Transcriptome Analysis Revealed the Embryo-Induced Gene Expression Patterns in the Endometrium from Meishan and Yorkshire Pigs

Revisiting the Transcriptome Landscape of Pig Embryo Implantation Site at Single-Cell Resolution

Litter size is one of the most economically important traits in commercial pig farming. It has been estimated that approximately 30% of porcine embryos are lost during the peri-implantation period. Despite rapid advances over recent years, the molecular mechanism underlying embryo implantation in pigs remains poorly understood. In this study, the conceptus together with a small amount of its surrounding endometrial tissues at the implantation site was collected and subjected to single-cell RNA-seq using the 10x platform. Because embryo and maternal endometrium were genetically different, we successfully dissected embryonic cells from maternal endometrial cells in the data according to single nucleotide polymorphism information captured by single-cell RNA-seq. Undoubtedly, the interaction between trophoblast cells and uterine epithelial cells represents the key mechanism of embryo implantation. Using the CellChat tool, we revealed cell-cell communications between these 2 cell types in terms of secreted signaling, ECM-receptor interaction and cell-cell contact. Additionally, by analyzing the non-pregnant endometrium as control, we were able to identify global gene expression changes associated with embryo implantation in each cell type. Our data provide a valuable resource for deciphering the molecular mechanism of embryo implantation in pigs.

Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs

BACKGROUND

Although lots of quantitative trait loci (QTLs) and genes present roles in litter size of some breeds, the information might not make it clear for the huge diversity of reproductive capability in pig breeds. To elucidate the inherent mechanisms of heterogeneity of reproductive capability in litter size of Xiang pig, we performed transcriptome analysis for the expression profile in ovaries using RNA-seq method.

RESULTS

We identified 1,419 up-regulated and 1,376 down-regulated genes in Xiang pigs with large litter size. Among them, 1,010 differentially expressed genes (DEGs) were differently spliced between two groups with large or small litter sizes. Based on GO and KEGG analysis, numerous members of genes were gathered in ovarian steroidogenesis, steroid biosynthesis, oocyte maturation and reproduction processes.

CONCLUSIONS

Combined with gene biological function, twelve genes were found out that might be related with the reproductive capability of Xiang pig, of which, eleven genes were recognized as hub genes. These genes may play a role in promoting litter size by elevating steroid and peptide hormones supply through the ovary and facilitating the processes of ovulation and in vivo fertilization.

Association of IL-4 and IL-4R Polymorphisms with Litter Size Traits in Pigs

Simple Summary

The IL-4 and IL-4R cytokine genes are responsible for immune response in the reproductive system and are related to embryonic implantation and fetal survival during pregnancy in females. However, to date, their effects on litter size traits in pigs have been not elucidated. Therefore, the present study was conducted to verify the porcine IL-4 and IL-4R polymorphisms and assess how they affect litter size traits in commercial pigs. The findings suggested that the porcine IL-4 g.134993898T > C and IL-4R c.1577A > T polymorphisms were associated with the litter size traits. Therefore, the porcine IL-4 and IL-4R genes may be potentially effective genetic markers to improve the litter size traits in pigs.

Abstract

The interleukin-4 (IL-4) and interleukin-4 receptor (IL-4R) are cytokines that are involved in the immune and reproductive systems. This study aimed to verify the polymorphisms in the porcine IL-4 and IL-4R genes and to assess their effects on litter size traits in commercial pigs. Single nucleotide polymorphisms (SNPs) in the porcine IL-4 and IL-4R genes were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. A non-coding SNP of IL-4 g.134993898T > C and a non-synonymous SNP of IL-4R c.1577A > T (amino acid change at position 526, Q526L) were found to be segregating in Landrace sows. The IL-4 g.134993898T > C polymorphism was significantly associated with the number of piglets weaned alive (NWA) trait. The IL-4R c.1577A > T polymorphism was significantly associated with the number born alive (NBA) and NWA traits. Moreover, the accumulation of favorable alleles of these two SNP markers revealed significant associations with the NBA, NWA, and mean weight of piglets at weaning (MWW) traits. These findings indicate that the porcine IL-4 and IL-4R genes may contribute to the reproductive traits of pigs and could be used as candidate genes to improve litter size traits in the pig breeding industry.

