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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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2
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Lobón-Iglesias MJ, Andrianteranagna M, Han ZY, Chauvin C, Masliah-Planchon J, Manriquez V, Tauziede-Espariat A, Turczynski S, Bouarich-Bourimi R, Frah M, Dufour C, Blauwblomme T, Cardoen L, Pierron G, Maillot L, Guillemot D, Reynaud S, Bourneix C, Pouponnot C, Surdez D, Bohec M, Baulande S, Delattre O, Piaggio E, Ayrault O, Waterfall JJ, Servant N, Beccaria K, Dangouloff-Ros V, Bourdeaut F. Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups. Nat Commun 2023; 14:6669. [PMID: 37863903 PMCID: PMC10589300 DOI: 10.1038/s41467-023-42371-7] [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: 06/10/2022] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26-CreERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.
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Affiliation(s)
- María-Jesús Lobón-Iglesias
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Mamy Andrianteranagna
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Zhi-Yan Han
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Céline Chauvin
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Julien Masliah-Planchon
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Valeria Manriquez
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Arnault Tauziede-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Paris Psychiatry and Neurosciences Institute (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Sandrina Turczynski
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Rachida Bouarich-Bourimi
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Magali Frah
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Christelle Dufour
- Department of Children and Adolescents Oncology, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Thomas Blauwblomme
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | | | - Gaelle Pierron
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Laetitia Maillot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Delphine Guillemot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Stéphanie Reynaud
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Christine Bourneix
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Célio Pouponnot
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Didier Surdez
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Mylene Bohec
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Olivier Delattre
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Eliane Piaggio
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Olivier Ayrault
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Nicolas Servant
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Kevin Beccaria
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | - Volodia Dangouloff-Ros
- Pediatric Radiology Department, AP-HP, Necker Sick Kids Hospital and Paris Cite Universiy INSERM 1299 and UMR 1163, Institut Imagine, Paris, France
| | - Franck Bourdeaut
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France.
- Department of Pediatric Oncology, SIREDO Oncology Center, Institut Curie Hospital, Paris, and Université de Paris, Paris, France.
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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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4
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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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5
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Tang PC, Chen L, Singh S, Groves AK, Koehler KR, Liu XZ, Nelson RF. Early Wnt Signaling Activation Promotes Inner Ear Differentiation via Cell Caudalization in Mouse Stem Cell-Derived Organoids. Stem Cells 2023; 41:26-38. [PMID: 36153788 PMCID: PMC9887082 DOI: 10.1093/stmcls/sxac071] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/14/2022] [Indexed: 02/02/2023]
Abstract
The inner ear is derived from the otic placode, one of the numerous cranial sensory placodes that emerges from the pre-placodal ectoderm (PPE) along its anterior-posterior axis. However, the molecular dynamics underlying how the PPE is regionalized are poorly resolved. We used stem cell-derived organoids to investigate the effects of Wnt signaling on early PPE differentiation and found that modulating Wnt signaling significantly increased inner ear organoid induction efficiency and reproducibility. Alongside single-cell RNA sequencing, our data reveal that the canonical Wnt signaling pathway leads to PPE regionalization and, more specifically, medium Wnt levels during the early stage induce (1) expansion of the caudal neural plate border (NPB), which serves as a precursor for the posterior PPE, and (2) a caudal microenvironment that is required for otic specification. Our data further demonstrate Wnt-mediated induction of rostral and caudal cells in organoids and more broadly suggest that Wnt signaling is critical for anterior-posterior patterning in the PPE.
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Affiliation(s)
- Pei-Ciao Tang
- Department of Otolaryngology—Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Otolaryngology—Head and Neck Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Li Chen
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Sunita Singh
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Andrew K Groves
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Karl R Koehler
- Department of Otolaryngology, Boston Children’s Hospital, Boston, MA, USA
- Department of Otolaryngology– Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Xue Zhong Liu
- Department of Otolaryngology—Head and Neck Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Rick F Nelson
- Department of Otolaryngology—Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
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Wang K, Zhou M, Zhang Y, Du Y, Li P, Guan C, Huang Z. IRX2 activated by jumonji domain-containing protein 2A is crucial for cardiac hypertrophy and dysfunction in response to the hypertrophic stimuli. Int J Cardiol 2023; 371:332-344. [PMID: 36181956 DOI: 10.1016/j.ijcard.2022.09.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/25/2022] [Accepted: 09/26/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Iroquois homeobox 2 (IRX2) is a member of the Iroquois family whose upregulation has been potentially correlated to cardiac hypertrophy. This work studied the function of IRX2 and its related molecules in hypertrophic cardiomyopathy (HCM). METHODS A GEO dataset GSE32453 was analyzed to identify aberrantly expressed genes in HCM. Altered expression of IRX2 was induced in mice by lentivirus injection, followed by angiotensin II (Ang II) treatment to induce HCM. The function of IRX2 knockdown in ventricular dysfunction, heart volume and pathological changes in mice, and in surface area, oxidative stress and apoptosis of isolated cardiomyocytes were examined. Binding relationship between jumonji domain-containing protein 2A (JMJD2A) and IRX2 was predicted by online tools and validated. The interaction between JMJD2A and IRX2 in HCM development was examined by joint interventions. RESULTS IRX2 was highly expressed in heart tissues with HCM. IRX2 knockdown prevented mice from Ang II-induced ventricular dysfunction, cardiac hypertrophy, inflammation and fibrosis in mouse heart, and it decreased the levels of cardiac hypertrophy-related markers, oxidative stress response, and apoptosis of Ang II-treated cardiomyocytes. JMJD2A catalyzed demethylation of H3K9me3 near the IRX2 promoter to activate its transcription. JMJD2A knockdown similarly exerted protective functions against cardiac hypertrophy in vivo and in vitro, but the protection was blocked upon further IRX2 upregulation. IRX2 was found to increase the Wnt/β-catenin signaling activation. CONCLUSION This work reports that JMJD2A activates IRX2 transcription and the Wnt/β-catenin signaling to induce cardiac hypertrophy and dysfunction in HCM.
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Affiliation(s)
- Kaihao Wang
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, Guangdong, PR China
| | - Min Zhou
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, Guangdong, PR China
| | - Youhong Zhang
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, Guangdong, PR China
| | - Yipeng Du
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, Guangdong, PR China
| | - Peixin Li
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, Guangdong, PR China
| | - Chang Guan
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, Guangdong, PR China
| | - Zheng Huang
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, Guangdong, PR China.
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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8
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Cocaine-related DNA methylation in caudate neurons alters 3D chromatin structure of the IRXA gene cluster. Mol Psychiatry 2021; 26:3134-3151. [PMID: 33046833 PMCID: PMC8039060 DOI: 10.1038/s41380-020-00909-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/14/2020] [Accepted: 10/01/2020] [Indexed: 02/01/2023]
Abstract
Epigenetic mechanisms, like those involving DNA methylation, are thought to mediate the relationship between chronic cocaine dependence and molecular changes in addiction-related neurocircuitry, but have been understudied in human brain. We initially used reduced representation bisulfite sequencing (RRBS) to generate a methylome-wide profile of cocaine dependence in human post-mortem caudate tissue. We focused on the Iroquois Homeobox A (IRXA) gene cluster, where hypomethylation in exon 3 of IRX2 in neuronal nuclei was associated with cocaine dependence. We replicated this finding in an independent cohort and found similar results in the dorsal striatum from cocaine self-administering mice. Using epigenome editing and 3C assays, we demonstrated a causal relationship between methylation within the IRX2 gene body, CTCF protein binding, three-dimensional (3D) chromatin interaction, and gene expression. Together, these findings suggest that cocaine-related hypomethylation of IRX2 contributes to the development and maintenance of cocaine dependence through alterations in 3D chromatin structure in the caudate nucleus.
