Bioinformatic analysis of endometrial miRNA expression profile at day 26-28 of pregnancy in the mare

The establishment of the fetomaternal interface depends on precisely regulated communication between the conceptus and the uterine environment. Recent evidence suggests that microRNAs (miRNAs) may play an important role in embryo-maternal dialogue. This study aimed to determine the expression profile of endometrial miRNAs during days 26-28 of equine pregnancy. Additionally, the study aimed to predict target genes for differentially expressed miRNAs (DEmiRs) and their potential role in embryo attachment, adhesion, and implantation. Using next-generation sequencing, we identified 81 DEmiRs between equine endometrium during the pre-attachment period of pregnancy (day 26-28) and endometrium during the mid-luteal phase of the estrous cycle (day 10-12). The identified DEmiRs appear to have a significant role in regulating the expression of genes that influence cell fate and properties, as well as endometrial receptivity formation. These miRNAs include eca-miR-21, eca-miR-126-3p, eca-miR-145, eca-miR-451, eca-miR-491-5p, members of the miR-200 family, and the miRNA-17-92 cluster. The target genes predicted for the identified DEmiRs are associated with ion channel activity and sphingolipid metabolism. Furthermore, it was noted that the expression of mucin 1 and leukemia inhibitory factor, genes potentially regulated by the identified DEmiRs, was up-regulated at day 26-28 of pregnancy. This suggests that miRNAs may play a role in regulating specific genes to create a favorable uterine environment that is necessary for proper attachment, adhesion, and implantation of the embryo in mares.

Changes in miRNA expression in the lungs of pigs supplemented with different levels and forms of vitamin D

BACKGROUND

Vitamin D is an immunomodulator, and its effects have been linked to many diseases, including the pathogenesis of cancer. However, the effect of vitamin D supplementation on the regulation of gene expression of the lungs is not fully understood. This study aims to determine the effect of the increased dose of cholecalciferol and a combination of cholecalciferol + calcidiol, as well as the replacement of cholecalciferol with calcidiol, on the miRNA profile of healthy swine lungs.

METHODS AND RESULTS

The swine were long-term (88 days) supplemented with a standard dose (2000IU/kg) of cholecalciferol and calcidiol, the increased dose (3000 IU/kg) of cholecalciferol, and the cholecalciferol + calcidiol combination: grower: 3000 IU/Kg of vitamin D (67% of cholecalciferol and 33% of calcidiol), finisher 2500 IU/Kg of vitamin D (60% of cholecalciferol and 40% of calcidiol). Swine lung tissue was used for Next Generation Sequencing (NGS) of miRNA. Long-term supplementation with the cholecalciferol + calcidiol combination caused significant changes in the miRNA profile. They embraced altered levels of the expression of miR-150, miR-193, miR-145, miR-574, miR-340, miR-381, miR-148 and miR-96 (q-value < 0.05). In contrast, raising the dose of cholecalciferol only changed the expression of miR-215, and the total replacement of cholecalciferol with calcidiol did not significantly affect the miRNAome profile.

CONCLUSIONS

The functional analysis of differentially expressed miRNAs suggests that the use of the increased dose of the cholecalciferol + calcidiol combination may affect tumorigenesis processes through, inter alia, modulation of gene regulation of the TGF- β pathway and pathways related to metabolism and synthesis of glycan.

Benchmarking of bioinformatics tools for NGS-based microRNA profiling with RT-qPCR method

MicroRNAs are vital gene expression regulators, extensively studied worldwide. The large-scale characterization of miRNAomes is possible using next-generation sequencing (NGS). This technology offers great opportunities, but these cannot be fully exploited without proper and comprehensive bioinformatics analysis. This may be achieved by the use of reliable dedicated software; however, different programs may generate divergent results, leading to additional discrepancies. Thus, the aim of this study was to compare three bioinformatic algorithms dedicated to NGS-based microRNA profiling and validate them using an alternative method, namely RT-qPCR. The comparison analysis revealed differences in the number and sets of identified miRNAs. The qPCR confirmed the expression of the investigated microRNAs. The correlation analysis of NGS and qPCR measurements showed strong and significant coefficients for a subset of the tested miRNAs, including those detected by all three algorithms. Single miRNA variants (isomiRs) showed different levels of correlation with the qPCR data. The obtained results revealed the good performance of all tested programs, despite the observed differences. Moreover, they implied that some specific miRNAs may be differentially estimated using NGS technology and the qPCR method, regardless of the used bioinformatics software. These discrepancies may stem from many factors, including the composition of the isomiR profile, their abundance, length, and investigated species. In conclusion, in this study, we shed light on the bioinformatics aspects of miRNAome profiling, elucidating its complexity and pinpointing potential features influencing validation. Thus, qPCR validation results should be open to interpretation when not fully concordant with NGS results until further, additional analyses are conducted.

