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1.
Cell ; 179(6): 1276-1288.e14, 2019 11 27.
Article in English | MEDLINE | ID: mdl-31778654

ABSTRACT

Although human genetic studies have implicated many susceptible genes associated with plasma lipid levels, their physiological and molecular functions are not fully characterized. Here we demonstrate that orphan G protein-coupled receptor 146 (GPR146) promotes activity of hepatic sterol regulatory element binding protein 2 (SREBP2) through activation of the extracellular signal-regulated kinase (ERK) signaling pathway, thereby regulating hepatic very low-density lipoprotein (VLDL) secretion, and subsequently circulating low-density lipoprotein cholesterol (LDL-C) and triglycerides (TG) levels. Remarkably, GPR146 deficiency reduces plasma cholesterol levels substantially in both wild-type and LDL receptor (LDLR)-deficient mice. Finally, aortic atherosclerotic lesions are reduced by 90% and 70%, respectively, in male and female LDLR-deficient mice upon GPR146 depletion. Taken together, these findings outline a regulatory role for the GPR146/ERK axis in systemic cholesterol metabolism and suggest that GPR146 inhibition could be an effective strategy to reduce plasma cholesterol levels and atherosclerosis.


Subject(s)
Atherosclerosis/metabolism , Hypercholesterolemia/metabolism , Receptors, G-Protein-Coupled/deficiency , Animals , Atherosclerosis/blood , Base Sequence , Cholesterol/blood , Dependovirus/metabolism , Extracellular Signal-Regulated MAP Kinases/metabolism , Fasting , Female , Hepatocytes/metabolism , Humans , Hypercholesterolemia/blood , Lipoproteins, VLDL/metabolism , Liver/metabolism , Mice , Mice, Inbred C57BL , RNA, Small Interfering/metabolism , Receptors, G-Protein-Coupled/metabolism , Receptors, LDL/metabolism , Signal Transduction , Sterol Regulatory Element Binding Protein 2/metabolism , Triglycerides/blood , Up-Regulation
2.
Cell ; 152(3): 642-54, 2013 Jan 31.
Article in English | MEDLINE | ID: mdl-23333102

ABSTRACT

Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin genome-wide in a large and diverse collection of human tissues and stem cells. The maps yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments. They also reveal global features of the epigenome, related to nuclear architecture, that also vary across cellular phenotypes. Specifically, developmental specification is accompanied by progressive chromatin restriction as the default state transitions from dynamic remodeling to generalized compaction. Exposure to serum in vitro triggers a distinct transition that involves de novo establishment of domains with features of constitutive heterochromatin. We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming.


Subject(s)
Chromatin Assembly and Disassembly , Chromatin/metabolism , Epigenesis, Genetic , Gene-Environment Interaction , Genome-Wide Association Study , Cell Nucleus , Cellular Senescence , Embryonic Stem Cells/metabolism , Gene Expression Regulation , Humans , Induced Pluripotent Stem Cells/metabolism , Organ Specificity
3.
Proc Natl Acad Sci U S A ; 117(33): 19854-19865, 2020 08 18.
Article in English | MEDLINE | ID: mdl-32759214

ABSTRACT

The blood-retina barrier and blood-brain barrier (BRB/BBB) are selective and semipermeable and are critical for supporting and protecting central nervous system (CNS)-resident cells. Endothelial cells (ECs) within the BRB/BBB are tightly coupled, express high levels of Claudin-5 (CLDN5), a junctional protein that stabilizes ECs, and are important for proper neuronal function. To identify novel CLDN5 regulators (and ultimately EC stabilizers), we generated a CLDN5-P2A-GFP stable cell line from human pluripotent stem cells (hPSCs), directed their differentiation to ECs (CLDN5-GFP hPSC-ECs), and performed flow cytometry-based chemogenomic library screening to measure GFP expression as a surrogate reporter of barrier integrity. Using this approach, we identified 62 unique compounds that activated CLDN5-GFP. Among them were TGF-ß pathway inhibitors, including RepSox. When applied to hPSC-ECs, primary brain ECs, and retinal ECs, RepSox strongly elevated barrier resistance (transendothelial electrical resistance), reduced paracellular permeability (fluorescein isothiocyanate-dextran), and prevented vascular endothelial growth factor A (VEGFA)-induced barrier breakdown in vitro. RepSox also altered vascular patterning in the mouse retina during development when delivered exogenously. To determine the mechanism of action of RepSox, we performed kinome-, transcriptome-, and proteome-profiling and discovered that RepSox inhibited TGF-ß, VEGFA, and inflammatory gene networks. In addition, RepSox not only activated vascular-stabilizing and barrier-establishing Notch and Wnt pathways, but also induced expression of important tight junctions and transporters. Taken together, our data suggest that inhibiting multiple pathways by selected individual small molecules, such as RepSox, may be an effective strategy for the development of better BRB/BBB models and novel EC barrier-inducing therapeutics.


