Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

Omonijo F, A Ganai N, M. Ibeagha-Awemu E, Mudasir Ahmad S. Immunotherapy in mastitis: state of knowledge, research gaps and way forward

Mastitis is an inflammatory condition that affects dairy cow's mammary glands. Traditional treatment approaches with antibiotics are increasingly leading to challenging scenarios such as antimicrobial resistance. In order to mitigate the unwanted side effects of antibiotics, alternative strategies such as those that harness the host immune system response, also known as immunotherapy, have been implemented. Immunotherapy approaches to treat bovine mastitis aims to enhance the cow's immune response against pathogens by promoting pathogen clearance, and facilitating tissue repair. Various studies have demonstrated the potential of immunotherapy for reducing the incidence, duration and severity of mastitis. Nevertheless, majority of reported therapies are lacking in specificity hampering their broad application to treat mastitis. Meanwhile, advancements in mastitis immunotherapy hold great promise for the dairy industry, with potential to provide effective and sustainable alternatives to traditional antibiotic-based approaches. This review synthesizes immunotherapy strategies, their current understanding and potential future perspectives. The future perspectives should focus on the development of precision immunotherapies tailored to address individual pathogens/group of pathogens, development of combination therapies to address antimicrobial resistance, and the integration of nano- and omics technologies. By addressing research gaps, the field of mastitis immunotherapy can make significant strides in the control, treatment and prevention of mastitis, ultimately benefiting both animal and human health/welfare, and environment health.

Effect of milk stasis on mammary gland involution and the microRNA profile

The presence of an autocrine factor in milk that can trigger mammary gland involution was proposed more than 50 yr ago. To provide evidence for the existence of one or more autocrine factors, 10 multiparous cows in late lactation were quarter-milked for 7 d. Following this baseline period, the right front quarter of each cow was left unmilked, and the other quarters were milked for 7 d. Before the last milking of that period, milk (mammary secretions) was collected aseptically from both front quarters. After that milking, 250 mL of the collected samples were infused in the cows' respective rear quarters. No quarters were milked for the following 7 d (milk stasis period), and quarter milking was then resumed in all quarters for the last 7 d of the experiment (remilking period). Quarter milk samples were collected during the baseline period, before the milk stasis period, and during the remilking period. These samples were used for measuring milk components and the concentration of involution markers (SCC, BSA, and lactoferrin). Samples of mammary secretions were collected manually from the quarters during the milk stasis period for involution marker determination. We extracted RNA from samples collected from front quarters before the last milking before the milk stasis period for microRNA (miRNA) determination. As anticipated, the longer milk stasis period implemented for the right front quarter resulted in a more advanced involution than in the left front quarter, based on the concentration of involution markers in the mammary secretions, lower milk production recovery, and changes in milk composition during the remilking period. All 3 involution marker concentrations in the mammary secretions increased in both rear quarters, but were greater in the right quarter secretions than in the left quarter secretions. Resuming milking reinitiated milk production in all quarters, but milk production recovery in the right rear quarters was less robust than that in the left rear quarters (54.3 ± 1.4% vs. 61.6 ± 1.4%, respectively). Milk from the quarters infused with mammary secretions (right rear) had a lower lactose content, but a higher milk protein content and higher SCC than the quarters infused with milk. We detected a total of 359 miRNAs, 76 of which were differentially expressed in milk and mammary secretions. Expression of bta-miR-221 and bta-miR-223 was upregulated in mammary secretions 34- and 40-fold, respectively. The results of the present experiment support the contention that milk stasis leads to the accumulation of one or more factors that trigger involution. The results also indicate that milk stasis leads to changes in the miRNA profile of the milk, but whether such changes are a cause or a consequence of the involution process remains to be established.

A systematic review of predictive, diagnostic, and prognostic biomarkers for detecting reproductive diseases in cattle using traditional and omics approaches

Reproductive diseases and illnesses pose significant challenges in cattle farming, affecting fertility, milk production, and overall herd health. In recent years, the integration of various omics approaches, including transcriptomics, proteomics, metagenomics, miRNAomics, and metabolomics, has revolutionized the study of these conditions. This systematic review summarised the findings from studies that investigated reproductive disease biomarkers in both male and female cattle. After extracting 6137 studies according to exclusion and inclusion criteria, a total of 60 studies were included in this review. All studies identified were associated with female cattle and none were related to reproductive diseases in bulls. The analysis highlights specific biomarkers, metabolic pathways, and microbial compositions associated with bovine reproductive disease conditions, providing valuable insights into the underlying molecular mechanisms of disease. Pro-inflammatory cytokines such as IL-1β, IL-8, IL-4, IL-6, TNFα and acute-phase response proteins such as SAA and HP have been identified as promising biomarkers for bovine reproductive diseases. However, further research is needed to validate these markers clinically and to explore potential strategies for improving cow reproductive health. The role of bulls as carriers of venereal diseases has been underestimated in the current literature and therefore needs more attention to understand their impact on infectious reproductive diseases of female cattle.

Milk-Derived Extracellular Vesicles: Biomedical Applications, Current Challenges, and Future Perspectives

Extracellular vesicles (EVs) are nano to-micrometer-sized sacs that are released by almost all animal and plant cells and act as intercellular communicators by transferring their cargos between the source and target cells. As a safe and scalable alternative to conditioned medium-derived EVs, milk-derived EVs (miEVs) have recently gained a great deal of popularity. Numerous studies have shown that miEVs have intrinsic therapeutic actions that can treat diseases and enhance human health. Additionally, they can be used as natural drug carriers and novel classes of biomarkers. However, due to the complexity of the milk, the successful translation of miEVs from benchtop to bedside still faces several unfilled gaps, especially a lack of standardized protocols for the isolation of high-purity miEVs. In this work, by comprehensively reviewing the bovine miEVs studies, we provide an overview of current knowledge and research on miEVs while highlighting their challenges and enormous promise as a novel class of theranostics. It is hoped that this study will pave the way for clinical applications of miEVs by addressing their challenges and opportunities.

Bovine Colostrum miR-30a-5p Targets the NF-κB Signaling Pathway to Alleviate Inflammation in Intestinal Epithelial Cells

Inflammatory bowel disease (IBD) is a common disease of the digestive system, and an excessive immune response mediated by the nuclear factor κ-B (NF-κB) signaling pathway is an essential etiology. Recent studies have found that bovine milk exosomes can improve intestinal mucosal health by delivering microRNA (miRNA), but the mechanism of action is so far unknown. In the present study, we analyzed the differential expression profiles of miRNA in colostrum and mature milk exosomes using high-throughput sequencing, based on the demonstration that colostrum exosomes inhibit the lipopolysaccharide (LPS)-induced intestinal epithelial NF-κB inflammatory pathway better than mature milk exosomes. The bta-miR-30a-5p, which is specifically highly expressed in colostrum, was screened, and its predicted target gene TRAM was found to be closely related to the NF-κB signaling pathway by functional enrichment analysis. Further, we used gene overexpression and silencing techniques and found that the bta-miR-30a-5p transfection treatment was confirmed to inhibit LPS-induced NF-κB signaling pathway activation and downstream pro-inflammatory factor expression, while the expression of its potential target gene, TRAM, was also suppressed. It is hypothesized that the high expression of bta-miR-30a-5p in colostrum, which targets TRAM to inhibit the downstream NF-κB inflammatory pathway, may be one of the molecular mechanisms responsible for its superior effect on resisting inflammatory attack compared to mature milk.