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9
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Welle A, Kasakow CV, Jungmann AM, Gobbo D, Stopper L, Nordström K, Salhab A, Gasparoni G, Scheller A, Kirchhoff F, Walter J. Epigenetic control of region-specific transcriptional programs in mouse cerebellar and cortical astrocytes. Glia 2021; 69:2160-2177. [PMID: 34028094 DOI: 10.1002/glia.24016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 01/07/2023]
Abstract
Astrocytes from the cerebral cortex (CTX) and cerebellum (CB) share basic molecular programs, but also form distinct spatial and functional subtypes. The regulatory epigenetic layers controlling such regional diversity have not been comprehensively investigated so far. Here, we present an integrated epigenome analysis of methylomes, open chromatin, and transcriptomes of astroglia populations isolated from the cortex or cerebellum of young adult mice. Besides a basic overall similarity in their epigenomic programs, cortical astrocytes and cerebellar astrocytes exhibit substantial differences in their overall open chromatin structure and in gene-specific DNA methylation. Regional epigenetic differences are linked to differences in transcriptional programs encompassing genes of region-specific transcription factor networks centered around Lhx2/Foxg1 in CTX astrocytes and the Zic/Irx families in CB astrocytes. The distinct epigenetic signatures around these transcription factor networks point to a complex interconnected and combinatorial regulation of region-specific transcriptomes. These findings suggest that key transcription factors, previously linked to temporal, regional, and spatial control of neurogenesis, also form combinatorial networks important for astrocytes. Our study provides a valuable resource for the molecular basis of regional astrocyte identity and physiology.
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Affiliation(s)
- Anna Welle
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Carmen V Kasakow
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Annemarie M Jungmann
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Davide Gobbo
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Laura Stopper
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Karl Nordström
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Abdulrahman Salhab
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Gilles Gasparoni
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Anja Scheller
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Frank Kirchhoff
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Jörn Walter
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
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10
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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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11
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Hezroni H, Ben-Tov Perry R, Gil N, Degani N, Ulitsky I. Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus. EMBO Rep 2020; 21:e51264. [PMID: 32969152 DOI: 10.15252/embr.202051264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/09/2022] Open
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs), yet the biological functions of most of them remain unknown. A particularly rich repertoire of lncRNAs found in mammalian brain and in the early embryo. We used RNA-seq and computational analysis to prioritize lncRNAs that may regulate commitment of pluripotent cells to a neuronal fate and perturbed their expression prior to neuronal differentiation. Knockdown by RNAi of two highly conserved and well-expressed lncRNAs, Reno1 (2810410L24Rik) and lnc-Nr2f1, decreased the expression of neuronal markers and led to massive changes in gene expression in the differentiated cells. We further show that the Reno1 locus forms increasing spatial contacts during neurogenesis with its adjacent protein-coding gene Bahcc1. Loss of either Reno1 or Bahcc1 leads to an early arrest in neuronal commitment, failure to induce a neuronal gene expression program, and to global reduction in chromatin accessibility at regions that are marked by the H3K4me3 chromatin mark at the onset of differentiation. Reno1 and Bahcc1 thus form a previously uncharacterized circuit required for the early steps of neuronal commitment.
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Affiliation(s)
| | | | - Noa Gil
- Weizmann Institute of Science, Rehovot, Israel
| | - Neta Degani
- Weizmann Institute of Science, Rehovot, Israel
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12
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Sim H, Lee JE, Yoo HM, Cho S, Lee H, Baek A, Kim J, Seo H, Kweon MN, Kim HG, Jeon YJ, Son MY, Kim J. Iroquois Homeobox Protein 2 Identified as a Potential Biomarker for Parkinson's Disease. Int J Mol Sci 2020; 21:E3455. [PMID: 32422864 PMCID: PMC7278941 DOI: 10.3390/ijms21103455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
The diagnosis of Parkinson's disease (PD) is initiated after the occurrence of motor symptoms, such as resting tremors, rigidity, and bradykinesia. According to previous reports, non-motor symptoms, notably gastrointestinal dysfunction, could potentially be early biomarkers in PD patients as such symptoms occur earlier than motor symptoms. However, connecting PD to the intestine is methodologically challenging. Thus, we generated in vitro human intestinal organoids from PD patients and ex vivo mouse small intestinal organoids from aged transgenic mice. Both intestinal organoids (IOs) contained the human LRRK2 G2019S mutation, which is the most frequent genetic cause of familial and sporadic PD. By conducting comprehensive genomic comparisons with these two types of IOs, we determined that a particular gene, namely, Iroquois homeobox protein 2 (IRX2), showed PD-related expression patterns not only in human pluripotent stem cell (PSC)-derived neuroectodermal spheres but also in human PSC-derived neuronal cells containing dopaminergic neurons. We expected that our approach of using various cell types presented a novel technical method for studying the effects of multi-organs in PD pathophysiology as well as for the development of diagnostic markers for PD.
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Affiliation(s)
- Hyuna Sim
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Joo-Eun Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
| | - Hee Min Yoo
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea;
| | - Sunwha Cho
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
| | - Hana Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Aruem Baek
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
| | - Jisun Kim
- Department of Molecular & Life Sciences, College of Science & Technology, Hanyang University, Ansan 15588, Korea; (J.K.); (H.S.)
| | - Hyemyung Seo
- Department of Molecular & Life Sciences, College of Science & Technology, Hanyang University, Ansan 15588, Korea; (J.K.); (H.S.)
| | - Mi-Na Kweon
- Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul 05505, Korea;
| | - Hyung Gun Kim
- Department of Pharmacology, College of Medicine, Dankook University, Cheonan 31116, Korea;
| | - Young-Joo Jeon
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
| | - Mi-Young Son
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Janghwan Kim
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.S.); (J.-E.L.); (S.C.); (H.L.); (A.B.); (Y.-J.J.)
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
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13
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Abdulrahim JW, Kwee LC, Grass E, Siegler IC, Williams R, Karra R, Kraus WE, Gregory SG, Shah SH. Epigenome-Wide Association Study for All-Cause Mortality in a Cardiovascular Cohort Identifies Differential Methylation in Castor Zinc Finger 1 ( CASZ1). J Am Heart Assoc 2019; 8:e013228. [PMID: 31642367 PMCID: PMC6898816 DOI: 10.1161/jaha.119.013228] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023]
Abstract
Background DNA methylation is implicated in many chronic diseases and may contribute to mortality. Therefore, we conducted an epigenome-wide association study (EWAS) for all-cause mortality with whole-transcriptome data in a cardiovascular cohort (CATHGEN [Catheterization Genetics]). Methods and Results Cases were participants with mortality≥7 days postcatheterization whereas controls were alive with≥2 years of follow-up. The Illumina Human Methylation 450K and EPIC arrays (Illumina, San Diego, CA) were used for the discovery and validation sets, respectively. A linear model approach with empirical Bayes estimators adjusted for confounders was used to assess difference in methylation (Δβ). In the discovery set (55 cases, 49 controls), 25 629 (6.5%) probes were differently methylated (P<0.05). In the validation set (108 cases, 108 controls), 3 probes were differentially methylated with a false discovery rate-adjusted P<0.10: cg08215811 (SLC4A9; log2 fold change=-0.14); cg17845532 (MATK; fold change=-0.26); and cg17944110 (castor zinc finger 1 [CASZ1]; FC=0.26; P<0.0001; false discovery rate-adjusted P=0.046-0.080). Meta-analysis identified 6 probes (false discovery rate-adjusted P<0.05): the 3 above, cg20428720 (intergenic), cg17647904 (NCOR2), and cg23198793 (CAPN3). Messenger RNA expression of 2 MATK isoforms was lower in cases (fold change=-0.24 [P=0.007] and fold change=-0.61 [P=0.009]). The CASZ1, NCOR2, and CAPN3 transcripts did not show differential expression (P>0.05); the SLC4A9 transcript did not pass quality control. The cg17944110 probe is located within a potential regulatory element; expression of predicted targets (using GeneHancer) of the regulatory element, UBIAD1 (P=0.01) and CLSTN1 (P=0.03), were lower in cases. Conclusions We identified 6 novel methylation sites associated with all-cause mortality. Methylation in CASZ1 may serve as a regulatory element associated with mortality in cardiovascular patients. Larger studies are necessary to confirm these observations.
