Negative energy balance and hepatic gene expression patterns in high-yielding dairy cows during the early postpartum period: a global approach

The effects of the housing system and milk productivity on serum and fecal levels of essential and toxic trace elements and minerals in Red Steppe dairy cows

The objective of the present study was to evaluate serum and fecal trace element and mineral levels in Red Steppe dairy cows with different daily milk yields during the transition from feedlot to pasture. Serum and fecal trace element and mineral levels were assessed using the inductively coupled plasma mass spectrometry. The obtained data demonstrate that serum Ca, Mg, K, and Na levels increased significantly in the pasture period, and this increase is more profound in cows with higher milk yield. In turn, circulating levels of B, Co, Cr, Fe, I, and Se significantly decreased in the pasture period. Despite the lack of group differences in the feedlot period, serum B, Cr, and Fe levels in the pasture period were higher in cows with higher milk yield. In turn, circulating Co and I concentrations were higher in the cows with lower milk yield. Finally, the levels of toxic trace elements in the pasture period were found to be higher in cows with lower milk productivity. Discriminant analysis demonstrated that the groups of cows with different milk productivity were clearly discriminated only in the pasture period. Despite a significant change in fecal trace element and mineral content upon transition from feedlot to pasture, only minor group differences between cows with different daily milk yields were observed. These findings demonstrate that despite the lack of differences in dietary trace element and mineral intake, cows with different milk productivity are characterized by distinct patterns of serum trace element and mineral content.

Genetic aspects of major blood metabolites in the Italian Simmental cattle population

The Simmental breed is widely known for its resilience, robustness, and resistance to disease, and the incidence of ketosis in this breed is therefore generally lower compared with Holsteins. Blood concentrations of nonesterified fatty acids (NEFA), BHB, and urea provide valuable information about the metabolic, health, and nutritional status of lactating animals. In the present study, we estimated h2 of BHB, NEFA, and urea in blood predicted from milk mid-infrared spectra and assessed their genetic correlation with milk yield and composition traits in the Italian Simmental cattle breed using phenotypes of 3,549 cows in 207 herds. Two sets were considered: early (1,920 records, 1 per cow, between 5 and 35 DIM) and whole (14,378 records, at least 3 per cow, between 5 and 305 DIM) lactation. In early lactation, h2 estimates were 0.06 for blood BHB as-is, 0.06 for log-transformed BHB, 0.18 for NEFA, 0.14 for log-transformed NEFA, and 0.05 for blood urea. In the whole lactation, the h2 were 0.09 for blood BHB as-is, 0.16 for log-transformed BHB, 0.03 for NEFA, 0.04 for log-transformed NEFA, and 0.04 for blood urea. As far as the genetic correlations were concerned, blood BHB was positively correlated with NEFA and blood urea. Blood BHB and NEFA were generally positively correlated with milk fat-to-protein ratio and milk, but only the first was negatively correlated with lactose content and positively with SCS. Sires' EBVs for BHB with accuracy ≥0.60 were extrapolated for a posteriori evaluation of the daughters' observed performance. The progeny of the top 5% of sires exhibited, on average, lower blood BHB, NEFA, and urea compared with the daughters of the bottom 5%. Overall, it is highly recommended to monitor the genetic variability of the metabolic traits in the dual-purpose Italian Simmental breed to monitor the incidence of metabolic diseases in future generations.

Associations between milk infrared-predicted plasma biomarkers of stress resilience and fertility in dairy cattle: Insights for enhancing breeding programs and herd management

Fertility is a crucial aspect of dairy herd efficiency and sustainability. Among factors influencing fertility in dairy cattle, metabolic stress and systemic inflammation of animals are of main relevance, especially in the postpartum stage when ovarian activity begins and cows are inseminated. Our study aimed to infer the associations between milk infrared-predicted blood biomarkers of stress resilience and fertility traits, namely the interval from calving to first service (iCF), days open (DO), and the pregnancy rate at first service (PRF) in a multibreed population of 89,097 dairy cows. The blood metabolites (15 blood biomarkers related to hepatic damage and function, oxidative stress, inflammation, and innate immunity) were predicted using milk Fourier-transform mid-infrared (MIR) spectroscopy. A gradient boosting machine approach with leave-one-batch-out cross-validation (R2 range from 0.45 to 0.82) was implemented to an independent calibration database of 1,367 lactating cows reared in 5 herds. Calibration equations were then applied to a population database of 1,799,186 MIR milk spectral data, that were then merged with fertility data collected by the Breeders Federation of Alto Adige (Bolzano province, Italy) generating a final database of 285,145 records. The 2 databases were merged according to the milk test day (and thus, the MIR spectrum) closest to the date of insemination. The interval fertility traits were fitted as the hazard of either receiving the first service after calving at time t for iCF or becoming pregnant after calving at time t for DO in a Cox proportional-hazards model. Statistical analyses were performed including in the model the number of lactations, year of calving, and herd as fixed effects. The independent effect of the MIR-based predictions of metabolites was also included with each metabolite evaluated separately and discretized into 7 levels based on percentiles. Pregnancy rate at first service, however, was analyzed using logistic regression and the same explanatory variables. The metabolites linked to liver function and damage, such as aspartate aminotransferase, total bilirubin, and alkaline phosphatase, had a relevant influence on iCF and DO in terms of the hazard ratio (HR). Relevant results were also obtained for the biomarkers related to oxidative stress, inflammation, and innate immunity. Specifically, increasing levels of ceruloplasmin, total reactive oxygen metabolites, and advanced oxidation protein products resulted in a relevant decrease in the HR of cows becoming pregnant. The logistic regression analysis did not reveal any significant effect of the aforementioned biomarkers on PRF, indicating that the effects of the stress response mainly concern the resumption of the ovarian cycle after calving. The results for the associations of the predicted biomarkers of the stress response with iCF and DO were consistent with expected physiological patterns. In conclusion, the predicted biomarkers investigated revealed to be promising novel phenotypes for assessing animal health and welfare, in the view of enhancing fertility in dairy cattle also through selective breeding, thus improving the overall efficiency of dairy herds.

Canonical Correlation of Milk Composition Parameters and Blood Biomarkers in High-Producing Dairy Cows During Different Lactation Stages

This study explores milk composition and blood markers in cows across lactation stages. Holstein cows were divided into four groups: beginning of lactation (BL; n = 21), peak of lactation (PL; n = 21), middle of lactation (ML; n = 21), and end of lactation (EL; n = 20). Blood (1 × 15 mL) and milk samples (1 × 100 mL) were collected for biomarker analysis. Blood chemistry profiles were determined using a clinical chemistry analyser, and milk lactose, fat, and protein levels (%) were determined using an infrared absorbance analyser. Minerals (Ca, P, and Mg) in milk were determined by atomic absorption spectrometry after mineralizing the samples. Glucose was higher in the EL group than in the BL group (p < 0.01), whereas D-beta-hydroxybutyrate (D-BHB) was higher in the BL group than in the PL and ML groups (p < 0.001). Cholesterol was higher in the PL, ML, and EL groups than in the BL group (p < 0.001). Gamma-glutamyl transferase was increased in the PL group compared to the BL group. Phosphorus levels were lower in the PL than in the BL group, whereas protein levels were higher in the EL than in the PL group. Spearman and partial correlation analysis showed several significant associations between the observed variables. Using canonical correlation analysis were identified three significant correlations (rc1 = 0.853; rc2 = 0.823; rc3 = 0.739). The main canonical correlation identified blood TG and milk urea as the strongest variables. According to the canonical loading, the biomarkers TG, Mg, urea, cholesterol, and alkaline phosphatase (U1) are the primary variables associated with milk parameters (V1), specifically with milk urea, milk Mg and P, protein, and lactose.

Liver transcriptome and proteome are modulated by nutrient restriction in early lactation cows challenged with intramammary lipopolysaccharide

The objective was to evaluate the effects of nutrient restriction on liver function 24 h after an intramammary lipopolysaccharide (LPS) challenge in early lactation cows using transcriptomic and proteomic analyses. Multiparous Holstein cows were fed a lactation diet (CONT, n = 8) throughout the study or were switched to a diet diluted with barley straw (48 % DM) for 96 h (REST, n = 8) starting at 24 (18 to 30) days in milk. At 72 h, a healthy rear mammary quarter was infused with 50 μg of LPS in all cows. Blood and liver biopsies were collected at 96 h, corresponding to 24 h after LPS challenge. Liver transcriptome was analyzed with a 44 K bovine microarray and proteome by LC MS/MS. Transcriptomic and proteomic data were analyzed using GeneSpring (moderated t-test with Westfall-Young correction) and the "between subject design", respectively. Data mining was performed using Panther and Pathway Studio software. By design, the negative energy balance was -68 and -37 MJ/d in REST and CONT, respectively. Plasma non-esterified FAs, and β-hydroxybutyrate were significantly greater in REST compared to CONT, which is consistent with 96 h of nutrient restriction in REST and ketosis induction. We detected 77 and 91 differentially expressed genes at mRNA and protein levels, respectively, between CONT and REST. Genes involved in fatty acid synthesis (e.g.: ACAT, FASN, SCD) were downregulated in REST, whereas those involved in fatty acid oxidation, detoxification, cholesterol synthesis, lipoprotein lipid secretion, and gluconeogenesis (e.g.: ACAD, CPT1A, CPT1B, CPT2) were upregulated. Differentially abundant mRNAs and proteins were consistent with negative energy balance and plasma metabolite concentrations, and reflected a state of intense lipomobilization, glucose deficit and ketogenesis in REST cows. Nutrient restriction did not change in deep liver expression of genes directly involved in immune function 24 h after an intramammary LPS challenge.

Effect of β-hydroxybutyrate acid on gene expression levels of antioxidant biomarkers and growth hormone-related genes in liver cell culture

Introduction

In dairy cattle, oxidative stress is a predominant problem associated with diseases and reproductive health issues. This study aimed to detect the variation in the antioxidant biomarkers by adding different concentrations of β-hydroxybutyric acid (BHBA) and sought to elucidate its effects on the gene expression levels of growth hormone (GH) and antioxidant biomarkers in bovine hepatocytes.