Subject(s)
Endothelial Cells/drug effects , Pluripotent Stem Cells/drug effects , Small Molecule Libraries/pharmacology , Animals , Blood-Brain Barrier/drug effects , Blood-Brain Barrier/metabolism , Blood-Retinal Barrier/drug effects , Blood-Retinal Barrier/metabolism , Cell Differentiation , Cell Line , Cell Proliferation/drug effects , Claudin-5/genetics , Claudin-5/metabolism , Drug Evaluation, Preclinical , Endothelial Cells/cytology , Endothelial Cells/metabolism , Gene Editing , Genome , Humans , Mice , Mice, Knockout , Pluripotent Stem Cells/cytology , Pluripotent Stem Cells/metabolism , Pyrazoles/pharmacology , Pyridines/pharmacology , Tight Junctions/metabolism , Vascular Endothelial Growth Factor A/metabolism
4.
Circ Res ; 126(3): 330-346, 2020 01 31.
Article in English | MEDLINE | ID: mdl-31739742

ABSTRACT

Rationale: Genome-wide association studies have identified genetic loci associated with insulin resistance (IR) but pinpointing the causal genes of a risk locus has been challenging. Objective: To identify candidate causal genes for IR, we screened regional and biologically plausible genes (16 in total) near the top 10 IR-loci in risk-relevant cell types, namely preadipocytes and adipocytes. Methods and Results: We generated 16 human Simpson-Golabi-Behmel syndrome preadipocyte knockout lines each with a single IR-gene knocked out by lentivirus-mediated CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system. We evaluated each gene knockout by screening IR-relevant phenotypes in the 3 insulin-sensitizing mechanisms, including adipogenesis, lipid metabolism, and insulin signaling. We performed genetic analyses using data on the genotype-tissue expression portal expression quantitative trait loci database and accelerating medicines partnership type 2 diabetes mellitus Knowledge Portal to evaluate whether candidate genes prioritized by our in vitro studies were expression quantitative trait loci genes in human subcutaneous adipose tissue, and whether expression of these genes is associated with risk of IR, type 2 diabetes mellitus, and cardiovascular diseases. We further validated the functions of 3 new adipose IR genes by overexpression-based phenotypic rescue in the Simpson-Golabi-Behmel syndrome preadipocyte knockout lines. Twelve genes, PPARG, IRS-1, FST, PEPD, PDGFC, MAP3K1, GRB14, ARL15, ANKRD55, RSPO3, COBLL1, and LYPLAL1, showed diverse phenotypes in the 3 insulin-sensitizing mechanisms, and the first 7 of these genes could affect all the 3 mechanisms. Five out of 6 expression quantitative trait loci genes are among the top candidate causal genes and the abnormal expression levels of these genes (IRS-1, GRB14, FST, PEPD, and PDGFC) in human subcutaneous adipose tissue could be associated with increased risk of IR, type 2 diabetes mellitus, and cardiovascular disease. Phenotypic rescue by overexpression of the candidate causal genes (FST, PEPD, and PDGFC) in the Simpson-Golabi-Behmel syndrome preadipocyte knockout lines confirmed their function in adipose IR. Conclusions: Twelve genes showed diverse phenotypes indicating differential roles in insulin sensitization, suggesting mechanisms bridging the association of their genomic loci with IR. We prioritized PPARG, IRS-1, GRB14, MAP3K1, FST, PEPD, and PDGFC as top candidate genes. Our work points to novel roles for FST, PEPD, and PDGFC in adipose tissue, with consequences for cardiometabolic diseases.


