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Multibacillary lesions are composed largely of infected epithelioid macrophages and paucibacillary lesions contain T cells but few bacteria. Multibacillary disease is similar to human lepromatous leprosy, with variable\/high levels of antibody and a dysfunctional immune response. Animals with paucibacillary disease have high cell-mediated immunity and variable levels of antibody. This study aims to characterize the immunological dysfunction using TruSeq analysis of the ileocaecal lymph node that drains disease lesions. Immune dysfunction is highlighted by repression of<jats:italic>TCR<\/jats:italic>\/<jats:italic>CD3<\/jats:italic>genes, T cell co-receptors\/co-stimulators, T cell activation and signal-transduction genes. Inflammation was an acute phase response and chronic inflammation, with little evidence of acute inflammation. The high levels of immunoglobulin and plasma cell transcripts is consistent with the anti-MAP antibody responses in paratuberculosis sheep. Also notable was the overwhelming reduction in mast cell transcripts, potentially affecting DC activation of the immune response. This study also shows that there were no fundamental differences in the gene expression patterns in multibacillary and paucibacillary disease, no shift in T cell genes from Th1 to Th2 pattern but rather an incremental decline into immune dysfunction leading to multibacillary pathology.<\/jats:p>","DOI":"10.1038\/srep46695","type":"journal-article","created":{"date-parts":[[2017,4,24]],"date-time":"2017-04-24T09:44:20Z","timestamp":1493027060000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Pathways and Genes Associated with Immune Dysfunction in Sheep Paratuberculosis"],"prefix":"10.1038","volume":"7","author":[{"given":"Anton","family":"Gossner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig","family":"Watkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Chianini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Hopkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,4,24]]},"reference":[{"key":"BFsrep46695_CR1","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1128\/CMR.14.3.489-512.2001","volume":"14","author":"NB Harris","year":"2001","unstructured":"Harris, N. 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