The effect of energy balance on the transcriptome of bovine granulosa cells at 60 days postpartum

Genome-wide association and functional annotation analysis for the calving interval in Nellore cattle

Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270-730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21, BCAR3), oocyte function (LHX8, CLPX, UTP23), immune system (TXK, TEC, NFATC2), endocrine function (LRRFIP2, GPR158), estrous cycle (SLC38A7), and female fertility (CCK, LYZL4, TRAK1, FOXP1, STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle.

Characterization of histone lysine β-hydroxybutyrylation in bovine tissues, cells, and cumulus-oocyte complexes

Besides their canonical roles as energy sources, short-chain fatty acids act as metabolic regulators of gene expression through histone posttranslational modifications. Ketone body β-hydroxybutyrate (BHB) causes a novel epigenetic modification, histone lysine β-hydroxybutyrylation (Kbhb), which is associated with genes upregulated in starvation-responsive metabolic pathways. Dairy cows increase BHB in early lactation, and the effects of this increase on cellular epigenomes are unknown. We searched for and identified that Kbhb is present in bovine tissues in vivo and confirmed that this epigenetic mark is responsive to BHB in bovine and human fibroblasts cultured in vitro in a dose-dependent manner. Maturation of cumulus-oocyte complexes with high concentrations of BHB did not affect the competence to complete meiotic maturation or to develop until the blastocyst stage. BHB treatment strongly induced H3K9bhb in cumulus cells, but faintly in oocytes. RNA-seq analysis in cumulus cells indicated that BHB treatment altered the expression of 345 genes. The downregulated genes were mainly involved in glycolysis and ribosome assembly pathways, while the upregulated genes were involved in mitochondrial metabolism and oocyte development. The genes and pathways altered by BHB will provide entry points to carry out functional experiments aiming to mitigate metabolic disorders and improve fertility in cattle.

How the environment affects early embryonic development

In the field of animal reproduction, the environment associated with gametes and embryos refers to the parents' condition as well as conditions surrounding gametes and embryos in vivo or in vitro . This environment is now known to influence not only the functionality of the early embryo but potentially the future phenotype of the offspring. Using transcriptomic and epigenetic molecular analysis, and the bovine model, recent research has shown that both the female and the male metabolic status, for example age, can affect gene expression and gene programming in the embryo. Evidence demonstrates that milking cows, which are losing weight at the time of conception, generates compromised embryos and offspring with a unique metabolic signature. A similar phenomenon has been associated with different culture conditions and the IVF procedure. The general common consequence of these situations is an embryo behaving on 'economy' mode where translation, cell division and ATP production is reduced, potentially to adapt to the perceived future environment. Few epidemiological studies have been done in bovines to assess if these changes result in a different phenotype and more studies are required to associate specific molecular changes in embryos with visible consequences later in life.

Cocultured porcine granulosa cells respond to excess non-esterified fatty acids during in vitro maturation

Background

Non-esterified fatty acids (NEFAs) are one of the main lipid components of follicular fluid at concentrations that depend on circulating levels. Elevated levels of NEFAs impair oocyte quality, development potential, and may subsequently influence the metabolism and reproductive fitness of offspring. Granulosa cells (GCs) are the follicular cells that are closely communicating with the oocyte. However, the responses of GCs exposed to high levels of NEFAs when cocultured with cumulus-oocyte complexes (COCs), and how they attenuate the negative effects of NEFAs on oocytes, are unclear.

Results

To better understand this protective effect, monolayers of porcine GCs were cocultured with COCs during in vitro maturation (IVM) in the presence of elevated levels of NEFAs. Genomic expression analysis was conducted to explore the responses of the GCs to the elevated levels of NEFAs. After limma algorithm analysis, 1,013 genes were differentially expressed between GCs cultured with and without elevated NEFAs. Among them, 438 genes were upregulated and 575 were downregulated. The differentially expressed genes were enriched in pathways related to metabolism, inflammation, and epithelial-mesenchymal transition.

Conclusions

The pathways and upstream regulators suggested that the cocultured GCs responded to the elevated NEFAs with (1) inhibition of the transition from granulosa to luteal cell, (2) interactions of metabolism change, anti-inflammation, mitochondrial function, and cell transition, (3) intercommunication with cocultured COCs of anti-inflammatory factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13048-021-00904-y.

