Development of a porcine (Sus scofa) embryo-specific microarray: array annotation and validation

Transcriptome and epigenome analysis of porcine embryos from non-esterified fatty acid-exposed oocytes

Increasing evidence indicates that maternal malnutrition leads to decreased female fertility and dysregulated metabolic homeostasis in offspring. High levels of non-esterified fatty acids (NEFAs) in follicular fluid were reported to be involved in these maternal nutritional effects, but the mechanisms remain unclear. This study explored the mechanisms of action of abnormal NEFA levels during porcine oocyte in vitro maturation (IVM) on early embryo development (blastocysts) using phenotypic, transcriptomic, and epigenetic analysis. The oocytes were treated during IVM with, in addition to the 1% (v/v) porcine follicular fluid in the control group, a combination of 468 μmol/L palmitic acid, 194 μmol/L stearic acid, and 534 μmol/L oleic acid supplemented to North Carolina State University-23 (NCSU-23) maturation medium to achieve a high level of NEFAs. After IVM, oocytes were in vitro fertilized and then cultured in regular conditions for blastocysts. Expanded blastocysts were collected to complete transcriptomic and epigenetic analysis. Macroscopically, high level of NEFAs impaired embryo development by reducing the blastocyst rate. Analysis of the transcriptome revealed that pathways related to inflammation, apoptosis, metabolism, and oxidative stress were the most affected. Moreover, DNA methylation data demonstrated differentially methylated regions in genes related to cellular metabolism and inflammation processes. Therefore, our conclusion is that high level of NEFAs during IVM might affect porcine early embryo development by diminishing blastocyst rate and altering gene expression, especially at the metabolism and cell status levels, which could further decrease the embryo quality.

Very late vasomotor responses and gene expression with bioresorbable scaffolds and metallic drug-eluting stents

OBJECTIVES

To investigate the long-term vasomotor response and inflammatory changes in Absorb bioresorbable vascular scaffold (BVS) and metallic drug-eluting stent (DES) implanted artery.

BACKGROUND

Clinical evidence has demonstrated that compared to DES, BVS is associated with higher rates of target lesion failure. However, it is not known whether the higher event rates observed with BVS are related to endothelial dysfunction or inflammation associated with polymer degradation.

METHODS

Ten Absorb BVS and six Xience V DES were randomly implanted in the main coronaries of six nonatherosclerotic swine. At 4-years, vasomotor response was evaluated in vivo by quantitative coronary angiography response to intracoronary infusion of Ach and ex vivo by the biomechanical response to prostaglandin F2-α (PGF2-α), substance P and bradykinin and gene expression analysis.

RESULTS

Absorb BVS implanted arteries showed significantly restored vasoconstrictive responses after Ach compared to in-stent Xience V. The contractility of Absorb BVS treated segments induced by PGF2-α was significantly greater compared to Xience V treated segments and endothelial-dependent vasorelaxation was greater with Absorb BVS compared to Xience V. Gene expression analyses indicated the pro-inflammatory lymphotoxin-beta receptor (LTβR) signaling pathway was significantly upregulated in arteries treated with a metallic stent compared to Absorb BVS treated arterial segments.

CONCLUSIONS

At 4 years, arteries treated with Absorb BVS compared with Xience V, demonstrate significantly greater restoration of vasomotor responses. Genetic analysis suggests mechanobiologic reparation of Absorb BVS treated arteries at 4 years as opposed to Xience V treated vessels.

Outcomes of a low birth weight phenotype on piglet gut microbial composition and intestinal transcriptomic profile

Decades of selection for increased litter size has caused a proportion of sows to consistently produce low birth weight (LBW) litters resulting in economic loss for producers due to reduced piglet survivability and growth. We hypothesized that piglets from LBW litters would have altered gut microbial composition, intestinal architecture, and intestinal transcriptomic profiles compared with piglets from high birth weight (HBW) litters. Sows were designated LBW (n = 45) or HBW (n = 46) based on litter birth weights of three successive parities. LBW piglets were 22% lighter (P < 0.001) at birth; however, no longer differed (P > 0.05) in weight at weaning compared with HBW piglets. LBW piglets had reduced (P < 0.05) fecal microbial diversity with a 114% increase in fecal Enterobacteriaceae (P < 0.05), as well as reduced (P < 0.05) abundance of cecal Roseburia and Faecalibacterium, fiber-degrading butyrate producers. Several genes associated with metabolic (PER2, CES1, KLHL38, and HK2) and immune pathways (IL-1B, IRF8, and TNIP3) were differentially expressed, suggesting altered metabolic and immune function in LBW piglets. In conclusion, LBW piglets had potentially unfavorable shifts in microbial structure in comparison to HBW piglets accompanied with alterations in metabolic and immune gene expression. Results indicate some biological consequences linking LBW phenotype to changes in production efficiency later in life.

