ABSTRACT
BACKGROUND: Exercise can protect myocardial infarction (MI) and downregulate cardiac Homeodomain-Interacting Protein Kinase 2 (HIPK2). However, the role of HIPK2 in MI is unclear. METHODS: HIPK2-/- mice and miR-222-/- rats, HIPK2 inhibitor (PKI1H) and adeno-associated virus serotype 9 (AAV9) carrying miR-222 were applied in the study. Animals were subjected to running, swimming, acute MI or post-MI remodeling. HIPK2 inhibition and P53 activator were used in neonatal rat cardiomyocytes (NRCMs) and human embryonic stem cell-derived cardiomyocytes (hESC-CMs) subjected to oxygen glucose deprivation/reperfusion (OGD/R). Serum miR-222 levels were analyzed in healthy people and MI patients that were survival or readmitted to the hospital and/or died. FINDINGS: Cardiac HIPK2 protein levels were reduced by exercise while increased in MI. In vitro, HIPK2 suppression by lentiviral vectors or inhibitor prevented apoptosis induced by OGD/R in NRCMs and hESC-CMs. HIPK2 inhibitor-treated mice and HIPK2-/- mice reduced infarct size after acute MI, and preserved cardiac function in MI remodeling. Mechanistically, protective effect against apoptosis by HIPK2 suppression was reversed by P53 activators. Furthermore, increasing levels of miR-222, targeting HIPK2, protected post-MI cardiac dysfunction, whereas cardiac dysfunction post-MI was aggravated in miR-222-/- rats. Moreover, serum miR-222 levels were significantly reduced in MI patients, as well as in MI patients that were readmitted to the hospital and/or died compared to those not. INTERPRETATION: Exercise-induced HIPK2 suppression attenuates cardiomyocytes apoptosis and protects MI by decreasing P-P53. Inhibition of HIPK2 represents a potential novel therapeutic intervention for MI. FUNDING: This work was supported by the grants from National Key Research and Development Project (2018YFE0113500 to JJ Xiao), National Natural Science Foundation of China (82020108002, 81722008, and 81911540486 to JJ Xiao, 81400647 to MJ Xu, 81800265 to YJ Liang), Innovation Program of Shanghai Municipal Education Commission (2017-01-07-00-09-E00042 to JJ Xiao), the grant from Science and Technology Commission of Shanghai Municipality (18410722200 and 17010500100 to JJ Xiao), the "Dawn" Program of Shanghai Education Commission (19SG34 to JJ Xiao), Shanghai Sailing Program (21YF1413200 to QL Zhou). JS is supported by Horizon2020 ERC-2016-COG EVICARE (725229).
Subject(s)
Carrier Proteins/genetics , Down-Regulation , Exercise/physiology , MicroRNAs/blood , MicroRNAs/genetics , Myocardial Infarction/genetics , Protein Serine-Threonine Kinases/genetics , Adult , Animals , Animals, Newborn , Carrier Proteins/metabolism , Case-Control Studies , Cells, Cultured , Dependovirus/genetics , Disease Models, Animal , Gene Knockout Techniques , Human Embryonic Stem Cells/chemistry , Human Embryonic Stem Cells/cytology , Human Embryonic Stem Cells/drug effects , Humans , Mice , Middle Aged , Myocardial Infarction/chemically induced , Myocardial Infarction/therapy , Myocytes, Cardiac/chemistry , Myocytes, Cardiac/cytology , Myocytes, Cardiac/drug effects , Protein Serine-Threonine Kinases/metabolism , Rats , Running/physiology , Swimming/physiologyABSTRACT
Metabolic homeostasis is critical for cell pluripotency and differentiation in human embryonic stem cells (hESCs). It has been reported that metabolic changes specifically regulate cellular signaling during hESC differentiation. This protocol describes procedures for both cell culture and detection of intracellular and extracellular metabolites in hESCs by liquid chromatography-mass spectrometry. Metabolites in glycolysis, citric acid cycle, pentose phosphate pathway, and other metabolic processes can be detected using this approach. For complete details on the use and execution of this protocol, please refer to Song et al., (2019), Yang et al., (2019), Meng et al., (2018), and Chen et al., (2011b).
