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1.
Circulation ; 2024 Apr 08.
Article En | MEDLINE | ID: mdl-38586957

BACKGROUND: Adult mammalian cardiomyocytes have limited proliferative capacity, but in specifically induced contexts they traverse through cell-cycle reentry, offering the potential for heart regeneration. Endogenous cardiomyocyte proliferation is preceded by cardiomyocyte dedifferentiation (CMDD), wherein adult cardiomyocytes revert to a less matured state that is distinct from the classical myocardial fetal stress gene response associated with heart failure. However, very little is known about CMDD as a defined cardiomyocyte cell state in transition. METHODS: Here, we leveraged 2 models of in vitro cultured adult mouse cardiomyocytes and in vivo adeno-associated virus serotype 9 cardiomyocyte-targeted delivery of reprogramming factors (Oct4, Sox2, Klf4, and Myc) in adult mice to study CMDD. We profiled their transcriptomes using RNA sequencing, in combination with multiple published data sets, with the aim of identifying a common denominator for tracking CMDD. RESULTS: RNA sequencing and integrated analysis identified Asparagine Synthetase (Asns) as a unique molecular marker gene well correlated with CMDD, required for increased asparagine and also for distinct fluxes in other amino acids. Although Asns overexpression in Oct4, Sox2, Klf4, and Myc cardiomyocytes augmented hallmarks of CMDD, Asns deficiency led to defective regeneration in the neonatal mouse myocardial infarction model, increased cell death of cultured adult cardiomyocytes, and reduced cell cycle in Oct4, Sox2, Klf4, and Myc cardiomyocytes, at least in part through disrupting the mammalian target of rapamycin complex 1 pathway. CONCLUSIONS: We discovered a novel gene Asns as both a molecular marker and an essential mediator, marking a distinct threshold that appears in common for at least 4 models of CMDD, and revealing an Asns/mammalian target of rapamycin complex 1 axis dependency for dedifferentiating cardiomyocytes. Further study will be needed to extrapolate and assess its relevance to other cell state transitions as well as in heart regeneration.

2.
Elife ; 132024 Jan 02.
Article En | MEDLINE | ID: mdl-38164941

Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites in vitro using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easy targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.


Genomics , Humans , Gene Expression , Transgenes , Cell Differentiation
3.
Nat Genet ; 55(6): 1009-1021, 2023 06.
Article En | MEDLINE | ID: mdl-37291193

Aldosterone-producing adenomas (APAs) are the commonest curable cause of hypertension. Most have gain-of-function somatic mutations of ion channels or transporters. Herein we report the discovery, replication and phenotype of mutations in the neuronal cell adhesion gene CADM1. Independent whole exome sequencing of 40 and 81 APAs found intramembranous p.Val380Asp or p.Gly379Asp variants in two patients whose hypertension and periodic primary aldosteronism were cured by adrenalectomy. Replication identified two more APAs with each variant (total, n = 6). The most upregulated gene (10- to 25-fold) in human adrenocortical H295R cells transduced with the mutations (compared to wildtype) was CYP11B2 (aldosterone synthase), and biological rhythms were the most differentially expressed process. CADM1 knockdown or mutation inhibited gap junction (GJ)-permeable dye transfer. GJ blockade by Gap27 increased CYP11B2 similarly to CADM1 mutation. Human adrenal zona glomerulosa (ZG) expression of GJA1 (the main GJ protein) was patchy, and annular GJs (sequelae of GJ communication) were less prominent in CYP11B2-positive micronodules than adjacent ZG. Somatic mutations of CADM1 cause reversible hypertension and reveal a role for GJ communication in suppressing physiological aldosterone production.


