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Geng X, Yuan J, Xu W, Zou D, Sun Y, Li J. YWHAB is regulated by IRX5 and inhibits the migration and invasion of breast cancer cells. Oncol Lett 2024; 28:469. [PMID: 39119237 PMCID: PMC11306988 DOI: 10.3892/ol.2024.14602] [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: 03/06/2024] [Accepted: 06/06/2024] [Indexed: 08/10/2024] Open
Abstract
Highly metastatic and heterogeneous breast cancer affects the health of women worldwide. Abnormal expression of tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein β (YWHAB), also known as 14-3-3β, is associated with the tumorigenesis and progression of bladder cancer, lung cancer and hepatocellular carcinoma; however, to the best of our knowledge, the role of YWHAB in breast cancer remains unknown. In the present study, a dual luciferase assay demonstrated that the transcription factor iroquois homeobox 5 may regulate YWHAB expression by affecting the promoter sequence upstream of its transcription start site. Subsequently, it was demonstrated that overexpression of YWHAB did not affect proliferation, but did reduce the migration and invasion of MDA-MB-231 cells. Furthermore, knockdown of YWHAB promoted the migration and invasion of MCF7 cells. Transcriptomics analysis demonstrated that when YWHAB was overexpressed, 61 genes were differentially expressed, of which 43 genes were upregulated and 18 genes were downregulated. These differentially expressed genes (DEGs) were enriched in cancer-related pathways, such as 'TNF signaling pathway' [Kyoto Encyclopedia of Genes and Genomes (KEGG): map04688]. The pathway with the largest number of DEGs was 'Rheumatoid arthritis' (KEGG: map05323). Notably, YWHAB downregulated vimentin, which is a mesenchymal marker, thus suggesting that it may weaken the mesenchymal properties of cells. These findings indicate that YWHAB may be a potential therapeutic target in breast cancer and further work should be performed to assess its actions as a potential tumor suppressor.
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Affiliation(s)
- Xuexia Geng
- School of Life Science, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Jun Yuan
- School of Life Science, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Wenjie Xu
- School of Life Science, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Deng Zou
- School of Life Science, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Yuxuan Sun
- School of Life Science, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Jun Li
- School of Life Science, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
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2
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Jiang B, Zheng J, Yao H, Wang Y, Song F, Huang C. IRX5 suppresses osteogenic differentiation of hBMSCs by inhibiting protein synthesis. J Cell Physiol 2024; 239:e31286. [PMID: 38666481 DOI: 10.1002/jcp.31286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
In our previous study, IRX5 has been revealed a significant role in adipogenesis of hBMSCs. Considering the expansion of adipose tissue in bone marrow in aged and ovariectomy-related osteoporosis, the effect of IRX5 on the osteogenesis of BMSCs still needs to be elucidated. In vivo, models of aging-induced and ovariectomy-induced osteoporotic mice, and in vitro studies of IRX5 gene gain- and loss-of-function in hBMSCs were employed. Histology, immunofluorescence, qRT-PCR, and Western blot analysis were performed to detect the functions of IRX5 in hBMSCs osteogenic differentiation. RNA-seq, transmission electron microscopy, Seahorse mito-stress assay, and Surface Sensing of Translation assay were conducted to explore the effect of mammalian/mechanistic target of rapamycin (mTOR)-mediated ribosomal translation and mitochondrial functions in the regulation of hBMSCs differentiation by IRX5. As a result, elevated IRX5 protein expression levels were observed in the bone marrow of osteoporotic mice compared to normal mice. IRX5 overexpression attenuated osteogenic processes, whereas IRX5 knockdown resulted in enhanced osteogenesis in hBMSCs. RNA-seq and enrichment analysis unveiled that IRX5 overexpression exerted inhibitory effects on ribosomal translation and mitochondrial functions. Furthermore, the application of the mTOR activator, MHY1485, effectively reversed the inhibitory impact of IRX5 on osteogenesis and mitochondrial functions in hBMSCs. In summary, our findings suggest that IRX5 restricts mTOR-mediated ribosomal translation, consequently impairing mitochondrial OxPhos, which in turn results in osteogenic dysfunction of hBMSCs.
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Affiliation(s)
- Bulin Jiang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Hubei, China
- Department of Prosthodontics, Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province; Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jiqi Zheng
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Hubei, China
| | - Hantao Yao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Hubei, China
| | - Yake Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Hubei, China
| | - Fangfang Song
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Hubei, China
| | - Cui Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Hubei, China
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3
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Catela C, Assimacopoulos S, Chen Y, Tsioras K, Feng W, Kratsios P. The Iroquois ( Iro/Irx) homeobox genes are conserved Hox targets involved in motor neuron development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596714. [PMID: 38853975 PMCID: PMC11160718 DOI: 10.1101/2024.05.30.596714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Iroquois (Iro/Irx) homeobox genes encode transcription factors with fundamental roles in animal development. Despite their link to various congenital conditions in humans, our understanding of Iro/Irx gene expression, function, and regulation remains incomplete. Here, we conducted a systematic expression analysis of all six mouse Irx genes in the embryonic spinal cord. We found five Irx genes (Irx1, Irx2, Irx3, Irx5, and Irx6) to be confined mostly to ventral spinal domains, offering new molecular markers for specific groups of post-mitotic motor neurons (MNs). Further, we engineered Irx2, Irx5, and Irx6 mouse mutants and uncovered essential but distinct roles for Irx2 and Irx6 in MN development. Last, we found that the highly conserved regulators of MN development across species, the HOX proteins, directly control Irx gene expression both in mouse and C. elegans MNs, critically expanding the repertoire of HOX target genes in the developing nervous system. Altogether, our study provides important insights into Iro/Irx expression and function in the developing spinal cord, and uncovers an ancient gene regulatory relationship between HOX and Iro/Irx genes.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Stavroula Assimacopoulos
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Konstantinos Tsioras
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
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4
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Lazarev D, Chau G, Bloemendal A, Churchhouse C, Neale BM. GUIDE deconstructs genetic architectures using association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592285. [PMID: 38766146 PMCID: PMC11100597 DOI: 10.1101/2024.05.03.592285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genome-wide association studies have revealed that the genetic architecture of most complex traits is characterized by a large number of distinct effects scattered across the genome. Functional enrichment analyses of these results suggest that the associations for any given complex trait are not purely random. Thus, we set out to leverage the genetic association results from many traits with a view to identifying the set of modules, or latent factors, that mediate these associations. The identification of such modules may aid in disease classification as well as the elucidation of complex disease mechanisms. We propose a method, Genetic Unmixing by Independent Decomposition (GUIDE), to estimate a set of statistically independent latent factors that best express the patterns of association across many traits. The resulting latent factors not only have desirable mathematical properties, such as sparsity and a higher variance explained (for both traits and variants), but are also able to single out and prioritize key biological features or pathophysiological mechanisms underlying a given trait or disease. Moreover, we show that these latent factors can index biological pathways as well as epidemiological and environmental influences that compose the genetic architecture of complex traits.
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5
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Petrikas M, Wingert RA. Slow down my beating heart: induction of cardiac fibrosis by Iroquois homeobox 2. Tissue Barriers 2024:2309036. [PMID: 38282252 DOI: 10.1080/21688370.2024.2309036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Cardiovascular diseases are a significant global health challenge and pervasive cause of mortality worldwide. Heart failure due to cardiovascular disease is characterized by the inability of the heart to pump blood efficiently to meet the metabolic demands of the body. The pathophysiology of heart failure involves myocardial remodeling due to excessive deposition of extracellular matrix proteins by cardiac myofibroblasts - structural changes which impair contractility, reduce compliance, and ultimately reduce stroke volume. Now, a recent report has uncovered an essential role for Iroquois homeobox 2 in the transcriptional regulation of cardiac fibrosis, illuminating new mechanistic insights that can be applied to developing future clinical therapies.
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Affiliation(s)
- Madeline Petrikas
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
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Cui Y, Xiao Q, Wang Z, Zhang Q, Liu Y, Hao W, Jiang J, Meng Q, Wei X. 1,2-bis(2,4,6-tribromophenoxy) ethane, a novel brominated flame retardant, disrupts intestinal barrier function via the IRX3/NOS2 axis in rat small intestine. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132597. [PMID: 37804762 DOI: 10.1016/j.jhazmat.2023.132597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/09/2023]
Abstract
Novel brominated flame retardants are widely used in electronics, textiles, furniture, and other products; they can enter the human body through ingestion and respiration and cause harm to the human body, and have been proven to have potential biological toxicity and accumulation effects. 1,2-bis(2,4,6-tribromophenoxy) ethane (BTBPE) is a widely used novel brominated flame retardant; however, there is a lack of research on its mechanism of toxicity, particularly that of intestinal toxicity. Currently, studies on the functionality of iroquois homeobox 3 (IRX3) are extremely limited. In our study, BTBPE was administered to Sprague-Dawley (SD) rats and rat small intestinal crypt epithelial cells (IEC6 cells) in vivo and in vitro, respectively, and hematoxylin and eosin (HE), immunohistochemical, Alcian blue-periodic acid-Schiff (AB-PAS), CCK8, acridine orange/ethidium bromide (AO/EB), fluorescent probes, qPCR, western blotting, and immunofluorescence analyses were performed. To explore the damage mechanism of BTBPE, we used siRNA to silence IRX3 and iNOs-IN-1 (yeast extract-peptone-wheat; YPW) to inhibit nitric oxide synthase 2 (NOS2). The results showed that BTBPE exposure caused inflammation and necroptosis in the jejunum and ileum, as well as destruction of the tight junctions and mucus layer. Moreover, BTBPE activated the IRX3/NOS2 axis both in vivo and in vitro. Silencing IRX3 or inhibiting NOS2 inhibits necroptosis and restores tight junctions in IEC6 cells. In conclusion, our study found that in the jejunum, ileum, and IEC6 cells, BTBPE exposure caused necroptosis and tight junction destruction by activating the IRX3/NOS2 axis. Blocking the IRX3/NOS2 axis can effectively inhibit necroptosis and restore tight junction. In addition, BTBPE exposure caused inflammation and loss of the mucous layer in the jejunum and ileum. Our study is the first to explore the mechanism of intestinal damage caused by BTBPE exposure and to discover new biological functions regulated by the IRX3/NOS2 axis, providing new research directions for necroptosis and tight junctions.
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Affiliation(s)
- Yuan Cui
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Qianqian Xiao
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Zhenyu Wang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Qiong Zhang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Yuetong Liu
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Weidong Hao
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Jianjun Jiang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Qinghe Meng
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Xuetao Wei
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, PR China.
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7
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Xu Q, Zhou W, Zhou Y, Zhang X, Jiang R, Ai Z, Chen J, Ma L. IRX2 regulates endometrial carcinoma oncogenesis by transcriptional repressing RUVBL1. Exp Cell Res 2024; 434:113866. [PMID: 38042247 DOI: 10.1016/j.yexcr.2023.113866] [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: 10/25/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 12/04/2023]
Abstract
Endometrial carcinoma (EC) is a rising concern among gynecological malignancies. Iroquois Homeobox 2 (IRX2), a member of the Iroquois homeobox gene family, demonstrates variable effects in different cancer types, emphasizing the need for extensive exploration of its involvement in EC progression. Utilizing TCGA and GEO databases, as well as performing immunohistochemistry (IHC) analysis on clinical samples, we assessed the expression levels of IRX2 and its promoter methylation in EC. To understand the functional roles of IRX2, we conducted various assays including in vitro CCK-8 assays, colony formation assays, cell invasion assays, and cell apoptosis assays. Moreover, we utilized in vivo subcutaneous xenograft mouse models. Additionally, we performed KEGG pathway and gene set enrichment analyses to gain insights into the underlying mechanisms. To validate the regulatory relationship between IRX2 and RUVBL1, we employed chromatin immunoprecipitation and luciferase reporter assays. Our results indicate significantly reduced levels of IRX2 expression in EC, correlating with higher histological grades, advanced clinical stages, and diminished overall survival. We observed that DNA methylation of the IRX2 promoter suppresses its expression in EC, with cg26333652 and cg11793269 playing critical roles as methylated sites. In contrast, ectopic overexpression of IRX2 substantially inhibits cell proliferation and invasion, and promotes cell apoptosis. Additionally, we discovered that IRX2 exerts negative regulation on the expression of RUVBL1, which is upregulated in EC and associated with a poorer prognosis. In conclusion, our findings indicate that decreased expression of IRX2 facilitates EC cell growth through the regulation of RUVBL1 expression, thereby contributing to the development of EC. Hence, targeting the IRX2-RUVBL1 axis holds promise as a potential therapeutic strategy for EC treatment.