Pleiotropic role of prokineticin 1 in the porcine endometrium during pregnancy establishment and embryo implantation †

Acquisition of endometrial receptivity for embryo implantation is one of the crucial processes during pregnancy and is induced mainly by progesterone and enhanced by conceptus signals. Prokineticin 1 (PROK1) is characterized as a secretory protein with diverse functions in various tissues, including the reproductive tract. PROK1, with its receptor PROKR1, are up-regulated in the porcine endometrium during implantation and in women's receptive endometrium and decidua. However, the function of PROK1 in embryo-maternal communication has still not been fully elucidated. Hence, we hypothesize that PROK1 is involved in endometrial receptivity development and implantation in pigs. In this study, using the porcine in vivo model of intrauterine infusions of estradiol-17β (E2) and prostaglandin E2 (PGE2), we revealed that these hormones elevated endometrial expression of PROK1 and PROKR1 mRNA, respectively. Moreover, E2, acting synergistically with PGE2, increased PROKR1 protein expression. We also evidenced that PROK1-PROKR1 signaling induced expression of following genes and/or proteins CCN2, CDH13, FGF2, NFATC2, ANGPT1, ANGPT2, CDH1, MUC4, SPP1, IFNG, IL6, LIF, LIFR, TNF, TGFB3, and FGF9, as well as phosphorylation of PTK2 and secretion of IL6 and IL11 by endometrial explants in vitro. Ingenuity pathway analysis revealed that functions associated with the PROK1-regulated genes/proteins include cell-to-cell contact, cell attachment, migration and viability, differentiation of epithelial tissue, leukocyte migration, inflammatory response, angiogenesis, and vasculogenesis. Summarizing, our study suggests that PROK1 acts pleiotropically as an embryonic signal mediator that regulates endometrial receptivity by increasing the expression of the genes and proteins involved in implantation and pregnancy establishment in pigs.

Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs

MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White pigs. Eighty-five circRNAs were differentially expressed between the two pig breeds. Of these, 37 were up-regulated and 48 were down-regulated in MeiShan pigs. Gene ontology enrichment analysis suggested that the differentially expressed circRNA were involved in the hormone-mediated signaling pathway. We verified that circSCIN and its parent gene, scinderin (SCIN), were differentially expressed by reverse transcription and quantitative PCR (RT-qPCR). Luciferase assays demonstrated that circSCIN can target and sponge miR-133 and miR-148a/b. The identification of differentially expressed circRNAs (DECs) and their regulatory functions increased our understanding of the differences in reproductive efficiency between MeiShan and Large White pigs.

Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy

During the early stages of pregnancy, the uterine endometrium undergoes dramatic morphologic and functional changes accompanied with dynamic variation in gene expression. Pregnancy-stage specific differentially expressed gene (DEG)-transcript-probes were investigated and identified by comparing endometrium transcriptome at 9th day (9D), 12th day (12D) and 16th day (16D) of early pregnancy in Polish large-white (PLW) gilts. Endometrium comparisons between 9D-vs-12D, 9D-vs-16D and 12D-vs-16D of early pregnancy identified 6049, 374 and 6034 highly significant DEG-transcript-probes (p < 0.001; >2 FC). GO term enrichment analysis identified commonly shared upregulated endometrial DEG-transcript-probes (p < 0.001; >2 FC), that were regulating the gene functions of anatomic structure development and transport (TG), DNA-binding and methyltransferase activity (ZBTB2), ion-binding and kinase activity (CKM), cell proliferation and apoptosis activity (IL1B). Downregulated DEG-transcript-probes (p < 0.001; >2 FC) were involved in regulating the gene functions of phosphatase activity (PTPN11), TC616413 gene-transcript and Sus-scrofa LOC100525539. Moreover, blastn comparison of microarray-probes sequences against sus-scrofa11 assembly identified commonly shared upregulated endometrial DEG-transcript-probes (E < 0.06; >2 FC), that were regulating the gene functions of reproduction and growth (SELENOP), cytoskeleton organization and kinase activity (CDC42BPA), phosphatase activity (MINPP1), enzyme-binding and cell-population proliferation (VAV3), cancer-susceptibility candidate gene (CASC4), cytoskeletal protein-binding (COBLL1), ion-binding, enzyme regulator activity (ACAP2) Downregulated endometrial DEG-transcript-probes (E < 0.06; >2FC) were involved in regulating the gene functions of signal-transduction (TMEM33), catabolic and metabolic processes (KLHL15). Microarray validation experiment on selected candidate genes showed complementarity to significant endometrial DEG-transcript-probes responsible for the regulation of immune response (IL1B, S100A11), lipid metabolism (FABP3, PPARG), cell-adhesion (ITGAV), angiogenesis (IL1B), intercellular transmission (NMB), cell-adhesion (OPN) and response to stimuli (RBP4) was confirmed by RT-PCR. This study provides a clue that identified pregnancy-stage specific microarray transcript probes could be considered as candidate genes for recognition and establishment of early pregnancy in the pig.