Material and Methods

Four antioxidant biomarkers, namely malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH Px) were evaluated using commercially available bovine ELISA kits. The expression levels of the bovine GH, its receptor (GHR), insulin-like growth factor (IGF), IGF-1, IGF-1 receptor, CAT, SOD, GSH-Px and β-actin (as a reference) genes in liver cell culture were determined by reverse transcriptase-PCR assay.

Results

With the increase of BHBA concentration and culture time, the activities of SOD, CAT, and GSH Px biomarkers in hepatocytes decreased. However, the content of MDA in hepatocytes increased gradually with the increase of hepatocyte culture time and BHBA concentration. The qPCR results revealed that after adding BHBA, gene expression levels of GSH-Px, SOD and IGF biomarkers in hepatocytes began to differ in the culture groups at 12 h, whereas the gene expression level of the CAT and GHR biomarkers in hepatocytes began to differ at 6 h.

Conclusion

Quantitative PCR results showed that the BHBA significantly downregulated the expression levels of the GHR gene and CAT, GSH Px and SOD antioxidant biomarker genes.

Hepatic metabolism of grazing cows of two Holstein strains under two feeding strategies with different levels of pasture inclusion

The objective of the study was to characterize adaptations of hepatic metabolism of dairy cows of two Holstein strains with varying proportions of grazing in the feeding strategy. Multiparous autumn calving Holstein cows of New Zealand (NZH) and North American (NAH) strains were assigned to a randomized complete block design with a 2 x 2 factorial arrangement with two feeding strategies that varied in the proportions of pasture and supplementation: maximum pasture and supplementation with a pelleted concentrate (MaxP) or fixed pasture and supplementation with a total mixed ration (FixP) from May through November of 2018. Hepatic biopsies were taken at - 45 ± 17, 21 ± 7, 100 ± 23 and 180 ± 23 days in milk (DIM), representing prepartum, early lactation, early mid-lactation and late mid-lactation. The effects of DIM, feeding strategy (FS), strain and their interactions were analyzed with mixed models using repeated measures. Cows of both strains had similar triglyceride levels, mitochondrial function and carnitine palmitoyltransferase activity in liver during lactation. However, there was an effect of DIM and FS as liver triglyceride was higher for the MaxP strategy at 21 DIM and both mitochondrial function and carnitine palmitoyltransferase activity in liver were lower for the MaxP strategy at 21 DIM. Hepatic mitochondrial function and acetylation levels were affected by the interaction between strain and feeding strategy as both variables were higher for NAH cows in the MaxP strategy. Mid-lactation hepatic gene expression of enzymes related to fatty acid metabolism and nuclear receptors was higher for NZH than NAH cows. This work confirms the association between liver triglyceride, decreased hepatic mitochondrial function and greater mitochondrial acetylation levels in cows with a higher inclusion of pasture and suggests differential adaptative mechanisms between NAH and NZH cows to strategies with varying proportions of grazing in the feeding strategy.

[The lipidosis of the liver of dairy cows: Part 1 - Role of insulin and the Growth Hormone-IGF-1 axis]

Lipidosis of the liver of dairy cows is a metabolic disease known since many years and is caused by an uptake of nonesterified fatty acids (NEFA) into the liver cells, limited metabolism of NEFA (oxidation and production of β-hydroxybutyrate), and resynthesis in relation to a low efflux as triglyceride (TG). The pathogenesis of lipidosis includes a) an augmented release of NEFA by mobilisation of adipose tissue, b) uptake of NEFA into the liver cells, c) metabolism of NEFA and d) re-synthesis of triglyceride and e) an efflux of TG as very low density lipoprotein (VLDL). The steps a-e are postpartum modified by hormones as an increase of growth hormone, a pronounced insulin resistance in combination with a decreased insulin and of IGF-1 concentrations. These hormonal changes are related to an uncoupling of the growth hormone-IGF-1-axis with enhanced lipolysis and consequences mentioned above. These alterations are associated with inflammation, oxidative and endoplasmatic stress. The metabolic and hormonal alterations are the result of the selection of dairy cows primarily for milk production without adequate food intake with the consequence of lipidosis, ketosis and further health risks (production diseases).

Investigating circulating miRNA in transition dairy cows: What miRNAomics tells about metabolic adaptation

In the current study, we investigated dairy cows’ circulating microRNA (miRNA) expression signature during several key time points around calving, to get insights into different aspects of metabolic adaptation. In a trial with 32 dairy cows, plasma samples were collected on days −21, 1, 28, and 63 relative to calving. Individually extracted total RNA was subjected to RNA sequencing using NovaSeq 6,000 (Illumina, CA) on the respective platform of IGA Technology Services, Udine, Italy. MiRDeep2 was used to identify known and novel miRNA according to the miRbase collection. Differentially expressed miRNA (DEM) were assessed at a threshold of fold-change &gt; 1.5 and false discovery rate &lt; 0.05 using the edgeR package. The MiRWalk database was used to predict DEM targets and their associated KEGG pathways. Among a total of 1,692 identified miRNA, 445 known miRNA were included for statistical analysis, of which 84, 59, and 61 DEM were found between days −21 to 1, 1 to 28, and 28 to 63, respectively. These miRNA were annotated to KEGG pathways targeting the insulin, MAPK, Ras, Wnt, Hippo, sphingolipid, T cell receptor, and mTOR signaling pathways. MiRNA-mRNA network analysis identified miRNA as master regulators of the biological process including miR-138, miR-149-5p, miR-2466-3p, miR-214, miR-504, and miR-6523a. This study provided new insights into the miRNA signatures of transition to the lactation period. Calving emerged as a critical time point when miRNA were most affected, while the following period appeared to be recovering from massive parturition changes. The primarily affected pathways were key signaling pathways related to establishing metabolic and immune adaptations.

Metabogenomic analysis to functionally annotate the regulatory role of long non-coding RNAs in the liver of cows with different nutrient partitioning phenotype

Long non-coding RNAs (lncRNAs) hold gene regulatory potential, but require substantial further functional annotation in livestock. Applying two metabogenomic approaches by combining transcriptomic and metabolomic analyses, we aimed to identify lncRNAs with potential regulatory function for divergent nutrient partitioning of lactating crossbred cows and to establish metabogenomic interaction networks comprising metabolites, genes and lncRNAs. Through correlation analysis of lncRNA expression with transcriptomic and metabolomic data, we unraveled lncRNAs that have a putative regulatory role in energy and lipid metabolism, the urea and tricarboxylic acid cycles, and gluconeogenesis. Especially FGF21, which correlated with a plentitude of differentially expressed genes, differentially abundant metabolites, as well as lncRNAs, suggested itself as a key metabolic regulator. Notably, lncRNAs in close physical proximity to coding-genes as well as lncRNAs with natural antisense transcripts appear to perform a fine-tuning function in gene expression involved in metabolic pathways associated with different nutrient partitioning phenotypes.

Investigation of β-hydroxybutyrate in early lactation of Simmental cows: Genetic parameters and genomic predictions

Genomic information allows for a more accurate calculation of relationships among animals than the pedigree information, leading to an increase in accuracy of breeding values. Here, we used pedigree-based and single-step genomic approaches to estimate variance components and breeding values for β-hydroxybutyrate milk content (BHB). Additionally, we performed a genome-wide association study (GWAS) to depict its genetic architecture. BHB concentrations within the first 90 days of lactation, estimated from milk medium infrared spectra, were available for 30,461 cows (70,984 records). Genotypes at 42,152 loci were available for 9,123 animals. Low heritabilities were found for BHB using pedigree-based (0.09 ± 0.01) and genomic (0.10 ± 0.01) approaches. Genetic correlation between BHB and milk traits ranged from -0.27 ± 0.06 (BHB and protein percentage) to 0.13 ± 0.07 (BHB and fat-to-protein ratio) using pedigree and from -0.26 ± 0.05 (BHB and protein percentage) to 0.13 ± 0.06 (BHB and fat-to-protein ratio) using genomics. Breeding values were validated for 344 genotyped cows using linear regression method. The genomic EBV (GEBV) had greater accuracy (0.51 vs. 0.45) and regression coefficient (0.98 vs. 0.95) compared to EBV. The correlation between two subsequent evaluations, without and with phenotypes for validation cows, was 0.85 for GEBV and 0.82 for EBV. Predictive ability (correlation between (G)EBV and adjusted phenotypes) was greater when genomic information was used (0.38) than in the pedigree-based approach (0.31). Validation statistics in the pairwise two-trait models (milk yield, fat and protein percentage, urea, fat/protein ratio, lactose and logarithmic transformation of somatic cells count) were very similar to the ones highlighted for the single-trait model. The GWAS allowed discovering four significant markers located on BTA20 (57.5-58.2 Mb), where the ANKH gene is mapped. This gene has been associated with lactose, alpha-lactalbumin and BHB. Results of this study confirmed the usefulness of genomic information to provide more accurate variance components and breeding values, and important insights about the genomic determination of BHB milk content.

Novel Facets of the Liver Transcriptome Are Associated with the Susceptibility and Resistance to Lipid-Related Metabolic Disorders in Periparturient Holstein Cows

Simple Summary

Energy and nutrient demands of the early lactation period can result in the development of metabolic disorders, such as ketosis and fatty liver, in dairy cows. Variability in the incidence of these disorders suggests that some cows have an ability to adapt. The objective of this study was to discover differences in liver gene expression that are associated with a cow’s susceptibility (disposition to disorder during typical conditions) or resistance (disposition to disorder onset and severity when presented a challenge) to metabolic disorders. Cows in a control treatment and a ketosis induction protocol treatment were retrospectively grouped into susceptibility and resistance groups, respectively, by a machine learning algorithm using lipid biomarker concentrations. Whole-transcriptome RNA sequencing was performed on liver samples from these cows. More susceptible cows had lower expression of glutathione metabolism genes, while less resistant cows had greater expression of eicosanoid-metabolism-related genes. Additionally, differentially expressed genes suggested a role for immune-response-related genes in conferring susceptibility and resistance to metabolic disorders. The overall inferred metabolism suggests that responses to oxidative stress may determine susceptibility and resistance to metabolic disorders, with novel implications for immunometabolism.