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Affiliation(s)
- Qinyang Xu
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wanzhen Zhou
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuedi Zhou
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xueying Zhang
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rongzhen Jiang
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihong Ai
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Chen
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Li Ma
- Department of Gynecology and Obstetrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Chan CH, Lam YY, Wong N, Geng L, Zhang J, Ahola V, Zare A, Li RA, Lanner F, Keung W, Cheung YF. Abnormal developmental trajectory and vulnerability to cardiac arrhythmias in tetralogy of Fallot with DiGeorge syndrome. Commun Biol 2023; 6:969. [PMID: 37740059 PMCID: PMC10516936 DOI: 10.1038/s42003-023-05344-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. Ventricular dysfunction and cardiac arrhythmias are well-documented complications in patients with repaired TOF. Whether intrinsic abnormalities exist in TOF cardiomyocytes is unknown. We establish human induced pluripotent stem cells (hiPSCs) from TOF patients with and without DiGeorge (DG) syndrome, the latter being the most commonly associated syndromal association of TOF. TOF-DG hiPSC-derived cardiomyocytes (hiPSC-CMs) show impaired ventricular specification, downregulated cardiac gene expression and upregulated neural gene expression. Transcriptomic profiling of the in vitro cardiac progenitors reveals early bifurcation, as marked by ectopic RGS13 expression, in the trajectory of TOF-DG-hiPSC cardiac differentiation. Functional assessments further reveal increased arrhythmogenicity in TOF-DG-hiPSC-CMs. These findings are found only in the TOF-DG but not TOF-with no DG (ND) patient-derived hiPSC-CMs and cardiac progenitors (CPs), which have implications on the worse clinical outcomes of TOF-DG patients.
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Affiliation(s)
- Chun-Ho Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yin-Yu Lam
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Nicodemus Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lin Geng
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jilin Zhang
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
| | - Virpi Ahola
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
| | - Aman Zare
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
| | - Ronald Adolphus Li
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, The University of Hong Kong, Hong Kong, China
| | - Fredrik Lanner
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavagen 9, 17165, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Wendy Keung
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, The University of Hong Kong, Hong Kong, China
| | - Yiu-Fai Cheung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China.
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, The University of Hong Kong, Hong Kong, China.
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Ma ZG, Yuan YP, Fan D, Zhang X, Teng T, Song P, Kong CY, Hu C, Wei WY, Tang QZ. IRX2 regulates angiotensin II-induced cardiac fibrosis by transcriptionally activating EGR1 in male mice. Nat Commun 2023; 14:4967. [PMID: 37587150 PMCID: PMC10432509 DOI: 10.1038/s41467-023-40639-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Cardiac fibrosis is a common feature of chronic heart failure. Iroquois homeobox (IRX) family of transcription factors plays important roles in heart development; however, the role of IRX2 in cardiac fibrosis has not been clarified. Here we report that IRX2 expression is significantly upregulated in the fibrotic hearts. Increased IRX2 expression is mainly derived from cardiac fibroblast (CF) during the angiotensin II (Ang II)-induced fibrotic response. Using two CF-specific Irx2-knockout mouse models, we show that deletion of Irx2 in CFs protect against pathological fibrotic remodelling and improve cardiac function in male mice. In contrast, Irx2 gain of function in CFs exaggerate fibrotic remodelling. Mechanistically, we find that IRX2 directly binds to the promoter of the early growth response factor 1 (EGR1) and subsequently initiates the transcription of several fibrosis-related genes. Our study provides evidence that IRX2 regulates the EGR1 pathway upon Ang II stimulation and drives cardiac fibrosis.
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Affiliation(s)
- Zhen-Guo Ma
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Yu-Pei Yuan
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Di Fan
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Xin Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Teng Teng
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Peng Song
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Chun-Yan Kong
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Can Hu
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Wen-Ying Wei
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China
| | - Qi-Zhu Tang
- Department of Cardiology, Renmin Hospital of Wuhan University, 430060, Wuhan, PR China.
- Cardiovascular Research Institute of Wuhan University, 430060, Wuhan, PR China.
- Hubei Key Laboratory of Metabolic and Chronic Diseases, 430060, Wuhan, PR China.
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10
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Astrof S, Arriagada C, Saijoh Y, Francou A, Kelly RG, Moon A. Aberrant differentiation of second heart field mesoderm prefigures cellular defects in the outflow tract in response to loss of FGF8. Dev Biol 2023; 499:10-21. [PMID: 37060937 PMCID: PMC10686765 DOI: 10.1016/j.ydbio.2023.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/17/2023]
Abstract
Development of the outflow tract of the heart requires specification, proliferation and deployment of a progenitor cell population from the second heart field to generate the myocardium at the arterial pole of the heart. Disruption of these processes leads to lethal defects in rotation and septation of the outflow tract. We previously showed that Fibroblast Growth Factor 8 (FGF8) directs a signaling cascade in the second heart field that regulates critical aspects of OFT morphogenesis. Here we show that in addition to the survival and proliferation cues previously described, FGF8 provides instructive and patterning information to OFT myocardial cells and their progenitors that prevents their aberrant differentiation along a working myocardial program.
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Affiliation(s)
- Sophie Astrof
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ, USA
| | - Cecilia Arriagada
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ, USA
| | - Yukio Saijoh
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, USA
| | - Alexandre Francou
- Aix-Marseille Université, CNRS UMR 7288, Developmental Biology Institute of Marseille, Marseille, France
| | - Robert G Kelly
- Aix-Marseille Université, CNRS UMR 7288, Developmental Biology Institute of Marseille, Marseille, France
| | - Anne Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, USA.
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11
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Plaisance I, Chouvardas P, Sun Y, Nemir M, Aghagolzadeh P, Aminfar F, Shen S, Shim WJ, Rochais F, Johnson R, Palpant N, Pedrazzini T. A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Cardiovasc Res 2023; 119:1361-1376. [PMID: 36537036 PMCID: PMC10262180 DOI: 10.1093/cvr/cvac191] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 03/25/2024] Open
Abstract
AIMS The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). The human lncRNA CARMEN, which is known to dictate specification toward the cardiomyocyte (CM) and the smooth muscle cell (SMC) fates, generates a diversity of alternatively spliced isoforms. METHODS AND RESULTS The CARMEN locus can be manipulated to direct human primary cardiac precursor cells (CPCs) into specific cardiovascular fates. Investigating CARMEN isoform usage in differentiating CPCs represents therefore a unique opportunity to uncover isoform-specific functions in lncRNAs. Here, we identify one CARMEN isoform, CARMEN-201, to be crucial for SMC commitment. CARMEN-201 activity is encoded within an alternatively spliced exon containing a MIRc short interspersed nuclear element. This element binds the transcriptional repressor REST (RE1 Silencing Transcription Factor), targets it to cardiogenic loci, including ISL1, IRX1, IRX5, and SFRP1, and thereby blocks the CM gene program. In turn, genes regulating SMC differentiation are induced. CONCLUSIONS These data show how a critical physiological switch is wired by alternative splicing and functional transposable elements in a long noncoding RNA. They further demonstrated the crucial importance of the lncRNA isoform CARMEN-201 in SMC specification during heart development.
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Affiliation(s)
- Isabelle Plaisance
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Yuliangzi Sun
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Mohamed Nemir
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Parisa Aghagolzadeh
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Farhang Aminfar
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Sophie Shen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Francesca Rochais
- Aix Marseille University, Marseille Medical Genetics, INSERM, U1251, Marseille, France
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University of Bern, Bern, Switzerland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nathan Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
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12
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Miles C, Boukens BJ, Scrocco C, Wilde AA, Nademanee K, Haissaguerre M, Coronel R, Behr ER. Subepicardial Cardiomyopathy: A Disease Underlying J-Wave Syndromes and Idiopathic Ventricular Fibrillation. Circulation 2023; 147:1622-1633. [PMID: 37216437 PMCID: PMC11073566 DOI: 10.1161/circulationaha.122.061924] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 03/27/2023] [Indexed: 05/24/2023]
Abstract
Brugada syndrome (BrS), early repolarization syndrome (ERS), and idiopathic ventricular fibrillation (iVF) have long been considered primary electrical disorders associated with malignant ventricular arrhythmia and sudden cardiac death. However, recent studies have revealed the presence of subtle microstructural abnormalities of the extracellular matrix in some cases of BrS, ERS, and iVF, particularly within right ventricular subepicardial myocardium. Substrate-based ablation within this region has been shown to ameliorate the electrocardiographic phenotype and to reduce arrhythmia frequency in BrS. Patients with ERS and iVF may also exhibit low-voltage and fractionated electrograms in the ventricular subepicardial myocardium, which can be treated with ablation. A significant proportion of patients with BrS and ERS, as well as some iVF survivors, harbor pathogenic variants in the voltage-gated sodium channel gene, SCN5A, but the majority of genetic susceptibility of these disorders is likely to be polygenic. Here, we postulate that BrS, ERS, and iVF may form part of a spectrum of subtle subepicardial cardiomyopathy. We propose that impaired sodium current, along with genetic and environmental susceptibility, precipitates a reduction in epicardial conduction reserve, facilitating current-to-load mismatch at sites of structural discontinuity, giving rise to electrocardiographic changes and the arrhythmogenic substrate.
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Affiliation(s)
- Chris Miles
- Cardiovascular Clinical Academic Group, St. George’s University Hospitals’ NHS Foundation Trust and Molecular and Clinical Sciences Institute, St. George’s, University of London, UK (C.M., C.S., E.R.B.)
| | - Bastiaan J. Boukens
- Department of Medical Biology, University of Amsterdam, the Netherlands (B.J.B.)
- University of Maastricht, Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, the Netherlands (B.J.B.)
| | - Chiara Scrocco
- Cardiovascular Clinical Academic Group, St. George’s University Hospitals’ NHS Foundation Trust and Molecular and Clinical Sciences Institute, St. George’s, University of London, UK (C.M., C.S., E.R.B.)
| | - Arthur A.M. Wilde
- Amsterdam UMC, University of Amsterdam, Department of Cardiology, the Netherlands (A.A.M.W.)
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, the Netherlands (A.A.M.W.)
- European Reference Network for rare, low-prevalence, and complex diseases of the heart: ERN GUARD-Heart (A.A.M.W., M.H.)
| | - Koonlawee Nademanee
- Center of Excellence in Arrhythmia Research Chulalongkorn University, Department of Medicine, Chulalongkorn University, Thailand (K.N.)
- Pacific Rim Electrophysiology Research Institute, Bumrungrad Hospital, Bangkok, Thailand (K.N.)
| | - Michel Haissaguerre
- European Reference Network for rare, low-prevalence, and complex diseases of the heart: ERN GUARD-Heart (A.A.M.W., M.H.)
- Institut Hospitalo-Universitaire Liryc, Electrophysiology and Heart Modeling Institute, Pessac, France (M.H.)
- Department of Electrophysiology and Cardiac Stimulation, Centre Hospitalier Universitaire de Bordeaux, France (M.H.)
| | - Ruben Coronel
- Department of Experimental Cardiology, Amsterdam University Medical Centers, Cardiovascular Science, the Netherlands (R.C.)
| | - Elijah R. Behr
- Cardiovascular Clinical Academic Group, St. George’s University Hospitals’ NHS Foundation Trust and Molecular and Clinical Sciences Institute, St. George’s, University of London, UK (C.M., C.S., E.R.B.)