Subject(s)
Cell Culture Techniques/methods , Extracellular Space , Human Embryonic Stem Cells , Intracellular Space , Metabolomics/methods , Cell Differentiation , Cells, Cultured , Chromatography, Liquid , Extracellular Space/chemistry , Extracellular Space/metabolism , Glycolysis/physiology , Human Embryonic Stem Cells/chemistry , Human Embryonic Stem Cells/metabolism , Humans , Intracellular Space/chemistry , Intracellular Space/metabolism , Mass Spectrometry , Metabolome/physiologyABSTRACT
Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing is a powerful technique that characterizes the genome-wide DNA-binding profile of a protein of interest. The general ChIP-seq workflow has been applied widely to many sample types and target proteins, but sample-specific optimization of various steps is necessary to achieve high-quality data. This protocol is specifically optimized for cultured human embryonic stem cells (hESCs), including steps to check sample quality and non-specific enrichment of "hyper-ChIPable" regions prior to sequencing. For complete details on the use and execution of this protocol, please refer to Gunne-Braden et al. (2020).
Subject(s)
Chromatin Immunoprecipitation Sequencing/methods , Human Embryonic Stem Cells , Cells, Cultured , DNA/chemistry , DNA/genetics , DNA/metabolism , Human Embryonic Stem Cells/chemistry , Human Embryonic Stem Cells/cytology , Human Embryonic Stem Cells/metabolism , HumansABSTRACT
F-53B and PFOS are two per- and polyfluoroalkyl substances (PFASs) widely utilized in the metal plating industry as mist suppressants. Recent epidemiological studies have linked PFASs to cardiovascular diseases and alterations in heart geometry. However, we still have limited understanding of the effects of F-53B and PFOS on the developing heart. In this study, we employed a human embryonic stem cell (hESC)-based cardiac differentiation system and whole transcriptomics analyses to evaluate the potential developmental cardiac toxicity of F-53B and PFOS. We utilized F-53B and PFOS concentrations of 0.1-60 µM, covering the levels detected in human blood samples. We demonstrated that both F-53B and PFOS inhibited cardiac differentiation and promoted epicardial specification via upregulation of the WNT signaling pathway. Most importantly, the effects of F-53B were more robust than those of PFOS. This was because F-53B treatment disrupted the expression of more genes and led to lower cardiac differentiation efficiency. These findings imply that F-53B may not be a safe replacement for PFOS.
Subject(s)
Alkanesulfonic Acids , Fluorocarbons , Human Embryonic Stem Cells/chemistry , Water Pollutants, Chemical/analysis , Animals , Cell Differentiation , Humans , Wnt Signaling Pathway , ZebrafishABSTRACT
OBJECTIVE: SOX9 is a key transcription factor with important roles in regulating proliferation and differentiation of various cell types. Dysregulation of SOX9 expression has been involved with pathogenesis of different developmental, degenerative, and neoplastic disorders. Natural antisense transcripts (NATs) are long non-coding RNAs with increasing significance in regulation of gene expression. However, the presence of a NAT at SOX9 locus has been so far unclear. RESULT: We detected a natural antisense transcript at SOX9 locus (SOX9-NAT) through strand-specific RT-PCR. In contrast to SOX9 sense RNA (mRNA), SOX9-NAT was down-regulated in cancer tissues and cell lines compared with their normal counterparts. In addition, reciprocal to SOX9 mRNA, SOX9-NAT was also down-regulated in human embryonic stem cells in comparison with human fibroblasts in vitro. CONCLUSION: The negative correlation between SOX9 mRNA and SOX9-NAT was confirmed by analyzing qPCR data, as well as RNA-Seq datasets of several human cancers. Our data suggest a functional role for SOX9-NAT in the regulation of SOX9 mRNA as a potential target in cancer treatment and regenerative medicine.