Subject(s)
Adipocytes/metabolism , Insulin Resistance/genetics , Quantitative Trait Loci , Adaptor Proteins, Signal Transducing/genetics , Cell Line , Dipeptidases/genetics , Follistatin/genetics , Genome-Wide Association Study/methods , Humans , Insulin Receptor Substrate Proteins/genetics , Loss of Function Mutation , Lymphokines/genetics , MAP Kinase Kinase Kinase 1/genetics , PPAR gamma/genetics , Platelet-Derived Growth Factor/genetics
5.
Proc Natl Acad Sci U S A ; 116(21): 10441-10446, 2019 05 21.
Article in English | MEDLINE | ID: mdl-31040209

ABSTRACT

Polymorphic HLAs form the primary immune barrier to cell therapy. In addition, innate immune surveillance impacts cell engraftment, yet a strategy to control both, adaptive and innate immunity, is lacking. Here we employed multiplex genome editing to specifically ablate the expression of the highly polymorphic HLA-A/-B/-C and HLA class II in human pluripotent stem cells. Furthermore, to prevent innate immune rejection and further suppress adaptive immune responses, we expressed the immunomodulatory factors PD-L1, HLA-G, and the macrophage "don't-eat me" signal CD47 from the AAVS1 safe harbor locus. Utilizing in vitro and in vivo immunoassays, we found that T cell responses were blunted. Moreover, NK cell killing and macrophage engulfment of our engineered cells were minimal. Our results describe an approach that effectively targets adaptive as well as innate immune responses and may therefore enable cell therapy on a broader scale.


Subject(s)
Genetic Engineering/methods , Pluripotent Stem Cells/immunology , CRISPR-Cas Systems , Cell Line , Gene Knockout Techniques , Genes, MHC Class I , Genes, MHC Class II , Humans
6.
Development ; 143(9): 1475-81, 2016 05 01.
Article in English | MEDLINE | ID: mdl-27143754

ABSTRACT

Hepatocyte-like cells (HLCs) are derived from human pluripotent stem cells (hPSCs) in vitro, but differentiation protocols commonly give rise to a heterogeneous mixture of cells. This variability confounds the evaluation of in vitro functional assays performed using HLCs. Increased differentiation efficiency and more accurate approximation of the in vivo hepatocyte gene expression profile would improve the utility of hPSCs. Towards this goal, we demonstrate the purification of a subpopulation of functional HLCs using the hepatocyte surface marker asialoglycoprotein receptor 1 (ASGR1). We analyzed the expression profile of ASGR1-positive cells by microarray, and tested their ability to perform mature hepatocyte functions (albumin and urea secretion, cytochrome activity). By these measures, ASGR1-positive HLCs are enriched for the gene expression profile and functional characteristics of primary hepatocytes compared with unsorted HLCs. We have demonstrated that ASGR1-positive sorting isolates a functional subpopulation of HLCs from among the heterogeneous cellular population produced by directed differentiation.


Subject(s)
Asialoglycoprotein Receptor/metabolism , Embryonic Stem Cells/cytology , Flow Cytometry/methods , Hepatocytes/metabolism , Induced Pluripotent Stem Cells/cytology , Albumins/metabolism , Cell Differentiation/physiology , Cell Line , Cell Membrane/metabolism , Cytochromes/metabolism , Humans , Urea/metabolism
7.
Proc Natl Acad Sci U S A ; 113(19): 5364-9, 2016 May 10.
Article in English | MEDLINE | ID: mdl-27078102

ABSTRACT

HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta. RNA-seq analysis demonstrated that Enhancer L specifically controls HLA-G expression. Moreover, DNase-seq and chromatin conformation capture (3C) defined Enhancer L as a cell type-specific enhancer that loops into the HLA-G promoter. Interestingly, MPRA-based saturation mutagenesis of Enhancer L identified motifs for transcription factors of the CEBP and GATA families essential for placentation. These factors associate with Enhancer L and regulate HLA-G expression. Our findings identify long-range chromatin looping mediated by core trophoblast transcription factors as the mechanism controlling tissue-specific HLA-G expression at the maternal-fetal interface. More broadly, these results establish the combination of MPRA and CRISPR/Cas9 deletion as a powerful strategy to investigate human immune gene regulation.