- Mayo Clinic Healthcare, London, UK (E.R.B.)
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13
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Lu SHA, Wu YH, Su LY, Hsu ZT, Weng TH, Wang HY, Yu C, Hsu PWC, Tsai SY. Cardiac myofibrillogenesis is spatiotemporally modulated by the molecular chaperone UNC45B. Stem Cell Reports 2023:S2213-6711(23)00184-4. [PMID: 37295424 PMCID: PMC10362501 DOI: 10.1016/j.stemcr.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 06/12/2023] Open
Abstract
Sarcomeres are fundamental to cardiac muscle contraction. Their impairment can elicit cardiomyopathies, leading causes of death worldwide. However, the molecular mechanism underlying sarcomere assembly remains obscure. We used human embryonic stem cell (hESC)-derived cardiomyocytes (CMs) to reveal stepwise spatiotemporal regulation of core cardiac myofibrillogenesis-associated proteins. We found that the molecular chaperone UNC45B is highly co-expressed with KINDLIN2 (KIND2), a marker of protocostameres, and later its distribution overlaps with that of muscle myosin MYH6. UNC45B-knockout CMs display essentially no contractility. Our phenotypic analyses further reveal that (1) binding of Z line anchor protein ACTN2 to protocostameres is perturbed because of impaired protocostamere formation, resulting in ACTN2 accumulation; (2) F-ACTIN polymerization is suppressed; and (3) MYH6 becomes degraded, so it cannot replace non-muscle myosin MYH10. Our mechanistic study demonstrates that UNC45B mediates protocostamere formation by regulating KIND2 expression. Thus, we show that UNC45B modulates cardiac myofibrillogenesis by interacting spatiotemporally with various proteins.
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Affiliation(s)
- Serena Huei-An Lu
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Hsuan Wu
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Liang-Yu Su
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Zi-Ting Hsu
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Han Weng
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Yu Wang
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chiao Yu
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Paul Wei-Che Hsu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County 350, Taiwan
| | - Su-Yi Tsai
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 10617, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University, Taipei 10617, Taiwan.
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14
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Iroquois Family Genes in Gastric Carcinogenesis: A Comprehensive Review. Genes (Basel) 2023; 14:genes14030621. [PMID: 36980893 PMCID: PMC10048635 DOI: 10.3390/genes14030621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Gastric cancer (GC) is the fifth leading cause of cancer-associated death worldwide, accounting for 768,793 related deaths and 1,089,103 new cases in 2020. Despite diagnostic advances, GC is often detected in late stages. Through a systematic literature search, this study focuses on the associations between the Iroquois gene family and GC. Accumulating evidence indicates that Iroquois genes are involved in the regulation of various physiological and pathological processes, including cancer. To date, information about Iroquois genes in GC is very limited. In recent years, the expression and function of Iroquois genes examined in different models have suggested that they play important roles in cell and cancer biology, since they were identified to be related to important signaling pathways, such as wingless, hedgehog, mitogen-activated proteins, fibroblast growth factor, TGFβ, and the PI3K/Akt and NF-kB pathways. In cancer, depending on the tumor, Iroquois genes can act as oncogenes or tumor suppressor genes. However, in GC, they seem to mostly act as tumor suppressor genes and can be regulated by several mechanisms, including methylation, microRNAs and important GC-related pathogens. In this review, we provide an up-to-date review of the current knowledge regarding Iroquois family genes in GC.
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15
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Wang J, Morgan W, Saini A, Liu T, Lough J, Han L. Single-cell transcriptomic profiling reveals specific maturation signatures in human cardiomyocytes derived from LMNB2-inactivated induced pluripotent stem cells. Front Cell Dev Biol 2022; 10:895162. [PMID: 36518540 PMCID: PMC9742441 DOI: 10.3389/fcell.2022.895162] [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: 03/13/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2023] Open
Abstract
Mammalian cardiomyocyte maturation entails phenotypic and functional optimization during the late fetal and postnatal phases of heart development, both processes driven and coordinated by complex gene regulatory networks. Cardiomyocytes derived from human induced pluripotent stem cells (iPSCs) are heterogenous and immature, barely resembling their adult in vivo counterparts. To characterize relevant developmental programs and maturation states during human iPSC-cardiomyocyte differentiation, we performed single-cell transcriptomic sequencing, which revealed six cardiomyocyte subpopulations, whose heterogeneity was defined by cell cycle and maturation states. Two of those subpopulations were characterized by a mature, non-proliferative transcriptional profile. To further investigate the proliferation-maturation transition in cardiomyocytes, we induced loss-of-function of LMNB2, which represses cell cycle progression in primary cardiomyocytes in vivo. This resulted in increased maturation in LMNB2-inactivated cardiomyocytes, characterized by transcriptional profiles related to myofibril structure and energy metabolism. Furthermore, we identified maturation signatures and maturational trajectories unique for control and LMNB2-inactivated cardiomyocytes. By comparing these datasets with single-cell transcriptomes of human fetal hearts, we were able to define spatiotemporal maturation states in human iPSC-cardiomyocytes. Our results provide an integrated approach for comparing in vitro-differentiated cardiomyocytes with their in vivo counterparts and suggest a strategy to promote cardiomyocyte maturation.
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Affiliation(s)
- Jie Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - William Morgan
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
- Division of Pediatric Cardiology, Herma Heart Institute, Children’s Hospital of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ankur Saini
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
- Division of Pediatric Cardiology, Herma Heart Institute, Children’s Hospital of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - John Lough
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Lu Han
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
- Division of Pediatric Cardiology, Herma Heart Institute, Children’s Hospital of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
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16
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Caillaud A, Lévêque A, Thédrez A, Girardeau A, Canac R, Bray L, Baudic M, Barc J, Gaborit N, Lamirault G, Gardie B, Idriss S, Rimbert A, Le May C, Cariou B, Si-Tayeb K. FACS-assisted CRISPR-Cas9 genome editing of human induced pluripotent stem cells. STAR Protoc 2022; 3:101680. [PMID: 36115027 PMCID: PMC9490201 DOI: 10.1016/j.xpro.2022.101680] [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: 03/22/2022] [Revised: 06/30/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023] Open
Abstract
This manuscript proposes an efficient and reproducible protocol for the generation of genetically modified human induced pluripotent stem cells (hiPSCs) by genome editing using CRISPR-Cas9 technology. Here, we describe the experimental strategy for generating knockout (KO) and knockin (KI) clonal populations of hiPSCs using single-cell sorting by flow cytometry. We efficiently achieved up to 15 kb deletions, molecular tag insertions, and single-nucleotide editing in hiPSCs. We emphasize the efficacy of this approach in terms of cell culture time. For complete details on the use and execution of this protocol, please refer to Canac et al. (2022) and Bray et al. (2022).
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Affiliation(s)
- Amandine Caillaud
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France,Corresponding author
| | - Antoine Lévêque
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Aurélie Thédrez
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Aurore Girardeau
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Robin Canac
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Lise Bray
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Manon Baudic
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Julien Barc
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Nathalie Gaborit
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Guillaume Lamirault
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Betty Gardie
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France,Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
| | - Salam Idriss
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Antoine Rimbert
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Cédric Le May
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Bertrand Cariou
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France,Corresponding author
| | - Karim Si-Tayeb
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
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17
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Okada D, Okamoto Y, Io T, Oka M, Kobayashi D, Ito S, Yamada R, Ishii K, Ono K. Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans. Biomolecules 2022; 12:biom12060859. [PMID: 35740984 PMCID: PMC9221511 DOI: 10.3390/biom12060859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies.
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Affiliation(s)
- Daigo Okada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Shogoinkawahara-cho, Kyoto 606-8507, Japan; (D.O.); (R.Y.)
| | - Yosuke Okamoto
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
- Correspondence:
| | - Toshiro Io
- Research Department, Ono Pharmaceutical Co., Ltd., Kyutaromachi, Osaka 618-8585, Japan; (T.I.); (M.O.)
| | - Miho Oka
- Research Department, Ono Pharmaceutical Co., Ltd., Kyutaromachi, Osaka 618-8585, Japan; (T.I.); (M.O.)
| | - Daiki Kobayashi
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
| | - Suzuka Ito
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
| | - Ryo Yamada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Shogoinkawahara-cho, Kyoto 606-8507, Japan; (D.O.); (R.Y.)
| | - Kuniaki Ishii
- Department of Pharmacology, Faculty of medicine, Yamagata University, Iida-Nishi, Yamagata 990-9585, Japan;
| | - Kyoichi Ono
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
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18
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Kim KH, Oh Y, Liu J, Dababneh S, Xia Y, Kim RY, Kim DK, Ban K, Husain M, Hui CC, Backx PH. Irx5 and transient outward K + currents contribute to transmural contractile heterogeneities in the mouse ventricle. Am J Physiol Heart Circ Physiol 2022; 322:H725-H741. [PMID: 35245131 DOI: 10.1152/ajpheart.00572.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous studies have established that fast transmural gradients of transient outward K+ current (Ito,f) correlate with regional differences in action potential (AP) profile and excitation-contraction coupling (ECC) with high Ito,f expression in the epimyocardium (EPI) being associated with short APs and low contractility and vice versa. Herein, we investigated the effects of disrupted Ito,f gradient on contractile properties using mouse models of Irx5 knockout (Irx5-KO) for selective Ito,f elevation in the endomyocardium (ENDO) of the left ventricle (LV) and Kcnd2 ablation (KV4.2-KO) for selective Ito,freduction in the EPI. Irx5-KO mice exhibited decreased global LV contractility in association with reductions in cell shortening and Ca2+ transient amplitudes in isolated ENDO but not EPI cardiomyocytes. Moreover, transcriptional profiling revealed that the primary effect of Irx5 ablation on ECC-related genes was to increase Ito,f gene expression (i.e. Kcnd2 and Kcnip2) in the ENDO, but not the EPI. Indeed, KV4.2-KO mice showed selective increases in cell shortening and Ca2+ transients in isolated EPI cardiomyocytes, leading to enhanced ventricular contractility and mice lacking both Irx5 and Kcnd2 displayed elevated ventricular contractility comparable to KV4.2-KO mice. Our findings demonstrate that the transmural electromechanical heterogeneities in the healthy ventricles depend on the Irx5-dependent Ito,f gradients. These observations provide a useful framework for assessing the molecular mechanisms underlying the alterations in contractile heterogeneity seen in the diseased heart.
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Affiliation(s)
- Kyoung-Han Kim
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Yena Oh
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jie Liu
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Saif Dababneh
- University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - Ying Xia
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ri Youn Kim
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Dae-Kyum Kim
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kiwon Ban
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Mansoor Husain
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter H Backx
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Biology, Faculty of Science, York University, Toronto, ON, Canada.,Toronto General Research Institute, University Health Network, Toronto, ON, Canada
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19
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Canac R, Caillaud A, Cimarosti B, Girardeau A, Hamamy H, Reversade B, Bonnard C, Al Sayed ZR, David L, Poschmann J, Lemarchand P, Lamirault G, Gaborit N. Generation of three human induced pluripotent stem cell lines with IRX5 knockout and knockin genetic editions using CRISPR-Cas9 system. Stem Cell Res 2021; 58:102627. [PMID: 34929443 DOI: 10.1016/j.scr.2021.102627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 12/12/2021] [Indexed: 11/30/2022] Open
Abstract
Studies on animal models have shown that Irx5 is an important regulator of cardiac development and that it regulates ventricular electrical repolarization gradient in the adult heart. Mutations in IRX5 have also been linked in humans to cardiac conduction defects. In order to fully characterize the role of IRX5 during cardiac development and in cardiomyocyte function, we generated three genetically-modified human induced pluripotent stem cell lines: two knockout lines (heterozygous and homozygous) and a knockin HA-tagged line (homozygous).