Integrated Analysis of miRNA-mRNA Network Reveals Different Regulatory Patterns in the Endometrium of Meishan and Duroc Sows during Mid-Late Gestation

Simple Summary

Meishan pigs have a lower fetal loss rate during mid-late gestation compared to Duroc pigs. Differentially expressed mRNAs and miRNAs detected in endometrial tissue from Meishan and Duroc sows at mid-late gestation are involved in regulating hormone and oxygen levels, blood vessel development, and developmental processes affecting reproduction. In addition, ssc-miR-503 and ssc-miR-671-5p were shown to target the EGF and ESR1 genes, respectively. These findings provided an important resource for studying embryonic mortality during mid-late gestation in pigs.

Abstract

Embryo loss is a major factor affecting profitability in the pig industry. Embryonic mortality occurs during peri-implantation and mid-late gestation in pigs. Previous investigations have shown that the embryo loss rate in Meishan pigs is significantly lower than in commercial breeds. Most studies have focused on embryonic mortality during early gestation, but little is known about losses during mid-late gestation. In this study, we performed a transcriptome analysis of endometrial tissue in mid-late gestation sows (gestation days 49 and 72) sampled from two breeds (Meishan (MS) and Duroc (DU)) that have different embryo loss rates. We identified 411, 1113, 697, and 327 differentially expressed genes, and 14, 36, 57, and 43 differentially expressed miRNAs in four comparisons (DU49 vs. DU72, DU49 vs. MS49, DU72 vs. MS72, and MS49 vs. MS72), respectively. Subsequently; seven differentially expressed mRNAs and miRNAs were validated using qPCR. Functional analysis suggested the differentially expressed genes and miRNAs target genes mainly involved in regulation of hormone levels, blood vessel development, developmental process involved in reproduction, embryonic placenta development, and the immune system. A network analysis of potential miRNA-gene interactions revealed that differentially expressed miRNAs in Meishan pigs are involved in the response to estradiol and oxygen levels, and affect angiogenesis and blood vessel development. The binding site on ssc-miR-503 for epidermal growth factor (EGF) and the binding site on ssc-miR-671-5p for estrogen receptor α (ESR1) were identified using a dual luciferase assay. The results of this study will enable further exploration of miRNA-mRNA interactions important in pig pregnancy and will help to uncover molecular mechanisms affecting embryonic mortality in pigs during mid-late gestation.

Protein expression profiles in Meishan and Duroc sows during mid-gestation reveal differences affecting uterine capacity, endometrial receptivity, and the maternal-fetal Interface

BACKGROUND

Embryonic mortality is a major concern in the commercial swine industry and primarily occurs early in gestation, but also during mid-gestation (~ days 50-70). Previous reports demonstrated that the embryonic loss rate was significant lower in Meishan than in commercial breeds (including Duroc). Most studies have focused on embryonic mortality in early gestation, but little is known about embryonic loss during mid-gestation.

RESULTS

In this study, protein expression patterns in endometrial tissue from Meishan and Duroc sows were examined during mid-gestation. A total of 2170 proteins were identified in both breeds. After statistical analysis, 70 and 114 differentially expressed proteins (DEPs) were identified in Meishan and Duroc sows, respectively. Between Meishan and Duroc sows, 114 DEPs were detected at day 49, and 98 DEPs were detected at day 72. Functional enrichment analysis revealed differences in protein expression patterns in the two breeds. Around half of DEPs were more highly expressed in Duroc at day 49 (DUD49), relative to DUD72 and Meishan at day 49 (MSD49). Many DEPs appear to be involved in metabolic process such as arginine metabolism. Our results suggest that the differences in expression affect uterine capacity, endometrial matrix remodeling, and maternal-embryo cross-talk, and may be major factors influencing the differences in embryonic loss between Meishan and Duroc sows during mid-gestation.

