1
|
Zare A, Salehpour A, Khoradmehr A, Bakhshalizadeh S, Najafzadeh V, Almasi-Turk S, Mahdipour M, Shirazi R, Tamadon A. Epigenetic Modification Factors and microRNAs Network Associated with Differentiation of Embryonic Stem Cells and Induced Pluripotent Stem Cells toward Cardiomyocytes: A Review. Life (Basel) 2023; 13:life13020569. [PMID: 36836926 PMCID: PMC9965891 DOI: 10.3390/life13020569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 02/22/2023] Open
Abstract
More research is being conducted on myocardial cell treatments utilizing stem cell lines that can develop into cardiomyocytes. All of the forms of cardiac illnesses have shown to be quite amenable to treatments using embryonic (ESCs) and induced pluripotent stem cells (iPSCs). In the present study, we reviewed the differentiation of these cell types into cardiomyocytes from an epigenetic standpoint. We also provided a miRNA network that is devoted to the epigenetic commitment of stem cells toward cardiomyocyte cells and related diseases, such as congenital heart defects, comprehensively. Histone acetylation, methylation, DNA alterations, N6-methyladenosine (m6a) RNA methylation, and cardiac mitochondrial mutations are explored as potential tools for precise stem cell differentiation.
Collapse
Affiliation(s)
- Afshin Zare
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Aria Salehpour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Shabnam Bakhshalizadeh
- Reproductive Development, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Vahid Najafzadeh
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Sahar Almasi-Turk
- Department of Basic Sciences, School of Medicine, Bushehr University of Medical Sciences, Bushehr 7514633341, Iran
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 5166653431, Iran
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 5166653431, Iran
- Correspondence: (M.M.); (R.S.); (A.T.)
| | - Reza Shirazi
- Department of Anatomy, School of Medical Sciences, Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (M.M.); (R.S.); (A.T.)
| | - Amin Tamadon
- PerciaVista R&D Co., Shiraz 7135644144, Iran
- Correspondence: (M.M.); (R.S.); (A.T.)
| |
Collapse
|
2
|
Epigenetic Evaluation of the TBX20 Gene and Environmental Risk Factors in Mexican Paediatric Patients with Congenital Septal Defects. Cells 2023; 12:cells12040586. [PMID: 36831251 PMCID: PMC9953838 DOI: 10.3390/cells12040586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
The TBX20 gene has a key role during cardiogenesis, and it has been related to epigenetic mechanisms in congenital heart disease (CHD). The purpose of this study was to assess the association between DNA methylation status and congenital septal defects. The DNA methylation of seven CpG sites in the TBX20 gene promoter was analyzed through pyrosequencing as a quantitative method in 48 patients with congenital septal defects and 104 individuals with patent ductus arteriosus (PDA). The average methylation was higher in patients than in PDA (p < 0.001). High methylation levels were associated with a higher risk of congenital septal defects (OR = 4.59, 95% CI = 1.57-13.44, p = 0.005). The ROC curve analysis indicated that methylation of the TBX20 gene could be considered a risk marker for congenital septal defects (AUC = 0.682; 95% CI = 0.58-0.77; p < 0.001). The analysis of environmental risk factors in patients with septal defects and PDA showed an association between the consumption of vitamins (OR = 0.10; 95% CI = 0.01-0.98; p = 0.048) and maternal infections (OR = 3.10; 95% CI = 1.26-7.60; p = 0.013). These results suggest that differences in DNA methylation of the TBX20 gene can be associated with septal defects.
