Demethylation Patterns Research Articles

Electrical stimulation alters DNA methylation and promotes neurite outgrowth.

Electrical stimulation (ES) influences neural regeneration and functionality. We here investigate whether ES regulates DNA demethylation, a critical epigenetic event known to influence nerve regeneration. Retinal ganglion cells (RGCs) have long served as a standard model for central nervous system neurons, whose growth and disease development are reportedly affected by DNA methylation. The current study focuses on the ability of ES to rescue RGCs and preserve vision by modulating DNA demethylation. To evaluate DNA demethylation pattern during development, RGCs from mice at different stages of development, were analyzed using qPCR for ten-eleven translocation (TETs) and immunostained for 5 hydroxymethylcytosine (5hmc) and 5 methylcytosine (5mc). To understand the effect of ES on neurite outgrowth and DNA demethylation, cells were subjected to ES at 75 µAmp biphasic ramp for 20 min and cultured for 5 days. ES increased TETs mediated neurite outgrowth, DNA demethylation, TET1 and growth associated protein 43 levels significantly. Immunostaining of PC12 cells following ES for histone 3 lysine 9 trimethylation showed cells attained an antiheterochromatin configuration. Cultured mouse and human retinal explants stained with β-III tubulin exhibited increased neurite growth following ES. Finally, mice subjected to optic nerve crush injury followed by ES exhibited improved RGCs function and phenotype as validated using electroretinogram and immunohistochemistry. Our results point to a possible therapeutic regulation of DNA demethylation by ES in neurons.

Cumulus-oocyte complexes from sows show differences in lipid metabolism compared to cumulus-oocyte complexes from prepubertal gilts during in vitro maturation.

This study aimed to evaluate the effects of donor age on lipid metabolism during in vitro maturation (IVM) of pigs cumulus-oocyte complexes (COCs). We evaluated transcript levels of genes, the percentage of ooplasm occupied by lipid droplets (LD) and evaluated DNA methylation in COCs from sows and prepubertal gilts. Transcript levels of six genes (ACACA, ACSS2, FASN, FABP3, SLC27A4, PLIN2), which were analyzed in cumulus cells (CCs), increased after 44 h of IVM in the sow group. In the gilt group, only FASN expression increased, while NR3C1 expression decreased after IVM. The measurement of LD in oocytes showed an accumulation of lipids in sow oocytes during IVM, while gilt oocytes showed a decrease in LD. FABP3 and NR3C1 methylation patterns exhibited a demethylation pattern in CCs and oocytes from gilts and sows and showed statistical differences between groups. CCs from sows had a better capacity to change transcription levels of the major genes involved in lipid metabolism during IVM than CCs from gilts. This difference may be involved in accumulation of lipids, acquisition of competence, and maturation of enclosed oocytes. Our results contribute to a better understanding of mechanisms involved in lipid metabolism and acquisition of competence in porcine COCs.

Data-driven identification and classification of nonlinear aging patterns reveals the landscape of associations between DNA methylation and aging

BackgroundAging affects the incidence of diseases such as cancer and dementia, so the development of biomarkers for aging is an important research topic in medical science. While such biomarkers have been mainly identified based on the assumption of a linear relationship between phenotypic parameters, including molecular markers, and chronological age, numerous nonlinear changes between markers and aging have been identified. However, the overall landscape of the patterns in nonlinear changes that exist in aging is unknown.ResultWe propose a novel computational method, Data-driven Identification and Classification of Nonlinear Aging Patterns (DICNAP), that is based on functional data analysis to identify biomarkers for aging and potential patterns of change during aging in a data-driven manner. We applied the proposed method to large-scale, public DNA methylation data to explore the potential patterns of age-related changes in methylation intensity. The results showed that not only linear, but also nonlinear changes in DNA methylation patterns exist. A monotonous demethylation pattern during aging, with its rate decreasing at around age 60, was identified as the candidate stable nonlinear pattern. We also analyzed the age-related changes in methylation variability. The results showed that the variability of methylation intensity tends to increase with age at age-associated sites. The representative variability pattern is a monotonically increasing pattern that accelerates after middle age.ConclusionDICNAP was able to identify the potential patterns of the changes in the landscape of DNA methylation during aging. It contributes to an improvement in our theoretical understanding of the aging process.

