The Transcriptome of Equine Peripheral Blood Mononuclear Cells

Pacholewska, Alicja; Drögemüller, Michaela; Klukowska‐Rötzler, Jolanta; Lanz, Simone; Hamza, Eman; Dermitzakis, Emmanouil T.; Marti, Eliane; Gerber, V.; Leeb, Tosso; Jagannathan, Vidhya

doi:10.1371/journal.pone.0122011

Cited by 20 publications

(35 citation statements)

References 50 publications

(44 reference statements)

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“…Using a large RNA-seq dataset generated in the context of previous studies [50, 56], we report here the effect of 24 h in vitro LPS-stimulation on the transcriptome of equine PBMCs and the effect of genetic background on these LPS-induced transcriptomic changes.…”

Section: Introductionmentioning

confidence: 99%

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

et al. 2017

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BackgroundLipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses.Results24 h-LPS challenge of equine immune cells resulted in substantial changes in the transcriptomic profile (1,265 differentially expressed genes) showing partial overlap with human data. One of the half-sib families showed a specific response different from the other two groups of horses. We also identified co-expressed gene modules that clearly differentiated 24 h-LPS- from non-stimulated samples. These modules consisted of 934 highly interconnected genes and included genes involved in the immune response (e.g. IL6, CCL22, CXCL6, CXCL2), however, none of the top ten hub genes of the modules have been annotated as responsive to LPS in gene ontology.ConclusionsUsing weighted gene co-expression network analysis we identified ten co-expressed gene modules significantly regulated by in vitro stimulation with LPS. Apart from 47 genes (5%) all other genes highly interconnected within the most up- and down-regulated modules were also significantly differentially expressed (FDR < 0.05). The LPS-regulated module hub genes have not yet been described as having a role in the immune response to LPS (e.g. VAT1 and TTC25).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3390-y) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

et al. 2017

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“…For example, horse specific miRNA in cartilage and bone have been already reported [10] and the existence of hundreds of horse specific transcripts may suggest the existence of more horse specific miRNAs [11]. Due to their strong sequence conservation, a majority of equine mature miRNAs have been perfectly matched to human miRNAs [4, 12].…”

Section: Introductionmentioning

confidence: 99%

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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“…Peripheral blood mononuclear cells (PBMCs), composed of cells, including lymphocytes, monocytes, and dendritic cells, can be easily obtained from blood and have been used as a tool in nutrition studies [9] and as a common target of immunological studies in animals and humans [10]. In addition, the transcriptome or gene expression analysis in PBMCs can reveal information on the lipid metabolism in obesity-associated organs, adipose tissue, and the liver [11].…”

Section: Introductionmentioning

confidence: 99%

Beneficial Effects of Pterocarpan-High Soybean Leaf Extract on Metabolic Syndrome in Overweight and Obese Korean Subjects: Randomized Controlled Trial

et al. 2016

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Pterocarpans are known to have antifungal and anti-inflammatory properties. However, little is known about the changes in transcriptional profiles in response to a pterocarpan-high soybean leaf extract (PT). Therefore, this study investigated the effects of PT on blood glucose and lipid levels, as well as on the inflammation-related gene expression based on a peripheral blood mononuclear cells (PBMCs) mRNA sequencing analysis in Korean overweight and obese subjects with mild metabolic syndrome. The participants were randomly assigned to two groups and were administered either placebo (starch, 3 g/day) or PT (2 g/day) for 12 weeks. The PT intervention did not change body weight, body fat percentage and body mass index (BMI). However, PT significantly decreased the glycosylated hemoglobin (HbA1c), plasma glucose, free fatty acid, total cholesterol, and non-HDL cholesterol levels after 12 weeks. Furthermore, PT supplementation significantly lowered the homeostatic index of insulin resistance, as well as the plasma levels of inflammatory markers. Finally, the mRNA sequencing analysis revealed that PT downregulated genes related to immune responses. PT supplementation is beneficial for the improvement of metabolic syndrome by altering the fasting blood and plasma glucose, HbA1c, plasma lipid levels and inflammation-related gene expression in PBMCs.

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The Transcriptome of Equine Peripheral Blood Mononuclear Cells

Cited by 20 publications

References 50 publications

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

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

Beneficial Effects of Pterocarpan-High Soybean Leaf Extract on Metabolic Syndrome in Overweight and Obese Korean Subjects: Randomized Controlled Trial

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