Milk-derived exosome nanovesicles: recent progress and daunting hurdles

Raw milk is the foundation of quality and safety in the dairy industry, and improving milk source management is the fundamental guarantee. Milk-derived exosomes (MDEs) are nanoscale information transfer molecules secreted by mammary cells with unique content and high stability, which can be used not only as potential markers to analyze key traits of lactation, reproduction, nutrition and health of animals, but also help farm managers to take timely interventions to improve animal welfare, milk quality, and functional traits. Our review first outlines the latest advances in MDEs isolation and purification, compositional analysis and characterization tools. We then provide a comprehensive summary of recent applications of MDEs liquid biopsy in breed selection, disease prevention and control, and feeding management. Finally, we evaluate the impact of processing on the stability of MDEs to offer guidance for dairy production and storage. The limitations and challenges in the development and use of MDEs markers are also discussed. As a noninvasive marker with high sensitivity and specificity, the MDEs-mediated assay technology is expected to be a powerful tool for measuring cow health and raw milk quality, enabling dynamic and precise regulation of dairy cows and full traceability of raw milk.

Review of exosomes and their potential for veterinary medicine

Small extracellular vesicles called exosomes are released by almost all cell types and play a crucial role in both healthy and pathological circumstances. Exosomes, found in biological fluids (including plasma, urine, milk, semen, saliva, abdominal fluid and cervical vaginal fluid) and ranging in size from 50 to 150 nm, are critical for intercellular communication. Analysis of exosomal cargos, including micro RNAs (miRNAs), proteins and lipids, has been proposed as valuable diagnostic and prognostic biomarkers of disease. Exosomes can also be used as novel, cell-free, treatment strategies. In this review, we discuss the role, significance and application of exosomes and their cargos in diseases of animals.

One-week storage of refrigerated bovine milk does not affect the size, concentration, or molecular properties of extracellular vesicles

Milk extracellular vesicles (EV) have gained extensive attention as promising diagnostic and therapeutic tools. Pre-analytical raw milk storage at low temperatures is an ordinary and usually necessary step after sample collection. It is known that direct freezing of unprocessed whole milk contaminates the native pool of milk EV with other cell structures. However, less evidence is available regarding prolonged cooling at 4°C. The current study assessed whether pre-analytical storage of bovine raw milk for several days affected EV isolation and further analysis. To confirm the independence from the health status of the mammary gland, we analyzed milk samples stored at 4°C for 1, 2, 3, and 7 d past collection, respectively, from 2 quarters of the same cow with different somatic cell counts (SCC). Seven days of refrigeration did not change the milk EV size, concentration, or morphology. We did not detect any changes in the EV cargo regarding the amount of protein and RNA, nor in the specific EV markers TSG101, CD9, and CD81 in milk from quarters with high and low SCC. Overall, we observed fewer CD81 and CD9 markers in quarters with high SCC. Moreover, we found no reduction in the mastitis-related miRNA bta-miR-223-3p, suggesting that refrigeration for several days up to 1 wk is a possible storage option compatible with further EV analyses. The findings of this study enhance the confidence that milk EV are highly stable in the raw milk matrix.

Milk exosomal microRNA profiling identified miR-375 and miR-199-5p for regulation of immune response during subclinical mastitis of crossbred cattle

BACKGROUND

The dairy industry has experienced significant economic losses as a result of mastitis, an inflammatory disease of cows, including both subclinical and clinical cases. Milk exosome microRNAs have gained attention due to their stable and selective wrapping nature, offering potential for the prognosis and diagnosis of bovine mastitis, the most common pathological condition of the mammary gland.

METHODS AND RESULTS

 In the present investigation, the microRNA profile of milk exosomes was explored using high-throughput small RNA sequencing data in sub-clinical mastitic and healthy crossbred Vrindavani cattle. In both groups, 349 microRNAs were identified, with 238 (68.19%) microRNAs co-expressed; however, 35 and 76 distinct microRNAs were found in subclinical mastitic and healthy cattle, respectively. Differential expression analysis revealed 11 microRNAs upregulated, and 18 microRNAs were downregulated in sub-clinical mastitic cattle. The functional annotation of the target genes of differentially expressed known and novel microRNAs including bta-miR-375, bta-miR-199-5p and bta-miR-12030 reveals their involvement in the regulation of immune response and inflammatory mechanisms and could be involved in development of mastitis.

CONCLUSIONS

The analysis of milk exosomal miRNAs cargos hold great promise as an approach to study the underlying molecular mechanisms associated with mastitis in high milk producing dairy cattle. Concurrently, the significantly downregulated miR-375 may upregulate key target genes, including CTLA4, IHH, IRF1, and IL7R. These genes are negative regulators of immune response pathways, which could be associated with impaired inflammatory mechanisms in mammary cells. According to the findings, bta-miR-375 could be a promising biomarker for the development of mastitis in dairy cattle.

Extracellular Vesicles Derived from Selenium-Deficient MAC-T Cells Aggravated Inflammation and Apoptosis by Triggering the Endoplasmic Reticulum (ER) Stress/PI3K-AKT-mTOR Pathway in Bovine Mammary Epithelial Cells

Selenium (Se) deficiency disrupts intracellular REDOX homeostasis and severely deteriorates immune and anti-inflammatory function in high-yielding periparturient dairy cattle. To investigate the damage of extracellular vesicles derived from Se-deficient MAC-T cells (SeD-EV) on normal mammary epithelial cells, an in vitro model of Se deficiency was established. Se-deficient MAC-T cells produced many ROS, promoting apoptosis and the release of inflammatory factors. Extracellular vesicles were successfully isolated by ultrahigh-speed centrifugation and identified by transmission electron microscopy, particle size analysis, and surface markers (CD63, CD81, HSP70, and TSG101). RNA sequencing was performed on exosomal RNA. A total of 9393 lncRNAs and 63,155 mRNAs transcripts were identified in the SeC and SeD groups, respectively, of which 126 lncRNAs and 955 mRNAs were differentially expressed. Furthermore, SeD-EV promoted apoptosis of normal MAC-T cells by TUNEL analysis. SeD-EV significantly inhibited Bcl-2, while Bax and Cleaved Caspase3 were greatly increased. Antioxidant capacity (CAT, T-AOC, SOD, and GSH-Px) was inhibited in SeD-EV-treated MAC-T cells. Additionally, p-PERK, p-eIF2α, ATF4, CHOP, and XBP1 were all elevated in MAC-T cells supplemented with SeD-EV. In addition, p-PI3K, p-Akt, and p-mTOR were decreased strikingly by SeD-EV. In conclusion, SeD-EV caused oxidative stress, thus triggering apoptosis and inflammation through endoplasmic reticulum stress and the PI3K-Akt-mTOR signaling pathway, which contributed to explaining the mechanism of Se deficiency causing mastitis.

Characterization and profiling of the microRNA in small extracellular vesicles isolated from goat milk samples collected during the first week postpartum

Colostrum contains nutrients, immunoglobulins, and various bioactive compounds such as microRNA (miRNA). Less is known about the temporal changes in miRNA profiles in ruminant milk samples during the first week postpartum. In this study, we characterized and compared the profiles of miRNA in the small extracellular vesicles (sEV) isolated from colostrum (CM, collected immediately after parturition, n = 8) and transition milk (TM, collected 7 d postpartum, n = 8) from eight 1-yr-old Guanzhong dairy goats with a milk yield of approximately 500 kg/year. A total of 192 unique sEV-associated miRNA (transcripts per million >1 at least 4 samples in either CM or TM) were identified in all samples. There were 29 miRNA uniquely identified in the TM samples while no miRNA was uniquely identified in the CM samples. The abundance of the top 10 miRNA accounted for 82.4% ± 4.0% (± SD) of the total abundance, with let-7 families (e.g., let-7a/b/c-5p) being predominant in all samples. The top 10 miRNA were predicted to target 1,008 unique genes that may regulate pathways such as focal adhesion, TGF-β signaling, and axon guidance. The expression patterns of EV miRNA were similar between the 2 sample groups, although the abundance of let-7c-5p and miR-30a-3p was higher, whereas that of let-7i-5p and miR-103-3p was lower in CM than in TM. In conclusion, the core miRNAome identified in the samples from CM and TM may play an important role in cell proliferation, bone homeostasis, and neuronal network formation in newborn goat kids. The lack of differential miRNA expression between the CM and TM samples may be due to a relatively short sampling interval in which diet composition, intake and health status of ewes, and environment were relatively stable.

