1
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Witman N, Zhou C, Häneke T, Xiao Y, Huang X, Rohner E, Sohlmér J, Grote Beverborg N, Lehtinen ML, Chien KR, Sahara M. Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development. Nat Commun 2023; 14:5435. [PMID: 37669989 PMCID: PMC10480216 DOI: 10.1038/s41467-023-41305-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/30/2023] [Indexed: 09/07/2023] Open
Abstract
Cardiogenic growth factors play important roles in heart development. Placental growth factor (PLGF) has previously been reported to have angiogenic effects; however, its potential role in cardiogenesis has not yet been determined. We analyze single-cell RNA-sequencing data derived from human and primate embryonic hearts and find PLGF shows a biphasic expression pattern, as it is expressed specifically on ISL1+ second heart field progenitors at an earlier stage and on vascular smooth muscle cells (SMCs) and endothelial cells (ECs) at later stages. Using chemically modified mRNAs (modRNAs), we generate a panel of cardiogenic growth factors and test their effects on enhancing cardiomyocyte (CM) and EC induction during different stages of human embryonic stem cell (hESC) differentiations. We discover that only the application of PLGF modRNA at early time points of hESC-CM differentiation can increase both CM and EC production. Conversely, genetic deletion of PLGF reduces generation of CMs, SMCs and ECs in vitro. We also confirm in vivo beneficial effects of PLGF modRNA for development of human heart progenitor-derived cardiac muscle grafts on murine kidney capsules. Further, we identify the previously unrecognized PLGF-related transcriptional networks driven by EOMES and SOX17. These results shed light on the dual cardiomyogenic and vasculogenic effects of PLGF during heart development.
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Affiliation(s)
- Nevin Witman
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
| | - Chikai Zhou
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
| | - Timm Häneke
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
| | - Yao Xiao
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
| | - Xiaoting Huang
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
| | - Eduarde Rohner
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
| | - Jesper Sohlmér
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
| | - Niels Grote Beverborg
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Miia L Lehtinen
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden
- Department of Cardiac Surgery, Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden.
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institutet, A6 Biomedicum, SE-171 77, Stockholm, Sweden.
- Department of Surgery, Yale University School of Medicine, 333 Cedar Street, New Haven, CN, 06510, USA.
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2
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Ho BX, Pang JKS, Chen Y, Loh YH, An O, Yang HH, Seshachalam VP, Koh JLY, Chan WK, Ng SY, Soh BS. Robust generation of human-chambered cardiac organoids from pluripotent stem cells for improved modelling of cardiovascular diseases. Stem Cell Res Ther 2022; 13:529. [PMID: 36544188 PMCID: PMC9773542 DOI: 10.1186/s13287-022-03215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Tissue organoids generated from human pluripotent stem cells are valuable tools for disease modelling and to understand developmental processes. While recent progress in human cardiac organoids revealed the ability of these stem cell-derived organoids to self-organize and intrinsically formed chamber-like structure containing a central cavity, it remained unclear the processes involved that enabled such chamber formation. METHODS Chambered cardiac organoids (CCOs) differentiated from human embryonic stem cells (H7) were generated by modulation of Wnt/ß-catenin signalling under fully defined conditions, and several growth factors essential for cardiac progenitor expansion. Transcriptomic profiling of day 8, day 14 and day 21 CCOs was performed by quantitative PCR and single-cell RNA sequencing. Endothelin-1 (EDN1) known to induce oxidative stress in cardiomyocytes was used to induce cardiac hypertrophy in CCOs in vitro. Functional characterization of cardiomyocyte contractile machinery was performed by immunofluorescence staining and analysis of brightfield and fluorescent video recordings. Quantitative PCR values between groups were compared using two-tailed Student's t tests. Cardiac organoid parameters comparison between groups was performed using two-tailed Mann-Whitney U test when sample size is small; otherwise, Welch's t test was used. Comparison of calcium kinetics parameters derived from the fluorescent data was performed using two-tailed Student's t tests. RESULTS Importantly, we demonstrated that a threshold number of cardiac progenitor was essential to line the circumference of the inner cavity to ensure proper formation of a chamber within the organoid. Single-cell RNA sequencing revealed improved maturation over a time course, as evidenced from increased mRNA expression of cardiomyocyte maturation genes, ion channel genes and a metabolic shift from glycolysis to fatty acid ß-oxidation. Functionally, CCOs recapitulated clinical cardiac hypertrophy by exhibiting thickened chamber walls, reduced fractional shortening, and increased myofibrillar disarray upon treatment with EDN1. Furthermore, electrophysiological assessment of calcium transients displayed tachyarrhythmic phenotype observed as a consequence of rapid depolarization occurring prior to a complete repolarization. CONCLUSIONS Our findings shed novel insights into the role of progenitors in CCO formation and pave the way for the robust generation of cardiac organoids, as a platform for future applications in disease modelling and drug screening in vitro.