Subject(s)
Down-Regulation , Neoplasms/genetics , RNA, Long Noncoding/genetics , SOX9 Transcription Factor/antagonists & inhibitors , A549 Cells , Cell Line, Tumor , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Human Embryonic Stem Cells/chemistry , Humans , Neoplastic Stem Cells/chemistry , Sequence Analysis, RNAABSTRACT
Induced pluripotent stem cells (iPS cells) are a prospective resource for regenerative biomedicine. iPS cells can differentiate into any type of stem, progenitor and somatic cells to help replace structures within damaged organs or tissues. However, iPS cells themselves, can produce malignant tumors if they are injected into the body of an immunocompatible or immunodeficient recipient. Thus, it is necessary to detect any residual iPS cells content in biomedical cell products obtained from iPS cells and destined for transplantation. In this article we describe searches for iPS cells in heterogeneous cell mixtures, using two different methods-quantitative RT-PCR and droplet digital PCR (ddPCR). In experiments with various heterogeneous mixtures, including mixtures with neural stem cells, we found that the OCT4, TDGF1 and LIN28 genes are the best markers for such a search, and droplet digital PCR provides the greatest measurement accuracy, which is 0.002%. Thus, we have confirmed the advantage of using droplet digital PCR in the search for pluripotent stem cells in heterogeneous cell mixtures. We hope that this data can be useful for biosafety control in regenerative biomedicine.
Subject(s)
Genetic Markers , Human Embryonic Stem Cells/cytology , Induced Pluripotent Stem Cells/cytology , Cell Line , Coculture Techniques , Containment of Biohazards , GPI-Linked Proteins/genetics , Human Embryonic Stem Cells/chemistry , Humans , Induced Pluripotent Stem Cells/chemistry , Intercellular Signaling Peptides and Proteins/genetics , Neoplasm Proteins/genetics , Octamer Transcription Factor-3/genetics , RNA-Binding Proteins/genetics , Real-Time Polymerase Chain Reaction , Regenerative MedicineABSTRACT
Recent studies have shown that long noncoding RNAs (lncRNAs) are crucial regulators of human embryonic stem cells (hESCs). However, modes of actions of lncRNAs in hESCs are not well illustrated. Here, we predicted a regulatory network in hESCs in which lncRNAs interact with TFs and thereby control the expressions of downstream targets of TFs. The predicted network is comprised of 2289 3-motif subgraphs which are characterized by 3 nodes: (i) a lncRNA which is predicted to interact with (ii) a TF and (iii) a gene which is a target of TF and coexpressing with lncRNA. We performed functional annotation of the network by identifying hub nodes followed by pathway enrichment study, which unveiled an active G1-S cell cycle phase transition-specific subnetwork that encompasses 2 lncRNAs, MALAT1 and DANCR. Our analysis revealed that MALAT1 and DANCR might be playing key roles in G1-S phase transition by acting as RNA decoy via interacting with crucial stemness maintaining TFs. We predicted that MALAT1 possibly compete with DNMT1 and CDCA7 genes to bind to E2F1 thereby interrupting repression of DNMT1 and activation of CDCA7 by E2F1 in hESCs, whereas DANCR possibly competes with IPO7 gene to bind to MYC thereby interrupting MYC-mediated activation of IPO7 in hESCs. Both of these are conjectured to contribute to rapid G1-S phase transition aiding in stemness maintenance of hESCs. This study presents a crucial TF target cross talks mediated by lncRNAs in hESCs regulating its properties which needs further investigation.
Subject(s)
Human Embryonic Stem Cells/cytology , RNA, Long Noncoding/genetics , Sequence Analysis, RNA/methods , Transcription Factors/genetics , Cell Cycle , Cells, Cultured , DNA (Cytosine-5-)-Methyltransferase 1/genetics , E2F1 Transcription Factor/genetics , Gene Regulatory Networks , Human Embryonic Stem Cells/chemistry , Humans , Molecular Sequence Annotation , Nuclear Proteins/genetics , RNA, Messenger/geneticsABSTRACT
Human embryonic stem cells (hESCs) have the capacity for self-renewal and multilineage differentiation, which are of clinical importance for regeneration medicine. Despite the significant progress of hESC study, the complete hESC proteome atlas, especially the surface protein composition, awaits delineation. According to the latest release of neXtProt database (January 17, 2018; 19â¯658 PE1, 2, 3, and 4 human proteins), membrane proteins present the major category (1047; 48%) among all 2186 missing proteins (MPs). We conducted a deep subcellular proteomics analysis of hESCs to identify the nuclear, cytoplasmic, and membrane proteins in hESCs and to mine missing membrane proteins in the very early cell status. To our knowledge, our study achieved the largest data set with confident identification of 11â¯970 unique proteins (1% false discovery rate at peptide, protein, and PSM levels), including the most-comprehensive description of 6â¯138 annotated membrane proteins in hESCs. Following the HPP guideline, we identified 26 gold (neXtProt PE2, 3, and 4 MPs) and 87 silver (potential MP candidates with a single unique peptide detected) MPs, of which 69 were membrane proteins, and the expression of 21 gold MPs was further verified either by multiple reaction monitoring mass spectrometry or by matching synthetic peptides in the Peptide Atlas database. Functional analysis of the MPs revealed their potential roles in the pluripotency-related pathways and the lineage- and tissue-specific differentiation processes. Our proteome map of hESCs may provide a rich resource not only for the identification of MPs in the human proteome but also for the investigation on self-renewal and differentiation of hESC. All mass spectrometry data were deposited in ProteomeXchange via jPOST with identifier PXD009840.