The chemorepellent, SLIT2, bolsters innate immunity against Staphylococcus aureus

Neutrophils are essential for host defense against Staphylococcus aureus (S. aureus). The neuro-repellent, SLIT2, potently inhibits neutrophil chemotaxis, and might, therefore, be expected to impair antibacterial responses. We report here that, unexpectedly, neutrophils exposed to the N-terminal SLIT2 (N-SLIT2) fragment kill extracellular S. aureus more efficiently. N-SLIT2 amplifies reactive oxygen species production in response to the bacteria by activating p38 mitogen-activated protein kinase that in turn phosphorylates NCF1, an essential subunit of the NADPH oxidase complex. N-SLIT2 also enhances the exocytosis of neutrophil secondary granules. In a murine model of S. aureus skin and soft tissue infection (SSTI), local SLIT2 levels fall initially but increase subsequently, peaking at 3 days after infection. Of note, the neutralization of endogenous SLIT2 worsens SSTI. Temporal fluctuations in local SLIT2 levels may promote neutrophil recruitment and retention at the infection site and hasten bacterial clearance by augmenting neutrophil oxidative burst and degranulation. Collectively, these actions of SLIT2 coordinate innate immune responses to limit susceptibility to S. aureus.

Comparison of goat and cow milk-derived extracellular vesicle miRNomes

miRNAs present in milk are mainly found in extracellular vesicles (EVs), which are nanosized membrane vesicles released by most of the cell types to ensure intercellular communication. The majority of the studies performed so far on these vesicles have been conducted on human and cow's milk and focused on their miRNA content. The objectives of this study were to profile the miRNA content of purified EVs from five healthy goats and to compare their miRNome to those obtained from five healthy cows, at an early stage of lactation. EV populations were morphologically characterized using Transmission Electron Microscopy and Nanoparticle Tracking Analysis. The presence of EV protein markers checked by Western blotting and the absence of contamination of preparations by milk proteins. The size distribution and concentration of bovine and goat milk-derived EVs were similar. RNA-sequencing were performed, and all sequences were mapped to the cow genome identifying a total of 295 miRNAs. This study reports for the first-time a goat miRNome from milk EVs and its validation using cow miRNomes.

Multifunctional Milk-Derived Small Extracellular Vesicles and Their Biomedical Applications

In recent years, small extracellular vesicles (sEVs) have been regarded as the next generation of novel delivery systems after lipid nanoparticles because of their advantages and huge prospects in drug delivery. Studies have shown that sEVs are abundant in milk and therefore can be a large and economical source of sEVs. Natural milk-derived small extracellular vesicles (msEVs) have important functions such as immune regulation, anti-bacterial infection, anti-oxidative, etc., and play a beneficial role in human health at multiple levels, including intestinal health, bone/muscle metabolism, and microbiota regulation. In addition, because they can pass the gastrointestinal barrier and have low immunogenicity, good biocompatibility, and stability, msEVs are considered a crucial oral drug delivery vehicle. Moreover, msEVs can be further engineered for targeted delivery to prolong the circulation time or enhance local drug concentrations. However, msEVs separation and purification, complex contents, and quality control hinder their application in drug delivery. This paper provides a comprehensive review of the biogenesis and characteristics, isolation and purification, composition, loading methods, and function of msEVs, based on which their applications in biomedical fields are further explored.

Regulatory Role of microRNA of Milk Exosomes in Mastitis of Dairy Cows

The aim of this study was to compare the cargos of miRNA in exosomes isolated from the milk of healthy (H) cows, cows at risk of mastitis (ARM), and cows with subclinical mastitis (SCM). Based on the number of somatic cells and the percentage of polymorphonuclear cells, 10 cows were assigned to group H, 11 to group ARM, and 11 to group SCM. After isolating exosomes in milk by isoelectric precipitation and ultracentrifugation, the extracted RNA was sequenced to 50 bp long single reads, and these were mapped against Btau_5.0.1. The resulting 225 miRNAs were uploaded to the miRNet suite, and target genes for Bos taurus were identified based on the miRTarBase and miRanda databases. The list of differentially expressed target genes resulting from the comparisons of the three groups was enriched using the Function Explorer of the Kyoto Encyclopedia of Genes and Genomes. A total of 38, 18, and 12 miRNAs were differentially expressed (DE, p < 0.05) in the comparisons of H vs. ARM, ARM vs. SCM, and H vs. SCM, respectively. Only 1 DE miRNA was shared among the three groups (bta-mir-221), 1 DE miRNA in the H vs. SCM comparison, 9 DE miRNAs in the ARM vs. SCM comparison, and 21 DE miRNAs in the H vs. ARM comparison. A comparison of the enriched pathways of target genes from the H, SCM, and ARM samples showed that 19 pathways were differentially expressed in the three groups, while 56 were expressed in the H vs. SCM comparison and 57 in the H vs. ARM comparison. Analyzing milk exosome miRNA cargos can be considered as a promising approach to study the complex molecular machinery set in motion in response to mastitis in dairy cows.

BMSC-Derived Exosomal CircHIPK3 Promotes Osteogenic Differentiation of MC3T3-E1 Cells via Mitophagy

Exosome-based therapy is emerging as a promising strategy to promote bone regeneration due to exosomal bioactive cargos, among which circular RNA (circRNA) has recently been recognized as the key effector. The role of exosomal circRNA derived from bone marrow mesenchymal stem cells (BMSCs) has not been well-defined. The present study aimed to clarify the regulatory function and molecular mechanism of BMSC-derived exosomal circRNA in osteogenesis. Exosomes derived from bone marrow mesenchymal stem cells (BMSC-Exos) were isolated and identified. BMSC-Exos' pro-osteogenic effect on MC3T3-E1 cells was validated by alkaline phosphatase (ALP) activity and Alizarin Red staining. Through bioinformatic analysis and molecular experiments, circHIPK3 was selected and verified as the key circRNA of BMSC-Exos to promote osteoblast differentiation of MC3T3-E1 cells. Mechanistically, circHIPK3 acted as an miR-29a-5p sponge and functioned in mitophagy via targeting miR-29a-5p and PINK1. Additionally, we showed that the mitophagy level of MC3T3-E1 cells were mediated by BMSC-Exos, which promoted the osteogenic differentiation. Collectively, our results revealed an important role for BMSC-derived exosomal circHIPK3 in osteogenesis. These findings provide a potentially effective therapeutic strategy for bone regeneration.

