Analysis of Biobanked Serum from a Mycobacterium avium subsp paratuberculosis Bovine Infection Model Confirms the Remarkable Stability of Circulating miRNA Profiles and Defines a Bovine Serum miRNA Repertoire

Abstract

Johne’s Disease (JD) is a chronic enteritis of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current disease control strategies are hampered by the lack of sensitive and specific diagnostic modalities. Therefore, novel diagnostic and prognostic tools are needed, and circulating microRNAs (miRNAs) may hold potential in this area. The aims of this study were twofold: (i) to address the stability of miRNA in bovine sera from biobanked samples, and (ii) to assess the potential of miRNAs as biomarkers for JD disease progression. To address these aims we used bovine sera from an experimental MAP infection model that had been stored at -20°C for over a decade, allowing us to also assess the stability of miRNA profiles in biobanked serum samples through comparison with fresh sera. Approximately 100–200 intact miRNAs were identified in each sample with 83 of these being consistently detected across all 57 samples. The miRNA profile of the biobanked sera stored at -20°C for over 10 years was highly similar to the profile of <1 year-old sera stored at -80°C, with an overlap of 73 shared miRNAs. IsomiR analysis also indicated a distinct bovine serum-specific isomiR profile as compared to previously reported bovine macrophage miRNA profiles. To explore the prognostic potential of miRNA profiles cattle defined as seropositive for anti-MAP antibodies (n = 5) were compared against seronegative cattle (n = 7). No significant differential expressed miRNAs were detected at either the early (6 months) or late (43, 46 and 49 months) intervals (FDR≤0.05, fold-change≥1.5) across seropositive or seronegative animals. However, comparing pre-infection sera to the early and late time-points identified increased miR-29a and miR-92b abundance (2-fold) that may be due to blood-cell population changes over time (P<0.001). In conclusion our study has demonstrated that bovine circulating miRNAs retain their integrity under long-term sub-optimal storage temperatures opening the way for increased miRNA analyses from biobanked samples for a range of infectious and non-infectious diseases.

Sensitivity and specificity of microRNA‐122 for liver disease in dogs

“…The median time in storage between blood sampling and RNA isolation was 402 days (IQR: 207‐593, n = 250) with 1091 days being the maximum storage time. This is less time in storage compared with published studies that demonstrate miRNA stability when frozen . miRNA was extracted using a miRNeasy Serum/Plasma kit (Qiagen, Venlo, Netherlands) following the manufacturer's instructions.…”

The role of IL-10 in Mycobacterium avium subsp. paratuberculosis infection

“…Recent studies on profiling of miRNAs during clinical and subclinical infection of MAP gave a new perspective to MAP control via miRNA techniques. These studies shown that circulating miRNAs in MAP infected animals retain their integrity under longterm suboptimal storage temperatures and are considered as potential biomarkers [164, 165] that can be exploited for devising the future paratuberculosis control strategies. Apart from miRNAs several compounds such as AS101, SD169 and niclosamide can be used to target IL-10 mediated anti-inflammatory activity.…”

Identification of microRNAs in bovine faeces and their potential as biomarkers of Johne’s Disease

“…Previous studies in MAP infected cattle have measured miRNA expression in serum 8 , whole blood 9 and ileal tissues 10 . We have previously investigated circulating miRNA expression in peripheral blood at silent and subclinical MAP infection stages but detected minimal changes that did not provide diagnostic benefit 11,12 . It may, however, be more rewarding to investigate extracellular miRNAs at a local level, with faeces providing a route to explore miRNA species and abundance in the context of the intestinal immune response.…”