Genome-wide DNA methylation analysis in jejunum of Sus scrofa with intrauterine growth restriction

Effects of maternal methyl donor intake during pregnancy on ileum methylation and function in an intrauterine growth restriction pig model

BACKGROUND

Intrauterine growth retardation (IUGR) affects intestinal growth, morphology, and function, which leads to poor growth performance and high mortality. The present study explored whether maternal dietary methyl donor (MET) supplementation alleviates IUGR and enhances offspring's growth performance by improving intestinal growth, function, and DNA methylation of the ileum in a porcine IUGR model.

METHODS

Forty multiparous sows were allocated to the control or MET diet groups from mating until delivery. After farrowing, 8 pairs of IUGR and normal birth weight piglets from 8 litters were selected for sampling before suckling colostrum.

RESULTS

The results showed that maternal MET supplementation tended to decrease the IUGR incidence and increased the average weaning weight of piglets. Moreover, maternal MET supplementation significantly reduced the plasma concentrations of isoleucine, cysteine, urea, and total amino acids in sows and newborn piglets. It also increased lactase and sucrase activity in the jejunum of newborn piglets. MET addition resulted in lower ileal methionine synthase activity and increased betaine homocysteine S-methyltransferase activity in the ileum of newborn piglets. DNA methylation analysis of the ileum showed that MET supplementation increased the methylation level of DNA CpG sites in the ileum of newborn piglets. Down-regulated differentially methylated genes were enriched in folic acid binding, insulin receptor signaling pathway, and endothelial cell proliferation. In contrast, up-regulated methylated genes were enriched in growth hormone receptor signaling pathway and nitric oxide biosynthetic process.

CONCLUSIONS

Maternal MET supplementation can reduce the incidence of IUGR and increase the weaning litter weight of piglets, which may be associated with better intestinal function and methylation status.

Maternal Oxidized Soybean Oil Administration in Rats during Pregnancy and Lactation Alters the Intestinal DNA Methylation in Offspring

As a food contaminant, oxidized oil or lipid oxidative products have been proven to exert toxicological effects on the growth and development of animals and humans. Research shows that maternal oxidative stress damage might transmit to another generation by epigenetic modulation. However, current evidence is still not clear on the mechanism of the effects of dietary oxidized oil during pregnancy on the two generations. This study employed a rat model fed with oxidized soybean oil (OSO) during pregnancy and lactation to explore the effects of the oxidative degree (0, 200, 400, and 800 mequiv of O₂/kg) on the placental RNA methylation and DNA methylation in offspring jejunum. The results showed that following the ingestion of OSO, the placental genes of different m⁶A methylation were significantly enriched to nutrient metabolic processes and hormone activity. In addition, the intestine in offspring hypofunctioned observably, such as reducing the height of villi and the level of anti-inflammatory cytokine. Furthermore, maternal intake of OSO during pregnancy can damage the intestinal barrier function of offspring by inhibiting the proliferation and differentiation of intestinal epithelial cells and reducing the activity of intestinal DNA methyltransferase. In conclusion, this study reinforces the assertion that maternal OSO consumption during gestation and lactation negatively affects the placental health and intestinal development of suckling pups.

Impact of quorum sensing signaling molecules in gram-negative bacteria on host cells: current understanding and future perspectives

Quorum sensing is a molecular signaling-based communication mechanism in prokaryotes. In the basic mode, signaling molecules released by certain bacteria are sensed by intracellular receptors or membrane-bound receptors of other members in the community, leading to the collective isogenic signaling molecule synthesis and synchronized activities. This regulation is important for the symbiosis of the bacterium with the host, as well as virulence and biofilm formation. Notably, quorum sensing signaling molecules are not only able to control microbial community behavior but can likewise regulate the physiological status of host cells. Here, we provide a comprehensive review of the importance of quorum sensing signaling molecules in gram-negative bacteria in regulating host cell function and gut health, and suggest possible opportunities for application in combating human and animal diseases by blocking the pathways through which quorum sensing signaling molecules exert their functions.

How Epigenetics Can Enhance Pig Welfare?