Reprogramming of fibroblast cells to totipotent state by DNA demethylation

Many attempts have been made to induce high-quality embryonic stem cells such as pluripotent stem cells and totipotent stem cells, but challenges remain to be overcome such as appropriate methods and sources. Demethylation of the genome after fertilization is an important step to initiate zygote gene activation, which can lead to the development of new embryos. Here, we tried to induce totipotent stem cells by mimicking DNA demethylation patterns of the embryo. Our data showed, after induction of DNA demethylation via chemicals or knockdown of Dnmts, cells positive for Nanog, and Cdx2 emerged. These cells could differentiate into the pluripotent and trophoblast lineage cells in-vitro. After transferring these cells to the uterus, they can implant and form embryo-like structures. Our study showed the importance of DNA demethylation roles in totipotent stem cell induction and a new and easy way to induce this cell type.

Regulatory T-cell stability and functional plasticity in health and disease.

FOXP3-expressing regulatory T cells (Treg ) are indispensable for immune homeostasis and tolerance, and in addition tissue-resident Treg have been found to perform noncanonical, tissue-specific functions. For optimal tolerogenic function during inflammatory disease, Treg are equipped with mechanisms that assure lineage stability. Treg lineage stability is closely linked to the installation and maintenance of a lineage-specific epigenetic landscape, specifically a Treg -specific DNA demethylation pattern. At the same time, for local and directed immune regulation Treg must possess a level of functional plasticity that requires them to partially acquire T helper cell (TH ) transcriptional programs-then referred to as TH -like Treg . Unleashing TH programs in Treg , however, is not without risk and may threaten the epigenetic stability of Treg with consequently pathogenic ex-Treg contributing to (auto-) inflammatory conditions. Here, we review how the Treg -stabilizing epigenetic landscape is installed and maintained, and further discuss the development, necessity and lineage instability risks of TH 1-, TH 2-, TH 17-like Treg and follicular Treg .

Global DNA methylation profiles of\xa0buffalo (Bubalus bubalis)\xa0preimplantation embryos produced by handmade cloning and in vitro fertilization

Somatic cell nuclear transfer technique (SCNT) has proved to be an outstanding method of multiplication of elite animals but accompanied with low efficiency and live birth rate of cloned animals. Epigenetic alterations of DNA has been one of the culprits behind this issue. Cloned embryos are found to deviate slightly from regular pattern of demethylation and re-methylation at the time of nuclear reprogramming and embryonic development when compared with embryos produced by in vitro fertilization (IVF). Thus, the present study was aimed at evaluating global DNA methylation profiles of cloned embryos at 2-cell, 8-cell and blastocyst stages and compare it with corresponding stages of embryos produced by IVF by using MeDIP-Sequencing on Illumina-based platform. We found out that cloned embryos exhibited significantly different DNA methylation pattern as compared to IVF embryos with respect to distribution of differentially methylated regions in different components of genome, CpG islands distribution and methylation status, gene ontological profiles and pathways affected throughout the developmental stages. The data generated from MeDIP-Seq was validated at blastocyst stage cloned and IVF embryos by bisulfite-sequencing PCR on five randomly selected gene regions.

Critical roles of the activation of ethylene pathway genes mediated by DNA demethylation in Arabidopsis hyperhydricity.