Collapse
|
3
|
In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
Collapse
|
4
|
Starcher AE, Peissig K, Stanton JB, Churchill GA, Cai D, Maxwell JT, Grider A, Love K, Chen SY, Coleman AE, Strauss E, Pazdro R. A systems approach using Diversity Outbred mice distinguishes the cardiovascular effects and genetics of circulating GDF11 from those of its homolog, myostatin. G3-GENES GENOMES GENETICS 2021; 11:6362884. [PMID: 34510201 PMCID: PMC8527520 DOI: 10.1093/g3journal/jkab293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/05/2021] [Indexed: 12/02/2022]
Abstract
Growth differentiation factor 11 (GDF11) is a member of the TGF-β protein family that has been implicated in the development of cardiac hypertrophy. While some studies have suggested that systemic GDF11 protects against cardiomyocyte enlargement and left ventricular wall thickening, there remains uncertainty about the true impact of GDF11 and whether its purported effects are actually attributable to its homolog myostatin. This study was conducted to resolve the statistical and genetic relationships among GDF11, myostatin, and cardiac hypertrophy in a mouse model of human genetics, the Diversity Outbred (DO) stock. In the DO population, serum GDF11 concentrations positively correlated with cardiomyocyte cross-sectional area, while circulating myostatin levels were negatively correlated with body weight, heart weight, and left ventricular wall thickness and mass. Genetic analyses revealed that serum GDF11 concentrations are modestly heritable (0.23) and identified a suggestive peak on murine chromosome 3 in close proximity to the gene Hey1, a transcriptional repressor. Bioinformatic analyses located putative binding sites for the HEY1 protein upstream of the Gdf11 gene in the mouse and human genomes. In contrast, serum myostatin concentrations were more heritable (0.57) than GDF11 concentrations, and mapping identified a significant locus near the gene FoxO1, which has binding motifs within the promoter regions of human and mouse myostatin genes. Together, these findings more precisely define the independent cardiovascular effects of GDF11 and myostatin, as well as their distinct regulatory pathways. Hey1 is a compelling candidate for the regulation of GDF11 and will be further evaluated in future studies.
Collapse
Affiliation(s)
- Abigail E Starcher
- Department of Nutritional Sciences, University of Georgia, Athens, GA 30602, USA
| | - Kristen Peissig
- Department of Nutritional Sciences, University of Georgia, Athens, GA 30602, USA
| | - James B Stanton
- Department of Pathology, University of Georgia College of Veterinary Medicine, Athens, GA 30602, USA
| | | | - Dunpeng Cai
- Department of Physiology, University of Georgia College of Veterinary Medicine, Athens, GA 30602, USA
| | - Joshua T Maxwell
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Arthur Grider
- Department of Nutritional Sciences, University of Georgia, Athens, GA 30602, USA
| | - Kim Love
- K. R. Love Quantitative Consulting and Collaboration, Athens, GA 30605, USA
| | - Shi-You Chen
- Department of Physiology, University of Georgia College of Veterinary Medicine, Athens, GA 30602, USA
| | - Amanda E Coleman
- Department of Small Animal Medicine & Surgery, University of Georgia College of Veterinary Medicine, Athens, GA 30602, USA
| | - Emma Strauss
- Department of Nutritional Sciences, University of Georgia, Athens, GA 30602, USA
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
5
|
Kim YJ, Tamadon A, Kim YY, Kang BC, Ku SY. Epigenetic Regulation of Cardiomyocyte Differentiation from Embryonic and Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:8599. [PMID: 34445302 PMCID: PMC8395249 DOI: 10.3390/ijms22168599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022] Open
Abstract
With the intent to achieve the best modalities for myocardial cell therapy, different cell types are being evaluated as potent sources for differentiation into cardiomyocytes. Embryonic stem cells and induced pluripotent stem cells have great potential for future progress in the treatment of myocardial diseases. We reviewed aspects of epigenetic mechanisms that play a role in the differentiation of these cells into cardiomyocytes. Cardiomyocytes proliferate during fetal life, and after birth, they undergo permanent terminal differentiation. Upregulation of cardiac-specific genes in adults induces hypertrophy due to terminal differentiation. The repression or expression of these genes is controlled by chromatin structural and epigenetic changes. However, few studies have reviewed and analyzed the epigenetic aspects of the differentiation of embryonic stem cells and induced pluripotent stem cells into cardiac lineage cells. In this review, we focus on the current knowledge of epigenetic regulation of cardiomyocyte proliferation and differentiation from embryonic and induced pluripotent stem cells through histone modification and microRNAs, the maintenance of pluripotency, and its alteration during cardiac lineage differentiation.