Comparing the whole genome methylation landscape of dairy calf blood cells revealed intergenerational inheritance of the maternal metabolism

This study evaluated the hypothesis that the maternal metabolic stressed status could be inherited to their F1 daughters via epigenetic mechanism. The maternal cow blood β-hydroxybutyric acid (BHB) level (≥0.9 mM/L) was used as an indicator of maternal metabolic stress. Eight newborn daughters' blood cells were used for methylation comparison and analysis. By Whole Genome Bisulphite Sequencing (WGBS), a total of 1,861 Differentially Methylated Regions (DMRs), including 944 differentially methylated cytosines (DMCs), were identified. Most DMRs were distributed in intronic and intergenic regions, and most of the DMR in promoter regions were hypermethylated. Differentially methylated genes (DMGs) with DMR methylation differences higher than 20% were mainly enriched in metabolism-related pathways. These results suggest that newborn calves' metabolic pathways were altered, with 64 DMGs being clustered with metabolic signalling by KEGG analysis. Our study revealed the whole epigenetic landscape of calf blood cells and suggested that the maternal metabolic status can affect the embryo's epigenetic status and metabolic-related pathways in offspring, providing further evidence for epigenetic intergenerational inheritance of metabolic stress in domestic animals. Besides, this study also contributed more evidence to support the Developmental Origins of Health and Disease (DOHAD) theory in large animals.

Uterine infection alters the transcriptome of the bovine reproductive tract three months later

Infection of the postpartum uterus with pathogenic bacteria is associated with infertility months later in dairy cattle. However, it is unclear whether these bacterial infections lead to long-term changes in the reproductive tract that might help explain this infertility. Here we tested the hypothesis that infusion of pathogenic bacteria into the uterus leads to changes in the transcriptome of the reproductive tract 3 months later. We used virgin Holstein heifers to avoid potential confounding effects of periparturient problems, lactation, and negative energy balance. Animals were infused intrauterine with endometrial pathogenic bacteria Escherichia coli and Trueperella pyogenes (n = 4) and compared with control animals (n = 6). Three months after infusion, caruncular and intercaruncular endometrium, isthmus and ampulla of the oviduct, and granulosa cells from ovarian follicles >8 mm diameter were profiled by RNA sequencing. Bacterial infusion altered the transcriptome of all the tissues when compared with control. Most differentially expressed genes were tissue specific, with 109 differentially expressed genes unique to caruncular endometrium, 57 in intercaruncular endometrium, 65 in isthmus, 298 in ampulla, and 83 in granulosa cells. Surprisingly, despite infusing bacteria into the uterus, granulosa cells had more predicted upstream regulators of differentially expressed genes than all the other tissues combined. In conclusion, there were changes in the transcriptome of the endometrium, oviduct and even granulosa cells, 3 months after intrauterine infusion of pathogenic bacteria. These findings imply that long-term changes throughout the reproductive tract could contribute to infertility after bacterial infections of the uterus.

Gene analysis of major signaling pathways regulated by gonadotropins in human ovarian granulosa tumor cells (KGN)†

The female reproductive function largely depends on timing and coordination between follicle-stimulating hormone (FSH) and luteinizing hormone. Even though it was suggested that these hormones act on granulosa cells via shared signaling pathways, mainly protein kinases A, B, and C (PKA, PKB, and PKC), there is still very little information available on how these signaling pathways are regulated by each hormone to provide such differences in gene expression throughout folliculogenesis. To obtain a global picture of the principal upstream factors involved in PKA, PKB, and PKC signaling in granulosa cells, human granulosa-like tumor cells (KGN) were treated with FSH or specific activators (forskolin, SC79, and phorbol 12-myristate 13-acetate) for each pathway to analyze gene expression with RNA-seq technology. Normalization and cutoffs (FC 1.5, P ≤ 0.05) revealed 3864 differentially expressed genes between treatments. Analysis of major upstream regulators showed that PKA is a master kinase of early cell differentiation as its activation resulted in the gene expression profile that accompanies granulosa cell differentiation. Our data also revealed that the activation of PKC in granulosa cells is also a strong differentiation signal that could control "advanced" differentiation in granulosa cells and the inflammatory cascade that occurs in the dominant follicle. According to our results, PKB activation provides support for PKA-stimulated gene expression and is also involved in granulosa cell survival throughout follicular development. Taken together, our results provide new information on PKA, PKB, and PKC signaling pathways and their roles in stimulating a follicle at the crossroad between maturation/ovulation and atresia.