Subject(s)
Enhancer Elements, Genetic/immunology , Gene Expression Regulation, Developmental/immunology , HLA-G Antigens/immunology , Histocompatibility, Maternal-Fetal/immunology , Maternal-Fetal Exchange/immunology , Pregnancy/immunology , Trophoblasts/immunology , Enhancer Elements, Genetic/genetics , Female , Gene Expression Regulation, Developmental/genetics , HLA-G Antigens/genetics , Histocompatibility, Maternal-Fetal/genetics , Humans , Immunogenetic Phenomena/genetics , Maternal-Fetal Exchange/genetics , Placenta/immunology
8.
Int J Mol Sci ; 20(24)2019 Dec 09.
Article in English | MEDLINE | ID: mdl-31835296

ABSTRACT

The kinase AKT2 (PKB) is an important mediator of insulin signaling, for which loss-of-function knockout (KO) mutants lead to early onset diabetes mellitus, and dominant active mutations lead to early development of obesity and endothelial cell (EC) dysfunction. To model EC dysfunction, we used edited human pluripotent stem cells (hPSCs) that carried either a homozygous deletion of AKT2 (AKT2 KO) or a dominant active mutation (AKT2 E17K), which, along with the parental wild type (WT), were differentiated into ECs. Profiling of EC lines indicated an increase in proinflammatory and a reduction in anti-inflammatory fatty acids, an increase in inflammatory chemokines in cell supernatants, increased expression of proinflammatory genes, and increased binding to the EC monolayer in a functional leukocyte adhesion assay for both AKT2 KO and AKT2 E17K. Collectively, these findings suggest that vascular endothelial inflammation that results from dysregulated insulin signaling (homeostasis) may contribute to coronary artery disease, and that either downregulation or upregulation of the insulin pathway may lead to inflammation of endothelial cells. This suggests that the standard of care for patients must be expanded from control of metabolic parameters to include control of inflammation, such that endothelial dysfunction and cardiovascular disorders can ultimately be prevented.


Subject(s)
Endothelial Cells/metabolism , Gene Editing , Metabolic Syndrome , Models, Biological , Pluripotent Stem Cells/metabolism , Gene Knockdown Techniques , Humans , Inflammation/genetics , Inflammation/metabolism , Metabolic Syndrome/genetics , Metabolic Syndrome/metabolism
9.
Biochem Biophys Res Commun ; 495(1): 254-260, 2018 01 01.
Article in English | MEDLINE | ID: mdl-29108996

ABSTRACT

Lipodystrophies are disorders that directly affect lipid metabolism and storage. Familial partial lipodystrophy type 2 (FPLD2) is caused by an autosomal dominant mutation in the LMNA gene. FPLD2 is characterized by abnormal adipose tissue distribution. This leads to metabolic deficiencies, such as insulin-resistant diabetes mellitus and hypertriglyceridemia. Here we have derived iPSC lines from two individuals diagnosed with FPLD2, and differentiated these cells into adipocytes. Adipogenesis and certain adipocyte functions are impaired in FPLD2-adipocytes. Consistent with the lipodystrophic phenotype, FPLD2-adipocytes appear to accumulate markers of autophagy and catabolize triglycerides at higher levels than control adipocytes. These data are suggestive of a mechanism causing the lack of adipose tissue in FPLD2 patients.


Subject(s)
Adipocytes/pathology , Induced Pluripotent Stem Cells/pathology , Lamin Type A/genetics , Lipid Metabolism , Lipodystrophy, Familial Partial/genetics , Point Mutation , Adipocytes/metabolism , Adipogenesis , Autophagy , Cells, Cultured , Humans , Induced Pluripotent Stem Cells/metabolism , Insulin Resistance , Lipodystrophy, Familial Partial/metabolism , Lipodystrophy, Familial Partial/pathology , Triglycerides/metabolism
10.
Arterioscler Thromb Vasc Biol ; 36(1): 15-8, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26543098

ABSTRACT

OBJECTIVE: To create isogenic human pluripotent stem cell-derived macrophages with and without ABCA1 expression as a model for reverse cholesterol transport. APPROACH AND RESULTS: The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) genome-editing system was used to introduce frameshift mutations into the coding sequence of ATP-binding cassette, subfamily A, member 1. Individual human pluripotent stem cell clones with deleterious mutations were identified, expanded, and differentiated into mature macrophages with a cytokine-based, feeder-free differentiation protocol. Wild-type cells demonstrated effective cholesterol efflux to apoAI acceptor, whereas ABCA1(-/-) cells displayed significantly reduced efflux ability and increased expression of proinflammatory cytokines. CONCLUSIONS: Human pluripotent stem cell-derived macrophages capable of reverse cholesterol transport can be rapidly generated and genetically edited with CRISPR/Cas9. Introduction of homozygous frameshift mutations results in loss of ABCA1 expression in differentiated macrophages and subsequent reduction of cholesterol efflux capability. This facile genome-editing approach and differentiation protocol pave the way for future studies of the molecular determinants of reverse cholesterol transport and other macrophage properties.