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Affiliation(s)
- Beatrice Xuan Ho
- grid.418812.60000 0004 0620 9243Disease Modelling and Therapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
| | - Jeremy Kah Sheng Pang
- grid.418812.60000 0004 0620 9243Disease Modelling and Therapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
| | - Ying Chen
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore ,grid.4280.e0000 0001 2180 6431Integrative Sciences and Engineering Programme, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077 Singapore ,grid.418812.60000 0004 0620 9243Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore
| | - Yuin-Han Loh
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore ,grid.418812.60000 0004 0620 9243Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore
| | - Omer An
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599 Singapore
| | - Henry He Yang
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599 Singapore
| | - Veerabrahma Pratap Seshachalam
- grid.510300.7Computational Phenomics Group, Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, 138670 Singapore
| | - Judice L. Y. Koh
- grid.510300.7Computational Phenomics Group, Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, 138670 Singapore
| | - Woon-Khiong Chan
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
| | - Shi Yan Ng
- grid.418812.60000 0004 0620 9243Neurotherapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117456 Singapore ,grid.276809.20000 0004 0636 696XNational Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433 Singapore
| | - Boon Seng Soh
- grid.418812.60000 0004 0620 9243Disease Modelling and Therapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
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Panfilio KA, Chuva de Sousa Lopes SM. The extended analogy of extraembryonic development in insects and amniotes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210268. [PMID: 36252225 PMCID: PMC9574626 DOI: 10.1098/rstb.2021.0268] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/14/2022] [Indexed: 12/22/2022] Open
Abstract
It is fascinating that the amnion and serosa/chorion, two extraembryonic (EE) tissues that are characteristic of the amniote vertebrates (mammals, birds and reptiles), have also independently evolved in insects. In this review, we offer the first detailed, macroevolutionary comparison of EE development and tissue biology across these animal groups. Some commonalities represent independent solutions to shared challenges for protecting the embryo (environmental assaults, risk of pathogens) and supporting its development, including clear links between cellular properties (e.g. polyploidy) and physiological function. Further parallels encompass developmental features such as the early segregation of the serosa/chorion compared to later, progressive differentiation of the amnion and formation of the amniotic cavity from serosal-amniotic folds as a widespread morphogenetic mode across species. We also discuss common developmental roles for orthologous transcription factors and BMP signalling in EE tissues of amniotes and insects, and between EE and cardiac tissues, supported by our exploration of new resources for global and tissue-specific gene expression. This highlights the degree to which general developmental principles and protective tissue features can be deduced from each of these animal groups, emphasizing the value of broad comparative studies to reveal subtle developmental strategies and answer questions that are common across species. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
| | - Susana M. Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Department for Reproductive Medicine, Ghent University Hospital, 9000 Ghent, Belgium
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4
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Morton SU, Quiat D, Seidman JG, Seidman CE. Genomic frontiers in congenital heart disease. Nat Rev Cardiol 2022; 19:26-42. [PMID: 34272501 PMCID: PMC9236191 DOI: 10.1038/s41569-021-00587-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The application of next-generation sequencing to study congenital heart disease (CHD) is increasingly providing new insights into the causes and mechanisms of this prevalent birth anomaly. Whole-exome sequencing analysis identifies damaging gene variants altering single or contiguous nucleotides that are assigned pathogenicity based on statistical analyses of families and cohorts with CHD, high expression in the developing heart and depletion of damaging protein-coding variants in the general population. Gene classes fulfilling these criteria are enriched in patients with CHD and extracardiac abnormalities, evidencing shared pathways in organogenesis. Developmental single-cell transcriptomic data demonstrate the expression of CHD-associated genes in particular cell lineages, and emerging insights indicate that genetic variants perturb multicellular interactions that are crucial for cardiogenesis. Whole-genome sequencing analyses extend these observations, identifying non-coding variants that influence the expression of genes associated with CHD and contribute to the estimated ~55% of unexplained cases of CHD. These approaches combined with the assessment of common and mosaic genetic variants have provided a more complete knowledge of the causes and mechanisms of CHD. Such advances provide knowledge to inform the clinical care of patients with CHD or other birth defects and deepen our understanding of the complexity of human development. In this Review, we highlight known and candidate CHD-associated human genes and discuss how the integration of advances in developmental biology research can provide new insights into the genetic contributions to CHD.
