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Li B, Xiong W, Zuo W, Shi Y, Wang T, Chang L, Wu Y, Ma H, Bian Q, Chang ACY. Proximal telomeric decompaction due to telomere shortening drives FOXC1-dependent myocardial senescence. Nucleic Acids Res 2024; 52:6269-6284. [PMID: 38634789 PMCID: PMC11194093 DOI: 10.1093/nar/gkae274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 02/29/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Telomeres, TTAGGGn DNA repeat sequences located at the ends of eukaryotic chromosomes, play a pivotal role in aging and are targets of DNA damage response. Although we and others have demonstrated presence of short telomeres in genetic cardiomyopathic and heart failure cardiomyocytes, little is known about the role of telomere lengths in cardiomyocyte. Here, we demonstrate that in heart failure patient cardiomyocytes, telomeres are shortened compared to healthy controls. We generated isogenic human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) with short telomeres (sTL-CMs) and normal telomeres (nTL-CMs) as model. Compared to nTL-CMs, short telomeres result in cardiac dysfunction and expression of senescent markers. Using Hi-C and RNASeq, we observe that short telomeres induced TAD insulation decrease near telomeric ends and this correlated with a transcription upregulation in sTL-CMs. FOXC1, a key transcription factor involved in early cardiogenesis, was upregulated in sTL-CMs and its protein levels were negatively correlated with telomere lengths in heart failure patients. Overexpression of FOXC1 induced hiPSC-CM aging, mitochondrial and contractile dysfunction; knockdown of FOXC1 rescued these phenotypes. Overall, the work presented demonstrate that increased chromatin accessibility due to telomere shortening resulted in the induction of FOXC1-dependent expression network responsible for contractile dysfunction and myocardial senescence.
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Affiliation(s)
- Bin Li
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Weiyao Xiong
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Wu Zuo
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yuanyuan Shi
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Teng Wang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Lingling Chang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yueheng Wu
- Department of Cardiovascular Medicine, Guangdong General Hospital, Guangzhou, Guangdong, China
| | - Heng Ma
- Department of Physiology and Pathophysiology, Fourth Military Medical University, No. 169 Changle West Rd, Xi'an 710032, China
| | - Qian Bian
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Alex C Y Chang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
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Wei W, Li B, Li F, Sun K, Jiang X, Xu R. Variants in FOXC1 and FOXC2 identified in patients with conotruncal heart defects. Genomics 2024; 116:110840. [PMID: 38580085 DOI: 10.1016/j.ygeno.2024.110840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/07/2024]
Abstract
Conotruncal heart defects (CTD), subtypes of congenital heart disease, result from abnormal cardiac outflow tract development (OFT). FOXC1 and FOXC2 are closely related members of the forkhead transcription factor family and play essential roles in the development of OFT. We confirmed their expression pattern in mouse and human embryos, identifying four variants in FOXC1 and three in FOXC2 by screening these two genes in 605 patients with sporadic CTD. Western blot demonstrated expression levels, while Dual-luciferase reporter assay revealed affected transcriptional abilities for TBX1 enhancer in two FOXC1 variants and three FOXC2 variants. This might result from the altered DNA-binding abilities of mutant proteins. These results indicate that functionally impaired FOXC1 and FOXC2 variants may contribute to the occurrence of CTD.
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Affiliation(s)
- Wei Wei
- Department of Pediatric Cardiology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Bojian Li
- Department of Pediatric Cardiology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Fen Li
- Shanghai Jiaotong University School of Medicine Shanghai Children's Medical Center, China
| | - Kun Sun
- Department of Pediatric Cardiology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Xuechao Jiang
- Scientific Research Center, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Rang Xu
- Scientific Research Center, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China.
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Su Y, Yu Z, Yang Y, Wong KC, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307280. [PMID: 38380499 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.
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Affiliation(s)
- Yanchi Su
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
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Jia Y, Pan J. CKLF1, transcriptionally activated by FOXC1, promotes hypoxia/reoxygenation‑induced oxidative stress and inflammation in H9c2 cells by NLRP3 inflammasome activation. Exp Ther Med 2024; 27:59. [PMID: 38234613 PMCID: PMC10790169 DOI: 10.3892/etm.2023.12347] [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: 07/12/2023] [Accepted: 08/11/2023] [Indexed: 01/19/2024] Open
Abstract
Myocardial ischemia/reperfusion (I/R) injury is a clinical challenge in the treatment of ischemic heart disease. The present study aimed to establish a hypoxia/reoxygenation (H/R)-induced H9c2 cell model to explore the role and mechanism of chemokine-like factor 1 (CKLF1) in myocardial I/R injury. First, CKLF1 expression was measured in H/R-induced H9c2 cells by reverse transcription-quantitative PCR and western blotting. Subsequently, after CKLF1 silencing, cell viability and apoptosis were evaluated by Cell Counting Kit-8 assay and flow cytometry. In addition, 2,7-dichlorodihydrofluorescein diacetate staining was used to assess the levels of cellular reactive oxygen species. Additionally, the levels of superoxide dismutase, glutathione peroxidase and malondialdehyde, and the contents of inflammatory factors IL-6, IL-1β and TNF-α were detected using corresponding commercially available kits. Western blotting was used to examine the expression levels of proteins involved in the NOD-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome. The JASPAR database predicted that forkhead box protein C1 (FOXC1) would bind to the CKLF1 promoter region, and dual luciferase and chromatin immunoprecipitation assays were performed to verify it. Subsequently, FOXC1 overexpression and CKLF1 silencing were used to clarify the regulatory mechanism of FOXC1 on CKLF1 in H/R-induced H9c2 cells. The results revealed that CKLF1 expression was markedly enhanced in H/R-stimulated H9c2 cells. CKLF1 knockdown enhanced the viability and inhibited the apoptosis of H9c2 cells exposed to H/R. Moreover, the oxidative stress and inflammation induced by H/R were alleviated following CKLF1 silencing. CKLF1 knockdown also inhibited NLRP3 inflammasome activation. Furthermore, FOXC1 bound to the CKLF1 promoter region to upregulate CKLF1 expression, and FOXC1 overexpression alleviated the effects of CKLF1 knockdown on H9c2 cell damage induced by H/R via activation of the NLRP3 inflammasome. In conclusion, CKLF1 transcriptionally activated by FOXC1 may promote H/R-induced oxidative stress and inflammation in H9c2 cells via NLRP3 inflammasome activation.