Subject(s)
Human Embryonic Stem Cells/chemistry , Membrane Proteins/analysis , Proteome/analysis , Cell Differentiation , Cell Lineage , Humans , Intracellular Membranes/chemistry , Proteomics/methodsABSTRACT
MRI for non-invasive cell tracking is recognized for enabling pre-clinical research on stem cell therapy. Yet, adoption of cellular imaging in stem cell research has been restricted to sites with experience in MR contrast agent synthesis and to small animal models that do not require scaled-up synthesis. In this study, we demonstrate the use of a gadolinium-free T1 contrast agent for tracking human embryonic stem cells. The agent, MnPNH2, is an easily synthesized manganese porphyrin that can be scaled for large cell numbers. MRI was performed on a 3 T clinical scanner. Cell pellets labeled at different MnPNH2 concentrations for 24 hours demonstrated a decrease in T1 relaxation time of nearly two-fold (P < 0.05), and cellular contrast was maintained for 24 hours (P < 0.05). Cell viability (Trypan blue) and differentiation (embryoid body formation) were unaffected. Cell uptake of Mn on inductively coupled plasma atomic emission spectroscopy corroborated MRI findings, and fluorescence microscopy revealed the agent localized mainly in cell-cell boundaries and cell nuclei. Labeled cells transplanted in rats demonstrated the superior sensitivity of MnPNH2 for in-vivo cell tracking.
Subject(s)
Cell Tracking/methods , Contrast Media/administration & dosage , Human Embryonic Stem Cells/transplantation , Magnetic Resonance Imaging/methods , Animals , Cell Culture Techniques , Cell Differentiation , Cell Nucleus/chemistry , Cell Survival , Contrast Media/chemical synthesis , Female , Human Embryonic Stem Cells/chemistry , Humans , Intravital Microscopy/methods , Manganese/chemistry , Microscopy, Fluorescence , Models, Animal , Porphyrins/chemistry , Rats , Rats, Sprague-Dawley , Sensitivity and Specificity , Spectrophotometry, AtomicABSTRACT
Cumulating epidemiological studies demonstrated that environmental exposure to endocrine disrupting chemicals (EDCs) during the early stages of fetal development is associated with the increase in disease susceptibility in later life. The fetal developmental plasticity is considered as a protective mechanism against an undesirable prenatal environment. Dioxin is one of the environmental contaminants and is considered a diabetogenic factor. Experimental animal and human epidemiological studies have revealed that dioxin exposure was associated with insulin resistance and altered beta cell function. But the effect of dioxin exposure in early stage of fetal development is still largely unknown. In this report, we used the human embryonic stem cell (hESC) line, VAL-3, as a model, together with Methyl-CpG Binding Domain (MBD) protein-enriched genome sequencing and transcriptome sequencing (RNA-seq), in order to determine the dynamic changes of the epigenetic landscape and transcriptional dysregulation in hESC upon dioxin exposure. The bioinformatics analyses including the Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis and Ingenuity Pathway Analysis (IPA) highlighted the predisposed neural, hepatic, cardiac and metabolic toxicological effects of dioxin during the fetal development.