Hyperhydricity (HH) often occurs in plant tissue culture, seriously influencing the commercial micropropagation and genetic improvement. DNA methylation has been studied for its function in plant development and stress responses. However, its potential role in HH is unknown. In this study, we report the first comparative DNA methylome analysis of normal and hyperhydric Arabidopsis thaliana (L.) Heynh. seedlings using whole-genome bisulfite sequencing (BS-seq). We found that the global methylation level decreased in hyperhydric seedlings, and most of the differentially methylated genes were CHH hypomethylated genes. Moreover, the bisulfite sequencing results showed that hyperhydric seedlings displayed CHH demethylation patterns in the promoter of the ACS1 and ETR1 genes, resulting in upregulated expression of both genes and increased ethylene accumulation. Furthermore, hyperhydric seedling displayed reduced stomatal aperture accompanied by decreased water loss and increased phosphorylation of aquaporins accompanied by increased water uptake. While silver nitrate (AgNO3 ) prevented HH by maintained the degree of methylation in the promoter regions of ACS1 and ETR1 and downregulated the transcription of both genes. AgNO3 also reduced the content of ethylene together with the phosphorylation of aquaporins and water uptake. Taken together, this study suggested that DNA demethylation is a key switch that activates ethylene pathway genes to enable ethylene synthesis and signal transduction, which may subsequently influence aquaporin phosphorylation and stomatal aperture, eventually causing HH; thus, DNA demethylation plays a crucial role in HH. These results provide insights into the epigenetic regulation mechanism of HH and confirm the role of ethylene and AgNO3 in hyperhydricity control.

ROS1 promotes low temperature-induced anthocyanin accumulation in apple by demethylating the promoter of anthocyanin-associated genes.

Low temperature can affect the growth and development of plants through changes in DNA demethylation patterns. Another known effect of low temperature is the accumulation of anthocyanin pigments. However, it is not known whether the two phenomena are linked, specifically whether DNA demethylation participates in anthocyanin accumulation in response to low-temperature stress. The ROS1 gene is involved in plant DNA demethylation and influences methylation levels in response to low-temperature stress. In this study, using RNA sequencing, we detected the transcription levels of MdROS1, as well as those of anthocyanin biosynthesis-related genes, correlate with the anthocyanin content in apple (Malus domestica), at low temperature. Genomic bisulfite sequencing showed that the methylation levels of the promoters of the anthocyanin-related genes MdCHS, MdCHI, MdF3′H, MdANS, MdUFGT, and MdMYB10 decreased in apple leaves after low-temperature treatment. Similar expression and methylation results were found in apple fruit. Transiently silencing MdROS1 in the leaves and fruit of apple cultivars inhibited the accumulation of anthocyanins and led to decreased expression of anthocyanin biosynthetic genes, and the opposite results were detected in MdROS1-overexpressing leaves and fruit. A promoter binding assay showed that the conserved RRD-DME domains of MdROS1 bind directly to the promoters of MdF3′H and MdUFGT. Taken together, these results suggest that ROS1 affects the anthocyanin biosynthetic pathway by decreasing the methylation level of anthocyanin-related gene promoters, thereby increasing their expression and increasing anthocyanin accumulation.

A Study on Preclinical Efficacy, Underlying Mechanisms, and Sensitivity Markers of a Novel Hypomethylating Agent Ntx-301 in Acute Myeloid Leukemia

