Skip to main content
ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #398238

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: Annotating cell transcriptomes in four immune tissues to establish a porcine single-cell Immune Atlas

item TUGGLE, CHRISTOPHER - Iowa State University
item DAHARSH, LANCE - Iowa State University
item SIVASANKARAN, SATHESH - Iowa State University
item Byrne, Kristen
item HERRERA-URIBE, JUBER - Iowa State University
item Loving, Crystal

Submitted to: Conference Research Workers Disease Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 1/20/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: A single cell-level understanding of the porcine immune system will provide tools for improving both disease resistance and use of the pig in biomedical modeling. We performed scRNA-seq on bone marrow, lymph node, spleen, and thymus from healthy adult pigs and sequenced a total of 65,782 cells. After quality control to remove duplicate cells and cells with high mitochondrial content, 50,559 cells and 18,673 genes were used for downstream analysis. Each tissue was individually mapped using non-linear dimensional reduction, and distinct clusters were found and analyzed using the following computational tools: IKAP, ROGUE, pair-wise differential gene expression testing, and random forest models. Using a combination of model defined and canonical immune cell markers, we were able to annotate each cluster as part of a diverse set of immune cell types identified. We used our previously published porcine PBMC scRNA-seq dataset to compare peripheral blood against tissue specific cell types. We were also able to confirm our cell type annotations across shared cell types. We further validated these annotations using publicly available human scRNA-seq datasets specific for each corresponding porcine immune tissue. We compared expression profiles between similarly annotated cell types between human and pig, and identified cells with expression profiles that were unique to pig immune tissues. Finally, we integrated all of the immune tissue data to compare all cell types across the four tissues, and were able to identify shared and tissue specific cell types. Our single cell-level transcriptomic study of immune tissues will be an important resource for improved annotation of porcine immune genes and cell types, including providing information for directed development of immune reagents to distinguish these cell types. These data can be compared to human single cell transcriptomes to inform human translational biomedical research using pigs as a biomedical model.