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Affiliation(s)
- Yinfeng Jia
- Department of Cardiovascular Medicine, The Second People's Hospital of Yueqing, Wenzhou, Zhejiang 325608, P.R. China
| | - Jiansheng Pan
- Department of Cardiovascular Medicine, The Second People's Hospital of Yueqing, Wenzhou, Zhejiang 325608, P.R. China
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Hridoy HM, Haidar MN, Khatun C, Sarker A, Hossain MP, Aziz MA, Hossain MT. In silico based analysis to explore genetic linkage between atherosclerosis and its potential risk factors. Biochem Biophys Rep 2023; 36:101574. [PMID: 38024867 PMCID: PMC10652116 DOI: 10.1016/j.bbrep.2023.101574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Atherosclerosis (ATH) is a chronic cardiovascular disease characterized by plaque formation in arteries, and it is a major cause of illness and death. Although therapeutic advances have significantly improved the prognosis of ATH, missing therapeutic targets pose a significant residual threat. This research used a systems biology approach to identify the molecular biomarkers involved in the onset and progression of ATH, analysing microarray gene expression datasets from ATH and tissues impacted by risk factors such as high cholesterol, adipose tissue, smoking, obesity, sedentary lifestyle, stress, alcohol consumption, hypertension, hyperlipidaemia, high fat, diabetes to find the differentially expressed genes (DEGs). Bioinformatic analyses of Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted on differentially expressed genes, revealing metabolic and signaling pathways (the chemokine signaling pathway, cytokine-cytokine receptor interaction, the cytosolic DNA-sensing pathway, the peroxisome proliferator-activated receptors signaling pathway, and the nuclear factor-kappa B signaling pathway), ten hubs proteins (CCL5, CCR1, TLR1, CCR2, FCGR2A, IL1B, CD163, AIF1, CXCL-1 and TNF), five transcription factors (YY1, FOXL1, FOXC1, SRF, and GATA2), and five miRNAs (mir-27a-3p, mir-124-3p, mir-16-5p, mir-129-2-3p, mir-1-3p). These findings identify potential biomarkers that may increase knowledge of the mechanisms underlying ATH and their connection to risk factors, aiding in the development of new therapies.
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Affiliation(s)
- Hossain Mohammad Hridoy
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Nasim Haidar
- Department of Electrical and Electronic Engineering, Rangpur Engineering College, Rangpur, Bangladesh
| | - Chadni Khatun
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Arnob Sarker
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Pervez Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Abdul Aziz
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Tofazzal Hossain
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
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Sadaf, Hazazi A, Alkhalil SS, Alsaiari AA, Gharib AF, Alhuthali HM, Rana S, Aloliqi AA, Eisa AA, Hasan MR, Dev K. Role of Fork-Head Box Genes in Breast Cancer: From Drug Resistance to Therapeutic Targets. Biomedicines 2023; 11:2159. [PMID: 37626655 PMCID: PMC10452497 DOI: 10.3390/biomedicines11082159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer has been acknowledged as one of the most notorious cancers, responsible for millions of deaths around the globe. Understanding the various factors, genetic mutations, comprehensive pathways, etc., that are involved in the development of breast cancer and how these affect the development of the disease is very important for improving and revitalizing the treatment of this global health issue. The forkhead-box gene family, comprising 19 subfamilies, is known to have a significant impact on the growth and progression of this cancer. The article looks into the various forkhead genes and how they play a role in different types of cancer. It also covers their impact on cancer drug resistance, interaction with microRNAs, explores their potential as targets for drug therapies, and their association with stem cells.
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Affiliation(s)
- Sadaf
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India;
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia;
| | - Samia S. Alkhalil
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 11961, Saudi Arabia;
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.F.G.); (H.M.A.)
| | - Amal F. Gharib
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.F.G.); (H.M.A.)
| | - Hayaa M. Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.F.G.); (H.M.A.)
| | - Shanika Rana
- School of Biosciences, Apeejay Stya University, Gurugram 122003, India;
| | - Abdulaziz A. Aloliqi
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Alaa Abdulaziz Eisa
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Medina 30002, Saudi Arabia;
| | - Mohammad Raghibul Hasan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 11961, Saudi Arabia;
| | - Kapil Dev
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India;
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Abstract
Axenfeld-Rieger syndrome is a rare multi-system disorder associated with cardiac anomalies. All patients with a diagnosis of Axenfeld-Rieger syndrome were identified from our electronic medical record. Chart review was performed to document the presence and types of CHD. Out of 58 patients, 14 (24.1%) had CHD and a wide variety of cardiac lesions were identified.
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Affiliation(s)
- Nishma Valikodath
- Department of Pediatrics, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, USA
| | - James A Johns
- Division of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, USA
| | - Justin Godown
- Division of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, USA
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8
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Fang Y, Ji Z, Zhou W, Abante J, Koldobskiy MA, Ji H, Feinberg A. DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence. Nucleic Acids Res 2023; 51:2046-2065. [PMID: 36762477 PMCID: PMC10018346 DOI: 10.1093/nar/gkad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 12/02/2022] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
Epigenetic information defines tissue identity and is largely inherited in development through DNA methylation. While studied mostly for mean differences, methylation also encodes stochastic change, defined as entropy in information theory. Analyzing allele-specific methylation in 49 human tissue sample datasets, we find that methylation entropy is associated with specific DNA binding motifs, regulatory DNA, and CpG density. Then applying information theory to 42 mouse embryo methylation datasets, we find that the contribution of methylation entropy to time- and tissue-specific patterns of development is comparable to the contribution of methylation mean, and methylation entropy is associated with sequence and chromatin features conserved with human. Moreover, methylation entropy is directly related to gene expression variability in development, suggesting a role for epigenetic entropy in developmental plasticity.
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Affiliation(s)
- Yuqi Fang
- Center for Epigenetics, Johns Hopkins University, 855 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Zhicheng Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jordi Abante
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University, 855 N. Wolfe St., Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University, 855 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, 600 N Wolfe St, Baltimore, MD 21205, USA
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9
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Davidsen N, Ramhøj L, Kugathas I, Evrard B, Darde TA, Chalmel F, Svingen T, Rosenmai AK. PFOS disrupts key developmental pathways during hiPSC-derived cardiomyocyte differentiation in vitro. Toxicol In Vitro 2022; 85:105475. [PMID: 36116746 DOI: 10.1016/j.tiv.2022.105475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/17/2022] [Accepted: 09/12/2022] [Indexed: 11/26/2022]
Abstract
Exposure to perfluorooctanesulfonic acid (PFOS) has been associated with congenital heart disease (CHD) and decreased birth weight. PFOS exposure can disrupt signaling pathways relevant for cardiac development in stem cell-derived cardiomyocyte assays, such as the PluriBeat assay, where spheroids of human induced pluripotent stem cells (hiPSCs) differentiate into contracting cardiomyocytes. Notably, cell line origin can also affect how the assay responds to chemical exposure. Herein, we examined the effect of PFOS on cardiomyocyte differentiation by transcriptomics profiling of two different hiPSC lines to see if they exhibit a common pattern of disruption. Two stages of differentiation were investigated: the cardiac progenitor stage and the cardiomyocyte stage. Many differentially expressed genes (DEGs) were observed between cell lines independent of exposure. However, 135 DEGs were identified as common between the two cell lines. Of these, 10 DEGs were associated with GO-terms related to the heart. PFOS exposure disrupted multiple signaling pathways relevant to cardiac development, including WNT, TGF, HH, and EGF. Of these pathways, genes related to the non-canonical WNTCa2+ signaling was particularly affected. PFOS thus has the capacity to disrupt pathways important for cardiac development and function.
