Stem Cell Models to Investigate the Role of DNA Methylation Machinery in Development of Neuropsychiatric Disorders

DNMT1 downregulation as well as its overexpression distinctly affect mostly overlapping genes implicated in schizophrenia, autism spectrum, epilepsy, and bipolar disorders

Data on schizophrenia (SZ), epilepsy (EPD) and bipolar disorders (BPD) suggested an association of DNMT1 overexpression whereas certain variants of the gene were predicted to result in its increased expression in autism spectrum disorder (ASD). In addition, loss of DNMT1 in frontal cortex resulted in behavioral abnormalities in mice. Here we investigated the effects of increased as well as lack of DNMT1 expression using Dnmt1tet/tet neurons as a model for abnormal neurogenesis and 10,861 genes showing transcript level dysregulation in datasets from the four disorders. In case of overexpression, 3,211 (∼ 30%) genes were dysregulated, affecting pathways involved in neurogenesis, semaphorin signaling, ephrin receptor activity, etc. A disproportionately higher proportion of dysregulated genes were associated with epilepsy. When transcriptome data of Dnmt1tet/tet neurons treated with doxycycline that downregulated DNMT1 was used, 3,356 genes (∼31%) were dysregulated with a significant proportion involved in pathways similar to those in untreated cells. Both conditions resulted in ∼68% of dysregulated genes wherein a majority showed similar patterns of transcript level changes. Among the genes with transcripts returning to normal levels, ribosome assembly/biogenesis was most significant whereas in absence of DNMT1, a new set of 903 genes became dysregulated and are involved in similar pathways as mentioned above. These findings provide support for overexpression of DNMT1 as well as its downregulation as risk factor for the four disorders and that its levels within a tight range are essential for normal neurodevelopment/mental health.

Generation of a transgenic mouse embryonic stem cell line overexpressing DNMT1

DNMT1 overexpression is reported in disorders like schizophrenia, bipolar, epilepsy and multiple cancer types. Here, we used non-homologous recombination to generate R1Dnmt1WT-1, a mouse embryonic stem cell (ESC) line carrying a Dnmt1 cDNA transgene to achieve about two-fold overexpression. This ESC line showed increased transcript levels of Sox2 pluripotency marker. R1Dnmt1WT-1 embryoid bodies showed increased levels of Lefty1 (endoderm), Tbxt and Acta2 (mesoderm), and Pax6 (ectoderm) transcripts. This new line showed normal karyotype and microsatellite profiles making it useful in studying carcinogenesis and abnormal neurogenesis due to DNMT1 overexpression.

Temporal Modulation of DNA Methylation and Gene Expression in Monolayer and 3D Spheroids of Dental Pulp Stem Cells during Osteogenic Differentiation: A Comparative Study

BACKGROUND

Human mesenchymal stem cells are being used for various regenerative applications in past decades. This study chronicled a temporal profile of the transcriptional pattern and promoter methylation status of the osteogenic related gene in dental pulp stem cells (DPSCs) derived from 3-dimensional spheroid culture (3D) vis a vis 2-dimensional (2D) monolayer culture upon osteogenic induction.

METHODS

Biomimetic properties of osteogenesis were determined by alkaline phosphatase assay and alizarin red staining. Gene expression and promoter methylation status of osteogenic genes such as runt-related transcription factor-2, collagen1α1, osteocalcin (OCN), and DLX5 (distal-homeobox) were performed by qPCR assay and bisulfite sequencing, respectively. Furthermore, µ-Computed tomography (micro-CT) was performed to examine the new bone formation in critical-sized rat calvarial bone defect model.

RESULTS

Our results indicated a greater inclination of spheroid culture-derived DPSCs toward osteogenic lineage than the monolayer culture. The bisulfite sequencing of the promoter region of osteogenic genes revealed sustenance of low methylation levels in DPSCs during the progression of osteogenic differentiation. However, the significant difference in the methylation pattern between 2D and 3D derived DPSCs were identified only for OCN gene promoter. We observed differences in the mRNA expression pattern of epigenetic writers such as DNA methyltransferases (DNMTs) and methyl-cytosine dioxygenases (TET) between the two culture conditions. Further, the DPSC spheroids showed enhanced new bone formation ability in an animal model of bone defect compared to the cells cultivated in a 2D platform which further substantiated our in-vitro observations.

CONCLUSION

The distinct cellular microenvironment induced changes in DNA methylation pattern and expression of epigenetic regulators such as DNMTs and TETs genes may lead to increase expression of osteogenic markers in 3D spheroid culture of DPSCs which make DPSCs spheroids suitable for osteogenic regeneration compared to monolayers.

