ABSTRACT
The DNA methyltransferase Dnmt3a has high expression in terminally differentiated macrophages; however, its role in innate immunity remains unknown. Here we report that deficiency in Dnmt3a selectively impaired the production of type I interferons triggered by pattern-recognition receptors (PRRs), but not that of the proinflammatory cytokines TNF and IL-6. Dnmt3a-deficient mice exhibited enhanced susceptibility to viral challenge. Dnmt3a did not directly regulate the transcription of genes encoding type I interferons; instead, it increased the production of type I interferons through an epigenetic mechanism by maintaining high expression of the histone deacetylase HDAC9. In turn, HDAC9 directly maintained the deacetylation status of the key PRR signaling molecule TBK1 and enhanced its kinase activity. Our data add mechanistic insight into the crosstalk between epigenetic modifications and post-translational modifications in the regulation of PRR signaling and activation of antiviral innate immune responses.
Subject(s)
DNA (Cytosine-5-)-Methyltransferases/metabolism , Immunity, Innate , Macrophages/immunology , Rhabdoviridae Infections/immunology , Vesicular stomatitis Indiana virus/immunology , Acetylation , Animals , DNA Methyltransferase 3A , Epigenesis, Genetic , HEK293 Cells , Histone Deacetylases/genetics , Histone Deacetylases/metabolism , Humans , Interferon Type I/metabolism , Macrophages/virology , Male , Mice , Mice, Inbred C57BL , Mice, Transgenic , Protein Serine-Threonine Kinases/metabolism , RAW 264.7 Cells , Receptors, Pattern Recognition/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism , Signal TransductionABSTRACT
Postnatal growth of mammalian oocytes is accompanied by a progressive gain of DNA methylation, which is predominantly mediated by DNMT3A, a de novo DNA methyltransferase1,2. Unlike the genome of sperm and most somatic cells, the oocyte genome is hypomethylated in transcriptionally inert regions2-4. However, how such a unique feature of the oocyte methylome is determined and its contribution to the developmental competence of the early embryo remains largely unknown. Here we demonstrate the importance of Stella, a factor essential for female fertility5-7, in shaping the oocyte methylome in mice. Oocytes that lack Stella acquire excessive DNA methylation at the genome-wide level, including in the promoters of inactive genes. Such aberrant hypermethylation is partially inherited by two-cell-stage embryos and impairs zygotic genome activation. Mechanistically, the loss of Stella leads to ectopic nuclear accumulation of the DNA methylation regulator UHRF18,9, which results in the mislocalization of maintenance DNA methyltransferase DNMT1 in the nucleus. Genetic analysis confirmed the primary role of UHRF1 and DNMT1 in generating the aberrant DNA methylome in Stella-deficient oocytes. Stella therefore safeguards the unique oocyte epigenome by preventing aberrant de novo DNA methylation mediated by DNMT1 and UHRF1.
Subject(s)
DNA (Cytosine-5-)-Methyltransferase 1/metabolism , DNA Methylation , Epigenesis, Genetic , Oocytes/metabolism , Repressor Proteins/metabolism , Animals , CCAAT-Enhancer-Binding Proteins , Cell Line , Cell Nucleus/metabolism , Chromosomal Proteins, Non-Histone , DNA (Cytosine-5-)-Methyltransferase 1/antagonists & inhibitors , Embryonic Development , Female , Genome/genetics , Humans , Mice , Nuclear Proteins/metabolism , Promoter Regions, Genetic/genetics , Repressor Proteins/deficiency , Repressor Proteins/genetics , Ubiquitin-Protein Ligases , Zygote/metabolismABSTRACT
Severe burns are one of the most devastating injuries, in which sustained inflammation and ischemia often delay the healing process. Pro-angiogenic growth factors such as vascular endothelial growth factor (VEGF) have been widely studied for promoting wound healing. However, the short half-life and instability of VEGF limit its clinical applications. In this study, we develop a photo-crosslinked hydrogel wound dressing from methacrylate hyaluronic acid (MeHA) bonded with a pro-angiogenic prominin-1-binding peptide (PR1P). The materials were extruded in wound bed and in situ formed a wound dressing via exposure to short-time ultraviolet radiation. The study shows that the PR1P-bonded hydrogel significantly improves VEGF recruitment, tubular formation, and cell migration in vitro. Swelling, Scanning Electron Microscope, and mechanical tests indicate the peptide does not affect the overall mechanical and physical properties of the hydrogels. For in vivo studies, the PR1P-bonded hydrogel dressing enhances neovascularization and accelerates wound closure in both deep second-degree burn and full-thickness excisional wound models. The Western blot assay shows such benefits can be related to the activation of the VEGF-Akt signaling pathway. These results suggest this photo-crosslinked hydrogel dressing efficiently promotes VEGF recruitment and angiogenesis in skin regeneration, indicating its potential for clinical applications in wound healing.