Contributions of RNA-seq to improve in vitro embryo production (IVP)

In Vitro Embryo Production (IVP) is widely used to improve the reproductive efficiency of livestock animals, however increasing the embryo development rates and pregnancy outcomes is still a challenge for some species. Thus, the lack of biological knowledge hinders developing specie-specific IVP protocols. Therefore, the contributions of RNA-seq to generate relevant biological knowledge and improve the efficiency of IVP in livestock animals are reviewed herein.

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform

Early embryonic loss is a large contributor to infertility in cattle. Moreover, bovine becomes an interesting model to study human preimplantation embryo development due to their similar developmental process. Although genetic factors are known to affect early embryonic development, the discovery of such factors has been a serious challenge. Microarray technology allows quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. One of the main decisions that have to be made when planning a microarray experiment is whether to use a one- or two-color approach. Two-color design increases technical replication, minimizes variability, improves sensitivity and accuracy as well as allows having loop designs, defining the common reference samples. Although microarray is a powerful biological tool, there are potential pitfalls that can attenuate its power. Hence, in this technical paper we demonstrate an optimized protocol for RNA extraction, amplification, labeling, hybridization of the labeled amplified RNA to the array, array scanning and data analysis using the two-color analysis strategy.

Morphologic and transcriptomic assessment of bovine embryos exposed to dietary long-chain fatty acids

The main objectives of this study were to determine the influence of diets enriched in α-linolenic, linoleic or oleic acid on the development and transcriptomic profile of embryos collected from dairy cattle. Non-lactating Holstein cows received one of the three diets supplemented with 8% rolled oilseeds: flax (FLX, n = 8), sunflower (SUN, n = 7) or canola (CAN, n = 8). After a minimum 35-day diet adaptation, cows were superovulated, artificially inseminated and ova/embryos recovered non-surgically after 7.5 days. Cows fed FLX had less degenerated embryos and more viable embryos than those fed CAN or SUN. In total, 175 genes were differentially expressed in blastocysts from cows fed FLX than in cows fed CAN or SUN. These differentially expressed genes were mainly involved in cellular growth and proliferation, cellular development, and cell survival and viability. In conclusion, dietary n-3 polyunsaturated fatty acids reduced early embryonic degeneration possibly through improving embryonic cell survival and viability.

Identification of differentially expressed genes in sexed pig embryos during post-hatching development in primiparous sows exposed to differing intermittent suckling and breeding strategies

The aim of commercial pig breeding programs is to maximize the number of pigs produced per sow per year. Given that sows exhibit an estrus during lactation is a potential means of increasing productivity of a pig breeding herd without reducing in lactation length, conventionally, weaning of piglets at a relatively young age is often related to post-weaning piglet performance which compromises piglet welfare. Therefore, intermittent suckling (IS) is a management technique in which lactating sows are separated from their piglets for a fixed period of the days and allowing sows to continue nursing piglets while exhibiting estrus and being breed during lactation, thereby promoting both piglet well-being and sow reproductive performance [1]. For this study, primiparous sows (PP) were exposed to 28 day (D28) lactation with intermittent suckling (IS) during the final week prior to weaning. The sows detected to be in estrus during lactation were either bred at this first estrus (FE) during lactation (IS21FE), or were “skipped” and bred at their second estrus which occurred after final weaning at D28 (IS21SE). Despite the benefits of IS, the effects of the maternal physiology related to breeding during lactation on embryonic transcriptome are largely unknown. Recent advances in the ability to assess embryonic gene expression in both sexes have made these analyses possible. Here, we describe the experimental procedures of two color microarray analyses and annotation of differentially expressed (DE) genes in detail corresponding to data deposited at NCBI in the Gene Expression Omnibus under accession number GSE53576 and GSE73020 for day 9 embryos (D9E) and day 30 embryos (D30E) respectively. Although only a few DE genes were discovered between IS21FE and IS21SE in both sexes from D9E or D30E, the raw data are still valuable for future use to understand the gene expression profiling from two different developmental stages.