Comparative Proteomic Analysis of Milk-Derived Extracellular Vesicles from Dairy Cows with Clinical and Subclinical Mastitis

Extracellular vesicles (EVs) are membranous vesicles found in biological fluids with essential functions. However, milk-derived EV proteins from clinical mastitis (CM) and subclinical mastitis (SM) cows have yet to be studied in detail. In this study, milk-derived EVs of CM, SM, and Healthy cows were extracted using a combination of acetic acid/ultracentrifugation and density gradient ultracentrifugation and analyzed using a shotgun proteomic by data-independent acquisition mode. A total of 1253 milk exosome proteins were identified and quantified. Differently enriched (DE) proteins were identified as given a Benjamini−Hochberg adjusted p < 0.05 and a fold change of at least 2. There were 53 and 1 DE proteins in milk-derived EVs from CM and SM cows compared with healthy cows. Protein S100-A9, Protein S100-A8, Chitinase-3-like protein 1, Haptoglobin, Integrin beta-2, and Chloride intracellular channel protein 1 were more abundant in the CM group (adjusted p < 0.05). Still, their enrichment in the SM group was not significant as in the Healthy group. The enrichment of DE proteins between CM and Healthy group was consistent with elevated GO (Gene Ontology) processes—defense response, defense response to Gram-positive bacterium, granulocyte chemotaxis also contributed to Reactome pathways—neutrophil degranulation, innate immune system, and antimicrobial peptides in the CM group. These results provide essential information on mastitis-associated proteins in milk-derived EVs and indicate the biological functions of milk-derived EVs proteins require further elucidation.

Extracellular Vesicles from Animal Milk: Great Potentialities and Critical Issues

Other than representing the main source of nutrition for newborn mammals, milk delivers a sophisticated signaling system from mother to child that promotes postnatal health. The bioactive components transferred through the milk intake are important for the development of the newborn immune system and include oligosaccharides, lactoferrin, lysozyme, α-La, and immunoglobulins. In the last 15 years, a pivotal role in this mother-to-child exchange has been attributed to extracellular vesicles (EVs). EVs are micro- and nanosized structures enclosed in a phospholipidic double-layer membrane that are produced by all cell types and released in the extracellular environment, reaching both close and distant cells. EVs mediate the intercellular cross-talk from the producing to the receiving cell through the transfer of molecules contained within them such as proteins, antigens, lipids, metabolites, RNAs, and DNA fragments. The complex cargo can induce a wide range of functional modulations in the recipient cell (i.e., anti-inflammatory, immunomodulating, angiogenetic, and pro-regenerative modulations) depending on the type of producing cells and the stimuli that these cells receive. EVs can be recovered from every biological fluid, including blood, urine, bronchoalveolar lavage fluid, saliva, bile, and milk, which is one of the most promising scalable vesicle sources. This review aimed to present the state-of-the-art of animal-milk-derived EV (mEV) studies due to the exponential growth of this field. A focus on the beneficial potentialities for human health and the issues of studying vesicles from milk, particularly for the analytical methodologies applied, is reported.

Comparative Study of the Expression Profiles of miRNAs of Milk-Derived Exosomes of Yak and Jeryak

The Jeryak is the hybrid offspring of yaks and Jersey cattle and exhibit improved milk and meat yields. Biomolecules carried within milk exosomes are important for cell growth, development, immune regulation, and various pathophysiological processes. Previous studies showed that miRNAs regulate mammary gland development, lactation, and milk quality. This study explored the relationship between milk exosomes miRNAs and lactation performance. A comparison of the milk content showed that yak milk was of a better quality compared to Jeryak milk (casein, fat, TS, SNF, lactose). Milk collected in December was superior to that collected in June for both yak and Jeryak, except for lactose concentrations. Exosomes were extracted by density gradient centrifugation and miRNA expression profiles in milk exosomes from three yaks and three Jeryaks collected in June and December were detected by small RNA sequencing. In all, 22, 120, 78, and 62 differentially expressed miRNAs (DEMs) were identified in Jun_ JY vs. Jun_ Y (P1: Jeryak in June vs. Yak in June), Jun_ JY vs. Dec_ JY (P2: Jeryak in June vs. Jeryak in December), Dec_ JY vs. Dec_ Y (P3: Jeryak in December vs. Yak in December), and Jun_ Y vs. Dec_ Y (P4: Yak in June vs. Yak in December) groups. These DEMs were enriched in functions and signaling pathways related to lactation performance. In conclusion, these findings are a reference tool to study the molecular basis of lactation performance.

Emerging roles of noncoding micro RNAs and circular RNAs in bovine mastitis: Regulation, breeding, diagnosis, and therapy

Bovine mastitis is one of the most troublesome and costly problems in the modern dairy industry, which is not only difficult to monitor, but can also cause economic losses while having significant implications on public health. However, efficacious preventative methods and therapy are still lacking. Moreover, new drugs and therapeutic targets are in increasing demand due to antibiotic restrictions. In recent years, noncoding RNAs have gained popularity as a topic in pathological and genetic studies. Meanwhile, there is growing evidence that they play a role in regulating various biological processes and developing novel treatment platforms. In light of this, this review focuses on two types of noncoding RNAs, micro RNAs and circular RNAs, and summarizes their characterizations, relationships, potential applications as selection markers, diagnostic or treatment targets and potential applications in RNA-based therapy, in order to shed new light on further research.

Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle

Data integration using hierarchical analysis based on the central dogma or common pathway enrichment analysis may not reveal non-obvious relationships among omic data. Here, we applied factor analysis (FA) and Bayesian network (BN) modeling to integrate different omic data and complex traits by latent variables (production, carcass, and meat quality traits). A total of 14 latent variables were identified: five for phenotype, three for miRNA, four for protein, and two for mRNA data. Pearson correlation coefficients showed negative correlations between latent variables miRNA 1 (mirna1) and miRNA 2 (mirna2) (-0.47), ribeye area (REA) and protein 4 (prot4) (-0.33), REA and protein 2 (prot2) (-0.3), carcass and prot4 (-0.31), carcass and prot2 (-0.28), and backfat thickness (BFT) and miRNA 3 (mirna3) (-0.25). Positive correlations were observed among the four protein factors (0.45-0.83): between meat quality and fat content (0.71), fat content and carcass (0.74), fat content and REA (0.76), and REA and carcass (0.99). BN presented arcs from the carcass, meat quality, prot2, and prot4 latent variables to REA; from meat quality, REA, mirna2, and gene expression mRNA1 to fat content; from protein 1 (prot1) and mirna2 to protein 5 (prot5); and from prot5 and carcass to prot2. The relations of protein latent variables suggest new hypotheses about the impact of these proteins on REA. The network also showed relationships among miRNAs and nebulin proteins. REA seems to be the central node in the network, influencing carcass, prot2, prot4, mRNA1, and meat quality, suggesting that REA is a good indicator of meat quality. The connection among miRNA latent variables, BFT, and fat content relates to the influence of miRNAs on lipid metabolism. The relationship between mirna1 and prot5 composed of isoforms of nebulin needs further investigation. The FA identified latent variables, decreasing the dimensionality and complexity of the data. The BN was capable of generating interrelationships among latent variables from different types of data, allowing the integration of omics and complex traits and identifying conditional independencies. Our framework based on FA and BN is capable of generating new hypotheses for molecular research, by integrating different types of data and exploring non-obvious relationships.

BMSC-derived exosomal miR-27a-3p and miR-196b-5p regulate bone remodeling in ovariectomized rats

Background

In the bone marrow microenvironment of postmenopausal osteoporosis (PMOP), bone marrow mesenchymal stem cell (BMSC)-derived exosomal miRNAs play an important role in bone formation and bone resorption, although the pathogenesis has yet to be clarified.

Methods

BMSC-derived exosomes from ovariectomized rats (OVX-Exo) and sham-operated rats (Sham-Exo) were co-cultured with bone marrow-derived macrophages to study their effects on osteoclast differentiation. Next-generation sequencing was utilized to identify the differentially expressed miRNAs (DE-miRNAs) between OVX-Exo and Sham-Exo, while target genes were analyzed using bioinformatics. The regulatory effects of miR-27a-3p and miR-196b-5p on osteogenic differentiation of BMSCs and osteoclast differentiation were verified by gain-of-function and loss-of-function analyses.