Introduction: While intensive induction chemotherapy has been standard-or-care for patients with acute myeloid leukemia (AML), intensive regimens have often been limited in elderly patients with comorbidities. As an alternative option, less intensive hypomethylating agents (HMAs), decitabine (DAC) and azacitidine (AZA), are currently being used in these unfit patients. However, their low response rates and adverse events when administered alone suggest a need to develop novel HMAs that elicit enhanced efficacy and reduced mortality. A recent study demonstrated pharmacological improvements of a novel 4′-thio-modified analog, 5-aza-4′-thio-2′-deoxycytidine (hereafter NTX-301), including enhanced chemical stability and incorporation into DNA and improved preclinical efficacy (Thottassery, 2014). However, the mechanism of action (MoA) of NTX-301 has not yet been understood. Herein, we aim to thoroughly investigate the preclinical efficacy and MoAs of NTX-301 in AML through comparative analysis with DAC and AZA. To this end, we used in vitro and in vivo preclinical models of AML and performed multiomics-based analyses.Results: We comprehensively examined viability of 200 cancer cell lines (CCLs) upon treatment with NTX-301. Consistent with the current use of HMAs as therapeutics for hematologic malignancies, this sensitivity profiling displayed the most remarkable potency of NTX-301 toward blood CCLs (OR=3.97, p=0.0003). In addition, phenotypic assays revealed that the anti-leukemic activity of NTX-301 was superior to that of DAC, which is attributed to more effective actions in inducing apoptosis, cell cycle arrest, and differentiation. Supporting the in vitro results, orally administrated NTX-301 led to more potent tumor regression, better tolerability, and survival benefits over DAC and AZA in both systemic (1.5-2.0 mg/kg, qdx5 then 2 days off, 5 days on, and 9 days off, for 3 cycles) and subcutaneous (0.2-1.5 mg/kg) xenograft models.To assess the underlying MoAs, we interrogated global alterations at the transcriptome and methylome levels upon treatment with NTX-301 in three AML cell lines using RNA sequencing and methylation array. Methylome analyses revealed that NTX-301-induced demethylation patterns were distinguished from DAC; DAC triggered stronger global demethylation than NTX-301 did, whereas NTX-301 derived rather selective demethylation, preferentially in early-replicating regions, H3K27ac-marked regions, and non-CpG islands. In transcriptome analyses compared with DAC, NTX-301 more markedly elicited a transcriptional reversal toward a normal myeloid-like signature by increasing a differentiation signature and suppressing a leukemic stem cell signature. NTX-301 also mediated more pronounced activation of DNA damage response and the p53 pathway, which are characterized by marked induction of pH2AX and pChk1 and increased stability of p53, respectively. Given the synthetic lethality of p53 activation and BCL2 inhibition (Rongqing, 2017), stronger p53 stabilization by NTX-301 may confer more benefits in combination with venetoclax. Indeed, the combination of NTX-301 + venetoclax produced a more synergistic combination index compared with DAC + venetoclax. Strikingly, the combined NTX-301 (0.5-2.0 mg/kg) + venetoclax (50 mg/kg) achieved complete tumor remission, no notable toxicity, and prolonged survival benefits over AZA (2.5 mg/kg) + venetoclax (50 mg/kg) in preclinical models of AML.By integrating sensitivity profiles and multiomics data of 200 CCLs, we interrogated molecular determinants associated with sensitivity to NTX-301. Intriguingly, when comparing methylomes between sensitive and resistant CCLs, we found a significantly biased global hypermethylation trend toward sensitive CCLs. A combinatorial set of the most significantly biased 352 differentially methylated regions (FDR<0.05) showed potential as a predictive sensitivity marker for NTX-301, exhibiting a significant correlation (r=0.69, p<0.0001) with sensitivity to NTX-301.Conclusions: Our study demonstrated an improved therapeutic index of NTX-301 over traditional HMAs, providing a rationale for further clinical development of the agent as a single-agent or in combination with other agents. We also believe that our study for MoAs and biomarkers will improve our understanding of NTX-301. DisclosuresLim: Pinotbio: Research Funding. Yoo: Pinotbio: Research Funding. Cho: Pinotbio: Research Funding. Choi: Pinotbio: Research Funding. Jung: Pinotbio: Research Funding. Jung: Pinotbio: Current Employment. Lee: Pinotbio: Current Employment. Chun: Pinotbio: Current Employment. Go: Pinotbio: Current Employment. Lee: Pinotbio: Current Employment. Choi: Pinotbio: Research Funding.