Subject(s)
Hydrogels , Neovascularization, Physiologic , Vascular Endothelial Growth Factor A , Wound Healing , Wound Healing/drug effects , Animals , Hydrogels/chemistry , Hydrogels/pharmacology , Vascular Endothelial Growth Factor A/metabolism , Neovascularization, Physiologic/drug effects , Humans , Mice , Hyaluronic Acid/chemistry , Hyaluronic Acid/pharmacology , Bandages , Cell Movement/drug effects , Burns/therapy , Burns/pathology , Male , Human Umbilical Vein Endothelial Cells , Peptides/chemistry , Peptides/pharmacology , Cross-Linking Reagents/chemistry , Angiogenesis Inducing Agents/pharmacology , Angiogenesis Inducing Agents/chemistryABSTRACT
BACKGROUND: Retinal degeneration (RD) is a group of disorders on irreversible vision loss. Multiple types of stem cells were used in clinical trials for RD treatment. However, it remains unknown what kinds of stem cells are most effective for the treatment. Therefore, we investigated the subretinal transplantation of several types of stem cells, human adipose-derived stem cells (hADSCs), amniotic fluid stem cells (hAFSCs), bone marrow stem cells (hBMSCs), dental pulp stem cells (hDPSCs), induced pluripotent stem cell (hiPSC), and hiPSC-derived retinal pigment epithelium (RPE) cells for protection effects, paracrine effects and treatment efficiency in an RD disease model rats. METHODS: The generation and characterization of these stem cells and hiPSC-derived RPE cells were performed before transplantation. The stem cells or hiPSC-derived RPE cell suspension labelled with CellTracker Green to detect transplanted cells were delivered into the subretinal space of 3-week-old RCS rats. The control group received subretinal PBS injection or non-injection. A series of detections including fundus photography, optomotor response (OMR) evaluations, light-dark box testing, electroretinography (ERG), and hematoxylin and eosin (HE) staining of retinal sections were conducted after subretinal injection of the cells. RESULTS: Each stem cell, hiPSC-derived RPE cell or PBS (blank experiment) was successfully transplanted into at least six RCS rats subretinally. Compared with the control rats, RCS rats subjected to subretinal transplantation of any stem cells except hiPSCs showed higher ERG waves (p < 0.05) and quantitative OMR (qOMR) index values (hADSCs: 1.166, hAFSCs: 1.249, hBMSCs: 1.098, hDPSCs: 1.238, hiPSCs: 1.208, hiPSC-RPE cells: 1.294, non-injection: 1.03, PBS: 1.06), which indicated better visual function, at 4Ā weeks post-injection. However, only rats that received hiPSC-derived RPE cells maintained their visual function at 8Ā weeks post-injection (p < 0.05). The outer nuclear layer thickness observed in histological sections after HE staining showed the same pattern as the ERG and qOMR results. CONCLUSIONS: Compared to hiPSC-derived RPE cells, adult and fetal stem cells yielded improvements in visual function for up to 4Ā weeks post-injection; this outcome was mainly based on the paracrine effects of several types of growth factors secreted by the stem cells. Patients with RD will benefit from the stem cell therapy.