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Affiliation(s)
- Sarah U. Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard University, Boston, MA, USA.,
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5
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Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer. Genes (Basel) 2021; 12:genes12050615. [PMID: 33919200 PMCID: PMC8143155 DOI: 10.3390/genes12050615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 01/19/2023] Open
Abstract
Alternative splicing (AS) is tightly regulated to maintain genomic stability in humans. However, tumor growth, metastasis and therapy resistance benefit from aberrant RNA splicing. Iroquois-class homeodomain protein 4 (IRX4) is a TALE homeobox transcription factor which has been implicated in prostate cancer (PCa) as a tumor suppressor through genome-wide association studies (GWAS) and functional follow-up studies. In the current study, we characterized 12 IRX4 transcripts in PCa cell lines, including seven novel transcripts by RT-PCR and sequencing. They demonstrate unique expression profiles between androgen-responsive and nonresponsive cell lines. These transcripts were significantly overexpressed in PCa cell lines and the cancer genome atlas program (TCGA) PCa clinical specimens, suggesting their probable involvement in PCa progression. Moreover, a PCa risk-associated SNP rs12653946 genotype GG was corelated with lower IRX4 transcript levels. Using mass spectrometry analysis, we identified two IRX4 protein isoforms (54.4 kDa, 57 kDa) comprising all the functional domains and two novel isoforms (40 kDa, 8.7 kDa) lacking functional domains. These IRX4 isoforms might induce distinct functional programming that could contribute to PCa hallmarks, thus providing novel insights into diagnostic, prognostic and therapeutic significance in PCa management.
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6
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Peng Y, Pang J, Hu J, Jia Z, Xi H, Ma N, Yang S, Liu J, Huang X, Tang C, Wang H. Clinical and molecular characterization of 12 prenatal cases of Cri-du-chat syndrome. Mol Genet Genomic Med 2020; 8:e1312. [PMID: 32500674 PMCID: PMC7434726 DOI: 10.1002/mgg3.1312] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Background This study aimed to define the molecular basis for 12 prenatal cases of Cri‐du‐chat syndrome (CdCS) and the potential genotyping‐phenotyping association. Methods Karyotyping and single nucleotide polymorphism array analyses for copy number variants were performed. Results Nine cases had 5p terminal deletions and three had 5p interstitial deletions, and these cases had variable deletion sizes with partial overlapping. Phenotypically, besides intrauterine growth restriction (IUGR) and brain as well as heart abnormalities, hypospadias, and lung dysplasia were observed. Potential genetic causes for specific phenotypes in these cases were identified. Conclusion This study defined the molecular bases for the patients of CdCS, which is important for genetic counseling for these families. The findings of present study expand the clinical features of CdCS in the fetal period, and provided important information for further refining the genotypic–phenotypic correlations for this syndrome.