Uterine infusion of bacteria alters the transcriptome of bovine oocytes

Postpartum uterine infection reduces fertility in dairy cattle; however, the mechanisms of uterine infection-mediated infertility are unknown. Paradoxically, infection-induced infertility persists after the resolution of disease. Oocytes are a finite resource, which are present at various stages of development during uterine infection. It is likely that oocyte development is influenced by uterine infection-induced changes to the follicular microenvironment. To better understand the impact of infection on oocyte quality we employed global transcriptomics of oocytes collected from heifers after receiving intrauterine infusion of pathogenic Escherichia coli and Trueperella pyogenes. We hypothesized that the oocyte transcriptome would be altered in response to intrauterine infection. A total of 452 differentially expressed genes were identified in oocytes collected from heifers 4 days after bacteria infusion compared to vehicle infusion, while 539 differentially expressed genes were identified in oocytes collected from heifers 60 days after bacteria infusion. Only 42 genes were differentially expressed in bacteria-infused heifers at both Day 4 and Day 60. Interferon, HMGB1, ILK, IL-6, and TGF-beta signaling pathways were downregulated in oocytes collected at Day 4 from bacteria-infused heifers, while interferon, ILK, and IL-6 signaling were upregulated in oocytes collected at Day 60 from bacteria-infused heifers. These data suggest that bacterial infusion alters the oocyte transcriptome differently at Day 4 and Day 60, suggesting different follicle stages are susceptible to damage. Characterizing the long-term impacts of uterine infection on the oocyte transcriptome aids in our understanding of how infection causes infertility in dairy cattle.

Embryonic response to high beta-hydroxybutyrate (BHB) levels in postpartum dairy cows

Cows at the beginning of lactation often do not meet their energy needs by feeding and therefore mobilize body fat, which produces ketone bodies, including β-hydroxybutyrate (BHB). They are nevertheless usually inseminated around 60 d postpartum, when they are still in this characteristic period of energy deficit. The aim of this study was to observe the effects of negative energy balance on embryo quality and to identify ways to improve the fertility of dairy cows. Holstein cows (n = 18) grouped as high or low BHB based on blood measurement at day 45 postpartum were estrus-synchronized and treated with follicle-stimulating hormone to obtain multiple follicle development, induced to ovulate and inseminated with sexed semen around day 60 postpartum. Of the 290 embryos collected over 16 mo, 159 were of quality I to IV. Based on microarray analysis of gene expression, exposure to an energy deficit metabolic environment (high BHB) during early development appeared to modify signaling by the mTOR and sirtuins pathways in the embryo, implying mitochondrial dysfunction and inhibition of transcription, leading to slower cell division, thus programming the embryo to be more energy efficient. Altered methylation markers suggested that such coping mechanisms might persist into adulthood.

Metabolism-associated genome-wide epigenetic changes in bovine oocytes during early lactation

Dietary intake in early lactating cows is outmatched by milk production. These cows experience a negative energy balance, resulting in a distinct blood metabolism and poor reproductive function due to impaired ovulation and increased embryo loss. We hypothesize that oocytes from lactating cows undergoing transient metabolic stress exhibit a different epigenetic profile crucial for developmental competence. To investigate this, we collected oocytes from metabolically-profiled cows at early- and mid-postpartum stages and characterized their epigenetic landscape compared with control heifers using whole-genome bisulfite sequencing. Early-postpartum cows were metabolically deficient with a significantly lower energy balance and significantly higher concentrations of non-esterified fatty acids and beta-hydroxybutyrate than mid-postpartum animals and control heifers. Accordingly, 32,990 early-postpartum-specific differentially methylated regions (DMRs) were found in genes involved in metabolic pathways, carbon metabolism, and fatty acid metabolism, likely descriptive of the epigenetic regulation of metabolism in early-postpartum oocytes. DMRs found overlapping CpG islands and exons of imprinted genes such as MEST and GNAS in early-postpartum oocytes suggest that early lactation metabolic stress may affect imprint acquisition, which could explain the embryo loss. This whole-genome approach introduces potential candidate genes governing the link between metabolic stress and the reproductive outcome of oocytes.