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Affiliation(s)
- Nichlas Davidsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Louise Ramhøj
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Indusha Kugathas
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000 Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000 Rennes, France
| | | | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000 Rennes, France
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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Lozano-Velasco E, Garcia-Padilla C, del Mar Muñoz-Gallardo M, Martinez-Amaro FJ, Caño-Carrillo S, Castillo-Casas JM, Sanchez-Fernandez C, Aranega AE, Franco D. Post-Transcriptional Regulation of Molecular Determinants during Cardiogenesis. Int J Mol Sci 2022; 23:ijms23052839. [PMID: 35269981 PMCID: PMC8911333 DOI: 10.3390/ijms23052839] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/19/2022] [Accepted: 02/26/2022] [Indexed: 12/15/2022] Open
Abstract
Cardiovascular development is initiated soon after gastrulation as bilateral precardiac mesoderm is progressively symmetrically determined at both sides of the developing embryo. The precardiac mesoderm subsequently fused at the embryonic midline constituting an embryonic linear heart tube. As development progress, the embryonic heart displays the first sign of left-right asymmetric morphology by the invariably rightward looping of the initial heart tube and prospective embryonic ventricular and atrial chambers emerged. As cardiac development progresses, the atrial and ventricular chambers enlarged and distinct left and right compartments emerge as consequence of the formation of the interatrial and interventricular septa, respectively. The last steps of cardiac morphogenesis are represented by the completion of atrial and ventricular septation, resulting in the configuration of a double circuitry with distinct systemic and pulmonary chambers, each of them with distinct inlets and outlets connections. Over the last decade, our understanding of the contribution of multiple growth factor signaling cascades such as Tgf-beta, Bmp and Wnt signaling as well as of transcriptional regulators to cardiac morphogenesis have greatly enlarged. Recently, a novel layer of complexity has emerged with the discovery of non-coding RNAs, particularly microRNAs and lncRNAs. Herein, we provide a state-of-the-art review of the contribution of non-coding RNAs during cardiac development. microRNAs and lncRNAs have been reported to functional modulate all stages of cardiac morphogenesis, spanning from lateral plate mesoderm formation to outflow tract septation, by modulating major growth factor signaling pathways as well as those transcriptional regulators involved in cardiac development.
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Affiliation(s)
- Estefania Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
| | - Carlos Garcia-Padilla
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Department of Anatomy, Embryology and Zoology, School of Medicine, University of Extremadura, 06006 Badajoz, Spain
| | - Maria del Mar Muñoz-Gallardo
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Francisco Jose Martinez-Amaro
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Sheila Caño-Carrillo
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Juan Manuel Castillo-Casas
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Cristina Sanchez-Fernandez
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
| | - Amelia E. Aranega
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
- Correspondence:
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Maderazo D, Flegg JA, Algama M, Ramialison M, Keith J. Detection and identification of cis-regulatory elements using change-point and classification algorithms. BMC Genomics 2022; 23:78. [PMID: 35078412 PMCID: PMC8790847 DOI: 10.1186/s12864-021-08190-0] [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: 04/12/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptional regulation is primarily mediated by the binding of factors to non-coding regions in DNA. Identification of these binding regions enhances understanding of tissue formation and potentially facilitates the development of gene therapies. However, successful identification of binding regions is made difficult by the lack of a universal biological code for their characterisation. RESULTS We extend an alignment-based method, changept, and identify clusters of biological significance, through ontology and de novo motif analysis. Further, we apply a Bayesian method to estimate and combine binary classifiers on the clusters we identify to produce a better performing composite. CONCLUSIONS The analysis we describe provides a computational method for identification of conserved binding sites in the human genome and facilitates an alternative interrogation of combinations of existing data sets with alignment data.
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Affiliation(s)
- Dominic Maderazo
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, 3010, VIC, Australia.
| | - Jennifer A Flegg
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Manjula Algama
- School of Mathematics, Monash University, Melbourne, 3800, VIC, Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Melbourne, 3800, VIC, Australia
| | - Jonathan Keith
- School of Mathematics, Monash University, Melbourne, 3800, VIC, Australia
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12
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Detection of Novel Potential Regulators of Stem Cell Differentiation and Cardiogenesis through Combined Genome-Wide Profiling of Protein-Coding Transcripts and microRNAs. Cells 2021; 10:cells10092477. [PMID: 34572125 PMCID: PMC8469649 DOI: 10.3390/cells10092477] [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: 08/01/2021] [Revised: 09/02/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
In vitro differentiation of embryonic stem cells (ESCs) provides a convenient basis for the study of microRNA-based gene regulation that is relevant for early cardiogenic processes. However, to which degree insights gained from in vitro differentiation models can be readily transferred to the in vivo system remains unclear. In this study, we profiled simultaneous genome-wide measurements of mRNAs and microRNAs (miRNAs) of differentiating murine ESCs (mESCs) and integrated putative miRNA-gene interactions to assess miRNA-driven gene regulation. To identify interactions conserved between in vivo and in vitro, we combined our analysis with a recent transcriptomic study of early murine heart development in vivo. We detected over 200 putative miRNA-mRNA interactions with conserved expression patterns that were indicative of gene regulation across the in vitro and in vivo studies. A substantial proportion of candidate interactions have been already linked to cardiogenesis, supporting the validity of our approach. Notably, we also detected miRNAs with expression patterns that closely resembled those of key developmental transcription factors. The approach taken in this study enabled the identification of miRNA interactions in in vitro models with potential relevance for early cardiogenic development. Such comparative approaches will be important for the faithful application of stem cells in cardiovascular research.
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13
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Ru W, Qi A, Shen X, Yue B, Zhang X, Wang J, Cao H, Chen H. The circular RNA circCPE regulates myoblast development by sponging miR-138. J Anim Sci Biotechnol 2021; 12:102. [PMID: 34493338 PMCID: PMC8424951 DOI: 10.1186/s40104-021-00618-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/05/2021] [Indexed: 01/19/2023] Open
Abstract
Background Skeletal muscle development, a long-term and complex process, is controlled by a set of the myogenic genes. Circular RNAs (circRNAs), a class of noncoding RNA, have been shown to regulate various biological processes. Recent studies indicate circRNAs may be involved in myogenesis, but the role and regulatory mechanism of circRNAs in myogenesis is largely unknown. In the present study, circCPE was firstly found to promote the bovine myoblast proliferation and inhibit cell apoptosis and differentiation by influencing the expression of FOXC1 in a miR138-mediated manner. And in vivo experiments revealed that overexpression of circCPE attenuates skeletal muscle regeneration. Results We identified a novel circular RNA circCPE by analyzing circRNAs sequencing data of bovine muscle tissue. Sequencing verification, RNase R treatment and Actinomycin D treatment confirmed the circular nature of circCPE in bovine muscle. Functional assays showed that overexpression of circCPE could inhibit bovine myoblast apoptosis and differentiation, as well as facilitate cell proliferation. Moreover, in vivo experiments revealed that overexpression of circCPE attenuates skeletal muscle regeneration. In consideration of circRNA action as miRNAs sponge, we found that circCPE harbors miR-138 binding sites and absorbed miR-138. Mechanistically, the rescue experiments showed that the overexpression of circCPE can counteract the inhibitory effect of miR-138 on the cell proliferation and the accelerated effects on the differentiation and apoptosis. Subsequently, we found that circCPE sequester the inhibitory effect of miR-138 on FOXC1 so as to involve in myogenesis. Conclusions Collectively, we constructed a novel circCPE/miR-138/FOXC1 regulatory network in bovine myogenesis, which further provide stronger evidence that circRNA involved in muscle development acting as miRNA sponge. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00618-7.