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Affiliation(s)
- Jawan W. Abdulrahim
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Lydia Coulter Kwee
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Elizabeth Grass
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Ilene C. Siegler
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNC
| | - Redford Williams
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNC
| | - Ravi Karra
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
| | - William E. Kraus
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
| | - Simon G. Gregory
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Svati H. Shah
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
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14
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Cri-du-Chat Syndrome interactome network: Correlating genotypic variations to associated phenotypes. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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ZIC1 Function in Normal Cerebellar Development and Human Developmental Pathology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:249-268. [PMID: 29442326 DOI: 10.1007/978-981-10-7311-3_13] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Zic genes are strongly expressed in the cerebellum. This feature leads to their initial identification and their name "zic," as the abbreviation of "zinc finger protein of the cerebellum." Zic gene function in cerebellar development has been investigated mainly in mice. However, association of heterozygous loss of ZIC1 and ZIC4 with Dandy-Walker malformation, a structural birth defect of the human cerebellum, highlights the clinical relevance of these studies. Two proposed mechanisms for Zic-mediated cerebellar developmental control have been documented: regulation of neuronal progenitor proliferation-differentiation and the patterning of the cerebellar primordium. Clinical studies have also revealed that ZIC1 gain of function mutations contribute to coronal craniosynostosis, a rare skull malformation. The molecular pathways contributing to these phenotypes are not fully explored; however, embryonic interactions with sonic hedgehog signaling, retinoic acid signaling, and TGFβ signaling have been described during mouse cerebellar development. Further, Zic1/2 target a multitude of genes associated with cerebellar granule cell maturation during postnatal mouse cerebellar development.
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16
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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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17
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Kiecker C, Graham A, Logan M. Differential Cellular Responses to Hedgehog Signalling in Vertebrates-What is the Role of Competence? J Dev Biol 2016; 4:jdb4040036. [PMID: 29615599 PMCID: PMC5831800 DOI: 10.3390/jdb4040036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 12/21/2022] Open
Abstract
A surprisingly small number of signalling pathways generate a plethora of cellular responses ranging from the acquisition of multiple cell fates to proliferation, differentiation, morphogenesis and cell death. These diverse responses may be due to the dose-dependent activities of signalling factors, or to intrinsic differences in the response of cells to a given signal—a phenomenon called differential cellular competence. In this review, we focus on temporal and spatial differences in competence for Hedgehog (HH) signalling, a signalling pathway that is reiteratively employed in embryos and adult organisms. We discuss the upstream signals and mechanisms that may establish differential competence for HHs in a range of different tissues. We argue that the changing competence for HH signalling provides a four-dimensional framework for the interpretation of the signal that is essential for the emergence of functional anatomy. A number of diseases—including several types of cancer—are caused by malfunctions of the HH pathway. A better understanding of what provides differential competence for this signal may reveal HH-related disease mechanisms and equip us with more specific tools to manipulate HH signalling in the clinic.
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Affiliation(s)
- Clemens Kiecker
- Department of Developmental Neurobiology, King's College London, Hodgkin Building, Guy's Hospital Campus, London SE1 1UL, UK.
| | - Anthony Graham
- Department of Developmental Neurobiology, King's College London, Hodgkin Building, Guy's Hospital Campus, London SE1 1UL, UK.
| | - Malcolm Logan
- Randall Division of Cell & Molecular Biophysics, King's College London, Hodgkin Building, Guy's Hospital Campus, London SE1 1UL, UK.
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18
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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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Capaldo E, Iulianella A. Cux2 serves as a novel lineage marker of granule cell layer neurons from the rhombic lip in mouse and chick embryos. Dev Dyn 2016; 245:881-96. [DOI: 10.1002/dvdy.24418] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/20/2016] [Accepted: 05/10/2016] [Indexed: 02/07/2023] Open
Affiliation(s)
- Emily Capaldo
- Department of Medical Neuroscience, Faculty of Medicine; Dalhousie University, Life Science Research Institute; Nova Scotia Canada
| | - Angelo Iulianella
- Department of Medical Neuroscience, Faculty of Medicine; Dalhousie University, Life Science Research Institute; Nova Scotia Canada
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20
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Harada H, Sato T, Nakamura H. Fgf8 signaling for development of the midbrain and hindbrain. Dev Growth Differ 2016; 58:437-45. [PMID: 27273073 DOI: 10.1111/dgd.12293] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/31/2023]
Abstract
In this paper, we review how midbrain and hindbrain are specified. Otx2 and Gbx2 are expressed from the early phase of development, and their expression abuts at the midbrain hindbrain boundary (MHB), where Fgf8 expression is induced, and functions as an organizing molecule for the midbrain and hindbrain. Fgf8 induces En1 and Pax2 expression at the region where Otx2 is expressed to specify midbrain. Fgf8 activates Ras-ERK pathway to specify hindbrain. Downstream of ERK, Pea3 specifies isthmus (rhombomere 0, r0), and Irx2 may specify r1, where the cerebellum is formed.
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Affiliation(s)
- Hidekiyo Harada
- Genetics and Development Division, Toronto Krembil Research Institute, Toronto, Ontario, Canada.,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Tatsuya Sato
- Department of Developmental Neuroscience, Graduate School of Medicine, Tohoku University, Sendai, 980-8575, Japan.,Frontier Research Institute for Interdisciplinary Science, Tohoku University, Sendai, 980-8578, Japan
| | - Harukazu Nakamura
- Frontier Research Institute for Interdisciplinary Science, Tohoku University, Sendai, 980-8578, Japan
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21
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Harada H, Omi M, Sato T, Nakamura H. Pea3 determines the isthmus region at the downstream of Fgf8-Ras-ERK signaling pathway. Dev Growth Differ 2015; 57:657-66. [DOI: 10.1111/dgd.12254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/25/2015] [Accepted: 10/25/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Hidekiyo Harada
- Department of Molecular Neurobiology; Institute of Development, Aging & Cancer and Graduate School of Life Sciences; Tohoku University; Sendai 980-8575 Miyagi Japan
| | - Minoru Omi
- Department of Molecular Neurobiology; Institute of Development, Aging & Cancer and Graduate School of Life Sciences; Tohoku University; Sendai 980-8575 Miyagi Japan
| | - Tatsuya Sato
- Department of Molecular Neurobiology; Institute of Development, Aging & Cancer and Graduate School of Life Sciences; Tohoku University; Sendai 980-8575 Miyagi Japan
| | - Harukazu Nakamura
- Department of Molecular Neurobiology; Institute of Development, Aging & Cancer and Graduate School of Life Sciences; Tohoku University; Sendai 980-8575 Miyagi Japan
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A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol 2015; 33:1173-81. [PMID: 26501951 PMCID: PMC4847940 DOI: 10.1038/nbt.3388] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/24/2015] [Indexed: 12/18/2022]
Abstract
The equivalence of human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) remains controversial. Here we use genetically matched hESC and hiPSC lines to assess the contribution of cellular origin (hESC vs. hiPSC), the Sendai virus (SeV) reprogramming method and genetic background to transcriptional and DNA methylation patterns while controlling for cell line clonality and sex. We find that transcriptional and epigenetic variation originating from genetic background dominates over variation due to cellular origin or SeV infection. Moreover, the 49 differentially expressed genes we detect between genetically matched hESCs and hiPSCs neither predict functional outcome nor distinguish an independently derived, larger set of unmatched hESC and hiPSC lines. We conclude that hESCs and hiPSCs are molecularly and functionally equivalent and cannot be distinguished by a consistent gene expression signature. Our data further imply that genetic background variation is a major confounding factor for transcriptional and epigenetic comparisons of pluripotent cell lines, explaining some of the previously observed differences between genetically unmatched hESCs and hiPSCs.