Sanitary program to reduce embryonic mortality associated with infectious diseases in cattle

Among reproductive disorders in dairy and beef cattle worldwide, embryonic mortalities stand out as one of the most frequent. Because of the multifactorial etiology, the clinical and laboratory diagnoses of embryonic mortality causes in cattle are quite complex. Often, infectious causes may account for up to 50% of bovine embryonic mortality rates after 30 days of conception. This review will address the main causes of early and late embryonic mortality, with emphasis on infectious causes and, particularly, those more frequent in the Brazilian cattle herds. In addition, we will discuss ways of controlling and prophylaxis including those related to reproductive and sanitary management, with emphasis on immunoprophylaxis of the three most frequent reproductive infectious diseases in Brazilian dairy and beef cattle herds.

Impact of the severity of negative energy balance on gene expression in the subcutaneous adipose tissue of periparturient primiparous Holstein dairy cows: Identification of potential novel metabolic signals for the reproductive system

The severity of negative energy balance (NEB) in high-producing dairy cows has a high incidence among health diseases. The cow’s energy status during early lactation critically affects metabolic and reproductive parameters. The first objective of this study was to investigate by RNA-seq analysis and RT-qPCR the gene expression profile in white adipose tissue and by gene ontology and upstream regulation tools the relationships with energy metabolism and reproduction in two groups of primiparous dairy cows with extreme NEB statuses (NEB < -9 Mcal/day vs. NEB > -9 Mcal/day) around parturition. The second objective was to determine the potential involvement of a new adipokine identified as a candidate for the regulation of ovarian function in our RNA-seq analysis by using bovine primary granulosa culture, thymidine incorporation to determine cell proliferation and ELISA assays to measure progesterone secretion. The RNA-seq analysis revealed that 514 genes were over-expressed and 695 were under-expressed in the adipose tissue of cows with severe NEB (SNEB) and cows with moderate NEB (MNEB) during the -4 and 16 wkpp period. In addition, 491 genes were over-expressed and 705 genes were under-expressed in the adipose tissue of SNEB cows compared to MNEB cows. Among these differently expressed genes (DEGs), 298 were related to metabolic functions and 264 to reproductive traits. A set of 19 DEGs were validated by RT-qPCR, including CCL21 (C-C motif chemokine ligand 21). Moreover, CCL21, a gene known to be secreted by adipose tissue, was chosen for further analysis in plasma and ovaries. The use of next-generation sequencing technologies allowed us to characterise the transcriptome of white adipose tissue from primiparous cows with different levels of NEB during lactation. This study highlighted the alteration of the expression of genes related to lipid metabolism, including CCL21, which is released in the bloodstream and associated with the in vitro regulation of ovarian functions.

Extracellular vesicle-coupled miRNA profiles in follicular fluid of cows with divergent post-calving metabolic status

Most high-yielding dairy cows enter a state of negative energy balance (NEB) during early lactation. This, in turn, results in changes in the level of various metabolites in the blood and follicular fluid microenvironment which contributes to disturbed fertility. Extracellular vesicles (EVs) are evolutionarily conserved communicasomes that transport cargo of miRNA, proteins and lipids. EV-coupled miRNAs have been reported in follicular fluid. However, the association between postpartum NEB and EV-coupled miRNA signatures in follicular fluid is not yet known. Energy balance analysis in lactating cows shortly after post-calving revealed that the majority of the cows exhibited transiently negative energy balance levels, whereas the remaining cows exhibited either consistently negative or consistently positive energy levels. Metabolic status was associated with EV-coupled miRNA composition in the follicular fluid. Cows experiencing NEB showed reduced expression of a large number of miRNAs while cows with positive energy balances primarily exhibited elevated expression of EV-coupled miRNAs. The miRNAs that were suppressed under NEB were found to be involved in various metabolic pathways. This is the first study to reveal the presence of an association between EV-coupled miRNA in follicular fluid and metabolic stress in dairy cows. The involvement of differentially expressed miRNAs in various pathways associated with follicular growth and oocyte maturation suggest the potential involvement of specific follicular miRNAs in oocyte developmental competence, which may partially explain reduced fertility in cows due to post-calving metabolic stress.