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Affiliation(s)
- Wenxiu Ru
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ao Qi
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xuemei Shen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Binglin Yue
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoyan Zhang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jian Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hui Cao
- Shaanxi Kingbull Livestock co.,LTD, Yangling, 712100, Shaanxi, China
| | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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14
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Ferre-Fernández JJ, Sorokina EA, Thompson S, Collery RF, Nordquist E, Lincoln J, Semina EV. Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome. Hum Mol Genet 2021; 29:2723-2735. [PMID: 32720677 DOI: 10.1093/hmg/ddaa163] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022] Open
Abstract
The Forkhead Box C1 (FOXC1) gene encodes a forkhead/winged helix transcription factor involved in embryonic development. Mutations in this gene cause dysgenesis of the anterior segment of the eye, most commonly Axenfeld-Rieger syndrome (ARS), often with other systemic features. The developmental mechanisms and pathways regulated by FOXC1 remain largely unknown. There are two conserved orthologs of FOXC1 in zebrafish, foxc1a and foxc1b. To further examine the role of FOXC1 in vertebrates, we generated foxc1a and foxc1b single knockout zebrafish lines and bred them to obtain various allelic combinations. Three genotypes demonstrated visible phenotypes: foxc1a-/- single homozygous and foxc1-/- double knockout homozygous embryos presented with similar characteristics comprised of severe global vascular defects and early lethality, as well as microphthalmia, periocular edema and absence of the anterior chamber of the eye; additionally, fish with heterozygous loss of foxc1a combined with homozygosity for foxc1b (foxc1a+/-;foxc1b-/-) demonstrated craniofacial defects, heart anomalies and scoliosis. All other single and combined genotypes appeared normal. Analysis of foxc1 expression detected a significant increase in foxc1a levels in homozygous and heterozygous mutant eyes, suggesting a mechanism for foxc1a upregulation when its function is compromised; interestingly, the expression of another ARS-associated gene, pitx2, was responsive to the estimated level of wild-type Foxc1a, indicating a possible role for this protein in the regulation of pitx2 expression. Altogether, our results support a conserved role for foxc1 in the formation of many organs, consistent with the features observed in human patients, and highlight the importance of correct FOXC1/foxc1 dosage for vertebrate development.
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Affiliation(s)
- Jesús-José Ferre-Fernández
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Elena A Sorokina
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Samuel Thompson
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Ross F Collery
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Emily Nordquist
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Joy Lincoln
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA.,Division of Pediatric Cardiology, Herma Heart Institute, Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Elena V Semina
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA.,Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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15
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Chen HY, Xiao ZZ, Ling X, Xu RN, Zhu P, Zheng SY. ELAVL1 is transcriptionally activated by FOXC1 and promotes ferroptosis in myocardial ischemia/reperfusion injury by regulating autophagy. Mol Med 2021; 27:14. [PMID: 33568052 PMCID: PMC7874472 DOI: 10.1186/s10020-021-00271-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
Aims Myocardial ischemia is the most common form of cardiovascular disease and the leading cause of morbidity and mortality. Understanding the mechanisms is very crucial for the development of effective therapy. Therefore, this study aimed to investigate the functional roles and mechanisms by which ELAVL1 regulates myocardial ischemia and reperfusion (I/R) injury. Methods Mouse myocardial I/R model and cultured myocardial cells exposed to hypoxia/reperfusion (H/R) were used in this study. Features of ferroptosis were evidenced by LDH activity, GPx4 activity, cellular iron, ROS, LPO, and GSH levels. The expression levels of autophagy markers (Beclin-1, p62, LC3), ELAVL1 and FOXC1 were measured by qRT-PCR, immunostaining and western blot. RIP assay, biotin-pull down, ChIP and dual luciferase activity assay were employed to examine the interactions of ELAVL1/Beclin-1 mRNA and FOXC1/ELAVL1 promoter. CCK-8 assay was used to examine viability of cells. TTC staining was performed to assess the myocardial I/R injury. Results Myocardial I/R surgery induced ferroptosis and up-regulated ELAVL1 level. Knockdown of ELAVL1 decreased ferroptosis and ameliorated I/R injury. Si-ELAVL1 repressed autophagy and inhibition of autophagy by inhibitor suppressed ferroptosis and I/R injury in myocardial cells. Increase of autophagy could reverse the effects of ELAVL1 knockdown on ferroptosis and I/R injury. ELAVL1 directly bound with and stabilized Beclin-1 mRNA. Furthermore, FOXC1 bound to ELAVL1 promoter region and activated its transcription upon H/R exposure. Conclusion FOXC1 transcriptionally activated ELAVL1 may promote ferroptosis during myocardial I/R by modulating autophagy, leading to myocardial injury. Inhibition of ELAVL1-mediated autophagic ferroptosis would be a new viewpoint in the treatment of myocardial I/R injury.
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Affiliation(s)
- Hui-Yong Chen
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, No.1838 North Guangzhou Avenue, Baiyun District, Guangzhou, 510515, Guangdong, People's Republic of China.,Department of Thoracic Surgery, Yuebei People's Hospital, Shantou University, Shaoguan, 512026, Guangdong, People's Republic of China
| | - Ze-Zhou Xiao
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, No.1838 North Guangzhou Avenue, Baiyun District, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xiao Ling
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, No.1838 North Guangzhou Avenue, Baiyun District, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Rong-Ning Xu
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, No.1838 North Guangzhou Avenue, Baiyun District, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Peng Zhu
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, No.1838 North Guangzhou Avenue, Baiyun District, Guangzhou, 510515, Guangdong, People's Republic of China.
| | - Shao-Yi Zheng
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, No.1838 North Guangzhou Avenue, Baiyun District, Guangzhou, 510515, Guangdong, People's Republic of China.
