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Background In pigs, genetic progress has led to an increase in perinatal mortality, mainly due to reduced piglet maturity. The end of gestation (90-110 days of gestation) plays a decisive role in the acquisition of fetal maturity. The endometrium is crucial for its acquisition as it provides nutrients to the fetus through the placenta. The aim of this study is to describe part of the metabolism of the endometrium in late pregnancy and in relation with neonatal survival. For this purpose, we performed untargeted metabolomic measurements by 1H nuclear magnetic resonance and gas chromatography coupled to a flame-ionization detector on 224 endometrial samples and compared the two days of the end of gestation (D90-D110, term at 114 days) and two maternal breeds with contrasted birth survival: Large White (LW, higher birth mortality) and Meishan (MS, lower birth mortality). Results Out of the 191 metabolites available in the ASICS package reference library, 46 metabolites and nine neutral lipids were quantified in the endometrial samples. Twenty-two metabolites showed a significant differential abundance in the endometrium between 90 and 110 days of gestation. These differences highlighted a decrease in the amount of glucogenic amino acids such as aspartate, glutamate, and glutamine at D110, indicating a depletion of energy resources in the endometrium. As a result of hypoxic catabolism to maintain energy levels, hypoxanthine and succinate accumulated, possibly contributing to the regulation of hypoxia, ROS and modulation of inflammation of the endometrium during late pregnancy. The study also documented ten endometrial metabolites with a significant differential abundance between LW and MS sows. Glutathione metabolism metabolites showed a decreased abundance in LW, which may contribute to increased oxidative stress. Furthermore, the accumulation of glutamine and phenylalanine may be a possible response to lower amino acid availability in LW, inducing more cellular autophagy and lower maternal immune tolerance in LW endometrium compared to MS. Conclusions For the first time, these data provide a metabolic status of the endometrium during late gestation and between two extreme breeds for piglet survival. They reinforce the role of succinate, glutamine, and phenylalanine in influencing piglet survival birth.

Background Genomic imprinting, a mechanism resulting in parent-of-origin expression of genes through epigenetic regulation, intersects with a broad range of biological fields, including evolution, molecular genetics and epigenetics, and determinism of complex traits. Although next generation sequencing technologies nowadays enable imprinted genes to be detected in a genome-wide manner, a wide spectrum of this phenomena is evaluated only in humans and rodents. Results Here, we propose to map genes showing a parental expression imbalance in hypothalamus, muscle and placenta in piglets around birth using an extensive strategy that minimized biases and relied on reciprocal crosses, reconstruction of parental phases after imputation, and statistical analyses discriminating parent-of-origin from allele-specific expression. We detected 141 genes with strong to exclusive parental expression imbalance (ratio > 25:75). A large proportion (80%) of these genes have never been shown to exhibit parent-of-origin expression and a small proportion (15%) are shared by at least two tissues, suggesting an overall weak conservation landscape of genomic imprinting. Interestingly, we identified novel parent-of-origin expressed genes involved in neurodevelopmental ( PREPL , Prolyl Endopeptidase Like) and fetal growth ( FAM20B , Glycosaminoglycan Xylosylkinase, and POU6F2 , POU Class 6 Homeobox 2) functions. In-depth analyses of specific loci highlighted specific imprinted isoforms of COPG2 (COPI Coat Complex Subunit Gamma 2) and confirmed livestock-specific imprinted genes such as the Zinc Finger Protein 300-like gene. Conclusions Altogether, our results provide an atlas of parent-of-origin expressed genes in the pig, making it the most documented species for genomic imprinting after humans and rodents. Our findings indicate weak conservation of this mechanism across species and tissues, suggesting a small number of core imprinted genes shared across eutherians and another imprinted genes that seem specific to species or tissues. These latter parent-of-origin expressed genes may have been subjected to evolutionary forces that have determine their imprinting status in either a livestock-specific or a tissue-specific manner.

