MAT2A promotes porcine adipogenesis by mediating H3K27me3 at Wnt10b locus and repressing Wnt/β-catenin signaling

Specific regulation of epigenome landscape by metabolic enzymes and metabolites

Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.

Epigenetic regulation of H3K27me3 in laying hens with fatty liver hemorrhagic syndrome induced by high-energy and low-protein diets

BACKGROUND

Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to FLHS is still lacking in terms of epigenetics.

RESULTS

In this study, we analyzed the genome-wide patterns of trimethylated lysine residue 27 of histone H3 (H3K27me3) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes in healthy and FLHS hens. The study results indicated that H3K27me3 levels were increased in the FLHS hens on a genome-wide scale. Additionally, H3K27me3 was found to occupy the entire gene and the distant intergenic region, which may function as silencer-like regulatory elements. The analysis of transcription factor (TF) motifs in hypermethylated peaks has demonstrated that 23 TFs are involved in the regulation of liver metabolism and development. Transcriptomic analysis indicated that differentially expressed genes (DEGs) were enriched in fatty acid metabolism, amino acid, and carbohydrate metabolism. The hub gene identified from PPI network is fatty acid synthase (FASN). Combined ChIP-seq and transcriptome analysis revealed that the increased H3K27me3 and down-regulated genes have significant enrichment in the ECM-receptor interaction, tight junction, cell adhesion molecules, adherens junction, and TGF-beta signaling pathways.

CONCLUSIONS

Overall, the trimethylation modification of H3K27 has been shown to have significant regulatory function in FLHS, mediating the expression of crucial genes associated with the ECM-receptor interaction pathway. This highlights the epigenetic mechanisms of H3K27me3 and provides insights into exploring core regulatory targets and nutritional regulation strategies in FLHS.

Genome-wide DNA methylation analysis reveals different methylation patterns in Chinese indigenous sheep with different type of tail

Background

The study was aimed to analyze the difference of genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which the typical breeds with different type tails, as to screen the differentially methylated genes (DMGs) that affect the type of tails.

Methods

In this study, three Lanzhou Large-tailed sheep, three Altay sheep and three Tibetan sheep were detected by whole genome bisulfite sequencing (WGBS). The degree of genome-wide DNA methylation, differentially methylated regions (DMRs) and DMGs were analyzed. The candidate genes affecting the tail type of sheep were identified by GO and KEGG pathway enrichment analysis of DMGs.

Results

we identified 68,603 different methylated regions (DMCs) and 75 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in biological process, cellular component and molecular function, Some of the genes in these pathways are involved in fat metabolism: NFATC4, LPIN2, MGAT2 and MAT2B.

Conclusion

Our results may help to further understand the epigenetic regulation mechanisms of deposition of fat in the tail of sheep and provide new basic data for the study of local sheep.

miR-503 targets MafK to inhibit subcutaneous preadipocyte adipogenesis causing a decrease of backfat thickness in Guanzhong Black pigs

Reducing backfat thickness (BFT), determined by subcutaneous fat deposition, is vital in Chinese developed pig breeds. The level of miR-503 in the backfat of Guanzhong Black pigs was found to be lower than that in Large White pigs, implying that miR-503 may be related to BFT. However, the effect and mechanism of miR-503 on adipogenic differentiation in subcutaneous preadipocytes remain unknown. Compared with Large White pigs, the BFT and body fat content of Guanzhong Black pigs were greater, but the level of miR-503 was lower in subcutaneous adipose tissue (SAT) at 180 days of age. Furthermore, miR-503 promoted preadipocyte proliferation by increasing the proportion of S-phase and EdU-positive cells. However, miR-503 inhibited preadipocyte differentiation by downregulating adipogenic gene expression. Mechanistically, miR-503 directly targeted musculoaponeurotic fibrosarcoma oncogene homolog K (MafK) in both proliferating and differentiating preadipocytes to repress adipogenesis. Our findings provide a novel miRNA biomarker for reducing pig BFT levels to improve carcass quality.