DNMT1: catalytic and non-catalytic roles in different biological processes

DNMT1 is the main enzyme that uses the information on DNA methylation patterns in the parent strand and methylates the daughter strand in freshly replicated hemimethylated DNA. It is widely known that DNMT1 is a component of the epigenetic machinery mediating gene repression via increased promoter methylation. However, recent data suggest that DNMT1 can also modulate gene expression independent of its catalytic activity and participates in multiple processes including the cell cycle, DNA damage repair and stem cell function. This review summarizes the noncanonical functions of DNMT1, some of which are clearly independent of maintenance methylation. Finally, phenotypic data on altered DNMT1 levels suggesting that maintenance of optimal levels of DNMT1 is vital for normal development and health is presented.

Dysregulation of schizophrenia-associated genes and genome-wide hypomethylation in neurons overexpressing DNMT1

Aim: To study the effects of DNMT1 overexpression on transcript levels of genes dysregulated in schizophrenia and on genome-wide methylation patterns. Materials & methods: Transcriptome and DNA methylome comparisons were made between R1 (wild-type) and Dnmt1^tet/tet mouse embryonic stem cells and neurons overexpressing DNMT1. Genes dysregulated in both Dnmt1^tet/tet cells and schizophrenia patients were studied further. Results & conclusions: About 50% of dysregulated genes in patients also showed altered transcript levels in Tet/Tet neurons in a DNA methylation-independent manner. These neurons unexpectedly showed genome-wide hypomethylation, increased transcript levels of Tet1 and Apobec 1-3 genes and increased activity and copy number of LINE-1 elements. The observed similarities between Tet/Tet neurons and schizophrenia brain samples reinforce DNMT1 overexpression as a risk factor.

Epigenetic Regulation of the Hippocampus, with Special Reference to Radiation Exposure

The hippocampus is crucial in learning, memory and emotion processing, and is involved in the development of different neurological and neuropsychological disorders. Several epigenetic factors, including DNA methylation, histone modifications and non-coding RNAs, have been shown to regulate the development and function of the hippocampus, and the alteration of epigenetic regulation may play important roles in the development of neurocognitive and neurodegenerative diseases. This review summarizes the epigenetic modifications of various cell types and processes within the hippocampus and their resulting effects on cognition, memory and overall hippocampal function. In addition, the effects of exposure to radiation that may induce a myriad of epigenetic changes in the hippocampus are reviewed. By assessing and evaluating the current literature, we hope to prompt a more thorough understanding of the molecular mechanisms that underlie radiation-induced epigenetic changes, an area which can be further explored.

Reproducible differentiation and characterization of neurons from mouse embryonic stem cells

Investigation on the effects of disease-associated mutations on neurodevelopment is an essential approach to understand the molecular basis of neurological disorders and can be achieved by generating suitable animal models. However, some of the mutations preclude development of animal models, leaving cell-based models as the only options. Mouse embryonic stem cells (mESCs) are attractive because of the well-established technologies for introducing disease-associated mutations and the feasibility of investigating the abnormalities during different stages of neurogenesis. Importantly, such transgenic mESCs enable large-scale screening and identification of the most promising small molecules and/or drug candidates before undertaking expensive animal studies. Although neuronal differentiation from mESCs is one of the earliest methods to be developed, we observed that the published as well as publicly available methods did not yield neurons consistently. Here, we describe a 16-day differentiation protocol that consistently induced differentiation of mESCs into neurons. This step-wise protocol enables monitoring of the neuronal differentiation process at different stages as well as characterization using the markers for immature and mature neurons by using immunocytochemistry and quantitative real-time PCRs.•Development of a method for differentiating mouse ES cells into neurons.•Differentiating the mouse ES cells into embryoid bodies prior to induction of neuronal differentiation results in better neuron formation.

Analysis of transcript levels of a few schizophrenia candidate genes in neurons from a transgenic mouse embryonic stem cell model overexpressing DNMT1