Subject(s)
ATP Binding Cassette Transporter 1/metabolism , Cholesterol/metabolism , Genome, Human , Macrophages/metabolism , Pluripotent Stem Cells/metabolism , ATP Binding Cassette Transporter 1/genetics , Apolipoprotein A-I/metabolism , Biological Transport , CRISPR-Associated Proteins/genetics , CRISPR-Associated Proteins/metabolism , CRISPR-Cas Systems , Cell Differentiation , Cell Line , Cytokines/metabolism , Frameshift Mutation , Gene Expression Regulation , Genotype , Humans , INDEL Mutation , Inflammation Mediators/metabolism , Phenotype
11.
Nature ; 470(7332): 95-100, 2011 Feb 03.
Article in English | MEDLINE | ID: mdl-21270795

ABSTRACT

Loss of kidney function underlies many renal diseases. Mammals can partly repair their nephrons (the functional units of the kidney), but cannot form new ones. By contrast, fish add nephrons throughout their lifespan and regenerate nephrons de novo after injury, providing a model for understanding how mammalian renal regeneration may be therapeutically activated. Here we trace the source of new nephrons in the adult zebrafish to small cellular aggregates containing nephron progenitors. Transplantation of single aggregates comprising 10-30 cells is sufficient to engraft adults and generate multiple nephrons. Serial transplantation experiments to test self-renewal revealed that nephron progenitors are long-lived and possess significant replicative potential, consistent with stem-cell activity. Transplantation of mixed nephron progenitors tagged with either green or red fluorescent proteins yielded some mosaic nephrons, indicating that multiple nephron progenitors contribute to a single nephron. Consistent with this, live imaging of nephron formation in transparent larvae showed that nephrogenic aggregates form by the coalescence of multiple cells and then differentiate into nephrons. Taken together, these data demonstrate that the zebrafish kidney probably contains self-renewing nephron stem/progenitor cells. The identification of these cells paves the way to isolating or engineering the equivalent cells in mammals and developing novel renal regenerative therapies.


Subject(s)
Kidney/cytology , Kidney/growth & development , Nephrons/cytology , Regeneration/physiology , Stem Cells/cytology , Zebrafish/growth & development , Aging/physiology , Animals , Animals, Genetically Modified , Cell Proliferation , Kidney/injuries , Kidney/metabolism , Larva , Models, Animal , Nephrons/growth & development , Organogenesis , Stem Cell Transplantation
12.
Biochem Biophys Res Commun ; 476(4): 487-492, 2016 08 05.
Article in English | MEDLINE | ID: mdl-27246738

ABSTRACT

Type 2 diabetes follows a well-defined progressive pathogenesis, beginning with insulin resistance in metabolic tissues such as the adipose. Intracellular signaling downstream of insulin receptor activation regulates critical metabolic functions of adipose tissue, including glucose uptake, lipogenesis, lipolysis and adipokine secretion. Previous studies have used the aP2 promoter to drive Cre recombinase expression in adipose tissue. Insulin receptor (IR) knockout mice created using this aP2-Cre strategy (FIRKO mice) were protected from obesity and glucose intolerance. Later studies demonstrated the promiscuity of the aP2 promoter, casting doubts upon the tissue specificity of aP2-Cre models. It is our goal to use the increased precision of the Adipoq promoter to investigate adipocyte-specific IR function. Towards this end we generated an adipocyte-specific IR knockout (AIRKO) mouse using an Adipoq-driven Cre recombinase. Here we report AIRKO mice are less insulin sensitive throughout life, and less glucose tolerant than wild-type (WT) littermates at the age of 16 weeks. In contrast to WT littermates, the insulin sensitivity of AIRKO mice is unaffected by age or dietary regimen. At any age, AIRKO mice are comparably insulin resistant to old or obese WT mice and have a significantly reduced lifespan. Similar results were obtained when these phenotypes were re-examined in FIRKO mice. We also found that the AIRKO mouse is protected from high-fat diet-induced weight gain, corresponding with a 90% reduction in tissue weight of major adipose depots compared to WT littermates. Adipose tissue mass reduction is accompanied by hepatomegaly and increased hepatic steatosis. These data indicate that adipocyte IR function is crucial to systemic energy metabolism and has profound effects on adiposity, hepatic homeostasis and lifespan.