Collapse
Affiliation(s)
- Yong-Jin Kim
- Department of Obstetrics and Gynecology, Korea University College of Medicine, Seoul 08308, Korea;
| | - Amin Tamadon
- Department of Marine Stem Cell and Tissue Engineering, Bushehr University of Medical Sciences, Bushehr 14174, Iran;
| | - Yoon-Young Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea;
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul 03080, Korea
| | - Byeong-Cheol Kang
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
| | - Seung-Yup Ku
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea;
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul 03080, Korea
| |
Collapse
|
6
|
Watanabe Y, Seya D, Ihara D, Ishii S, Uemoto T, Kubo A, Arai Y, Isomoto Y, Nakano A, Abe T, Shigeta M, Kawamura T, Saito Y, Ogura T, Nakagawa O. Importance of endothelial Hey1 expression for thoracic great vessel development and its distal enhancer for Notch-dependent endothelial transcription. J Biol Chem 2020; 295:17632-17645. [PMID: 33454003 PMCID: PMC7762959 DOI: 10.1074/jbc.ra120.015003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Thoracic great vessels such as the aorta and subclavian arteries are formed through dynamic remodeling of embryonic pharyngeal arch arteries (PAAs). Previous work has shown that loss of a basic helix-loop-helix transcription factor Hey1 in mice causes abnormal fourth PAA development and lethal great vessel anomalies resembling congenital malformations in humans. However, how Hey1 mediates vascular formation remains unclear. In this study, we revealed that Hey1 in vascular endothelial cells, but not in smooth muscle cells, played essential roles for PAA development and great vessel morphogenesis in mouse embryos. Tek-Cre-mediated Hey1 deletion in endothelial cells affected endothelial tube formation and smooth muscle differentiation in embryonic fourth PAAs and resulted in interruption of the aortic arch and other great vessel malformations. Cell specificity and signal responsiveness of Hey1 expression were controlled through multiple cis-regulatory regions. We found two distal genomic regions that had enhancer activity in endothelial cells and in the pharyngeal epithelium and somites, respectively. The novel endothelial enhancer was conserved across species and was specific to large-caliber arteries. Its transcriptional activity was regulated by Notch signaling in vitro and in vivo, but not by ALK1 signaling and other transcription factors implicated in endothelial cell specificity. The distal endothelial enhancer was not essential for basal Hey1 expression in mouse embryos but may likely serve for Notch-dependent transcriptional control in endothelial cells together with the proximal regulatory region. These findings help in understanding the significance and regulation of endothelial Hey1 as a mediator of multiple signaling pathways in embryonic vascular formation.
Collapse
Affiliation(s)
- Yusuke Watanabe
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan; Graduate School of Medical Sciences, Nara Medical University, Kashihara, Nara, Japan.
| | - Daiki Seya
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Dai Ihara
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan; Laboratory of Stem Cell and Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Shuhei Ishii
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan; Graduate School of Medical Sciences, Nara Medical University, Kashihara, Nara, Japan
| | - Taiki Uemoto
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan; Graduate School of Medical Sciences, Nara Medical University, Kashihara, Nara, Japan
| | - Atsushi Kubo
- Department of Developmental Neurobiology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Yuji Arai
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan; Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Yoshie Isomoto
- Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Atsushi Nakano
- Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mayo Shigeta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Teruhisa Kawamura
- Laboratory of Stem Cell and Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Yoshihiko Saito
- Graduate School of Medical Sciences, Nara Medical University, Kashihara, Nara, Japan; Department of Cardiovascular Medicine, Nara Medical University, Kashihara, Nara, Japan
| | - Toshihiko Ogura
- Department of Developmental Neurobiology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Osamu Nakagawa
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan; Graduate School of Medical Sciences, Nara Medical University, Kashihara, Nara, Japan.
| |
Collapse
|
7
|
Gholipoorfeshkecheh R, Agarwala S, Krishnappa S, Savitha M, Narayanappa D, Ramachandra NB. Variants in HEY genes manifest in Ventricular Septal Defects of Congenital Heart Disease. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
8
|
Formaldehyde Exposure and Epigenetic Effects: A Systematic Review. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Formaldehyde (FA) is a general living and occupational pollutant, classified as carcinogenic for humans. Although genotoxicity is recognized as a FA mechanism of action, a potential contribution of epigenetic effects cannot be excluded. Therefore, aim of this review is to comprehensively assess possible epigenetic alterations induced by FA exposure in humans, animals, and cellular models. A systematic review of Pubmed, Scopus, and Isi Web of Science databases was performed. DNA global methylation changes were demonstrated in workers exposed to FA, and also in human bronchial cells. Histone alterations, i.e., the reduction in acetylation of histone lysine residues, in human lung cells were induced by FA. Moreover, a dysregulation of microRNA expression in human lung adenocarcinoma cells as well as in the nose, olfactory bulb and white blood cells of rodents and nonhuman primates was reported. Although preliminary, these findings suggest the role of epigenetic modifications as possible FA mechanisms of action that need deeper qualitative and quantitative investigation. This may allow to define the role of such alterations as indicators of early biological effect and the opportunity to include such information in future risk assessment and management strategies for public and occupationally FA-exposed populations.