Genome-wide distribution of 5hmC in the dental pulp of mouse molars and incisors

The dental pulp is critical for the production of odontoblasts to create reparative dentin. In recent years, dental pulp has become a promising source of mesenchymal stem cells that are capable of differentiating into multiple cell types. To elucidate the transcriptional control mechanisms specifying the early phases of odontoblast differentiation, we analysed the DNA demethylation pattern associated with 5-hydroxymethylcytosine (5hmC) in the primary murine dental pulp. 5hmC plays an important role in chromatin accessibility and transcriptional control by modelling a dynamic equilibrium between DNA methylation and demethylation. Our research revealed 5hmC enrichment along genes and non-coding regulatory regions associated with specific developmental pathways in the genome of mouse incisor and molar dental pulp. Although the overall distribution of 5hmC is similar, the intensity and location of the 5hmC peaks significantly differs between the incisor and molar pulp genome, indicating cell type-specific epigenetic variations. Our study suggests that the differential DNA demethylation pattern could account for the distinct regulatory mechanisms underlying the tooth-specific ontogenetic programs.

Two Distinctive POMC Promoters Modify Gene Expression in Cushing Disease.

ContextMechanisms underlying pituitary corticotroph adenoma adrenocorticotropin (ACTH) production are poorly understood, yet circulating ACTH levels closely correlate with adenoma phenotype and clinical outcomes.ObjectiveWe characterized the 5′ ends of proopiomelanocortin (POMC) gene transcripts, which encode the precursor polypeptide for ACTH, in order to investigate additional regulatory mechanisms of POMC gene transcription and ACTH production.MethodsWe examined 11 normal human pituitary tissues, 32 ACTH-secreting tumors, as well as 6 silent corticotroph adenomas (SCAs) that immunostain for but do not secrete ACTH.ResultsWe identified a novel regulatory region located near the intron 2/exon 3 junction in the human POMC gene, which functions as a second promoter and an enhancer. In vitro experiments demonstrated that CREB binds the second promoter and regulates its transcriptional activity. The second promoter is highly methylated in SCAs, partially demethylated in normal pituitary tissue, and highly demethylated in pituitary and ectopic ACTH-secreting tumors. In contrast, the first promoter is demethylated in all POMC-expressing cells and is highly demethylated only in pituitary ACTH-secreting tumors harboring the ubiquitin-specific protease 8 (USP8) mutation. Demethylation patterns of the second promoter correlate with clinical phenotypes of Cushing disease.ConclusionWe identified a second POMC promoter regulated by methylation status in ACTH-secreting pituitary tumors. Our findings open new avenues for elucidating subcellular regulation of the hypothalamic-pituitary-adrenal axis and suggest the second POMC promoter may be a target for therapeutic intervention to suppress excess ACTH production.

The people behind the papers - Brandon Carpenter and David Katz.

A dynamic pattern of histone methylation and demethylation controls gene expression during development, with some processes such as formation of the zygote involving large-scale reprogramming of methylation states. A new paper in Development investigates how inherited histone methylation regulates developmental timing and the germline/soma distinction in Caenorhabditis elegans To hear more about the story we caught up with first author and postdoctoral researcher Brandon Carpenter, and his supervisor David Katz, Associate Professor in the Department of Cell Biology at Emory University School of Medicine in Atlanta, Georgia.

Selenium accumulation characteristics of Cyphomandra betacea (Solanum betaceum) seedlings.

A pot experiment was conducted to study the selenium (Se) accumulation characteristics and the tolerance of Cyphomandra betacea (Solanum betaceum) seedlings under different soil Se concentrations. The 5mg/kg soil Se concentration increased the C. betacea seedling biomass and photosynthetic pigment contents (chlorophyll a, chlorophyll b, total chlorophyll, and carotenoid), whereas the other soil Se concentrations (10, 25, and 50mg/kg) inhibited seedling growth. Increases in the soil Se concentrations tended to decrease the superoxide dismutase activity and soluble protein content, but had the opposite effect on the peroxidase and catalase activities. The 5, 10, and 25mg/kg soil Se concentrations decreased the DNA methylation levels of C. betacea seedlings because of an increase in demethylation patterns (versus 0mg/kg), whereas the 50mg/kg soil Se concentration increased the DNA methylation levels because of an increase in hypermethylation patterns (versus 0mg/kg). Increases in the soil Se concentrations were accompanied by an increasing trend in the Se content of C. betacea seedlings. Moreover, the amount of Se extracted by the shoots was highest for the 25mg/kg soil Se concentration. Therefore, C. betacea may be able to accumulate relatively large amounts of Se and its growth may be promoted in 5mg/kg soil Se.

