these cattle, only having been placed in a commercial auction setting for a relatively short period of time, were exposed and immunologically responded to a virulent virus or viruses [ 17 , 60 , 61 , 62 , 63 ]. Interestingly, these antiviral-related gene expression signatures were not necessarily associated with clinical BRD development and severity during backgrounding, as seen in previous RNA-Seq studies [ 39 , 42 , 45 , 64 ]. Future studies should pair RNA-Seq with host genetic and/or epigenetic evaluation and pathogen or microbiome identification methods to more clearly associate pathogen exposure and regulation with regards to these DEGs.…”

Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

“…Genetic variations in BOLA-DQA2, a Bovine Leukocyte Antigen (BOLA) class II gene, have been associated with resistance to dairy cow mastitis [ 80 ]. MGC126945, an uncharacterized protein, was found as highly variable in bovine respiratory disease [ 81 ].…”

Hematological and gene co-expression network analyses of high-risk beef cattle defines immunological mechanisms and biological complexes involved in bovine respiratory disease and weight gain

“…Based on our previous work, it can be inferred that host gene expression captured at facility arrival is variable across BRD severity cohorts [ 20 , 40 , 41 ]. Therefore, we assessed whether the at-arrival co-expression patterns and modules found in this study were well preserved across an RNA-Seq data set from an independent population of cattle.…”

“…Hub gene identification analysis included co-expressed genes from the following modules: violet (54), orange (68), royalblue (100), mediumpurple3 (41), and steelblue (59). The k ME and GS value cutoffs within each module resulted in 24, 46, 30, 22, and 32 BRD-associated hub genes from the violet, orange, royalblue, mediumpurple3, and steelblue modules, respectively (S5 Table ).…”