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.

Association between pre-breeding metabolic profiles and reproductive performance in heifers and lactating dairy cows

Lactating cows and nulliparous heifers are in distinctive and unique physiological conditions when they are approaching the planned time of breeding, at approximately 60 days in milk and 13-15 months of age, respectively. This study aimed to profile the metabolic milieu in heifers (N = 14) and lactating cows (N = 15) in the weeks leading up to planned time of breeding. All cows were followed for a period of 15 weeks, from 3 weeks pre-calving to 12 weeks post-calving, while heifers were monitored for a period of 4 weeks leading up to the tentative week of breeding (pre-breeding period). For data analysis, we further divided cows into primiparous (N = 8) and multiparous (N = 7) cows owing to the significant difference in their milk yield. Assessment of reproductive performance showed that primiparous and multiparous cows tended to have lower pregnancy rates compared to heifers (P < 0.1). Plasma concentrations of β-hydroxybutyric acid were about 2-fold higher in multiparous cows than those of heifers in the week leading up to planned time of breeding (P < 0.05). Total bile acid levels during the pre-breeding period were higher in all lactating cows compared to heifers (P < 0.05) and glucose levels were lower in lactating cows (P < 0.05). Triglyceride concentrations were lowest in multiparous cows compared to both primiparous cows and nulliparous heifers (P < 0.05). In addition, lactating cows had higher concentrations of total-cholesterol and the high-density lipoprotein and low-density lipoprotein compared to heifers (P < 0.05). Conversely, concentrations of very low-density lipoprotein were lower in multiparous cows than primiparous cows and nulliparous heifers (P < 0.05). There were no differences in plasma glutathione levels, as measured by liquid chromatography-tandem mass spectrometry, between the groups, but the ferric reducing ability of plasma was higher in lactating cows compared to heifers (P < 0.05). These data establish the differences in the profile of metabolic and oxidative markers during the period approaching planned time of breeding in lactating cows compared to nulliparous heifers. As certain metabolites in the plasma have been shown to be represented in the ovarian follicular microenvironment, the unique profiles may influence reproductive performance in dairy cattle in different physiological stages.

Comparative analysis of granulosa cell gene expression in association with oocyte competence in FSH-stimulated Holstein cows

Ovarian stimulation with exogenous FSH followed by FSH withdrawal or ‘coasting’ is an effective means of increasing the number of oocytes obtainable for the in vitro production of cattle embryos. However, the quality of the oocytes thus obtained varies considerably from one cow to the next. The aim of the present study was to gain a better understanding of the follicular conditions associated with low oocyte developmental competence. Granulosa cells from 94 Holstein cows in a commercial embryo production facility were collected following ovarian stimulation and coasting. Microarray analysis showed 120 genes expressed with a differential of at least 1.5 when comparing donors of mostly competent with donors of mostly incompetent oocytes. Using ingenuity pathway analysis, we revealed the main biological functions and potential upstream regulators that distinguish donors of mostly incompetent oocytes. These are involved in cell proliferation, apoptosis, lipid metabolism, retinol availability and insulin signalling. In summary, we demonstrated that differences in follicle maturity at collection could explain differences in oocyte competence associated with individual animals. We also revealed deficiencies in lipid metabolism and retinol signalling in granulosa cells from donors of mostly incompetent oocytes.

Embryo development in dairy cattle

During the past 50 years, the fertility of high-producing lactating dairy cows has decreased, associated with intensive selection for increased milk production. The physiological and metabolic changes associated with high milk production, including decreased (glucose, insulin, IGF-I) or increased (nonesterified fatty acids, ketone bodies) concentrations of circulating metabolites during nutrient partitioning associated with negative energy balance as well as uterine and nonuterine diseases have been linked with poor reproductive efficiency. Fertilization is typically above 80% and does not seem to be the principal factor responsible for the low fertility in dairy cows. However, early embryonic development is compromised in high-producing dairy cows, as observed by most embryonic losses occurring during the first 2 weeks after fertilization and may be linked to compromised oocyte quality due to a poor follicular microenvironment, suboptimal reproductive tract environment for the embryo, and/or inadequate maternal-embryonic communication. These and other factors related to embryo development will be discussed.