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Lu J, Song G, Tang Q, Zou C, Han F, Zhao Z, Yong B, Yin J, Xu H, Xie X, Kang T, Lam Y, Yang H, Shen J, Wang J. IRX1 hypomethylation promotes osteosarcoma metastasis via induction of CXCL14/NF-κB signaling. J Clin Invest 2015; 125:1839-56. [PMID: 25822025 DOI: 10.1172/jci78437] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/19/2015] [Indexed: 12/13/2022] Open
Abstract
Osteosarcoma is a common malignant bone tumor with a propensity to metastasize to the lungs. Epigenetic abnormalities have been demonstrated to underlie osteosarcoma development; however, the epigenetic mechanisms that are involved in metastasis are not yet clear. Here, we analyzed 2 syngeneic primary human osteosarcoma cell lines that exhibit disparate metastatic potential for differences in epigenetic modifications and expression. Using methylated DNA immunoprecipitation (MeDIP) and microarray expression analysis to screen for metastasis-associated genes, we identified Iroquois homeobox 1 (IRX1). In both human osteosarcoma cell lines and clinical osteosarcoma tissues, IRX1 overexpression was strongly associated with hypomethylation of its own promoter. Furthermore, experimental modulation of IRX1 in osteosarcoma cell lines profoundly altered metastatic activity, including migration, invasion, and resistance to anoikis in vitro, and influenced lung metastasis in murine models. These prometastatic effects of IRX1 were mediated by upregulation of CXCL14/NF-κB signaling. In serum from osteosarcoma patients, the presence of IRX1 hypomethylation in circulating tumor DNA reduced lung metastasis-free survival. Together, these results identify IRX1 as a prometastatic gene, implicate IRX1 hypomethylation as a potential molecular marker for lung metastasis, and suggest that epigenetic reversion of IRX1 activation may be beneficial for controlling osteosarcoma metastasis.
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MESH Headings
- Animals
- Anoikis
- Base Sequence
- Bone Neoplasms/genetics
- Bone Neoplasms/metabolism
- Bone Neoplasms/pathology
- Cell Line, Tumor
- Cell Movement
- Chemokines, CXC/physiology
- DNA Methylation
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/genetics
- High-Throughput Screening Assays
- Homeodomain Proteins/biosynthesis
- Homeodomain Proteins/blood
- Homeodomain Proteins/genetics
- Homeodomain Proteins/physiology
- Humans
- Lung Neoplasms/secondary
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Molecular Sequence Data
- NF-kappa B/physiology
- Neoplasm Invasiveness
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/blood
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Neoplasm Transplantation
- Osteosarcoma/genetics
- Osteosarcoma/metabolism
- Osteosarcoma/secondary
- Promoter Regions, Genetic/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Transcription Factors/biosynthesis
- Transcription Factors/blood
- Transcription Factors/genetics
- Transcription Factors/physiology
- Transcription, Genetic
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24
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Karlsson J, Lilljebjörn H, Holmquist Mengelbier L, Valind A, Rissler M, Øra I, Fioretos T, Gisselsson D. Activation of human telomerase reverse transcriptase through gene fusion in clear cell sarcoma of the kidney. Cancer Lett 2015; 357:498-501. [DOI: 10.1016/j.canlet.2014.11.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 10/24/2022]
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25
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Pose-Méndez S, Candal E, Mazan S, Rodríguez-Moldes I. Genoarchitecture of the rostral hindbrain of a shark: basis for understanding the emergence of the cerebellum at the agnathan–gnathostome transition. Brain Struct Funct 2015; 221:1321-35. [DOI: 10.1007/s00429-014-0973-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 12/17/2014] [Indexed: 12/14/2022]
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26
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Yamaguchi M, Shima N, Kimoto M, Ebihara N, Murakami A, Yamagami S. Markers for distinguishing cultured human corneal endothelial cells from corneal stromal myofibroblasts. Curr Eye Res 2014; 40:1211-7. [PMID: 25546361 DOI: 10.3109/02713683.2014.993087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE Eliminating contamination by corneal stromal cells is critical when preparing cultured human corneal endothelial cells (CECs) transplantation. We investigated markers for the purification of cultured human CECs and markers for excluding cultured human corneal stromal myofibroblasts (CSMFs) from cultured human CECs. MATERIALS AND METHODS CECs and CSMFs were obtained from human donor corneas by culturing separately in serum-containing medium. Candidate markers of CECs and CSMFs were screened with microarray analysis in the fourth passaged CECs and CSMFs. Then, selected factors were evaluated in reverse transcription polymerase chain reaction (RT-PCR), western blot, immunocytochemistry, and flow cytometry to investigate differential markers for each cell. RESULTS Among the genes identified by microarray analysis, cultured human CECs, but not CSMFs, expressed integrin alpha 3 (ITGA3 and CD49c) protein according to immunocytochemistry and western blotting. Iroquois homeobox 2 (IRX2) gene was a marker that distinguished CSMFs from cultured human CECs by RT-PCR. The IRX2 gene can be used as a marker of CSMFs contaminating cultured CECs. CONCLUSION These molecules could be important markers for the production of highly purified cultured CECs for regenerative medicine.
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Affiliation(s)
- Masahiro Yamaguchi
- a Corneal Regeneration Research Team, Foundation for Biomedical Research and Innovation , Kobe , Japan .,b Department of Ophthalmology , Juntendo University School of Medicine , Tokyo , Japan
| | - Nobuyuki Shima
- a Corneal Regeneration Research Team, Foundation for Biomedical Research and Innovation , Kobe , Japan .,c Department of Ophthalmology , University of Tokyo Graduate School of Medicine , Tokyo , Japan
| | - Miwa Kimoto
- a Corneal Regeneration Research Team, Foundation for Biomedical Research and Innovation , Kobe , Japan
| | - Nobuyuki Ebihara
- b Department of Ophthalmology , Juntendo University School of Medicine , Tokyo , Japan .,d Department of Ophthalmology , Juntendo University Urayasu Hospital , Chiba , Japan and
| | - Akira Murakami
- b Department of Ophthalmology , Juntendo University School of Medicine , Tokyo , Japan
| | - Satoru Yamagami
- a Corneal Regeneration Research Team, Foundation for Biomedical Research and Innovation , Kobe , Japan .,e Corneal Transplantation Section, University of Tokyo Graduate School of Medicine , Tokyo , Japan
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27
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Chuang HN, Hsiao KM, Chang HY, Wu CC, Pan H. The homeobox transcription factor Irxl1 negatively regulates MyoD expression and myoblast differentiation. FEBS J 2014; 281:2990-3003. [PMID: 24814716 DOI: 10.1111/febs.12837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/07/2014] [Accepted: 04/30/2014] [Indexed: 11/29/2022]
Abstract
Irxl1/Mkx (Iroquois homeobox-like 1/Mohawk) encodes a member of the TALE subfamily of homeodomain proteins. It is expressed in multiple mesoderm-derived tissues and has recently been shown to regulate tendon differentiation during mouse embryonic development. Previously we showed that knockdown of Irxl1 in zebrafish caused a deficit in neural crest cells which consequently resulted in deformation of craniofacial muscles and arch cartilages. Here, we further demonstrate that loss of Irxl1 function results in deformed somites with disordered muscle fibers and myotendinous junctions. Because expression of myoD is increased in the somites of Irxl1 knockdown morphants, we test whether Irxl1 negatively regulates myoD expression. When stable C2C12 myoblasts overexpressing Irxl1/Mkx were induced to differentiate, myotube formation was inhibited and protein levels of myoD and myosin heavy chain were decreased accordingly. A series of deletion constructs of myoD promoter fragments were tested by luciferase reporter assays, which identified a promoter fragment that is necessary and sufficient for Irxl1-mediated repression. Direct interaction of Irxl1 and myoD promoter was subsequently elucidated by yeast one-hybrid assays, electrophoretic mobility shift assays and chromatin immunoprecipitation analysis. Furthermore, mouse Mkx also binds to and represses myoD promoter. These results indicate that Irxl1/Mkx can repress myoD expression through direct binding to its promoter and may thus play a negative regulatory role in muscle differentiation.
