Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition

Lee, Seung-Woo; Hwang, Seungwoo; Yu, Hee Jeong; Oh, Dayoung; Choi, Yu Jung; Kim, Myungchul; Kim, Yongbaek; Ryu, Doug-Young

doi:10.1371/journal.pone.0146374

Cited by 17 publications

(26 citation statements)

References 38 publications

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“…The high-confidence novel miRNAs were combined with the known equine miRNAs from miRBase and expression profiling followed by differential expression analysis was performed. In agreement with previous reports of plasma expressed miRNAs in horses, one of the top expressed miRNAs across all samples was eca-miR-486-5p [ 65 ].…”

Section: Discussionsupporting

confidence: 91%

Differential Expression of Serum MicroRNAs Supports CD4+ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma

Pacholewska

Kraft

Gerber

et al. 2017

Genes

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MicroRNAs (miRNAs) regulate post-transcriptional gene expression and may be exported from cells via exosomes or in partnership with RNA-binding proteins. MiRNAs in body fluids can act in a hormone-like manner and play important roles in disease initiation and progression. Hence, miRNAs are promising candidates as biomarkers. To identify serum miRNA biomarkers in the equine model of asthma we investigated small RNA derived from the serum of 34 control and 37 asthmatic horses. These samples were used for next generation sequencing, novel miRNA identification and differential miRNA expression analysis. We identified 11 significantly differentially expressed miRNAs between case and control horses: eca-miR-128, eca-miR-744, eca-miR-197, eca-miR-103, eca-miR-107a, eca-miR-30d, eca-miR-140-3p, eca-miR-7, eca-miR-361-3p, eca-miR-148b-3p and eca-miR-215. Pathway enrichment using experimentally validated target genes of the human homologous miRNAs showed a significant enrichment in the regulation of epithelial-to-mesenchymal transition (key player in airway remodeling in asthma) and the phosphatidylinositol (3,4,5)-triphosphate (PIP3) signaling pathway (modulator of CD4+ T cell maturation and function). Downregulated miR-128 and miR-744 supports a Th2/Th17 type immune response in severe equine asthma.

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Section: Discussionsupporting

confidence: 91%

Differential Expression of Serum MicroRNAs Supports CD4+ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma

Pacholewska

Kraft

Gerber

et al. 2017

Genes

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“…Interestingly two of them were not expressed (at >10 cpm level) in either cartilage or bone, but in blood (Additional file 3: Table S2 and Additional file 4: Table S3). From five most abundantly expressed novel putative miRNA reported in equine plasma by Lee et al [37], only one miRNA was identified in our study in bone and blood tissues with a mature sequenced shorter by three nucleotides from 5’ end. From the 329 novel miRNAs reported by Kim et al [9] only 11 had exactly the same mature sequence as novel miRNAs reported here.…”

Section: Discussionmentioning

confidence: 63%

Novel equine tissue miRNAs and breed-related miRNA expressed in serum

et al. 2016

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BackgroundMiRNAs regulate multiple genes at the post-transcriptional level and therefore play an important role in many biological processes. It has been suggested that miRNA exported outside the cells contribute to inter-cellular communication. Consequently, circulating miRNAs are of particular interest and are promising biomarkers for many diseases. The number of miRNAs annotated in the horse genome is much lower compared to model organisms like human and mouse. We therefore aimed to identify novel equine miRNAs for tissue types and breed in serum.ResultsWe analysed 71 small RNA-seq libraries derived from nine tissues (gluteus medius, platysma, masseter muscle, heart, liver, cartilage, bone, total blood and serum) using miRDeep2 and miRdentify tools. Known miRNAs represented between 2.3 and 62.9 % of the reads in 71 libraries. A total of 683 novel miRNAs were identified. Breed and tissue type affected the number of miRNAs detected and interestingly, affected its average intensity. A total of 50 miRNAs in serum proved to be potential biomarkers to differentiate specific breed types, of which miR-122, miR-200, miR-483 were over-expressed and miR-328 was under-expressed in ponies compared to Warmbloods. The different miRNAs profiles, as well as the differences in their expression levels provide a foundation for more hypotheses based on the novel miRNAs discovered.ConclusionsWe identified 683 novel equine miRNAs expressed in seven solid tissues, blood and serum. Additionally, our approach evidenced that such data supported identification of specific miRNAs as markers of functions related to breeds or disease tissues.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3168-2) contains supplementary material, which is available to authorized users.

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“…From a confirmative viewpoint, these findings are similar to those reported for human SEs (34), suggesting that these miRNAs can be involved in similar modulatory processes in both species. Furthermore, the let-7 family of miRNAs as well as mir-21 are highly abundant in equine serum and plasma and also expressed in diverse tissue types (59,(75)(76)(77)(78)(79)(80). Validation of the miRNA sequencing data by RT-qPCR confirmed specific downregulation of eca-mir-128 in long-term persistently infected stallions, an intronic miRNA encoded by two distinct genes, eca-mir-128-1 and eca-mir-128-2, located on (81).…”

Section: Discussionmentioning

confidence: 82%

Downregulation of MicroRNA eca-mir-128 in Seminal Exosomes and Enhanced Expression of CXCL16 in the Stallion Reproductive Tract Are Associated with Long-Term Persistence of Equine Arteritis Virus

Carossino

Dini

Kalbfleisch

et al. 2018

J Virol

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Equine arteritis virus (EAV) can establish long-term persistent infection in the reproductive tract of stallions and is shed in the semen. Previous studies showed that long-term persistence is associated with a specific allele of the gene () and that persistent infection is maintained despite the presence of a local inflammatory and humoral and mucosal antibody responses. In this study, we demonstrated that equine seminal exosomes (SEs) are enriched in a small subset of microRNAs (miRNAs). Most importantly, we demonstrated that long-term EAV persistence is associated with the downregulation of an SE-associated miRNA (eca-mir-128) and with an enhanced expression of CXCL16 in the reproductive tract, a putative target of eca-mir-128. The findings presented here suggest that SE eca-mir-128 is implicated in the regulation of the CXCL16/CXCR6 axis in the reproductive tract of persistently infected stallions, a chemokine axis strongly implicated in EAV persistence. This is a novel finding and warrants further investigation to identify its specific mechanism in modulating the CXCL16/CXCR6 axis in the reproductive tract of the EAV long-term carrier stallion. Equine arteritis virus (EAV) has the ability to establish long-term persistent infection in the stallion reproductive tract and to be shed in semen, which jeopardizes its worldwide control. Currently, the molecular mechanisms of viral persistence are being unraveled, and these are essential for the development of effective therapeutics to eliminate persistent infection. Recently, it has been determined that long-term persistence is associated with a specific allele of the gene () and is maintained despite induction of local inflammatory, humoral, and mucosal antibody responses. This study demonstrated that long-term persistence is associated with the downregulation of seminal exosome miRNA eca-mir-128 and enhanced expression of its putative target, CXCL16, in the reproductive tract. For the first time, this study suggests complex interactions between eca-mir-128 and cellular elements at the site of EAV persistence and implicates this miRNA in the regulation of the CXCL16/CXCR6 axis in the reproductive tract during long-term persistence.

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Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition

Cited by 17 publications

References 38 publications

Differential Expression of Serum MicroRNAs Supports CD4+ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma

Differential Expression of Serum MicroRNAs Supports CD4+ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma

Novel equine tissue miRNAs and breed-related miRNA expressed in serum

Downregulation of MicroRNA eca-mir-128 in Seminal Exosomes and Enhanced Expression of CXCL16 in the Stallion Reproductive Tract Are Associated with Long-Term Persistence of Equine Arteritis Virus

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