Results

Osteoclast differentiation was significantly enhanced in the OVX-Exo treatment group compared to the Sham-Exo group. Twenty DE-miRNAs were identified between OVX-Exo and Sham-Exo, among which miR-27a-3p and miR-196b-5p promoted the expressions of osteogenic differentiation markers in BMSCs. In contrast, knockdown of miR-27a-3p and miR-196b-5p increased the expressions of osteoclastic markers in osteoclast. These 20 DE-miRNAs were found to target 11435 mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these target genes were involved in several biological processes and osteoporosis-related signaling pathways.

Conclusion

BMSC-derived exosomal miR-27a-3p and miR-196b-5p may play a positive regulatory role in bone remodeling.

Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases

Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.

Assessment of microRNA profiles in small extracellular vesicles isolated from bovine colostrum with different immunoglobulin G concentrations

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The RNA concentration in sEV isolated from bovine colostrum was highest using the combination of the miRCURY Cell/Urine/CSF and miRNeasy Mini kits.

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The top 50 miRNA were the same using miRDeep2 and sRNAbench, predominated by let-7b, let-7a-5p, miR-30a-5p, and miR-148a.

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Predicted target genes of the top 50 miRNA regulate PI3K-Akt and MAPK signaling pathways, axon guidance, and focal adhesion.

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The abundance of miR-27a-3p was higher in colostrum with high IgG concentrations.

The consumption of bovine colostrum by newborn calves during the first days of life is essential to ensure the transfer of passive immunity. In addition to critical IgG, colostrum also contains non-IgG biomolecules, including microRNA (miRNA). The present study investigated the profiles of miRNA in small extracellular vesicles (sEV) isolated from bovine colostrum with high (256.5 ± 5.7 mg/mL, mean ± standard deviation, n = 4) and low (62.8 ± 3.6 mg/mL, n = 4) concentrations of IgG. Different combination of sEV extraction methods and bioinformatic pipelines (miRDeep2 and sRNAbench) for miRNA analysis were evaluated. Results showed that miRCURY exosome Cell/Urine/CSF and miRNeasy Mini kits yielded the highest RNA concentration. The miRNA-seq data analysis showed miRDeep2 yielded more comprehensive miRNAome compared with sRNAbench (527 versus 392 unique miRNA), whereas 389 shared miRNA were identified using both approaches. The profiles of top 50 miRNA were the same using both approaches, and their abundance contributed to 91.7% and 94.3% of total abundance of miRNA using miRDeep2 and sRNAbennch, respectively. These core miRNA were predicted to target 2,655 genes, which regulate 78 KEGG (Kyoto Encyclopedia of Genes and Genomes) level-3 pathways including PI3K-Akt and MAPK signaling pathway, axon guidance, and focal adhesion. The expression profiles of sEV-associated miRNA were similar between high- and low-IgG colostrum samples, despite the fact that the abundance of miR-27a-3p was higher in colostrum with high concentrations of IgG. In conclusion, a core miRNAome in bovine colostrum may play a role in regulating health and developmental stages in neonatal calves, independent of IgG concentration.

Insight of Melatonin: The Potential of Melatonin to Treat Bacteria-Induced Mastitis

Bovine mastitis is a common inflammatory disease, mainly induced by bacterial pathogens, such as Staphylococcus aureus, Escherichia coli, and Streptococcus agalactiae. Mastitis has negative effects on the production and quality of milk, resulting in huge economic losses. Melatonin, which is synthesized and secreted by the pineal gland and other organs, is ubiquitous throughout nature and has different effects on different tissues. Melatonin is crucial in modulating oxidative stress, immune responses, and cell autophagy and apoptosis, via receptor-mediated or receptor-independent signaling pathways. The potent antioxidative and anti-inflammatory activities of melatonin and its metabolites suggest that melatonin can be used to treat various infections. This article reviews the potential for melatonin to alleviate bovine mastitis through its pleiotropic effect on reducing oxidative stress, inhibiting pro-inflammatory cytokines, and regulating the activation of NF-κB, STATs, and their cascade reactions. Therefore, it is promising that melatonin supplementation may be an alternative to antibiotics for the treatment of bovine mastitis.

The global trend of exosome in diabetes research: A bibliometric approach

BACKGROUND AND AIMS

Exosome as a novel biomarker reflecting cell behavior in normal and pathological conditions such as diabetes is being the center of academic attention. Therefore, we aimed to study the research output of exosome in diabetes globally.

METHODS

We conducted a bibliometric approach to analyze publications on exosome and diabetes from the beginning to 2021 based on keyword search in the Scopus. Annual publications, citations, contributions, co-authorships, and co-occurrences were analyzed and plotted using VOSviewer and GraphPad Prism.

RESULTS

410 original articles and 149 reviews have published between 2009 and 2021. China and the USA were top countries in research output, sponsorship, and international collaborations. The top journals were Scientific Reports, Stem Cell Research and Therapy and Diabetes. The top institution was the University of Queensland in Australia. The top author was Chopp M. Co-occurrence analysis indicated that researchers focused on 1) extracellular vesicles in insulin resistance induced by metabolic disorders like obesity and diabetes mellitus; 2) diagnostic applicability of exosomal microRNAs as biomarkers for diabetic nephropathy; 3) therapeutic effect of exosome in wound healing and endothelial dysfunction during diabetes mellitus; and 4) The oxidative stress, autophagy, apoptosis, fibrosis, inflammation and angiogenesis mediated by exosomes during diabetes.

CONCLUSION

The trend in research output has been increased in this field, and advanced countries are involved much more than other countries in terms of research, financial support, and international collaboration. The bibliometric results could be beneficial for further studies in better understanding of novel ideas in exosome and diabetes fields.

MiRNAs in milk can be used towards early prediction of mammary gland inflammation in cattle

Considering the importance of early disease detection for reducing the huge financial and animal welfare impact of bovine mastitis globally, improved tools are urgently needed that can accurately detect early mammary inflammation. MiRNAs have demonstrated value as disease biomarkers, however, their potential for accurately detecting early mammary inflammation has not been examined in detail. To address this, we investigated the association between levels of four inflammation-associated miRNAs (bta-miR-26a, bta-miR-142-5p, bta-miR-146a and bta-miR-223) and CMT scores (0 to 3) obtained from a large number of individual quarter milk samples (n = 236) collected from dairy cows at different lactations (1 to 4). Initial analyses (n = 21 samples) confirmed that the levels of each of bta-miR-142-5p, bta-miR-146a and bta-miR-223 in whole milk were significantly correlated with mRNA levels of known inflammatory markers (HP, TNF, CXCL8 and IL1B) in milk cells (Rho ≥ 0.49, P < 0.005). Subsequent analyses (n = 215 samples) revealed a significant effect of CMT score on each of the four miRNAs analysed (P < 0.0001), characterised by a progressive increase in miRNA levels in milk as CMT score increase from 0 to > 1. Moreover, a significant effect of lactation number (P < 0.01) for bta-miR-26a, bta-miR-142-5p and bta-miR-146a was attributed to higher miRNA levels during lactation 1 than later lactations. Finally, by generating ROC curves we showed that bta-miR-223 and bta-miR-142-5p levels could identify early inflammatory changes in individual quarter milk samples (CMT1) with high accuracy (100% sensitivity, > 81% specificity). Our results provide novel proof of the value of miRNAs as early diagnostic biomarkers of bovine mastitis.

