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Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579143. [PMID: 38370833 PMCID: PMC10871202 DOI: 10.1101/2024.02.06.579143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining in situ polyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.
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Affiliation(s)
- Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Dingyao Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Tao
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shuozhen Bao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Xiaolong Tian
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Ningning Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yang Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mina L. Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology, Yale University School of Medicine, New Haven, CT 06520, USA
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Personalized Medicine Approach in a DCM Patient with LMNA Mutation Reveals Dysregulation of mTOR Signaling. J Pers Med 2022; 12:jpm12071149. [PMID: 35887646 PMCID: PMC9323361 DOI: 10.3390/jpm12071149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Mutations in the Lamin A/C (LMNA) gene are responsible for about 6% of all familial dilated cardiomyopathy (DCM) cases which tend to present at a young age and follow a fulminant course. Methods: We report a 47-year-old DCM patient with severely impaired left ventricular ejection fraction and NYHA functional class IV despite optimal heart failure treatment. Whole-exome sequencing revealed an LMNA E161K missense mutation as the pathogenetic cause for DCM in this patient. We generated a patient-specific LMNA-knock in (LMNA-KI) in vitro model using mES cells. Results: Beta adrenergic stimulation of cardiomyocytes derived from LMNA-KI mES cells resulted in augmented mTOR signaling and increased dysregulation of action potentials, which could be effectively prevented by the mTOR-inhibitor rapamycin. A cardiac biopsy confirmed strong activation of the mTOR-signaling pathway in the patient. An off-label treatment with oral rapamycin was initiated and resulted in an improvement in left ventricular ejection fraction (27.8% to 44.5%), NT-BNP (8120 ng/L to 2210 ng/L) and NYHA functional class. Conclusion: We have successfully generated the first in vitro model to recapitulate a patient-specific LMNA E161K mutation which leads to a severe form of DCM. The model may serve as a template for individualized and specific treatment of heart failure.
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Dessouki FBA, Singal PK, Singla DK. Rat-Induced Pluripotent Stem Cells-Derived Cardiac Myocytes in a Cell Culture Dish. Methods Mol Biol 2022; 2520:37-51. [PMID: 34128207 PMCID: PMC10716860 DOI: 10.1007/7651_2021_406] [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] [Indexed: 01/24/2023]
Abstract
Induced pluripotent stem (iPS) cells are genetically reprogrammed somatic cells that exhibit embryonic stem cell-like characteristics such as self-renewal and pluripotency. These cells have broad differentiation capability to convert into diverse cell types that make up the primary germ layers during embryonic development. iPS cells can spontaneously differentiate and form cell aggregates termed embryoid bodies (EBs) in the absence of differentiation inhibitory factors. Unlike other methods used to generate EBs, "the hanging drop" method offers reproducibility and homogeneity from a set number of iPS cells. As such, we describe the differentiation of rat-induced pluripotent stem cells into cardiac myocytes in vitro using the hanging drop method. Both the confirmation and identification of the cardiac myocytes are done using immunocytochemistry, RT-PCR, Western Blot, and Flow Cytometry. Briefly, a specific number of iPS cells are placed in droplets on the lid of culture dishes and incubated for 2 days, yielding embryoid bodies, which are suspended and plated. Spontaneous beating of cardiomyocytes can be seen 7-14 days after the plating of EBs and specific cardiac markers can be observed through identification assays.