Collapse
|
9
|
Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies. Nat Commun 2020; 11:1585. [PMID: 32221292 PMCID: PMC7101316 DOI: 10.1038/s41467-020-15298-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/02/2020] [Indexed: 01/28/2023] Open
Abstract
Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative and scalable computational method, iDEA, to perform joint DE and GSE analysis through a hierarchical Bayesian framework. By integrating DE and GSE analyses, iDEA can improve the power and consistency of DE analysis and the accuracy of GSE analysis. Importantly, iDEA uses only DE summary statistics as input, enabling effective data modeling through complementing and pairing with various existing DE methods. We illustrate the benefits of iDEA with extensive simulations. We also apply iDEA to analyze three scRNA-seq data sets, where iDEA achieves up to five-fold power gain over existing GSE methods and up to 64% power gain over existing DE methods. The power gain brought by iDEA allows us to identify many pathways that would not be identified by existing approaches in these data. Differential expression (DE) and gene set enrichment (GSE) analysis tend to be carried out separately. Here, the authors present iDEA (integrative Differential expression and gene set Enrichment Analysis) for the analysis of scRNAseq data which uses a Baysian approach to jointly model DE and GSE for improved power in both tasks.
Collapse
|
10
|
Abstract
Virtually all adults with Down syndrome (DS) show the neuropathological changes of Alzheimer disease (AD) by the age of 40 years. This association is partially due to overexpression of amyloid precursor protein, encoded by APP, as a result of the location of this gene on chromosome 21. Amyloid-β accumulates in the brain across the lifespan of people with DS, which provides a unique opportunity to understand the temporal progression of AD and the epigenetic factors that contribute to the age of dementia onset. This age dependency in the development of AD in DS can inform research into the presentation of AD in the general population, in whom a longitudinal perspective of the disease is not often available. Comparison of the risk profiles, biomarker profiles and genetic profiles of adults with DS with those of individuals with AD in the general population can help to determine common and distinct pathways as well as mechanisms underlying increased risk of dementia. This Review evaluates the similarities and differences between the pathological cascades and genetics underpinning DS and AD with the aim of providing a platform for common exploration of these disorders.
Collapse
Affiliation(s)
- Ira T Lott
- Department of Pediatrics and Neurology, School of Medicine, University of California, Irvine, CA, USA.
| | - Elizabeth Head
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
11
|
Ménard M, Costechareyre C, Ichim G, Blachier J, Neves D, Jarrosson-Wuilleme L, Depping R, Koster J, Saintigny P, Mehlen P, Tauszig-Delamasure S. Hey1- and p53-dependent TrkC proapoptotic activity controls neuroblastoma growth. PLoS Biol 2018; 16:e2002912. [PMID: 29750782 PMCID: PMC5965893 DOI: 10.1371/journal.pbio.2002912] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/23/2018] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
The neurotrophin-3 (NT-3) receptor tropomyosin receptor kinase C (TrkC/NTRK3) has been described as a dependence receptor and, as such, triggers apoptosis in the absence of its ligand NT-3. This proapoptotic activity has been proposed to confer a tumor suppressor activity to this classic tyrosine kinase receptor (RTK). By investigating interacting partners that might facilitate TrkC-induced cell death, we have identified the basic helix-loop-helix (bHLH) transcription factor Hey1 and importin-α3 (karyopherin alpha 4 [KPNA4]) as direct interactors of TrkC intracellular domain, and we show that Hey1 is required for TrkC-induced apoptosis. We propose here that the cleaved proapoptotic portion of TrkC intracellular domain (called TrkC killer-fragment [TrkC-KF]) is translocated to the nucleus by importins and interacts there with Hey1. We also demonstrate that Hey1 and TrkC-KF transcriptionally silence mouse double minute 2 homolog (MDM2), thus contributing to p53 stabilization. p53 transcriptionally regulates the expression of TrkC-KF cytoplasmic and mitochondrial interactors cofactor of breast cancer 1 (COBRA1) and B cell lymphoma 2–associated X (BAX), which will subsequently trigger the intrinsic pathway of apoptosis. Of interest, TrkC was proposed to constrain tumor progression in neuroblastoma (NB), and we demonstrate in an avian model that TrkC tumor suppressor activity requires Hey1 and p53. Tropomyosin receptor kinase C (TrkC) is a transmembrane receptor at the cell surface and has been described to work paradoxically both as an oncogene and as a tumor suppressor. We partly solved this paradox in a previous study, demonstrating that TrkC is a double-facet receptor: Upon interaction with its ligand neurotrophin-3 (NT-3), TrkC has a tyrosine kinase activity and induces survival and proliferation of the cell; conversely, in the absence of the ligand, TrkC is cleaved and releases a "killer-fragment" that triggers apoptosis. In this study, we analyze the fate of this fragment and show that TrkC killer-fragment is translocated to the nucleus, where it stabilizes the apoptosis inducer p53. We further find that p53 activates the transcription of cytoplasmic molecular partners, which interact with TrkC killer-fragment and induce apoptosis. We also demonstrate that alteration of this mechanism favors tumor growth in neuroblastoma (NB), an avian tumor progression model for a pediatric cancer.
