Abstract
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) that affects cervid species throughout North America. We evaluated gene expression in white‐tailed deer collected by Illinois Department of Natural Resource wildlife managers during annual population reduction (e.g., sharpshooting) and disease monitoring efforts throughout the CWD‐endemic area of northcentral Illinois. We conducted comparative transcriptomic analysis of liver and retropharyngeal lymph node tissue samples between CWD‐positive (n = 5) and CWD‐not detected (n = 5) deer. A total of 74,479 transcripts were assembled, and 51,661 (69.36%) transcripts were found to have matched proteins in NCBI‐NR and UniProt. Our analysis of functional categories showed 40,308 transcripts were assigned to at least one Gene Ontology term and 37,853 transcripts were involved in at least one pathway. We identified a total of 59 differentially expressed genes (DEGs) in CWD‐positive deer, of which 36 and 23 were associated with liver and retropharyngeal lymph node tissues, respectively. Functions of DEGs lend support to previous relationships between misfolded PrP and cellular membranes (e.g., STXBP5), and internal cellular components. We identified several genes that suggest a link between CWD and retroviruses and identified the gene ADIPOQ that acts as a tumor necrosis factor (TNF) antagonist. This gene may lead to reduced production of TNF and impact disease progression and clinical symptoms associated with CWD (i.e., wasting syndrome). Use of candidate genes identified in this study suggests the activation of endogenous processes in CWD‐positive deer, which in turn may enable earlier detection of the disease.
Highlights
The resulting data matrix that contained FPKM expression values for liver and retropharyngeal lymph node tissues of each individual was generated by “rsem‐generate‐data‐matrix” script. This data matrix with FPKM values was imported into edgeR 2.14 (Robinson, McCarthy, & Smyth, 2010) to create a pairwise com‐ parison between Chronic wasting disease (CWD)‐positive and CWD‐ND deer, and identify dif‐ ferentially expressed genes (DEGs) with fold change > 22 and a p‐ value < .001 for false discovery rate
Several differentially expressed genes identified in our study (i.e., ADIPOQ, CCL3; Table 3) are related to tumor necrosis factor (TNF), a cytokine that produces an immune response to help prevent the spread of infection
TA B L E 5 Gene ontology (GO) classifications for differentially expressed genes (DEGs) in liver (LV) and retropharyngeal lymph node (RPLN) tissue of chronic wasting disease‐positive white‐tailed deer collected in the chronic wasting disease‐endemic area of northern Illinois during annual population reduction, winter 2015 may have down‐regulated TNF production at the time of sampling
Summary
From January to March 2015, liver, obex, and retropharyngeal lymph node samples were collected from 380 free‐ranging adult The resulting data matrix that contained FPKM expression values for liver and retropharyngeal lymph node tissues of each individual was generated by “rsem‐generate‐data‐matrix” script This data matrix with FPKM values was imported into edgeR 2.14 (Robinson, McCarthy, & Smyth, 2010) to create a pairwise com‐ parison between CWD‐positive and CWD‐ND deer, and identify dif‐ ferentially expressed genes (DEGs) with fold change > 22 (log fold change = log 2 [CWD‐positive FPKM/CWD‐ND FPKM]) and a p‐ value < .001 for false discovery rate. TA B L E 2 Number of Gene Ontology (GO) analysis identified white‐tailed deer transcripts with a cutoff E‐value of
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