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Affiliation(s)
- Fatima Bianca A Dessouki
- Division of Metabolic and Cardiovascular Sciences, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Pawan K Singal
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Dinender K Singla
- Division of Metabolic and Cardiovascular Sciences, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
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Chen YS, Ouyang XP, Yu XH, Novák P, Zhou L, He PP, Yin K. N6-Adenosine Methylation (m 6A) RNA Modification: an Emerging Role in Cardiovascular Diseases. J Cardiovasc Transl Res 2021; 14:857-872. [PMID: 33630241 DOI: 10.1007/s12265-021-10108-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/15/2021] [Indexed: 12/27/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant and prevalent epigenetic modification of mRNA in mammals. This dynamic modification is regulated by m6A methyltransferases and demethylases, which control the fate of target mRNAs through influencing splicing, translation and decay. Recent studies suggest that m6A modification plays an important role in the progress of cardiac remodeling and cardiomyocyte contractile function. However, the exact roles of m6A in cardiovascular diseases (CVDs) have not been fully explained. In this review, we summarize the current roles of the m6A methylation in the progress of CVDs, such as cardiac remodeling, heart failure, atherosclerosis (AS), and congenital heart disease. Furthermore, we seek to explore the potential risk mechanisms of m6A in CVDs, including obesity, inflammation, adipogenesis, insulin resistance (IR), hypertension, and type 2 diabetes mellitus (T2DM), which may provide novel therapeutic targets for the treatment of CVDs.
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Affiliation(s)
- Ye-Shi Chen
- School of Nursing, University of South China, Hengyang, Hunan, 421001, China
- Guangxi Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, 541100, China
| | - Xin-Ping Ouyang
- Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Department of Physiology, The Neuroscience Institute, Hengyang Medical College, University of South China, Hengyang, 421001, Hunan, China
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, Hunan, China
| | - Xiao-Hua Yu
- Institute of Clinical Medicine, The Second Affiliated Hospital of Hainan Medical University, Haikou, 460106, Hainan, China
| | - Petr Novák
- Guangxi Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, 541100, China
| | - Le Zhou
- Guangxi Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, 541100, China
| | - Ping-Ping He
- School of Nursing, University of South China, Hengyang, Hunan, 421001, China.
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, Hunan, China.
| | - Kai Yin
- Guangxi Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, 541100, China.
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McCann KL, Kavari SL, Burkholder AB, Phillips BT, Hall TMT. H/ACA snoRNA levels are regulated during stem cell differentiation. Nucleic Acids Res 2020; 48:8686-8703. [PMID: 32710630 DOI: 10.1093/nar/gkaa612] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
H/ACA small nucleolar RNAs (snoRNAs) guide pseudouridylation as part of a small nucleolar ribonucleoprotein complex (snoRNP). Disruption of H/ACA snoRNA levels in stem cells impairs pluripotency, yet it remains unclear how H/ACA snoRNAs contribute to differentiation. To determine if H/ACA snoRNA levels are dynamic during differentiation, we comprehensively profiled H/ACA snoRNA abundance in multiple murine cell types and during differentiation in three cellular models, including mouse embryonic stem cells and mouse myoblasts. We determined that the profiles of H/ACA snoRNA abundance are cell-type specific, and we identified a subset of snoRNAs that are specifically regulated during differentiation. Additionally, we demonstrated that a decrease in Snora27 abundance upon differentiation corresponds to a decrease in pseudouridylation of its target site within the E-site transfer RNA (tRNA) binding region of the 28S ribosomal RNA (rRNA) in the large ribosomal subunit. Together, these data point toward a potential model in which H/ACA snoRNAs are specifically regulated during differentiation to alter pseudouridylation and fine tune ribosome function.
