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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #400434

Research Project: Intestinal Microbial Ecology and Non-Antibiotic Strategies to Limit Shiga Toxin-Producing Escherichia coli (STEC) and Antimicrobial Resistance Transmission in Food Animals

Location: Food Safety and Enteric Pathogens Research

Title: 3’mRNA-Seq analysis of the effects of weaning and influenza infection on gene expression in whole blood of pigs

item MEEKS, CARRIE - Iowa State University
item TUGGLE, CHRISTOPHER - Iowa State University
item KAPOOR, MUSKAN - Iowa State University
item KRAMER, LUKE - Iowa State University
item Byrne, Kristen
item LIM, KYU-SANG - Kongiu National University
item DEKKERS, JACK - Iowa State University
item Loving, Crystal

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Advantages of whole blood (WB) in transcriptomic studies include simplicity of collecting and frequent sampling of the same individual, and whole blood transcriptomics has been used to study response to infection and vaccination in pigs. Interpretation of this type of data, however, can result in complexities due to variations in the proportion of cell types among blood samples, both intrinsically as well as due to immune responses, both of which can cause differences in observed gene expression patterns. We utilized RNA from pig WB samples collected under weaning stress and influenza infection to determine the differentially expressed genes (DEGs) and their functions through 3’mRNA-seq analysis using DESeq2 . No significant DEGs were detected between day 1 post-wean and 4 days prior to weaning, indicating that WB RNA may not be ideal for evaluating the effect of weaning stress on gene expression. Nine days post-influenza infection compared to day 0 predicted 884 DEGs; 736 and 148 genes were found to be increased or decreased in expression, respectively. Gene ontology analysis identified 146 of the increased expression genes as expressed in hematopoietic cells. Gene set enrichment analysis showed the MIR7_1_3P pathway to be enriched in DEGs that showed increased expression. Future work will include using flow cytometry data to estimate cell type proportions and determine what fraction of this differential RNA abundance is due to transcriptional differences in specific cell populations.