Organelles coordinate milk production and secretion during lactation: Insights into mammary pathologies

The mammary gland undergoes a spectacular series of changes during its development and maintains a remarkable capacity to remodel and regenerate during progression through the lactation cycle. This flexibility of the mammary gland requires coordination of multiple processes including cell proliferation, differentiation, regeneration, stress response, immune activity, and metabolic changes under the control of diverse cellular and hormonal signaling pathways. The lactating mammary epithelium orchestrates synthesis and apical secretion of macromolecules including milk lipids, milk proteins, and lactose as well as other minor nutrients that constitute milk. Knowledge about the subcellular compartmentalization of these metabolic and signaling events, as they relate to milk production and secretion during lactation, is expanding. Here we review how major organelles (endoplasmic reticulum, Golgi apparatus, mitochondrion, lysosome, and exosome) within mammary epithelial cells collaborate to initiate, mediate, and maintain lactation, and how study of these organelles provides insight into options to maintain mammary/breast health.

Exosomal lnc-AFTR as a novel translation regulator of FAS ameliorates Staphylococcus aureus-induced mastitis

Although the specific expression of long noncoding RNA (lncRNA) in mastitis tissue has been reported, few studies have involved the differential expression of lncRNA in mastitis exosomes (Exo) and its mechanism and function. We screened an lncRNA associated with FAS translational regulation (lnc-AFTR) through exosomal RNA sequencing, and clarified its function and molecular mechanism. Lnc-AFTR is markedly downregulated in Staphylococcus aureus-Exo and S. aureus-induced MAC-T cell as well as mastitis tissue. Overexpression of lnc-AFTR exosomes (oe-AFTR-Exo) significantly improves cell damage induced by S. aureus, including inhibiting apoptosis, promoting proliferation, and increasing the production of pro-inflammatory cytokines (tumor necrosis factor-α [TNF-α] and interleukin-1β [IL-1β]). Oe-AFTR-Exo also suppressed the activation of Caspase-8, Caspase-3, and JNK. Dual-luciferase report analysis confirmed that lnc-AFTR interacts with FAS mRNA directly to hinder translation process, but does not degrade FAS mRNA. Overexpression of lnc-AFTR in MAC-T cells obviously reduced S. aureus-induced apoptosis and inflammation. Knockdown of lnc-AFTR significantly increased FAS and promoted the activation of Caspase-8, Caspase-3, and JNK caused by S. aureus. In summary, these results revealed the mechanism by which lnc-AFTR directly bound FAS mRNA to prevent translation, and confirmed that the exosomal lnc-AFTR exerted anti-inflammatory and anti-apoptotic effects by inhibiting the activation of TNF signaling pathway and mitogen-activated protein kinases (MAPK) signaling pathway.

Differentially Expressed Extracellular Vesicle, Exosome and Non-Exosome miRNA Profile in High and Low Tick-Resistant Beef Cattle

Heavy tick burden on beef cattle account for huge economic losses globally, with an estimated value of US$22-30 billion per annum. In Australia, ticks cost the northern beef industry approximately A$170-200 million. Methods to evaluate and predict tick resistance would therefore be of great value to the global cattle trade. Exosomes (EX) are small extracellular vesicles (EVs) of ~30-150nm diameter and have gained popularity for their diagnostic and prognostic potential. EX contain, among other biomolecules, various types of RNA including micro-RNA (miRNA) and long noncoding RNA (lncRNA). MiRNA specifically have been validated as therapeutic biomarkers as they perform regulatory functions at the post-transcriptional level and are differentially expressed between divergent groups. The objective of the present study was to evaluate the miRNA profiles of EV and fractionated exosomal samples of high and low tick-resistant beef cattle to highlight potential miRNA biomarkers of tick resistance. Cows (n = 3/group) were classified into high or low tick resistant groups according to a novel scoring system. EVs and EX were isolated and fractionated from the blood plasma of high and low tick resistant cattle using established isolation and enrichment protocols. The resultant EX and non-EX samples were processed for next generation miRNA sequencing. Offspring of the cows in each high and low tick resistant group underwent the same processing for blood plasma EX, non-EX and miRNA analysis to evaluate the heritability of miRNA associated with tick resistance. A total of 2631 miRNAs were identified in EX and non-EX fractionated samples from high and low tick-resistant beef cattle. MiR-449a was highly expressed in maternal high tick-resistant EX samples. Of these, 174 were novel miRNAs, and 10 were differentially expressed (DE) (FDR < 0.05). These 10 DE miRNAs were also present in EVs, and three miRNAs were highly expressed: miR-2419-3p, miR-7861-3p and miR-2372-5p. Although 196 novel miRNAs were identified in fractionated samples of offspring, no miRNA were differentially expressed in these animals.

MicroRNAs: Potential biomarkers for reproduction, diagnosis, prognosis, and therapeutic in domestic animals

MicroRNA (miRNAs) are small non-coding RNA molecules involved in a wide range of biological processes through the post-transcriptional regulation of gene expression. Most studies evaluated microRNA expression in human, and despite fewer studies in veterinary medicine, this topic is one of the most exciting areas of modern veterinary medicine. miRNAs showed to be part of the pathogenesis of diseases and reproduction physiology in animals, making them biomarkers candidates. This review provides an overview of the current knowledge regarding miRNAs' role in reproduction and animal diseases, diagnostic and therapy.

Regulatory network of miRNA, lncRNA, transcription factor and target immune response genes in bovine mastitis

Pre- and post-transcriptional modifications of gene expression are emerging as foci of disease studies, with some studies revealing the importance of non-coding transcripts, like long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). We hypothesize that transcription factors (TFs), lncRNAs and miRNAs modulate immune response in bovine mastitis and could potentially serve as disease biomarkers and/or drug targets. With computational analyses, we identified candidate genes potentially regulated by miRNAs and lncRNAs base pair complementation and thermodynamic stability of binding regions. Remarkably, we found six miRNAs, two being bta-miR-223 and bta-miR-24-3p, to bind to several targets. LncRNAs NONBTAT027932.1 and XR_003029725.1, were identified to target several genes. Functional and pathway analyses revealed lipopolysaccharide-mediated signaling pathway, regulation of chemokine (C-X-C motif) ligand 2 production and regulation of IL-23 production among others. The overarching interactome deserves further in vitro/in vivo explication for specific molecular regulatory mechanisms during bovine mastitis immune response and could lay the foundation for development of disease markers and therapeutic intervention.

Ruminant Milk-Derived Extracellular Vesicles: A Nutritional and Therapeutic Opportunity?

Milk has been shown to contain a specific fraction of extracellular particles that are reported to resist digestion and are purposefully packaged with lipids, proteins, and nucleic acids to exert specific biological effects. These findings suggest that these particles may have a role in the quality of infant nutrition, particularly in the early phase of life when many of the foundations of an infant's potential for health and overall wellness are established. However, much of the current research focuses on human or cow milk only, and there is a knowledge gap in how milk from other species, which may be more commonly consumed in different regions, could also have these reported biological effects. Our review provides a summary of the studies into the extracellular particle fraction of milk from a wider range of ruminants and pseudo-ruminants, focusing on how this fraction is isolated and characterised, the stability and uptake of the fraction, and the reported biological effects of these fractions in a range of model systems. As the individual composition of milk from different species is known to differ, we propose that the extracellular particle fraction of milk from non-traditional and minority species may also have important and distinct biological properties that warrant further study.