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Affiliation(s)
- Kathleen L McCann
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Sanam L Kavari
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Adam B Burkholder
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Bart T Phillips
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Zakariyah A, Rajgara R, Shelton M, Blais A, Skerjanc IS, Burgon PG. Combinatorial Utilization of Murine Embryonic Stem Cells and In Vivo Models to Study Human Congenital Heart Disease. ACTA ACUST UNITED AC 2018; 48:e75. [PMID: 30548532 DOI: 10.1002/cpsc.75] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have established an in vitro model of the human congenital heart defect (CHD)-associated mutation NKX2.5 R141C. We describe the use of the hanging drop method to differentiate Nkx2.5R141C/+ murine embryonic stem cells (mESCs) along with Nkx2.5+/+ control cells. This method allows us to recapitulate the early stages of embryonic heart development in tissue culture. We also use qRT-PCR and immunofluorescence to examine samples at different time points during differentiation to validate our data. The in vivo model is a mouse line with a knock-in of the same mutation. We describe the isolation of RNA from embryonic day 8.5 (E8.5) embryos and E9.5 hearts of wild-type and mutant mice. We found that the in vitro model shows reduced cardiomyogenesis, similar to Nkx2.5R141C/+ embryos at E8.5, indicating a transient loss of cardiomyogenesis at this time point. These results suggest that our in vitro model can be used to study very early changes in heart development that cause CHD. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Abeer Zakariyah
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Rashida Rajgara
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Shelton
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Alexandre Blais
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Center for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Ilona S Skerjanc
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Patrick G Burgon
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Center for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada.,Department of Medicine, Division of Cardiology, University of Ottawa, Ottawa, Ontario, Canada.,University of Ottawa Heart Institute, Ottawa, Ontario, Canada
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7
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HIRA directly targets the enhancers of selected cardiac transcription factors during in vitro differentiation of mouse embryonic stem cells. Mol Biol Rep 2018; 45:1001-1011. [PMID: 30030774 PMCID: PMC6156767 DOI: 10.1007/s11033-018-4247-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/08/2018] [Indexed: 01/06/2023]
Abstract
HIRA is a histone chaperone known to modulate gene expression through the deposition of H3.3. Conditional knockout of Hira in embryonic mouse hearts leads to cardiac septal defects. Loss of function mutation in HIRA, together with other chromatin modifiers, was found in patients with congenital heart diseases. However, the effects of HIRA on gene expression at earlier stages of cardiogenic mesoderm differentiation have not yet been studied. Differentiation of mouse embryonic stem cells (mESCs) towards cardiomyocytes mimics some of these early events and is an accepted model of these early stages. We performed RNA-Seq and H3.3-HA ChIP-seq on both WT and Hira-null mESCs and early cardiomyocyte progenitors of both genotypes. Analysis of RNA-seq data showed differential down regulation of cardiovascular development-related genes in Hira-null cardiomyocytes compared to WT cardiomyocytes. We found HIRA-dependent H3.3 deposition at these genes. In particular, we observed that HIRA influenced directly the expression of the transcription factors Gata6, Meis1 and Tbx2, essential for cardiac septation, through H3.3 deposition. We therefore identified new direct targets of HIRA during cardiac differentiation.
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8
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Liu H, Ren C, Liu W, Jiang X, Wang L, Zhu B, Jia W, Lin J, Tan J, Liu X. Embryotoxicity estimation of commonly used compounds with embryonic stem cell test. Mol Med Rep 2017; 16:263-271. [PMID: 28487962 PMCID: PMC5482095 DOI: 10.3892/mmr.2017.6552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 02/27/2017] [Indexed: 01/05/2023] Open
Abstract
The embryonic stem cell test (EST), an alternative model to animal studies, is a reliable and scientifically validated in vitro system for testing embryotoxicity. In contrast to most in vivo animal tests, two permanent cell lines, murine fibroblasts (BALB/c-3T3 cells) and murine embryonic stem cells (mES-D3 cells), are used in EST instead of animals in standard tests of toxicity. The embryotoxic potential of compounds (non, weak or strong embryotoxicity) may be obtained with a biostatistics-based prediction model and calculated from three different experimental endpoint values: The potency to inhibit growth of i) BALB/c-3T3 cells and ii) mES-D3 cells (IC503T3 and IC50ES) as presented using a cell cytotoxicity assay, and iii) the potency to inhibit differentiation of mES-D3 cells into contracting cardiomyocytes (ID50 D3) as demonstrated in a mES-D3 cell differentiation assay. In the present study, a model of EST with mES-D3 cells and BALB/c-3T3 cells was established, according to the standard EST system of the EU Center for the Validation of Alternative Methods, and verified it with 5-fluorouracil (strong embryotoxicity) as a positive control and penicillin G (non-embryotoxic) as a negative control. In addition, the authors further assessed the embryotoxicity of four compounds (eugenol, carnosic acid, procyanidin and dioctyl phthalate) with this model. The embryotoxic potentials of the four compounds were successfully classified by the EST system. Eugenol exhibited strong embryotoxicity, carnosic acid and dioctyl phthalate exhibited weak embryotoxicity, while procyanidin exhibited non-embryotoxicity.