Collapse
Affiliation(s)
- Marie Ménard
- Apoptosis, Cancer and Development Laboratory—Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Clélia Costechareyre
- Apoptosis, Cancer and Development Laboratory—Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Gabriel Ichim
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Jonathan Blachier
- Apoptosis, Cancer and Development Laboratory—Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - David Neves
- Apoptosis, Cancer and Development Laboratory—Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Loraine Jarrosson-Wuilleme
- Apoptosis, Cancer and Development Laboratory—Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Reinhard Depping
- Universität zu Lübeck, Institut für Physiologie, Zentrum für Medizinische Struktur und Zellbiologie, Lübeck, Germany
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Pierre Saintigny
- Department of translational Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory—Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
- Department of translational Research and Innovation, Centre Léon Bérard, Lyon, France
- * E-mail: (PM); (ST)
| | - Servane Tauszig-Delamasure
- Apoptosis, Cancer and Development Laboratory—Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
- * E-mail: (PM); (ST)
| |
Collapse
|
12
|
Nerys-Junior A, Braga-Dias LP, Pezzuto P, Cotta-de-Almeida V, Tanuri A. Comparison of the editing patterns and editing efficiencies of TALEN and CRISPR-Cas9 when targeting the human CCR5 gene. Genet Mol Biol 2018; 41:167-179. [PMID: 29583154 PMCID: PMC5901495 DOI: 10.1590/1678-4685-gmb-2017-0065] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/07/2017] [Indexed: 01/02/2023] Open
Abstract
The human C-C chemokine receptor type-5 (CCR5) is the major transmembrane
co-receptor that mediates HIV-1 entry into target CD4+ cells. Gene therapy to
knock-out the CCR5 gene has shown encouraging results in providing a functional
cure for HIV-1 infection. In gene therapy strategies, the initial region of the
CCR5 gene is a hotspot for producing functional gene knock-out. Such target gene
editing can be done using programmable endonucleases such as transcription
activator-like effector nucleases (TALEN) or clustered regularly interspaced
short palindromic repeats (CRISPR-Cas9). These two gene editing approaches are
the most modern and effective tools for precise gene modification. However,
little is known of potential differences in the efficiencies of TALEN and
CRISPR-Cas9 for editing the beginning of the CCR5 gene. To examine which of
these two methods is best for gene therapy, we compared the patterns and amount
of editing at the beginning of the CCR5 gene using TALEN and CRISPR-Cas9
followed by DNA sequencing. This comparison revealed that CRISPR-Cas9 mediated
the sorting of cells that contained 4.8 times more gene editing than TALEN+
transfected cells.