Subject(s)
Adipocytes/metabolism , Receptor, Insulin/metabolism , Adipose Tissue/anatomy & histology , Adipose Tissue/metabolism , Aging/metabolism , Animals , Blood Glucose/metabolism , Diabetes Mellitus, Type 2/etiology , Diabetes Mellitus, Type 2/metabolism , Diabetes Mellitus, Type 2/pathology , Diet, High-Fat/adverse effects , Female , Insulin Resistance/physiology , Longevity/physiology , Male , Mice , Mice, Knockout , Receptor, Insulin/deficiency , Receptor, Insulin/genetics , Signal Transduction
13.
Circ Res ; 115(5): 488-92, 2014 Aug 15.
Article in English | MEDLINE | ID: mdl-24916110

ABSTRACT

RATIONALE: Individuals with naturally occurring loss-of-function proprotein convertase subtilisin/kexin type 9 (PCSK9) mutations experience reduced low-density lipoprotein cholesterol levels and protection against cardiovascular disease. OBJECTIVE: The goal of this study was to assess whether genome editing using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system can efficiently introduce loss-of-function mutations into the endogenous PCSK9 gene in vivo. METHODS AND RESULTS: We used adenovirus to express CRISPR-associated 9 and a CRISPR guide RNA targeting Pcsk9 in mouse liver, where the gene is specifically expressed. We found that <3 to 4 days of administration of the virus, the mutagenesis rate of Pcsk9 in the liver was as high as >50%. This resulted in decreased plasma PCSK9 levels, increased hepatic low-density lipoprotein receptor levels, and decreased plasma cholesterol levels (by 35-40%). No off-target mutagenesis was detected in 10 selected sites. CONCLUSIONS: Genome editing with the CRISPR-CRISPR-associated 9 system disrupts the Pcsk9 gene in vivo with high efficiency and reduces blood cholesterol levels in mice. This approach may have therapeutic potential for the prevention of cardiovascular disease in humans.


Subject(s)
Clustered Regularly Interspaced Short Palindromic Repeats , Liver/enzymology , Mutation , Proprotein Convertases/genetics , RNA Editing , RNA, Guide, Kinetoplastida/genetics , Serine Endopeptidases/genetics , 3T3-L1 Cells , Adenoviridae/genetics , Animals , Biomarkers/blood , Cardiovascular Diseases/enzymology , Cardiovascular Diseases/genetics , Cardiovascular Diseases/prevention & control , Cholesterol/blood , Female , Gene Expression Regulation, Enzymologic , Genetic Vectors , Genotype , Male , Mice , Mice, Inbred C57BL , Phenotype , Proprotein Convertase 9 , Proprotein Convertases/blood , Protective Factors , RNA, Guide, Kinetoplastida/metabolism , Receptors, LDL/metabolism , Serine Endopeptidases/blood , Time Factors , Transfection
14.
Nature ; 466(7307): 714-9, 2010 Aug 05.
Article in English | MEDLINE | ID: mdl-20686566

ABSTRACT

Recent genome-wide association studies (GWASs) have identified a locus on chromosome 1p13 strongly associated with both plasma low-density lipoprotein cholesterol (LDL-C) and myocardial infarction (MI) in humans. Here we show through a series of studies in human cohorts and human-derived hepatocytes that a common noncoding polymorphism at the 1p13 locus, rs12740374, creates a C/EBP (CCAAT/enhancer binding protein) transcription factor binding site and alters the hepatic expression of the SORT1 gene. With small interfering RNA (siRNA) knockdown and viral overexpression in mouse liver, we demonstrate that Sort1 alters plasma LDL-C and very low-density lipoprotein (VLDL) particle levels by modulating hepatic VLDL secretion. Thus, we provide functional evidence for a novel regulatory pathway for lipoprotein metabolism and suggest that modulation of this pathway may alter risk for MI in humans. We also demonstrate that common noncoding DNA variants identified by GWASs can directly contribute to clinical phenotypes.