Adrenal Cortex Neoplasms , Adrenocortical Adenoma , Hyperaldosteronism , Hypertension , Humans , Aldosterone , Cytochrome P-450 CYP11B2 , Gap Junctions , Mutation , Cell Adhesion Molecule-1
4.
Oxid Med Cell Longev ; 2022: 9180267, 2022.
Article En | MEDLINE | ID: mdl-35391931

Doxorubicin is an anthracycline widely used for the treatment of various cancers; however, the drug has a common deleterious side effect, namely a dose-dependent cardiotoxicity. Doxorubicin treatment increases the generation of reactive oxygen species, which leads to oxidative stress in the cardiac cells and ultimately DNA damage and cell death. The most common DNA lesion produced by oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoguanine), and the enzyme responsible for its repair is the 8-oxoguanine DNA glycosylase (OGG1), a base excision repair enzyme. Here, we show that the OGG1 deficiency has no major effect on cardiac function at baseline or with pressure overload; however, we found an exacerbation of cardiac dysfunction as well as a higher mortality in Ogg1 knockout mice treated with doxorubicin. Our transcriptomic analysis also showed a more extensive dysregulation of genes in the hearts of Ogg1 knockout mice with an enrichment of genes involved in inflammation. These results demonstrate that OGG1 attenuates doxorubicin-induced cardiotoxicity and thus plays a role in modulating drug-induced cardiomyopathy.


DNA Glycosylases , Heart Diseases , Animals , Cardiotoxicity , DNA Damage , DNA Glycosylases/genetics , DNA Glycosylases/metabolism , DNA Repair , Doxorubicin/adverse effects , Guanine/analogs & derivatives , Mice , Mice, Knockout , Oxidative Stress
5.
Nat Genet ; 53(9): 1360-1372, 2021 09.
Article En | MEDLINE | ID: mdl-34385710

Most aldosterone-producing adenomas (APAs) have gain-of-function somatic mutations of ion channels or transporters. However, their frequency in aldosterone-producing cell clusters of normal adrenal gland suggests a requirement for codriver mutations in APAs. Here we identified gain-of-function mutations in both CTNNB1 and GNA11 by whole-exome sequencing of 3/41 APAs. Further sequencing of known CTNNB1-mutant APAs led to a total of 16 of 27 (59%) with a somatic p.Gln209His, p.Gln209Pro or p.Gln209Leu mutation of GNA11 or GNAQ. Solitary GNA11 mutations were found in hyperplastic zona glomerulosa adjacent to double-mutant APAs. Nine of ten patients in our UK/Irish cohort presented in puberty, pregnancy or menopause. Among multiple transcripts upregulated more than tenfold in double-mutant APAs was LHCGR, the receptor for luteinizing or pregnancy hormone (human chorionic gonadotropin). Transfections of adrenocortical cells demonstrated additive effects of GNA11 and CTNNB1 mutations on aldosterone secretion and expression of genes upregulated in double-mutant APAs. In adrenal cortex, GNA11/Q mutations appear clinically silent without a codriver mutation of CTNNB1.


Adrenal Cortex Neoplasms/genetics , Adrenocortical Adenoma/genetics , Aldosterone/biosynthesis , GTP-Binding Protein alpha Subunits/genetics , beta Catenin/genetics , Adolescent , Adrenal Cortex Neoplasms/pathology , Adrenocortical Adenoma/pathology , Adult , Female , GTP-Binding Protein alpha Subunits, Gq-G11/genetics , Humans , Hyperaldosteronism/pathology , Male , Menopause/metabolism , Middle Aged , Pregnancy , Puberty/metabolism
6.
Mol Biol Evol ; 38(10): 4463-4474, 2021 09 27.
Article En | MEDLINE | ID: mdl-34152401

The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.76-6.49%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.65-1.51%), southern Chinese (0.86%, 0.50-1.23%), and northern Chinese (0.25%, 0.18-0.32%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.