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Affiliation(s)
- Ying Peng
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Jialun Pang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Jiancheng Hu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Zhengjun Jia
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Hui Xi
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Na Ma
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Shuting Yang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Jing Liu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Xiaoliang Huang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Chengyuan Tang
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
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7
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Zhang Z, Nam YJ. Analysis of Cardiac Chamber Development During Mouse Embryogenesis Using Whole Mount Epifluorescence. J Vis Exp 2019. [PMID: 31058904 DOI: 10.3791/59413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The goal of this protocol is to describe a method for the dissection of mouse embryos and visualization of embryonic mouse ventricular chambers during heart development using ventricular specific fluorescent reporter knock-in mice (MLC-2v-tdTomato mice). Heart development involves a linear heart tube formation, the heart tube looping, and four chamber septation. These complex processes are highly conserved in all vertebrates. The mouse embryonic heart has been widely used for heart developmental studies. However, due to their extremely small size, dissecting mouse embryonic hearts is technically challenging. In addition, visualization of cardiac chamber formation often needs in situ hybridization, beta-galactosidase staining using LacZ reporter mice, or immunostaining of sectioned embryonic hearts. Here, we describe how to dissect mouse embryonic hearts and directly visualize ventricular chamber formation of MLC-2v-tdTomato mice using whole mount epifluorescent microscopy. With this method, it is possible to directly examine heart tube formation and looping, and four chamber formation without further experimental manipulation of mouse embryos. Although the MLC-2v-tdTomato reporter knock-in mouse line is used in this protocol as an example, this protocol can be applied to other heart-specific fluorescent reporter transgenic mouse lines.
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Affiliation(s)
- Zhentao Zhang
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center; Department of Cell and Developmental Biology, Vanderbilt University; Vanderbilt Center for Stem Cell Biology, Vanderbilt University
| | - Young-Jae Nam
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center; Department of Cell and Developmental Biology, Vanderbilt University; Vanderbilt Center for Stem Cell Biology, Vanderbilt University;
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8
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Cri-du-Chat Syndrome interactome network: Correlating genotypic variations to associated phenotypes. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Abstract
Reprogramming the human genome toward any desirable state is within reach; application of select transcription factors drives cell types toward different lineages in many settings. We introduce the concept of data-guided control in building a universal algorithm for directly reprogramming any human cell type into any other type. Our algorithm is based on time series genome transcription and architecture data and known regulatory activities of transcription factors, with natural dimension reduction using genome architectural features. Our algorithm predicts known reprogramming factors, top candidates for new settings, and ideal timing for application of transcription factors. This framework can be used to develop strategies for tissue regeneration, cancer cell reprogramming, and control of dynamical systems beyond cell biology. The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton’s laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control. We construct an approximate model for the natural evolution of a cell-cycle–synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points during the cell cycle. To arrive at a model of moderate complexity, we cluster gene expression based on division of the genome into topologically associating domains (TADs) and then model the dynamics of TAD expression levels. Based on this dynamical model and additional data, such as known TF binding sites and activity, we develop a methodology for identifying the top TF candidates for a specific cellular reprogramming task. Our data-guided methodology identifies a number of TFs previously validated for reprogramming and/or natural differentiation and predicts some potentially useful combinations of TFs. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes.
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10
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Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest. Proc Natl Acad Sci U S A 2017; 114:E8372-E8381. [PMID: 28916735 DOI: 10.1073/pnas.1707316114] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mammalian heart undergoes maturation during postnatal life to meet the increased functional requirements of an adult. However, the key drivers of this process remain poorly defined. We are currently unable to recapitulate postnatal maturation in human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs), limiting their potential as a model system to discover regenerative therapeutics. Here, we provide a summary of our studies, where we developed a 96-well device for functional screening in human pluripotent stem cell-derived cardiac organoids (hCOs). Through interrogation of >10,000 organoids, we systematically optimize parameters, including extracellular matrix (ECM), metabolic substrate, and growth factor conditions, that enhance cardiac tissue viability, function, and maturation. Under optimized maturation conditions, functional and molecular characterization revealed that a switch to fatty acid metabolism was a central driver of cardiac maturation. Under these conditions, hPSC-CMs were refractory to mitogenic stimuli, and we found that key proliferation pathways including β-catenin and Yes-associated protein 1 (YAP1) were repressed. This proliferative barrier imposed by fatty acid metabolism in hCOs could be rescued by simultaneous activation of both β-catenin and YAP1 using genetic approaches or a small molecule activating both pathways. These studies highlight that human organoids coupled with higher-throughput screening platforms have the potential to rapidly expand our knowledge of human biology and potentially unlock therapeutic strategies.