Subject(s)
Human Embryonic Stem Cells/chemistry , Polychlorinated Dibenzodioxins/chemistry , Transcriptome/genetics , HumansABSTRACT
Human embryonic stem cells (hESCs) exhibit high levels of proteasome activity, an intrinsic characteristic required for their self-renewal, pluripotency and differentiation. However, the mechanisms by which enhanced proteasome activity maintains hESC identity are only partially understood. Besides its essential role for the ability of hESCs to suppress misfolded protein aggregation, we hypothesize that enhanced proteasome activity could also be important to degrade endogenous regulatory factors. Since E3 ubiquitin ligases are responsible for substrate selection, we first define which E3 enzymes are increased in hESCs compared with their differentiated counterparts. Among them, we find HECT-domain E3 ligases such as HERC2 and UBE3A as well as several RING-domain E3s, including UBR7 and RNF181. Systematic characterization of their interactome suggests a link with hESC identity. Moreover, loss of distinct up-regulated E3s triggers significant changes at the transcriptome and proteome level of hESCs. However, these alterations do not dysregulate pluripotency markers and differentiation ability. On the contrary, global proteasome inhibition impairs diverse processes required for hESC identity, including protein synthesis, rRNA maturation, telomere maintenance and glycolytic metabolism. Thus, our data indicate that high proteasome activity is coupled with other determinant biological processes of hESC identity.
Subject(s)
Human Embryonic Stem Cells/enzymology , Proteasome Endopeptidase Complex/analysis , Ubiquitin-Protein Ligases/analysis , Ubiquitin/analysis , Cells, Cultured , Gene Expression Profiling , Human Embryonic Stem Cells/chemistry , Humans , Protein Interaction Mapping , Protein Interaction Maps , ProteomicsABSTRACT
Background: Genetic predisposition and epigenetic alterations are both considered to contribute to sporadic neurodegenerative diseases (NDDs) such as Parkinson's disease (PD). Since cell reprogramming and the generation of induced pluripotent stem cells (iPSCs) are themselves associated with major epigenetic remodeling, it remains unclear to what extent iPSC-derived neurons lend themselves to model epigenetic disease-associated changes. A key question to be addressed in this context is whether iPSC-derived neurons exhibit epigenetic signatures typically observed in neurons derived from non-reprogrammed human embryonic stem cells (hESCs). Results: Here, we compare mature neurons derived from hESC and isogenic human iPSC generated from hESC-derived neural stem cells. Genome-wide 450 K-based DNA methylation and HT12v4 gene array expression analyses were complemented by a deep analysis of selected genes known to be involved in NDD. Our studies show that DNA methylation and gene expression patterns of isogenic hESC- and iPSC-derived neurons are markedly preserved on a genome-wide and single gene level. Conclusions: Overall, iPSC-derived neurons exhibit similar DNA methylation patterns compared to isogenic hESC-derived neurons. Further studies will be required to explore whether the epigenetic patterns observed in iPSC-derived neurons correspond to those detectable in native brain neurons.
Subject(s)
DNA Methylation , Human Embryonic Stem Cells/cytology , Induced Pluripotent Stem Cells/cytology , Neurons/chemistry , Cell Differentiation , Cells, Cultured , Epigenesis, Genetic , Gene Expression Profiling , Human Embryonic Stem Cells/chemistry , Humans , Induced Pluripotent Stem Cells/chemistry , Oligonucleotide Array Sequence Analysis , Sequence Analysis, DNA , alpha-Synuclein/geneticsABSTRACT
Human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) can provide sources for midbrain dopaminergic (mDA) neural progenitors (NPCs) for cell therapy to treat Parkinson's disease (PD) patients. However, the well-known line-to-cell line variability in the differentiation capacity of individual cell lines needs to be improved for the success of this therapy. To address this issue, we sought to identify mDA NPC specific cell surface markers for fluorescence activated cell sorting (FACS). Through RNA isolation after sorting for NPCs based on staining for cell-specific transcription factors followed by microarray, we identified two positive cell surface markers (CORIN and CD166) and one negative cell surface marker (CXCR4) for mDA NPC sorting. These three markers can enrich floor plate NPCs to 90% purity, and the sorted NPCs more efficiently differentiate to mature dopaminergic neurons compared to unsorted or CORIN+ alone mDA NPCs. This surface marker identification strategy can be used broadly to facilitate isolation of cell subtypes of interest from heterogeneous cultures.