Subject(s)
Induced Pluripotent Stem Cells , Mesenchymal Stem Cells , Retinal Degeneration , Adult , Humans , Rats , Animals , Retinal Degeneration/therapy , Induced Pluripotent Stem Cells/metabolism , Induced Pluripotent Stem Cells/pathology , Retina/pathology , Electroretinography , Mesenchymal Stem Cells/metabolism , Retinal Pigment Epithelium/pathologyABSTRACT
Zika virus (ZIKV) infection during pregnancy is linked to various developmental brain disorders. Infants who are asymptomatic at birth might have postnatal neurocognitive complications. However, animal models recapitulating these neurocognitive phenotypes are lacking, and the circuit mechanism underlying behavioral abnormalities is unknown. Here, we show that ZIKV infection during mouse pregnancy induces maternal immune activation (MIA) and leads to autistic-like behaviors including repetitive self-grooming and impaired social memory in offspring. In the medial prefrontal cortex (mPFC), ZIKV-affected offspring mice exhibit excitation and inhibition imbalance and increased cortical activity. This could be explained by dysregulation of inhibitory neurons and synapses, and elevated neural activity input from mPFC-projecting ventral hippocampus (vHIP) neurons. We find structure alterations in the synaptic connections and pattern of vHIP innervation of mPFC neurons, leading to hyperconnectivity of the vHIP-mPFC pathway. Decreasing the activity of mPFC-projecting vHIP neurons with a chemogenetic strategy rescues social memory deficits in ZIKV offspring mice. Our studies reveal a hyperconnectivity of vHIP to mPFC projection driving social memory deficits in mice exposed to maternal inflammation by ZIKV.
Subject(s)
Zika Virus Infection , Zika Virus , Animals , Female , Hippocampus , Inflammation , Mice , Prefrontal Cortex , PregnancyABSTRACT
Multipotent trophoblasts undergo dynamic morphological movement and cellular differentiation after conceptus implantation to generate placenta. However, the mechanism controlling trophoblast development and differentiation during peri-implantation development in human remains elusive. In this study, we modeled human conceptus peri-implantation development from blastocyst to early postimplantation stages by using an in vitro coculture system and profiled the transcriptome of 476 individual trophoblast cells from these conceptuses. We revealed the genetic networks regulating peri-implantation trophoblast development. While determining when trophoblast differentiation happens, our bioinformatic analysis identified T-box transcription factor 3 (TBX3) as a key regulator for the differentiation of cytotrophoblast (CT) into syncytiotrophoblast (ST). The function of TBX3 in trophoblast differentiation is then validated by a loss-of-function experiment. In conclusion, our results provided a valuable resource to study the regulation of trophoblasts development and differentiation during human peri-implantation development.
Subject(s)
Gene Expression Regulation, Developmental , Gene Regulatory Networks , Models, Biological , T-Box Domain Proteins/genetics , Transcriptome , Trophoblasts/metabolism , Cell Culture Techniques , Cell Differentiation , Computational Biology/methods , Embryo Implantation/genetics , High-Throughput Nucleotide Sequencing , Humans , Single-Cell Analysis , T-Box Domain Proteins/metabolism , Trophoblasts/cytology , ZygoteABSTRACT
BACKGROUND: Genetic programs underlying preimplantation development and early lineage segregation are highly conserved across mammals. It has been suggested that nonhuman primates would be better model organisms for human embryogenesis, but a limited number of studies have investigated the monkey preimplantation development. In this study, we collect single cells from cynomolgus monkey preimplantation embryos for transcriptome profiling and compare with single-cell RNA-seq data derived from human and mouse embryos. RESULTS: By weighted gene-coexpression network analysis, we found that cynomolgus gene networks have greater conservation with human embryos including a greater number of conserved hub genes than that of mouse embryos. Consistently, we found that early ICM/TE lineage-segregating genes in monkeys exhibit greater similarity with human when compared to mouse, so are the genes in signaling pathways such as LRP1 and TCF7 involving in WNT pathway. Last, we tested the role of one conserved pre-EGA hub gene, SIN3A, using a morpholino knockdown of maternal RNA transcripts in monkey embryos followed by single-cell RNA-seq. We found that SIN3A knockdown disrupts the gene-silencing program during the embryonic genome activation transition and results in developmental delay of cynomolgus embryos. CONCLUSION: Taken together, our study provided new insight into evolutionarily conserved and divergent transcriptome dynamics during mammalian preimplantation development.