Epigenetics works as an interface between the individual and its environment to provide phenotypic plasticity to increase individual adaptation capabilities. Recently, a wide variety of epi-genetic findings have indicated evidence for its application in the development of putative epi-biomarkers of stress in farm animals. The purpose of this study was to evaluate previously reported stress epi-biomarkers in swine and encourage researchers to investigate potential paths for the development of a robust molecular tool for animal welfare certification. In this literature review, we report on the scientific concerns in the swine production chain, the management carried out on the farms, and the potential implications of these practices for the animals' welfare and their epigenome. To assess reported epi-biomarkers, we identified, from previous studies, potentially stress-related genes surrounding epi-biomarkers. With those genes, we carried out a functional enrichment analysis of differentially methylated regions (DMRs) of the DNA of swine subjected to different stress-related conditions (e.g., heat stress, intrauterine insult, and sanitary challenges). We identified potential epi-biomarkers for target analysis, which could be added to the current guidelines and certification schemes to guarantee and certify animal welfare on farms. We believe that this technology may have the power to increase consumers' trust in animal welfare.

DNA methylation as a regulator of intestinal gene expression

The intestinal tract is the entry gate for nutrients and symbiotic organisms, being in constant contact with external environment. DNA methylation is one of the keys to how environmental conditions, diet and nutritional status included, shape functionality in the gut and systemically. This review aims to summarise findings on the importance of methylation to gut development, differentiation and function. Evidence to date on how external factors such as diet, dietary supplements, nutritional status and microbiota modifications modulate intestinal function through DNA methylation is also presented.

N-Acyl-Homoserine Lactones May Affect the Gut Health of Low-Birth-Weight Piglets by Altering Intestinal Epithelial Cell Barrier Function and Amino Acid Metabolism

BACKGROUND

In piglets, low birth weight (LBW) is associated with intestinal dysfunction, which affects their growth performance and causes economic losses.

OBJECTIVES

This study was designed to test whether microbial quorum sensing (QS) affects LBW-induced intestinal developmental defects in piglets.

METHODS

Seven normal-birth-weight (NBW; 1.36 ± 0.01 kg) and 7 LBW (0.89 ± 0.01 kg) piglets were selected. Feces were collected from piglets on 2, 21, and 50 days of age for detection of the QS signaling molecules, N-acyl-homoserine lactones (AHLs), and microbiota analysis. The associations between 2 long-chain AHLs [N-3-oxo-dodecanoyl-l-homoserine lactone (3OC12-HSL) and N-3-oxo-tetradecanoyl-l-homoserine lactone (3OC14-HSL)] and the microbes were tested using Spearman correlation coefficients. The effect of 3OC12-HSL and 3OC14-HSL on intestinal porcine epithelial cell-jejunum 2 (IPEC-J2) cell viability was investigated by cholecystokinin octapeptide assay. Transcriptomic analysis was performed by RNA sequencing on cells treated with 3OC12-HSL.

RESULTS

The concentrations of 3OC12-HSL and 3OC14-HSL in the feces of LBW piglets were higher than those in NBW piglets at age 50 d by 2.5- and 2.24-fold, respectively (P < 0.05). The microbial α diversity (observed species, abundance-based coverage estimator, and Shannon index) of LBW piglets was 81-91% lower than that of NBW piglets (P < 0.05). The relative abundance of Ruminococcaceae UCG-002/UCG-013 was 43.0% and 30.0% lower, respectively, in feces from LBW compared with NBW piglets (P < 0.05). 3OC12-HSL and Ruminococcaceae UCG-002/UCG-005/UCG-010 abundance were negatively correlated (ρ  ≤  -0.58). Treatment with 400 μM 3OC12-HSL markedly reduced IPEC-J2 cell viability by 47.5%. Transcriptomic data showed that 3OC12-HSL mainly changed the "import across plasma membrane" and "arginine and proline metabolism" of IPEC-J2 cells.

CONCLUSIONS

3OC12-HSL is a QS signaling molecule with an ability to impair gut health of LBW piglets. This finding adds to our understanding of the mechanisms responsible for gut injury in LBW piglets.