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16
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Lee JA, An J, Taniguchi J, Kashiwazaki G, Pandian GN, Parveen N, Kang TM, Sugiyama H, De D, Kim KK. Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells. J Cell Physiol 2020; 236:3946-3962. [PMID: 33164232 DOI: 10.1002/jcp.30140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/25/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
The epigenome has an essential role in orchestrating transcriptional activation and modulating key developmental processes. Previously, we developed a library of pyrrole-imidazole polyamides (PIPs) conjugated with suberoylanilide hydroxamic acid (SAHA), a histone deacetylase (HDAC) inhibitor, for the purpose of sequence-specific modification of epigenetics. Based on the gene expression profile of SAHA-PIPs and screening studies using the α-myosin heavy chain promoter-driven reporter and SAHA-PIP library, we identified that SAHA-PIP G activates cardiac-related genes. Studies in mouse ES cells showed that SAHA-PIP G could enhance the generation of spontaneous beating cells, which is consistent with upregulation of several cardiac-related genes. Moreover, ChIP-seq results confirmed that the upregulation of cardiac-related genes is highly correlated with epigenetic activation, relevant to the sequence-specific binding of SAHA-PIP G. This proof-of-concept study demonstrating the applicability of SAHA-PIP not only improves our understanding of epigenetic alterations involved in cardiomyogenesis but also provides a novel chemical-based strategy for stem cell differentiation.
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Affiliation(s)
- Jin-A Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Jieun An
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Ganesh N Pandian
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Nazia Parveen
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Tong Mook Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Debojyoti De
- Department of Biotechnology, National Institute of Technology, Durgapur, Burdwan, West Bengal, India
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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17
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Johnson CJ, Razy-Krajka F, Stolfi A. Expression of smooth muscle-like effectors and core cardiomyocyte regulators in the contractile papillae of Ciona. EvoDevo 2020; 11:15. [PMID: 32774829 PMCID: PMC7397655 DOI: 10.1186/s13227-020-00162-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/22/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The evolution of vertebrate smooth muscles is obscured by lack of identifiable smooth muscle-like cells in tunicates, the invertebrates most closely related to vertebrates. A recent evolutionary model was proposed in which smooth muscles arose before the last bilaterian common ancestor, and were later diversified, secondarily lost or modified in the branches leading to extant animal taxa. However, there is currently no data from tunicates to support this scenario. METHODS AND RESULTS Here, we show that the axial columnar cells, a unique cell type in the adhesive larval papillae of the tunicate Ciona, are enriched for orthologs of vertebrate smooth/non-muscle-specific effectors of contractility, in addition to developing from progenitors that express conserved cardiomyocyte regulatory factors. We show that these cells contract during the retraction of the Ciona papillae during larval settlement and metamorphosis. CONCLUSIONS We propose that the axial columnar cells of Ciona are a myoepithelial cell type required for transducing external stimuli into mechanical forces that aid in the attachment of the motile larva to its final substrate. Furthermore, they share developmental and functional features with vertebrate myoepithelial cells, vascular smooth muscle cells, and cardiomyocytes. We discuss these findings in the context of the proposed models of vertebrate smooth muscle and cardiomyocyte evolution.
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18
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FoxC1-Induced Vascular Niche Improves Survival and Myocardial Repair of Mesenchymal Stem Cells in Infarcted Hearts. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7865395. [PMID: 32963702 PMCID: PMC7490631 DOI: 10.1155/2020/7865395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
Abstract
Aims Forkhead box C1 (FoxC1) is essential for maintaining the hair follicle stem cell niche. The role of FoxC1 in maintaining mesenchymal stem cell (MSC) niches after myocardial infarction (MI) has not been directly determined to date. In this study, we determined to explore the possible roles and mechanisms of FoxC1 on MSC survival and function in the ischemic niche. Methods and Results MI model was established in this study, and expression level of FoxC1 was overexpressed or knocked down through efficient delivery of FoxC1 transfection or siFoxC1. Fifteen days later, the animals were allocated randomly to receive phosphate-buffered saline (PBS) injection or MSC transplantation. We identified FoxC1 as a key regulator of maintaining the vascular niche in the infarcted hearts (IHs) by driving proangiogenic and anti-inflammatory cytokines while repressing inflammatory and fibrotic factor expression. This vascular niche improved MSC survival and capacity in the IHs. Importantly, FoxC1 interacted with MSCs and was required for vessel specification and differentiation of engrafted MSCs in the ischemic niches, promoting myocardial repair. Inhibiting FoxC1 abolished these effects. Conclusion These results definitively implicate FoxC1 signaling in maintaining ischemic vascular niche, which may be helpful in myocardial repair induced by MSC therapy.
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19
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Haidar MN, Islam MB, Chowdhury UN, Rahman MR, Huq F, Quinn JMW, Moni MA. Network-based computational approach to identify genetic links between cardiomyopathy and its risk factors. IET Syst Biol 2020; 14:75-84. [PMID: 32196466 PMCID: PMC8687405 DOI: 10.1049/iet-syb.2019.0074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/23/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Cardiomyopathy (CMP) is a group of myocardial diseases that progressively impair cardiac function. The mechanisms underlying CMP development are poorly understood, but lifestyle factors are clearly implicated as risk factors. This study aimed to identify molecular biomarkers involved in inflammatory CMP development and progression using a systems biology approach. The authors analysed microarray gene expression datasets from CMP and tissues affected by risk factors including smoking, ageing factors, high body fat, clinical depression status, insulin resistance, high dietary red meat intake, chronic alcohol consumption, obesity, high-calorie diet and high-fat diet. The authors identified differentially expressed genes (DEGs) from each dataset and compared those from CMP and risk factor datasets to identify common DEGs. Gene set enrichment analyses identified metabolic and signalling pathways, including MAPK, RAS signalling and cardiomyopathy pathways. Protein-protein interaction (PPI) network analysis identified protein subnetworks and ten hub proteins (CDK2, ATM, CDT1, NCOR2, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E and HIST1H4L). Five transcription factors (FOXC1, GATA2, FOXL1, YY1, CREB1) and five miRNAs were also identified in CMP. Thus the authors' approach reveals candidate biomarkers that may enhance understanding of mechanisms underlying CMP and their link to risk factors. Such biomarkers may also be useful to develop new therapeutics for CMP.