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Affiliation(s)
- Robin Canac
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Amandine Caillaud
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Bastien Cimarosti
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Aurore Girardeau
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, Geneva University, Geneva 1211, Switzerland
| | - Bruno Reversade
- Genome Institute of Singapore, A*STAR, Singapore, Singapore; Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey; Department of Paediatrics, National, University of Singapore, Singapore, Singapore; Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore; Reproductive Biology Laboratory, Amsterdam UMC, Amsterdam-Zuidoost, the Netherlands
| | - Carine Bonnard
- Skin Research Institute of Singapore, A*STAR, Singapore, Singapore
| | - Zeina R Al Sayed
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Laurent David
- Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS, UMS 3556, F-44000 Nantes, France; Université de Nantes, CHU Nantes, INSERM, CRTI, UMR 1064, ITUN, F-44000 Nantes, France
| | - Jeremie Poschmann
- Université de Nantes, CHU Nantes, INSERM, CRTI, UMR 1064, ITUN, F-44000 Nantes, France
| | - Patricia Lemarchand
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Guillaume Lamirault
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Nathalie Gaborit
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France.
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20
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Dou Z, Son JE, Hui CC. Irx3 and Irx5 - Novel Regulatory Factors of Postnatal Hypothalamic Neurogenesis. Front Neurosci 2021; 15:763856. [PMID: 34795556 PMCID: PMC8593166 DOI: 10.3389/fnins.2021.763856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022] Open
Abstract
The hypothalamus is a brain region that exhibits highly conserved anatomy across vertebrate species and functions as a central regulatory hub for many physiological processes such as energy homeostasis and circadian rhythm. Neurons in the arcuate nucleus of the hypothalamus are largely responsible for sensing of peripheral signals such as leptin and insulin, and are critical for the regulation of food intake and energy expenditure. While these neurons are mainly born during embryogenesis, accumulating evidence have demonstrated that neurogenesis also occurs in postnatal-adult mouse hypothalamus, particularly in the first two postnatal weeks. This second wave of active neurogenesis contributes to the remodeling of hypothalamic neuronal populations and regulation of energy homeostasis including hypothalamic leptin sensing. Radial glia cell types, such as tanycytes, are known to act as neuronal progenitors in the postnatal mouse hypothalamus. Our recent study unveiled a previously unreported radial glia-like neural stem cell (RGL-NSC) population that actively contributes to neurogenesis in the postnatal mouse hypothalamus. We also identified Irx3 and Irx5, which encode Iroquois homeodomain-containing transcription factors, as genetic determinants regulating the neurogenic property of these RGL-NSCs. These findings are significant as IRX3 and IRX5 have been implicated in FTO-associated obesity in humans, illustrating the importance of postnatal hypothalamic neurogenesis in energy homeostasis and obesity. In this review, we summarize current knowledge regarding postnatal-adult hypothalamic neurogenesis and highlight recent findings on the radial glia-like cells that contribute to the remodeling of postnatal mouse hypothalamus. We will discuss characteristics of the RGL-NSCs and potential actions of Irx3 and Irx5 in the regulation of neural stem cells in the postnatal-adult mouse brain. Understanding the behavior and regulation of neural stem cells in the postnatal-adult hypothalamus will provide novel mechanistic insights in the control of hypothalamic remodeling and energy homeostasis.
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Affiliation(s)
- Zhengchao Dou
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Joe Eun Son
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chi-chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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21
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Yao J, Wu D, Zhang C, Yan T, Zhao Y, Shen H, Xue K, Huang X, Wang Z, Qiu Y. Macrophage IRX3 promotes diet-induced obesity and metabolic inflammation. Nat Immunol 2021; 22:1268-1279. [PMID: 34556885 DOI: 10.1038/s41590-021-01023-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 08/04/2021] [Indexed: 02/07/2023]
Abstract
Metabolic inflammation is closely linked to obesity, and is implicated in the pathogenesis of metabolic diseases. FTO harbors the strongest genetic association with polygenic obesity, and IRX3 mediates the effects of FTO on body weight. However, in what cells and how IRX3 carries out this control are poorly understood. Here we report that macrophage IRX3 promotes metabolic inflammation to accelerate the development of obesity and type 2 diabetes. Mice with myeloid-specific deletion of Irx3 were protected against diet-induced obesity and metabolic diseases via increasing adaptive thermogenesis. Mechanistically, macrophage IRX3 promoted proinflammatory cytokine transcription and thus repressed adipocyte adrenergic signaling, thereby inhibiting lipolysis and thermogenesis. JNK1/2 phosphorylated IRX3, leading to its dimerization and nuclear translocation for transcription. Further, lipopolysaccharide stimulation stabilized IRX3 by inhibiting its ubiquitination, which amplified the transcriptional capacity of IRX3. Together, our findings identify a new player, macrophage IRX3, in the control of body weight and metabolic inflammation, implicating IRX3 as a therapeutic target.
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Affiliation(s)
- Jingfei Yao
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Dongmei Wu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chunyan Zhang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ting Yan
- School of life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yiheng Zhao
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Hongyu Shen
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Kaili Xue
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xun Huang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zihao Wang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yifu Qiu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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22
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Lindström NO, Sealfon R, Chen X, Parvez RK, Ransick A, De Sena Brandine G, Guo J, Hill B, Tran T, Kim AD, Zhou J, Tadych A, Watters A, Wong A, Lovero E, Grubbs BH, Thornton ME, McMahon JA, Smith AD, Ruffins SW, Armit C, Troyanskaya OG, McMahon AP. Spatial transcriptional mapping of the human nephrogenic program. Dev Cell 2021; 56:2381-2398.e6. [PMID: 34428401 PMCID: PMC8396064 DOI: 10.1016/j.devcel.2021.07.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/06/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022]
Abstract
Congenital abnormalities of the kidney and urinary tract are among the most common birth defects, affecting 3% of newborns. The human kidney forms around a million nephrons from a pool of nephron progenitors over a 30-week period of development. To establish a framework for human nephrogenesis, we spatially resolved a stereotypical process by which equipotent nephron progenitors generate a nephron anlage, then applied data-driven approaches to construct three-dimensional protein maps on anatomical models of the nephrogenic program. Single-cell RNA sequencing identified progenitor states, which were spatially mapped to the nephron anatomy, enabling the generation of functional gene networks predicting interactions within and between nephron cell types. Network mining identified known developmental disease genes and predicted targets of interest. The spatially resolved nephrogenic program made available through the Human Nephrogenesis Atlas (https://sckidney.flatironinstitute.org/) will facilitate an understanding of kidney development and disease and enhance efforts to generate new kidney structures.
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Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Rachel Sealfon
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xi Chen
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guilherme De Sena Brandine
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern, Los Angeles, CA 90089, USA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bill Hill
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jian Zhou
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alicja Tadych
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Aaron Watters
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Aaron Wong
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Elizabeth Lovero
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Brendan H Grubbs
- Maternal Fetal Medicine Division, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew E Thornton
- Maternal Fetal Medicine Division, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern, Los Angeles, CA 90089, USA
| | - Seth W Ruffins
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chris Armit
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; BGI Hong Kong, 26/F, Kings Wing Plaza 2, 1 On Kwan Street, Shek Mun, NT, Hong Kong
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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23
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Farmer DT, Patel P, Choi R, Liu CY, Crump JG. A comprehensive series of Irx cluster mutants reveals diverse roles in facial cartilage development. Development 2021; 148:271157. [PMID: 34338288 DOI: 10.1242/dev.197244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 07/21/2021] [Indexed: 12/28/2022]
Abstract
Proper function of the vertebrate skeleton requires the development of distinct articulating embryonic cartilages. Irx transcription factors are arranged in co-regulated clusters that are expressed in the developing skeletons of the face and appendages. IrxB cluster genes are required for the separation of toes in mice and formation of the hyoid joint in zebrafish, yet whether Irx genes have broader roles in skeletal development remains unclear. Here, we perform a comprehensive loss-of-function analysis of all 11 Irx genes in zebrafish. We uncover conserved requirements for IrxB genes in formation of the fish and mouse scapula. In the face, we find a requirement for IrxAb genes and irx7 in formation of anterior neural crest precursors of the jaw, and for IrxBa genes in formation of endodermal pouches and gill cartilages. We also observe extensive joint loss and cartilage fusions in animals with combinatorial losses of Irx clusters, with in vivo imaging revealing that at least some of these fusions arise through inappropriate chondrogenesis. Our analysis reveals diverse roles for Irx genes in the formation and later segmentation of the facial skeleton.
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Affiliation(s)
- D'Juan T Farmer
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Punam Patel
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Rachelle Choi
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Chih-Yu Liu
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - J Gage Crump
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
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24
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Son JE, Dou Z, Kim KH, Wanggou S, Cha VSB, Mo R, Zhang X, Chen X, Ketela T, Li X, Huang X, Hui CC. Irx3 and Irx5 in Ins2-Cre + cells regulate hypothalamic postnatal neurogenesis and leptin response. Nat Metab 2021; 3:701-713. [PMID: 33859429 DOI: 10.1038/s42255-021-00382-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/08/2021] [Indexed: 12/24/2022]
Abstract
Obesity is mainly due to excessive food intake. IRX3 and IRX5 have been suggested as determinants of obesity in connection with the intronic variants of FTO, but how these genes contribute to obesity via changes in food intake remains unclear. Here, we show that mice doubly heterozygous for Irx3 and Irx5 mutations exhibit lower food intake with enhanced hypothalamic leptin response. By lineage tracing and single-cell RNA sequencing using the Ins2-Cre system, we identify a previously unreported radial glia-like neural stem cell population with high Irx3 and Irx5 expression in early postnatal hypothalamus and demonstrate that reduced dosage of Irx3 and Irx5 promotes neurogenesis in postnatal hypothalamus leading to elevated numbers of leptin-sensing arcuate neurons. Furthermore, we find that mice with deletion of Irx3 in these cells also exhibit a similar food intake and hypothalamic phenotype. Our results illustrate that Irx3 and Irx5 play a regulatory role in hypothalamic postnatal neurogenesis and leptin response.
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Affiliation(s)
- Joe Eun Son
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zhengchao Dou
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Kyoung-Han Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Ottawa Heart Institute and Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Siyi Wanggou
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Vincent Su Bin Cha
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rong Mo
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaoyun Zhang
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xinyu Chen
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Troy Ketela
- Princess Margaret Genomics Centre, University Health Network, Toronto, Ontario, Canada
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Huang
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chi-Chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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25
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Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer. Genes (Basel) 2021; 12:genes12050615. [PMID: 33919200 PMCID: PMC8143155 DOI: 10.3390/genes12050615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 01/19/2023] Open
Abstract
Alternative splicing (AS) is tightly regulated to maintain genomic stability in humans. However, tumor growth, metastasis and therapy resistance benefit from aberrant RNA splicing. Iroquois-class homeodomain protein 4 (IRX4) is a TALE homeobox transcription factor which has been implicated in prostate cancer (PCa) as a tumor suppressor through genome-wide association studies (GWAS) and functional follow-up studies. In the current study, we characterized 12 IRX4 transcripts in PCa cell lines, including seven novel transcripts by RT-PCR and sequencing. They demonstrate unique expression profiles between androgen-responsive and nonresponsive cell lines. These transcripts were significantly overexpressed in PCa cell lines and the cancer genome atlas program (TCGA) PCa clinical specimens, suggesting their probable involvement in PCa progression. Moreover, a PCa risk-associated SNP rs12653946 genotype GG was corelated with lower IRX4 transcript levels. Using mass spectrometry analysis, we identified two IRX4 protein isoforms (54.4 kDa, 57 kDa) comprising all the functional domains and two novel isoforms (40 kDa, 8.7 kDa) lacking functional domains. These IRX4 isoforms might induce distinct functional programming that could contribute to PCa hallmarks, thus providing novel insights into diagnostic, prognostic and therapeutic significance in PCa management.