Low birth weight female piglets show altered intestinal development, gene expression, and epigenetic changes at key developmental loci

Intestinal development is compromised in low birth weight (LBW) pigs, negatively impacting their growth, health, and resilience. We investigated the molecular mechanisms of the altered intestinal maturation observed in neonatal and juvenile LBW female piglets by comparing the changes in intestinal morphology, gene expression, and methylation in LBW versus normal birth weight (NBW) female piglets. A total of 16 LBW/NBW sibling pairs were sacrificed at 0 hours, 8 hours, 10 days, and 8 weeks of age. The gastrointestinal tract was weighed, measured, and the small intestine was sampled for histomorphology, gene expression, and methylation analyses. Impaired intestinal development, with shorter villi and shallower crypts, was observed in LBW female piglets. The expression of intestinal development markers (ALPI and OLFM) rapidly peaked after birth in NBW but not in LBW female piglets. The lower expression of genes involved in nutrient digestion (ANPEP and SI) and barrier function (OCLN and CLDN4) in LBW, together with their delayed development of intestinal villi and crypts could help to explain the compromised health and growth potential of LBW female piglets. The changes in methylation observed in LBW in key regulators of intestinal development (OLFM4 and FZD5) suggest long-term effects of BW on intestinal gene expression, development, and function. Accordingly, experimental demethylation induced in IPEC-J2 cells led to increased expression of intestinal genes (MGA, DPP4, and GLUT2). Overall, we have identified the alterations in transcription or epigenetic marking at a number of genes critical to intestinal development, which may contribute to both the short- and long-term failure of LBW female piglets to thrive.

Postnatal growth retardation is associated with deteriorated intestinal mucosal barrier function using a porcine model

Individuals with postnatal growth retardation (PGR) are prone to developing chronic diseases. Abnormal development in small intestine is casually implicated in impaired growth. However, the exact mechanism is still implausible. In this present study, PGR piglets (aged 42 days) were employed as a good model to analyze developmental changes in intestinal mucosal barrier function. Our data demonstrated that PGR piglets exhibited impaired jejunal and ileal epithelial villous morphology and permeability, accompanied by decreased cell proliferation ability and increased apoptosis rate. In addition, the expression of tight junction proteins (ZO-1, claudin 1, and occludin) and E-cadherin was markedly inhibited by PGR. The expression of P-glycoprotein was significantly reduced in PGR piglets, as well as decreased activity of lysozyme. Moreover, the mRNA abundance and content of inflammatory cytokines were significantly increased in the intestinal mucosa and plasma of PGR piglets, respectively. PGR also contributed to lower level of sIgA, and higher level of CD68-positive rate, β-defensins, and protein expression involved p38 MAPK/NF-κB pathway. Furthermore, PGR altered the intestinal microbial community such as decreased genus Alloprevotella and Oscillospira abundances, and led to lower microbial-derived butyrate production, which may be potential targets for treatment. Collectively, our findings indicated that the intestinal mucosal barrier function of PGR piglets could develop the nutritional intervention strategies in prevention and treatment of the intestinal mucosal barrier dysfunction in piglets and humans.

AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species

BACKGROUND

Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysis, differential epigenomic analysis or co-expression network analysis. While tools have been developed to identify biological functions that are enriched in the genes sets, there remains a need for comprehensive tools that identify functional enrichment of genes for both model and non-model species from a different function classification perspective.

RESULTS

We developed AllEnricher, a tool that calculates gene set function enrichment, with user-defined updatable libraries backing up for both model and non-model species as well as providing comprehensive functional interpretation from multiple dimensions, including GO, KEGG, Reactome, DO and DisGeNET.

CONCLUSIONS

AllEnricher incorporates up to date information from different public resources and provides a comprehensive resolution for biologists to make sense out of specific gene sets, making it an advanced open-source tool for gene set function analysis.