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Affiliation(s)
- Md Nasim Haidar
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj 6751, Bangladesh
| | - Fazlul Huq
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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20
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Gong R, Lin W, Gao A, Liu Y, Li J, Sun M, Chen X, Han S, Men C, Sun Y, Liu J. Forkhead box C1 promotes metastasis and invasion of non-small cell lung cancer by binding directly to the lysyl oxidase promoter. Cancer Sci 2019; 110:3663-3676. [PMID: 31597217 PMCID: PMC6890438 DOI: 10.1111/cas.14213] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/19/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence indicates that human forkhead box C1 (FOXC1) plays important roles in tumor development and metastasis. However, the underlying molecular mechanism of FOXC1 in non–small cell lung cancer (NSCLC) metastasis remains unclear. Here, we identified FOXC1 as an independent prognostic factor in NSCLC and showed clear biological implications in invasion and metastasis. FOXC1 overexpression enhanced the proliferation, migration and invasion of NSCLC cells, whereas FOXC1 silencing impaired the effects both in vitro and in vivo. Importantly, we found a positive correlation between FOXC1 expression and lysyl oxidase (LOX) expression in NSCLC cells and patient samples. Downregulation of LOX or LOX activity inhibition in NSCLC cells inhibited the FOXC1‐driven effects on cellular migration and invasion. Xenograft models showed that inhibition of LOX activity by β‐aminopropionitrile monofumarate decreased the number of lung metastases. Mechanistically, we demonstrated a novel FOXC1‐LOX mechanism that was involved in the invasion and metastasis of NSCLC. Dual‐luciferase assay and ChIP identified that FOXC1 bound directly in the LOX promoter region and activated its transcription. Collectively, the present study offered new insight into FOXC1 in the mediation of NSCLC metastasis through interaction with the LOX promoter and further revealed that targeted inhibition of LOX protein activity could prevent lung metastasis in murine xenograft models. These data implicated FOXC1 as a potential therapeutic strategy for the treatment of NSCLC metastasis.
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Affiliation(s)
- Rumei Gong
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Wenli Lin
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Aiqin Gao
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Yanli Liu
- Provincial Key Laboratory of Radio-Oncology, Shandong Cancer Hospital and Institute, Jinan, China
| | - Juan Li
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Meili Sun
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Xiaozheng Chen
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Shuyi Han
- Genetic and Molecular Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Chengsong Men
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Yuping Sun
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
| | - Jie Liu
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Jinan, China
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21
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Yoda K, Ohnuki Y, Masui S, Kurosawa H. Optimized conditions for the supplementation of human-induced pluripotent stem cell cultures with a GSK-3 inhibitor during embryoid body formation with the aim of inducing differentiation into mesodermal and cardiac lineage. J Biosci Bioeng 2019; 129:371-378. [PMID: 31615734 DOI: 10.1016/j.jbiosc.2019.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/27/2019] [Accepted: 09/21/2019] [Indexed: 01/19/2023]
Abstract
We optimized the conditions for the differentiation of human induced pluripotent stem cells (hiPSCs) into mesoderm lineage-committed cells by supplementing the cultures with CHIR, a selective GSK-3 inhibitor, during embryoid body (EB) formation. In vitro treatment with 4 μM CHIR during the late 2 days of a 4-day suspension culture period was most effective at promoting mesodermal differentiation. The resulting EBs showed a significant increase in the expression levels of mesoderm-associated genes (WNT3A, T, DKK1, GATA4, FOXC1, and MESP1) and a maintenance of OCT3/4 and NANOG expressions. Upon subsequent differentiation into a cardiac cell lineage, these EBs were shown to generate contractile cardiomyocytes. When shortening the CHIR treatment period to 1 day, the resulting EBs showed reduced expression of mesoderm-associated genes in comparison to the 2-day CHIR treatment. In particular, the expression level of FOXC1 in the 1-day CHIR-treated EBs was much lower than that of the 2-day CHIR-treated EBs. When the treatment period with CHIR was extended to 4 days, the resulting EBs presented significantly reduced expression of WNT3A, OCT3/4, and NANOG upon CHIR concentrations above 4 μM. Similarly, when CHIR treatment was conducted after the formation of EBs, the effectiveness of the GSK-3 inhibitor was reduced compared to a treatment performed during EB formation. Our results indicate that spatiotemporal constraints associated with EB formation, i.e., three-dimensional structuration and cell development in EBs, should be taken into account when designing EB formation-based differentiation protocol involving CHIR treatment.
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Affiliation(s)
- Kiyomi Yoda
- Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Yoshitsugu Ohnuki
- Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Shinji Masui
- Advanced Biotechnology Center, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Hiroshi Kurosawa
- Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan.
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22
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Liu P, Pu J, Zhang J, Chen Z, Wei K, Shi L. Bioinformatic analysis of miR-4792 regulates Radix Tetrastigma hemsleyani flavone to inhibit proliferation, invasion, and induce apoptosis of A549 cells. Onco Targets Ther 2019; 12:1401-1412. [PMID: 30863107 PMCID: PMC6389004 DOI: 10.2147/ott.s182525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Radix Tetrastigma hemsleyani, a kind of Chinese medicinal herb, contains multiple medicinal ingredients and can exert a variety of pharmacological activities. Our previous study revealed that miR-4792 was significantly upregulated in Radix Tetrastigma hemsleyani flavone (RTHF)-treated A549 cells; however, the regulatory mechanism of RTHF-treated A549 cells remains unclear. MATERIALS AND METHODS In this study, we investigated the antitumor mechanism and regulatory pathway of miR-4792 in RTHF-treated A549 cells, and the target genes were predicted and pathway enrichment of miR-4792 was performed using bioinformatic analysis. RESULTS Our results confirmed that the upregulated expression of miR-4792 could inhibit cell proliferation and invasion, provoke cell cycle arrest, and induce apoptosis in A549 cells. Gene Ontology analysis showed that target genes of miR-4792 were enriched in protein binding, cytosol, cytoplasm, plasma membrane, and metal ion binding. Kyoto Encyclopedia of Genes and Genomes analysis showed that target genes of miR-4792 were enriched in aminoacyltRNA biosynthesis, AGE-RAGE signaling pathway in diabetic complications, sphingolipid signaling pathway, neuroactive ligand-receptor interaction, glycosaminoglycan degradation, and regulation of lipolysis in adipocytes. Additionally, FOXC1 was identified as an important target gene of miR-4792 in RTHF-treated A549 cells, and miR-4792 may be the target of some apoptotic-related proteins involved in induction of apoptosis in A549 cells by RTHF. Moreover, the intracellular Ca2+ levels of A549 cells were increased after RTHF treatment, which may be involved in the anticancer regulatory process of miR-4792 in RTHF-treated A549 cells. CONCLUSION These findings suggest a novel therapeutic approach for lung cancer that will be investigated in future studies.