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26
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Kim KH, Backx PH. Understanding the role of Iroquois homeobox transcription factor 5 (IRX5) in cardiac function: getting to the (human) heart of the matter. Cardiovasc Res 2021; 117:1989-1991. [PMID: 33739382 DOI: 10.1093/cvr/cvab098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kyoung-Han Kim
- University of Ottawa Heart Institute, 40 Ruskin Street, Ottawa, ON K1Y 4W7, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth road, Ottawa, ON K1N 6N5, Canada
| | - Peter H Backx
- Department of Biology, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada.,Division of Cardiology and the Peter Munk Cardiac Centre, University Health Network, 101 College St, Toronto, ON M5G 1L7, Canada
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27
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Reichlmeir M, Elias L, Schulte D. Posttranslational Modifications in Conserved Transcription Factors: A Survey of the TALE-Homeodomain Superclass in Human and Mouse. Front Cell Dev Biol 2021; 9:648765. [PMID: 33768097 PMCID: PMC7985065 DOI: 10.3389/fcell.2021.648765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022] Open
Abstract
Transcription factors (TFs) guide effector proteins like chromatin-modifying or -remodeling enzymes to distinct sites in the genome and thereby fulfill important early steps in translating the genome’s sequence information into the production of proteins or functional RNAs. TFs of the same family are often highly conserved in evolution, raising the question of how proteins with seemingly similar structure and DNA-binding properties can exert physiologically distinct functions or respond to context-specific extracellular cues. A good example is the TALE superclass of homeodomain-containing proteins. All TALE-homeodomain proteins share a characteristic, 63-amino acid long homeodomain and bind to similar sequence motifs. Yet, they frequently fulfill non-redundant functions even in domains of co-expression and are subject to regulation by different signaling pathways. Here we provide an overview of posttranslational modifications that are associated with murine and human TALE-homeodomain proteins and discuss their possible importance for the biology of these TFs.
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Affiliation(s)
- Marina Reichlmeir
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Lena Elias
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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28
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Corporan D, Onohara D, Amedi A, Saadeh M, Guyton RA, Kumar S, Padala M. Hemodynamic and transcriptomic studies suggest early left ventricular dysfunction in a preclinical model of severe mitral regurgitation. J Thorac Cardiovasc Surg 2021; 161:961-976.e22. [PMID: 33277035 PMCID: PMC7889661 DOI: 10.1016/j.jtcvs.2020.08.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Primary mitral regurgitation is a valvular lesion in which the left ventricular ejection fraction remains preserved for long periods, delaying a clinical trigger for mitral valve intervention. In this study, we sought to investigate whether adverse left ventricular remodeling occurs before a significant fall in ejection fraction and characterize these changes. METHODS Sixty-five rats were induced with severe mitral regurgitation by puncturing the mitral valve leaflet with a 23-G needle using ultrasound guidance. Rats underwent longitudinal cardiac echocardiography at biweekly intervals and hearts explanted at 2 weeks (n = 15), 10 weeks (n = 15), 20 weeks (n = 15), and 40 weeks (n = 15). Sixty age- and weight-matched healthy rats were used as controls. Unbiased RNA-sequencing was performed at each terminal point. RESULTS Regurgitant fraction was 40.99 ± 9.40%, with pulmonary flow reversal in the experimental group, and none in the control group. Significant fall in ejection fraction occurred at 14 weeks after mitral regurgitation induction. However, before 14 weeks, end-diastolic volume increased by 93.69 ± 52.38% (P < .0001 compared with baseline), end-systolic volume increased by 118.33 ± 47.54% (P < .0001 compared with baseline), and several load-independent pump function indices were reduced. Transcriptomic data at 2 and 10 weeks before fall in ejection fraction indicated up-regulation of myocyte remodeling and oxidative stress pathways, whereas those at 20 and 40 weeks indicated extracellular matrix remodeling. CONCLUSIONS In this rodent model of mitral regurgitation, left ventricular ejection fraction was preserved for a long duration, yet rapid and severe left ventricular dilatation, and biological remodeling occurred before a clinically significant fall in ejection fraction.
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Affiliation(s)
- Daniella Corporan
- Structural Heart Research and Innovation Laboratory, Carlyle Fraser Heart Center at Emory University Hospital Midtown, Atlanta, Ga
| | - Daisuke Onohara
- Structural Heart Research and Innovation Laboratory, Carlyle Fraser Heart Center at Emory University Hospital Midtown, Atlanta, Ga
| | - Alan Amedi
- Structural Heart Research and Innovation Laboratory, Carlyle Fraser Heart Center at Emory University Hospital Midtown, Atlanta, Ga
| | - Maher Saadeh
- Structural Heart Research and Innovation Laboratory, Carlyle Fraser Heart Center at Emory University Hospital Midtown, Atlanta, Ga
| | - Robert A Guyton
- Structural Heart Research and Innovation Laboratory, Carlyle Fraser Heart Center at Emory University Hospital Midtown, Atlanta, Ga; Division of Cardiothoracic Surgery, Department of Surgery, Emory University School of Medicine, Atlanta, Ga
| | - Sandeep Kumar
- Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, Ga
| | - Muralidhar Padala
- Structural Heart Research and Innovation Laboratory, Carlyle Fraser Heart Center at Emory University Hospital Midtown, Atlanta, Ga; Division of Cardiothoracic Surgery, Department of Surgery, Emory University School of Medicine, Atlanta, Ga.
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29
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Abstract
Cardiac development is a complex developmental process that is initiated soon after gastrulation, as two sets of precardiac mesodermal precursors are symmetrically located and subsequently fused at the embryonic midline forming the cardiac straight tube. Thereafter, the cardiac straight tube invariably bends to the right, configuring the first sign of morphological left–right asymmetry and soon thereafter the atrial and ventricular chambers are formed, expanded and progressively septated. As a consequence of all these morphogenetic processes, the fetal heart acquired a four-chambered structure having distinct inlet and outlet connections and a specialized conduction system capable of directing the electrical impulse within the fully formed heart. Over the last decades, our understanding of the morphogenetic, cellular, and molecular pathways involved in cardiac development has exponentially grown. Multiples aspects of the initial discoveries during heart formation has served as guiding tools to understand the etiology of cardiac congenital anomalies and adult cardiac pathology, as well as to enlighten novels approaches to heal the damaged heart. In this review we provide an overview of the complex cellular and molecular pathways driving heart morphogenesis and how those discoveries have provided new roads into the genetic, clinical and therapeutic management of the diseased hearts.
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30
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Küster MM, Schneider MA, Richter AM, Richtmann S, Winter H, Kriegsmann M, Pullamsetti SS, Stiewe T, Savai R, Muley T, Dammann RH. Epigenetic Inactivation of the Tumor Suppressor IRX1 Occurs Frequently in Lung Adenocarcinoma and Its Silencing Is Associated with Impaired Prognosis. Cancers (Basel) 2020; 12:E3528. [PMID: 33256112 PMCID: PMC7760495 DOI: 10.3390/cancers12123528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Iroquois homeobox (IRX) encodes members of homeodomain containing genes which are involved in development and differentiation. Since it has been reported that the IRX1 gene is localized in a lung cancer susceptibility locus, the epigenetic regulation and function of IRX1 was investigated in lung carcinogenesis. We observed frequent hypermethylation of the IRX1 promoter in non-small cell lung cancer (NSCLC) compared to small cell lung cancer (SCLC). Aberrant IRX1 methylation was significantly correlated with reduced IRX1 expression. In normal lung samples, the IRX1 promoter showed lower median DNA methylation levels (<10%) compared to primary adenocarcinoma (ADC, 22%) and squamous cell carcinoma (SQCC, 14%). A significant hypermethylation and downregulation of IRX1 was detected in ADC and SQCC compared to matching normal lung samples (p < 0.0001). Low IRX1 expression was significantly correlated with impaired prognosis of ADC patients (p = 0.001). Reduced survival probability was also associated with higher IRX1 promoter methylation (p = 0.02). Inhibition of DNA methyltransferase (DNMT) activity reactivated IRX1 expression in human lung cancer cell lines. Induced DNMT3A and EZH2 expression was correlated with downregulation of IRX1. On the cellular level, IRX1 exhibits nuclear localization and expression of IRX1 induced fragmented nuclei in cancer cells. Localization of IRX1 and induction of aberrant nuclei were dependent on the presence of the homeobox of IRX1. By data mining, we showed that IRX1 is negatively correlated with oncogenic pathways and IRX1 expression induces the proapoptotic regulator BAX. In conclusion, we report that IRX1 expression is significantly associated with improved survival probability of ADC patients. IRX1 hypermethylation may serve as molecular biomarker for ADC diagnosis and prognosis. Our data suggest that IRX1 acts as an epigenetically regulated tumor suppressor in the pathogenesis of lung cancer.
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Affiliation(s)
- Miriam M. Küster
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Marc A. Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Antje M. Richter
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Sarah Richtmann
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Hauke Winter
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Surgery, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Mark Kriegsmann
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Pathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Soni S. Pullamsetti
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thorsten Stiewe
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, 35032 Marburg, Germany
| | - Rajkumar Savai
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Reinhard H. Dammann
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
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31
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Mikryukov AA, Mazine A, Wei B, Yang D, Miao Y, Gu M, Keller GM. BMP10 Signaling Promotes the Development of Endocardial Cells from Human Pluripotent Stem Cell-Derived Cardiovascular Progenitors. Cell Stem Cell 2020; 28:96-111.e7. [PMID: 33142114 DOI: 10.1016/j.stem.2020.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 06/03/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022]
Abstract
The embryonic endocardium is essential for early heart development as it functions to induce trabecular myocardium, the first heart tissue to form, and is the source of the cells that make up the valves and a portion of the coronary vasculature. With this potential, human endocardial cells could provide unique therapeutic opportunities that include engineering biological valves and cell-based therapy strategies to replace coronary vasculature in damaged hearts. To access human endocardial cells, we generated a human pluripotent stem cell (hPSC)-derived endothelial population that displays many characteristics of endocardium, including expression of the cohort of genes that identifies this lineage in vivo, the capacity to induce a trabecular fate in immature cardiomyocytes in vitro, and the ability to undergo an endothelial-to-mesenchymal transition. Analyses of the signaling pathways required for development of the hPSC-derived endocardial cells identified a novel role for BMP10 in the specification of this lineage from cardiovascular mesoderm.
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Affiliation(s)
| | - Amine Mazine
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G1L7, Canada; Division of Cardiac Surgery, Department of Surgery, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Bei Wei
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Donghe Yang
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Yifei Miao
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford School of Medicine, Stanford, CA 94305, USA; Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mingxia Gu
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford School of Medicine, Stanford, CA 94305, USA; Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Gordon M Keller
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada.
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32
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Tao H, Lambert JP, Yung TM, Zhu M, Hahn NA, Li D, Lau K, Sturgeon K, Puviindran V, Zhang X, Gong W, Chen XX, Anderson G, Garry DJ, Henkelman RM, Sun Y, Iulianella A, Kawakami Y, Gingras AC, Hui CC, Hopyan S. IRX3/5 regulate mitotic chromatid segregation and limb bud shape. Development 2020; 147:dev.180042. [PMID: 32907847 DOI: 10.1242/dev.180042] [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: 04/30/2019] [Accepted: 08/25/2020] [Indexed: 01/19/2023]
Abstract
Pattern formation is influenced by transcriptional regulation as well as by morphogenetic mechanisms that shape organ primordia, although factors that link these processes remain under-appreciated. Here we show that, apart from their established transcriptional roles in pattern formation, IRX3/5 help to shape the limb bud primordium by promoting the separation and intercalation of dividing mesodermal cells. Surprisingly, IRX3/5 are required for appropriate cell cycle progression and chromatid segregation during mitosis, possibly in a nontranscriptional manner. IRX3/5 associate with, promote the abundance of, and share overlapping functions with co-regulators of cell division such as the cohesin subunits SMC1, SMC3, NIPBL and CUX1. The findings imply that IRX3/5 coordinate early limb bud morphogenesis with skeletal pattern formation.