Isolation of extracellular vesicles from byproducts of cheesemaking by tangential flow filtration yields heterogeneous fractions of nanoparticles

Extracellular vesicles (EV) in milk, particularly exosomes, have attracted considerable attention as bioactive food compounds and for their use in drug delivery. The utility of small EV in milk (sMEV) as an animal feed additive and in drug delivery would be enhanced by cost-effective large-scale protocols for the enrichment of sMEV from byproducts in dairy plants. Here, we tested the hypothesis that sMEV may be enriched from byproducts of cheesemaking by tangential flow filtration (EV-FF) and that the sMEV have properties similar to sMEV prepared by ultracentrifugation (sMEV-UC). Three fractions of EV were purified from the whey fraction of cottage cheese making by using EV-FF that passed through a membrane with a 50-kDa cutoff (50 penetrate; 50P), and subfractions of 50P that were retained (100 retentate; 100R) or passed through (100 penetrate; 100P) a membrane with a 100-kDa cutoff; sMEV-UC controls were prepared by serial ultracentrifugation. The abundance of sMEV (<200 nm) was less than 0.3% in EV-FF compared with sMEV-UC (10¹²/mL of milk). Despite the low EV count, the protein content (mg/mL) of 100R (63 ± 0.02; ± standard deviation) was higher than that of 50P (0.75 ± 0.10), 100P (0.65 ± 0.40), and sMEV-UC (27 ± 0.02). There were 17, 14, 35, and 75 distinct proteins detected by nontargeted mass spectrometry analysis in 50P, 100R, 100P, and sMEV-UC, respectively. Exosome markers CD9, CD63, CD81, HSP-70, PDCD6IP, and TSG101 were detected in control sMEV-UC but not in EV-FF by using targeted mass spectrometry and immunoblot analyses. Negative exosome markers, APOB, β-integrin, and histone H3 were below the limit of detection in EV-FF and control sMEV-UC analyzed by immunoblotting. The abundance of the major milk fat globule protein butyrophilin showed the following pattern: 100R ≫ 100P = 50P > sMEV-UC. More than 100 mature microRNA were detected in sMEV-UC by using sequencing analysis, compared with 36 to 60 microRNA in EV-FF. Only 100R and sMEV-UC yielded mRNA in quantities and qualities sufficient for sequencing analysis; an average of 276,000 and 838,000 reads were mapped to approximately 14,600 and 18,500 genes in 100R and sMEV-UC, respectively. In principal component analysis, microRNA, mRNA, and protein in EV-FF preparations clustered separately from control sMEV-UC. We conclude that under the conditions used here, flow filtration yields a heterogeneous population of milk EV.

Proteomic analysis of liver tissues in chicken embryo at Day 16 and Day 20 reveals antioxidant mechanisms

To investigate the mechanisms of the defense system and antioxidant defense system during chicken embryo development, protein profiling of liver tissues in chicken embryo at Day 16 and Day 20 was conducted. TMT was used to analyze the liver tissues proteomes with significantly different activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in chicken embryo. PRM was operated to validate the target differentially abundant proteins (DAPs) using the same samples. The result showed a total of 34 DAPs were identified. Among these, 9 were upregulated and 25 were downregulated. The screened DAPs strictly related to regulation of oxidoreductase activity (DDO and GAS2L1), response to stress (ERAD2 and SAA), immune system process (GAL3 and PDCD4), and lipid regulation and metabolism (ETNPPL, APOV1, LIPM, and APOA4). These analyses indicated that the antioxidant enzyme activity of chicken embryo is regulated through different pathways. Correlation analysis revealed a linear relationship between mRNA and protein expression and 12 genes (ORM1, C8B, KPNA2, CA4, C1S, SULT1B, ETNPPL, ERCC6L, DDO, SERPINF1, VAT1L, and APOA4) were detected to be differently expressed both at mRNA and protein levels. In consequence, these findings are an important resource that can be used in future studies of antioxidant mechanisms in chicken embryo. BIOLOGICAL SIGNIFICANCE: The genetic mechanisms of antioxidant activity are still unclear in chicken embryo. In the article, the combined transcriptomic and proteomic analysis is used to further explore potential signaling pathways and differentially abundant proteins related to antioxidant activity. These findings will facilitate a better understanding of the mechanism and these DAPs can be further investigated as candidate markers to predict the activity of antioxidant enzymes.

miRNA Regulatory Functions in Farm Animal Diseases, and Biomarker Potentials for Effective Therapies

MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression post-transcriptionally by targeting either the 3′ untranslated or coding regions of genes. They have been reported to play key roles in a wide range of biological processes. The recent remarkable developments of transcriptomics technologies, especially next-generation sequencing technologies and advanced bioinformatics tools, allow more in-depth exploration of messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), including miRNAs. These technologies have offered great opportunities for a deeper exploration of miRNA involvement in farm animal diseases, as well as livestock productivity and welfare. In this review, we provide an overview of the current knowledge of miRNA roles in major farm animal diseases with a particular focus on diseases of economic importance. In addition, we discuss the steps and future perspectives of using miRNAs as biomarkers and molecular therapy for livestock disease management as well as the challenges and opportunities for understanding the regulatory mechanisms of miRNAs related to disease pathogenesis.

Exosomal Cargo May Hold the Key to Improving Reproductive Outcomes in Dairy Cows

The reproductive status of dairy cows remains a challenge for dairy farmers worldwide, with impaired fertility linked to a significant reduction in herd profitability, due in part to impaired immunity, increased metabolic pressure, and longer postpartum anestrous interval (PPAI). Exosomes are nanovesicles released from a variety of cell types and end up in circulation, and carry proteins, bioactive peptides, lipids, and nucleic acids specific to the place of origin. As such, their role in health and disease has been investigated in humans and animals. This review discusses research into exosomes in the context of reproduction in dairy herds and introduces recent advances in mass-spectrometry (MS) based proteomics that have a potential to advance quantitative profiling of exosomal protein cargo in a search for early biomarkers of cattle fertility.

Circulating Adiponectin and Its Association with Metabolic Traits and Type 2 Diabetes: Gene-Diet Interactions Focusing on Selected Gene Variants and at the Genome-Wide Level in High-Cardiovascular Risk Mediterranean Subjects

Adiponectin is gaining renewed interest since, in addition to its possible protective role against insulin resistance and arteriosclerosis, recent studies suggest other additional favorable effects. However, the influence of gene-diet interactions on plasma adiponectin levels is still little understood. We analyzed the association between plasma adiponectin levels and various metabolic traits in a high-cardiovascular risk Mediterranean population, as well as the genetic effect of four candidate single-nucleotide polymorphisms (SNPs) in the adiponectin gene (ADIPOQ) and their interactions with the Mediterranean dietary pattern. Additionally, we explored, at the genome-wide level, the SNPs most associated with plasma adiponectin levels, as well as gene-diet interactions with the Mediterranean diet. In the 954 participants studied (aged 55-80 years), plasma adiponectin levels were strongly associated with plasma HDL-C concentrations (p = 6.6 × 10^-36) and inversely related to triglycerides (p = 4.7 × 10^-18), fasting glucose (p = 3.5 × 10^-16) and type 2 diabetes (p = 1.4 × 10^-7). Of the four pre-selected ADIPOQ candidate SNPs, the one most associated with plasma adiponectin was the -11391G > A (rs17300539) promoter SNP (p = 7.2 × 10^-5, in the multivariable adjusted model). No significant interactions with the Mediterranean diet pattern were observed for these SNPs. Additionally, in the exploratory genome-wide association study (GWAS), we found new SNPs associated with adiponectin concentrations at the suggestive genome-wide level (p < 1 × 10^-5) for the whole population, including the lead SNP rs9738548 (intergenic) and rs11647294 in the VAT1L (Vesicle Amine Transport 1 Like) gene. We also found other promising SNPs on exploring different strata such as men, women, diabetics and non-diabetics (p = 3.5 × 10^-8 for rs2850066). Similarly, we explored gene-Mediterranean diet interactions at the GWAS level and identified several SNPs with gene-diet interactions at p < 1 × 10^-5. A remarkable gene-diet interaction was revealed for the rs2917570 SNP in the OPCML (Opioid Binding Protein/Cell Adhesion Molecule Like) gene, previously reported to be associated with adiponectin levels in some populations. Our results suggest that, in this high-cardiovascular risk Mediterranean population, and even though adiponectin is favorably associated with metabolic traits and lower type 2 diabetes, the gene variants more associated with adiponectin may be population-specific, and some suggestive gene-Mediterranean diet interactions were detected.