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Affiliation(s)
- Han-Ni Chuang
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan; Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
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28
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Xiao L, Harrell JC, Perou CM, Dudley AC. Identification of a stable molecular signature in mammary tumor endothelial cells that persists in vitro. Angiogenesis 2013; 17:511-8. [PMID: 24257808 DOI: 10.1007/s10456-013-9409-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/13/2013] [Indexed: 12/25/2022]
Abstract
Long-term, in vitro propagation of tumor-specific endothelial cells (TEC) allows for functional studies and genome-wide expression profiling of clonally derived, well-characterized subpopulations. Using a genetically engineered mouse model of mammary adenocarcinoma, we have optimized an isolation procedure and defined growth conditions for long-term propagation of mammary TEC. The isolated TEC maintain their endothelial specification and phenotype in culture. Furthermore, gene expression profiling of multiple TEC subpopulations revealed striking, persistent overexpression of several candidate genes including Irx2 and Zfp503 (transcription factors), Alcam and Cd133 (cell surface markers), Ccl4 and neurotensin (Nts) (angiocrine factors), and Gpr182 and Cnr2 (G protein-coupled receptors). Taken together, we have developed an effective method for isolating and culture-expanding mammary TEC, and uncovered several new TEC-selective genes whose overexpression persists even after long-term in vitro culture. These results suggest that the tumor microenvironment may induce changes in vascular endothelium in vivo that are stably transmittable in vitro.
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Affiliation(s)
- Lin Xiao
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 3340C Medical Biomolecular Research Building, Chapel Hill, NC, 27599, USA
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29
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Affiliation(s)
| | - Richard Hawkes
- Department of Cell Biology and Anatomy, Genes and Development Research Group and Hotchkiss Brain Institute, Faculty of Medicine, University of Calgary
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30
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The Iroquois complex is required in the dorsal mesoderm to ensure normal heart development in Drosophila. PLoS One 2013; 8:e76498. [PMID: 24086746 PMCID: PMC3781054 DOI: 10.1371/journal.pone.0076498] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 08/27/2013] [Indexed: 12/23/2022] Open
Abstract
Drosophila heart development is an invaluable system to study the orchestrated action of numerous factors that govern cardiogenesis. Cardiac progenitors arise within specific dorsal mesodermal regions that are under the influence of temporally coordinated actions of multiple signaling pathways. The Drosophila Iroquois complex (Iro-C) consists of the three homeobox transcription factors araucan (ara), caupolican (caup) and mirror (mirr). The Iro-C has been shown to be involved in tissue patterning leading to the differentiation of specific structures, such as the lateral notum and dorsal head structures and in establishing the dorsal-ventral border of the eye. A function for Iro-C in cardiogenesis has not been investigated yet. Our data demonstrate that loss of the whole Iro complex, as well as loss of either ara/caup or mirr only, affect heart development in Drosophila. Furthermore, the data indicate that the GATA factor Pannier requires the presence of Iro-C to function in cardiogenesis. Furthermore, a detailed expression pattern analysis of the members of the Iro-C revealed the presence of a possibly novel subpopulation of Even-skipped expressing pericardial cells and seven pairs of heart-associated cells that have not been described before. Taken together, this work introduces Iro-C as a new set of transcription factors that are required for normal development of the heart. As the members of the Iro-C may function, at least partly, as competence factors in the dorsal mesoderm, our results are fundamental for future studies aiming to decipher the regulatory interactions between factors that determine different cell fates in the dorsal mesoderm.
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31
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Response to the dorsal anterior gradient of EGFR signaling in Drosophila oogenesis is prepatterned by earlier posterior EGFR activation. Cell Rep 2013; 4:791-802. [PMID: 23972992 DOI: 10.1016/j.celrep.2013.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/21/2013] [Accepted: 07/26/2013] [Indexed: 11/22/2022] Open
Abstract
Spatially restricted epidermal growth factor receptor (EGFR) activity plays a central role in patterning the follicular epithelium of the Drosophila ovary. In midoogenesis, localized EGFR activation is achieved by the graded dorsal anterior localization of its ligand, Gurken. Graded EGFR activity determines multiple dorsal anterior fates along the dorsal-ventral axis but cannot explain the sharp posterior limit of this domain. Here, we show that posterior follicle cells express the T-box transcription factors Midline and H15, which render cells unable to adopt a dorsal anterior fate in response to EGFR activation. The posterior expression of Midline and H15 is itself induced in early oogenesis by posteriorly localized EGFR signaling, defining a feedback loop in which early induction of Mid and H15 confers a molecular memory that fundamentally alters the outcome of later EGFR signaling. Spatial regulation of the EGFR pathway thus occurs both through localization of the ligand and through localized regulation of the cellular response.
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32
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Brain-derived neurotrophic factor signaling rewrites the glucocorticoid transcriptome via glucocorticoid receptor phosphorylation. Mol Cell Biol 2013; 33:3700-14. [PMID: 23878391 DOI: 10.1128/mcb.00150-13] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Abnormal glucocorticoid and neurotrophin signaling has been implicated in numerous psychiatric disorders. However, the impact of neurotrophic signaling on glucocorticoid receptor (GR)-dependent gene expression is not understood. We therefore examined the impact of brain-derived neurotrophic factor (BDNF) signaling on GR transcriptional regulatory function by gene expression profiling in primary rat cortical neurons stimulated with the selective GR agonist dexamethasone (Dex) and BDNF, alone or in combination. Simultaneous treatment with BDNF and Dex elicited a unique set of GR-responsive genes associated with neuronal growth and differentiation and also enhanced the induction of a large number of Dex-sensitive genes. BDNF via its receptor TrkB enhanced the transcriptional activity of a synthetic GR reporter, suggesting a direct effect of BDNF signaling on GR function. Indeed, BDNF treatment induces the phosphorylation of GR at serine 155 (S155) and serine 287 (S287). Expression of a nonphosphorylatable mutant (GR S155A/S287A) impaired the induction of a subset of BDNF- and Dex-regulated genes. Mechanistically, BDNF-induced GR phosphorylation increased GR occupancy and cofactor recruitment at the promoter of a BDNF-enhanced gene. GR phosphorylation in vivo is sensitive to changes in the levels of BDNF and TrkB as well as stress. Therefore, BDNF signaling specifies and amplifies the GR transcriptome through a coordinated GR phosphorylation-dependent detection mechanism.
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Kim KH, Rosen A, Bruneau BG, Hui CC, Backx PH. Iroquois homeodomain transcription factors in heart development and function. Circ Res 2012; 110:1513-24. [PMID: 22628575 DOI: 10.1161/circresaha.112.265041] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Numerous cardiac transcription factors play overlapping roles in both the specification and proliferation of the cardiac tissues and chambers during heart development. It has become increasingly apparent that cardiac transcription factors also play critical roles in the regulation of expression of many functional genes in the prenatal and postnatal hearts. Accordingly, mutations of cardiac transcription factors cannot only result in congenital heart defects but also alter heart function thereby predisposing to heart disease and cardiac arrhythmias. In this review, we summarize the roles of Iroquois homeobox (Irx) family of transcription factors in heart development and function. In all, 6 Irx genes are expressed with distinct and overlapping patterns in the mammalian heart. Studies in several animal models demonstrate that Irx genes are important for the establishment of ventricular chamber properties, the ventricular conduction system, as well as heterogeneity of the ventricular repolarization. The molecular mechanisms by which Irx proteins regulate gene expression and the clinical relevance of Irx functions in the heart are discussed.