Methylome and transcriptome data integration reveals aberrantly regulated genes in equine sarcoids

DNA methylation is a key mechanism in transcription regulation, and aberrant methylation is a common and important mechanism in tumor initiation, maintenance, and progression. To find genes that are aberrantly regulated by altered methylation in horse sarcoids, we used reduced representation bisulfite sequencing (RRBS) accompanied by RNA sequencing (RNA-Seq) for methylome (whole genome DNA methylation sequencing) and transcriptome profiling, respectively. We found that the DNA methylation level was generally lower in lesion samples than in controls. In the analyzed samples, a total of 14,692 differentially methylated sites (DMSs) in the context of CpG (where cytosine and guanine are separated by a phosphate), and 11,712 differentially expressed genes (DEGs) were identified. The integration of the methylome and transcriptome data suggests that aberrant DNA methylation may be involved in the deregulation of expression of the 493 genes in equine sarcoid. Furthermore, enrichment analysis of the genes demonstrated the activation of multiple molecular pathways related to extracellular matrix (ECM), oxidative phosphorylation (OXPHOS), immune response, and disease processes that can be related to tumor progression. The results provide further insight into the epigenetic alterations in equine sarcoids and provide a valuable resource for follow-up studies to identify biomarkers for predicting susceptibility to this common condition in horses.

The potential role of miRNAs and regulation of their expression in the development of mare endometrial fibrosis

Mare endometrial fibrosis (endometrosis), is one of the main causes of equine infertility. Despite the high prevalence, both ethology, pathogenesis and the nature of its progression remain poorly understood. Recent studies have shown that microRNAs (miRNAs) are important regulators in multiple cellular processes and functions under physiological and pathological circumstances. In this article, we reported changes in miRNA expression at different stages of endometrosis and the effect of transforming growth factor (TGF)-β1 on the expression of the most dysregulated miRNAs. We identified 1, 26, and 5 differentially expressed miRNAs (DEmiRs), in categories IIA (mild fibrosis), IIB (moderate fibrosis), and III (severe fibrosis) groups compared to category I (no fibrosis) endometria group, respectively (Padjusted < 0.05, log2FC ≥ 1.0/log2FC ≤  - 1.0). This study indicated the potential involvement of miRNAs in the regulation of the process associated to the development and progression of endometrosis. The functional enrichment analysis revealed, that DEmiRs target genes involved in the mitogen-activated protein kinases, Hippo, and phosphoinositide-3-kinase (PI3K)-Akt signalling pathways, focal adhesion, and extracellular matrix-receptor interaction. Moreover, we demonstrated that the most potent profibrotic cytokine-TGF-β1-downregulated novel-eca-miR-42 (P < 0.05) expression in fibroblasts derived from endometria at early-stage endometrosis (category IIA).

Silver birch pollen-derived microRNAs promote NF-κB-mediated inflammation in human lung cells

The pollen of Betula pendula Roth (silver birch) is considered to be the main cause of allergy-related rhinitis in Europe and its protein-based allergens such as Bet v 1 are well characterized. However, little is known about non-protein components of birch pollen, e.g., small RNAs and their proinflammatory activity. In the present study, next-generation sequencing (NGS) and bioinformatic approaches were used for silver birch pollen (SBP)-derived microRNA profiling and evaluation of microRNA target genes and pathways in human. Human lung cells, namely WI-38 fibroblasts and A549 alveolar epithelial cells were then stimulated with SBP microRNA in vitro and imaging cytometry-based analysis of the levels of proinflammatory cytokines, autophagy parameters and small RNA processing regulators was conducted. Bioinformatic analysis revealed that SBP microRNA may interfere with autophagy, inflammation and allergy pathways in human. SBP and SBP-derived microRNA induced NF-κB-mediated proinflammatory response in human lung cells as judged by increased levels of NF-κB p65, IL-8 and TNFα. NSUN2 and NSUN5 were involved in pollen-derived microRNA processing. Pollen-derived microRNA also modulated autophagic pathway by changes in the pools of LC3B and p62 that may affect autophagy-based adaptive responses during allergic lung inflammation. We postulate that SBP-derived microRNAs can be considered as novel proinflammatory environmental agents.

Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome

MicroRNAs (miRNAs) are recognized as gene expression regulators, indirectly orchestrating a plethora of biological processes. Single nucleotide polymorphism (SNP), one of the most common genetic variations in the genome, is established to affect miRNA functioning and influence complex traits and diseases. SNPs in miRNAs have also been associated with important production traits in livestock. Thus, the aim of our study was to reveal the SNP variability of miRNA genes in the genome of the pig, which is a significant farm animal and large-mammal human model. To this end, we applied the targeted sequencing approach, enabling deep sequencing of specified genomic regions. As a result, 73 SNPs localized in 50 distinct pre-miRNAs were identified. In silico analysis revealed that many of the identified SNPs influenced the structure and energy of the hairpin precursors. Moreover, SNPs localized in the seed regions were shown to alter targeted genes and, as a result, enrich different biological pathways. The obtained results corroborate a significant impact of SNPs on the miRNA processing and broaden the state of knowledge in the field of animal genomics. We also report the targeted sequencing approach to be a promising alternative for the whole genome sequencing in miRNA genes focused studies.