Gene expression of porcine blastocysts from gilts fed organic or inorganic selenium and pyridoxine

In this study, we determined how maternal dietary supplementation with pyridoxine combined with different sources of selenium (Se) affected global gene expression of porcine expanded blastocysts (PEB) during pregnancy. Eighteen gilts were randomly assigned to one of the three experimental diets (n=6 per treatment): i) basal diet without supplemental Se or pyridoxine (CONT); ii) CONT+0.3 mg/kg of Na-selenite and 10 mg/kg of HCl-pyridoxine (MSeB610); and iii) CONT+0.3 mg/kg of Se-enriched yeast and 10 mg/kg of HCl-pyridoxine (OSeB610). All gilts were inseminated at their fifth post-pubertal estrus and killed 5 days later for embryo harvesting. A porcine embryo-specific microarray was used to detect differentially gene expression between MSeB610 vs CONT, OSeB610 vs CONT, and OSeB610 vs MSeB610. CONT gilts had lower whole blood Se and erythrocyte pyridoxal-5-P concentrations than supplemented gilts (P<0.05). No treatment effect was observed on blood plasma Se-glutathione peroxidase activity (P=0.57). There were 10, 247, and 96 differentially expressed genes for MSeB610 vs CONT, OSeB610 vs CONT, and OSeB610 vs MSeB610 respectively. No specific biological process was associated with MSeB610 vs CONT. However, for OSeB610 vs CONT, upregulated genes were related with global protein synthesis but not to selenoproteins. The stimulation of some genes related with monooxygenase and thioredoxin families was confirmed by quantitative real-time RT-PCR. In conclusion, OSeB610 affects PEB metabolism more markedly than MSeB610. Neither Se sources with pyridoxine influenced the Se-glutathione peroxidase metabolic pathway in the PEB, but OSeB610 selectively stimulated genes involved with antioxidant defense.

The porcine innate immune system: an update

Over the last few years, we have seen an increasing interest and demand for pigs in biomedical research. Domestic pigs (Sus scrofa domesticus) are closely related to humans in terms of their anatomy, genetics, and physiology, and often are the model of choice for the assessment of novel vaccines and therapeutics in a preclinical stage. However, the pig as a model has much more to offer, and can serve as a model for many biomedical applications including aging research, medical imaging, and pharmaceutical studies to name a few. In this review, we will provide an overview of the innate immune system in pigs, describe its anatomical and physiological key features, and discuss the key players involved. In particular, we compare the porcine innate immune system to that of humans, and emphasize on the importance of the pig as model for human disease.

Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum

Background

Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cell recognition genes, however, little is known about the genetic basis of self/non-self recognition in this species. Based on the key hypothesis that there should be differential expression of genes if D. discoideum cells were interacting with non-clone mates, we performed transcriptomic profiling study in this species during clonal vs. chimeric development. The transcriptomic profiles of D. discoideum cells in clones vs. different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed.

Results

We find 1,759 genes significantly different between chimera and clone, 1,144 genes associated significant strain differences, and 6,586 genes developmentally regulated over time. Principal component analysis showed a small amount of the transcriptional variance to chimerism-related factors (Chimerism: 0.18%, Chimerism × Timepoint: 0.03%). There are 162 genes specifically regulated under chimeric development, with continuous small differences between chimera vs. clone over development. Almost 60% of chimera-associated differential genes were differentially expressed at the 4 h aggregate stage, which corresponds to the initial transition of D. discoideum from solitary life to a multicellular phase.

Conclusions

A relatively small proportion of over-all variation in gene expression is explained by differences between chimeric and clonal development. The relatively small modifications in gene expression associated with chimerism is compatible with the high level of cooperation observed among different strains of D. discoideum; cells of distinct genetic backgrounds will co-aggregate indiscriminately and co-develop into fruiting bodies. Chimeric development may involve re-programming of the transcriptome through small modifications of the developmental genetic network, which may also indicate that response to social interaction involves many genes with individually small transcriptional effect.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-616) contains supplementary material, which is available to authorized users.