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11
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Nelson DO, Lalit PA, Biermann M, Markandeya YS, Capes DL, Addesso L, Patel G, Han T, John MC, Powers PA, Downs KM, Kamp TJ, Lyons GE. Irx4 Marks a Multipotent, Ventricular-Specific Progenitor Cell. Stem Cells 2016; 34:2875-2888. [PMID: 27570947 DOI: 10.1002/stem.2486] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/18/2016] [Indexed: 12/11/2022]
Abstract
While much progress has been made in the resolution of the cellular hierarchy underlying cardiogenesis, our understanding of chamber-specific myocardium differentiation remains incomplete. To better understand ventricular myocardium differentiation, we targeted the ventricle-specific gene, Irx4, in mouse embryonic stem cells to generate a reporter cell line. Using an antibiotic-selection approach, we purified Irx4+ cells in vitro from differentiating embryoid bodies. The isolated Irx4+ cells proved to be highly proliferative and presented Cxcr4, Pdgfr-alpha, Flk1, and Flt1 on the cell surface. Single Irx4+ ventricular progenitor cells (VPCs) exhibited cardiovascular potency, generating endothelial cells, smooth muscle cells, and ventricular myocytes in vitro. The ventricular specificity of the Irx4+ population was further demonstrated in vivo as VPCs injected into the cardiac crescent subsequently produced Mlc2v+ myocytes that exclusively contributed to the nascent ventricle at E9.5. These findings support the existence of a newly identified ventricular myocardial progenitor. This is the first report of a multipotent cardiac progenitor that contributes progeny specific to the ventricular myocardium. Stem Cells 2016;34:2875-2888.
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Affiliation(s)
- Daryl O Nelson
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Pratik A Lalit
- Department of Medicine, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mitch Biermann
- Department of Medicine, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yogananda S Markandeya
- Department of Medicine, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Deborah L Capes
- Department of Medicine, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Luke Addesso
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Gina Patel
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Tianxiao Han
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Manorama C John
- University of Wisconsin Biotechnology Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Patricia A Powers
- University of Wisconsin Biotechnology Center, University of Wisconsin, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Karen M Downs
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,Department of Medicine, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gary E Lyons
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Hartman ME, Dai DF, Laflamme MA. Human pluripotent stem cells: Prospects and challenges as a source of cardiomyocytes for in vitro modeling and cell-based cardiac repair. Adv Drug Deliv Rev 2016; 96:3-17. [PMID: 25980938 DOI: 10.1016/j.addr.2015.05.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/27/2015] [Accepted: 05/07/2015] [Indexed: 12/13/2022]
Abstract
Human pluripotent stem cells (PSCs) represent an attractive source of cardiomyocytes with potential applications including disease modeling, drug discovery and safety screening, and novel cell-based cardiac therapies. Insights from embryology have contributed to the development of efficient, reliable methods capable of generating large quantities of human PSC-cardiomyocytes with cardiac purities ranging up to 90%. However, for human PSCs to meet their full potential, the field must identify methods to generate cardiomyocyte populations that are uniform in subtype (e.g. homogeneous ventricular cardiomyocytes) and have more mature structural and functional properties. For in vivo applications, cardiomyocyte production must be highly scalable and clinical grade, and we will need to overcome challenges including graft cell death, immune rejection, arrhythmogenesis, and tumorigenic potential. Here we discuss the types of human PSCs, commonly used methods to guide their differentiation into cardiomyocytes, the phenotype of the resultant cardiomyocytes, and the remaining obstacles to their successful translation.