The role of WNT10B in physiology and disease: A 10-year update

WNT10B, a member of the WNT family of secreted glycoproteins, activates the WNT/β-catenin signaling cascade to control proliferation, stemness, pluripotency, and cell fate decisions. WNT10B plays roles in many tissues, including bone, adipocytes, skin, hair, muscle, placenta, and the immune system. Aberrant WNT10B signaling leads to several diseases, such as osteoporosis, obesity, split-hand/foot malformation (SHFM), fibrosis, dental anomalies, and cancer. We reviewed WNT10B a decade ago, and here we provide a comprehensive update to the field. Novel research on WNT10B has expanded to many more tissues and diseases. WNT10B polymorphisms and mutations correlate with many phenotypes, including bone mineral density, obesity, pig litter size, dog elbow dysplasia, and cow body size. In addition, the field has focused on the regulation of WNT10B using upstream mediators, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). We also discussed the therapeutic implications of WNT10B regulation. In summary, research conducted during 2012-2022 revealed several new, diverse functions in the role of WNT10B in physiology and disease.

Single Nucleotide Polymorphisms of ALDH18A1 and MAT2A Genes and Their Genetic Associations with Milk Production Traits of Chinese Holstein Cows

Our preliminary work had suggested two genes, aldehyde dehydrogenase 18 family member A1 (ALDH18A1) and methionine adenosyltransferase 2A (MAT2A), related to amino acid synthesis and metabolism as candidates affecting milk traits by analyzing the liver transcriptome and proteome of dairy cows at different lactation stages. In this study, the single nucleotide polymorphisms (SNPs) of ALDH18A1 and MAT2A genes were identified and their genetic effects and underlying causative mechanisms on milk production traits in dairy cattle were analyzed, with the aim of providing effective genetic information for the molecular breeding of dairy cows. By resequencing the entire coding and partial flanking regions of ALDH18A1 and MAT2A, we found eight SNPs located in ALDH18A1 and two in MAT2A. Single-SNP association analysis showed that most of the 10 SNPs of these two genes were significantly associated with the milk yield traits, 305-day milk yield, fat yield, and protein yield in the first and second lactations (corrected p ≤ 0.0488). Using Haploview 4.2, we found that the seven SNPs of ALDH18A1 formed two haplotype blocks; subsequently, the haplotype-based association analysis showed that both haplotypes were significantly associated with 305-day milk yield, fat yield, and protein yield (corrected p ≤ 0.014). Furthermore, by Jaspar and Genomatix software, we found that 26:g.17130318 C>A and 11:g.49472723G>C, respectively, in the 5′ flanking region of ALDH18A1 and MAT2A genes changed the transcription factor binding sites (TFBSs), which might regulate the expression of corresponding genes to affect the phenotypes of milk production traits. Therefore, these two SNPs were considered as potential functional mutations, but they also require further verification. In summary, ALDH18A1 and MAT2A were proved to probably have genetic effects on milk production traits, and their valuable SNPs might be used as candidate genetic markers for dairy cattle’s genomic selection (GS).

LINC00092 Modulates Oxidative Stress and Glycolysis of Breast Cancer Cells via Pyruvate Carboxylase-Mediated AKT/mTOR Pathway

Background

The discovery of noncoding RNAs (ncRNAs) offers new options for cancer-targeted therapy. This study is aimed at exploring the regulatory function of LINC00092 on breast cancer (BC) oxidative stress and glycolysis, along with internal mechanism concerning pyruvate carboxylase (PC).

Methods

Bioinformatics analysis was used to explore LINC00092 (or friend leukemia virus integration 1 (FLI1)) expression on BC progression, as well as oxidative stress and glycolysis in BC. After LINC00092 overexpression or silence, BC cell viability, proliferation, migration, invasion, oxidative stress, glycolysis, and AKT/mTOR pathway were detected. Following 2-DG, SC79, or MK2206 treatment, effects of LINC00092 on BC cells were measured. Moreover, regulatory activity of LINC00092 in PC expression was analyzed. Whether PC participated in the modulation of LINC00092 on BC cell functions was explored.

Results

LINC00092 was lowly expressed in BC and negatively related to BC progression. FLI1 bound to LINC00092 promoter to positively modulate LINC00092. LINC00092 overexpression inhibited BC cell proliferation, migration, invasion, oxidative stress, glycolysis, and AKT/mTOR pathway and likewise suppressed BC growth in vivo. Silence of LINC00092 had opposite influences. 2-DG partially reversed the LINC00092 silence-resulted increase of BC cell proliferation. SC79 alleviated the function of LINC00092 overexpression on BC cell functions. MK2206 had the contrary influence of SC79. Besides, LINC00092 bound to PC to modulate ubiquitination degradation of PC protein. PC took part in the influences of LINC00092 on BC cell functions.

Conclusions

LINC0092 modulates oxidative stress and glycolysis of BC cells via the PC-mediated AKT/mTOR pathway, which is possibly a target for BC diagnosis and therapy.