Evaluation of the Epigenetic Demethylation of NRF2, a Master Transcription Factor for Antioxidant Enzymes, in Colorectal Cancer

Epigenetic changes in CpG islands of the promoter regions of homeostasis-related genes, including nuclear factor erythroid 2-related factor 2 (NRF2), have been shown to hold a significant role in the development of colorectal cancer. Therefore, we aimed to examine the DNA demethylation pattern of the NRF2 promoter region in cancerous lesions from patients with colorectal cancer and the association of methylation status with clinicopathological features in the Iranian population. In this cross-sectional study, 114 colorectal tissue samples were collected. These samples included: 34 tumour tissue samples, 60 precancerous polyps, and 20 normal tissue samples. The promoter methylation status of the NRF2 gene was examined using methylation-specific PCR. Additionally, the relationship between the methylation status and the clinicopathological features was investigated. The frequency of NRF2 demethylation in the tumour samples was significantly higher compared to the polyp tissues (p= 0.003) and normal tissue (p= 0.009), indicating that cancerous colorectal tissues exhibit increased demethylation of the NRF2 promoter. After examining the demethylation status of tissue samples, the clinicopathological features were compared to the demethylation results. No significant association was found between NRF2 promoter demethylation and the clinicopathological features of patient samples. Our findings suggest that the epigenetic modifications leading to NRF2 demethylation found in colorectal tumour samples may contribute to cancer progression from precancerous polyps to cancerous lesions.

Transdifferentiation of α-1,3-galactosyltransferase knockout pig bone marrow derived mesenchymal stem cells into pancreatic β-like cells by microenvironment modulation.

ObjectiveTo evaluate the pancreatic differentiation potential of α-1,3-galactosyltransferase knockout (GalTKO) pig-derived bone marrow-derived mesenchymal stem cells (BM-MSCs) using epigenetic modifiers with different pancreatic induction media.MethodsThe BM-MSCs have been differentiated into pancreatic β-like cells by inducing the overexpression of key transcription regulatory factors or by exposure to specific soluble inducers/small molecules. In this study, we evaluated the pancreatic differentiation of GalTKO pig-derived BM-MSCs using epigenetic modifiers, 5-azacytidine (5-Aza) and valproic acid (VPA), and two types of pancreatic induction media – advanced Dulbecco’s modified Eagle’s medium (ADMEM)-based and N2B27-based media. GalTKO BM-MSCs were treated with pancreatic induction media and the expression of pancreas-islets-specific markers was evaluated by real-time quantitative polymerase chain reaction, Western blotting, and immunofluorescence. Morphological changes and changes in the 5′-C-phosphate-G-3′ (CpG) island methylation patterns were also evaluated.ResultsThe expression of the pluripotent marker (POU class 5 homeobox 1 [OCT4]) was upregulated upon exposure to 5-Aza and/or VPA. GalTKO BM-MSCs showed increased expression of neurogenic differentiation 1 in the ADMEM-based (5-Aza) media, while the expression of NK6 homeobox 1 was elevated in cells induced with the N2B27-based (5-Aza) media. Moreover, the morphological transition and formation of islets-like cellular clusters were also prominent in the cells induced with the N2B27-based media with 5-Aza. The higher insulin expression revealed the augmented trans-differentiation ability of GalTKO BM-MSCs into pancreatic β-like cells in the N2B27-based media than in the ADMEM-based media.Conclusion5-Aza treated GalTKO BM-MSCs showed an enhanced demethylation pattern in the second CpG island of the OCT4 promoter region compared to that in the GalTKO BM-MSCs. The exposure of GalTKO pig-derived BM-MSCs to the N2B27-based microenvironment can significantly enhance their trans-differentiation ability into pancreatic β-like cells.