Selective packaged circular RNAs in milk extracellular vesicles during Staphylococcus aureus infection may have potential against bacterial infection

Extracellular vesicles (EVs) provide a novel intercellular communication mechanism to transfer biologically important molecules to target cells. Although several pieces of evidence have shown that EVs have potential to respond to bacterial infections, our knowledge about the role of circular RNA (circRNA), an important cargo of EV, behind this process remains poor. In particular, the mechanism by which circRNAs are packaged into EVs remains elusive during bacterial infection. In the present study, EVs from bovine milk samples with or without Staphylococcus aureus (S. aureus) infection were isolated. The presence of circRNAs in milk-derived EVs (MEVs) was validated for the first time by PCR amplification with convergent and divergent primers and the RNase R resistance test. Through high-throughput sequencing, the expression profile of circRNAs in EVs was found to be changed during S. aureus infection. Moreover, we demonstrated that circRNAs were selectively packaged into EVs. Finally, bioinformatic analyses predicted the involvement of differentially expressed circRNAs in immune functions. In summary, our findings offer an insight into the packaging mechanism of EV circRNAs and underscore the potential by which host used the EV circRNAs in response to pathogenic bacterial infections.

Genome-Wide DNA Methylation Analysis of Mammary Gland Tissues From Chinese Holstein Cows With Staphylococcus aureus Induced Mastitis

Staphylococcus aureus intramammary infection is one of the most common causes of chronic mastitis in dairy cows, whose development may be associated with epigenetic changes in the expression of important host defense genes. This study aimed to construct a genome-wide DNA methylation profile of the mammary gland of Chinese Holstein cows (n = 3) following experimentally induced S. aureus mastitis, and to explore the potential gene regulatory mechanisms affected by DNA methylation during S. aureus mastitis. DNA was extracted from S. aureus-positive (n = 3) and S. aureus-negative (n = 3) mammary gland quarters and subjected to methylation-dependent restriction-site associated DNA sequencing (Methyl-RAD Seq). Results showed that CmCGG/CmCWGG DNA methylation sites were unevenly distributed and concentrated on chromosomes 5, 11, and 19, and within intergenic regions and intron regions of genes. Compared with healthy control quarters, 9,181 significantly differentially methylated (DM) CmCGG sites and 1,790 DM CmCWGG sites were found in the S. aureus-positive quarters (P < 0.05, |log2FC| > 1). Furthermore, 363 CmCGG differently methylated genes (DMGs) and 301 CmCWGG DMGs (adjusted P < 0.05, |log2FC| > 1) were identified. Gene ontology and KEGG enrichment analysis indicated that CmCGG DMGs are involved in immune response pathways, while the CmCWGG DMGs were mainly enriched in gene ontology terms related to metabolism. The mRNAs of 526 differentially methylated CmCGG genes and 124 differentially methylated CmCWGG genes were also significantly differentially expressed (RNA-Seq data) in the same samples, herein denoted differentially methylated and expressed genes (DMEGs) (P < 0.05). Functional enrichment analysis of DMEGs revealed roles related to biological processes, especially the regulation of immune response to diseases. CmCGG DMEGs like IL6R, TNF, BTK, IL1R2, and TNFSF8 enriched in several immune-related GO terms and pathways indicated their important roles in host immune response and their potential as candidate genes for S. aureus mastitis. These results suggest potential regulatory roles for DNA methylation in bovine mammary gland processes during S. aureus mastitis and serves as a reference for future epigenetic regulation and mechanistic studies.

Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus)

Infertility is a challenging phenomenon in cattle that reduces the sustainability of beef production worldwide. Here, we tested the hypothesis that gene expression profiles of protein-coding genes expressed in peripheral white blood cells (PWBCs), and circulating micro RNAs in plasma, are associated with female fertility, measured by pregnancy outcome. We drew blood samples from 17 heifers on the day of artificial insemination and analyzed transcript abundance for 10,496 genes in PWBCs and 290 circulating micro RNAs. The females were later classified as pregnant to artificial insemination, pregnant to natural breeding or not pregnant. We identified 1860 genes producing significant differential coexpression (eFDR < 0.002) based on pregnancy outcome. Additionally, 237 micro RNAs and 2274 genes in PWBCs presented differential coexpression based on pregnancy outcome. Furthermore, using a machine learning prediction algorithm we detected a subset of genes whose abundance could be used for blind categorization of pregnancy outcome. Our results provide strong evidence that transcript abundance in circulating white blood cells is associated with fertility in heifers.

Impact of processing method on donated human breast milk microRNA content

Pasteurization of donated human milk preserves it for storage and makes it safe for feeding, but at the expense of its composition, nutritional values and functions. Here, we aimed to investigate the impact of Holder Pasteurization (HoP) and High Pressure Processing (HPP) methods on miRNA in human milk and to evaluate impact of these changes on miRNA functions. Milk samples obtained from women in 50th day of lactation (n = 3) were subjected either to HoP, HPP or remained unpasteurized as a control. Subsequently, miRNA was isolated from whole material and exosomal fraction and sequenced with Illumina NextSeq 500. Sequencing data were processed, read counts were mapped to miRNA and analyzed both quantitatively with DESeq2 and functionally with DIANA mirPath v.3. While HPP caused statistically insignificant decrease in number of miRNA reads compared to unprocessed material, HoP led to 82-fold decrease in whole material (p = 0.0288) and 302-fold decrease in exosomes (p = 0.0021) not leaving enough reads for further analysis. Changes in composition of miRNA fraction before and after HPP indicated uneven stability of individual miRNAs under high pressure conditions, with miR-30d-5p identified as relatively stable and miR-29 family as sensitive to HPP. Interestingly, about 2/3 of unprocessed milk miRNA content consists of only 10 distinct miRNAs with miR-148a-3p at the top. Functional analysis of most abundant human milk miRNAs showed their involvement in signaling pathways, cell communication, proliferation and metabolism that are obviously important in rapidly growing infants. Functions of miRNAs which suffered the greatest depletion during HPP were similar to roles of the majority of unprocessed human milk's miRNA, which indicates that those functions may be weakened although not completely lost. Our findings indicate that HPP is less detrimental to human milk miRNAs than HoP and should be considered in further research on recommended processing procedures for human milk banks.

MicroRNA Milk Exosomes: From Cellular Regulator to Genomic Marker

Recent advances in ruminants' milk-derived exosomes (EXO) have indicated a role of microRNAs (miRNAs) in cell-to-cell communication in dairy ruminants. The miRNAs EXO retain peculiar mechanisms of uptake from recipient cells, which enables the selective delivery of cargos, with a specific regulation of target genes. Although many studies have been published on the miRNAs contained in milk, less information is available on the role of miRNAs EXO, which are considered stable over time and resistant to digestion and milk processing. Several miRNAs EXO have been implicated in the cellular signaling pathway, as in the regulation of immune response. Moreover, they exert epigenetic control, as extenuating the expression of DNA methyltransferase 1. However, the study of miRNAs EXO is still challenging due to the difficulty of isolating EXO. In fact, there are not agreed protocols, and different methods, often time-consuming, are used, making it difficult to routinely process a large number of samples. The regulation of cell functions in mammary glands by miRNAs EXO, and their applications as genomic markers in livestock, is presented.