Asian People , Genetics, Population , Asia, Southeastern , Asian People/genetics , China , Female , Humans , Whole Genome Sequencing
7.
J Mol Cell Cardiol ; 160: 15-26, 2021 11.
Article En | MEDLINE | ID: mdl-34146546

AIMS: Direct cardiac reprogramming represents an attractive way to reversing heart damage caused by myocardial infarction because it removes fibroblasts, while also generating new functional cardiomyocytes. Yet, the main hurdle for bringing this technique to the clinic is the lack of efficacy with current reprogramming protocols. Here, we describe our unexpected discovery that DMSO is capable of significantly augmenting direct cardiac reprogramming in vitro. METHODS AND RESULTS: Upon induction with cardiac transcription factors- Gata4, Hand2, Mef2c and Tbx5 (GHMT), the treatment of mouse embryonic fibroblasts (MEFs) with 1% DMSO induced ~5 fold increase in Myh6-mCherry+ cells, and significantly upregulated global expression of cardiac genes, including Myh6, Ttn, Nppa, Myh7 and Ryr2. RNA-seq confirmed upregulation of cardiac gene programmes and downregulation of extracellular matrix-related genes. Treatment of TGF-ß1, DMSO, or SB431542, and the combination thereof, revealed that DMSO most likely targets a separate but parallel pathway other than TGF-ß signalling. Subsequent experiments using small molecule screening revealed that DMSO enhances direct cardiac reprogramming through inhibition of the CBP/p300 bromodomain, and not its acetyltransferase property. CONCLUSION: In conclusion, our work points to a direct molecular target of DMSO, which can be used for augmenting GHMT-induced direct cardiac reprogramming and possibly other cell fate conversion processes.


Cellular Reprogramming/drug effects , Dimethyl Sulfoxide/pharmacology , Fibroblasts/cytology , Myocytes, Cardiac/cytology , Protein Domains/drug effects , Signal Transduction/drug effects , p300-CBP Transcription Factors/chemistry , Animals , Benzamides/pharmacology , Cells, Cultured , Dioxoles/pharmacology , Down-Regulation/drug effects , Down-Regulation/genetics , Embryo, Mammalian/cytology , Female , Fibroblasts/drug effects , Fibroblasts/metabolism , GATA4 Transcription Factor/metabolism , Male , Mice , Mice, Transgenic , Myocytes, Cardiac/drug effects , Myocytes, Cardiac/metabolism , Pregnancy , Transforming Growth Factor beta1/pharmacology , Up-Regulation/drug effects , Up-Regulation/genetics
8.
Dev Dyn ; 250(12): 1759-1777, 2021 12.
Article En | MEDLINE | ID: mdl-34056790

BACKGROUND: Biomechanical stimuli are known to be important to cardiac development, but the mechanisms are not fully understood. Here, we pharmacologically disrupted the biomechanical environment of wild-type zebrafish embryonic hearts for an extended duration and investigated the consequent effects on cardiac function, morphological development, and gene expression. RESULTS: Myocardial contractility was significantly diminished or abolished in zebrafish embryonic hearts treated for 72 hours from 2 dpf with 2,3-butanedione monoxime (BDM). Image-based flow simulations showed that flow wall shear stresses were abolished or significantly reduced with high oscillatory shear indices. At 5 dpf, after removal of BDM, treated embryonic hearts were maldeveloped, having disrupted cardiac looping, smaller ventricles, and poor cardiac function (lower ejected flow, bulboventricular regurgitation, lower contractility, and slower heart rate). RNA sequencing of cardiomyocytes of treated hearts revealed 922 significantly up-regulated genes and 1,698 significantly down-regulated genes. RNA analysis and subsequent qPCR and histology validation suggested that biomechanical disruption led to an up-regulation of inflammatory and apoptotic genes and down-regulation of ECM remodeling and ECM-receptor interaction genes. Biomechanics disruption also prevented the formation of ventricular trabeculation along with notch1 and erbb4a down-regulation. CONCLUSIONS: Extended disruption of biomechanical stimuli caused maldevelopment, and potential genes responsible for this are identified.