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Affiliation(s)
- Hirotaka Tao
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Theodora M Yung
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Min Zhu
- Department of Mechanical and Industrial Engineering, University of Toronto, ON M5S 3G8, Canada
| | - Noah A Hahn
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Danyi Li
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kimberly Lau
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kendra Sturgeon
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Vijitha Puviindran
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Xiaoyun Zhang
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiao Xiao Chen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory Anderson
- Mouse Imaging Centre, Hospital for Sick Children, Toronto Centre for Phenogenomics, Department of Medical Biophysics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto Centre for Phenogenomics, Department of Medical Biophysics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, ON M5S 3G8, Canada
| | - Angelo Iulianella
- Department of Medical Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sevan Hopyan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Division of Orthopaedic Surgery, Hospital for Sick Children and University of Toronto, Toronto M5G 1X8, Canada
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33
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Zhu X, Wei Y, Zhan Q, Yan A, Feng J, Liu L, Tang D. CRISPR/Cas9-Mediated Biallelic Knockout of IRX3 Reduces the Production and Survival of Somatic Cell-Cloned Bama Minipigs. Animals (Basel) 2020; 10:E501. [PMID: 32192102 PMCID: PMC7142520 DOI: 10.3390/ani10030501] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/11/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
Bama minipigs are a local pig breed that is unique to China and has a high development and utilization value. However, its high fat content, low feed utilization rate, and slow growth rate have limited its popularity and utilization. Compared with the long breeding cycle and high cost of traditional genetic breeding of pigs, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) endonuclease 9 system (CRISPR/Cas9)-mediated gene editing can cost-effectively implement targeted mutations in animal genomes, thereby providing a powerful tool for rapid improvement of the economic traits of Bama minipigs. The iroquois homeobox 3 (IRX3) gene has been implicated in human obesity. Mouse experiments have shown that knocking out IRX3 significantly enhances basal metabolism, reduces fat content, and controls body mass and composition. This study aimed to knock out IRX3 using the CRISPR/Cas9 gene editing method to breed Bama minipigs with significantly reduced fat content. First, the CRISPR/Cas9 gene editing method was used to efficiently obtain IRX3-/- cells. Then, the gene-edited cells were used as donor cells to produce surviving IRX3-/- Bama minipigs using somatic cell cloning. The results show that the use of IRX3-/- cells as donor cells for the production of somatic cell-cloned pigs results in a significant decrease in the average live litter size and a significant increase in the average number of stillbirths. Moreover, the birth weight of surviving IRX3-/- somatic cell-cloned pigs is significantly lower, and viability is poor such that all piglets die shortly after birth. Therefore, the preliminary results of this study suggest that IRX3 may have important biological functions in pigs, and IRX3 should not be used as a gene editing target to reduce fat content in Bama minipigs. Moreover, this study shows that knocking out IRX3 does not favor the survival of pigs, and whether targeted regulation of IRX3 in the treatment of human obesity will also induce severe adverse consequences requires further investigation.
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Affiliation(s)
- Xiangxing Zhu
- Guangdong Provincial Engineering and Technology Research Center for Gene Editing, School of Medical Engineering, Foshan University, Foshan 528225, China; (A.Y.); (J.F.); (L.L.)
| | - Yanyan Wei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; (Y.W.); (Q.Z.)
| | - Qunmei Zhan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; (Y.W.); (Q.Z.)
| | - Aifen Yan
- Guangdong Provincial Engineering and Technology Research Center for Gene Editing, School of Medical Engineering, Foshan University, Foshan 528225, China; (A.Y.); (J.F.); (L.L.)
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; (Y.W.); (Q.Z.)
| | - Juan Feng
- Guangdong Provincial Engineering and Technology Research Center for Gene Editing, School of Medical Engineering, Foshan University, Foshan 528225, China; (A.Y.); (J.F.); (L.L.)
| | - Lian Liu
- Guangdong Provincial Engineering and Technology Research Center for Gene Editing, School of Medical Engineering, Foshan University, Foshan 528225, China; (A.Y.); (J.F.); (L.L.)
| | - Dongsheng Tang
- Guangdong Provincial Engineering and Technology Research Center for Gene Editing, School of Medical Engineering, Foshan University, Foshan 528225, China; (A.Y.); (J.F.); (L.L.)
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; (Y.W.); (Q.Z.)
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34
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Sapkota Y, Cheung YT, Moon W, Shelton K, Wilson CL, Wang Z, Mulrooney DA, Zhang J, Armstrong GT, Hudson MM, Robison LL, Krull KR, Yasui Y. Whole-Genome Sequencing of Childhood Cancer Survivors Treated with Cranial Radiation Therapy Identifies 5p15.33 Locus for Stroke: A Report from the St. Jude Lifetime Cohort Study. Clin Cancer Res 2019; 25:6700-6708. [PMID: 31462438 DOI: 10.1158/1078-0432.ccr-19-1231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/10/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE To identify genetic factors associated with risk of stroke among survivors of childhood cancer treated with cranial radiotherapy (CRT). EXPERIMENTAL DESIGN We analyzed whole-genome sequencing (36.8-fold) data of 686 childhood cancer survivors of European ancestry [median (range), 40.4 (12.4-64.7) years old; 54% male] from the St. Jude Lifetime Cohort study treated with CRT, of whom 116 (17%) had clinically diagnosed stroke. Association analyses (single-variant and Burden/SKAT tests) were performed, adjusting for demographic characteristics and childhood cancer treatment exposures. RESULTS We identified a genome-wide significant association between 5p15.33 locus and stroke [rs112896372: HR = 2.55; P = 1.42 × 10-8], with a stronger association (HR = 3.68) among survivors treated with CRT dose 25-50 Gray (Gy) and weaker associations among those treated with CRT doses <20 or 20-25 or >50 Gy (HRs = 2.14, 2.40, and 2.28). The association was replicated in 90 CRT-exposed African survivors (HR = 3.05; P = 0.034). In CRT-exposed Europeans, rs112896372 significantly (P < 0.001) improved predictive ability (AUC = 0.717) for determining stroke risk than nongenetic factors alone (AUC = 0.663) at 30 years since diagnosis, with significant improvement among African survivors (P = 0.047). SNP rs112896372 was further evaluated in three independent datasets including 1,641 European (HR = 1.54; P = 0.055) and 316 African survivors (HR = 1.88; P = 0.283) not treated with CRT, and 166,988 males in the UK Biobank (OR = 1.0012; P = 0.042). CONCLUSIONS A novel locus 5p15.33 is associated with stroke risk among childhood cancer survivors, with a possible CRT dose-specific effect. The locus is of potential clinical utility in characterizing individuals who may benefit from surveillance and intervention strategies.
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Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Yin Ting Cheung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T. Hong Kong
| | - Wonjong Moon
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kyla Shelton
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Daniel A Mulrooney
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kevin R Krull
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
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35
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Anderson DJ, Kaplan DI, Bell KM, Koutsis K, Haynes JM, Mills RJ, Phelan DG, Qian EL, Leitoguinho AR, Arasaratnam D, Labonne T, Ng ES, Davis RP, Casini S, Passier R, Hudson JE, Porrello ER, Costa MW, Rafii A, Curl CL, Delbridge LM, Harvey RP, Oshlack A, Cheung MM, Mummery CL, Petrou S, Elefanty AG, Stanley EG, Elliott DA. NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network. Nat Commun 2018; 9:1373. [PMID: 29636455 PMCID: PMC5893543 DOI: 10.1038/s41467-018-03714-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/05/2018] [Indexed: 12/19/2022] Open
Abstract
Congenital heart defects can be caused by mutations in genes that guide cardiac lineage formation. Here, we show deletion of NKX2-5, a critical component of the cardiac gene regulatory network, in human embryonic stem cells (hESCs), results in impaired cardiomyogenesis, failure to activate VCAM1 and to downregulate the progenitor marker PDGFRα. Furthermore, NKX2-5 null cardiomyocytes have abnormal physiology, with asynchronous contractions and altered action potentials. Molecular profiling and genetic rescue experiments demonstrate that the bHLH protein HEY2 is a key mediator of NKX2-5 function during human cardiomyogenesis. These findings identify HEY2 as a novel component of the NKX2-5 cardiac transcriptional network, providing tangible evidence that hESC models can decipher the complex pathways that regulate early stage human heart development. These data provide a human context for the evaluation of pathogenic mutations in congenital heart disease. A gene regulatory network, including the transcription factor Nkx2-5, regulates cardiac development. Here, the authors show that on deletion of NKX2-5 from human embryonic stem cells, there is impaired cardiomyogenesis and changes in action potentials, and that this is regulated via HEY2.
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Affiliation(s)
- David J Anderson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - David I Kaplan
- The Florey Institute of Neuroscience and Mental Health; Centre for Neuroscience, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Katrina M Bell
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Katerina Koutsis
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - John M Haynes
- Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade Parkville, Victoria, 3052, Australia
| | - Richard J Mills
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dean G Phelan
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Elizabeth L Qian
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Ana Rita Leitoguinho
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Deevina Arasaratnam
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Tanya Labonne
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Elizabeth S Ng
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Richard P Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Simona Casini
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Robert Passier
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - James E Hudson
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Enzo R Porrello
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Arash Rafii
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar Qatar Foundation, Doha, Qatar.,Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Clare L Curl
- Department of Physiology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Lea M Delbridge
- Department of Physiology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2052, Australia.,St. Vincent's Clinical School and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, 2052, Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Michael M Cheung
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.,Department of Pediatrics, The Royal Children's Hospital, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christine L Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Stephen Petrou
- The Florey Institute of Neuroscience and Mental Health; Centre for Neuroscience, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Andrew G Elefanty
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.,Department of Pediatrics, The Royal Children's Hospital, University of Melbourne, Parkville, VIC, 3052, Australia.,Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Edouard G Stanley
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.,Department of Pediatrics, The Royal Children's Hospital, University of Melbourne, Parkville, VIC, 3052, Australia.,Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - David A Elliott
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia. .,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. .,School of Biosciences, University of Melbourne, Parkville, VIC, 3052, Australia.
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Man J, Barnett P, Christoffels VM. Structure and function of the Nppa-Nppb cluster locus during heart development and disease. Cell Mol Life Sci 2018; 75:1435-1444. [PMID: 29302701 PMCID: PMC5852170 DOI: 10.1007/s00018-017-2737-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/07/2017] [Accepted: 12/20/2017] [Indexed: 01/20/2023]
Abstract
Atrial natriuretic factor and brain natriuretic peptide are two important biomarkers in clinical cardiology. These two natriuretic peptide hormones are encoded by the paralogous genes Nppa and Nppb, which are evolutionary conserved. Both genes are predominantly expressed by the heart muscle during the embryonic and fetal stages, and in particular Nppa expression is strongly reduced in the ventricles after birth. Upon cardiac stress, Nppa and Nppb are strongly upregulated in the ventricular myocardium. Much is known about the molecular and physiological ques inducing Nppa and Nppb expression; however, the transcriptional regulatory mechanisms of the Nppa-Nppb cluster in vivo has proven to be quite complex and is not well understood. In this review, we will provide recent insights into the dynamic and complex regulation of Nppa and Nppb during heart development and hypertrophy, and the association of this gene cluster with the cardiomyocyte-intrinsic program of heart regeneration.
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Affiliation(s)
- Joyce Man
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Phil Barnett
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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Hu W, Xin Y, Zhang L, Hu J, Sun Y, Zhao Y. Iroquois Homeodomain transcription factors in ventricular conduction system and arrhythmia. Int J Med Sci 2018; 15:808-815. [PMID: 30008591 PMCID: PMC6036080 DOI: 10.7150/ijms.25140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/29/2018] [Indexed: 02/05/2023] Open
Abstract
Iroquois homeobox genes, Irx, encode cardiac transcription factors, Irx1-6 in most mammals. These six transcription factors are expressed in different patterns mainly in the ventricular part of the heart. Existing researches show that Irx genes play key roles in the differentiation and development of ventricular conduction system and the establishment and maintenance of gradient expression of potassium channels, Kv4.2. Our main focus of this review is on the recent advances in the discovery of above-mentioned genes and the function of the encoding products, how Irx genes establish ventricular conduction system and regulate ventricular repolarization, how the individual and complementary functions can be verified to complement our cognition and leads to novel therapeutic approaches.