Subject(s)
Biomarkers/analysis , Flow Cytometry/methods , Human Embryonic Stem Cells/chemistry , Human Embryonic Stem Cells/physiology , Induced Pluripotent Stem Cells/chemistry , Induced Pluripotent Stem Cells/physiology , Membrane Proteins/analysis , Antigens, CD/analysis , Cell Adhesion Molecules, Neuronal/analysis , Fetal Proteins/analysis , Human Embryonic Stem Cells/classification , Humans , Induced Pluripotent Stem Cells/classification , Receptors, CXCR4/analysis , Serine Endopeptidases/analysisABSTRACT
BACKGROUND: Human embryonic stem cells (hESCs) hold tremendous promise for cell replacement therapies for a range of degenerative diseases. In order to provide cost-effective treatments affordable by public health systems, HLA-matched allogeneic tissue banks of the highest quality clinical-grade hESCs will be required. However only a small number of existing hESC lines are suitable for clinical use; they are limited by moral and ethical concerns and none of them apply Good Manufacturing Practice (GMP) standards to the earliest and critical stages of gamete and embryo procurement. We thus aimed to derive new clinical grade hESC lines of highest quality from fresh surplus GMP grade human embryos. METHODS: A comprehensive screen was performed for suitable combinations of culture media with supporting feeder cells or feeder-free matrix, at different stages, to support expansion of the inner cell mass and to establish new hESC lines. RESULTS: We developed a novel two-step and sequential media system of clinical-grade hESC derivation and successfully generated seven new hESC lines of widely varying HLA type, carefully screened for genetic health, from human embryos donated under the highest ethical and moral standards under an integrated GMP system which extends from hESC banking all the way back to gamete and embryo procurement. CONCLUSIONS: The present study, for the first time, reports the successful derivation of highest-quality clinical-grade hESC lines from fresh poor-quality surplus human embryos generated in a GMP-grade IVF laboratory. The availability of hESC lines of this status represents an important step towards more widespread application of regenerative medicine therapies.
Subject(s)
Cell Culture Techniques , Embryo, Mammalian/cytology , Human Embryonic Stem Cells/cytology , Regenerative Medicine/standards , Animals , Biomarkers/analysis , Blastocyst Inner Cell Mass/chemistry , Blastocyst Inner Cell Mass/cytology , Cell Differentiation , Cell Line , Cell Proliferation , Cell Separation , Culture Media/chemistry , Feeder Cells/chemistry , Haplotypes/genetics , Human Embryonic Stem Cells/chemistry , Humans , Pluripotent Stem Cells/chemistryABSTRACT
Human embryonic stem cells (hESCs) are pluripotent stem cells that offer a wide range of applications in regenerative medicine. In addition, they have been proposed as an appropriate alternative source of hepatocytes. In this work, hESCs were differentiated into definitive endodermal cells (DECs), followed by maturation into hepatocyte-like cells (HLCs). Their cell-surface N-glycome was profiled and also compared with that of primary human hepatocytes (PHHs). Undifferentiated hESCs contained large amounts of high-mannose N-glycans. In contrast, complex-type N-glycans such as asialylated or monosialylated biantennary and triantennary N-glycans were dominant in HLCs, and fully galactosylated structures were significantly more abundant than in undifferentiated hESCs. The cell-surface N-glycosylation of PHHs was more biologically processed than that of HLCs, with bisialylated biantennary and trisialylated triantennary structures predominant. This is the first report of the cell surface N-glycome of PHHs and of HLCs being directly generated from hESCs without embryoid body formation.