Abstract

Lipid-related metabolic disorders (LRMD) are prevalent in early lactation dairy cows, and have detrimental effects on productivity and health. Our objectives were to identify cows resistant or susceptible to LRMD using a ketosis induction protocol (KIP) to discover differentially expressed liver genes and metabolic pathways associated with disposition. Clustering cows based on postpartum lipid metabolite concentrations within dietary treatments identified cows more or less susceptible (MS vs. LS) to LRMD within the control treatment, and more or less resistant (MR vs. LR) within the KIP treatment. Whole-transcriptome RNA sequencing was performed on liver samples (−28, +1, and +14 days relative to calving) to assess differential gene and pathway expression (LS vs. MS; MR vs. LR; n = 3 cows per cluster). Cows within the MS and LR clusters had evidence of greater blood serum β-hydroxybutyrate concentration and liver triglyceride content than the LS and MR clusters, respectively. The inferred metabolism of differentially expressed genes suggested a role of immune response (i.e., interferon-inducible proteins and major histocompatibility complex molecules). Additionally, unique roles for glutathione metabolism and eicosanoid metabolism in modulating susceptibility and resistance, respectively, were implicated. Overall, this research provides novel insight into the role of immunometabolism in LRMD pathology, and suggests the potential for unique control points for LRMD progression and severity.

Single-step genomic best linear unbiased predictor genetic parameter estimations and genome-wide associations for milk fatty acid profiles, interval from calving to first insemination, and ketosis in Holstein cattle

Milk fatty acids (FA) have been suggested as biomarkers for early-lactation metabolic diseases and for female fertility status. The aim of the present study was to infer associations between FA, the metabolic disorder ketosis (KET), and the interval from calving to first insemination (ICF) genetically and genomically. In this regard, we focused on a single-step genomic BLUP approach, allowing consideration of genotyped and ungenotyped cows simultaneously. The phenotypic data set considered 38,375 first-lactation Holstein cows, kept in 45 large-scale co-operator herds from 2 federal states in Germany. The calving years for these cows were from 2014 to 2017. Concentrations in milk from the first official milk recording test-day for saturated, unsaturated (UFA), monounsaturated (MUFA), polyunsaturated, palmitic, and stearic (C18:0) FA were determined via Fourier-transform infrared spectroscopy. Ketosis was defined as a binary trait according to a veterinarian diagnosis key, considering diagnoses within a 6-wk interval after calving. A subset of 9,786 cows was genotyped for 40,989 SNP markers. Variance components and heritabilities for all Gaussian distributed FA and for ICF, and for binary KET were estimated by applying single-step genomic BLUP single-trait linear and threshold models, respectively. Genetic correlations were estimated in series of bivariate runs. Genomic breeding values for the single-step genomic BLUP estimations were dependent traits in single-step GWAS. Heritabilities for FA were moderate in the range from 0.09 to 0.20 (standard error = 0.02-0.03), but quite small for ICF (0.08, standard error = 0.01) and for KET (0.05 on the underlying liability scale, posterior standard deviation = 0.02). Genetic correlations between KET and UFA, MUFA, and C18:0 were large (0.74 to 0.85, posterior standard deviation = 0.14-0.19), and low positive between KET and ICF (0.17, posterior standard deviation = 0.22). Genetic correlations between UFA, MUFA, and C18:0 with ICF ranged from 0.34 to 0.46 (standard error = 0.12). In single-step GWAS, we identified a large proportion of overlapping genomic regions for the different FA, especially for UFA and MUFA, and for saturated and palmitic FA. One identical significantly associated SNP was identified for C18:0 and KET on BTA 15. However, there was no genomic segment simultaneously significantly affecting all trait categories ICF, FA, and KET. Nevertheless, some of the annotated potential candidate genes DGKA, IGFBP4, and CXCL8 play a role in lipid metabolism and fertility mechanisms, and influence production diseases in early lactation. Genetic and genomic associations indicate that Fourier-transform infrared spectroscopy FA concentrations in milk from the first official test-day are valuable predictors for KET and for ICF.

Characterization of the liver proteome in dairy cows experiencing negative energy balance at early lactation

Negative energy balance (NEB) is associated with metabolic disorders in early lactation dairy cows. Therefore, our objective was to characterize the liver proteome in cows experiencing either NEB or positive energy balance (PEB). Forty-two multiparous Holstein dairy cows were milked either 2 or 3 times daily for the first 30 days in milk (DIM) to alter EB, and were classified retrospectively as NEB (n = 18) or PEB (n = 22). Liver biopsies were collected from 10 cows (n = 5 from each milking frequency) at 17 ± 3 DIM (NEB, n = 6; PEB, n = 4). The liver proteome was characterized using label-free quantitative shotgun proteomics and Ingenuity Pathway Analysis used to identify key affected canonical pathways. Overall, 2741 proteins were identified, and 68 of those were differentially abundant (P ≤ 0.05 and FC ± 1.5). ENO3 (FC = 10.3, P < 0.01) and FABP5 (FC = -12.5, P = 0.045) were the most dramatically upregulated and downregulated proteins, respectively, in NEB cows. Numerous mitochondrial proteins (NDUFA5, NDUFS3, NDUFA6, COX7A2L, COX6C, and COA5) were differentially abundant. Canonical pathways associated with NEB were LPS/IL-1 mediated inhibition of RXR function, oxidative phosphorylation, and mitochondrial dysfunction. Additionally, cows experiencing NEB had less hepatic IL10 transcript abundance than PEB. Together, NEB was associated with altered hepatic inflammatory status, likely due to oxidative stress from mitochondrial dysfunction. SIGNIFICANCE: Our manuscript describes the associations of negative energy balance with the liver proteome in early lactation dairy cows, when metabolic stress and the incidence of diseases is increased. Specifically, we found associations of negative energy balance with shifts in hepatic protein abundance involved in fatty acid uptake, impaired anti-inflammatory responses, and mitochondrial dysfunction. Moving forward, differentially abundant proteins found in this study may be useful as either biological markers for disease or therapeutic targets to improve metabolic adaptations to lactation in postpartum dairy cattle.

An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake

The selection of cattle with enhanced feed efficiency is of importance with regard to reducing feed costs in the beef industry. Global transcriptome profiling was undertaken on liver and skeletal muscle biopsies from Simmental heifers and bulls divergent for residual feed intake (RFI), a widely acknowledged feed efficiency phenotype, in order to identify genes that may be associated with this trait. We identified 5 genes (adj. p < 0.1) to be differentially expressed in skeletal muscle between high and low RFI heifers with all transcripts involved in oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (adj. p < 0. 1) were differentially expressed in liver tissue between high and low RFI bulls with differentially expressed genes related to amino and nucleotide metabolism as well as endoplasmic reticulum protein processing. No genes were identified as differentially expressed in either heifer liver or bull muscle analyses. Results from this study show that the molecular control of RFI in young cattle is modified according to gender, which may be attributable to differences in physiological maturity between heifers and bulls of the same age. Despite this we have highlighted a number of genes that may hold potential as molecular biomarkers for RFI cattle.

Effect of overconditioning on the hepatic global gene expression pattern of dairy cows at the end of pregnancy

Overconditioning is a risk factor for upregulated pre- and postpartum fat mobilization. Therefore, we hypothesized that overconditioning at the end of pregnancy leads to the accumulation of lipids in the liver and modifications of the hepatic gene expression pattern. The aim of this study was to evaluate the effect of normal- versus overconditioning on the hepatic transcriptomic profile of dairy cows at the end of pregnancy. Ten dry multiparous Holstein cows were killed 2 wk before expected calving. Body condition score (BCS) and backfat thickness (BFT) were evaluated, and blood samples for nonesterified fatty acids (NEFA) were taken before cows were killed. After cows were killed, liver biopsy samples were collected for further assessment of total lipids and RNA sequencing. Five cows were classified as normal-conditioned (median BCS = 3, range 2.75-3.5) and 5 as overconditioned (median BCS = 4, range 4-5). Regression models confirmed that normal-conditioned cows had lower BFT (1.29 ± 0.29 cm; least squares means ± standard error) and serum NEFA (0.16 ± 0.04 mmol/L) in comparison to overconditioned cows (3.14 ± 0.43 cm and 0.38 ± 0.07 mmol/L for BFT and NEFA, respectively). Total liver lipid percentage tended to be lower in normal- versus overconditioned cows (4.63 ± 0.40% and 6.06 ± 0.44%, respectively). In comparison to the mean liver lipid percentage of the normal- and overconditioned cows, 1 overconditioned cow had a relatively low (5.21%) and 1 normal-conditioned cow had a relatively high (6.07%) liver lipid percentage. Differentially expressed genes analysis (edgeR quasi-likelihood method) showed that normal-conditioned cows presented 11 upregulated and 12 downregulated genes in comparison to overconditioned cows. Linear discriminant analysis effects size revealed 133 differentially expressed genes between normal- versus overconditioned cows. Notably, the liver of normal-conditioned cows had upregulated genes associated with liver functionality (ALB, SELENOP, IGF1, and IGF2). On the other hand, overconditioned cows had upregulated genes associated with the acute-phase response (C3, HPX, and, LBP). High basal lipolysis in overconditioned cows at the end of pregnancy increased liver lipid content, and this may alter the hepatic gene expression pattern to a pro-inflammatory state.