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Affiliation(s)
- Kyoung-Han Kim
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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34
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Affiliation(s)
- Clemens Kiecker
- Medical Research Council (MRC) Center for Developmental Neurobiology, King's College, London SE1 1UL, United Kingdom; ,
| | - Andrew Lumsden
- Medical Research Council (MRC) Center for Developmental Neurobiology, King's College, London SE1 1UL, United Kingdom; ,
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35
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Crespo-Enriquez I, Partanen J, Martinez S, Echevarria D. Fgf8-related secondary organizers exert different polarizing planar instructions along the mouse anterior neural tube. PLoS One 2012; 7:e39977. [PMID: 22792203 PMCID: PMC3391221 DOI: 10.1371/journal.pone.0039977] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/30/2012] [Indexed: 12/11/2022] Open
Abstract
Early brain patterning depends on proper arrangement of positional information. This information is given by gradients of secreted signaling molecules (morphogens) detected by individual cells within the responding tissue, leading to specific fate decisions. Here we report that the morphogen FGF8 exerts initially a differential signal activity along the E9.5 mouse neural tube. We demonstrate that this polarizing activity codes by RAS-regulated ERK1/2 signaling and depends on the topographical location of the secondary organizers: the isthmic organizer (IsO) and the anterior neural ridge (anr) but not on zona limitans intrathalamica (zli). Our results suggest that Sprouty2, a negative modulator of RAS/ERK pathway, is important for regulating Fgf8 morphogenetic signal activity by controlling Fgf8-induced signaling pathways and positional information during early brain development.
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Affiliation(s)
- Ivan Crespo-Enriquez
- Instituto de Neurociencias de Alicante, Consejo Superior de Investigaciones Científicas–Universidad Miguel Hernandez, Alicante, Spain
| | - Juha Partanen
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | - Salvador Martinez
- Instituto de Neurociencias de Alicante, Consejo Superior de Investigaciones Científicas–Universidad Miguel Hernandez, Alicante, Spain
| | - Diego Echevarria
- Instituto de Neurociencias de Alicante, Consejo Superior de Investigaciones Científicas–Universidad Miguel Hernandez, Alicante, Spain
- * E-mail:
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36
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Mattes B, Weber S, Peres J, Chen Q, Davidson G, Houart C, Scholpp S. Wnt3 and Wnt3a are required for induction of the mid-diencephalic organizer in the caudal forebrain. Neural Dev 2012; 7:12. [PMID: 22475147 PMCID: PMC3349543 DOI: 10.1186/1749-8104-7-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 04/04/2012] [Indexed: 01/05/2023] Open
Abstract
Background A fundamental requirement for development of diverse brain regions is the function of local organizers at morphological boundaries. These organizers are restricted groups of cells that secrete signaling molecules, which in turn regulate the fate of the adjacent neural tissue. The thalamus is located in the caudal diencephalon and is the central relay station between the sense organs and higher brain areas. The mid-diencephalic organizer (MDO) orchestrates the development of the thalamus by releasing secreted signaling molecules such as Shh. Results Here we show that canonical Wnt signaling in the caudal forebrain is required for the formation of the Shh-secreting MD organizer in zebrafish. Wnt signaling induces the MDO in a narrow time window of 4 hours - between 10 and 14 hours post fertilization. Loss of Wnt3 and Wnt3a prevents induction of the MDO, a phenotype also observed upon blockage of canonical Wnt signaling per se. Pharmaceutical activation of the canonical Wnt pathways in Wnt3/Wnt3a compound morphant embryos is able to restore the lack of the MDO. After blockage of Wnt signaling or knock-down of Wnt3/Wnt3a we find an increase of apoptotic cells specifically within the organizer primordium. Consistently, blockage of apoptosis restores the thalamus organizer MDO in Wnt deficient embryos. Conclusion We have identified canonical Wnt signaling as a novel pathway, that is required for proper formation of the MDO and consequently for the development of the major relay station of the brain - the thalamus. We propose that Wnt ligands are necessary to maintain the primordial tissue of the organizer during somitogenesis by suppressing Tp53-mediated apoptosis.
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Affiliation(s)
- Benjamin Mattes
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Karlsruhe, Germany
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37
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Suzuki A, Harada H, Nakamura H. Nuclear translocation of FGF8 and its implication to induce Sprouty2. Dev Growth Differ 2012; 54:463-73. [PMID: 22404534 DOI: 10.1111/j.1440-169x.2012.01332.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fibroblast growth factor 8 (FGF8) functions as a local organizing signal for the tectum and cerebellum. FGF8 activates Ras-ERK signaling pathway to induce cerebellar development. We paid attention to the difference in the expression pattern of the molecules that are induced by FGF8 in the mid-hind brain region during normal development and after FGF8 misexpression; some are expressed in the area corresponding to the ERK activation domain but the others are expressed corresponding to the Fgf8 expression domain. Since some of the FGF family members are localized in the nucleus, we wondered if FGF8 could localize in the nuclei and function in the nucleus. We first show that in cultured NIH3T3 cells transfected FGF8b could localize in the nucleus. Transfected FGF8b could also localize in the nucleus of the cells in the chick neural tube. In mouse embryonic neural tube, we detected endogenous FGF8 in the nuclei. Implantation of an FGF8b-soaked bead showed that exogenous FGF8b could be translocated to the nuclei in the isthmus. Furthermore, signal-peptide-deletion mutant of FGF8b mainly localized in the nuclei, and induced Sprouty2 without activating ERK in the mesencephalon. Signal-peptide-deletion mutant of FGF8b could not induce Pax2 expression. Taken together, we concluded that FGF8b could be translocated to the nuclei, and that the nuclear FGF8 could function as transcriptional regulator to induce Sprouty2 in the isthmus.
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Affiliation(s)
- Ayumu Suzuki
- Department of Molecular Neurobiology, Graduate School of Life Sciences and Institute of Development, Aging and Cancer, Tohoku University, Seiryo-machi 4-1, Aoba-ku, 980-8575 Sendai, Japan
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A transcriptional program promotes remodeling of GABAergic synapses in Caenorhabditis elegans. J Neurosci 2011; 31:15362-75. [PMID: 22031882 DOI: 10.1523/jneurosci.3181-11.2011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Although transcription factors are known to regulate synaptic plasticity, downstream genes that contribute to neural circuit remodeling are largely undefined. In Caenorhabditis elegans, GABAergic Dorsal D (DD) motor neuron synapses are relocated to new sites during larval development. This remodeling program is blocked in Ventral D (VD) GABAergic motor neurons by the COUP-TF (chicken ovalbumin upstream promoter transcription factor) homolog, UNC-55. We exploited this UNC-55 function to identify downstream synaptic remodeling genes that encode a diverse array of protein types including ion channels, cytoskeletal components, and transcription factors. We show that one of these targets, the Iroquois-like homeodomain protein, IRX-1, functions as a key regulator of remodeling in DD neurons. Our discovery of irx-1 as an unc-55-regulated target defines a transcriptional pathway that orchestrates an intricate synaptic remodeling program. Moreover, the well established roles of these conserved transcription factors in mammalian neural development suggest that a similar cascade may also control synaptic plasticity in more complex nervous systems.