MicroRNA expression profile in bovine mammary gland parenchyma infected by coagulase-positive or coagulase-negative staphylococci

MicroRNAs (miRNAs) are short, non-coding RNAs, 21-23 nucleotides in length which are known to regulate biological processes that greatly impact immune system activity. The aim of the study was to compare the miRNA expression in non-infected (H) mammary gland parenchyma samples with that of glands infected with coagulase-positive staphylococci (CoPS) or coagulase-negative staphylococci (CoNS) using next-generation sequencing. The miRNA profile of the parenchyma was found to change during mastitis, with its profile depending on the type of pathogen. Comparing the CoPS and H groups, 256 known and 260 potentially new miRNAs were identified, including 32 that were differentially expressed (p ≤ 0.05), of which 27 were upregulated and 5 downregulated. Comparing the CoNS and H groups, 242 known and 171 new unique miRNAs were identified: 10 were upregulated (p ≤ 0.05), and 2 downregulated (p ≤ 0.05). In addition, comparing CoPS with H and CoNS with H, 5 Kyoto Encyclopedia of Genes and Genomes pathways were identified; in both comparisons, differentially-expressed miRNAs were associated with the bacterial invasion of epithelial cells and focal adhesion pathways. Four gene ontology terms were identified in each comparison, with 2 being common to both immune system processes and signal transduction. Our results indicate that miRNAs, especially miR-99 and miR-182, play an essential role in the epigenetic regulation of a range of cellular processes, including immunological systems bacterial growth in dendritic cells and disease pathogenesis (miR-99), DNA repair and tumor progression (miR-182).

MicroRNA profiling of the pig periaqueductal grey (PAG) region reveals candidates potentially related to sex-dependent differences

Background

MicroRNAs indirectly orchestrate myriads of essential biological processes. A wide diversity of miRNAs of the neurodevelopmental importance characterizes the brain tissue, which, however, exhibits region-specific miRNA profile differences. One of the most conservative regions of the brain is periaqueductal grey (PAG) playing vital roles in significant functions of this organ, also those observed to be sex-influenced. The domestic pig is an important livestock species but is also believed to be an excellent human model. This is of particular importance for neurological research because of the similarity of pig and human brains as well as difficult access to human samples. However, the pig PAG profile has not been characterized so far. Moreover, molecular bases of sex differences connected with brain functioning, including miRNA expression profiles, have not been fully deciphered yet.

Methods

Thus, in this study, we applied next-generation sequencing to characterize pig PAG expressed microRNAs. Furthermore, we performed differential expression analysis between females and males to identify changes of the miRNA profile and reveal candidates underlying sex-related differences.

Results

As a result, known brain-enriched, and new miRNAs which will expand the available profile, were identified. The downstream analysis revealed 38 miRNAs being differentially expressed (DE) between female and male samples. Subsequent pathway analysis showed that they enrich processes vital for neuron growth and functioning, such as long-term depression and axon guidance. Among the identified sex-influenced miRNAs were also those associated with the PAG physiology and diseases related to this region.

Conclusions

The obtained results broaden the knowledge on the porcine PAG miRNAome, along with its dynamism reflected in different isomiR signatures. Moreover, they indicate possible mechanisms associated with sex-influenced differences mediated via miRNAs in the PAG functioning. They also provide candidate miRNAs for further research concerning, i.e., sex-related bases of physiological and pathological processes occurring in the nervous system.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13293-020-00343-2.

Identification of Molecular Mechanisms Related to Pig Fatness at the Transcriptome and miRNAome Levels

Fat deposition and growth rate are closely related to pork quality and fattening efficiency. The next-generation sequencing (NGS) approach for transcriptome and miRNAome massive parallel sequencing of adipocyte tissue was applied to search for a molecular network related to fat deposition in pigs. Pigs were represented by three breeds (Large White, Pietrain, and Hampshire) that varied in fat content within each breed. The obtained results allowed for the detection of significant enrichment of Gene Ontology (GO) terms and pathways associated directly and indirectly with fat deposition via regulation of fatty acid metabolism, fat cell differentiation, inflammatory response, and extracellular matrix (ECM) organization and disassembly. Moreover, the results showed that adipocyte tissue content strongly affected the expression of leptin and other genes related to a response to excessive feed intake. The findings indicated that modification of genes and miRNAs involved in ECM rearrangements can be essential during fat tissue growth and development in pigs. The identified molecular network within genes and miRNAs that were deregulated depending on the subcutaneous fat level are proposed as candidate factors determining adipogenesis, fatness, and selected fattening characteristics in pigs.