Biomechanical Phenomena/drug effects , Diacetyl/analogs & derivatives , Heart/embryology , Zebrafish , Animals , Animals, Genetically Modified , Biomechanical Phenomena/physiology , Diacetyl/pharmacology , Embryo, Nonmammalian/drug effects , Embryonic Development/drug effects , Embryonic Development/genetics , Gene Expression Regulation, Developmental/drug effects , Heart/drug effects , Heart/physiology , Hydrodynamics , Myocardial Contraction/drug effects , Myocardium/metabolism , Organogenesis/drug effects , Organogenesis/genetics , Organogenesis/physiology , Stress, Mechanical , Zebrafish/embryology , Zebrafish/genetics
9.
Dev Cell ; 56(6): 747-760.e6, 2021 03 22.
Article En | MEDLINE | ID: mdl-33667344

Loss of insulin-secreting pancreatic ß cells through apoptosis contributes to the progression of type 2 diabetes, but underlying mechanisms remain elusive. Here, we identify a pathway in which the cell death inhibitor ARC paradoxically becomes a killer during diabetes. While cytoplasmic ARC maintains ß cell viability and pancreatic architecture, a pool of ARC relocates to the nucleus to induce ß cell apoptosis in humans with diabetes and several pathophysiologically distinct mouse models. ß cell death results through the coordinate downregulation of serpins (serine protease inhibitors) not previously known to be synthesized and secreted by ß cells. Loss of the serpin α1-antitrypsin from the extracellular space unleashes elastase, triggering the disruption of ß cell anchorage and subsequent cell death. Administration of α1-antitrypsin to mice with diabetes prevents ß cell death and metabolic abnormalities. These data uncover a pathway for ß cell loss in type 2 diabetes and identify an FDA-approved drug that may impede progression of this syndrome.


Apoptosis , Cell Nucleus/metabolism , Cytoskeletal Proteins/metabolism , Diabetes Mellitus, Experimental/pathology , Diabetes Mellitus, Type 2/pathology , Insulin-Secreting Cells/pathology , Nerve Tissue Proteins/metabolism , alpha 1-Antitrypsin/chemistry , Animals , Apoptosis Regulatory Proteins/physiology , Cytoplasm/metabolism , Cytoskeletal Proteins/genetics , Diabetes Mellitus, Experimental/etiology , Diabetes Mellitus, Experimental/metabolism , Diabetes Mellitus, Type 2/etiology , Diabetes Mellitus, Type 2/metabolism , Female , Humans , Insulin-Secreting Cells/metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Muscle Proteins/physiology , Nerve Tissue Proteins/genetics , alpha 1-Antitrypsin/genetics , alpha 1-Antitrypsin/metabolism
10.
Arch Dis Child ; 106(1): 31-37, 2021 01.
Article En | MEDLINE | ID: mdl-32819910

OBJECTIVE: Use next-generation sequencing (NGS) technology to improve our diagnostic yield in patients with suspected genetic disorders in the Asian setting. DESIGN: A diagnostic study conducted between 2014 and 2019 (and ongoing) under the Singapore Undiagnosed Disease Program. Date of last analysis was 1 July 2019. SETTING: Inpatient and outpatient genetics service at two large academic centres in Singapore. PATIENTS: Inclusion criteria: patients suspected of genetic disorders, based on abnormal antenatal ultrasound, multiple congenital anomalies and developmental delay. EXCLUSION CRITERIA: patients with known genetic disorders, either after clinical assessment or investigations (such as karyotype or chromosomal microarray). INTERVENTIONS: Use of NGS technology-whole exome sequencing (WES) or whole genome sequencing (WGS). MAIN OUTCOME MEASURES: (1) Diagnostic yield by sequencing type, (2) diagnostic yield by phenotypical categories, (3) reduction in time to diagnosis and (4) change in clinical outcomes and management. RESULTS: We demonstrate a 37.8% diagnostic yield for WES (n=172) and a 33.3% yield for WGS (n=24). The yield was higher when sequencing was conducted on trios (40.2%), as well as for certain phenotypes (neuromuscular, 54%, and skeletal dysplasia, 50%). In addition to aiding genetic counselling in 100% of the families, a positive result led to a change in treatment in 27% of patients. CONCLUSION: Genomic sequencing is an effective method for diagnosing rare disease or previous 'undiagnosed' disease. The clinical utility of WES/WGS is seen in the shortened time to diagnosis and the discovery of novel variants. Additionally, reaching a diagnosis significantly impacts families and leads to alteration in management of these patients.