Subject(s)
Blastomeres/metabolism , Embryonic Development/genetics , Macaca fascicularis/embryology , Adult , Animals , Blastocyst , Blastomeres/cytology , Cell Lineage/genetics , Cells, Cultured , Embryo, Mammalian , Embryonic Development/physiology , Female , Gene Expression Profiling , Gene Expression Regulation, Developmental , Gene Regulatory Networks/physiology , Humans , Macaca fascicularis/genetics , Macaca mulatta , Male , Mice , Pregnancy , Sin3 Histone Deacetylase and Corepressor Complex/genetics , Sin3 Histone Deacetylase and Corepressor Complex/physiology , Single-Cell Analysis/veterinary , Transcriptome/geneticsABSTRACT
Patient-derived xenograft (PDX) animal models allow the exogenous growth of human tumors, offering an irreplaceable preclinical tool for oncology research. Mice are the most commonly used host for human PDX models, however their small body size limits the xenograft growth, sample collection, and drug evaluation. Therefore, we sought to develop a novel rat model that could overcome many of these limitations. We knocked out Rag1, Rag2, and Il2rg in Sprague Dawley (SD) rats by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 technology. The development of lymphoid organs is significantly impaired in Rag1-/-Rag2-/-Il2rg-/Y (designated as SD-RG) rats. Consequently, SD-RG rats are severely immunodeficient with an absence of mature T, B, and NK cells in the immune system. After subcutaneous injection of tumor cell lines of different origin, such as NCI-H460, U-87MG, and MDA-MB-231, the tumors grow significantly faster and larger in SD-RG rats than in nonobese diabetic- Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice. Most important of all, we successfully established a PDX model of lung squamous cell carcinoma in which the grafts recapitulate the histopathologic features of the primary tumor for several passages. In conclusion, the severely immunodeficient SD-RG rats support fast growth of PDX compared with mice, thus holding great potential to serve as a new model for oncology research.-He, D., Zhang, J., Wu, W., Yi, N., He, W., Lu, P., Li, B., Yang, N., Wang, D., Xue, Z., Zhang, P., Fan, G., Zhu, X. A novel immunodeficient rat model supports human lung cancer xenografts.
Subject(s)
Disease Models, Animal , Lung Neoplasms/immunology , Lung Neoplasms/pathology , Animals , Apoptosis , Cell Proliferation , Female , Humans , Male , Mice , Mice, Inbred NOD , Mice, SCID , Rats , Rats, Sprague-Dawley , Tumor Cells, Cultured , Xenograft Model Antitumor AssaysABSTRACT
Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primate in biomedical research, have the largest natural geographic distribution of any nonhuman primate, and have been the focus of much evolutionary and behavioral investigation. Consequently, rhesus macaques are one of the most thoroughly studied nonhuman primate species. However, little is known about genome-wide genetic variation in this species. A detailed understanding of extant genomic variation among rhesus macaques has implications for the use of this species as a model for studies of human health and disease, as well as for evolutionary population genomics. Whole-genome sequencing analysis of 133 rhesus macaques revealed more than 43.7 million single-nucleotide variants, including thousands predicted to alter protein sequences, transcript splicing, and transcription factor binding sites. Rhesus macaques exhibit 2.5-fold higher overall nucleotide diversity and slightly elevated putative functional variation compared with humans. This functional variation in macaques provides opportunities for analyses of coding and noncoding variation, and its cellular consequences. Despite modestly higher levels of nonsynonymous variation in the macaques, the estimated distribution of fitness effects and the ratio of nonsynonymous to synonymous variants suggest that purifying selection has had stronger effects in rhesus macaques than in humans. Demographic reconstructions indicate this species has experienced a consistently large but fluctuating population size. Overall, the results presented here provide new insights into the population genomics of nonhuman primates and expand genomic information directly relevant to primate models of human disease.
Subject(s)
High-Throughput Nucleotide Sequencing/methods , Macaca mulatta/genetics , Whole Genome Sequencing/methods , Animals , Evolution, Molecular , Female , Genetic Fitness , Macaca mulatta/classification , Models, Animal , Polymorphism, Single Nucleotide , Population DensityABSTRACT
Mammalian pre-implantation development is a complex process involving dramatic changes in the transcriptional architecture. We report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos, using single-cell RNA sequencing. Based on single-nucleotide variants in human blastomere messenger RNAs and paternal-specific single-nucleotide polymorphisms, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25 to 53%). By weighted gene co-expression network analysis, we find that each developmental stage can be delineated concisely by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation and metabolism, acting in a step-wise fashion from cleavage to morula. Cross-species comparisons with mouse pre-implantation embryos reveal that the majority of human stage-specific modules (7 out of 9) are notably preserved, but developmental specificity and timing differ between human and mouse. Furthermore, we identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely to be key in driving mammalian pre-implantation development. Together, the results provide a valuable resource to dissect gene regulatory mechanisms underlying progressive development of early mammalian embryos.