Knockdown of nuclear receptor binding SET domain-containing protein 1 (NSD1) inhibits proliferation and facilitates apoptosis in paclitaxel-resistant breast cancer cells via inactivating the Wnt/β-catenin signaling pathway

The burden of breast cancer (BC) has exacerbated over decades. Paclitaxel resistance is responsible for increasing BC treatment burden. Nuclear receptor binding SET domain-containing protein 1 (NSD1) is positively correlated with a poor prognosis in patients with BC. This study investigates the function of NSD1 in paclitaxel-resistant (PR) BC cells. The high levels of NSD1 and Wnt10b in PR BC cell lines (MCF-7/PR) or MCF-7 parental cells were determined by RT-qPCR. Western blotting was conducted to measure the levels of NSD1 protein, apoptosis-associated proteins, Wnt10b protein, H3K36me2 protein, H3K27me3 protein, and signal pathway-associated proteins in MCF-7/PR cells or MCF-7 cells or in vivo subcutaneous xenografted tumor model, and the results demonstrated that NSD1 inhibited cell apoptosis and promoted cell proliferation and tumor growth via activating Wnt/β-catenin pathway. Cell apoptosis and viability were estimated using cell counting kit-8 assays and flow cytometry. Positive correlation between NSD1 and Wnt10b was identified by chromatin immunoprecipitation assay. The distribution of β-catenin was determined by immunofluorescence assays. We conclude that NSD1 knockdown inhibits the viability and promotes the apoptosis of paclitaxel-resistant BC cells by inactivating the NSD1/H3K27me3/Wnt10b/β-catenin signaling pathway.

Genome-Wide Analysis of H3K27me3 in Porcine Embryonic Muscle Development

The trimethylation of histone H3 lysine 27 (H3K27me3) is one of the most important chromatin modifications, which is generally presented as a repressive mark in various biological processes. However, the dynamic and global-scale distribution of H3K27me3 during porcine embryonic muscle development remains unclear. Here, our study provided a comprehensive genome-wide view of H3K27me3 and analyzed the matching transcriptome in the skeletal muscles on days 33, 65, and 90 post-coitus from Duroc fetuses. Transcriptome analysis identified 4,124 differentially expressed genes (DEGs) and revealed the key transcriptional properties in three stages. We found that the global H3K27me3 levels continually increased during embryonic development, and the H3K27me3 level was negatively correlated with gene expression. The loss of H3K27me3 in the promoter was associated with the transcriptional activation of 856 DEGs in various processes, including skeletal muscle development, calcium signaling, and multiple metabolic pathways. We also identified for the first time that H3K27me3 could enrich in the promoter of genes, such as DES, MYL1, TNNC1, and KLF5, to negatively regulate gene expression in porcine satellite cells (PSCs). The loss of H3K27me3 could promote muscle cell differentiation. Taken together, this study provided the first genome-wide landscape of H3K27me3 in porcine embryonic muscle development. It revealed the complex and broad function of H3K27me3 in the regulation of embryonic muscle development from skeletal muscle morphogenesis to myofiber maturation.

Effect of rare earth element lanthanum on lipid deposition and Wnt10b signaling in the liver of male zebrafish

This paper investigates the effect of lanthanum (La) on lipid deposition and Wnt10b signaling in the liver of male zebrafish with exposure of 0, 10, 20, and 30 μmol/L La. It suggests that La can be accumulated in liver, and its treatments decrease the activities and gene expression of enzymes related to fatty acid synthesis. The levels of total cholesterol (TC), triglyceride (TG), and nonesterified fatty acids (NEFA) as well as the size of lipid droplets are decreased by La treatments. Moreover, La treatments affect the composition of fatty acids and the content of nutrient elements. Meanwhile, they also induce the gene expression of wnt10b, β-catenin, pparα, and pparγ, but inhibit gsk-3β gene expression in liver. Further study on the result of wnt10b gene interference shows that Wnt10b/β-catenin signaling plays a crucial role in the regulatory process of hepatic lipid deposition. Taken together, our observations suggest that La accumulation affects lipid deposition in the liver of male zebrafish, and Wnt10b signaling pathway may be involved in this process.