Abnormalities, Multiple/genetics , Developmental Disabilities/genetics , High-Throughput Nucleotide Sequencing , Undiagnosed Diseases/genetics , Abnormalities, Multiple/diagnosis , Adolescent , Adult , Child , Child, Preschool , Developmental Disabilities/diagnosis , Female , Humans , Infant , Male , Singapore , Undiagnosed Diseases/diagnosis , Young Adult
12.
Cell Death Dis ; 11(5): 354, 2020 05 11.
Article En | MEDLINE | ID: mdl-32393784

Human pluripotent stem cells (hPSCs)-derived cardiovascular progenitor cells (CVPCs) are a promising source for myocardial repair, while the mechanisms remain largely unknown. Extracellular vesicles (EVs) are known to mediate cell-cell communication, however, the efficacy and mechanisms of hPSC-CVPC-secreted EVs (hCVPC-EVs) in the infarct healing when given at the acute phase of myocardial infarction (MI) are unknown. Here, we report the cardioprotective effects of the EVs secreted from hESC-CVPCs under normoxic (EV-N) and hypoxic (EV-H) conditions in the infarcted heart and the long noncoding RNA (lncRNA)-related mechanisms. The hCVPC-EVs were confirmed by electron microscopy, nanoparticle tracking, and immunoblotting analysis. Injection of hCVPC-EVs into acutely infracted murine myocardium significantly improved cardiac function and reduced fibrosis at day 28 post MI, accompanied with the improved vascularization and cardiomyocyte survival at border zones. Consistently, hCVPC-EVs enhanced the tube formation and migration of human umbilical vein endothelial cells (HUVECs), improved the cell viability, and attenuated the lactate dehydrogenase release of neonatal rat cardiomyocytes (NRCMs) with oxygen glucose deprivation (OGD) injury. Moreover, the improvement of the EV-H in cardiomyocyte survival and tube formation of HUVECs was significantly better than these in the EV-N. RNA-seq analysis revealed a high abundance of the lncRNA MALAT1 in the EV-H. Its abundance was upregulated in the infarcted myocardium and cardiomyocytes treated with hCVPC-EVs. Overexpression of human MALAT1 improved the cell viability of NRCM with OGD injury, while knockdown of MALAT1 inhibited the hCVPC-EV-promoted tube formation of HUVECs. Furthermore, luciferase activity assay, RNA pull-down, and manipulation of miR-497 levels showed that MALAT1 improved NRCMs survival and HUVEC tube formation through targeting miR-497. These results reveal that hCVPC-EVs promote the infarct healing through improvement of cardiomyocyte survival and angiogenesis. The cardioprotective effects of hCVPC-EVs can be enhanced by hypoxia-conditioning of hCVPCs and are partially contributed by MALAT1 via targeting the miRNA.


Extracellular Vesicles/transplantation , Human Embryonic Stem Cells/transplantation , Myocardial Infarction/surgery , Myocardium/metabolism , Myocytes, Cardiac/transplantation , Ventricular Function, Left , Ventricular Remodeling , Animals , Cell Hypoxia , Cell Line , Disease Models, Animal , Extracellular Vesicles/metabolism , Extracellular Vesicles/ultrastructure , Fibrosis , Human Embryonic Stem Cells/metabolism , Human Embryonic Stem Cells/ultrastructure , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Male , Mice, Inbred C57BL , MicroRNAs/genetics , MicroRNAs/metabolism , Myocardial Infarction/metabolism , Myocardial Infarction/pathology , Myocardial Infarction/physiopathology , Myocardium/pathology , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/ultrastructure , Neovascularization, Physiologic , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Recovery of Function
13.
Circulation ; 139(16): 1937-1956, 2019 04 16.
Article En | MEDLINE | ID: mdl-30717603