To compare the analgesic effect of ultrasound-guided Transversus Abdominis Plane (TAP) block versus Continuous Wound Infusion (CWI) with levobupivacaine after caesarean delivery. We recruited parturients undergoing elective caesareans for this multicenter study. Following written informed consent, they received a spinal anaesthetic without intrathecal morphine for their caesarean section. The postoperative analgesia was randomized to either a bilateral ultrasound guided TAP block (levobupivicaine = 150 mg) or a CWI through an elastomeric pump for 48 hours (levobupivacaine = 150 mg the first day and 12.5 mg/h thereafter). Every woman received regular analgesics along with oral morphine if required. The primary outcome was comparison of the 48-hour area under the curve (AUC) pain scores. Secondary outcomes included morphine consumption, adverse events, and persistent pain one month postoperatively. Recruitment of 120 women was planned but the study was prematurely terminated due to the occurrence of generalized seizures in one patient of the TAP group. By then, 36 patients with TAP and 29 with CWI had completed the study. AUC of pain at rest and during mobilization were not significantly different: 50 [22.5-80] in TAP versus 50 [27.5-130] in CWI (P = 0.4) and 190 [130-240] versus 160 [112.5-247.5] (P = 0.5), respectively. Morphine consumption (0 [0-20] mg in the TAP group and 10 [0-32.5] mg in the CWI group (P = 0.09)) and persistent pain at one month were similar in both groups (respectively 29.6% and 26.6% (P = 0.73)). In cases of morphine-free spinal anesthesia for cesarean delivery, no difference between TAP block and CWI for postoperative analgesia was suggested. TAP block may induce seizures in this specific context. Consequently, such a technique after a caesarean section cannot be recommended. ClinicalTrials.gov NCT01151943.

Background Successful achievement of early folliculogenesis is crucial for female reproductive function. The process is finely regulated by cell-cell interactions and by the coordinated expression of genes in both the oocyte and in granulosa cells. Despite many studies, little is known about the cell-specific gene expression driving early folliculogenesis. The very small size of these follicles and the mixture of types of follicles within the developing ovary make the experimental study of isolated follicular components very difficult. The recently developed laser capture microdissection (LCM) technique coupled with microarray experiments is a promising way to address the molecular profile of pure cell populations. However, one main challenge was to preserve the RNA quality during the isolation of single cells or groups of cells and also to obtain sufficient amounts of RNA. Using a new LCM method, we describe here the separate expression profiles of oocytes and follicular cells during the first stages of sheep folliculogenesis. Results We developed a new tissue fixation protocol ensuring efficient single cell capture and RNA integrity during the microdissection procedure. Enrichment in specific cell types was controlled by qRT-PCR analysis of known genes: six oocyte-specific genes ( SOHLH2 , MAEL , MATER , VASA , GDF9 , BMP15 ) and three granulosa cell-specific genes ( KL , GATA4 , AMH ). A global gene expression profile for each follicular compartment during early developmental stages was identified here for the first time, using a bovine Affymetrix chip. Most notably, the granulosa cell dataset is unique to date. The comparison of oocyte vs. follicular cell transcriptomes revealed 1050 transcripts specific to the granulosa cell and 759 specific to the oocyte. Functional analyses allowed the characterization of the three main cellular events involved in early folliculogenesis and confirmed the relevance and potential of LCM-derived RNA. Conclusions The ovary is a complex mixture of different cell types. Distinct cell populations need therefore to be analyzed for a better understanding of their potential interactions. LCM and microarray analysis allowed us to identify novel gene expression patterns in follicular cells at different stages and in oocyte populations.