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Affiliation(s)
- Wenyu Hu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yanguo Xin
- Department of Cardiology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Zhang
- Department of Cardiology, Jinqiu Hosipital Of Liaoning Province, Shenyang, Liaoning110001, China
| | - Jian Hu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yingxian Sun
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yinan Zhao
- Department of Neurology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
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Multiple Roles of Pitx2 in Cardiac Development and Disease. J Cardiovasc Dev Dis 2017; 4:jcdd4040016. [PMID: 29367545 PMCID: PMC5753117 DOI: 10.3390/jcdd4040016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022] Open
Abstract
Cardiac development is a complex morphogenetic process initiated as bilateral cardiogenic mesoderm is specified at both sides of the gastrulating embryo. Soon thereafter, these cardiogenic cells fuse at the embryonic midline configuring a symmetrical linear cardiac tube. Left/right bilateral asymmetry is first detected in the forming heart as the cardiac tube bends to the right, and subsequently, atrial and ventricular chambers develop. Molecular signals emanating from the node confer distinct left/right signalling pathways that ultimately lead to activation of the homeobox transcription factor Pitx2 in the left side of distinct embryonic organ anlagen, including the developing heart. Asymmetric expression of Pitx2 has therefore been reported during different cardiac developmental stages, and genetic deletion of Pitx2 provided evidence of key regulatory roles of this transcription factor during cardiogenesis and thus congenital heart diseases. More recently, impaired Pitx2 function has also been linked to arrhythmogenic processes, providing novel roles in the adult heart. In this manuscript, we provide a state-of-the-art review of the fundamental roles of Pitx2 during cardiogenesis, arrhythmogenesis and its contribution to congenital heart diseases.
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Gomez-Velazquez M, Badia-Careaga C, Lechuga-Vieco AV, Nieto-Arellano R, Tena JJ, Rollan I, Alvarez A, Torroja C, Caceres EF, Roy AR, Galjart N, Delgado-Olguin P, Sanchez-Cabo F, Enriquez JA, Gomez-Skarmeta JL, Manzanares M. CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart. PLoS Genet 2017; 13:e1006985. [PMID: 28846746 PMCID: PMC5591014 DOI: 10.1371/journal.pgen.1006985] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/08/2017] [Accepted: 08/17/2017] [Indexed: 11/27/2022] Open
Abstract
Cardiac progenitors are specified early in development and progressively differentiate and mature into fully functional cardiomyocytes. This process is controlled by an extensively studied transcriptional program. However, the regulatory events coordinating the progression of such program from development to maturation are largely unknown. Here, we show that the genome organizer CTCF is essential for cardiogenesis and that it mediates genomic interactions to coordinate cardiomyocyte differentiation and maturation in the developing heart. Inactivation of Ctcf in cardiac progenitor cells and their derivatives in vivo during development caused severe cardiac defects and death at embryonic day 12.5. Genome wide expression analysis in Ctcf mutant hearts revealed that genes controlling mitochondrial function and protein production, required for cardiomyocyte maturation, were upregulated. However, mitochondria from mutant cardiomyocytes do not mature properly. In contrast, multiple development regulatory genes near predicted heart enhancers, including genes in the IrxA cluster, were downregulated in Ctcf mutants, suggesting that CTCF promotes cardiomyocyte differentiation by facilitating enhancer-promoter interactions. Accordingly, loss of CTCF disrupts gene expression and chromatin interactions as shown by chromatin conformation capture followed by deep sequencing. Furthermore, CRISPR-mediated deletion of an intergenic CTCF site within the IrxA cluster alters gene expression in the developing heart. Thus, CTCF mediates local regulatory interactions to coordinate transcriptional programs controlling transitions in morphology and function during heart development. Properly regulated gene expression in time and space during development and differentiation requires not only transcriptional inputs, but also specific structuring of the chromatin. CTCF is a DNA binding factor that is believed to be critical for this process through binding to tens of thousands of sites across the genome. Despite the knowledge gained in recent years on the role of CTCF in genome organization, its functions in vivo are poorly understood. To address this issue, we studied the effect of genetically deleting CTCF in differentiating cardiomyocytes at early stages of mouse development. Surprisingly only a fraction of genes change their expression when CTCF is removed. Importantly, misregulated genes control opposing genetic programs in charge of development and patterning on one hand, and cardiomyocyte maturation on the other. This imbalance leads to faulty mitochondria and incorrect expression of cardiac patterning genes, and subsequent embryonic lethality. Our results suggest that CTCF is not necessary for maintenance of global genome structure, but coordinates dynamic genetic programs controlling phenotypic transitions in developing cells and tissues.
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Affiliation(s)
| | | | - Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Isabel Rollan
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Alba Alvarez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Carlos Torroja
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Eva F. Caceres
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Anna R. Roy
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Paul Delgado-Olguin
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Heart and Stroke Richard Lewar Centre of Excellence, Toronto, Ontario, Canada
| | | | | | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- * E-mail:
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Tamamura Y, Katsube K, Mera H, Itokazu M, Wakitani S. Irx3 and Bmp2 regulate mouse mesenchymal cell chondrogenic differentiation in both a Sox9-dependent and -independent manner. J Cell Physiol 2017; 232:3317-3336. [PMID: 28059449 DOI: 10.1002/jcp.25776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 12/31/2016] [Accepted: 01/05/2017] [Indexed: 01/22/2023]
Abstract
Sox9, a master regulator of cartilage development, controls the cell fate decision to differentiate from mesenchymal to chondrogenic cells. In addition, Sox9 regulates the proliferation and differentiation of chondrocytes, as well as the production of cartilage-specific proteoglycans. The existence of Sox9-independent mechanisms in cartilage development remains to be determined. Here, we attempted to identify genes involved in such putative mechanisms via microarray analysis using a mouse chondrogenic cell line, N1511. We first focused on transcription factors that exhibited upregulated expression following Bmp2 treatment, which was not altered by subsequent treatment with Sox9 siRNA. Among these, we selected positive regulators for chondrogenesis and identified Iroquois-related homeobox 3 (Irx3) as one of the candidate genes. Irx3 expression gradually increased with chondrocyte terminal differentiation in a reciprocal manner to Sox9 expression, and promoted the chondrogenic differentiation of mesenchymal cells upon Bmp2 treatment. Furthermore, Irx3 partially rescued impaired chondrogenesis by upregulating the expression of epiphycan and lumican under reduced Sox9 expression. Finally, Irx3 was shown to act in concert with Bmp2 signaling to activate the p38 MAPK pathway, which in turn stimulated Sox9 expression, as well as the expression of epiphycan and lumican in a Sox9-independent manner. These results indicate that Irx3 represents a novel chondrogenic factor of mesenchymal cells, acts synergistically with Bmp2-mediated signaling, and regulates chondrogenesis independent of the transcriptional machinery associated with Sox9-mediated regulation.
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Affiliation(s)
- Yoshihiro Tamamura
- School of Health and Sports Science, Mukogawa Women's University, Nishinomiya, Japan
| | - Kenichi Katsube
- Faculty of Human Care, Department of Nursing Science, Tohto College of Health Sciences, Saitama, Japan
| | - Hisashi Mera
- School of Health and Sports Science, Mukogawa Women's University, Nishinomiya, Japan
| | - Maki Itokazu
- School of Health and Sports Science, Mukogawa Women's University, Nishinomiya, Japan.,Department of Orthopedic Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Shigeyuki Wakitani
- School of Health and Sports Science, Mukogawa Women's University, Nishinomiya, Japan
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41
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Corrêa S, Panis C, Binato R, Herrera AC, Pizzatti L, Abdelhay E. Identifying potential markers in Breast Cancer subtypes using plasma label-free proteomics. J Proteomics 2017; 151:33-42. [DOI: 10.1016/j.jprot.2016.07.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 07/17/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
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42
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Cardeña-Núñez S, Sánchez-Guardado LÓ, Corral-San-Miguel R, Rodríguez-Gallardo L, Marín F, Puelles L, Aroca P, Hidalgo-Sánchez M. Expression patterns of Irx genes in the developing chick inner ear. Brain Struct Funct 2016; 222:2071-2092. [PMID: 27783221 DOI: 10.1007/s00429-016-1326-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
The vertebrate inner ear is a complex three-dimensional sensorial structure with auditory and vestibular functions. The molecular patterning of the developing otic epithelium creates various positional identities, consequently leading to the stereotyped specification of each neurosensory and non-sensory element of the membranous labyrinth. The Iroquois (Iro/Irx) genes, clustered in two groups (A: Irx1, Irx2, and Irx4; and B: Irx3, Irx5, and Irx6), encode for transcriptional factors involved directly in numerous patterning processes of embryonic tissues in many phyla. This work presents a detailed study of the expression patterns of these six Irx genes during chick inner ear development, paying particular attention to the axial specification of the otic anlagen. The Irx genes seem to play different roles at different embryonic periods. At the otic vesicle stage (HH18), all the genes of each cluster are expressed identically. Both clusters A and B seem involved in the specification of the lateral and posterior portions of the otic anlagen. Cluster B seems to regulate a larger area than cluster A, including the presumptive territory of the endolymphatic apparatus. Both clusters seem also to be involved in neurogenic events. At stages HH24/25-HH27, combinations of IrxA and IrxB genes participate in the specification of most sensory patches and some non-sensory components of the otic epithelium. At stage HH34, the six Irx genes show divergent patterns of expression, leading to the final specification of the membranous labyrinth, as well as to cell differentiation.
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Affiliation(s)
- Sheila Cardeña-Núñez
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain
| | - Luis Óscar Sánchez-Guardado
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain
| | - Rubén Corral-San-Miguel
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Lucía Rodríguez-Gallardo
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain
| | - Faustino Marín
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Pilar Aroca
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Matías Hidalgo-Sánchez
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain.
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43
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Plaisance I, Perruchoud S, Fernandez-Tenorio M, Gonzales C, Ounzain S, Ruchat P, Nemir M, Niggli E, Pedrazzini T. Cardiomyocyte Lineage Specification in Adult Human Cardiac Precursor Cells Via Modulation of Enhancer-Associated Long Noncoding RNA Expression. JACC Basic Transl Sci 2016; 1:472-493. [PMID: 29707678 PMCID: PMC5916868 DOI: 10.1016/j.jacbts.2016.06.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human CPCs produce predominantly smooth muscle cells. CPCs can be redirected to the cardiomyocyte fate by transient activation followed by inhibition of NOTCH signaling. Inhibition of NOTCH signaling during differentiation represses MIR-143/145 expression and blocks smooth muscle differentiation. Expression of the microRNAs is under control of CARMEN, a long noncoding RNA associated with an enhancer located in the MIR-143/145 locus and target of NOTCH signaling. The CARMEN/MIR-145/143 locus represents a promising therapeutic target to favor production of cardiomyocytes in cell replacement therapies.
The mechanisms controlling differentiation in adult cardiac precursor cells (CPCs) are still largely unknown. In this study, CPCs isolated from the human heart were found to produce predominantly smooth muscle cells but could be redirected to the cardiomyocyte fate by transient activation followed by inhibition of NOTCH signaling. NOTCH inhibition repressed MIR-143/145 expression, and blocked smooth muscle differentiation. Expression of the microRNAs is under control of CARMEN, a long noncoding RNA associated with an enhancer located in the MIR-143/145 locus and target of NOTCH signaling. The CARMEN/MIR-145/143 axis represents, therefore, a promising target to favor production of cardiomyocytes in cell replacement therapies.