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Affiliation(s)
- Hui Liu
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, P.R. China
| | - Caiping Ren
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, P.R. China
| | - Weidong Liu
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, P.R. China
| | - Xingjun Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Lei Wang
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, P.R. China
| | - Bin Zhu
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, P.R. China
| | - Wei Jia
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, P.R. China
| | - Jianxing Lin
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, P.R. China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Xiuying Liu
- Hunan Provincial Center for Disease Control and Prevention, Changsha, Hunan 410005, P.R. China
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Popowski M, Lee BK, Rhee C, Iyer VR, Tucker HO. Arid3a regulates mesoderm differentiation in mouse embryonic stem cells. JOURNAL OF STEM CELL THERAPY AND TRANSPLANTATION 2017; 1:52-62. [PMID: 31080945 PMCID: PMC6510499 DOI: 10.29328/journal.jsctt.1001005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Research into regulation of the differentiation of stem cells is critical to understanding early developmental decisions and later development growth. The transcription factor ARID3A previously was shown to be critical for trophectoderm and hematopoetic development. Expression of ARID3A increases during embryonic differentiation, but the underlying reason remained unclear. Here we show that Arid3a null embryonic stem (ES) cells maintain an undifferentiated gene expression pattern and form teratomas in immune-compromised mice. However, Arid3a null ES cells differentiated in vitro into embryoid bodies (EBs) significantly faster than control ES cells, and the majority forming large cystic embryoid EBs. Analysis of gene expression during this transition indicated that Arid3a nulls differentiated spontaneously into mesoderm and neuroectoderm lineages. While young ARID3A-deficient mice showed no gross tissue morphology, proliferative and structural abnormalities were observed in the kidneys of older null mice. Together these data suggest that ARID3A is not only required hematopoiesis, but is critical for early mesoderm differentiation.
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Affiliation(s)
- Melissa Popowski
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-kyu Lee
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Cathy Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vishwanath R Iyer
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Haley O Tucker
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Address for Correspondence: Haley O Tucker, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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10
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Yang P, Chen X, Kaushal S, Reece EA, Yang P. High glucose suppresses embryonic stem cell differentiation into cardiomyocytes : High glucose inhibits ES cell cardiogenesis. Stem Cell Res Ther 2016; 7:187. [PMID: 27938398 PMCID: PMC5148851 DOI: 10.1186/s13287-016-0446-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 12/18/2022] Open
Abstract
Background Babies born to mothers with pregestational diabetes have a high risk for congenital heart defects (CHD). Embryonic stem cells (ESCs) are excellent in vitro models for studying the effect of high glucose on cardiac lineage specification because ESCs can be differentiated into cardiomyocytes. ESC maintenance and differentiation are currently performed under high glucose conditions, whose adverse effects have never been clarified. Method We investigated the effect of high glucose on cardiomyocyte differentiation from a well-characterized ESC line, E14, derived from mouse blastocysts. E14 cells maintained under high glucose (25 mM) failed to generate any beating cardiomyocytes using the hanging-drop embryonic body method. We created a glucose-responsive E14 cell line (GR-E14) through a graduated low glucose adaptation. The expression of stem cell markers was similar in the parent E14 cells and the GR-E14 cells. Results Glucose transporter 2 gene was increased in GR-E14 cells. When GR-E14 cells were differentiated into cardiomyocytes under low (5 mM) or high (25 mM) glucose conditions, high glucose significantly delayed the appearance and reduced the number of TNNT2 (Troponin T Type 2)-positive contracting cardiomyocytes. High glucose suppressed the expression of precardiac mesoderm markers, cardiac transcription factors, mature cardiomyocyte markers, and potassium channel proteins. High glucose impaired the functionality of ESC-derived cardiomyocytes by suppressing the frequencies of Ca2+ wave and contraction. Conclusions Our findings suggest that high glucose inhibits ESC cardiogenesis by suppressing key developmental genes essential for the cardiac program. Electronic supplementary material The online version of this article (doi:10.1186/s13287-016-0446-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Penghua Yang
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, BRB11-039, 655W. Baltimore Street, Baltimore, MD, 21201, USA
| | - Xi Chen