BACKGROUND: The human genome folds in 3 dimensions to form thousands of chromatin loops inside the nucleus, encasing genes and cis-regulatory elements for accurate gene expression control. Physical tethers of loops are anchored by the DNA-binding protein CTCF and the cohesin ring complex. Because heart failure is characterized by hallmark gene expression changes, it was recently reported that substantial CTCF-related chromatin reorganization underpins the myocardial stress-gene response, paralleled by chromatin domain boundary changes observed in CTCF knockout. METHODS: We undertook an independent and orthogonal analysis of chromatin organization with mouse pressure-overload model of myocardial stress (transverse aortic constriction) and cardiomyocyte-specific knockout of Ctcf. We also downloaded published data sets of similar cardiac mouse models and subjected them to independent reanalysis. RESULTS: We found that the cardiomyocyte chromatin architecture remains broadly stable in transverse aortic constriction hearts, whereas Ctcf knockout resulted in ≈99% abolition of global chromatin loops. Disease gene expression changes correlated instead with differential histone H3K27-acetylation enrichment at their respective proximal and distal interacting genomic enhancers confined within these static chromatin structures. Moreover, coregulated genes were mapped out as interconnected gene sets on the basis of their multigene 3D interactions. CONCLUSIONS: This work reveals a more stable genome-wide chromatin framework than previously described. Myocardial stress-gene transcription responds instead through H3K27-acetylation enhancer enrichment dynamics and gene networks of coregulation. Robust and intact CTCF looping is required for the induction of a rapid and accurate stress response.


Aortic Valve Stenosis/genetics , CCCTC-Binding Factor/metabolism , Chromatin/metabolism , Heart Failure/genetics , Myocytes, Cardiac/physiology , Acetylation , Animals , CCCTC-Binding Factor/genetics , Cells, Cultured , Chromatin Assembly and Disassembly , Disease Models, Animal , Epigenesis, Genetic , Gene Expression Regulation , Gene Ontology , Gene Regulatory Networks , Histones/metabolism , Humans , Mice , Mice, Inbred C57BL , Mice, Knockout , Stress, Physiological
14.
Nat Commun ; 8(1): 225, 2017 08 09.
Article En | MEDLINE | ID: mdl-28790305

Cardiac regeneration may revolutionize treatment for heart failure but endogenous progenitor-derived cardiomyocytes in the adult mammalian heart are few and pre-existing adult cardiomyocytes divide only at very low rates. Although candidate genes that control cardiomyocyte cell cycle re-entry have been implicated, expression heterogeneity in the cardiomyocyte stress-response has never been explored. Here, we show by single nuclear RNA-sequencing of cardiomyocytes from both mouse and human failing, and non-failing adult hearts that sub-populations of cardiomyocytes upregulate cell cycle activators and inhibitors consequent to the stress-response in vivo. We characterize these subgroups by weighted gene co-expression network analysis and discover long intergenic non-coding RNAs (lincRNA) as key nodal regulators. KD of nodal lincRNAs affects expression levels of genes related to dedifferentiation and cell cycle, within the same gene regulatory network. Our study reveals that sub-populations of adult cardiomyocytes may have a unique endogenous potential for cardiac regeneration in vivo.Adult mammalian cardiomyocytes are predominantly binucleated and unable to divide. Using single nuclear RNA-sequencing of cardiomyocytes from mouse and human failing and non-failing adult hearts, See et al. show that some cardiomyocytes respond to stress by dedifferentiation and cell cycle re-entry regulated by lncRNAs.