Subject(s)
Embryo, Mammalian/embryology , Embryo, Mammalian/metabolism , Embryonic Development/genetics , Gene Expression Regulation, Developmental , Sequence Analysis, RNA , Single-Cell Analysis , Alleles , Animals , Blastocyst/cytology , Blastocyst/metabolism , Cell Cycle/genetics , Embryo, Mammalian/cytology , Gene Expression Profiling , Humans , Mice , Morula/cytology , Morula/metabolism , Oocytes/cytology , Oocytes/metabolismABSTRACT
PURPOSE: The aim of this study was to identify the morphological features of the retina and choroid in Macaca fascicularis of different ages using multimodal imaging. METHODS: A total of 27 Macaca fascicularis with no ocular diseases were studied (mean age, 104.2Ā months; range, 1.2-223.6Ā months). Multimodal imaging was obtained from each subject. The morphological features were compared within four subgroups according to age. RESULTS: On spectrum-domain optical coherence tomography (SD-OCT), four hyper-reflective bands could be observed in the outer retina in non-infant macaques (21/21, 100%), while the interdigitation zone could not be observed in the six infant macaques. A narrow hypo-reflective band just posterior to the retinal pigment epithelium (RPE) was noted in most eyes (25/27, 92.6%). The choroidal-scleral junction (CSJ) was visible in 83.3% of infants but only in 12.5% of adults and 14.3% of the geriatric population, and it could not be seen in juveniles. There was a significant difference in CSJ visibility between the infant group and the other three groups (P < 0.001). Tessellated fundus, in which the choroidal vessels are visible through the retina, could be observed clearly with near-infrared reflectance imaging (NIR). Some granular spots were noted in juveniles, and they accumulated dramatically with age, but were absent in infants. CONCLUSION: Notable morphological features can be observed in the Macaca fascicularis subjects using multimodal imaging, and these features vary distinctly according to their age. It is important to note that infant macaques had no interdigitation zone, while the other macaques had no visible CSJ but did have well-defined choroidal capillaries. Age and the features should be considered seriously in future animal studies.
Subject(s)
Aging , Choroid/diagnostic imaging , Multimodal Imaging , Retina/diagnostic imaging , Animals , Fluorescein Angiography/methods , Fundus Oculi , Macaca fascicularis , Models, Animal , Reference Values , Reproducibility of Results , Tomography, Optical Coherence/methods , Visual Field TestsABSTRACT
BACKGROUND: To investigate the clinical value of the alpha-fetoprotein (AFP) response following transcatheter arterial chemoembolization (TACE) in intermediate-stage hepatocellular carcinoma (HCC). METHODS: Data on patients with Barcelona Clinic Liver Cancer B staging system were analyzed. An AFP response was defined as a decrease in AFP of more than 20% after a TACE session. The association between AFP response and treatment outcome regarding imaging response and overall survival (OS) was explored. Cox proportional hazards models were applied to identify independent risk factors for OS after TACE. RESULTS: Of the enrolled 376 patients with elevated serum AFP >20Ā ng/mL, 214 (57%) with AFP responses were identified. AFP responders had improved median survival than non-responders (20 vs. 12 months, PĀ =Ā 0.002). AFP response was significantly correlated with imaging response (PĀ <Ā 0.001). The Cox proportional hazards model revealed that AFP response was an independent factor for OS (hazard ratio, 0.59; 95% confidence interval, 0.45-0.78; PĀ <Ā 0.001). In stratified analyses, an AFP response achieved improved survival in patients with tumor diameters ≤5Ā cm, diameters >5Ā cm, tumor number ≤3 and without underlying cirrhosis. CONCLUSIONS: The AFP response indicates enhanced survival after TACE in patients with intermediate-stage BCLC.