CONCLUSIONS

Our data showed differential protein expression pattern in endometrium between Meishan and Duroc sows and provides insight into the development process of endometrium. These findings could help us further uncover the molecular mechanism involved in prolificacy.

Human Endometrial Extracellular Vesicles Functionally Prepare Human Trophectoderm Model for Implantation: Understanding Bidirectional Maternal-Embryo Communication

Embryo implantation into maternal endometrium is critical for initiation and establishment of pregnancy, requiring developmental synchrony between endometrium and blastocyst. However, factors regulating human endometrial-embryo cross talk and facilitate implantation remain largely unknown. Extracellular vesicles (EVs) are emerging as important mediators of this process. Here, a trophectoderm spheroid-based in vitro model mimicking the pre-implantation human embryo is used to recapitulate important functional aspects of blastocyst implantation. Functionally, human endometrial EVs, derived from hormonally treated cells synchronous with implantation, are readily internalized by trophectoderm cells, regulating adhesive and invasive capacity of human trophectoderm spheroids. To gain molecular insights into mechanisms underpinning endometrial EV-mediated enhancement of implantation, quantitative proteomics reveal critical alterations in trophectoderm cellular adhesion networks (cell adhesion molecule binding, cell-cell adhesion mediator activity, and cell adherens junctions) and metabolic and gene expression networks, and the soluble secretome from human trophectodermal spheroids. Importantly, transfer of endometrial EV cargo proteins to trophectoderm to mediate changes in trophectoderm function is demonstrated. This is highlighted by correlation among endometrial EVs, the trophectodermal proteome following EV uptake, and EV-mediated trophectodermal cellular proteome, important for implantation. This work provides an understanding into molecular mechanisms of endometrial EV-mediated regulation of human trophectoderm functions-fundamental in understanding human endometrium-embryo signaling during implantation.

Distinct Patterns of PPARγ Promoter Usage, Lipid Degradation Activity, and Gene Expression in Subcutaneous Adipose Tissue of Lean and Obese Swine

Subcutaneous adipose tissue is a loose connective tissue specializing in the regulation of energy storage and metabolization. In domesticated pigs (Sus scrofa), the temporal development of subcutaneous adipose tissue is critical for meat production. However, the regulation of adipose tissue development remains unclear. Here, the subcutaneous adipose tissue development was characterized and compared in lean (Danish-Landrace) and obese (Min) pigs at juvenile and the juvenile-to-adult growth stages. Using RNA sequencing, we profiled the transcriptome of subcutaneous adipose tissue isolated from 4- and 16-week-old pigs and identified 24,718 expressed transcription units. Of them, 6327 genes were differentially expressed between the breeds and/or developmental stages. Compared with obese pigs, upregulated genes in lean pigs showed significant function and pathway enrichment in fatty acid degradation and mitochondrial functions. Further analysis uncovered the distinct usage preferences of the three alternative peroxisomeproliferator-activatedreceptorγ (PPARγ) promoters associated with the development of subcutaneous adipose tissue in both breeds. Transcriptome analysis of subcutaneous adipose tissue in lean and obese pigs suggested that marker-assisted selection of fatty acid degradation and PPARγ signaling pathways could be important directions for future pork quality improvement and modern breeding.

Effect of orexin B on CYP17A1 and CYP19A3 expression and oestradiol, oestrone and testosterone secretion in the porcine uterus during early pregnancy and the oestrous cycle