MiR-26b-5p-modified hUB-MSCs derived exosomes attenuate early brain injury during subarachnoid hemorrhage via MAT2A-mediated the p38 MAPK/STAT3 signaling pathway

Early brain injury (EBI) is a major cause of adverse outcomes following subarachnoid hemorrhage (SAH). There is evidence that mesenchymal stem cells (MSCs) - derived exosomes are involved in the repair of SAH. Exosomes were extracted from human umbilical cord mesenchymal stem cells (hubMSCs) and identified. OxyHb treated PC12 cells were transfected with exosomes alone or together with miR-26b-5p inhibitor. Hub-MSCs derived exosomes promote cell proliferation, inhibit apoptosis and reduce inflammatory mediator expression. Transfection of miR-26b-5p inhibitor abolished the promoting effect of exosomes on the proliferation of PC12 cells, as well as the inhibitory effect on cell apoptosis. In addition, methionine adenosyltransferase II alpha (MAT2A) was one target gene of miR-26b-5p. OxyHb treated PC12 cells were transfected with exosomes alone or together with pcDNA-MAT2A and observed that the promoting effect of exosomes on PC12 cell proliferation was abolished by pcDNA-MAT2A, which was the same as the effect of miR-26b-5p inhibitor. OxyHb treated PC cells incubated with exosomes were transfected with miR-26b-5p inhibitor alone or together with si-MAT2A, respectively, and it was observed that exosomes decreased the phosphorylation levels of p38 MAPK and STAT3 proteins, inhibited cell apoptosis and inflammatory mediator expression, and miR-26b-5p inhibitor abrogated the effects of exosomes, while transfection of si-MAT2A reversed the effects of miR-26b-5p inhibitor. Moreover, injection of miR-26b-5p inhibitor resulted in increased MAT2A and pathway protein expression, increased inflammatory mediators, and aggravated neurological symptoms in the brain tissues of SAH rats.

SYVN1-MTR4-MAT2A Signaling Axis Regulates Methionine Metabolism in Glioma Cells

Methionine is one of the essential amino acids. How tumor cells adapt and adjust their signal transduction networks to avoid apoptosis in a methionine-restricted environment is worthy of further exploration. In this study, we investigated the molecular mechanism of glioma response to methionine restriction, providing a theoretical basis for new treatment strategies for glioma.

Proteinase-activated receptor 2 promotes 3T3-L1 preadipocyte differentiation through activation of the PI3K/AKT signalling pathway and MAT2A gene expression

The present study aimed to investigate the function and mechanisms of PAR2 in preadipocyte differentiation. This study found that the expression level of PAR2 was increased during 3T3-L1 mouse preadipocyte differentiation towards adipocytes. In addition, PAR2 overexpression significantly stimulated the expression of adipogenic proteins including ACC1, PPARγ, and SREBF1. Moreover, PAR2 overexpression increased the content of triglyceride (TG) in 3T3-L1 preadipocytes. Knockdown of PAR2 suppressed 3T3-L1 preadipocyte differentiation and adipogenesis. Mechanistically, PAR2 promoted 3T3-L1 preadipocyte differentiation and TG production through activation of the PI3K/AKT signalling pathway and MAT2A gene expression. The research sheds light on the adipogenic effects of PAR2 and its underlying mechanisms. Thus, PAR2 may have therapeutic significance for obesity.

MiR-370 enhances cell cycle and represses lipid accumulation in porcine adipocytes

MicroRNAs (miRNAs) are emerging as an important regulator during adipose development. Previous studies have revealed that miR-370 is related to lipid metabolic homeostasis, however, its roles in lipid accumulation remain to be established. In this study, we demonstrated that ssc-miR-370 was highly conserved across domestic animals, and relatively enriched in adipose tissues and skeletal muscles. Overexpression of ssc-miR-370 significantly promoted the proliferation of porcine preadipocytes through facilitating G₁/S phase transition. Meanwhile, ssc-miR-370 mimics dramatically suppressed adipogenic differentiation, indicated by reduced triglyceride deposition as well as downregulated PPARγ and aP2 expressions. Furthermore, ssc-miR-370 was demonstrated to repress FoxO1 expression via directly targeting FoxO1 3'-UTR using dual luciferase activity assay. Our data evaluates miR-370 as a novel adipogenic modulator, which may be a potential target to reduce backfat thickness in pigs and fight obesity in humans.

CRISPR/Cas9-mediated knockout of NSD1 suppresses the hepatocellular carcinoma development via the NSD1/H3/Wnt10b signaling pathway

Background

The NSD family of histone lysine methyltransferases have emerged as important biomarkers that participate in a variety of malignancies. Recent evidence has indicated that somatic dysregulation of the nuclear receptor binding SET domain-containing protein 1 (NSD1) is associated with the tumorigenesis in HCC, suggesting that NSD1 may serve as a prognostic target for this malignant tumor. However, its mechanism in human hepatocellular carcinoma (HCC), the major primary malignant tumor in the human liver, remains unclear. Hence, we investigated how NSD1 regulated HCC progression via regulation of the Wnt/β-catenin signaling pathway.