Subject(s)
Carcinoma, Hepatocellular/therapy , Chemoembolization, Therapeutic , Liver Neoplasms/therapy , Neoplasms, Multiple Primary/therapy , alpha-Fetoproteins/metabolism , Adult , Aged , Aged, 80 and over , Carcinoma, Hepatocellular/blood , Carcinoma, Hepatocellular/mortality , Carcinoma, Hepatocellular/pathology , Chemoembolization, Therapeutic/adverse effects , Chemoembolization, Therapeutic/mortality , Female , Humans , Liver Neoplasms/blood , Liver Neoplasms/mortality , Liver Neoplasms/pathology , Male , Middle Aged , Neoplasm Staging , Neoplasms, Multiple Primary/blood , Neoplasms, Multiple Primary/mortality , Neoplasms, Multiple Primary/pathology , Retrospective Studies , Risk Assessment , Risk Factors , Time Factors , Treatment Outcome , Tumor BurdenABSTRACT
DNA methylation is an epigenetic mechanism that regulates gene transcription without changing primary nucleotide sequences. In mammals, DNA methylation involves the covalent addition of a methyl group to the 5-carbon position of cytosine by DNA methyltransferases (DNMTs). The change of DNA methylation and its pathological role in acute kidney injury (AKI) remain largely unknown. Here, we analyzed genome-wide DNA methylation during cisplatin-induced AKI by reduced representation bisulfite sequencing. This technique identified 215 differentially methylated regions between the kidneys of control and cisplatin-treated animals. While most of the differentially methylated regions were in the intergenic, intronic, and coding DNA sequences, some were located in the promoter or promoter-regulatory regions of 15 protein-coding genes. To determine the pathological role of DNA methylation, we initially examined the effects of the DNA methylation inhibitor 5-aza-2'-deoxycytidine and showed it increased cisplatin-induced apoptosis in a rat kidney proximal tubular cell line. We further established a kidney proximal tubule-specific DNMT1 (PT-DNMT1) knockout mouse model, which showed more severe AKI during cisplatin treatment than wild-type mice. Finally, interferon regulatory factor 8 (Irf8), a pro-apoptotic factor, was identified as a hypomethylated gene in cisplatin-induced AKI, and this hypomethylation was associated with a marked induction of Irf8. In the rat kidney proximal tubular cells, the knockdown of Irf8 suppressed cisplatin-induced apoptosis, supporting a pro-death role of Irf8 in renal tubular cells. Thus, DNA methylation plays a protective role in cisplatin-induced AKI by regulating specific genes, such as Irf8.
Subject(s)
Acute Kidney Injury/genetics , Antineoplastic Agents/adverse effects , Cisplatin/adverse effects , DNA (Cytosine-5-)-Methyltransferase 1/metabolism , DNA Methylation , Interferon Regulatory Factors/genetics , Acute Kidney Injury/chemically induced , Acute Kidney Injury/pathology , Animals , Apoptosis/drug effects , Azacitidine/analogs & derivatives , Azacitidine/pharmacology , Cell Line , DNA (Cytosine-5-)-Methyltransferase 1/genetics , Decitabine , Disease Models, Animal , Epigenesis, Genetic , Gene Knockdown Techniques , Genome , Humans , Interferon Regulatory Factors/metabolism , Kidney Tubules, Proximal/cytology , Kidney Tubules, Proximal/pathology , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Neoplasms/drug therapy , Rats , Sequence Analysis, DNA/methodsABSTRACT
Immunodeficiency, centromeric instability and facial anomalies type I (ICF1) syndrome is a rare genetic disease caused by mutations in DNA methyltransferase (DNMT) 3B, a de novo DNA methyltransferase. However, the molecular basis of how DNMT3B deficiency leads to ICF1 pathogenesis is unclear. Induced pluripotent stem cell (iPSC) technology facilitates the study of early human developmental diseases via facile in vitro paradigms. Here, we generate iPSCs from ICF Type 1 syndrome patient fibroblasts followed by directed differentiation of ICF1-iPSCs to mesenchymal stem cells (MSCs). By performing genome-scale bisulfite sequencing, we find that DNMT3B-deficient iPSCs exhibit global loss of non-CG methylation and select CG hypomethylation at gene promoters and enhancers. Further unbiased scanning of ICF1-iPSC methylomes also identifies large megabase regions of CG hypomethylation typically localized in centromeric and subtelomeric regions. RNA sequencing of ICF1 and control iPSCs reveals abnormal gene expression in ICF1-iPSCs relevant to ICF syndrome phenotypes, some directly associated with promoter or enhancer hypomethylation. Upon differentiation of ICF1 iPSCs to MSCs, we find virtually all CG hypomethylated regions remained hypomethylated when compared with either wild-type iPSC-derived MSCs or primary bone-marrow MSCs. Collectively, our results show specific methylome and transcriptome defects in both ICF1-iPSCs and differentiated somatic cell lineages, providing a valuable stem cell system for further in vitro study of the molecular pathogenesis of ICF1 syndrome. GEO accession number: GSE46030.