Cell Cycle , Cell Dedifferentiation , Gene Expression Regulation , Heart Failure/genetics , Myocytes, Cardiac/cytology , Nodal Protein/genetics , RNA, Long Noncoding/metabolism , Animals , Gene Regulatory Networks , Heart Failure/metabolism , Heart Failure/physiopathology , Humans , Male , Mice , Mice, Inbred C57BL , Myocytes, Cardiac/metabolism , RNA, Long Noncoding/genetics , Stress, Physiological , Transcriptome
15.
Mol Cancer Ther ; 16(9): 2035-2044, 2017 09.
Article En | MEDLINE | ID: mdl-28533437

There is increasing preclinical evidence suggesting that metformin, an antidiabetic drug, has anticancer properties against various malignancies, including colorectal cancer. However, the majority of evidence, which was derived from cancer cell lines and xenografts, was likely to overestimate the benefit of metformin because these models are inadequate and require supraphysiologic levels of metformin. Here, we generated patient-derived xenograft (PDX) lines from 2 colorectal cancer patients to assess the properties of metformin and 5-fluorouracil (5-FU), the first-line drug treatment for colorectal cancer. Metformin (150 mg/kg) as a single agent inhibits the growth of both PDX tumors by at least 50% (P < 0.05) when administered orally for 24 days. In one of the PDX models, metformin given concurrently with 5-FU (25 mg/kg) leads to an 85% (P = 0.054) growth inhibition. Ex vivo culture of organoids generated from PDX demonstrates that metformin inhibits growth by executing metabolic changes to decrease oxygen consumption and activating AMPK-mediated pathways. In addition, we also performed genetic characterizations of serial PDX samples with corresponding parental tissues from patients using next-generation sequencing (NGS). Our pilot NGS study demonstrates that PDX represents a useful platform for analysis in cancer research because it demonstrates high fidelity with parental tumor. Furthermore, NGS analysis of PDX may be useful to determine genetic identifiers of drug response. This is the first preclinical study using PDX and PDX-derived organoids to investigate the efficacy of metformin in colorectal cancer. Mol Cancer Ther; 16(9); 2035-44. ©2017 AACR.


Antineoplastic Agents/pharmacology , Colorectal Neoplasms/metabolism , Energy Metabolism/drug effects , Hypoglycemic Agents/pharmacology , Metformin/pharmacology , Animals , Biomarkers , Cell Line, Tumor , Cell Proliferation/drug effects , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , DNA Mutational Analysis , Disease Models, Animal , Female , Fluorouracil/pharmacology , Humans , MAP Kinase Signaling System/drug effects , Mice , Microsatellite Instability , Mutation , Oxygen Consumption/drug effects , Tumor Suppressor Protein p53/genetics , Xenograft Model Antitumor Assays
16.
Oncol Lett ; 13(3): 1625-1630, 2017 Mar.
Article En | MEDLINE | ID: mdl-28454300

Although bulk high-throughput genomic profiling studies have led to a significant increase in the understanding of cancer biology, there is increasing awareness that bulk profiling approaches do not completely elucidate tumor heterogeneity. Single-cell genomic profiling enables the distinction of tumor heterogeneity, and may improve clinical diagnosis through the identification and characterization of putative subclonal populations. In the present study, the challenges associated with a single-cell genomics profiling workflow for clinical diagnostics were investigated. Single-cell RNA-sequencing (RNA-seq) was performed on 20 cells from an acute myeloid leukemia bone marrow sample. Putative blasts were identified based on their gene expression profiles and principal component analysis was performed to identify outlier cells. Variant calling was performed on the single-cell RNA-seq data. The present pilot study demonstrates a proof of concept for clinical single-cell genomic profiling. The recognized limitations include significant stochastic RNA loss and the relatively low throughput of the current proposed platform. Although the results of the present study are promising, further technological advances and protocol optimization are necessary for single-cell genomic profiling to be clinically viable.

17.
Nat Commun ; 8: 4565, 2017 02 27.
Article En | MEDLINE | ID: mdl-28240289

Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.