Subject(s)
Adaptor Proteins, Vesicular Transport/metabolism , Cholesterol, LDL/metabolism , Chromosomes, Human, Pair 1/genetics , Genetic Predisposition to Disease/genetics , Polymorphism, Single Nucleotide/genetics , Adaptor Proteins, Vesicular Transport/biosynthesis , Adaptor Proteins, Vesicular Transport/deficiency , Adaptor Proteins, Vesicular Transport/genetics , Animals , Base Sequence , Binding Sites , CCAAT-Enhancer-Binding Proteins/metabolism , Cells, Cultured , Cholesterol, LDL/blood , Cohort Studies , Coronary Artery Disease/blood , Coronary Artery Disease/genetics , Europe/ethnology , Gene Expression Regulation , Gene Knockdown Techniques , Genome-Wide Association Study , Haplotypes/genetics , Hepatocytes/metabolism , Humans , Lipids/blood , Lipoproteins, VLDL/blood , Lipoproteins, VLDL/metabolism , Liver/cytology , Liver/metabolism , Mice , Myocardial Infarction/blood , Myocardial Infarction/genetics , Phenotype , Transcription, Genetic
15.
Commun Biol ; 6(1): 1298, 2023 12 21.
Article in English | MEDLINE | ID: mdl-38129665

ABSTRACT

Biallelic mutations of the chromatin regulator SMARCAL1 cause Schimke Immunoosseous Dysplasia (SIOD), characterized by severe growth defects and premature mortality. Atherosclerosis and hyperlipidemia are common among SIOD patients, yet their onset and progression are poorly understood. Using an integrative approach involving proteomics, mouse models, and population genetics, we investigated SMARCAL1's role. We found that SmarcAL1 interacts with angiopoietin-like 3 (Angptl3), a key regulator of lipoprotein metabolism. In vitro and in vivo analyses demonstrate SmarcAL1's vital role in maintaining cellular lipid homeostasis. The observed translocation of SmarcAL1 to cytoplasmic peroxisomes suggests a potential regulatory role in lipid metabolism through gene expression. SmarcAL1 gene inactivation reduces the expression of key genes in cellular lipid catabolism. Population genetics investigations highlight significant associations between SMARCAL1 genetic variations and body mass index, along with lipid-related traits. This study underscores SMARCAL1's pivotal role in cellular lipid metabolism, likely contributing to the observed lipid phenotypes in SIOD patients.


Subject(s)
Immunologic Deficiency Syndromes , Animals , Humans , Mice , Chromatin , DNA Helicases/genetics , DNA Helicases/metabolism , Immunologic Deficiency Syndromes/genetics , Immunologic Deficiency Syndromes/metabolism , Lipid Metabolism/genetics , Lipids
16.
Curr Opin Genet Dev ; 18(4): 324-9, 2008 Aug.
Article in English | MEDLINE | ID: mdl-18625311

ABSTRACT

Human embryonic stem cells possess the unique ability to differentiate into any adult cell type. Recent advances in the understanding of stem cell biology make new applications possible for stem cell based technology. Of note, it is now possible to reprogram terminally differentiated human somatic cells into pluripotent cells that are functionally equivalent to embryonic stem cells. These induced pluripotent cells may become the substrate for future disease models and cell-based therapies. In addition, novel techniques for genetic manipulation have increased the ease with which genes can be modified into stem cells. In this review, we describe these novel technologies as well as developments in the understanding of basic biology of stem cell pluripotency and differentiation.


Subject(s)
Biomedical Technology/methods , Biomedical Technology/trends , Embryonic Stem Cells/cytology , Cell Differentiation/physiology , Cell Proliferation , Humans , Models, Biological
17.
PLoS Genet ; 4(10): e1000242, 2008 Oct.
Article in English | MEDLINE | ID: mdl-18974828

ABSTRACT

In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes -- the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells.


Subject(s)
Chromatin/metabolism , CpG Islands , Embryonic Stem Cells/metabolism , Epigenesis, Genetic , Genome, Human , Genome , Repressor Proteins/metabolism , Animals , Chromatin/chemistry , Chromatin Immunoprecipitation , Chromosome Mapping , Computational Biology , Histones/metabolism , Humans , Jumonji Domain-Containing Histone Demethylases , Methylation , Mice , Oxidoreductases, N-Demethylating/metabolism , Pluripotent Stem Cells/metabolism , Polycomb-Group Proteins , Promoter Regions, Genetic , Protein Structure, Tertiary , Repressor Proteins/genetics
18.
Science ; 372(6543): 716-721, 2021 05 14.
Article in English | MEDLINE | ID: mdl-33986176

ABSTRACT

Transcription and metabolism both influence cell function, but dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. We discovered, using a chemical suppressor screen, that inhibition of the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) rescues erythroid differentiation in bloodless zebrafish moonshine (mon) mutant embryos defective for transcriptional intermediary factor 1 gamma (tif1γ). This rescue depends on the functional link of DHODH to mitochondrial respiration. The transcription elongation factor TIF1γ directly controls coenzyme Q (CoQ) synthesis gene expression. Upon tif1γ loss, CoQ levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A CoQ analog rescues mon's bloodless phenotype. These results demonstrate that mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.