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Affiliation(s)
- Peigang Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China,
- Department of Chinese Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Jinbao Pu
- Department of Chinese Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Junhui Zhang
- RuoHeng Family Farm, Zhejiang Dou Dou Bao Traditional Chinese Medicine Research Co., Ltd, Taizhou, Zhejiang, People's Republic of China
| | - Zhilu Chen
- Department of Hematology, Zhejiang Provincial Tongde Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Kemin Wei
- Department of Chinese Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang, People's Republic of China
- Department of Hematology, Zhejiang Provincial Tongde Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Lian'gen Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China,
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23
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Liu Z, Xu S, Chu H, Lu Y, Yuan P, Zeng X. Silencing FOXC1 inhibits growth and migration of human oral squamous cell carcinoma cells. Exp Ther Med 2018; 16:3369-3376. [PMID: 30233683 PMCID: PMC6143893 DOI: 10.3892/etm.2018.6627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/13/2018] [Indexed: 01/19/2023] Open
Abstract
Forkhead box C1 (FOXC1) is a transcription factor that serves an important role in regulating tumorigenesis and cancer progression. However, the expression and functional role of FOXC1 in oral squamous cell carcinoma (OSCC) remains unclear. FOXC1 protein expression was determined using immunohistochemical staining of OSCC tissues and normal tissues. Cell Counting Kit-8, colony formation, migration and 5-ethynyl-2′-deoxyuridine assays were performed to investigate the role and underlying mechanism of action of FOXC1 in OSCC. A consistent increase in the immunoreactive intensity of FOXC1 in OSCC tissues as compared with that in adjacent normal tissues was demonstrated. Knockdown of FOXC1 impaired cell growth and colony formation by inhibiting cell proliferation and reducing cyclin B1 and cyclin D1 levels in OSCC cells. FOXC1-silenced OSCC cells exhibited decreased migration compared with that demonstrated by the control cells, accompanied by a downregulation of matrix metalloproteinase (MMP)-2 and MMP-9. Collectively, the results of the present study demonstrated that FOXC1 functions as an oncogene in OSCC and may be an important therapeutic target and predictive biomarker for OSCC.
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Affiliation(s)
- Zhongjun Liu
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Shuaimei Xu
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Hongxing Chu
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Yu Lu
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Peiyan Yuan
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Xiongqun Zeng
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
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24
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Johnson J, Choi M, Dadmanesh F, Han B, Qu Y, Yu-Rice Y, Zhang X, Bagaria S, Taylor C, Giuliano AE, Amersi F, Cui X. FOXC1 identifies basal-like breast cancer in a hereditary breast cancer cohort. Oncotarget 2018; 7:75729-75738. [PMID: 27708239 PMCID: PMC5342773 DOI: 10.18632/oncotarget.12370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022] Open
Abstract
Breast cancers arising in the setting of the hereditary breast cancer genes BRCA1 and BRCA2 are most commonly classified as basal-like breast cancer (BLBC) or luminal breast cancer, respectively. BLBC is an aggressive subtype of breast cancer associated with liver and lung metastases and poorer prognosis than other subtypes and for which chemotherapy is the only systemic therapy. Multiple immunohistochemical markers are used to identify the basal-like subtype, including the absence of estrogen receptor alpha, progesterone receptor, and human epidermal growth factor receptor 2. Forkhead box C1 (FOXC1) has been identified as a specific marker expressed in BLBC in general breast cancer cohorts. We examined an institutional cohort of breast cancer patients with germline BRCA1 (n=46) and BRCA2 (n=35) mutations and found that FOXC1 expression on immunohistochemical staining is associated with BRCA1 vs BRCA2 mutations [30/46 vs. 6/35]. In BRCA1 mutant tumors, FOXC1 was expressed in 28/31 BLBC tumors and 2/13 non-BLBC tumors, In BRCA2 mutant tumors, FOXC1 was expressed in 5/5 BLBC tumors and 1/30 non-BLBC tumors. In cell culture models of BRCA1-mutant breast cancer, FOXC1 is associated with increased proliferation and may serve as a marker for sensitivity to PARP-inhibitor therapy with olaparib.
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Affiliation(s)
- Jeff Johnson
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael Choi
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Farnaz Dadmanesh
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Bingchen Han
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ying Qu
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yi Yu-Rice
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xiao Zhang
- Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sanjay Bagaria
- Department of Surgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Clive Taylor
- Department of Pathology and Laboratory Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Farin Amersi
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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25
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Yue Y, Jiang M, He L, Zhang Z, Zhang Q, Gu C, Liu M, Li N, Zhao Q. The transcription factor Foxc1a in zebrafish directly regulates expression of nkx2.5, encoding a transcriptional regulator of cardiac progenitor cells. J Biol Chem 2017; 293:638-650. [PMID: 29162723 DOI: 10.1074/jbc.ra117.000414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/17/2017] [Indexed: 01/19/2023] Open
Abstract
Cardiogenesis is a tightly controlled biological process required for formation of a functional heart. The transcription factor Foxc1 not only plays a crucial role in outflow tract development in mice, but is also involved in cardiac structure formation and normal function in humans. However, the molecular mechanisms by which Foxc1 controls cardiac development remain poorly understood. Previously, we reported that zebrafish embryos deficient in foxc1a, an ortholog of mammalian Foxc1, display pericardial edemas and die 9-10 days postfertilization. To further investigate Foxc1a's role in zebrafish cardiogenesis and identify its downstream target genes during early heart development, we comprehensively analyzed the cardiovascular phenotype of foxc1a-null zebrafish embryos. Our results confirmed that foxc1a-null mutants exhibit disrupted cardiac morphology, structure, and function. Performing transcriptome analysis on the foxc1a mutants, we found that the expression of the cardiac progenitor marker gene nkx2.5 was significantly decreased, but the expression of germ layer-patterning genes was unaffected. Dual-fluorescence in situ hybridization assays revealed that foxc1a and nkx2.5 are co-expressed in the anterior lateral plate mesoderm at the somite stage. Chromatin immunoprecipitation and promoter truncation assays disclosed that Foxc1a regulates nkx2.5 expression via direct binding to two noncanonical binding sites in the proximal nkx2.5 promoter. Moreover, functional rescue experiments revealed that developmental stage-specific nkx2.5 overexpression partially rescues the cardiac defects of the foxc1a-null embryos. Taken together, our results indicate that during zebrafish cardiogenesis, Foxc1a is active directly upstream of nkx2.5.
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Affiliation(s)
- Yunyun Yue
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Mingyang Jiang
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Luqingqing He
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Zhaojunjie Zhang
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Qinxin Zhang
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Chun Gu
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Meijing Liu
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Nan Li
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
| | - Qingshun Zhao
- From the Model Animal Research Center, Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing 210061, China
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26
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Wang J, Li W, Zheng X, Pang X, Du G. Research progress on the forkhead box C1. Oncotarget 2017; 9:12471-12478. [PMID: 29552326 PMCID: PMC5844762 DOI: 10.18632/oncotarget.22527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 11/01/2017] [Indexed: 01/19/2023] Open
Abstract
FOXC1 is a vital member of FOX families which play important roles in biological processes including proliferation, differentiation, apoptosis, migration, invasion, metabolism, and longevity. Here we are focusing on roles of FOXC1 and their mechanisms in cancers. FOXC1 promoted progress of many cancers, such as breast cancer (especially basal-like breast cancer), hepatocellular carcinoma, gastric cancer and so on. FOXC1 was also found to be associated with drug resistance of cancers. FOXC1 promoted metastasis of cancers by increasing expression of MMP7, NEDD9 and Snail. Proliferation and invasion of cancers were increased by FOXC1 by mediating NF-κB, MST1R and KLF4 expression. FOXC1 was associated with development by regulating expression of FGF19 and MSX1. Recently, FOXC1 was found to be required for niche of stem cells or development of stem cells by mediating expression of Gli2, CXCL12, SCF, NFATC1, BMP and Myh7. Overall, FOXC1 exerts its functions by many mechanisms and may be used as a potential biomarker for diseases.