CRISPR Editing of Mutant IDH1 R132H Induces a CpG Methylation-Low State in Patient-Derived Glioma Models of G-CIMP.

Mutations in isocitrate dehydrogenases 1 and 2 (IDH) occur in the majority of World Health Organization grade II and III gliomas. IDH1/2 active site mutations confer a neomorphic enzyme activity producing the oncometabolite D-2-hydroxyglutarate (D-2HG), which generates the glioma CpG island methylation phenotype (G-CIMP). While IDH1/2 mutations and G-CIMP are commonly retained during tumor recurrence, recent work has uncovered losses of the IDH1 mutation in a subset of secondary glioblastomas. Cooccurrence of the loss of the mutant allele with extensive methylation changes suggests a possible link between the two phenomena. Here, we utilize patient-derived IDH1R132H/WT glioma cell lines and CRISPR-Cas9-mediated gene knockout to model the genetic loss of IDH1 R132H, and characterize the effects of this deletion on DNA methylation. After D-2HG production has been abolished by deletions within the IDH1 alleles, these models show persistent DNA hypermethylation at seven CpG sites previously used to define G-CIMP-positivity in patient tumor samples. Despite these defining G-CIMP sites showing persistent hypermethylation, we observed a genome-wide pattern of DNA demethylation, enriched for CpG sites located within open sea regions of the genome, as well as in CpG-island shores of transcription start sites, after loss of D-2HG production. These results suggest that inhibition of D-2HG from genetic deletion of IDH alleles is not sufficient to reverse hypermethylation of all G-CIMP-defining CpG sites, but does result in more demethylation globally and may contribute to the formation of a G-CIMP-low-like phenotype. IMPLICATIONS: These findings show that loss of the IDH1 mutation in malignant glioma cells leads to a pattern of DNA methylation alterations, and shows plausibility of IDH1 mutation loss being causally related to the gain of a G-CIMP-low-like phenotype.

DNA methylation regulated by ascorbic acids in yak preimplantation embryo helps to improve blastocyst quality.

DNA methylation as an important, essential epigenetic modification is critical for the successful development of mammalian embryos. In recent years, the important role of ascorbic acid (AA) as an irreplaceable cofactor for epigenetic regulation has been confirmed. However, the effect of AA on DNA methylation in preimplantation embryo development of plateau yak remains unknown. In this study, we explored whether AA can help regulates DNA methylation in yak preimplantation embryos to improve the blastocyst quality. First, our results indicate that the preimplantation of the yak still follows the classical pattern of DNA demethylation and remethylation, however, remethylation occurs in the blastocyst stage. Second, the unique expression pattern of the ten-eleven translocation enzyme (TET3) in the cytoplasm plays a key role in the demethylation mechanism. Third, in the blastocyst stage, the pluripotency gene CDX2 promoter region was in a hypomethylated state, and the POU5F1, SOX2, and NANOG promoter regions were in moderate methylation states. In addition, treatment with 50 μg/ml AA mainly improved the expression levels of DNMT1, DNMT3a, and TET3, ensured the establishment, maintenance and transition of 5-methylcytosine. After AA treatment, the methylation level of the pluripotency genes NANOG promoter regions was significantly reduced, and the mRNA transcript abundance of the pluripotency genes NANOG, POU5F1, and CDX2 was upregulated. In conclusion, our findings suggest that AA could increase blastocyst cell numbers by regulating DNA methylation of yak preimplantation embryos .