Collapse
Affiliation(s)
- Arildo Nerys-Junior
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Luciene P Braga-Dias
- Laboratório do Serviço de Biotecnologia e Desenvolvimento Animal, Instituto de Ciência e Tecnologia em Biomodelos, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Paula Pezzuto
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| |
Collapse
|
13
|
Qiu JJ, Liu YN, Ren ZR, Yan JB. Dysfunctions of mitochondria in close association with strong perturbation of long noncoding RNAs expression in down syndrome. Int J Biochem Cell Biol 2017; 92:115-120. [DOI: 10.1016/j.biocel.2017.09.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 08/23/2017] [Accepted: 09/23/2017] [Indexed: 01/07/2023]
|
14
|
Veerman CC, Podliesna S, Tadros R, Lodder EM, Mengarelli I, de Jonge B, Beekman L, Barc J, Wilders R, Wilde AAM, Boukens BJ, Coronel R, Verkerk AO, Remme CA, Bezzina CR. The Brugada Syndrome Susceptibility Gene HEY2 Modulates Cardiac Transmural Ion Channel Patterning and Electrical Heterogeneity. Circ Res 2017. [PMID: 28637782 DOI: 10.1161/circresaha.117.310959] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RATIONALE Genome-wide association studies previously identified an association of rs9388451 at chromosome 6q22.3 (near HEY2) with Brugada syndrome. The causal gene and underlying mechanism remain unresolved. OBJECTIVE We used an integrative approach entailing transcriptomic studies in human hearts and electrophysiological studies in Hey2+/- (Hey2 heterozygous knockout) mice to dissect the underpinnings of the 6q22.31 association with Brugada syndrome. METHODS AND RESULTS We queried expression quantitative trait locus data acquired in 190 human left ventricular samples from the genotype-tissue expression consortium for cis-expression quantitative trait locus effects of rs9388451, which revealed an association between Brugada syndrome risk allele dosage and HEY2 expression (β=+0.159; P=0.0036). In the same transcriptomic data, we conducted genome-wide coexpression analysis for HEY2, which uncovered KCNIP2, encoding the β-subunit of the channel underlying the transient outward current (Ito), as the transcript most robustly correlating with HEY2 expression (β=+1.47; P=2×10-34). Transcript abundance of Hey2 and the Ito subunits Kcnip2 and Kcnd2, assessed by quantitative reverse transcription-polymerase chain reaction, was higher in subepicardium versus subendocardium in both left and right ventricles, with lower levels in Hey2+/- mice compared with wild type. Surface ECG measurements showed less prominent J waves in Hey2+/- mice compared with wild-type. In wild-type mice, patch-clamp electrophysiological studies on cardiomyocytes from right ventricle demonstrated a shorter action potential duration and a lower Vmax in subepicardium compared with subendocardium cardiomyocytes, which was paralleled by a higher Ito and a lower sodium current (INa) density in subepicardium versus subendocardium. These transmural differences were diminished in Hey2+/- mice because of changes in subepicardial cardiomyocytes. CONCLUSIONS This study uncovers a role of HEY2 in the normal transmural electrophysiological gradient in the ventricle and provides compelling evidence that genetic variation at 6q22.31 (rs9388451) is associated with Brugada syndrome through a HEY2-dependent alteration of ion channel expression across the cardiac ventricular wall.
Collapse
Affiliation(s)
- Christiaan C Veerman
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Svitlana Podliesna
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Rafik Tadros
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Elisabeth M Lodder
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Isabella Mengarelli
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Berend de Jonge
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Leander Beekman
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Julien Barc
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Ronald Wilders
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Arthur A M Wilde
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Bastiaan J Boukens
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Ruben Coronel
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Arie O Verkerk
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Carol Ann Remme
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.)
| | - Connie R Bezzina
- From the Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, Amsterdam, The Netherlands (C.C.V., S.P., R.T., E.M.L., I.M., L.B., A.A.M.W., R.C., A.O.V., C.A.R., C.R.B.); Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute, Canada (R.T.); Université de Montréal, Canada (R.T.); Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.d.J., R.W., B.J.B., A.O.V.); INSERM, CNRS, Université de Nantes, L'institut du Thorax, Nantes, France (J.B.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Saudi Arabia (A.A.M.W.); and Electrophysiology and Heart Modeling Institute LIRYC, Université de Bordeaux, France (R.C.).
| |
Collapse
|
15
|
Liu Z, Sanders AJ, Liang G, Song E, Jiang WG, Gong C. Hey Factors at the Crossroad of Tumorigenesis and Clinical Therapeutic Modulation of Hey for Anticancer Treatment. Mol Cancer Ther 2017; 16:775-786. [PMID: 28468863 DOI: 10.1158/1535-7163.mct-16-0576] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Zihao Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Andrew J Sanders
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Gehao Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom.
| | - Chang Gong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetic and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| |
Collapse
|
16
|
Epigenomic engineering for Down syndrome. Neurosci Biobehav Rev 2016; 71:323-327. [DOI: 10.1016/j.neubiorev.2016.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/11/2016] [Accepted: 09/15/2016] [Indexed: 12/27/2022]
|
17
|
Therapeutic Potential of Stem Cells Strategy for Cardiovascular Diseases. Stem Cells Int 2016; 2016:4285938. [PMID: 27829839 PMCID: PMC5088322 DOI: 10.1155/2016/4285938] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/09/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
Despite development of medicine, cardiovascular diseases (CVDs) are still the leading cause of mortality and morbidity worldwide. Over the past 10 years, various stem cells have been utilized in therapeutic strategies for the treatment of CVDs. CVDs are characterized by a broad range of pathological reactions including inflammation, necrosis, hyperplasia, and hypertrophy. However, the causes of CVDs are still unclear. While there is a limit to the currently available target-dependent treatments, the therapeutic potential of stem cells is very attractive for the treatment of CVDs because of their paracrine effects, anti-inflammatory activity, and immunomodulatory capacity. Various studies have recently reported increased therapeutic potential of transplantation of microRNA- (miRNA-) overexpressing stem cells or small-molecule-treated cells. In addition to treatment with drugs or overexpressed miRNA in stem cells, stem cell-derived extracellular vesicles also have therapeutic potential because they can deliver the stem cell-specific RNA and protein into the host cell, thereby improving cell viability. Here, we reported the state of stem cell-based therapy for the treatment of CVDs and the potential for cell-free based therapy.
