Use of nCounter mRNA profiling to identify at-arrival gene expression patterns for predicting bovine respiratory disease in beef cattle
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Author
Scott, M.A.Woolums, A.R.
Swiderski, C.E.
Thompson, A.C.
Perkins, A.D.
Nanduri, B.
Karisch, B.B.
Goehl, D.R.
Affiliation
School of Animal and Comparative Biomedical Sciences, University of ArizonaIssue Date
2022Keywords
Beef cattleBioinformatics
Biomarkers
Bovine respiratory disease
Disease prediction
Gene expression
Host immunology
Infectious disease
mRNA
NanoString
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BioMed Central LtdCitation
Scott, M. A., Woolums, A. R., Swiderski, C. E., Thompson, A. C., Perkins, A. D., Nanduri, B., Karisch, B. B., & Goehl, D. R. (2022). Use of nCounter mRNA profiling to identify at-arrival gene expression patterns for predicting bovine respiratory disease in beef cattle. BMC Veterinary Research.Journal
BMC Veterinary ResearchRights
Copyright © The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License.Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.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. © 2022, The Author(s).Note
Open access journalISSN
1746-6148PubMed ID
35197051Version
Final published versionae974a485f413a2113503eed53cd6c53
10.1186/s12917-022-03178-8
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Except where otherwise noted, this item's license is described as Copyright © The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License.
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