PARP Inhibitor Affects Long-term Heat-stress Response via Changes in DNA Methylation

Resilience to stress can be obtained by adjusting the stress-response set point during postnatal sensory development. Recent studies have implemented epigenetic mechanisms to play leading roles in improving resilience. We previously found that better resilience to heat stress in chicks can be achieved by conditioning them to moderate heat stress during their critical developmental period of thermal control establishment, 3 days posthatch. Furthermore, the expression level of corticotropin-releasing hormone (CRH) was found to play a direct role in determining future resilience or vulnerability to heat stress by alterations in its DNA-methylation and demethylation pattern. Here we demonstrate how intraperitoneal injection of poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) influences the DNA methylation pattern, thereby affecting the long-term heat-stress response. Single PARPi administration, induced a reduction in both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), without affecting body temperature. The accumulated effect of three PARPi doses brought about a long-term decrease in 5mC% and 5hmC%. These changes coincided with a reduction in body temperature in non-conditioned chicks, similar to that occurring in moderately conditioned heat-stress-resilient chicks. The observed changes in DNA methylation can be explained by decreased activity of the enzyme DNA methyltransferase as a result of the PARPi injection. Furthermore, evaluation of the DNA-methylation pattern along the CRH intron showed a reduction in 5mC% as a result of PARPi treatment, alongside a reduction in CRH mRNA expression. Thus, PARPi treatment can affect DNA methylation, which can alter hypothalamic–pituitary–adrenal (HPA) axis anchors such as CRH, thereby potentially enhancing long-term resilience to heat stress.

Single-cell multiomics sequencing and analyses of human colorectal cancer

Although genomic instability, epigenetic abnormality, and gene expression dysregulation are hallmarks of colorectal cancer, these features have not been simultaneously analyzed at single-cell resolution. Using optimized single-cell multiomics sequencing together with multiregional sampling of the primary tumor and lymphatic and distant metastases, we developed insights beyond intratumoral heterogeneity. Genome-wide DNA methylation levels were relatively consistent within a single genetic sublineage. The genome-wide DNA demethylation patterns of cancer cells were consistent in all 10 patients whose DNA we sequenced. The cancer cells' DNA demethylation degrees clearly correlated with the densities of the heterochromatin-associated histone modification H3K9me3 of normal tissue and those of repetitive element long interspersed nuclear element 1. Our work demonstrates the feasibility of reconstructing genetic lineages and tracing their epigenomic and transcriptomic dynamics with single-cell multiomics sequencing.

In vitro assessment of cord blood–derived proinsulin-specific regulatory T cells for cellular therapy in type 1 diabetes

BackgroundAntigen-specific regulatory T cells (Tregs) have proven to be effective in reversing established autoimmunity in type 1 diabetes (T1D). Cord blood (CB) can serve as an efficient and safe source for Tregs for antigen-specific immunomodulation in T1D, a strategy that is yet to be explored. Therefore, we assessed the potential of CB in generation of proinsulin (PI)-specific Tregs by using HLA class II tetramers. MethodsWe analyzed the frequency of PI-specific natural Tregs (nTregs) and induced Tregs (iTregs) derived from the CB as well as peripheral blood (PB) of patients with T1D and healthy control subjects. For this, CD4+CD25+CD127low and CD4+CD25-T cells were cultured in the presence of PI-derived peptides, transforming growth factor (TGF)-β and rapamycin. PI-specific Tregs were then selected using allele-specific HLA II tetramers loaded with PI-derived peptides, followed by suppression assays. ResultsFollowing stimulation, we observed that CB harbors a significantly higher frequency of PI-specific Tregs than PB of subjects with T1D (P = 0.0003). Further, the proportion of PI-specific Tregs was significantly higher in both the nTreg (P = 0.01) and iTreg (P = 0.0003) compartments of CB as compared with PB of subjects with T1D. In co-culture experiments, the PI-specific Tregs suppressed the proliferation of effector T cells significantly (P = 0.0006). The expanded nTregs were able to retain hypomethylation status at their Tregs-specific demethylated region (TSDR), whereas iTregs were unable to acquire the characteristic demethylation pattern. ConclusionOur study demonstrates that CB can serve as an excellent source for generation of functional antigen-specific Tregs for immunotherapeutic approaches in subjects with T1D.