Collapse
|
18
|
Spatiotemporal regulation of enhancers during cardiogenesis. Cell Mol Life Sci 2016; 74:257-265. [PMID: 27497925 PMCID: PMC5219004 DOI: 10.1007/s00018-016-2322-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/20/2016] [Accepted: 08/02/2016] [Indexed: 01/02/2023]
Abstract
With the advance in chromatin immunoprecipitation followed by high-throughput sequencing, there has been a dramatic increase in our understanding of distal enhancer function. In the developing heart, the identification and characterisation of such enhancers have deepened our knowledge of the mechanisms of transcriptional regulation that drives cardiac differentiation. With next-generation sequencing techniques becoming widely accessible, the quantity of data describing the genome-wide distribution of cardiac-specific transcription factor and chromatin modifiers has rapidly increased and it is now becoming clear that the usage of enhancers is highly dynamic and complex, both during the development and in the adult. The identification of those enhancers has revealed new insights into the transcriptional mechanisms of how tissue-specific gene expression patterns are established, maintained, and change dynamically during development and upon physiological stress.
Collapse
|
19
|
Abdolazimi Y, Stojanova Z, Segil N. Selection of cell fate in the organ of Corti involves the integration of Hes/Hey signaling at the Atoh1 promoter. Development 2016; 143:841-50. [PMID: 26932672 DOI: 10.1242/dev.129320] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Determination of cell fate within the prosensory domain of the developing cochlear duct relies on the temporal and spatial regulation of the bHLH transcription factor Atoh1. Auditory hair cells and supporting cells arise in a wave of differentiation that patterns them into discrete rows mediated by Notch-dependent lateral inhibition. However, the mechanism responsible for selecting sensory cells from within the prosensory competence domain remains poorly understood. We show in mice that rather than being upregulated in rows of cells, Atoh1 is subject to transcriptional activation in groups of prosensory cells, and that highly conserved sites for Hes/Hey repressor binding in the Atoh1 promoter are needed to select the hair cell and supporting cell fate. During perinatal supporting cell transdifferentiation, which is a model of hair cell regeneration, we show that derepression is sufficient to induce Atoh1 expression, suggesting a mechanism for priming the 3' Atoh1 autoregulatory enhancer needed for hair cell expression.
Collapse
Affiliation(s)
- Yassan Abdolazimi
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USC, 1425 San Pablo St., Los Angeles, CA 90033, USA GMCB Graduate Program, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USC, 1425 San Pablo St., Los Angeles, CA 90033, USA
| | - Zlatka Stojanova
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USC, 1425 San Pablo St., Los Angeles, CA 90033, USA
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USC, 1425 San Pablo St., Los Angeles, CA 90033, USA Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of Medicine of the University of Southern California, 1450 San Pablo St., Suite 5100, Los Angeles, CA 90033, USA
| |
Collapse
|
20
|
Quintes S, Brinkmann BG, Ebert M, Fröb F, Kungl T, Arlt FA, Tarabykin V, Huylebroeck D, Meijer D, Suter U, Wegner M, Sereda MW, Nave KA. Zeb2 is essential for Schwann cell differentiation, myelination and nerve repair. Nat Neurosci 2016; 19:1050-1059. [PMID: 27294512 PMCID: PMC4964942 DOI: 10.1038/nn.4321] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/04/2016] [Indexed: 12/12/2022]
Abstract
Schwann cell development and peripheral nerve myelination require the serial expression of transcriptional activators, such as Sox10, Oct6 (also called Scip or Pou3f1) and Krox20 (also called Egr2). Here we show that transcriptional repression, mediated by the zinc-finger protein Zeb2 (also known as Sip1), is essential for differentiation and myelination. Mice lacking Zeb2 in Schwann cells develop a severe peripheral neuropathy, caused by failure of axonal sorting and virtual absence of myelin membranes. Zeb2-deficient Schwann cells continuously express repressors of lineage progression. Moreover, genes for negative regulators of maturation such as Sox2 and Ednrb emerge as Zeb2 target genes, supporting its function as an 'inhibitor of inhibitors' in myelination control. When Zeb2 is deleted in adult mice, Schwann cells readily dedifferentiate following peripheral nerve injury and become repair cells. However, nerve regeneration and remyelination are both perturbed, demonstrating that Zeb2, although undetectable in adult Schwann cells, has a latent function throughout life.