Glucose and Fatty Acid Metabolism of Dairy Cows in a Total Mixed Ration or Pasture-Based System During Lactation

In this study, we explored mechanisms related to glucose and fatty acid metabolism in Holstein–Friesian multiparous dairy cows during lactation under two feeding strategies. From 0 to 180 days postpartum, cows were fed total mixed ration (TMR) ad libitum (non-grazing group, G0) or grazed Festuca arundinacea or Medicago sativa and were supplemented with 5.4 kg DM/d of an energy-protein concentrate (grazing group, G1). From 180 to 250 days postpartum, all cows grazed F. arundinacea and were supplemented with TMR. Plasma samples and liver biopsies were collected at −14, 35, 60, 110, 180, and 250 days in milk (DIM) for metabolite, hormone, gene expression, and western blot analysis. Our results showed increased levels of negative energy balance markers: plasma non-esterified fatty acids (NEFA), liver triglyceride and plasma β-hydroxybutyrate (BHB) (P &lt; 0.01), triglyceride and β-hydroxybutyrate concentration were especially elevated for G1 cows. Also, hepatic mRNA expression of gluconeogenic enzymes was upregulated during early lactation (P &lt; 0.05). In particular, methymalonyl-CoA mutase expression was increased for G0 cows (P &lt; 0.05) while pyruvate carboxylase (PC) expression was increased for G1 cows (P &lt; 0.05), suggesting differential gluconeogenic precursors for different feeding strategies. Phosphorylation of AMP-activated protein kinase was increased in early lactation vs. late lactation (P &lt; 0.01) and negatively correlated with PC mRNA levels. The positive association of gluconeogenic genes with proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) hepatic expression supported the importance of this transcription factor in glucose metabolism. The peroxisome proliferator-activated receptor alpha (PPARA) mRNA was increased during early lactation (P &lt; 0.05), and was positively associated to PPARGC1A, carnitine palmitoyl-transferase 1, and hydroxymethylglutaryl-CoA synthase 2 (HMGCS2) mRNA expression. Alongside, hepatic mRNA expression of FABP was decreased for G1 vs. G0 cows (P &lt; 0.05), possibly linked to impaired fatty acid transport and related to accumulation of liver triglycerides, evidencing G1 cows fail to adapt to the demands of early lactation. In sum, our results showed that metabolic adaptations related to early lactation negative energy balance can be affected by feeding strategy and might be regulated by the metabolic sensors AMPK, SIRT1, and coordinated by transcription factors PPARGC1A and PPARA.

Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation

Homeorhetic mechanisms assist dairy cows in the transition from pregnancy to lactation. Less successful cows develop severe negative energy balance (NEB), placing them at risk of metabolic and infectious diseases and reduced fertility. We have previously placed multiparous Holstein Friesian cows from 4 herds into metabolic clusters, using as biomarkers measurements of plasma nonesterified fatty acids, β-hydroxybutyrate, glucose and IGF-1 collected at 14 and 35 d in milk (DIM). This study characterized the global transcriptomic profiles of liver and circulating leukocytes from the same animals to determine underlying mechanisms associated with their metabolic and immune function. Liver biopsy and whole-blood samples were collected around 14 DIM for RNA sequencing. All cows with available RNA sequencing data were placed into balanced (BAL, n = 44), intermediate (n = 44), or imbalanced (IMBAL, n = 19) metabolic cluster groups. Differential gene expression was compared between the 3 groups using ANOVA, but only the comparison between BAL and IMBAL cows is reported. Pathway analysis was undertaken using DAVID Bioinformatic Resources (https://david.ncifcrf.gov/). Milk yields did not differ between BAL and IMBAL cows but dry matter intake was less in IMBAL cows and they were in greater energy deficit at 14 DIM (-4.48 v -11.70 MJ/d for BAL and IMBAL cows). Significantly differentially expressed pathways in hepatic tissue included AMPK signaling, glucagon signaling, adipocytokine signaling, and insulin resistance. Genes involved in lipid metabolism and cholesterol transport were more highly expressed in IMBAL cows but IGF1 and IGFALS were downregulated. Leukocytes from BAL cows had greater expression of histones and genes involved in nucleosomes and cell division. Leukocyte expression of heat shock proteins increased in IMBAL cows, suggesting an unfolded protein response, and several key genes involved in immune responses to pathogens were upregulated (e.g., DEFB13, HP, OAS1Z, PTX3, and TLR4). Differentially expressed genes upregulated in IMBAL cows in both tissues included CD36, CPT1, KFL11, and PDK4, all central regulators of energy metabolism. The IMBAL cows therefore had greater difficulty maintaining glucose homeostasis and had dysregulated hepatic lipid metabolism. Their energy deficit was associated with a reduced capacity for cell division and greater evidence of stress responses in the leukocyte population, likely contributing to an increased risk of infectious disease.

Green tea polyphenols supplementation alters immunometabolism and oxidative stress in dairy cows with hyperketonemia

Peripartal cows often experience negative energy balance, and are therefore prone to suffering from metabolic diseases such as hyperketonemia, which causes financial losses in dairy farms. This study aimed to investigate the effect of green tea polyphenol (GTP) supplementation during the periparturient period on production performance, oxidative stress and immunometabolism in dairy cows with hyperketonemia. One hundred Holstein cows were assigned to GTP (0.2 g/kg DM; n = 50) or control (without GTP; n = 50) group based on body weight, previous milk yield, and parity on d 15 before expected parturition. Subsequently, 10 cows with hyperketonemia were selected from each group, according to blood β-hydroxybutyric acid (BHBA) concentration between 1.2 and 2.9 mmol/L from 2 to 3 d postpartum. All cows were fed a close-up diet and a lactation diet with or without GTP supply from 15 d prepartum until 30 d postpartum. Milk and blood samples were obtained from 20 cows selected with hyperketonemia on 10, 20, and 30 d postpartum. Compared with control cows, greater milk yield and lower somatic cell count were observed in GTP cows. The GTP group had lower concentrations of BHBA, free fatty acids, cholesterol, triglyceride, reactive oxygen species, malondialdehyde, and hydrogen peroxide, greater concentrations of glucose, lower activities of aspartate aminotransferase, alanine aminotransferase, and glutamyl transpeptidase, alongside greater activities of superoxide dismutase, glutathione peroxidase, and total antioxidant capacity. Additionally, GTP supplementation up-regulated concentrations of interleukin-6 and interleukin-10, but down-regulated concentrations of tumor necrosis factor-α, interleukin-1β, interleukin-2, interleukin-8, and interferon-γ in plasma. Greater concentrations of plasma immunoglobulin G were also detected in the GTP group. Overall, the data suggested that GTP supplementation from 15 d prepartum to 30 d postpartum improved the milk yield and health status in cows with hyperketonemia during early lactation.

Genetic and nongenetic profiling of milk β-hydroxybutyrate and acetone and their associations with ketosis in Holstein cows

Ketosis is a metabolic disorder of increasing importance in high-yielding dairy cows, but accurate population-wide binary health trait recording is difficult to implement. Against this background, proper Gaussian indicator traits, which can be routinely measured in milk, are needed. Consequently, we focused on the ketone bodies acetone and β-hydroxybutyrate (BHB), measured via Fourier-transform infrared spectroscopy (FTIR) in milk. In the present study, 62,568 Holstein cows from large-scale German co-operator herds were phenotyped for clinical ketosis (KET) according to a veterinarian diagnosis key. A sub-sample of 16,861 cows additionally had first test-day observations for FTIR acetone and BHB. Associations between FTIR acetone and BHB with KET and with test-day traits were studied phenotypically and quantitative genetically. Furthermore, we estimated SNP marker effects for acetone and BHB (application of genome-wide association studies) based on 40,828 SNP markers from 4,384 genotyped cows, and studied potential candidate genes influencing body fat mobilization. Generalized linear mixed models were applied to infer the influence of binary KET on Gaussian-distributed acetone and BHB (definition of an identity link function), and vice versa, such as the influence of acetone and BHB on KET (definition of a logit link function). Additionally, linear models were applied to study associations between BHB, acetone and test-day traits (milk yield, fat percentage, protein percentage, fat-to-protein ratio and somatic cell score) from the first test-day after calving. An increasing KET incidence was statistically significant associated with increasing FTIR acetone and BHB milk concentrations. Acetone and BHB concentrations were positively associated with fat percentage, fat-to-protein ratio and somatic cell score. Bivariate linear animal models were applied to estimate genetic (co)variance components for KET, acetone, BHB and test-day traits within parities 1 to 3, and considering all parities simultaneously in repeatability models. Pedigree-based heritabilities were quite small (i.e., in the range from 0.01 in parity 3 to 0.07 in parity 1 for acetone, and from 0.03-0.04 for BHB). Heritabilites from repeatability models were 0.05 for acetone, and 0.03 for BHB. Genetic correlations between acetone and BHB were moderate to large within parities and considering all parities simultaneously (0.69-0.98). Genetic correlations between acetone and BHB with KET from different parities ranged from 0.71 to 0.99. Genetic correlations between acetone across parities, and between BHB across parities, ranged from 0.55 to 0.66. Genetic correlations between KET, acetone, and BHB with fat-to-protein ratio and with fat percentage were large and positive, but negative with milk yield. In genome-wide association studies, we identified SNP on BTA 4, 10, 11, and 29 significantly influencing acetone, and on BTA 1 and 16 significantly influencing BHB. The identified potential candidate genes NRXN3, ACOXL, BCL2L11, HIBADH, KCNJ1, and PRG4 are involved in lipid and glucose metabolism pathways.