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Affiliation(s)
- Isabelle Plaisance
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Stéphanie Perruchoud
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Christine Gonzales
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Samir Ounzain
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Patrick Ruchat
- Department of Cardiovascular Surgery, University of Lausanne Medical School, Lausanne, Switzerland
| | - Mohamed Nemir
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Ernst Niggli
- Department of Physiology, University of Bern, Bern, Switzerland
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
- Reprint requests and correspondence: Dr. Thierry Pedrazzini, Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland.
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44
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Enrichment of risk SNPs in regulatory regions implicate diverse tissues in Parkinson's disease etiology. Sci Rep 2016; 6:30509. [PMID: 27461410 PMCID: PMC4962314 DOI: 10.1038/srep30509] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/04/2016] [Indexed: 12/15/2022] Open
Abstract
Recent genome-wide association studies (GWAS) of Parkinson’s disease (PD) revealed at least 26 risk loci, with associated single nucleotide polymorphisms (SNPs) located in non-coding DNA having unknown functions in risk. In order to explore in which cell types these SNPs (and their correlated surrogates at r2 ≥ 0.8) could alter cellular function, we assessed their location overlap with histone modification regions that indicate transcription regulation in 77 diverse cell types. We found statistically significant enrichment of risk SNPs at 12 loci in active enhancers or promoters. We investigated 4 risk loci in depth that were most significantly enriched (−logeP > 14) and contained 8 putative enhancers in the different cell types. These enriched loci, along with eQTL associations, were unexpectedly present in non-neuronal cell types. These included lymphocytes, mesendoderm, liver- and fat-cells, indicating that cell types outside the brain are involved in the genetic predisposition to PD. Annotating regulatory risk regions within specific cell types may unravel new putative risk mechanisms and molecular pathways that contribute to PD development.
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45
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WANG PEI, ZHUANG CHUNBO, HUANG DA, XU KESHU. Downregulation of miR-377 contributes to IRX3 deregulation in hepatocellular carcinoma. Oncol Rep 2016; 36:247-52. [DOI: 10.3892/or.2016.4815] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/26/2016] [Indexed: 11/06/2022] Open
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46
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Affiliation(s)
- Maiko Matsui
- Ion Channel Research Unit, Duke University Medical Center, Durham, NC, USA Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Geoffrey S Pitt
- Ion Channel Research Unit, Duke University Medical Center, Durham, NC, USA Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, USA Department of Neurobiology; Duke University Medical Center, Durham, NC, USA
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47
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Cain CJ, Gaborit N, Lwin W, Barruet E, Ho S, Bonnard C, Hamamy H, Shboul M, Reversade B, Kayserili H, Bruneau BG, Hsiao EC. Loss of Iroquois homeobox transcription factors 3 and 5 in osteoblasts disrupts cranial mineralization. Bone Rep 2016; 5:86-95. [PMID: 27453922 PMCID: PMC4926823 DOI: 10.1016/j.bonr.2016.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 02/02/2016] [Indexed: 01/13/2023] Open
Abstract
Cranial malformations are a significant cause of perinatal morbidity and mortality. Iroquois homeobox transcription factors (IRX) are expressed early in bone tissue formation and facilitate patterning and mineralization of the skeleton. Mice lacking Irx5 appear grossly normal, suggesting that redundancy within the Iroquois family. However, global loss of both Irx3 and Irx5 in mice leads to significant skeletal malformations and embryonic lethality from cardiac defects. Here, we study the bone-specific functions of Irx3 and Irx5 using Osx-Cre to drive osteoblast lineage-specific deletion of Irx3 in Irx5(-/-) mice. Although we found that the Osx-Cre transgene alone could also affect craniofacial mineralization, newborn Irx3 (flox/flox) /Irx5(-/-)/Osx-Cre (+) mice displayed additional mineralization defects in parietal, interparietal, and frontal bones with enlarged sutures and reduced calvarial expression of osteogenic genes. Newborn endochondral long bones were largely unaffected, but we observed marked reductions in 3-4-week old bone mineral content of Irx3 (flox/flox) /Irx5(-/-)/Osx-Cre (+) mice. Our findings indicate that IRX3 and IRX5 can work together to regulate mineralization of specific cranial bones. Our results also provide insight into the causes of the skeletal changes and mineralization defects seen in Hamamy syndrome patients carrying mutations in IRX5.
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Affiliation(s)
- Corey J Cain
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Nathalie Gaborit
- Inserm, UMR 1087, l'institut du thorax, Nantes, France; CNRS, UMR 6291, Nantes, France; Université de Nantes, France
| | - Wint Lwin
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Emilie Barruet
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Samantha Ho
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Carine Bonnard
- Human Embryology and Genetics Laboratory, Institute of Medical Biology, ASTAR, Singapore 138648, Singapore
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, Geneva University, Geneva 1211, Switzerland
| | - Mohammad Shboul
- Human Embryology and Genetics Laboratory, Institute of Medical Biology, ASTAR, Singapore 138648, Singapore
| | - Bruno Reversade
- Human Embryology and Genetics Laboratory, Institute of Medical Biology, ASTAR, Singapore 138648, Singapore
| | - Hülya Kayserili
- Medical Genetics Department, Koc University School of Medicine, Rumelifeneri Yolu, Sarıyer, Istanbul 34450, Turkey; Medical Genetics Department, Istanbul Medical Faculty, Istanbul University Topkapi, Fatih, 34093 lstanbul, Turkey
| | - Benoit G Bruneau
- Gladstone Institute for Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Edward C Hsiao
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
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48
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Kim KH, Rosen A, Hussein SMI, Puviindran V, Korogyi AS, Chiarello C, Nagy A, Hui CC, Backx PH. Irx3 is required for postnatal maturation of the mouse ventricular conduction system. Sci Rep 2016; 6:19197. [PMID: 26786475 PMCID: PMC4726432 DOI: 10.1038/srep19197] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/07/2015] [Indexed: 12/17/2022] Open
Abstract
The ventricular conduction system (VCS) orchestrates the harmonious contraction in every heartbeat. Defects in the VCS are often associated with life-threatening arrhythmias and also promote adverse remodeling in heart disease. We have previously established that the Irx3 homeobox gene regulates rapid electrical propagation in the VCS by modulating the transcription of gap junction proteins Cx40 and Cx43. However, it is unknown whether other factors contribute to the conduction defects observed in Irx3 knockout (Irx3(-/-)) mice. In this study, we show that during the early postnatal period, Irx3(-/-) mice develop morphological defects in the VCS which are temporally dissociated from changes in gap junction expression. These morphological defects were accompanied with progressive changes in the cardiac electrocardiogram including right bundle branch block. Hypoplastic VCS was not associated with increased apoptosis of VCS cardiomyocytes but with a lack of recruitment and maturation of ventricular cardiomyocytes into the VCS. Computational analysis followed by functional verification revealed that Irx3 promotes VCS-enriched transcripts targeted by Nkx2.5 and/or Tbx5. Altogether, these results indicate that, in addition to ensuring the appropriate expression of gap junctional channels in the VCS, Irx3 is necessary for the postnatal maturation of the VCS, possibly via its interactions with Tbx5 and Nkx2.5.
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Affiliation(s)
- Kyoung-Han Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Anna Rosen
- The Heart and Stroke Richard Lewar Centre of Excellence, University of Toronto, Toronto, ON M5S 3E2, Canada
- Departments of Physiology and Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Samer M. I. Hussein
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada
| | - Vijitha Puviindran
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Adam S. Korogyi
- The Heart and Stroke Richard Lewar Centre of Excellence, University of Toronto, Toronto, ON M5S 3E2, Canada
- Departments of Physiology and Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Carmelina Chiarello
- The Heart and Stroke Richard Lewar Centre of Excellence, University of Toronto, Toronto, ON M5S 3E2, Canada
- Departments of Physiology and Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Institute of Medical Science and Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5T 3H7, Canada
| | - Chi-chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peter H. Backx
- The Heart and Stroke Richard Lewar Centre of Excellence, University of Toronto, Toronto, ON M5S 3E2, Canada
- Departments of Physiology and Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Peter Munk Cardiac Centre and Division of Cardiology, University Health Network, Toronto ON
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Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells. BMC Cancer 2015; 15:896. [PMID: 26560478 PMCID: PMC4642646 DOI: 10.1186/s12885-015-1907-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background Disseminated tumor cells (DTCs) can be detected using ultrasensitive immunocytochemical assays and their presence in the bone marrow can predict the subsequent occurrence of overt metastasis formation and metastatic relapse. Using expression profiling on early stage primary breast tumors, low IRX2 expression was previously shown to be associated with the presence of DTCs in the bone marrow, suggesting a possible role of IRX2 in the early steps of metastasis formation. The purpose of this study is to gain insights into the significance of IRX2 protein function in the progression of breast cancer. Methods To assess the physiological relevance of IRX2 in breast cancer, we evaluated IRX2 expression in a large breast cancer cohort (n = 1992). Additionally, constitutive IRX2 over expression was established in BT-549 and Hs578T breast cancer cell lines. Subsequently we analyzed whether IRX2 overexpression effects chemokine secretion and cellular motility of these cells. Results Low IRX2 mRNA expression was found to correlate with high tumor grade, positive lymph node status, negative hormone receptor status, and basal type of primary breast tumors. Also in cell lines low IRX2 expression was associated with mainly basal breast cancer cell lines. The functional studies show that overexpression of the IRX2 transcription factor in basal cell lines suppressed secretion of the pro-metastatic chemokines and inhibited cellular motility but did not influence cell proliferation. Conclusion Our results imply that the IRX2 transcription factor might represent a novel metastasis associated protein that acts as a negative regulator of cellular motility and as a repressor of chemokine expression. Loss of IRX2 expression could therefore contribute to early hematogenous dissemination of breast cancer by sustaining chemokine secretion and enabling mobilization of tumor cells. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1907-4) contains supplementary material, which is available to authorized users.
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Scarlett K, Pattabiraman V, Barnett P, Liu D, Anderson LM. The proangiogenic effect of iroquois homeobox transcription factor Irx3 in human microvascular endothelial cells. J Biol Chem 2015; 290:6303-15. [PMID: 25512384 PMCID: PMC4358267 DOI: 10.1074/jbc.m114.601146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 12/14/2014] [Indexed: 12/29/2022] Open
Abstract
Angiogenesis is a dynamic process required for embryonic development. However, postnatal vascular growth is characteristic of multiple disease states. Despite insights into the multistep process in which adhesion molecules, extracellular matrix proteins, growth factors, and their receptors work in concert to form new vessels from the preexisting vasculature, there remains a lack of insight of the nuclear transcriptional mechanisms that occur within endothelial cells (ECs) in response to VEGF. Iroquois homeobox gene 3 (Irx3) is a transcription factor of the Iroquois family of homeobox genes. Irx homeodomain transcription factors are involved in the patterning and development of several tissues. Irx3 is known for its role during embryogenesis in multiple organisms. However, the expression and function of Irx3 in human postnatal vasculature remains to be investigated. Here we show that Irx3 is expressed in human microvascular endothelial cells, and expression is elevated by VEGF stimulation. Genetic Irx3 gain and loss of function studies in human microvascular endothelial cells resulted in the modulation of EC migration during wound healing, chemotaxis and invasion, and tubulogenesis. Additionally, we observed increased delta-like ligand 4 (Dll4) expression, which suggests an increase in EC tip cell population. Finally, siRNA screening studies revealed that transient knockdown of Hey1, a downstream Notch signaling mediator, resulted in increased Irx3 expression in response to VEGF treatment. Strategies to pharmacologically regulate Irx3 function in adult endothelial cells may provide new therapies for angiogenesis.
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Affiliation(s)
| | | | - Petrina Barnett
- the Cancer Center for Therapeutic Development, Clark Atlanta University, Atlanta, Georgia 30314
| | - Dong Liu
- From the Cardiovascular Research Institute and Department of Physiology, Morehouse School of Medicine, Atlanta, Georgia 30310 and
| | - Leonard M Anderson
- From the Cardiovascular Research Institute and Department of Physiology, Morehouse School of Medicine, Atlanta, Georgia 30310 and
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