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, BRB11-039, 655W. Baltimore Street, Baltimore, MD, 21201, USA
| | - Sunjay Kaushal
- Division of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - E Albert Reece
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, BRB11-039, 655W. Baltimore Street, Baltimore, MD, 21201, USA.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Peixin Yang
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, BRB11-039, 655W. Baltimore Street, Baltimore, MD, 21201, USA. .,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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11
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Zhang M, Cheng L, Jia Y, Liu G, Li C, Song S, Bradley A, Huang Y. Aneuploid embryonic stem cells exhibit impaired differentiation and increased neoplastic potential. EMBO J 2016; 35:2285-2300. [PMID: 27558554 DOI: 10.15252/embj.201593103] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 07/27/2016] [Indexed: 11/09/2022] Open
Abstract
Aneuploidy leads to severe developmental defects in mammals and is also a hallmark of cancer. However, whether aneuploidy is a driving cause or a consequence of tumor formation remains controversial. Paradoxically, existing studies based on aneuploid yeast and mouse fibroblasts have shown that aneuploidy is usually detrimental to cellular fitness. Here, we examined the effects of aneuploidy on mouse embryonic stem (ES) cells by generating a series of cell lines that each carries an extra copy of single chromosomes, including trisomy 6, 8, 11, 12, or 15. Most of these aneuploid cell lines had rapid proliferation rates and enhanced colony formation efficiencies. They were less dependent on growth factors for self-renewal and showed a reduced capacity to differentiate in vitro Moreover, trisomic stem cells formed teratomas more efficiently, from which undifferentiated cells can be recovered. Further investigations demonstrated that co-culture of wild-type and aneuploid ES cells or supplementation with extracellular BMP4 rescues the differentiation defects of aneuploid ES cells.
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Affiliation(s)
- Meili Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Cheng
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuyan Jia
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guang Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Cuiping Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Shuhui Song
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China .,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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12
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Bisson JA, Mills B, Paul Helt JC, Zwaka TP, Cohen ED. Wnt5a and Wnt11 inhibit the canonical Wnt pathway and promote cardiac progenitor development via the Caspase-dependent degradation of AKT. Dev Biol 2014; 398:80-96. [PMID: 25482987 DOI: 10.1016/j.ydbio.2014.11.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 01/09/2023]
Abstract
Wnt proteins regulate cell behavior via a canonical signaling pathway that induces β-catenin dependent transcription. It is now appreciated that Wnt/β-catenin signaling promotes the expansion of the second heart field (SHF) progenitor cells that ultimately give-rise to the majority of cardiomyocytes. However, activating β-catenin can also cause the loss of SHF progenitors, highlighting the necessity of precise control over β-catenin signaling during heart development. We recently reported that two non-canonical Wnt ligands, Wnt5a and Wnt11, act cooperatively to attenuate canonical Wnt signaling that would otherwise disrupt the SHF. While these data reveal the essential role of this anti-canonical Wnt5a/Wnt11 signaling in SHF development, the mechanisms by which these ligands inhibit the canonical Wnt pathway are unclear. Wnt11 was previously shown to inhibit β-catenin and promote cardiomyocyte maturation by activating a novel apoptosis-independent function of Caspases. Consistent with these data, we now show that Wnt5a and Wnt11 are capable of inducing Caspase activity in differentiating embryonic stem (ES) cells and that hearts from Wnt5a(-/-); Wnt11(-/-) embryos have diminished Caspase 3 (Casp3) activity. Furthermore, SHF markers are reduced in Casp3 mutant ES cells while the treatment of wild type ES cells with Caspase inhibitors blocked the ability of Wnt5a and Wnt11 to promote SHF gene expression. This finding was in agreement with our in vivo studies in which injecting pregnant mice with Caspase inhibitors reduced SHF marker expression in their gestating embryos. Caspase inhibition also blocked other Wnt5a/Wnt11 induced effects, including the suppression of β-catenin protein expression and activity. Interestingly, Wnt5a/Wnt11 treatment of differentiating ES cells reduced both phosphorylated and total Akt through a Caspase-dependent mechanism and phosphorylated Akt levels were increased in the hearts Caspase inhibitor treated. Surprisingly, inhibition of either Akt or PI3K in ES cells was an equally effective means of increasing SHF markers compared to treatment with Wnt5a/Wnt11. Moreover, Akt inhibition restored SHF gene expression in Casp3 mutant ES cells. Taken together, these findings suggest that Wnt5a/Wnt11 inhibit β-catenin to promote SHF development through Caspase-dependent Akt degradation.