Knockdown of phosphatase and tensin homolog (PTEN) inhibits fatty acid oxidation and reduces very low density lipoprotein assembly and secretion in calf hepatocytes

Dairy cows with fatty liver exhibit hepatic lipid accumulation and disturbances in fatty acid oxidation and lipid transport. Phosphatase and tensin homolog (PTEN), a lipid phosphatase, regulates intrahepatic fatty acid oxidation and lipid transport in mice. Whether PTEN play a role in fatty acid oxidation and very low density lipoprotein (VLDL) assembly in calf hepatocytes are unknown. Hepatocytes isolated from 3 healthy female Holstein calves (1 d old, 30-40 kg) were infected with empty adenovirus with green fluorescent protein for 48 h (Ad-GFP group) or infected with PTEN knockdown adenovirus for 48 h (Ad-shPTEN group), or cultured in RPMI-1640 without Ad-shPTEN or Ad-GFP (control group). Compared with the Ad-GFP group, PTEN knockdown decreased mRNA and protein abundance and the activity of fatty acid oxidation-related molecules, including acyl-coA synthetase long-chain 1, carnitine palmitoyltransferase 1, carnitine palmitoyltransferase 2, and 3-hydroxy acyl-coA dehydrogenase. Furthermore, PTEN knockdown decreased mRNA and protein abundance of VLDL assembly-related molecules, including apolipoprotein B100, apolipoprotein E, microsomal triglyceride transfer protein, and low density lipoprotein receptor. Importantly, PTEN knockdown promoted triglyceride accumulation in hepatocytes and reduced the VLDL content in culture medium. A subsequent study was conducted on the following 4 groups: cells infected with Ad-GFP for 48 h and then treated with 2% BSA for another 24 h (Ad-GFP + BSA); cells infected with Ad-GFP for 48 h and then treated with 1.2 mM free fatty acids (FFA) and 2% BSA for another 24 h (Ad-GFP + 1.2 mM FFA); cells infected with Ad-shPTEN for 48 h and then treated with 2% BSA for another 24 h (Ad-shPTEN + BSA); cells infected with Ad-shPTEN for 48 h and then treated with 1.2 mM FFA and 2% BSA for another 24 h (Ad-shPTEN + 1.2 mM FFA). Compared with Ad-GFP + BSA, the abundances of PTEN and of fatty acid oxidation- and VLDL assembly-related proteins were lower in the Ad-GFP + 1.2 mM FFA group. Importantly, PTEN knockdown heightened the increase in triglyceride accumulation of hepatocytes and the decrease in VLDL content in culture medium induced by FFA. Overall, these in vitro data indicate that FFA inhibits PTEN expression, leading to triglyceride accumulation and the inhibition of VLDL assembly in calf hepatocytes. These findings suggest that PTEN may be a potential therapeutic target for FFA-induced hepatic steatosis in dairy cows.

Assessing selection signatures within and between selected lines of dual-purpose black and white and German Holstein cattle

The aim of this study was to detect selection signatures considering cows from the German Holstein (GH) and the local dual-purpose black and white (DSN) population, as well as from generated sub-populations. The 4654 GH and 261 DSN cows were genotyped with the BovineSNP50 Genotyping BeadChip. The geographical herd location was used as an environmental descriptor to create the East-DSN and West-DSN sub-populations. In addition, two further sub-populations of GH cows were generated, using the extreme values for solutions of residual effects of cows for the claw disorder dermatitis digitalis. These groups represented the most susceptible and most resistant cows. We used cross-population extended haplotype homozygosity methodology (XP-EHH) to identify the most recent selection signatures. Furthermore, we calculated Wright's fixation index (F_ST ). Chromosomal segments for the top 0.1 percentile of negative or positive XP-EHH scores were studied in detail. For gene annotations, we used the Ensembl database and we considered a window of 250 kbp downstream and upstream of each core SNP corresponding to peaks of XP-EHH. In addition, functional interactions among potential candidate genes were inferred via gene network analyses. The most outstanding XP-EHH score was on chromosome 12 (at 77.34 Mb) for DSN and on chromosome 20 (at 36.29-38.42 Mb) for GH. Selection signature locations harbored QTL for several economically important milk and meat quality traits, reflecting the different breeding goals for GH and DSN. The average F_ST value between GH and DSN was quite low (0.068), indicating shared founders. For group stratifications according to cow health, several identified potential candidate genes influence disease resistance, especially to dermatitis digitalis.

Hepatic metabolomics and transcriptomics to study susceptibility to ketosis in response to prepartal nutritional management

Background

Ketosis in dairy cows is associated with body fat mobilization during the peripartal period. Sub-clinical and clinical ketosis arise more frequently in cows that are overfed energy during the entire dry (last 50 to 45 days prior to parturition) or close-up period (last ~ 28 days prepartum).

Methods

A retrospective analysis was performed on 12 cows from a larger cohort that were fed a higher-energy diet [1.54 Mcal/kg of dry matter (DM); 35.9% of DM corn silage and 13% of DM ground corn] during the close-up dry period, of which 6 did not develop clinical ketosis (OVE, 0.83 mmol/L plasma hydroxybutyrate; BHB) and 6 were diagnosed with clinical ketosis (KET, 1.4 mmol/L BHB) during the first week postpartum. A whole-transcriptome bovine microarray (Agilent Technologies) and metabolomics (GC-MS, LC-MS; Metabolon® Inc.) were used to perform transcript and metabolite profiling of liver tissue harvested at − 10 days relative to parturition which allowed to establish potential associations between prepartal transcriptome/metabolome profiles and susceptibility to clinical ketosis postpartum.

Results

Cows in KET had greater (P = 0.01) overall body weight between − 2 and 1 week around parturition, but similar body condition score than OVE. Although dry matter intake (DMI) did not differ prepartum, KET cows had lower (P < 0.01) DMI and similar milk yield as OVE cows during the first week postpartum. Transcriptome analysis revealed a total of 3065 differentially expressed genes (DEG; P ≤ 0.05) in KET. Metabolomics identified 15 out of 313 total biochemical compounds significantly affected (P ≤ 0.10) in KET. Among those, greater concentrations (P ≤ 0.06, + 2.3-fold) of glycochenodeoxycholate in KET cows also have been detected in humans developing non-alcoholic fatty liver disease. Bioinformatics analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database and the DEG revealed that, among the top 20 most-impacted metabolic pathway categories in KET, 65% were overall downregulated. Those included ‘Metabolism of cofactors and vitamins’, ‘Biosynthesis of other secondary metabolites’, ‘Lipid’, ‘Carbohydrate’, and ‘Glycan biosynthesis and metabolism’. The lower relative concentration of glucose-6-phosphate and marked downregulation of fructose-1,6-bisphosphatase 2 and pyruvate dehydrogenase kinase 4 support a strong impairment in gluconeogenesis in prepartal liver of cows developing KET postpartum. Among the top 20 most-impacted non-metabolic pathways, 85% were downregulated. Pathways such as ‘mTOR signalling’ and ‘Insulin signalling’ were among those. ‘Ribosome’, ‘Nucleotide excision repair’, and ‘Adherens junctions’ were the only upregulated pathways in cows with KET.

Conclusions

The combined data analyses revealed more extensive alterations of the prepartal liver transcriptome than metabolome in cows overfed energy and developing ketosis postpartum. The causative link between these tissue-level adaptations and onset of clinical ketosis needs to be studied further.

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health

Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.

Different mitochondrial DNA copy number in liver and mammary gland of lactating cows with divergent genetic background for milk production

Adequate metabolic adaptation of key tissues playing an essential role for bioenergetic homeostasis and lactogenesis is critical in cows to adapt to changes in energy requirements and physiological processes during the lactation period. Mitochondria are recognized as central to meet energy needs and maintaining of metabolic homeostasis because mitochondrial DNA (mtDNA) is template for several polypeptides of the respiratory chain complexes essential for ATP generation. The quantity of mtDNA in a cell has been widely used as a surrogate marker for the capacity of cells for energy generation. In our study we analyzed the mtDNA copy number and the mRNA expression of important nuclear encoded genes controlling mitochondrial biogenesis in liver and mammary gland. We compared cows with a nuclear genome dairy × beef crossbred make-up to purebred German Holstein dairy cows. The study revealed tissue-specific variations of mtDNA copy number and expression levels of nuclear genes involved in mitochondrial biogenesis when comparing lactating cows with different genetic predisposition regarding milk performance. This may reflect nuclear genome-determined genetic differences between the cow groups in coping with metabolic demands and physiological changes during lactation. The results indicate that mitochondrial biogenesis processes in the liver and mammary gland appear to be impaired in high lactating dairy cows, which consequently, would point to a disturbed energy adaptation. The results provide a basis to further elucidate the adaptive and regulatory modulation of the mitochondrial biogenesis in response to lactation-associated metabolic challenges in lactating cows.

STAT6, PBX2, and PBRM1 Emerge as Predicted Regulators of 452 Differentially Expressed Genes Associated With Puberty in Brahman Heifers

The liver plays a central role in metabolism and produces important hormones. Hepatic estrogen receptors and the release of insulin-like growth factor 1 (IGF1) are critical links between liver function and the reproductive system. However, the role of liver in pubertal development is not fully understood. To explore this question, we applied transcriptomic analyses to liver samples of pre- and post-pubertal Brahman heifers and identified differentially expressed (DE) genes and genes encoding transcription factors (TFs). Differential expression of genes suggests potential biological mechanisms and pathways linking liver function to puberty. The analyses identified 452 DE genes and 82 TF with significant contribution to differential gene expression by using a regulatory impact factor metric. Brain-derived neurotrophic factor was observed as the most down-regulated gene (P = 0.003) in post-pubertal heifers and we propose this gene influences pubertal development in Brahman heifers. Additionally, co-expression network analysis provided evidence for three TF as key regulators of liver function during pubertal development: the signal transducer and activator of transcription 6, PBX homeobox 2, and polybromo 1. Pathway enrichment analysis identified transforming growth factor-beta and Wnt signaling pathways as significant annotation terms for the list of DE genes and TF in the co-expression network. Molecular information regarding genes and pathways described in this work are important to further our understanding of puberty onset in Brahman heifers.

Integrated regulatory network reveals novel candidate regulators in the development of negative energy balance in cattle

Negative energy balance (NEB) is an altered metabolic state in modern high-yielding dairy cows. This metabolic state occurs in the early postpartum period when energy demands for milk production and maintenance exceed that of energy intake. Negative energy balance or poor adaptation to this metabolic state has important effects on the liver and can lead to metabolic disorders and reduced fertility. The roles of regulatory factors, including transcription factors (TFs) and micro RNAs (miRNAs) have often been separately studied for evaluating of NEB. However, adaptive response to NEB is controlled by complex gene networks and still not fully understood. In this study, we aimed to discover the integrated gene regulatory networks involved in NEB development in liver tissue. We downloaded data sets including mRNA and miRNA expression profiles related to three and four cows with severe and moderate NEB, respectively. Our method integrated two independent types of information: module inference network by TFs, miRNAs and mRNA expression profiles (RNA-seq data) and computational target predictions. In total, 176 modules were predicted by using gene expression data and 64 miRNAs and 63 TFs were assigned to these modules. By using our integrated computational approach, we identified 13 TF-module and 19 miRNA-module interactions. Most of these modules were associated with liver metabolic processes as well as immune and stress responses, which might play crucial roles in NEB development. Literature survey results also showed that several regulators and gene targets have already been characterized as important factors in liver metabolic processes. These results provided novel insights into regulatory mechanisms at the TF and miRNA levels during NEB. In addition, the method described in this study seems to be applicable to construct integrated regulatory networks for different diseases or disorders.