An integrated platform for bovine DNA methylome analysis suitable for small samples

Background

Oocytes and early embryos contain minute amounts of DNA, RNA and proteins, making the study of early mammalian development highly challenging. The study of the embryo epigenome, in particular the DNA methylome, has been made accessible thanks to the possibility of amplifying specific sequences according to their initial methylation status. This paper describes a novel platform dedicated to the genome-wide study of bovine DNA methylation, including a complete pipeline for data analysis and visualization. The platform allows processing and integrating of DNA methylome and transcriptome data from the same sample. Procedures were optimized for genome-wide analysis of 10 ng of DNA (10 bovine blastocysts). Bovine sperm and blastocysts were compared as a test of platform capability.

Results

The hypermethylation of bovine sperm DNA compared to the embryo genome was confirmed. Differentially methylated regions were distributed across various classes of bovine sperm genomic feature including primarily promoter, intronic and exonic regions, non-CpG-island regions (shore, shelf and open-sea) and CpG islands with low-to-intermediate CpG density. The blastocyst genome bore more methylation marks than sperm DNA only in CpG islands with high CpG density. Long-terminal-repeat retrotransposons (LTR), LINE and SINE were more methylated in sperm DNA, as were low-complexity repetitive elements in blastocysts.

Conclusions

This is the first early embryo compatible genome-wide epigenetics platform for bovine. Such platforms should improve the study of the potential epigenetic risks of assisted reproductive technologies (ART), the establishment sequence of embryonic cell lines and potential deviations in both gene expression and DNA methylation capable of having long-term impact.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-451) contains supplementary material, which is available to authorized users.

Genomic profiling to improve embryogenesis in the pig

Over the past decade the technology to characterize transcription during embryogenesis has progressed from estimating a single transcript to a reliable description of the entire transcriptome. Northern blots were followed by sequencing ESTs, quantitative real time PCR, cDNA arrays, custom oligo arrays, and more recently, deep sequencing. The amount of information that can be generated is overwhelming. The challenge now is how to glean information from these vast data sets that can be used to understand development and to improve methods for creating and culturing embryos in vitro, and for reducing reproductive loss. The use of ESTs permitted the identification of SPP1 as an oviductal component that could reduce polyspermy. Microarrays identified LDL and NMDA as components to replace BSA in embryo culture media. Deep sequencing implicated arginine, glycine, and folate as components that should be adjusted in our current culture system, and identified a characteristic of embryo metabolism that is similar to cancer and stem cells. Not only will these characterizations aid in improving in vitro production of embryos, but will also be useful for identifying, or creating conditions for donor cells that will be more likely to result in normal development of cloned embryos. The easily found targets have been identified, and now more sophisticated methods are being employed to advance our understanding of embryogenesis. Here the technology to study the global transcriptome is reviewed followed by specific examples of how the technology has been used to understand and improve porcine embryogenesis both in vitro and in vivo.

Characterization of the altered gene expression profile in early porcine embryos generated from parthenogenesis and somatic cell chromatin transfer

The in vitro production of early porcine embryos is of particular scientific and economic interest. In general, embryos produced from in vitro Assisted Reproductive Technologies (ART) manipulations, such as somatic cell chromatin transfer (CT) and parthenogenetic activation (PA), are less developmentally competent than in vivo–derived embryos. The mechanisms underlying the deficiencies of embryos generated from PA and CT have not been completely understood. To characterize the altered genes and gene networks in embryos generated from CT and PA, comparative transcriptomic analyses of in vivo (IVV) expanded blastocysts (XB), IVV hatched blastocyst (HB), PA XB, PA HB, and CT HB were performed using a custom microarray platform enriched for genes expressed during early embryonic development. Differential expressions of 1492 and 103 genes were identified in PA and CT HB, respectively, in comparison with IVV HB. The “eIF2 signalling”, “mitochondrial dysfunction”, “regulation of eIF4 and p70S6K signalling”, “protein ubiquitination”, and “mTOR signalling” pathways were down-regulated in PA HB. Dysregulation of notch signalling–associated genes were observed in both PA and CT HB. TP53 was predicted to be activated in both PA and CT HB, as 136 and 23 regulation targets of TP53 showed significant differential expression in PA and CT HB, respectively, in comparison with IVV HB. In addition, dysregulations of several critical pluripotency, trophoblast development, and implantation-associated genes (NANOG, GATA2, KRT8, LGMN, and DPP4) were observed in PA HB during the blastocyst hatching process. The critical genes that were observed to be dysregulated in CT and PA embryos could be indicative of underlying developmental deficiencies of embryos produced from these technologies.