Subject(s)
Erythropoiesis , Mitochondria/metabolism , Transcription Factors/metabolism , Transcription, Genetic , Zebrafish Proteins/metabolism , Animals , Citric Acid Cycle , DNA Methylation , Dihydroorotate Dehydrogenase , Electron Transport , Embryo, Nonmammalian/metabolism , Enzyme Inhibitors/pharmacology , Gene Expression Regulation , Histones/metabolism , Leflunomide/pharmacology , Metabolic Networks and Pathways , Methylation , Oxidoreductases Acting on CH-CH Group Donors/antagonists & inhibitors , Oxygen Consumption , Transcription Factors/genetics , Ubiquinone/metabolism , Zebrafish/embryology , Zebrafish/genetics , Zebrafish Proteins/genetics
19.
J Cell Physiol ; 222(2): 278-81, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19877154

ABSTRACT

Induced pluripotent stem cell (iPSC) technology has emerged as the most promising method for generating patient-specific human embryonic stem (ES) cells and adult stem cells (Takahashi et al., 2007, Cell 131:861-872; Wernig et al., 2007, Nature 448:318-324; Park et al., 2008, Nature 451:141-146). So far, most studies of direct reprogramming have been done by using lentiviruses/retroviruses encoding the reprogramming factors. This represents a major limitation to therapeutic applications since viral integration in the host genome increases the risk of tumorigenicity, and low-level residual expression of reprogramming factors may alter the differentiation potential of the human iPSCs (hiPSCs). As a result, more attention has been paid to developing new techniques to manipulate the human genome, with the goal of making safer hiPSCs that have fewer or no lesions or alterations in the genome. Additionally, the efficiency of reprogramming and of homologous recombination in gene therapy must be improved, if iPSC technology is to be a viable tool in regenerative medicine. Here, we summarize the recent developments in human genome manipulation for generating hiPSCs and advances in homologous recombination for gene targeting.


Subject(s)
Embryonic Stem Cells/physiology , Gene Expression Regulation, Developmental , Gene Targeting , Genetic Therapy/methods , Genome, Human , Pluripotent Stem Cells/physiology , Recombination, Genetic , Animals , DNA Transposable Elements , Genetic Therapy/adverse effects , Genetic Vectors , Genomic Instability , Humans , Lentivirus/genetics , Retroviridae/genetics
20.
Sci Rep ; 10(1): 3886, 2020 03 03.
Article in English | MEDLINE | ID: mdl-32127614

ABSTRACT

Endothelial cells (ECs) display remarkable plasticity during development before becoming quiescent and functionally mature. EC maturation is directed by several known transcription factors (TFs), but the specific set of TFs responsible for promoting high-resistance barriers, such as the blood-brain barrier (BBB), have not yet been fully defined. Using expression mRNA data from published studies on ex vivo ECs from the central nervous system (CNS), we predicted TFs that induce high-resistance barrier properties of ECs as in the BBB. We used our previously established method to  generate ECs from human pluripotent stem cells (hPSCs), and then we overexpressed the candidate TFs in hPSC-ECs and measured barrier resistance and integrity using electric cell-substrate impedance sensing, trans-endothelial electrical resistance and FITC-dextran permeability assays. SOX18 and TAL1 were the strongest EC barrier-inducing TFs, upregulating Wnt-related signaling and EC junctional gene expression, respectively, and downregulating EC proliferation-related genes. These TFs were combined with SOX7 and ETS1 that together effectively induced EC barrier resistance, decreased paracellular transport and increased protein expression of tight junctions and induce mRNA expression of several genes involved in the formation of EC barrier and transport. Our data shows identification of a transcriptional network that controls barrier resistance in ECs. Collectively this data may lead to novel approaches for generation of in vitro models of the BBB.


Subject(s)
Endothelial Cells/metabolism , Transcription Factors/metabolism , Blood-Brain Barrier/cytology , Cell Differentiation , Endothelial Cells/cytology , Humans , Pluripotent Stem Cells/cytology
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