Subject(s)
Cell Membrane/chemistry , Glycomics , Hepatocytes/chemistry , Human Embryonic Stem Cells/chemistry , Polysaccharides/chemistry , Biomarkers/metabolism , Carbohydrate Conformation , Carbohydrate Sequence , Cell Differentiation , Cell Membrane/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Energy Metabolism , Gene Expression , Glycosylation , Hepatocytes/cytology , Hepatocytes/metabolism , Human Embryonic Stem Cells/cytology , Human Embryonic Stem Cells/metabolism , Humans , Mannose/chemistry , Mannose/metabolism , Polysaccharides/metabolism , Primary Cell Culture , Transcription Factors/genetics , Transcription Factors/metabolismABSTRACT
As the functions of proteins are associated with their cellular localization, the comprehensive sub-cellular proteome knowledge of human embryonic stem cells (hESCs) is indispensable for ensuring a therapeutic effect. Here, we have utilized a sub-cellular proteomics approach to analyze the localization of proteins in the nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomes. Out of 2002 reproducibly identified proteins, we detected 762 proteins in a single organelle whereas 160 proteins were found in all sub-cellular fractions. We verified the localization of identified proteins through databases and discussed the consistency of the obtained results. With regards to the ambiguity in the definition of a membrane protein, we tried to clearly define the plasma membrane, peripheral membrane and membrane proteins by annotation of these proteins in databases, along with predictions of transmembrane helices. Among ten enriched signaling pathways highlighted in our results, non-canonical Wnt signaling were analyzed in greater detail. The functions of three novel hESC membrane proteins (ERBB4, GGT1 and ZDHHC13) have been assessed in terms of pluripotency. Our report is the most comprehensive for organellar proteomics of hESCs. SIGNIFICANCE: Mass spectrometric identification of proteins using a TripleTOF 5600 from nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomal fractions highlighted the significance of the non-canonical Wnt signaling in human embryonic stem cells.
Subject(s)
Human Embryonic Stem Cells/chemistry , Proteome/analysis , Acyltransferases/physiology , Databases, Protein , Humans , Membrane Proteins , Organelles/chemistry , Proteomics/methods , Receptor, ErbB-4/physiology , Subcellular Fractions/chemistry , Wnt Signaling Pathway , gamma-Glutamyltransferase/physiologyABSTRACT
CTG repeat expansions in DMPK cause myotonic dystrophy (DM1) with a continuum of severity and ages of onset. Congenital DM1 (CDM1), the most severe form, presents distinct clinical features, large expansions, and almost exclusive maternal transmission. The correlation between CDM1 and expansion size is not absolute, suggesting contributions of other factors. We determined CpG methylation flanking the CTG repeat in 79 blood samples from 20 CDM1-affected individuals; 21, 27, and 11 individuals with DM1 but not CDM1 (henceforth non-CDM1) with maternal, paternal, and unknown inheritance; and collections of maternally and paternally derived chorionic villus samples (7 CVSs) and human embryonic stem cells (4 hESCs). All but two CDM1-affected individuals showed high levels of methylation upstream and downstream of the repeat, greater than non-CDM1 individuals (p = 7.04958 × 10-12). Most non-CDM1 individuals were devoid of methylation, where one in six showed downstream methylation. Only two non-CDM1 individuals showed upstream methylation, and these were maternally derived childhood onset, suggesting a continuum of methylation with age of onset. Only maternally derived hESCs and CVSs showed upstream methylation. In contrast, paternally derived samples (27 blood samples, 3 CVSs, and 2 hESCs) never showed upstream methylation. CTG tract length did not strictly correlate with CDM1 or methylation. Thus, methylation patterns flanking the CTG repeat are stronger indicators of CDM1 than repeat size. Spermatogonia with upstream methylation may not survive due to methylation-induced reduced expression of the adjacent SIX5, thereby protecting DM1-affected fathers from having CDM1-affected children. Thus, DMPK methylation may account for the maternal bias for CDM1 transmission, larger maternal CTG expansions, age of onset, and clinical continuum, and may serve as a diagnostic indicator.
Subject(s)
CpG Islands , DNA Methylation , Myotonic Dystrophy/genetics , Myotonin-Protein Kinase/genetics , Adolescent , Adult , Base Sequence , Cell Line , Child , Female , Human Embryonic Stem Cells/chemistry , Humans , Linear Models , Male , Pedigree , Pregnancy , Promoter Regions, Genetic , Sequence Analysis, DNA , Young AdultABSTRACT
We present a fully defined culture system (adapted Essential8TM [E8TM ] medium in combination with vitronectin) for human embryonic stem cells that can be used for SILAC purposes. Although a complete incorporation of the labels was observed after 4 days in culture, over 90% of precursors showed at least 10% conversion. To reduce this arginine conversion, E8TM medium was modified by adding (1) l-proline, (2) l-ornithine, (3) Nω -hydroxy-nor-l-arginine acetate, or by (4) lowering the arginine concentration. Reduction of arginine conversion was best obtained by adding 5 mM l-ornithine, followed by 3.5 mM l-proline and by lowering the arginine concentration in the medium to 99.5 µM. No major changes in pluripotency and cell amount could be observed for the adapted E8TM media with ornithine and proline. However, our subsequent ion mobility assisted data-independent acquisition (high-definition MS) proteome analysis cautions for ongoing changes in the proteome when aiming at longer term suppression of arginine conversion.