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Affiliation(s)
- Joseph A Bisson
- Division of Endocrinology and Metabolism, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Bradley Mills
- Division of Endocrinology and Metabolism, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Jay-Christian Paul Helt
- Division of Endocrinology and Metabolism, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Thomas P Zwaka
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ethan David Cohen
- Division of Endocrinology and Metabolism, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.
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13
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Ounzain S, Pezzuto I, Micheletti R, Burdet F, Sheta R, Nemir M, Gonzales C, Sarre A, Alexanian M, Blow MJ, May D, Johnson R, Dauvillier J, Pennacchio LA, Pedrazzini T. Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease. J Mol Cell Cardiol 2014; 76:55-70. [PMID: 25149110 PMCID: PMC4445080 DOI: 10.1016/j.yjmcc.2014.08.009] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 08/07/2014] [Accepted: 08/07/2014] [Indexed: 01/17/2023]
Abstract
The key information processing units within gene regulatory networks are enhancers. Enhancer activity is associated with the production of tissue-specific noncoding RNAs, yet the existence of such transcripts during cardiac development has not been established. Using an integrated genomic approach, we demonstrate that fetal cardiac enhancers generate long noncoding RNAs (lncRNAs) during cardiac differentiation and morphogenesis. Enhancer expression correlates with the emergence of active enhancer chromatin states, the initiation of RNA polymerase II at enhancer loci and expression of target genes. Orthologous human sequences are also transcribed in fetal human hearts and cardiac progenitor cells. Through a systematic bioinformatic analysis, we identified and characterized, for the first time, a catalog of lncRNAs that are expressed during embryonic stem cell differentiation into cardiomyocytes and associated with active cardiac enhancer sequences. RNA-sequencing demonstrates that many of these transcripts are polyadenylated, multi-exonic long noncoding RNAs. Moreover, knockdown of two enhancer-associated lncRNAs resulted in the specific downregulation of their predicted target genes. Interestingly, the reactivation of the fetal gene program, a hallmark of the stress response in the adult heart, is accompanied by increased expression of fetal cardiac enhancer transcripts. Altogether, these findings demonstrate that the activity of cardiac enhancers and expression of their target genes are associated with the production of enhancer-derived lncRNAs.
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Affiliation(s)
- Samir Ounzain
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland.
| | - Iole Pezzuto
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Rudi Micheletti
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Frédéric Burdet
- VitalIT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Razan Sheta
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Mohamed Nemir
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Christine Gonzales
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Alexandre Sarre
- Cardiovascular Assessment Facility, University of Lausanne, Lausanne, Switzerland
| | - Michael Alexanian
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Matthew J Blow
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Dalit May
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rory Johnson
- Bioinformatics and Genomics Group, Centre for Genomic Regulation, Barcelona, Spain
| | - Jérôme Dauvillier
- VitalIT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Len A Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland.
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14
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Abstract
The reprogramming of adult somatic cells into an embryonic stem cell (ESC) state by various means has opened a new chapter in basic and applied life science. While this technology will create great opportunities for regenerative medicine, the more immediate impact is likely to be found in human disease modeling and drug testing/development. An important aspect in the latter contexts is the ability to reliably monitor the pluripotent stem cell state, in particular with respect to human cell reprogramming using patient-specific somatic cells and high-throughput screens. Undifferentiated transcription factor 1 (UTF1) belongs to the core transcriptional network characterizing pluripotency. UTF1 is involved in ESC-specific chromatin organization, and its expression pattern during cell reprogramming and subsequent differentiation appears to be tightly connected with the pluripotent stem cell state. Here, we capitalized on these features and generated a reliable reporter system that was used to monitor induced pluripotent stem cell (iPSC) formation and subsequent differentiation. Our reporter cassette comprises less than 2.3 kb and remains functional during many cell passages after genomic integration. The fact that the human UTF1 genetic control elements work in a mouse background and the demonstrated functionality of the reporter in an epigenetic state further qualifies this system as a versatile new tool for iPSC research.