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Affiliation(s)
- Jinhua Wang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China.,Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Wan Li
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Xiangjin Zheng
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Xiaocong Pang
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Guanhua Du
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China.,Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
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27
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Wang J, Li W, Zhao Y, Kang D, Fu W, Zheng X, Pang X, Du G. Members of FOX family could be drug targets of cancers. Pharmacol Ther 2017; 181:183-196. [PMID: 28830838 DOI: 10.1016/j.pharmthera.2017.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FOX families play important roles in biological processes, including metabolism, development, differentiation, proliferation, apoptosis, migration, invasion and longevity. Here we are focusing on roles of FOX members in cancers, FOX members and drug resistance, FOX members and stem cells. Finally, FOX members as drug targets of cancer treatment were discussed. Future perspectives of FOXC1 research were described in the end.
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Affiliation(s)
- Jinhua Wang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Wan Li
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Ying Zhao
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - De Kang
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Weiqi Fu
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Xiangjin Zheng
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Xiaocong Pang
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Guanhua Du
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China.
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28
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Hopkins A, Coatham ML, Berry FB. FOXC1 Regulates FGFR1 Isoform Switching to Promote Invasion Following TGFβ-Induced EMT. Mol Cancer Res 2017; 15:1341-1353. [DOI: 10.1158/1541-7786.mcr-17-0185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/13/2017] [Accepted: 07/03/2017] [Indexed: 11/16/2022]
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29
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Lin YJ, Shyu WC, Chang CW, Wang CC, Wu CP, Lee HT, Chen LJ, Hsieh CH. Tumor Hypoxia Regulates Forkhead Box C1 to Promote Lung Cancer Progression. Theranostics 2017; 7:1177-1191. [PMID: 28435457 PMCID: PMC5399585 DOI: 10.7150/thno.17895] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
Forkhead box C1 (FOXC1) is a member of the forkhead family of transcription factors that are characterized by a DNA-binding forkhead domain. Increasing evidence indicates that FOXC1 is involved in tumor progression. However, the role of tumor hypoxia in FOXC1 regulation and its impact on lung cancer progression are unclear. Here, we report that FOXC1 was upregulated in hypoxic areas of lung cancer tissues from rodents or humans. Hypoxic stresses significantly induced FOXC1 expression. Moreover, hypoxia activated FOXC1 transcription via direct binding of hypoxia-inducible factor-1α (HIF-1α) to the hypoxia-responsive element (HRE) in the FOXC1 promoter. FOXC1 gain-of-function in lung cancer cells promoted cell proliferation, migration, invasion, angiogenesis, and epithelial-mesenchymal transition in vitro. However, a knockdown of FOXC1 in lung cancer cells inhibited these effects. Notably, knockdown of tumor hypoxia-induced FOXC1 expression via HIF-1-mediated FOXC1 shRNAs in lung cancer xenograft models suppressed tumor growth and angiogenesis. Finally, systemic delivery of FOXC1 siRNA encapsulated in lipid nanoparticles inhibited tumor growth and increased survival time in lung cancer-bearing mice. Taken together, these data indicate that FOXC1 is a novel hypoxia-induced transcription factor and plays a critical role in tumor microenvironment-promoted lung cancer progression. Systemic FOXC1 blockade therapy may be an effective therapeutic strategy for lung cancer.
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30
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Slagle CE, Conlon FL. Emerging Field of Cardiomics: High-Throughput Investigations into Transcriptional Regulation of Cardiovascular Development and Disease. Trends Genet 2016; 32:707-716. [PMID: 27717505 DOI: 10.1016/j.tig.2016.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/25/2016] [Accepted: 09/01/2016] [Indexed: 01/19/2023]
Abstract
Congenital heart defects remain a leading cause of infant mortality in the western world, despite decades of research focusing on cardiovascular development and disease. With the recent emergence of several high-throughput technologies including RNA sequencing, chromatin-immunoprecipitation-coupled sequencing, mass-spectrometry-based proteomics analyses, and the numerous variations of these strategies, investigations into cardiac development have been transformed from candidate-based studies into whole-genome, -transcriptome, and -proteome undertakings. In this review, we discuss several reports that have emerged from our laboratory and others over the past 5 years that emphasize the versatility of large dataset-based investigations of cardiogenic transcription factors, from phenotypic validations and new gene implications to the identification of novel roles of well-studied transcriptional regulators.
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Affiliation(s)
- Christopher E Slagle
- McAllister Heart Institute, Lineberger Comprehensive Cancer Center, Integrative Program for Biological & Genome Sciences, Departments of Biology and Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Frank L Conlon
- McAllister Heart Institute, Lineberger Comprehensive Cancer Center, Integrative Program for Biological & Genome Sciences, Departments of Biology and Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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31
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Yeo HC, Ting S, Brena RM, Koh G, Chen A, Toh SQ, Lim YM, Oh SKW, Lee DY. Genome-Wide Transcriptome and Binding Sites Analyses Identify Early FOX Expressions for Enhancing Cardiomyogenesis Efficiency of hESC Cultures. Sci Rep 2016; 6:31068. [PMID: 27501774 PMCID: PMC4977469 DOI: 10.1038/srep31068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 07/14/2016] [Indexed: 01/19/2023] Open
Abstract
The differentiation efficiency of human embryonic stem cells (hESCs) into heart muscle cells (cardiomyocytes) is highly sensitive to culture conditions. To elucidate the regulatory mechanisms involved, we investigated hESCs grown on three distinct culture platforms: feeder-free Matrigel, mouse embryonic fibroblast feeders, and Matrigel replated on feeders. At the outset, we profiled and quantified their differentiation efficiency, transcriptome, transcription factor binding sites and DNA-methylation. Subsequent genome-wide analyses allowed us to reconstruct the relevant interactome, thereby forming the regulatory basis for implicating the contrasting differentiation efficiency of the culture conditions. We hypothesized that the parental expressions of FOXC1, FOXD1 and FOXQ1 transcription factors (TFs) are correlative with eventual cardiomyogenic outcome. Through WNT induction of the FOX TFs, we observed the co-activation of WNT3 and EOMES which are potent inducers of mesoderm differentiation. The result strengthened our hypothesis on the regulatory role of the FOX TFs in enhancing mesoderm differentiation capacity of hESCs. Importantly, the final proportions of cells expressing cardiac markers were directly correlated to the strength of FOX inductions within 72 hours after initiation of differentiation across different cell lines and protocols. Thus, we affirmed the relationship between early FOX TF expressions and cardiomyogenesis efficiency.
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Affiliation(s)
- Hock Chuan Yeo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Sherwin Ting
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore
| | - Romulo Martin Brena
- USC Epigenome Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Geoffrey Koh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore
| | - Allen Chen
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore
| | - Siew Qi Toh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Yu Ming Lim
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore
| | - Steve Kah Weng Oh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
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