Orexin A (OXA) and B (OXB) are hypothalamic neuropeptides identified as regulators of food intake, energy homoeostasis, sleep-wake cycle and arousal. They also create an integrative link between energy homoeostasis and reproduction. Although their functions in the ovaries and testes have been partially explored, to date, less attention has been focused on the role of the peptides in the uterus. The aim of this study was to investigate the effect of one of orexins - orexin B on oestradiol (E2), oestrone (E1) and testosterone (T) secretion by porcine endometrial and myometrial slices as well as the gene expression of key steroidogenic enzymes responsible for steroid production (CYP17A1, CYP19A3) during the luteal phase of the oestrous cycle (days 10 to 11) and early pregnancy (days 10 to 11, 12 to 13, 15 to 16, 27 to 28). Orexin B suppressed E2 secretion by endometrial slices on days 10 to 11 and 15 to 16 of pregnancy, and days 10 to 11 of the cycle. In the myometrium, OXB inhibited E2 production on days 10 to 11 of pregnancy, whereas on days 12 to 13 it enhanced steroid output. Endometrial E1 release was potentiated by the peptide during all studied periods of the cycle and pregnancy, with the exception of days 12 to 13, when an inhibitory effect was observed. Myometrial secretion of E1 was increased, except on days 27 to 28. Testosterone secretion by endometrial slices was increased on days 12 to 13 and 27 to 28 of pregnancy. On days 10 to 11 of the cycle, T release was stimulated in response to the lowest and decreased under the influence of the highest dose of OXB. In the myometrium, T production was inhibited by OXB on days 10 to 11 of pregnancy and during the corresponding period of the cycle. On days 27 to 28 of pregnancy, T release was potentiated by the lowest dose of OXB. Expression of both genes was modified by OXB depending on the period of pregnancy and the type of examined uterine tissues. Our findings suggest that OXB, through modulation of uterine steroidogenesis, may have a regulatory role in the uterus.

The effect of orexin A on CYP17A1 and CYP19A3 expression and on oestradiol, oestrone and testosterone secretion in the porcine uterus during early pregnancy and the oestrous cycle

Orexin A (OXA) is a hypothalamic neuropeptide known for its role in the regulation of food intake and arousal. It is also considered as a link between energy homeostasis and reproduction. Nevertheless, very little is known on the role of this peptide in the uterus. The objective of this study was to investigate OXA effect on oestradiol (E₂), oestrone (E₁), and testosterone (T) secretion by porcine endometrial and myometrial explants and gene expression of key steroidogenic enzymes involved in steroid production, namely cytochrome P450c17 (CYP17A1) and cytochrome P450 aromatase (CYP19A3), on days 10-11, 12 to 13, 15 to 16 and 27 to 28 of pregnancy and on days 10-11 of the cycle. In endometrium, OXA increased E₁ secretion on days 10-11 and 15 to 27 of gestation, and T release on days 12-13. A decrease in E₂, E₁ and T secretion was noted on days 27-28, 12 to 13 and 10 to 11 of gestation, respectively. OXA enhanced CYP17A1 and CYP19A3 expression on days 15-28 of pregnancy, whereas decreased their expression on days 10-13. In the myometrium, OXA increased E₁ secretion on days 10-16 of pregnancy, whereas inhibited the release of E₂ and T on days 10-11. CYP17A1 and CYP19A3 genes expression was enhanced on days 27-28 and 12 to 13 of pregnancy, respectively. The expression of both genes was suppressed on days 10-11 and 15 to 16 of pregnancy (P < 0.05). Our findings suggest that OXA, via its influence on steroidogenesis, may play a regulatory role in the uterus.

Genetic determinants of pig birth weight variability

Background

Piglet birth weight variability, a trait also known as the within-litter homogeneity of birth weight, reflects the sow’s prolificacy, because it is positively genetically correlated with preweaning mortality but negatively correlated with the mean growth of piglets during sucking. In addition, the maternal additive genetic variance and heritability has been found exist for this trait, thus, reduction in the variability of piglet birth weight to improve the sow prolificacy is possible by selective breeding.

Results

We performed a genome wide association study (GWAS) in 82 sows with extreme standard deviation of birth weights within the first parity to identify significant SNPs, and finally 266 genome-wide significant SNPs (p < 0.01) were identified. These SNPs were mainly enriched on chromosome 7, 1, 13, 14, 15 and 18. We further scanned genes of the top 50 SNPs with the lowest p values and found some genes involved in plasma glucose homeostasis (GLP1R) and lipid metabolism as well as maternal-fetal lipid transport (AACS, APOB, OSBPL10 and LRP1B) which may contribute to the birth weight variability trait.

Conclusions

Birth weight variability trait has a low heritability. It is not easy to get significant signal by GWAS using small sample size. Herein, we identified some candidate chromosome regions especially chromosome 7 and suggested five genes which may provide some information for the further study.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0309-6) contains supplementary material, which is available to authorized users.