Overexpression of DNA Methyltransferase I (DNMT1) is considered as one of the etiological factors for schizophrenia (SZ). However, information on genes subjected to dysregulation because of DNMT1 overexpression is limited. To test whether a larger group of SZ-associated genes are affected, we selected 15 genes reported to be dysregulated in patients (Gad1, Reln, Ank3, Cacna1c, Dkk3, As3mt, Ppp1r11, Smad5, Syn1, Wnt1, Pdgfra, Gsk3b, Cxcl12, Tcf4 and Fez1). Transcript levels of these genes were compared between neurons derived from Dnmt1^tet/tet (Tet/Tet) mouse embryonic stem cells (ESCs) that overexpress DNMT1 with R1 (wild-type) neurons. Transcript levels of thirteen genes were significantly altered in Tet/Tet neurons of which, the dysregulation patterns of 11 were similar to patients. Transcript levels of eight out of these eleven were also significantly altered in Tet/Tet ESCs, but the dysregulation patterns of only five were similar to neurons. Comparative analyses among ESCs, embryoid bodies and neurons divided the 15 genes into four distinct groups with a majority showing developmental stage-specific patterns of dysregulation. Reduced Representational Bisulfite Sequencing data from neurons did not show any altered promoter DNA methylation for the dysregulated genes. Doxycycline treatment of Tet/Tet ESCs that eliminated DNMT1, reversed the direction of dysregulation of only four genes (Gad1, Dkk3, As3mt and Syn1). These results suggest that 1. Increased DNMT1 affected the levels of a majority of the transcripts studied, 2. Dysregulation appears to be independent of promoter methylation, 3. Effects of increased DNMT1 levels were reversible for only a subset of the genes studied, and 4. Increased DNMT1 levels may affect transcript levels of multiple schizophrenia-associated genes.

MiR-148a promotes myocardial differentiation of human bone mesenchymal stromal cells via DNA methyltransferase 1 (DNMT1)

MicroRNAs have potential to modulate the differentiation of stem cells. In previous study, we found that miR-148a was up-regulated in myocardial differentiation of human bone mesenchymal stromal cells (hBMSCs) induced by 5'-azacytidine. However, the role of miR-148a in regulating this process still remains unclear. In this study, we investigated the function and molecular mechanism of miR-148a in myocardial differentiation of hBMSCs. We found that miR-148a was significantly increased while DNA methyltransferase 1 (DNMT1) was significantly decreased in myocardial differentiation of hBMSCs. Then, the dual luciferase reporter assays method indicated that DNMT1 was the direct target of miR-148a. In addition, we showed that up-regulation of miR-148a could enhance myocardial differentiation of hBMSCs, while down-regulation of miR-148a could inhibit myocardial differentiation process. Moreover, knockdown of DNMT1 could block the role of miR-148a in promoting myocardial differentiation of hBMSCs. Finally, MiR-148a acted on methylation level of GATA-4 and knockdown of DNMT1 could block this function. Therefore, our results indicate that miR-148a plays a vital role in regulating myocardial differentiation of hBMSCs by targeting DNMT1.

Neurodevelopment at Age 10 Years of Children Born <28 Weeks With Fetal Growth Restriction

OBJECTIVES

We sought to evaluate the relationships between fetal growth restriction (FGR) (both severe and less severe) and assessments of cognitive, academic, and adaptive behavior brain function at age 10 years.

METHODS

At age 10 years, the Extremely Low Gestational Age Newborns Cohort Study assessed the cognitive function, academic achievement, social-communicative function, psychiatric symptoms, and overall quality of life of 889 children born before 28 weeks' gestation. A pediatric epileptologist also interviewed parents as part of a seizure evaluation. The 52 children whose birth weight z scores were <-2 were classified as having severe FGR, and the 113 whose birth weight z scores were between -2 and -1 were considered to have less severe FGR.

RESULTS

The more severe the growth restriction in utero, the lower the level of function on multiple cognitive and academic achievement assessments performed at age 10 years. Growth-restricted children were also more likely than their extremely preterm peers to have social awareness impairments, autistic mannerisms, autism spectrum diagnoses, difficulty with semantics and speech coherence, and diminished social and psychosocial functioning. They also more frequently had phobias, obsessions, and compulsions (according to teacher, but not parent, report).

CONCLUSIONS

Among children born extremely preterm, those with severe FGR appear to be at increased risk of multiple cognitive and behavioral dysfunctions at age 10 years, raising the possibility that whatever adversely affected their intrauterine growth also adversely affected multiple domains of cognitive and neurobehavioral development.

Deciphering the Epigenetic Code in Embryonic and Dental Pulp Stem Cells

A close cooperation between chromatin states, transcriptional modulation, and epigenetic modifications is required for establishing appropriate regulatory circuits underlying self-renewal and differentiation of adult and embryonic stem cells. A growing body of research has established that the epigenome topology provides a structural framework for engaging genes in the non-random chromosomal interactions to orchestrate complex processes such as cell-matrix interactions, cell adhesion and cell migration during lineage commitment. Over the past few years, the functional dissection of the epigenetic landscape has become increasingly important for understanding gene expression dynamics in stem cells naturally found in most tissues. Adult stem cells of the human dental pulp hold great promise for tissue engineering, particularly in the skeletal and tooth regenerative medicine. It is therefore likely that progress towards pulp regeneration will have a substantial impact on the clinical research. This review summarizes the current state of knowledge regarding epigenetic cues that have evolved to regulate the pluripotent differentiation potential of embryonic stem cells and the lineage determination of developing dental pulp progenitors.