Expression of hepatic genes related to energy metabolism during the transition period of Holstein and F1 Holstein-Gir cows

The aim of this study was to investigate the expression of genes encoding enzymes and other factors involved with carbohydrate and lipid metabolism in the liver of 2 genetic groups of dairy cows during the transition period. We analyzed the expression of glucose-6-phosphatase (G6PC), cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C), methylmalonyl-CoA mutase (MUT), β-hydroxybutyrate dehydrogenase-2 (BDH2), acetyl-CoA carboxylase (ACC), carnitine palmitoyltransferase-2 (CPT2), 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), glucose transporter-2 (SLC2A2), and the transcription factor peroxisome proliferator-activated receptor α (PPARA). Blood concentrations of glucose, nonesterified fatty acids, and β-hydroxybutyrate were also determined. Liver biopsies and blood samples were taken at d 15 prepartum and at d 6, 21, 36, 51, and 66 postpartum from Holsteins (n = 6) and F₁ Holstein-Gir (n = 6) cows. Cows were kept under the same prepartum and postpartum management conditions. The results showed that the expression of G6PC, PEPCK-C, BDH2, ACC, CPT2, HMGCR, SLC2A2, and PPARA genes did not differ between genetic groups. Except for PEPCK-C, no interaction between genetic groups and the experimental period was observed. Within both groups of cows, G6PC and PEPCK-C gene expression decreased when comparing prepartum gene expression with 21 and 36 DIM, and increased in d 51 postpartum. MUT mRNA levels differed between the 2 genetic groups and displayed a significant increase after d 36 postpartum, whereas mRNA levels of HMGCR tended to increase when comparing d 21 and 36 to d 51 postpartum. Glucose concentrations also differed between genetic groups, being significantly higher in the plasma of F₁ Holstein-Gir cows than in Holstein cows, but no differences were found within each group during the analysis period. β-Hydroxybutyrate and nonesterified fatty acid concentrations did not differ between genetic groups, but displayed increased levels from prepartum to d 6 and 21 postpartum. Our results indicated that expression in the liver of genes involved with glucose and fatty acid metabolism were similar in both groups of cows and significant differences were observed between the 2 groups in the expression of MUT, a gene involved in propionate metabolism.

Linoleic acid, α-linolenic acid and enterolactone affect lipid oxidation and expression of lipid metabolism and antioxidant-related genes in hepatic tissue of dairy cows

Although beneficial effects have been attributed to PUFA supplementation in high-yielding dairy cows, diets rich in PUFA may also increase oxidative stress in tissues such as the liver. To fully exploit the health benefits of PUFA, we believe that the addition of natural antioxidants could help in preventing oxidative damage. Using an in vitro precision-cut liver slices (PCLS) tissue culture system, we investigated the effects of different linoleic acid (LA, n-6):α-linolenic acid (ALA, n-3) ratios (LA:ALA ratio of 4, LA:ALA ratio of 15 and LA:ALA ratio of 25) in the presence or absence of the antioxidant enterolactone (ENL) on (1) the mRNA abundance of genes with key roles in hepatic lipid metabolism, oxidative stress response and inflammatory processes, (2) oxidative damages to lipids and proteins and (3) superoxide dismutase activity in early-lactating dairy cows. The addition of LA and ALA to PCLS culture media increased oxidative damage to lipids as suggested by higher concentrations of thiobarbituric acid reactive substances and increased the expression of nuclear factor erythroid 2-related factor 2 target genes. The addition of ENL was effective in preventing lipid peroxidation caused by LA and ALA. Transcript abundance of sterol regulatory element-binding transcription factor 1 and its lipogenic target genes acetyl-CoA carboxylase α, fatty acid synthase (FASN) and stearoyl-CoA desaturase (SCD) was decreased with LA and ALA, whereas ENL decreased FASN and SCD gene expression. Our results show that addition of LA and ALA to PCLS culture media lowers hepatic lipogenic gene expression and increases oxidative damages to lipids. On the other hand, addition of ENL prevents oxidative damages provoked by these PUFA.

Hanging Drop, A Best Three-Dimensional (3D) Culture Method for Primary Buffalo and Sheep Hepatocytes

Livestock, having close resemblance to humans, could be a better source of primary hepatocytes than rodents. Herein, we successfully developed three-dimensional (3D) culturing system for primary sheep and buffalo hepatocytes. The 3D-structures of sheep hepatocytes were formed on the fifth-day and maintained until the tenth-day on polyHEMA-coated plates and in hanging drops with William’s E media (HDW). Between the cultured and fresh cells, we observed a similar expression of GAPDH, HNF4α, ALB, CYP1A1, CK8 and CK18. Interestingly, a statistically significant increase was noted in the TAT, CPS, AFP, AAT, GSP and PCNA expression. In buffalo hepatocytes culture, 3D-like structures were formed on the third-day and maintained until the sixth-day on polyHEMA and HDW. The expression of HNF4α, GSP, CPS, AFP, AAT, PCNA and CK18 was similar between cultured and fresh cells. Further, a statistically significant increase in the TAT and CK8 expression, and a decrease in the GAPDH, CYP1A1 and ALB expression were noted. Among the culture systems, HDW maintained the liver transcript markers more or less similar to the fresh hepatocytes of the sheep and buffalo for ten and six days, respectively. Taken together, hanging drop is an efficient method for 3D culturing of primary sheep and buffalo hepatocytes.

RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

Background

The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE.

Results

The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450.

Conclusion

We used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular pathways. The DEGs that were identified were the CYP’s and GIMAP genes for the Holstein and Jersey cows, respectively, which are related to the primary immunodeficiency pathway and play a major role in feed utilization and the metabolism of lipids, sugars and proteins.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3622-9) contains supplementary material, which is available to authorized users.

Supplements of vitamins B9 and B12 affect hepatic and mammary gland gene expression profiles in lactating dairy cows

Background

A combined supplement of vitamins B9 and B12 was reported to increase milk and milk component yields of dairy cows without effect on feed intake. The present study was undertaken to verify whether this supplementation positively modifies the pathways involved in milk and milk component synthesis. Thus, by studying the transcriptome activity in these tissues, the effect of supplements of both vitamins on the metabolism of both liver and mammary gland, was investigated. For this study, 24 multiparous Holstein dairy cows were assigned to 6 blocks of 4 animals each according to previous 305-day milk production. Within each block, cows were randomly assigned to weekly intramuscular injections of 5 mL of either saline 0.9 % NaCl, 320 mg of vitamin B9, 10 mg of vitamin B12 or a combination of both vitamins (B9 + B12). The experimental period began 3 weeks before the expected calving date and lasted 9 weeks of lactation. Liver and mammary biopsies were performed on lactating dairy cows 64 ± 3 days after calving. Samples from both tissues were analyzed by microarray and qPCR to identify genes differentially expressed in hepatic and mammary tissues.

Results

Microarray analysis identified 47 genes in hepatic tissue and 16 genes in the mammary gland whose expression was modified by the vitamin supplements. Gene ontology (GO) categorizes genes in non-overlapping domains of molecular biology. Panther is one of the online GO resources used for gene function classification. It classifies the 63 genes according to Molecular Function, Biological Process and Protein Class. Most of the biological processes modulated by the vitamin supplements were associated to developmental process, protein metabolic process, transport and response to inflammation. In the liver, most of the genes modulated by the vitamin treatments involved protein metabolic process while developmental process appeared to be more affected by the treatments in mammary gland. Out of 25 genes analysed by qPCR, 7 were validated.

Conclusion

The results indicate that several metabolic processes were modulated by the supplementation of vitamins in early-lactating dairy cows. In addition, the results suggest that the vitamin supplements promoted liver regeneration and reduced catabolism of lipids in early lactation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2872-2) contains supplementary material, which is available to authorized users.

Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of hepatic tissue in cattle

Background

Compensatory growth (CG) is an accelerated growth phenomenon observed in animals upon re-alimentation following a period of dietary restriction. It is typically utilised in livestock systems to reduce feed costs during periods of reduced feed availability. The biochemical mechanisms controlling this phenomenon, however, are yet to be elucidated. This study aimed to uncover the molecular mechanisms regulating the hepatic expression of CG in cattle, utilising RNAseq. RNAseq was performed on hepatic tissue of bulls following 125 days of dietary restriction (RES) and again following 55 days of subsequent re-alimentation during which the animals exhibited significant CG. The data were compared with those of control animals offered the same diet on an ad libitum basis throughout (ADLIB). Elucidation of the molecular control of CG may yield critical information on genes and pathways which could be targeted as putative molecular biomarkers for the selection of animals with improved CG potential.

Results

Following a period of differential feeding, body-weight and liver weight were 161 and 4 kg higher, respectively, for ADLIB compared with RES animals. At this time RNAseq analysis of liver tissue revealed 1352 significantly differentially expressed genes (DEG) between the two treatments. DEGs indicated down-regulation of processes including nutrient transport, cell division and proliferation in RES. In addition, protein synthesis genes were up-regulated in RES following a period of restricted feeding. The subsequent 55 days of ad libitum feeding for both groups resulted in the body-weight difference reduced to 84 kg, with no difference in liver weight between treatment groups. At the end of 55 days of unrestricted feeding, 49 genes were differentially expressed between animals undergoing CG and their continuously fed counterparts. In particular, hepatic expression of cell proliferation and growth genes were greater in animals undergoing CG.