Methods

Reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot analysis was performed to identify the expression of NSD1 in HCC cells and clinically obtained tissues. The relationship between NSD1 expression and prognosis was analyzed by Kaplan-Meier survival curve. Further, a NSD1 knockout cell line was constructed by CRISPR/Cas9 genomic editing system, which was investigated in a battery of assays such as HCC cell proliferation, migration and invasion, followed by the investigation into NSD1 regulation on histone H3, Wnt10b and Wnt/β-catenin signaling pathway via ChIP. Finally, a nude mouse xenograft model was conducted in order to assess tumorigenesis affected by NSD1 knockout in vivo.

Results

NSD1 was overexpressed in HCC tissues and cell lines in association with poor prognosis. Knockout of NSD1 inhibited the proliferation, migration and invasion abilities of HCC cells. CRISPR/Cas9-mediated knockout of NSD1 promoted methylation of H3K27me3 and reduced methylation of H3K36me2, which inhibited Wnt10b expression. The results thereby indicated an inactivation of the Wnt/β-catenin signaling pathway suppressed cell proliferation, migration and invasion in HCC. Moreover, these in vitro findings were reproduced in vivo on tumor xenograft in nude mice.

Conclusion

In conclusion, the study provides evidence that CRISPR/Cas9-mediated NSD1 knockout suppresses HCC cell proliferation and migration via the NSD1/H3/Wnt10b signaling pathway, suggesting that NSD1, H3 and Wnt10b may serve as potential targets for HCC.

MAT2A/2B promote porcine intramuscular preadipocyte proliferation through ERK signaling pathway

Intramuscular fat (IMF) content has been identified as a crucial factor of porcine meat quality. MAT2A and MAT2B coordinately catalyzes the synthesis of the major biological methyl donor S-adenosylmethionine (SAMe). However, the regulatory effect of MAT2A and MAT2B on porcine intramuscular preadipocyte proliferation has not been clarified. In this study, we investigated the effect of MAT2A and MAT2B and its potential mechanism during porcine intramuscular proliferation. We demonstrated that overexpression of MAT2A and MAT2B promoted the cell cycle progression of porcine preadipocyte by flow cytometry and EdU-labeling assay, as well as promoted the expression of cell cycle marker genes including Cyclin B, Cyclin D, and Cyclin-dependent kinase 4, but reduced the expression of cell cycle inhibitor P27. Consistently, knockdown of MAT2A and MAT2B inhibited cell cycle progression and downregulated the mRNA and protein levels of the above genes. Furthermore, overexpression of MAT2A and MAT2B activated the phosphorylation of ERK1/2. Moreover, the inhibitory effect of U0126 (a specific ERK1/2 inhibitor) on the ERK1/2 activities was partially recovered by overexpression of MAT2A and MAT2B in porcine intramuscular preadipocytes. Taken together, our findings suggested that MAT2A and MAT2B promote porcine preadipocyte proliferation by ERK1/2 signaling pathway.

Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux

Metabolism has been shown to alter cell fate in human pluripotent stem cells (hPSC). However, current understanding is almost exclusively based on work performed at 20% oxygen (air), with very few studies reporting on hPSC at physiological oxygen (5%). In this study, we integrated metabolic, transcriptomic, and epigenetic data to elucidate the impact of oxygen on hPSC. Using ¹³C-glucose labeling, we show that 5% oxygen increased the intracellular levels of glycolytic intermediates, glycogen, and the antioxidant response in hPSC. In contrast, 20% oxygen increased metabolite flux through the TCA cycle, activity of mitochondria, and ATP production. Acetylation of H3K9 and H3K27 was elevated at 5% oxygen while H3K27 trimethylation was decreased, conforming to a more open chromatin structure. RNA-seq analysis of 5% oxygen hPSC also indicated increases in glycolysis, lysine demethylases, and glucose-derived carbon metabolism, while increased methyltransferase and cell cycle activity was indicated at 20% oxygen. Our findings show that oxygen drives metabolite flux and specifies carbon fate in hPSC and, although the mechanism remains to be elucidated, oxygen was shown to alter methyltransferase and demethylase activity and the global epigenetic landscape.