Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus
Date
2021-04-22
Journal Title
Journal ISSN
Volume Title
Publisher
Frontiers Media
Abstract
Bovine respiratory disease (BRD) causes substantial morbidity and mortality, affecting
cattle of all ages. One of the main causes of BRD is an initial inflammatory response
to bovine respiratory syncytial virus (BRSV). MicroRNAs are novel and emerging noncoding
small RNAs that regulate many biological processes and are implicated in
various inflammatory diseases. The objective of the present study was to elucidate
the changes in the bovine bronchial lymph node miRNA transcriptome in response
to BRSV following an experimental viral challenge. Holstein-Friesian calves were either
administered a challenge dose of BRSV (103:5 TCID50/ml 15 ml) (n = 12) or were
mock inoculated with sterile phosphate buffered saline (n = 6). Daily scoring of clinical
signs was performed and calves were euthanized at day 7 post-challenge. Bronchial
lymph nodes were collected for subsequent RNA extraction and sequencing (75 bp).
Read counts for known miRNAs were generated using the miRDeep2 package using
the UMD3.1 reference genome and the bovine mature miRNA sequences from the
miRBase database (release 22). EdgeR was used for differential expression analysis
and Targetscan was used to identify target genes for the differentially expressed (DE)
miRNAs. Target genes were examined for enriched pathways and gene ontologies using
Ingenuity Pathway Analysis (Qiagen). Multi-dimensional scaling (MDS) based on miRNA
gene expression changes, revealed a clearly defined separation between the BRSV
challenged and control calves, although the clinical manifestation of disease was only
mild. One hundred and nineteen DE miRNAs (P < 0.05, FDR < 0.1, fold change > 1.5)
were detected between the BRSV challenged and control calves. The DE miRNAs
were predicted to target 465 genes which were previously found to be DE in bronchial
lymph node tissue, between these BRSV challenged and control calves. Of the DE
predicted target genes, 455 had fold changes that were inverse to the corresponding
DE miRNAs. There were eight enriched pathways among the DE predicted target genes
with inverse fold changes to their corresponding DE miRNA including: granulocyte
and agranulocyte adhesion and diapedesis, interferon signalling and role of pathogen recognition receptors in recognition of bacteria and viruses. Functions predicted to be
increased included: T cell response, apoptosis of leukocytes, immune response of cells
and stimulation of cells. Pathogen recognition and proliferation of cytotoxic T cells are
vital for the recognition of the virus and its subsequent elimination.
Description
Publication history: Accepted - 19 March 2021; Published - 22 April 2021.
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Article
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Keywords
miRNA, small RNA-Seq, dairy calves, pneumonia, bovine respiratory disease, BRSV challenge
Citation
Johnston, D., Earley, B., McCabe, M. S., Kim, J., Taylor, J. F., Lemon, K., McMenamy, M., Duffy, C., Cosby, S. L. and Waters, S. M. (2021) ‘Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus’, Frontiers in Genetics. Frontiers Media SA, 12. doi: 10.3389/fgene.2021.633125.