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39
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Iroquois homeobox gene 3 establishes fast conduction in the cardiac His-Purkinje network. Proc Natl Acad Sci U S A 2011; 108:13576-81. [PMID: 21825130 DOI: 10.1073/pnas.1106911108] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rapid electrical conduction in the His-Purkinje system tightly controls spatiotemporal activation of the ventricles. Although recent work has shed much light on the regulation of early specification and morphogenesis of the His-Purkinje system, less is known about how transcriptional regulation establishes impulse conduction properties of the constituent cells. Here we show that Iroquois homeobox gene 3 (Irx3) is critical for efficient conduction in this specialized tissue by antithetically regulating two gap junction-forming connexins (Cxs). Loss of Irx3 resulted in disruption of the rapid coordinated spread of ventricular excitation, reduced levels of Cx40, and ectopic Cx43 expression in the proximal bundle branches. Irx3 directly represses Cx43 transcription and indirectly activates Cx40 transcription. Our results reveal a critical role for Irx3 in the precise regulation of intercellular gap junction coupling and impulse propagation in the heart.
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40
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Carrasco-Rando M, Tutor AS, Prieto-Sánchez S, González-Pérez E, Barrios N, Letizia A, Martín P, Campuzano S, Ruiz-Gómez M. Drosophila araucan and caupolican integrate intrinsic and signalling inputs for the acquisition by muscle progenitors of the lateral transverse fate. PLoS Genet 2011; 7:e1002186. [PMID: 21811416 PMCID: PMC3141015 DOI: 10.1371/journal.pgen.1002186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 05/28/2011] [Indexed: 01/23/2023] Open
Abstract
A central issue of myogenesis is the acquisition of identity by individual muscles. In Drosophila, at the time muscle progenitors are singled out, they already express unique combinations of muscle identity genes. This muscle code results from the integration of positional and temporal signalling inputs. Here we identify, by means of loss-of-function and ectopic expression approaches, the Iroquois Complex homeobox genes araucan and caupolican as novel muscle identity genes that confer lateral transverse muscle identity. The acquisition of this fate requires that Araucan/Caupolican repress other muscle identity genes such as slouch and vestigial. In addition, we show that Caupolican-dependent slouch expression depends on the activation state of the Ras/Mitogen Activated Protein Kinase cascade. This provides a comprehensive insight into the way Iroquois genes integrate in muscle progenitors, signalling inputs that modulate gene expression and protein activity. In Drosophila, as in vertebrates, the muscular system consists of different types of muscles that must act in coordination with the nervous system to control the adequate release of contraction power required for the proper functioning of the organism. Therefore, the acquisition of specific identities by individual muscles is a key step in the generation of the muscular system. In Drosophila, muscle progenitors (specific myoblasts that seed the formation of mature muscles) integrate positional and temporal signalling inputs, resulting in the expression of unique combinations of muscle identity genes, which confer on them specific fates. Up to now, very little was known of how this integration takes place at a molecular level and how a particular code is translated into a specific muscle fate. Here we show that the acquisition of the lateral transverse muscle fate requires the repression mediated by Araucan and Caupolican, two homeoproteins of the Iroquois Complex, of other muscle identity genes, like slouch and vestigial. The repressor or activator function of the Iroquois proteins depends on the activity of the Ras signalling pathway. Therefore, our work places Iroquois genes at a nodal point that integrates signalling inputs and regulates protein activity and cell fate determination.
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Affiliation(s)
- Marta Carrasco-Rando
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio S. Tutor
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
| | - Silvia Prieto-Sánchez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
| | - Esther González-Pérez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
| | - Natalia Barrios
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
| | - Annalisa Letizia
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Paloma Martín
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
| | - Sonsoles Campuzano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
| | - Mar Ruiz-Gómez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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The atypical homeodomain transcription factor Mohawk controls tendon morphogenesis. Mol Cell Biol 2010; 30:4797-807. [PMID: 20696843 DOI: 10.1128/mcb.00207-10] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mohawk homeobox (Mkx) gene encodes a new atypical homeodomain-containing protein with transcriptional repressor activity. Mkx mRNA exhibited dynamic expression patterns during development of the palate, somite, kidney, and testis, suggesting that it may be an important regulator of multiple developmental processes. To investigate the roles of Mkx in organogenesis, we generated mice carrying a null mutation in this gene. Mkx(-/-) mice survive postnatally and exhibit a unique wavy-tail phenotype. Close examination revealed that the mutant mice had smaller tendons than wild-type littermates and that the rapid postnatal growth of collagen fibrils in tendons was disrupted in Mkx(-/-) mice. Defects in tendon development were detected in the mutant mouse embryos as early as embryonic day 16.5 (E16.5). Although collagen fibril assembly initially appeared normal, the tendons of Mkx(-/-) embryos expressed significantly reduced amounts of collagen I, fibromodulin, and tenomodulin in comparison with control littermates. We found that Mkx mRNA was strongly expressed in differentiating tendon cells during embryogenesis and in the tendon sheath cells in postnatal stages. In addition to defects in tendon collagen fibrillogenesis, Mkx(-/-) mutant mice exhibited abnormal tendon sheaths. These results identify Mkx as an important regulator of tendon development.
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Scholpp S, Lumsden A. Building a bridal chamber: development of the thalamus. Trends Neurosci 2010; 33:373-80. [PMID: 20541814 PMCID: PMC2954313 DOI: 10.1016/j.tins.2010.05.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 12/26/2022]
Abstract
The thalamus is a central brain region that plays a crucial role in distributing incoming sensory information to appropriate regions of the cortex. The thalamus develops in the posterior part of the embryonic forebrain, where early cell fate decisions are controlled by a local signaling center – the mid-diencephalic organizer – which forms at the boundary between prospective prethalamus and thalamus. In this review we discuss recent observations of early thalamic development in zebrafish, chick, and mouse embryos, that reveal a conserved set of interactions between homeodomain transcription factors. These interactions position the organizer along the neuraxis. The most prominent of the organizer's signals, Sonic hedgehog, is necessary for conferring regional identity on the prethalamus and thalamus and for patterning their differentiation.
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Affiliation(s)
- Steffen Scholpp
- Karlsruhe Institute of Technology, Institute for Toxicology and Genetics, 76021 Karlsruhe, Germany
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43
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Agoston Z, Schulte D. Meis2 competes with the Groucho co-repressor Tle4 for binding to Otx2 and specifies tectal fate without induction of a secondary midbrain-hindbrain boundary organizer. Development 2009; 136:3311-22. [DOI: 10.1242/dev.037770] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The transcription factor Otx2 is expressed throughout the anterior neuroectoderm and is required for the formation of all forebrain- and midbrain-derived structures. The molecular determinants that cooperate with Otx2 to subdivide its expression domain into distinct functional units are, however, poorly understood at present. We show here that the TALE-homeodomain protein Meis2 is expressed in the chick tectal anlage and is both necessary and sufficient for tectal development. Unlike known tectum-inducing genes, the ability of Meis2 to initiate tectal development does not involve the formation of a secondary midbrain-hindbrain boundary organizer, but instead requires direct interaction with Otx2. Using an Otx2-dependent reporter assay we demonstrate that Meis2 competes with the Groucho co-repressor Tle4 (Grg4) for binding to Otx2 and thereby restores Otx2 transcriptional activator function. Together, our data suggest a model in which the balance between a co-repressor and a co-activator, which compete for binding to Otx2 in the mesencephalic vesicle, provides spatial and temporal control over tectal development. Controlled formation of Meis2-containing higher order protein complexes might thus serve as a general mechanism to achieve subdivision of the anterior neuroectoderm into distinct functional units during embryogenesis.