Subject(s)
DNA (Cytosine-5-)-Methyltransferases/genetics , Epigenesis, Genetic , Genome, Human , Immunologic Deficiency Syndromes/genetics , Induced Pluripotent Stem Cells/enzymology , Mesenchymal Stem Cells/enzymology , Cell Differentiation , DNA (Cytosine-5-)-Methyltransferases/deficiency , DNA Methylation , Enhancer Elements, Genetic , Fibroblasts/enzymology , Fibroblasts/pathology , Humans , Immunologic Deficiency Syndromes/enzymology , Immunologic Deficiency Syndromes/pathology , Induced Pluripotent Stem Cells/pathology , Mesenchymal Stem Cells/pathology , Promoter Regions, Genetic , DNA Methyltransferase 3BABSTRACT
Corneal endothelial cells (CECs) are a monolayer of cells covering the inner-side of cornea, playing a pivotal role in keeping the cornea transparent. Because adult CECs have no proliferative capacity, the loss of CECs during aging or under pathological conditions would lead to corneal edema, eventually leading to the blindness. Clinically, donated CECs have been successfully transplanted to treat the diseases of CEC deficiency; however, the source of CEC donation is very limited. As an alternative cell source for CEC transplantation, CEC-like cells can be obtained via inĀ vitro differentiation of human pluripotent stem cells. In this study, we introduced a modified two-stage differentiation method to convert H9 human embryonic stem cells (hESCs) to neural crest cells (NCCs), then further into CEC-like cells. The CEC-like cells treated with bovine CEC conditional medium morphologically best resembled primary CECs among all the culture conditions. By whole transcriptome analysis, we found that the typical markers of CECs, such as Na+-K+-ATPase, AQP1, Col8a and ZO-1, are highly expressed in hESC-derived CEC-like cells. By comparing RNA transcriptome of hESC-derived CEC-like cells with human primary fetal and adult CECs, we further identified shared molecular markers such as TRIT1, HSPB11, CRY1 that can be used to quality control CEC derivatives from hESCs. Our study paves the way for the quality-control and future application of hESC-derived CECs in the treatment of CEC deficiency disorders.
Subject(s)
Endothelium, Corneal/cytology , Gene Expression Profiling/methods , Human Embryonic Stem Cells/cytology , Transcriptome/genetics , Animals , Cattle , Cell Differentiation , Cells, Cultured , Corneal Diseases/genetics , Corneal Diseases/metabolism , Corneal Diseases/pathology , Flow Cytometry , Human Embryonic Stem Cells/metabolism , Humans , Mice , RNA/genetics , Reverse Transcriptase Polymerase Chain ReactionABSTRACT
Preimplantation genetic diagnosis/screening (PGD/PGS) aims to help couples lower the risks of transmitting genetic defects to their offspring, implantation failure, and/or miscarriage during in vitro fertilization (IVF) cycles. However, it is still being debated with regard to the practicality and diagnostic accuracy of PGD/PGS due to the concern of invasive biopsy and the potential mosaicism of embryos. Recently, several non-invasive and high-throughput assays have been developed to help overcome the challenges encountered in the conventional invasive biopsy and low-throughput analysis in PGD/PGS. In this mini-review, we will summarize the recent progresses of these new methods for PGD/PGS and discuss their potential applications in IVF clinics.
