Differential microRNA expression in jejunal tissue and jejunal lymph nodes following naturally occurring Mycobacterium avium subspecies paratuberculosis infection in Holstein cows

Abstract Mycobacterium avium subsp. Paratuberculosis (MAP) is the causal agent of Johne’s disease (JD), a chronic intestinal disease affecting ruminants worldwide. This study investigated miRNA expression in jejunal intestine (JE) and jejunal lymph nodes (JELN), and the potential regulatory roles of miRNAs during JD progression. JE and JELN tissues were collected from 5 MAP positive (JD subclinical stage) Holstein cows and 5 MAP negative cows. Following miRNA sequencing, bioinformatic processing with a standard pipeline and functional analysis with ClueGo, 272 and 333 miRNAs were identified in JE and JELN, respectively. Compared with MAP negative cows, 13 and 71 miRNAs were differently expressed (DE) (P < 0.05) in MAP infected JE and JELN, respectively. The most up-regulated and down-regulated miRNAs were bta-miR-485 (fold change = 6.18) and bta-miR-451 (fold change = -6.81), and bta-miR-331-5p (fold change = 35.56) and bta-miR-2285bk (fold change = -61.25) in JE and JELN, respectively. In JE, some DE miRNAs (miR-147 and miR-199a-5p) have been associated with glucose metabolism while several DE miRNAs in JELN have associations with immune response to disease (e.g. miR-146a and miR-146b have been associated with bovine mastitis and miR331-5p and miR-184 are important for human cancers). Target genes of JELN DE miRNAs were enriched (P < 0.05) for more gene ontology terms (n = 180) and KEGG pathways (n = 123) as compared with JE (n = 90 and 25, respectively). Furthermore, JELN DE miRNAs were uniquely enriched in several immune related pathways including immune response regulating/activating signal transduction, T-cell/B-cell receptor signaling, Toll-like receptor signaling, TNF signaling pathways, etc., suggesting potential regulatory roles for JELN DE miRNAs in the host immune response to JD. In addition, interactions between DE miRNAs and DE mRNAs (expressed in the same samples) demonstrated important functions for miR-2284/2285 family members in JELN response to MAP infection. In conclusion, these results suggest site specific regulatory roles for miRNAs during MAP infection.