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15
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Abstract
This chapter broadly reviews the use of stem cells as a means to accelerate wound healing, focusing first on the properties of stem cells that make them attractive agents to influence repair, both alone and as vehicles for growth factor delivery. Major stem cell reservoirs are described, including adult, embryonic, and induced pluripotent cell sources, outlining the advantages and limitations of each source as wound healing agents, as well as the possible mechanisms responsible for wound healing acceleration. Finally, the chapter includes a materials and methods section that provides an in-depth description of adult tissue harvest techniques.
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Affiliation(s)
- Allison C Nauta
- Hagey Laboratory for Pediatric and Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Ao A, Hao J, Hopkins CR, Hong CC. DMH1, a novel BMP small molecule inhibitor, increases cardiomyocyte progenitors and promotes cardiac differentiation in mouse embryonic stem cells. PLoS One 2012; 7:e41627. [PMID: 22848549 PMCID: PMC3407188 DOI: 10.1371/journal.pone.0041627] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/22/2012] [Indexed: 01/24/2023] Open
Abstract
The possibility of using cell-based therapeutics to treat cardiac failure has generated significant interest since the initial introduction of stem cell-based technologies. However, the methods to quickly and robustly direct stem cell differentiation towards cardiac cell types have been limited by a reliance on recombinant growth factors to provide necessary biological cues. We report here the use of dorsomorphin homologue 1 (DMH1), a second-generation small molecule BMP inhibitor based on dorsomorphin, to efficiently induce beating cardiomyocyte formation in mouse embryonic stem cells (ESCs) and to specifically upregulate canonical transcriptional markers associated with cardiac development. DMH1 differs significantly from its predecessor by its ability to enrich for pro-cardiac progenitor cells that respond to late-stage Wnt inhibition using XAV939 and produce secondary beating cardiomyocytes. Our study demonstrates the utility of small molecules to complement existing in vitro cardiac differentiation protocols and highlights the role of transient BMP inhibition in cardiomyogenesis.
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Affiliation(s)
- Ada Ao
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail: (AA); (CCH)
| | - Jijun Hao
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Corey R. Hopkins
- Vanderbilt Institute of Chemical Biology, Department of Pharmacology, Center for Neuroscience Drug Discovery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Charles C. Hong
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Vanderbilt Institute of Chemical Biology, Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Research Medicine, Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
- * E-mail: (AA); (CCH)
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Chou YF, Yabuuchi A. Murine embryonic stem cell derivation, in vitro pluripotency characterization, and in vivo teratoma formation. ACTA ACUST UNITED AC 2012; Chapter 2:Unit2.22. [PMID: 22058054 DOI: 10.1002/0471140856.tx0222s50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The derivation of embryonic stem (ES) cells represents one of the most important breakthroughs in mammalian developmental biology. In addition to their utility in a wide array of in vitro studies, ES cells are also one of the most useful starting materials for the generation of mutants by homologous recombination in mice (Thomson and Solter, 1988). When ES cells are injected into host blastocysts and transferred to the uterus of a pseudo-pregnant mouse, they can contribute to different types of tissues in chimeric mice, including the germ line (Bradley et al., 1984). Hundreds of genes have been studied through genetic manipulation of ES cells to model human genetic diseases. In this unit, the ES cell lines are derived from the 129SvEv mice strain, which has a high probability of promoting germ line transmission. Procedures for validating and characterizing ES cell pluripotency are also described in detail.
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Affiliation(s)
- Yu-Fen Chou
- Wadsworth Center, New York State Department of Health, Albany, USA
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