Corn dried distillers grains with solubles (cDDGS) in the diet of pigs change the expression of adipose genes that are potential therapeutic targets in metabolic and cardiovascular diseases

Background

Corn dried distillers grains with solubles (cDDGS) are a byproduct of biofuel and alcohol production. cDDGS have been used in pig feed for many years, because they are readily available and rich in protein, fiber, unsaturated fatty acids and phytosterols. However, feed mixtures too high in cDDGS result in the worsening of backfat quality. We performed RNA-sequencing analysis of backfat from crossbred pigs fed different diets. The diets were isoenergetic but contained different amounts of cDDGS and various sources of fats. The animals were divided into four dietary groups during the two months of experimentation: group I (control (-cDDGS+rapeseed oil)), group II (+cDDGS+rapeseed oil), group III (+cDDGS+beef tallow), and group IV (+cDDGS+coconut oil). The aim of the present experiment was to evaluate changes in the backfat transcriptome of pigs fed isoenergetic diets that differed in cDDGS presence.

Results

Via DESeq2 software, we identified 93 differentially expressed genes (DEGs) between groups I and II, 13 between groups I and III, and 125 between groups I and IV. DEGs identified between group I (-cDDGS+rapeseed oil) and group II (+cDDGS+rapeseed oil) were highly overrepresented in several KEGG pathways: metabolic pathways (FDR < 1.21e-06), oxidative phosphorylation (FDR < 0.00189), fatty acid biosynthesis (FDR < 0.00577), Huntington’s disease (FDR < 0.00577), fatty acid metabolism (FDR < 0.0112), Parkinson’s disease (FDR < 0.0151), non-alcoholic fatty liver disease (NAFLD) (FDR < 0.016), Alzheimer’s disease (FDR < 0.0211) and complement and coagulation cascades (FDR < 0.02).

Conclusions

We observed that the addition of cDDGS positively affects the expression of several genes that have been recently proposed as potential targets for the treatment of obesity, diabetes, cardiovascular disease, and Alzheimer’s disease (e.g., FASN, AACS, ALAS1, HMGCS1, and VSIG4). Thus, our results support the idea of including cDDGS into the diets of companion animals and humans and encourage research into the bioactive ingredients of cDDGS.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5265-x) contains supplementary material, which is available to authorized users.

Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data

Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Pietrain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-β signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs.

Evaluation of changes arising in the pig mesenchymal stromal cells transcriptome following cryopreservation and Trichostatin A treatment

Cryopreservation is an important procedure in maintenance and clinical applications of mesenchymal stem/stromal cells (MSCs). Although the methods of cell freezing using various cryoprotectants are well developed and allow preserving structurally intact living cells, the freezing process can be considered as a severe cellular stress associated with ice formation, osmotic damage, cryoprotectants migration/cytotoxicity or rapid cell shrinkage. The cellular response to freezing stress is aimed at the restoring of homeostasis and repair of cell damage and is crucial for cell viability. In this study we evaluated the changes arising in the pig mesenchymal stromal cell transcriptome following cryopreservation and showed the vast alterations in cell transcriptional activity (5,575 genes with altered expression) suggesting the engagement in post-thawing cell recovery of processes connected with cell membrane tension regulation, membrane damage repair, cell shape maintenance, mitochondria-connected energy homeostasis and apoptosis mediation. We also evaluated the effect of known gene expression stimulator—Trichostain A (TSA) on the frozen/thawed cells transcriptome and showed that TSA is able to counteract to a certain extent transcriptome alterations, however, its specificity and advantages for cell recovery after cryopreservation require further studies.

Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome

Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation. To this end, Equine SNP64K Illumina microarrays were applied along with bioinformatics tools dedicated for signal intensity analysis. The analysis revealed increased instability of the genome of sarcoid cells compared with unaltered skin tissue samples, which was manifested by the prevalence of CNV and cnLOH events. Many of the identified CNVs overlapped with the other research results, but the simultaneously observed variability in the number and sizes of detected aberrations indicated a need for further studies and the development of more reliable bioinformatics algorithms. The functional analysis of genes co-localized with the identified aberrations revealed that these genes are engaged in vital cellular processes. In addition, a number of these genes directly contribute to neoplastic transformation. Furthermore, large numbers of cnLOH events identified in the sarcoids suggested that they may play no less significant roles than CNVs in the carcinogenesis of this tumor. Thus, our results indicate the importance of cnLOH and CNV in equine sarcoid oncogenesis and present a direction of future research.