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Kokkinopoulos I, Ishida H, Saba R, Ruchaya P, Cabrera C, Struebig M, Barnes M, Terry A, Kaneko M, Shintani Y, Coppen S, Shiratori H, Ameen T, Mein C, Hamada H, Suzuki K, Yashiro K. Single-Cell Expression Profiling Reveals a Dynamic State of Cardiac Precursor Cells in the Early Mouse Embryo. PLoS One 2015; 10:e0140831. [PMID: 26469858 PMCID: PMC4607431 DOI: 10.1371/journal.pone.0140831] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/29/2015] [Indexed: 01/07/2023] Open
Abstract
In the early vertebrate embryo, cardiac progenitor/precursor cells (CPs) give rise to cardiac structures. Better understanding their biological character is critical to understand the heart development and to apply CPs for the clinical arena. However, our knowledge remains incomplete. With the use of single-cell expression profiling, we have now revealed rapid and dynamic changes in gene expression profiles of the embryonic CPs during the early phase after their segregation from the cardiac mesoderm. Progressively, the nascent mesodermal gene Mesp1 terminated, and Nkx2-5+/Tbx5+ population rapidly replaced the Tbx5low+ population as the expression of the cardiac genes Tbx5 and Nkx2-5 increased. At the Early Headfold stage, Tbx5-expressing CPs gradually showed a unique molecular signature with signs of cardiomyocyte differentiation. Lineage-tracing revealed a developmentally distinct characteristic of this population. They underwent progressive differentiation only towards the cardiomyocyte lineage corresponding to the first heart field rather than being maintained as a progenitor pool. More importantly, Tbx5 likely plays an important role in a transcriptional network to regulate the distinct character of the FHF via a positive feedback loop to activate the robust expression of Tbx5 in CPs. These data expands our knowledge on the behavior of CPs during the early phase of cardiac development, subsequently providing a platform for further study.
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Affiliation(s)
- Ioannis Kokkinopoulos
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Hidekazu Ishida
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Rie Saba
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Prashant Ruchaya
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Physiology and Pathology, University of São Paulo State – UNESP, Araraquara School of Dentistry, Araraquara, São Paulo, Brazil
| | - Claudia Cabrera
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Monika Struebig
- Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Michael Barnes
- Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Anna Terry
- Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Masahiro Kaneko
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Yasunori Shintani
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Steven Coppen
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Hidetaka Shiratori
- Department of Developmental Genetics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Torath Ameen
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Charles Mein
- Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Hiroshi Hamada
- Department of Developmental Genetics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Ken Suzuki
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Kenta Yashiro
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- * E-mail:
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Bhattacharya S, Burridge PW, Kropp EM, Chuppa SL, Kwok WM, Wu JC, Boheler KR, Gundry RL. High efficiency differentiation of human pluripotent stem cells to cardiomyocytes and characterization by flow cytometry. J Vis Exp 2014:52010. [PMID: 25286293 DOI: 10.3791/52010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
There is an urgent need to develop approaches for repairing the damaged heart, discovering new therapeutic drugs that do not have toxic effects on the heart, and improving strategies to accurately model heart disease. The potential of exploiting human induced pluripotent stem cell (hiPSC) technology to generate cardiac muscle "in a dish" for these applications continues to generate high enthusiasm. In recent years, the ability to efficiently generate cardiomyogenic cells from human pluripotent stem cells (hPSCs) has greatly improved, offering us new opportunities to model very early stages of human cardiac development not otherwise accessible. In contrast to many previous methods, the cardiomyocyte differentiation protocol described here does not require cell aggregation or the addition of Activin A or BMP4 and robustly generates cultures of cells that are highly positive for cardiac troponin I and T (TNNI3, TNNT2), iroquois-class homeodomain protein IRX-4 (IRX4), myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC2v) and myosin regulatory light chain 2, atrial isoform (MLC2a) by day 10 across all human embryonic stem cell (hESC) and hiPSC lines tested to date. Cells can be passaged and maintained for more than 90 days in culture. The strategy is technically simple to implement and cost-effective. Characterization of cardiomyocytes derived from pluripotent cells often includes the analysis of reference markers, both at the mRNA and protein level. For protein analysis, flow cytometry is a powerful analytical tool for assessing quality of cells in culture and determining subpopulation homogeneity. However, technical variation in sample preparation can significantly affect quality of flow cytometry data. Thus, standardization of staining protocols should facilitate comparisons among various differentiation strategies. Accordingly, optimized staining protocols for the analysis of IRX4, MLC2v, MLC2a, TNNI3, and TNNT2 by flow cytometry are described.
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Affiliation(s)
| | - Paul W Burridge
- Stanford Cardiovascular Institute, Stanford University School of Medicine
| | - Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin
| | | | - Wai-Meng Kwok
- Department of Anesthesiology, Medical College of Wisconsin
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine
| | - Kenneth R Boheler
- Stem Cell and Regenerative Medicine Consortium, LKS Faculty of Medicine, Hong Kong University; Division of Cardiology, Johns Hopkins University School of Medicine
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin; Cardiovascular Research Center, Biotechnology and Bioengineering Center, Medical College of Wisconsin;
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