Background The successful achievement of early ovarian folliculogenesis is important for fertility and reproductive life span. This complex biological process requires the appropriate expression of numerous genes at each developmental stage, in each follicular compartment. Relatively little is known at present about the molecular mechanisms that drive this process, and most gene expression studies have been performed in rodents and without considering the different follicular compartments. Results We used RNA-seq technology to explore the sheep transcriptome during early ovarian follicular development in the two main compartments: oocytes and granulosa cells. We documented the differential expression of 3,015 genes during this phase and described the gene expression dynamic specific to these compartments. We showed that important steps occurred during primary/secondary transition in sheep. We also described the in vivo molecular course of a number of pathways. In oocytes, these pathways documented the chronology of the acquisition of meiotic competence, migration and cellular organization, while in granulosa cells they concerned adhesion, the formation of cytoplasmic projections and steroid synthesis. This study proposes the involvement in this process of several members of the integrin and BMP families. The expression of genes such as Kruppel-like factor 9 (KLF9) and BMP binding endothelial regulator (BMPER) was highlighted for the first time during early follicular development, and their proteins were also predicted to be involved in gene regulation. Finally, we selected a data set of 24 biomarkers that enabled the discrimination of early follicular stages and thus offer a molecular signature of early follicular growth. This set of biomarkers includes known genes such as SPO11 meiotic protein covalently bound to DSB (SPO11), bone morphogenetic protein 15 (BMP15) and WEE1 homolog 2 (S. pombe)(WEE2) which play critical roles in follicular development but other biomarkers are also likely to play significant roles in this process. Conclusions To our knowledge, this is the first in vivo spatio-temporal exploration of transcriptomes derived from early follicles in sheep.

Background The crucial role of the major histocompatibility complex (MHC) for the immune response to infectious diseases is well-known, but no information is available on the 3D nuclear organization of this gene-dense region in immune cells, whereas nuclear architecture is known to play an essential role on genome function regulation. We analyzed the spatial arrangement of the three MHC regions (class I, III and II) in macrophages using 3D-FISH. Since this complex presents major differences in humans and pigs with, notably, the presence of the centromere between class III and class II regions in pigs, the analysis was implemented in both species to determine the impact of this organization on the 3D conformation of the MHC. The expression level of the three genes selected to represent each MHC region was assessed by quantitative real-time PCR. Resting and lipopolysaccharide (LPS)-activated states were investigated to ascertain whether a response to a pathogen modifies their expression level and their 3D organization. Results While the three MHC regions occupy an intermediate radial position in porcine macrophages, the class I region was clearly more peripheral in humans. The BAC center-to-center distances allowed us to propose a 3D nuclear organization of the MHC in each species. LPS/IFNγ activation induces a significant decompaction of the chromatin between class I and class III regions in pigs and between class I and class II regions in humans. We detected a strong overexpression of TNFα (class III region) in both species. Moreover, a single nucleus analysis revealed that the two alleles can have either the same or a different compaction pattern. In addition, macrophage activation leads to an increase in alleles that present a decompacted pattern in humans and pigs. Conclusions The data presented demonstrate that: (i) the MHC harbors a different 3D organization in humans and pigs; (ii) LPS/IFNγ activation induces chromatin decompaction, but it is not the same area affected in the two species. These findings were supported by the application of an original computation method based on the geometrical distribution of the three target genes. Finally, the position of the centromere inside the swine MHC could influence chromatin reorganization during the activation process.

Background The successful achievement of early ovarian folliculogenesis is important for fertility and reproductive life span. This complex biological process requires the appropriate expression of numerous genes at each developmental stage, in each follicular compartment. Relatively little is known at present about the molecular mechanisms that drive this process, and most gene expression studies have been performed in rodents and without considering the different follicular compartments. Results We used RNA-seq technology to explore the sheep transcriptome during early ovarian follicular development in the two main compartments: oocytes and granulosa cells. We documented the differential expression of 3,015 genes during this phase and described the gene expression dynamic specific to these compartments. We showed that important steps occurred during primary/secondary transition in sheep. We also described the in vivo molecular course of a number of pathways. In oocytes, these pathways documented the chronology of the acquisition of meiotic competence, migration and cellular organization, while in granulosa cells they concerned adhesion, the formation of cytoplasmic projections and steroid synthesis. This study proposes the involvement in this process of several members of the integrin and BMP families. The expression of genes such as Kruppel-like factor 9 (KLF9) and BMP binding endothelial regulator (BMPER) was highlighted for the first time during early follicular development, and their proteins were also predicted to be involved in gene regulation. Finally, we selected a data set of 24 biomarkers that enabled the discrimination of early follicular stages and thus offer a molecular signature of early follicular growth. This set of biomarkers includes known genes such as SPO11 meiotic protein covalently bound to DSB (SPO11), bone morphogenetic protein 15 (BMP15) and WEE1 homolog 2 (S. pombe)(WEE2) which play critical roles in follicular development but other biomarkers are also likely to play significant roles in this process. Conclusions To our knowledge, this is the first in vivo spatio-temporal exploration of transcriptomes derived from early follicles in sheep.