Conclusions

Greater expression of cell cycle and cell proliferation genes during CG was associated with a 100 % recovery of liver weight during re-alimentation. Additionally, an apparent up-regulation in capacity for cellular protein synthesis during restricted feeding may contribute to and sustain CG during re-alimentation. DEGs identified are potential candidate genes for the identification of biomarkers for CG, which may be incorporated into future breeding programmes.

Electronic supplementary material

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Liver condition of Holstein cows affects mitochondrial function and fertilization ability of oocytes

The aim of the present study was to examine the fertilization ability and mitochondrial function of oocytes derived from cows with or without liver damage. Oocytes were collected from the ovaries of cows with damaged livers (DL) and those of cows with healthy livers (HL), subjected to in vitro maturation, and fertilized in vitro. A significantly high abnormal fertilization rate was observed for oocytes from DL cows compared to oocytes from HL cows. The time to dissolve the zona pellucida by protease before fertilization was similar between the two liver conditions, whereas after fertilization treatment this time was shorter for DL cows than for HL cows. The percentage of oocytes with equivalent cortical granule distributions underneath the membrane was greater for in vitro matured oocytes from HL cows, whereas an immature distribution pattern was observed for oocytes from DL cows. In addition, a greater percentage of oocytes derived from HL cows released cortical granules following fertilization compared with oocytes from DL cows. Mitochondrial function determined by ATP content and membrane potential were similar at the germinal vesicle stage, but post-in vitro maturation, the oocytes derived from HL cows showed higher values than DL cows. The mitochondrial DNA copy number in oocytes was similar between the two liver conditions for both the germinal vesicle and post-in vitro maturation oocytes. In conclusion, liver damage induces low fertilization, likely because of incomplete cortical granule distribution and release, and the maturation of oocytes from DL cows contain low-functioning mitochondria compared to their HL counterparts.

Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis

BACKGROUND

The regulation of endometrial inflammation has important consequences for the resumption of bovine fertility postpartum. All cows experience bacterial influx into the uterus after calving; however a significant proportion fail to clear infection leading to the development of cytological endometritis (CE) and compromised fertility. We hypothesised that early immunological changes could not only act as potential prognostic biomarkers for the subsequent development of disease but also shed light on the pathogenesis of endometritis in the postpartum dairy cow.

METHODS

Endometrial biopsy RNA was extracted from 15 cows at 7 and 21 days postpartum (DPP), using the Qiagen RNeasy(®) Plus Mini kit and quality determined using an Agilent 2100 bioanalyser. Disease status was determined by histpathology based on inflammatory cell infiltrate. RNA-seq of both mRNA and miRNA libraries were performed on an Illumina® HiSeq(™) 2000. Paired reads were aligned to the bovine genome with Bowtie2 and differentially expressed genes were identified using EdgeR. Significantly over-represented Gene Ontology terms were identified using GO-seq, and pathway analysis was performed using KEGG. Quanititative real-time PCR was also performed for validation (ABI 7500 fast). Haematology was assessed using an automated ADVIA 2120 analyser. Serum proteins were evaluated by ELISA and metabolite analysis was performed using a Beckman Coulter AU 400 clinical analyser. Terminal-restriction fragment length polymorphism (T-RFLP) was used to obtain fingerprints of the microbial communities present.

RESULTS

Next-generation sequencing from endometrial biopsies taken at 7 DPP identified significant induction of inflammatory gene expression in all cows. Despite the common inflammatory profile and enrichment of the Toll-like receptor and NFκB pathways, 73 genes and 31 miRNAs were significantly differentially expressed between healthy cows (HC, n = 9) and cows which subsequently developed CE at 7 DPP (n = 6, FDR < 0.1). While significant differential expression of 4197 genes in the transcriptome of healthy cows between 7 and 21 DPP showed the transition from a proinflammatory to tissue profliferation and repair, only 31 genes were differentially expressed in cows with CE (FDR < 0.1), indicating the arrest of such a transition. A link betwene the dysregulated inflammatory response and the composition of the uterine microbial communities was suggested by the presence of significant differences in uterine bacterial tRFLP profiles between HC and CE groups. Furthermore, inflammatory activity was not confined to the uterus; decreased circulating granulocytes and increased Acute Phase Protein (SAA and HP) expression levels were detected in plasma at 7 DPP in cows that developed CE.

CONCLUSION

Our data suggests that the IL1 and IL17 inflammatory cascade activated early postpartum is resolved thereby restoring homeostasis in healthy cows by 21 DPP, but this transition fails to occur in cows which develop CE. Despite a common early inflammatory profile, elevated and differential expression of specific immune genes may identify cows at risk of prolonged inflammation and the development of CE postpartum.

Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes

BACKGROUND

Efficiency of feed utilization is important for animal production because it can reduce greenhouse gas emissions and improve industry profitability. However, the genetic basis of feed utilization in livestock remains poorly understood. Recent developments in molecular genetics, such as platforms for genome-wide genotyping and sequencing, provide an opportunity to identify genes and pathways that influence production traits. It is known that transcriptional networks influence feed efficiency-related traits such as growth and energy balance. This study sought to identify differentially expressed genes in animals genetically divergent for Residual Feed Intake (RFI), using RNA sequencing methodology (RNA-seq) to obtain information from genome-wide expression profiles in the liver tissues of Nelore cattle.

RESULTS

Differential gene expression analysis between high Residual Feed Intake (HRFI, inefficient) and low Residual Feed Intake (LRFI, efficient) groups was performed to provide insights into the molecular mechanisms that underlie feed efficiency-related traits in beef cattle. A total of 112 annotated genes were identified as being differentially expressed between animals with divergent RFI phenotypes. These genes are involved in ion transport and metal ion binding; act as membrane or transmembrane proteins; and belong to gene clusters that are likely related to the transport and catalysis of molecules through the cell membrane and essential mechanisms of nutrient absorption. Genes with functions in cellular signaling, growth and proliferation, cell death and survival were also differentially expressed. Among the over-represented pathways were drug or xenobiotic metabolism, complement and coagulation cascades, NRF2-mediated oxidative stress, melatonin degradation and glutathione metabolism.

CONCLUSIONS

Our data provide new insights and perspectives on the genetic basis of feed efficiency in cattle. Some previously identified mechanisms were supported and new pathways controlling feed efficiency in Nelore cattle were discovered. We potentially identified genes and pathways that play key roles in hepatic metabolic adaptations to oxidative stress such as those involved in antioxidant mechanisms. These results improve our understanding of the metabolic mechanisms underlying feed efficiency in beef cattle and will help develop strategies for selection towards the desired phenotype.

Integrative analyses of hepatic differentially expressed genes and blood biomarkers during the peripartal period between dairy cows overfed or restricted-fed energy prepartum

Using published dairy cattle liver transcriptomics dataset along with novel blood biomarkers of liver function, metabolism, and inflammation we have attempted an integrative systems biology approach applying the classical functional enrichment analysis using DAVID, a newly-developed Dynamic Impact Approach (DIA), and an upstream gene network analysis using Ingenuity Pathway Analysis (IPA). Transcriptome data was generated from experiments evaluating the impact of prepartal plane of energy intake [overfed (OF) or restricted (RE)] on liver of dairy cows during the peripartal period. Blood biomarkers uncovered that RE vs. OF led to greater prepartal liver distress accompanied by a low-grade inflammation and larger proteolysis (i.e., higher haptoglobin, bilirubin, and creatinine). Post-partum the greater bilirubinaemia and lipid accumulation in OF vs. RE indicated a large degree of liver distress. The re-analysis of microarray data revealed that expression of >4,000 genes was affected by diet × time. The bioinformatics analysis indicated that RE vs. OF cows had a liver with a greater lipid and amino acid catabolic capacity both pre- and post-partum while OF vs. RE cows had a greater activation of pathways/functions related to triglyceride synthesis. Furthermore, RE vs. OF cows had a larger (or higher capacity to cope with) ER stress likely associated with greater protein synthesis/processing, and a higher activation of inflammatory-related functions. Liver in OF vs. RE cows had a larger cell proliferation and cell-to-cell communication likely as a response to the greater lipid accumulation. Analysis of upstream regulators indicated a pivotal role of several lipid-related transcription factors (e.g., PPARs, SREBPs, and NFE2L2) in priming the liver of RE cows to better face the early postpartal metabolic and inflammatory challenges. An all-encompassing dynamic model was proposed based on the findings.

Effects of herbage allowance of native grasslands in purebred and crossbred beef cows: metabolic, endocrine and hepatic gene expression profiles through the gestation-lactation cycle

Our objective was to evaluate the metabolic, endocrine and hepatic mRNA profiles through the gestation-lactation cycle in purebred (PU: Angus and Hereford) and crossbred (CR: reciprocal F1 crosses) mutliparous beef cows (n=32), grazing on two herbage allowances of native pastures (2.5 v. 4 kg dry matter/kg BW; LO v. HI) and their associations with cow's productive performance (calf birth weight, milk production and commencement of luteal activity). Cow BW, body condition score (BCS) and blood samples were collected monthly, starting at -165 days relative to calving (days), and every 2 weeks after calving until +60 days of lactation. Liver biopsies were collected at -165, -75, -45, -15±10, and +15 and +60±3 days. Metabolic, endocrine and hepatic gene expression profiles, and calf birth weight, milk yield and postpartum commencement of luteal activity were evaluated. Overall, the most pronounced changes in metabolic, endocrine and hepatic gene expression occurred during winter gestation (-165 to -45 days), when all cows experienced the onset of a negative energy balance (decreased BCS, glucose and insulin, and increased non-esterified fatty acid concentrations, P<0.008). Concentrations of insulin and IGF-I were greater (P<0.037) in HI than in LO cows. However, serum IGF-I concentrations and hepatic growth hormone receptor (GHR) and IGF1 mRNA decreased (P<0.05) during the winter gestation period only in HI cows. Although IGF-I concentrations decreased (P<0.05) during the early postpartum (-15 v.+15 days) for all cows, the typical molecular mechanism that control the uncoupling of the growth hormone-IGF1 axis during the transition period of the dairy cattle (reduced hepatic GHR1A and IGF-I mRNA) was not observed in this study. The hepatic mRNA expression of key transcripts involved in gluconeogenesis and fatty-acid oxidation were upregulated (P<0.05) during winter gestation (from -165 to -45, -15 or +15 days, depending on the cow groups). Particularly, acyl-CoA oxidase-1 mRNA was greater for CR than for PU cows during winter gestation (-75 and -45 days), and fibroblast growth factor-21 mRNA was downregulated (P<0.01) only for HI cows during the transition (-15 v. 15 days) and lactation period (+15 to +60 days, P<0.01). These results, together with the greater BCS, estimated energy intake, increased milk yield and shorter commencement of luteal activity in HI than in LO, and in CR than in PU cows (P<0.018), would indicate that HI and CR cows were able to adapt more efficiently to changes in nutrient and energy supply through the gestation-lactation cycle.