Subject(s)
Arginine/metabolism , Culture Media/metabolism , Human Embryonic Stem Cells/metabolism , Proteome/analysis , Proteomics/methods , Arginine/analysis , Cell Count , Cell Culture Techniques/methods , Cell Line , Culture Media/chemistry , Human Embryonic Stem Cells/chemistry , Human Embryonic Stem Cells/cytology , Humans , Isotope Labeling/methods , Octamer Transcription Factor-3/analysis , Octamer Transcription Factor-3/metabolism , Proteome/metabolism , Tandem Mass Spectrometry/methodsABSTRACT
Human embryonic stem cells (hESCs) are promising in regenerative medicine (RM) due to their differentiation plasticity and proliferation potential. However, a major challenge in RM is the generation of a vascular system to support nutrient flow to newly synthesized tissues. Here we refined an existing method to generate tight vessels by differentiating hESCs in CD34(+) vascular progenitor cells using chemically defined media and growth conditions. We selectively purified these cells from CD34(-) outgrowth populations also formed. To analyze these differentiation processes, we compared the proteomes of the hESCs with those of the CD34(+) and CD34(-) populations using high resolution mass spectrometry, label-free quantification, and multivariate analysis. Eighteen protein markers validate the differentiated phenotypes in immunological assays; nine of these were also detected by proteomics and show statistically significant differential abundance. Another 225 proteins show differential abundance between the three cell types. Sixty-three of these have known functions in CD34(+) and CD34(-) cells. CD34(+) cells synthesize proteins implicated in endothelial cell differentiation and smooth muscle formation, which support the bipotent phenotype of these progenitor cells. CD34(-) cells are more heterogeneous synthesizing muscular/osteogenic/chondrogenic/adipogenic lineage markers. The remaining >150 differentially abundant proteins in CD34(+) or CD34(-) cells raise testable hypotheses for future studies to probe vascular morphogenesis.
Subject(s)
Cell Differentiation , Human Embryonic Stem Cells/cytology , Proteome/analysis , Stem Cells/cytology , Antigens, CD34 , Cells, Cultured , Culture Media/pharmacology , Endothelial Cells/chemistry , Endothelial Cells/cytology , Human Embryonic Stem Cells/chemistry , Humans , Mass Spectrometry , Muscle, Smooth, Vascular/chemistry , Muscle, Smooth, Vascular/cytology , Stem Cells/chemistryABSTRACT
BACKGROUND: Anesthetic preconditioning can improve survival of cardiac progenitor cells exposed to oxidative stress. We investigated the role of protein kinase C and isoform protein kinase C-ε in isoflurane-induced preconditioning of cardiac progenitor cells exposed to oxidative stress. METHODS: Cardiac progenitor cells were obtained from undifferentiated human embryonic stem cells. Immunostaining with anti-Nkx2.5 was used to confirm the differentiated cardiac progenitor cells. Oxidative stress was induced by H2O2 and FeSO4. For anesthetic preconditioning, cardiac progenitor cells were exposed to 0.25, 0.5, and 1.0 mM of isoflurane. PMA and chelerythrine were used for protein kinase C activation and inhibition, while εψRACK and εV1-2 were used for protein kinase C -ε activation and inhibition, respectively. RESULTS: Isoflurane-preconditioning decreased the death rate of Cardiac progenitor cells exposed to oxidative stress (death rates isoflurane 0.5 mM 12.7 ± 9.3%, 1.0 mM 12.0 ± 7.7% vs. control 31.4 ± 10.2%). Inhibitors of both protein kinase C and protein kinase C -ε abolished the preconditioning effect of isoflurane 0.5 mM (death rates 27.6 ± 13.5% and 25.9 ± 8.7% respectively), and activators of both protein kinase C and protein kinase C - ε had protective effects from oxidative stress (death rates 16.0 ± 3.2% and 10.6 ± 3.8% respectively). CONCLUSIONS: Both PKC and PKC-ε are involved in isoflurane-induced preconditioning of human embryonic stem cells -derived Nkx2.5(+) Cardiac progenitor cells under oxidative stress.