Carcinoma, Hepatocellular/pathology , Liver Neoplasms/pathology , Biopsy , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/virology , DNA Copy Number Variations/genetics , Genome, Human , Humans , Liver/pathology , Liver/virology , Liver Neoplasms/genetics , Liver Neoplasms/virology , Mutation/genetics , Neoplasm Metastasis , Phenotype , Phylogeny , Sequence Analysis, DNA , Virus Integration
18.
Cardiovasc Res ; 113(3): 298-309, 2017 03 01.
Article En | MEDLINE | ID: mdl-28082450

Aims: Circular RNA (circRNA) is a newly validated class of single-stranded RNA, ubiquitously expressed in mammalian tissues and possessing key functions including acting as microRNA sponges and as transcriptional regulators by binding to RNA-binding proteins. While independent studies confirm the expression of circRNA in various tissue types, genome-wide circRNA expression in the heart has yet to be described in detail. Methods and results: We performed deep RNA-sequencing on ribosomal-depleted RNA isolated from 12 human hearts, 25 mouse hearts and across a 28-day differentiation time-course of human embryonic stem cell-derived cardiomyocytes. Using purpose-designed bioinformatics tools, we uncovered a total of 15 318 and 3017 cardiac circRNA within human and mouse, respectively. Their abundance generally correlates with the abundance of their cognate linear RNA, but selected circRNAs exist at disproportionately higher abundance. Top highly expressed circRNA corresponded to key cardiac genes including Titin (TTN), RYR2, and DMD. The most abundant cardiac-expressed circRNA is a cytoplasmic localized single-exon circSLC8A1-1. The longest human transcript TTN alone generates up to 415 different exonic circRNA isoforms, the majority (83%) of which originates from the I-band domain. Finally, we confirmed the expression of selected cardiac circRNA by RT-PCR, Sanger sequencing and single molecule RNA-fluorescence in situ hybridization. Conclusions: Our data provide a detailed circRNA expression landscape in hearts. There is a high-abundance of specific cardiac-expressed circRNA. These findings open up a new avenue for future investigation into this emerging class of RNA.


Embryonic Stem Cells/metabolism , Heart Diseases/genetics , Myocytes, Cardiac/metabolism , RNA/genetics , Animals , Case-Control Studies , Cell Differentiation , Cell Line , Computational Biology , Databases, Genetic , Gene Expression Regulation, Developmental , Genetic Association Studies , Genetic Markers , Genetic Predisposition to Disease , Heart Diseases/diagnosis , High-Throughput Nucleotide Sequencing , Humans , In Situ Hybridization, Fluorescence , Mice , Phenotype , Polymerase Chain Reaction , RNA/metabolism , RNA, Circular , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sequence Analysis, RNA , Single Molecule Imaging , Time Factors
19.
EBioMedicine ; 5: 211-6, 2016 Mar.
Article En | MEDLINE | ID: mdl-27077130

BACKGROUND: In Western cohorts, the prevalence of incidental findings (IFs) or incidentalome, referring to variants in genes that are unrelated to the patient's primary condition, is between 0.86% and 8.8%. However, data on prevalence and type of IFs in Asian population is lacking. METHODS: In 2 cohorts of individuals with genomic sequencing performed in Singapore (total n = 377), we extracted and annotated variants in the 56 ACMG-recommended genes and filtered these variants based on the level of pathogenicity. We then analyzed the precise distribution of IFs, class of genes, related medical conditions, and potential clinical impact. RESULTS: We found a total of 41,607 variants in the 56 genes in our cohort of 377 individuals. After filtering for rare and coding variants, we identified 14 potential variants. After reviewing primary literature, only 4 out of the 14 variants were classified to be pathogenic, while an additional two variants were classified as likely pathogenic. Overall, the cumulative prevalence of IFs (pathogenic and likely pathogenic variants) in our cohort was 1.6%. CONCLUSION: The cumulative prevalence of IFs through genomic sequencing is low and the incidentalome may not be a significant barrier to implementation of genomics for personalized medicine.


Genetic Variation , Genome, Human , Incidental Findings , Precision Medicine , Chromosome Mapping , Databases, Genetic , Exome/genetics , Genomics , High-Throughput Nucleotide Sequencing , Humans , Molecular Sequence Annotation , Mutation , Singapore
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