The miRNAome of the postpartum dairy cow liver in negative energy balance

Background

Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB), short read RNA sequencing was carried out. To identify putative targets of differentially expressed miRNAs among differentially expressed hepatic genes reported previously in dairy cows in SNEB computational target identification was employed.

Results

Our results indicate that the dairy cow liver expresses 53 miRNAs at a lower threshold of 10 reads per million. Of these, 10 miRNAs accounted for greater than 95% of the miRNAome (miRNA content). Of the highly expressed miRNAs, miR-122 constitutes 75% followed by miR-192 and miR-3596. Five out of thirteen let-7 miRNA family members are also among the highly expressed miRNAs. miR-143, down-regulated in SNEB, was found to have 4 putative up-regulated gene targets associated with SNEB including LRP2 (low density lipoprotein receptor-related protein 2), involved in lipid metabolism and up-regulated in SNEB.

Conclusions

This is the first liver miRNA-seq profiling study of moderate yielding dairy cows in the early postpartum period. Tissue specific miR-122 and liver enriched miR-192 are two of the most abundant miRNAs in the postpartum dairy cow liver. miR-143 is significantly down-regulated in SNEB and putative targets of miRNA-143 which are up-regulated in SNEB, include a gene involved in lipid metabolism.

Overfeeding Dairy Cattle During Late-Pregnancy Alters Hepatic PPARα-Regulated Pathways Including Hepatokines: Impact on Metabolism and Peripheral Insulin Sensitivity

Hepatic metabolic gene networks were studied in dairy cattle fed control (CON, 1.34 Mcal/kg) or higher energy (overfed (OVE), 1.62 Mcal/kg) diets during the last 45 days of pregnancy. A total of 57 target genes encompassing PPARα-targets/co-regulators, hepatokines, growth hormone (GH)/insulin-like growth factor 1 (IGF-1) axis, lipogenesis, and lipoprotein metabolism were evaluated on −14, 7, 14, and 30 days around parturition. OVE versus CON cows were in more negative energy balance (NEB) postpartum and had greater serum non-esterified fatty acids (NEFA), β-hydroxybutyrate (BHBA), and liver triacylglycerol (TAG) concentrations. Milk synthesis rate did not differ. Liver from OVE cows responded to postpartal NEB by up-regulating expression of PPARα-targets in the fatty acid oxidation and ketogenesis pathways, along with gluconeogenic genes. Hepatokines (fibroblast growth factor 21 (FGF21), angiopoietin-like 4 (ANGPTL4)) and apolipoprotein A-V (APOA5) were up-regulated postpartum to a greater extent in OVE than CON. OVE led to greater blood insulin prepartum, lower NEFA:insulin, and greater lipogenic gene expression suggesting insulin sensitivity was not impaired. A lack of change in APOB, MTTP, and PNPLA3 coupled with upregulation of PLIN2 postpartum in cows fed OVE contributed to TAG accumulation. Postpartal responses in NEFA and FGF21 with OVE support a role of this hepatokine in diminishing adipose insulin sensitivity.

Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle

BACKGROUND

In both beef and dairy cattle, the majority of early embryo loss occurs within the first 14 days following insemination. During this time-period, embryos are completely dependent on their maternal uterine environment for development, growth and ultimately survival, therefore an optimum uterine environment is critical to their survival. The objective of this study was to investigate whether differences in endometrial gene expression during the mid-luteal phase of the estrous cycle exist between crossbred beef heifers ranked as either high (HF) or low fertility (LF) (following four rounds of artificial insemination (AI)) using the Affymetrix® 23 K Bovine Gene Chip.

RESULTS

Conception rates for each of the four rounds of AI were within a normal range: 70-73.3%. Microarray analysis of endometrial tissue collected on day 7 of the estrous cycle detected 419 differentially expressed genes (DEG) between HF (n = 6) and LF (n = 6) animals. The main gene pathways affected were, cellular growth and proliferation, angiogenesis, lipid metabolism, cellular and tissue morphology and development, inflammation and metabolic exchange. DEG included, FST, SLC45A2, MMP19, FADS1 and GALNT6.

CONCLUSIONS

This study highlights, some of the molecular mechanisms potentially controlling uterine endometrial function during the mid-luteal phase of the estrous cycle, which may contribute to uterine endometrial mediated impaired fertility in cattle. Differentially expressed genes are potential candidate genes for the identification of genetic variation influencing cow fertility, which may be incorporated into future breeding programmes.

Effects of parturition and feed restriction on concentrations and distribution of the insulin-like growth factor-binding proteins in plasma and cerebrospinal fluid of dairy cows

Hormones and metabolites act as satiety signals in the brain and play an important role in the control of feed intake (FI). These signals can reach the hypothalamus and brainstem, 2 major centers of FI regulation, via the blood stream or the cerebrospinal fluid (CSF). During the early lactation period of high-yielding dairy cows, the increase of FI is often insufficient. Recently, it has been demonstrated that insulin-like growth factors (IGF) may control FI. Thus, we asked in the present study if IGF-binding proteins (IGFBP) are regulated during the periparturient period and in response to feed restriction and therefore might affect FI as well. In addition, we specifically addressed conditional distribution of IGFBP in plasma and CSF. In one experiment, 10 multiparous German Holstein dairy cows were fed ad libitum and samples of CSF and plasma were obtained before morning feeding on d -20, -10, +1, +10, +20, and +40 relative to calving. In a second experiment, 7 cows in second mid-lactation were sampled for CSF and plasma after ad libitum feeding and again after feeding 50% of the previous ad libitum intake for 4 d. Intact IGFBP-2, IGFBP-3, and IGFBP-4 were detected in plasma by quantitative Western ligand blot analysis. In CSF, we were able to predominantly identify intact IGFBP-2 and a specific IGFBP-2 fragment containing detectable binding affinities for biotinylated IGF-II. Whereas plasma concentrations of IGFBP-2 and IGFBP-4 increased during the periparturient period, IGFBP-3 was unaffected over time. In CSF, concentrations of IGFBP-2, both intact and fragmented, were not affected during the periparturient period. Plasma IGF-I continuously decreased until calving but remained at a lower concentration in early lactation than in late pregnancy. Food restriction did not affect concentrations of IGF components present in plasma or CSF. We could show that the IGFBP profiles in plasma and CSF are clearly distinct and that changes in IGFBP in plasma do not simply correspond in the brain. We thus assume independent control of IGFBP distribution between plasma and CSF. Due to the known anorexic effect of IGF-I, elevated plasma concentrations of IGFBP-2 and IGFBP-4 during the postpartum period in conjunction with reduced plasma IGF-I concentrations may be interpreted as an endocrine response against negative energy balance in early lactation in dairy cows.

Alterations in hepatic miRNA expression during negative energy balance in postpartum dairy cattle

BACKGROUND

Negative energy balance (NEB), an altered metabolic state, occurs in early postpartum dairy cattle when energy demands to support lactation exceed energy intake. During NEB the liver undergoes oxidative stress and increased breakdown of fatty acids accompanied by changes in gene expression. It is now known that micro RNAs (miRNA) can have a role in mediating such alterations in gene expression through repression or degradation of target mRNAs. miRNA expression is known to be altered by metabolism and environmental factors and miRNAs are implicated in expression modulation of metabolism related genes.

RESULTS

miRNA expression was profiled in the liver of moderate yielding dairy cattle under severe NEB (SNEB) and mild NEB (MNEB) using the Affymetrix Gene Chip miRNA_2.0 array with 679 probe sets for Bos-taurus miRNAs. Ten miRNAs were found to be differentially expressed using the 'samr' statistical package (delta = 0.6) at a q-value FDR of < 12%. Five miRNAs including miR-17-5p, miR-31, miR-140, miR-1281 and miR-2885 were validated using RT-qPCR, to be up-regulated under SNEB. Liver diseases associated with these miRNAs include non-alcoholic fatty liver (NAFLD) and hepatocellular carcinoma (HCC). miR-140 and miR-17-5p are known to show differential expression under oxidative stress. A total of 32 down-regulated putative target genes were also identified among 418 differentially expressed hepatic genes previously reported for the same animal model. Among these, GPR37 (G protein-coupled receptor 37), HEYL (hairy/enhancer-of-split related with YRPW motif-like), DNJA1, CD14 (Cluster of differentiation 14) and GNS (glucosamine (N-acetyl)-6-sulfatase) are known to be associated with hepatic metabolic disorders. In addition miR-140 and miR-2885 have binding sites on the most down-regulated of these genes, FADS2 (Fatty acid desaturase 2) which encodes an enzyme critical in lipid biosynthesis. Furthermore, HNF3-gamma (Hepatocyte nuclear factor 3-gamma), a hepatic transcription factor (TF) that is involved in IGF-1 expression regulation and maintenance of glucose homeostasis is a putative target of miR-31.

CONCLUSIONS

This study shows that SNEB affects liver miRNA expression and these miRNAs have putative targets in hepatic genes down-regulated under this condition. This study highlights the potential role of miRNAs in transcription regulation of hepatic gene expression during SNEB in dairy cattle.