Collapse
Affiliation(s)
- Susanne Quintes
- Max Planck Institute of Experimental Medicine, Department of
Neurogenetics, Göttingen, Germany
- University Medical Center Göttingen (UMG), Department of
Clinical Neurophysiology, Göttingen, Germany
| | - Bastian G Brinkmann
- Max Planck Institute of Experimental Medicine, Department of
Neurogenetics, Göttingen, Germany
| | - Madlen Ebert
- Max Planck Institute of Experimental Medicine, Department of
Neurogenetics, Göttingen, Germany
| | - Franziska Fröb
- Institut für Biochemie, Emil-Fischer-Zentrum,
Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - Theresa Kungl
- Max Planck Institute of Experimental Medicine, Department of
Neurogenetics, Göttingen, Germany
| | - Friederike A Arlt
- Max Planck Institute of Experimental Medicine, Department of
Neurogenetics, Göttingen, Germany
| | - Victor Tarabykin
- Institute for Cell and Neurobiology, Center for Anatomy,
Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Danny Huylebroeck
- Laboratory of Molecular Biology (Celgen), Department of Development
and Regeneration, KU Leuven, Leuven, Belgium
- Department of Cell Biology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - Dies Meijer
- Centre for Neuroregeneration, University of Edinburgh, Edinburgh,
United Kingdom
| | - Ueli Suter
- Institute of Molecular Health Sciences, Department of Biology, ETH
Zürich, Zürich, Switzerland
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum,
Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - Michael W Sereda
- Max Planck Institute of Experimental Medicine, Department of
Neurogenetics, Göttingen, Germany
- University Medical Center Göttingen (UMG), Department of
Clinical Neurophysiology, Göttingen, Germany
| | - Klaus-Armin Nave
- Max Planck Institute of Experimental Medicine, Department of
Neurogenetics, Göttingen, Germany
| |
Collapse
|
21
|
Hartley SW, Mullikin JC. Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq. Nucleic Acids Res 2016; 44:e127. [PMID: 27257077 PMCID: PMC5009739 DOI: 10.1093/nar/gkw501] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/24/2016] [Indexed: 12/14/2022] Open
Abstract
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In particular, JunctionSeq is capable of detecting differential usage of novel splice junctions without the need for an additional isoform assembly step, greatly improving performance when the available transcript annotation is flawed or incomplete. JunctionSeq also provides a powerful and streamlined visualization toolset that allows bioinformaticians to quickly and intuitively interpret their results. We tested our method on publicly available data from several experiments performed on the rat pineal gland and Toxoplasma gondii, successfully detecting known and previously validated AIR genes in 19 out of 19 gene-level hypothesis tests. Due to its ability to query novel splice sites, JunctionSeq is still able to detect these differences even when all alternative isoforms for these genes were not included in the transcript annotation. JunctionSeq thus provides a powerful method for detecting alternative isoform regulation even with low-quality annotations. An implementation of JunctionSeq is available as an R/Bioconductor package.
Collapse
Affiliation(s)
- Stephen W Hartley
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Mullikin
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
22
|
Notch signaling: an emerging therapeutic target for cancer treatment. Cancer Lett 2015; 369:20-7. [PMID: 26341688 DOI: 10.1016/j.canlet.2015.07.048] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/28/2015] [Accepted: 07/31/2015] [Indexed: 12/14/2022]
Abstract
The Notch pathway is involved in cell proliferation, differentiation and survival. The Notch signaling pathway is one of the most commonly activated signaling pathways in cancer. Alterations include activating mutations and amplification of the Notch pathway, which play key roles in the progression of cancer. Accumulating evidence suggests that the pharmacological inhibition of this pathway can overcome chemoresistance. Efforts have been taken to develop Notch inhibitors as a single agent or in combination with clinically used chemotherapeutics to treat cancer. Some Notch inhibitors have been demonstrated to have therapeutic efficacy in preclinical studies. This review summarizes the recent studies and clinical evaluations of the Notch inhibitors in cancer.
Collapse
|