Subject(s)
Abortion, Spontaneous/genetics , Fertilization in Vitro/trends , Genetic Testing/methods , Preimplantation Diagnosis/methods , Abortion, Spontaneous/physiopathology , Aneuploidy , Comparative Genomic Hybridization , Embryo Transfer , Female , Fertilization in Vitro/adverse effects , Genetic Testing/trends , Humans , Pregnancy , Preimplantation Diagnosis/trendsABSTRACT
Obesity rates continue to rise throughout the world. Recent evidence has suggested that environmental factors contribute to altered energy balance regulation. However, the role of epigenetic modifications to the central control of energy homeostasis remains unknown. To investigate the role of DNA methylation in the regulation of energy balance, we investigated the role of the de novo DNA methyltransferase, Dnmt3a, in Single-minded 1 (Sim1) cells, including neurons in the paraventricular nucleus of the hypothalamus (PVH). Dnmt3a expression levels were decreased in the PVH of high-fat-fed mice. Mice lacking Dnmt3a specifically in the Sim1 neurons, which are expressed in the forebrain, including PVH, became obese with increased amounts of abdominal and subcutaneous fat. The mice were also found to have hyperphagia, decreased energy expenditure, and glucose intolerance with increased serum insulin and leptin. Furthermore, these mice developed hyper-LDL cholesterolemia when fed a high-fat diet. Gene expression profiling and DNA methylation analysis revealed that the expression of tyrosine hydroxylase and galanin were highly upregulated in the PVH of Sim1-specific Dnmt3a deletion mice. DNA methylation levels of the tyrosine hydroxylase promoter were decreased in the PVH of the deletion mice. These results suggest that Dnmt3a in the PVH is necessary for the normal control of body weight and energy homeostasis and that tyrosine hydroxylase is a putative target of Dnmt3a in the PVH. These results provide evidence for a role for Dnmt3a in the PVH to link environmental conditions to altered energy homeostasis.
Subject(s)
Basic Helix-Loop-Helix Transcription Factors/metabolism , DNA (Cytosine-5-)-Methyltransferases/physiology , Energy Metabolism/physiology , Homeostasis , Neurons/metabolism , Repressor Proteins/metabolism , Adipose Tissue/physiology , Animals , Cholesterol, LDL/blood , DNA (Cytosine-5-)-Methyltransferases/genetics , DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA Methylation , DNA Methyltransferase 3A , Diet, High-Fat , Female , Galanin/biosynthesis , Gene Expression Profiling , Glucose Intolerance/genetics , Glucose Intolerance/physiopathology , Hyperphagia/complications , Hyperphagia/genetics , Hyperphagia/physiopathology , Insulin/blood , Leptin/blood , Male , Mice , Mice, Knockout , Obesity/blood , Obesity/complications , Obesity/genetics , Obesity/physiopathology , Paraventricular Hypothalamic Nucleus/metabolism , Tyrosine 3-Monooxygenase/biosynthesis , Up-RegulationABSTRACT
The corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs), which is essential for maintaining corneal transparency. To better characterize CECs in different developmental stages, we profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells. By comparing CECs with 12 other tissue types, we identified 245 and 284 signature genes that are highly expressed in fetal and adult CECs, respectively. Functionally, these genes are enriched in pathways characteristic of CECs, including inorganic anion transmembrane transporter, extracellular matrix structural constituent and cyclin-dependent protein kinase inhibitor activity. Importantly, several of these genes are disease target genes in hereditary corneal dystrophies, consistent with their functional significance in CEC physiology. We also identified stage-specific markers associated with CEC development, such as specific members in the transforming growth factor beta and Wnt signaling pathways only expressed in fetal, but not in adult CECs. Lastly, by the immunohistochemistry of ocular tissues, we demonstrated the unique protein localization for Wnt5a, S100A4, S100A6 and IER3, the four novel markers for fetal and adult CECs. The identification of a new panel of stage-specific markers for CECs would be very useful for characterizing CECs derived from stem cells or ex vivo expansion for cell replacement therapy.
Subject(s)
Endothelial Cells/metabolism , Endothelium, Corneal/cytology , Eye Proteins/genetics , Transcriptome , Apoptosis Regulatory Proteins/genetics , Apoptosis Regulatory Proteins/metabolism , Biomarkers/metabolism , Cells, Cultured , Eye Proteins/metabolism , Fetus/cytology , Gene Expression Profiling , Humans , Membrane Proteins/genetics , Membrane Proteins/metabolism , Organ Specificity , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , S100 Proteins/genetics , S100 Proteins/metabolism , Wnt Proteins/genetics , Wnt Proteins/metabolism , Wnt Signaling Pathway , Wnt-5a ProteinABSTRACT
Supramolecular nanosubstrate-mediated delivery (SNSMD) leverages the power of molecular self-assembly and a nanostructured substrate platform for the low toxicity, highly efficient co-delivery of biological factors encapsulated in a nanovector. Human fibroblasts are successfully reprogrammed into induced pluripotent stems and transdifferentiated into induced neuronal-like cells.