Birthweight determines intestinal microvasculature development and alters endothelial nitric oxide synthase density in young piglets

Blood supply to enterocytes dictates intestinal health and nutrient absorption. These two aspects are impaired in low birthweight (LBW) piglets, but whether the perfusion to intestinal tissues is implicated as well is still unknown. Thus, structural changes in the microvasculature of LBW and normal birthweight (NBW) piglets were investigated during early postnatal development. Additionally, the presence of endothelial nitric oxide synthase (eNOS) in the intestinal mucosa was assessed given its important role to assure perfusion. A total of 22 pigs (11 LBW and 11 NBW) were sacrificed at days 0, 3, 8 and 19 of life. Body weight and intestinal length were recorded and a piece of the small intestine was sampled for immunohistochemical analysis of von Willebrand Factor (vWF, an endothelial cell marker) and eNOS. LBW piglets had a relatively (to body weight) longer intestine than their NBW counterparts. Age did not affect microvasculature, which was more abundant (85% larger vWF-positive area) in NBW than LBW pigs. However, an interaction age*BW was observed for eNOS-IR, showing that eNOS presence peaked in NBW piglets on the first day of life and subsequently decreased. This pattern was not observed in LBW piglets. The less abundant intestinal endothelial mass and the different pattern of eNOS expression observed in LBW piglets suggests microcirculation as a contributing factor in the impaired digestive functioning and gut health of LBW pigs. However, revealing whether the origin of this alteration is prenatal or postnatal, for example due to a lower milk intake, needs further study.

Small intestinal transcriptome analysis revealed changes of genes involved in nutrition metabolism and immune responses in growth retardation piglets1

Postnatal growth retardation (PGR) is common in piglets. Abnormal development in small intestine was casually implicated in impaired growth, but the exact mechanism is still implausible. The present study unveiled transcriptome profile of jejunal mucosa, the major site of nutrient absorption, in PGR and healthy piglets using RNA-sequencing (RNA-seq). The middle segments of jejunum and ileum, and jejunal mucosa were obtained from healthy and PGR piglets at 42 d of age. Total RNA samples extracted from jejunal mucosa of healthy and PGR piglets were submitted for RNA-seq. Lower villus height was observed in both jejunum and ileum from PGR piglets suggesting structural impairment in small intestine (P < 0.05). RNA-seq libraries were constructed and sequenced, and produced average 4.8 × 107 clean reads. Analysis revealed a total of 499 differently expressed genes (DEGs), of which 320 DEGs were downregulated in PGR piglets as compared to healthy piglets. The functional annotation based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) highlighted that most DEGs were involved in nutrient metabolism and immune responses. Our results further indicated decreased gene expression associated with glucose, lipid, protein, mineral, and vitamin metabolic process, detoxication ability, oxidoreductase activity, and mucosal barrier function; as well as the increased insulin resistance and inflammatory response in the jejunal mucosa of PGR piglets. These results characterized the transcriptomic profile of the jejunal mucosa in PGR piglets, and could provide valuable information with respect to better understanding the nutrition metabolism and immune responses in the small intestine of piglets.

Intrauterine Growth Restriction Alters the Genome-Wide DNA Methylation Profiles in Small Intestine, Liver and Longissimus Dorsi Muscle of Newborn Piglets

Intrauterine growth restriction (IUGR) remains a major problem in swine production since the associated low birth weight leads to high rates of pre-weaning morbidity and mortality, and permanent retardation of growth and development. The underlying regulatory mechanisms from the aspects of epigenetic modification has received widespread attention. Studies explore the changes in genome wide methylation in small intestine (SI), liver and longissimus dorsi muscle (LDM) between IUGR and normal birth weight (NBW) newborn piglets using a methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) approach. The data demonstrated that methylated peaks were prominently distributed in distal intergenic regions and the quantities of peaks in IUGR piglets were more than that of NBW piglets. IUGR piglets had relatively high methylated level in promoters, introns and coding exons in all the three tissues. Through KEGG pathway analysis of differentially methylated genes found that 33, 54 and 5 differentially methylated genes in small intestine, liver and longissimus dorsi muscle between NBW and IUGR piglets, respectively, which are related to development and differentiation, carbohydrate and energy metabolism, lipid metabolism, protein turnover, immune response, detoxification, oxidative stress and apoptosis pathway. The objective of this review is to assess the impact of differentially methylation status on developmental delay, metabolic disorders and immune deficiency of IUGR piglets.