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Affiliation(s)
- Zsuzsa Agoston
- Department of Neuroanatomy, Max-Planck Institute for Brain Research,Deutschordenstr. 46, Frankfurt, Germany
| | - Dorothea Schulte
- Department of Neuroanatomy, Max-Planck Institute for Brain Research,Deutschordenstr. 46, Frankfurt, Germany
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Kadota M, Sato M, Duncan B, Ooshima A, Yang HH, Diaz-Meyer N, Gere S, Kageyama SI, Fukuoka J, Nagata T, Tsukada K, Dunn BK, Wakefield LM, Lee MP. Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA. Cancer Res 2009; 69:7357-65. [PMID: 19706770 DOI: 10.1158/0008-5472.can-09-0064] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To identify genetic events that characterize cancer progression, we conducted a comprehensive genetic evaluation of 161 primary breast tumors. Similar to the "mountain-and-hill" view of mutations, gene amplification also shows high- and low-frequency alterations in breast cancers. The frequently amplified genes include the well-known oncogenes ERBB2, FGFR1, MYC, CCND1, and PIK3CA, whereas other known oncogenes that are amplified, although less frequently, include CCND2, EGFR, FGFR2, and NOTCH3. More importantly, by honing in on minimally amplified regions containing three or fewer genes, we identified six new amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4. We found that both the IRX2 and TBL1XR1 proteins showed higher expression in the malignant cell lines MCF10CA1h and MCF10CA1a than in their precursor, MCF10A, a normal immortalized mammary epithelial cell line. To study oncogenic roles of TBL1XR1, we performed knockdown experiments using a short hairpin RNA approach and found that depletion of TBL1XR1 in MCF10CA1h cells resulted in reduction of cell migration and invasion as well as suppression of tumorigenesis in mouse xenografts. Intriguingly, our mutation analysis showed the presence of activation mutations in the PIK3CA gene in a subset of tumors that also had DNA copy number increases in the PIK3CA locus, suggesting an additive effect of coexisting activating amino acid substitution and dosage increase from amplification. Our gene amplification and somatic mutation analysis of breast primary tumors provides a coherent picture of genetic events, both corroborating and novel, offering insight into the genetic underpinnings of breast cancer progression.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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45
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Developmental expression of the three iroquois genes of amphioxus (BfIrxA, BfIrxB, and BfIrxC) with special attention to the gastrula organizer and anteroposterior boundaries in the central nervous system. Gene Expr Patterns 2009; 9:329-34. [DOI: 10.1016/j.gep.2009.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 02/06/2009] [Accepted: 02/11/2009] [Indexed: 11/16/2022]
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46
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Functional mode of FoxD1/CBF2 for the establishment of temporal retinal specificity in the developing chick retina. Dev Biol 2009; 331:300-10. [PMID: 19450575 DOI: 10.1016/j.ydbio.2009.05.549] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 05/12/2009] [Accepted: 05/12/2009] [Indexed: 12/13/2022]
Abstract
Two winged-helix transcription factors, FoxG1 (previously called chick brain factor1, CBF1) and FoxD1 (chick brain factor2, CBF2), are expressed specifically in the nasal and temporal regions of the developing chick retina, respectively. We previously demonstrated that FoxG1 controls the expression of topographic molecules including FoxD1, and determines the regional specificity of the nasal retina. FoxD1 is known to prescribe temporal specificity, however, molecular mechanisms and downstream targets have not been elucidated. Here we addressed the genetic mechanisms for establishing temporal specificity in the developing retina using an in ovo electroporation technique. Fibroblast growth factor (Fgf) and Wnt first play pivotal roles in inducing the region-specific expression of FoxG1 and FoxD1 in the optic vesicle. Misexpression of FoxD1 represses the expression of FoxG1, GH6, SOHo1, and ephrin-A5, and induces that of EphA3 in the retina. GH6 and SOHo1 repress the expression of FoxD1. In contrast to the inhibitory effect of FoxG1 on bone morphogenic protein (BMP) signaling, FoxD1 does not alter the expression of BMP4 or BMP2. Studies with chimeric mutants of FoxD1 showed that FoxD1 acts as a transcription repressor in controlling its downstream targets in the retina. Taken together with previous findings, our data suggest that FoxG1 and FoxD1 are located at the top of the gene cascade for regional specification along the nasotemporal (anteroposterior) axis in the retina, and FoxD1 determines temporal specificity.
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Anderson DM, Beres BJ, Wilson-Rawls J, Rawls A. The homeobox gene Mohawk represses transcription by recruiting the sin3A/HDAC co-repressor complex. Dev Dyn 2009; 238:572-80. [PMID: 19235719 DOI: 10.1002/dvdy.21873] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mohawk is an atypical homeobox gene expressed in embryonic progenitor cells of skeletal muscle, tendon, and cartilage. We demonstrate that Mohawk functions as a transcriptional repressor capable of blocking the myogenic conversion of 10T1/2 fibroblasts. The repressor activity is located in three small, evolutionarily conserved domains (MRD1-3) in the carboxy-terminal half of the protein. Point mutation analysis revealed six residues in MRD1 are sufficient for repressor function. The carboxy-terminal half of Mohawk is able to recruit components of the Sin3A/HDAC co-repressor complex (Sin3A, Hdac1, and Sap18) and a subset of Polymerase II general transcription factors (Tbp, TFIIA1 and TFIIB). Furthermore, Sap18, a protein that bridges the Sin3A/HDAC complex to DNA-bound transcription factors, is co-immunoprecipitated by MRD1. These data predict that Mohawk can repress transcription through recruitment of the Sin3A/HDAC co-repressor complex, and as a result, repress target genes required for the differentiation of cells to the myogenic lineage.
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Affiliation(s)
- Douglas M Anderson
- School of Life Sciences, Center for Evolutionary Functional Genomics, Arizona State University, Tempe, Arizona 85287-4501, USA
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Rodríguez-Seguel E, Alarcón P, Gómez-Skarmeta JL. The Xenopus Irx genes are essential for neural patterning and define the border between prethalamus and thalamus through mutual antagonism with the anterior repressors Fezf and Arx. Dev Biol 2009; 329:258-68. [PMID: 19268445 DOI: 10.1016/j.ydbio.2009.02.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 02/20/2009] [Accepted: 02/24/2009] [Indexed: 12/17/2022]
Abstract
The Iroquois (Irx) genes encode homeoproteins conserved during evolution. Vertebrate genomes contain six Irx genes organized in two clusters, IrxA (which harbors Irx1, Irx2 and Irx4) and IrxB (which harbors Irx3, Irx5 and Irx6). To determine the precise role of these genes during development and their putative redundancies, we conducted a comparative expression analysis and a comprehensive loss-of-function study of all the early expressed Irx genes (Irx1-5) using specific morpholinos in Xenopus. We found that the five Irx genes display largely overlapping expression patterns and contribute to neural patterning. All Irx genes are required for proper formation of posterior forebrain, midbrain, hindbrain and, to a lesser an extent, spinal cord. Nevertheless, Irx1 and Irx3 seem to have a predominant role during regionalization of the neural plate. In addition, we find that the common anterior limit of Irx gene expression, which will correspond to the future border between the prethalamus and thalamus, is defined by mutual repression between Fezf and Irx proteins. This mutual repression is likely direct. Finally, we show that Arx, another anteriorly expressed repressor, also contribute to delineate the anterior border of Irx expression.
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Affiliation(s)
- Elisa Rodríguez-Seguel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013 Sevilla, Spain
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49
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A functional interaction between Irx and Meis patterns the anterior hindbrain and activates krox20 expression in rhombomere 3. Dev Biol 2009; 327:566-77. [DOI: 10.1016/j.ydbio.2008.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 11/17/2008] [Accepted: 12/16/2008] [Indexed: 11/20/2022]
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50
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Kiecker C, Lumsden A. Recent advances in neural development. F1000 BIOLOGY REPORTS 2009; 1:1. [PMID: 20948677 PMCID: PMC3100780 DOI: 10.3410/b1-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A surprisingly small number of signalling pathways are used reiteratively during neural development, eliciting very different responses depending on the cellular context. Thus, the way a neural cell responds to a given signal is as important as the signal itself and this responsiveness, also called competence, changes with time. Here we describe recent advances in elucidating the signalling pathways that operate in brain development.
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Affiliation(s)
- Clemens Kiecker
- MRC Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
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