PURPOSE: The purpose of this study is to describe the time course of gene expression in a skeletal muscle local injury induced by an intramuscular (IM) injection, and to compare the dynamics of gene expression with pathological events. MATERIALS AND METHODS: Ten piglets received 4 IM injections of propylene glycol in the longissimus dorsi muscles 6 h, 2, 7, and 21 days before euthanasia, where control and injected muscle sites were sampled for RNA isolation and microscopic examination. The hybridization of nylon cDNA microarrays was carried out with radioactive probes obtained from the muscle RNA. RESULTS: 153 genes were found under- or over-expressed at least once among the investigated time-conditions. The eight most discriminant genes were also identified: Two genes (GTP-binding protein RAD and Ankyrin repeat domain protein) were over-expressed at 6 h and six genes between 2 and 21 days (Osteonectin, Fibronectin, Matrix metalloproteinase-2, Collagen alpha 1(I) chain, Collagen alpha 2(I) chain, and Thymosin beta-4). Necrosis, inflammation and regeneration were observed through both the dynamics of gene expression profiles and through the microscopic examinations. CONCLUSION: Our data demonstrate that several pathways are involved in post-injection muscle injury, and that necrosis, inflammation and regeneration are not sequential but occur in parallel.

Together with environmental factors, physiological maturity at birth is a major determinant for neonatal survival and postnatal development in mammalian species. Maturity at birth is the outcome of complex mechanisms of intra-uterine development and maturation during the end of gestation. In pig production, piglet preweaning mortality averages 20% of the litter and thus, maturity is a major welfare and economic concern. Here, we used both targeted and untargeted metabolomic approaches to provide a deeper understanding of the maturity in a model of lines of pigs divergently selected on residual feed intake (RFI), previously shown to have contrasted signs of maturity at birth. Analyses were conducted on plasma metabolome of piglets at birth and integrated with other phenotypic characteristics associated to maturity. We confirmed proline and myo-inositol, previously described for their association with delayed growth, as potential markers of maturity. Urea cycle and energy metabolism were found more regulated in piglets from high and low RFI lines, respectively, suggesting a better thermoregulation ability for the low RFI (with higher feed efficiency) piglets.

Background Successful early folliculogenesis is crucial for female reproductive function. It requires appropriate gene specific expression of the different types of ovarian cells at different developmental stages. To date, most gene expression studies on the ovary were conducted in rodents and did not distinguish the type of cell. In mono-ovulating species, few studies have addressed gene expression profiles and mainly concerned human oocytes. Results We used a laser capture microdissection method combined with RNA-seq technology to explore the transcriptome in oocytes and granulosa cells (GCs) during development of the sheep ovarian follicle. We first documented the expression profile of 15 349 genes, then focused on the 5 129 genes showing differential expression between oocytes and GCs. Enriched functional categories such as oocyte meiotic arrest and GC steroid synthesis reflect two distinct cell fates. We identified the implication of GC signal transduction pathways such as SHH, WNT and RHO GTPase. In addition, signaling pathways (VEGF, NOTCH, IGF1, etc.) and GC transzonal projections suggest the existence of complex cell-cell interactions. Finally, we highlighted several transcription regulators and specifically expressed genes that likely play an important role in early folliculogenesis. Conclusions To our knowledge, this is the first comprehensive exploration of transcriptomes derived from in vivo oocytes and GCs at key stages in early follicular development in sheep . Collectively, our data advance our understanding of early folliculogenesis in mono-ovulating species and will be a valuable resource for unraveling human ovarian dysfunction such as premature ovarian failure (POF).