Maternal imprinting of the neonatal microbiota colonization in intrauterine growth restricted piglets: a review

Early colonization of intestinal microbiota during the neonatal stage plays an important role on the development of intestinal immune system and nutrients absorption of the host. Compared to the normal birth weight (NBW) piglets, intrauterine growth restricted (IUGR) piglets have a different intestinal microbiota during their early life, which is related to maternal imprinting on intestinal microbial succession during gestation, at birth and via suckling. Imbalanced allocation of limited nutrients among fetuses during gestation could be one of the main causes for impaired intestinal development and microbiota colonization in neonatal IUGR piglets. In this review, we summarized the potential impact of maternal imprinting on the colonization of the intestinal microbiota in IUGR piglets, including maternal undernutrition, imbalanced allocation of nutrients among fetuses, as well as vertical microbial transmission from mother to offspring during gestation and lactation. At the same time, we give information about the current maternal nutritional strategies (mainly breastfeeding, probiotics and prebiotics) to help colonization of the advantageous intestinal microbiota for IUGR piglets.

Original low birth weight deteriorates the hindgut epithelial barrier function in pigs at the growing stage

The deteriorative effect of low birth weight (LBW) on the mucosal permeability of the small intestine in piglets has been widely confirmed. However, whether the hindgut epithelial barrier function in LBW pigs is deteriorated during the growing stage is still unclear. Our study investigated differences in the hindgut epithelial barrier function between LBW and normal birth weight pigs during the growing stage (d 90). Our data demonstrated that the hindgut epithelium of LBW pigs has a high histopathological score, accompanied by decreased antioxidant capacity and increased apoptosis rate, as well as elevated expression and activity of caspase-3. In addition, the number of intestinal goblet cells and gene expression of mucin 2 were significantly down-regulated in LBW pigs. The expression of tight junction proteins (ZO-1 and occludin) was markedly inhibited by the LBW. The mRNA abundance of inflammatory cytokines such as TNF-α, IL-1β, and IL-8 was significantly increased in the hindgut mucosa of LBW pigs. Furthermore, our data revealed that LBW altered the intestinal microbial community in the hindgut mucosa of pigs. Collectively, these finding add to our understanding of the mechanisms responsible for hindgut epithelial barrier dysfunction in LBW pigs during the growing stage and facilitate the development of nutritional intervention strategies.-Tao, S., Bai, Y., Li, T., Li, N., Wang, J. Original low birth weight deteriorates the hindgut epithelial barrier function in pigs at the growing stage.

Are Global DNA methylation and telomere length useful biomarkers for identifying intrauterine growth restricted neonates?

Background: Intrauterine growth restriction (IUGR) is manifested by decreased growth rate of fetus than its normal genetic growth potential. Global DNA methylation is a crucial investigation for identification of epigenetic changes. Epigenetic change regulates Gene transcription, maintenance of genomic stability, and telomere length.Objectives: To investigate whether the global DNA methylation and telomere length are useful for identifying intrauterine growth restriction.Methods: This cohort study was conducted in the Neonatology Department of JIPMER during the period of November 2016 to December 2017. Forty (40) IUGR and forty (40) AGA neonates were recruited. Umbilical cord blood samples were collected at birth. DNA has been separated from the blood samples and using 5-mC DNA ELISA method, the percentage of genomic DNA methylated in these neonates was established. Telomere length (T/S ratio) was measured by using quantitative real time PCR. Data were expressed as a mean ± standard deviation.Results: Genomic DNA methylation varied significantly between IUGR and AGA neonates (IUGR: 3.12 ± 1.24; AGA: 4.40 ± 2.03; p: < .01). There was significant DNA hypo methylation in IUGR neonates. However, telomere length (T/S ratio) was (IUGR: 1.25 ± 0.13; AGA: 1.26 ± 0.22; p: 0.228 (NS)) similar in both groups.Conclusion: Although there is no significant difference in telomere length between IUGR and AGA neonates, global DNA methylation of 3.45 would identify IUGR with a sensitivity and specificity of 69 and 65% respectively.