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Chongtham MC, Wang H, Thaller C, Hsiao NH, Vachkov IH, Pavlov SP, Williamson LH, Yamashima T, Stoykova A, Yan J, Eichele G, Tonchev AB. Transcriptome Response and Spatial Pattern of Gene Expression in the Primate Subventricular Zone Neurogenic Niche After Cerebral Ischemia. Front Cell Dev Biol 2020; 8:584314. [PMID: 33344448 PMCID: PMC7744782 DOI: 10.3389/fcell.2020.584314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/20/2020] [Indexed: 11/13/2022] Open
Abstract
The main stem cell niche for neurogenesis in the adult mammalian brain is the subventricular zone (SVZ) that extends along the cerebral lateral ventricles. We aimed at characterizing the initial molecular responses of the macaque monkey SVZ to transient, global cerebral ischemia. We microdissected tissue lining the anterior horn of the lateral ventricle (SVZa) from 7 day post-ischemic and sham-operated monkeys. Transcriptomics shows that in ischemic SVZa, 541 genes were upregulated and 488 genes were down-regulated. The transcription data encompassing the upregulated genes revealed a profile typical for quiescent stem cells and astrocytes. In the primate brain the SVZ is morphologically subdivided in distinct and separate ependymal and subependymal regions. The subependymal contains predominantly neural stem cells (NSC) and differentiated progenitors. To determine in which SVZa region ischemia had evoked transcriptional upregulation, sections through control and ischemic SVZa were analyzed by high-throughput in situ hybridization for a total of 150 upregulated genes shown in the www.monkey-niche.org image database. The majority of the differentially expressed genes mapped to the subependymal layers on the striatal or callosal aspect of the SVZa. Moreover, a substantial number of upregulated genes was expressed in the ependymal layer, implicating a contribution of the ependyma to stem cell biology. The transcriptome analysis yielded several novel gene markers for primate SVZa including the apelin receptor that is strongly expressed in the primate SVZa niche upon ischemic insult.
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Affiliation(s)
- Monika C Chongtham
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Christina Thaller
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Nai-Hua Hsiao
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ivan H Vachkov
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stoyan P Pavlov
- Department of Anatomy and Cell Biology, Faculty of Medicine, Medical University, Varna, Bulgaria.,Department of Stem Cell Biology and Advanced Computational Bioimaging, Research Institute, Medical University, Varna, Bulgaria
| | - Lorenz H Williamson
- Department of Anatomy and Cell Biology, Faculty of Medicine, Medical University, Varna, Bulgaria.,Department of Stem Cell Biology and Advanced Computational Bioimaging, Research Institute, Medical University, Varna, Bulgaria
| | - Tetsumori Yamashima
- Department of Psychiatry and Behavioral Science, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Anastassia Stoykova
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Gregor Eichele
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Anton B Tonchev
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Anatomy and Cell Biology, Faculty of Medicine, Medical University, Varna, Bulgaria.,Department of Stem Cell Biology and Advanced Computational Bioimaging, Research Institute, Medical University, Varna, Bulgaria
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2
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Urban I, Kerimoglu C, Sakib MS, Wang H, Benito E, Thaller C, Zhou X, Yan J, Fischer A, Eichele G. TIP60/KAT5 is required for neuronal viability in hippocampal CA1. Sci Rep 2019; 9:16173. [PMID: 31700011 PMCID: PMC6838100 DOI: 10.1038/s41598-019-50927-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
Aberrant histone acetylation contributes to age-dependent cognitive decline and neurodegenerative diseases. We analyze the function of lysine acetyltransferase TIP60/KAT5 in neurons of the hippocampus using an inducible mouse model. TIP60-deficiency in the adult forebrain leads within days to extensive transcriptional dysfunction characterized by the presence of a neurodegeneration-related signature in CA1. Cell cycle- and immunity-related genes are upregulated while learning- and neuronal plasticity-related genes are downregulated. The dysregulated genes seen under TIP60-deficiency overlap with those in the well-characterized CK-p25 neurodegeneration model. We found that H4K12 is hypoacetylated at the transcriptional start sites of those genes whose expression is dampened in TIP60-deficient mice. Transcriptional dysregulation is followed over a period of weeks by activation of Caspase 3 and fragmentation of β-actin in CA1 neurites, eventually leading to severe neuronal loss. TIP60-deficient mice also develop mild memory impairment. These phenotypes point to a central role of TIP60 in transcriptional networks that are critical for neuronal viability.
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Affiliation(s)
- Inga Urban
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Cemil Kerimoglu
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany
| | - M Sadman Sakib
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Eva Benito
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany.,European Molecular Biology Organization (EMBO), 69117, Heidelberg, Germany
| | - Christina Thaller
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Xunlei Zhou
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Institute of Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, China
| | - André Fischer
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany. .,Department for Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075, Göttingen, Germany.
| | - Gregor Eichele
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
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3
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Şişecioğlu M, Budak H, Geffers L, Çankaya M, Çiftci M, Thaller C, Eichele G, Küfrevioğlu Öİ, Özdemir H. A compendium of expression patterns of cholesterol biosynthetic enzymes in the mouse embryo. J Lipid Res 2015; 56:1551-9. [PMID: 26108225 PMCID: PMC4513996 DOI: 10.1194/jlr.m059634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/20/2022] Open
Abstract
Cholesterol and its biosynthetic pathway intermediates and derivatives are required for many developmental processes including membrane biogenesis, transmembrane receptor signaling, steroid biogenesis, nuclear receptor activation, and posttranslational modification of hedgehog (Hh) proteins. To perform such multifaceted tasks depends on stringent regulation of expression of cholesterol biosynthetic enzymes (CBEs). We established for a whole organism, for the first time, the 3D expression pattern of all genes required for cholesterol biosynthesis (CBS), starting from acetyl-CoA and ending with cholesterol. This data was produced by high-throughput in situ hybridization on serial sections through the mouse fetus. The textually annotated image data were seamlessly integrated into the METscout and GenePaint public databases. This novel information helps in the understanding of why CBEs are expressed at particular locations within the fetus. For example, strong CBE expression is detected at sites of cell proliferation and also where cell growth increases membrane surface, such as in neurons sprouting axons and forming synapses. The CBE data also sheds light on the spatial relationship of cells and tissue that express sonic Hh (Shh) and produce cholesterol, respectively. We discovered that not all cells expressing Shh are capable of CBS. This finding suggests novel ways by which cholesterylation of Shh is regulated.
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Affiliation(s)
- Melda Şişecioğlu
- Departments of Molecular Biology and Genetics Faculty of Science, Ataturk University, 25240 Erzurum, Turkey
| | - Harun Budak
- Departments of Molecular Biology and Genetics Faculty of Science, Ataturk University, 25240 Erzurum, Turkey Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37077 Goettingen, Germany
| | - Lars Geffers
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37077 Goettingen, Germany
| | - Murat Çankaya
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37077 Goettingen, Germany Department of Biology, Faculty of Arts and Sciences, Erzincan University, 24100 Erzincan, Turkey
| | - Mehmet Çiftci
- Chemistry, Faculty of Science, Ataturk University, 25240 Erzurum, Turkey Department of Chemistry, Faculty of Arts and Sciences, Bingol University, 12000 Bingol, Turkey
| | - Christina Thaller
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37077 Goettingen, Germany
| | - Gregor Eichele
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37077 Goettingen, Germany
| | | | - Hasan Özdemir
- Chemistry, Faculty of Science, Ataturk University, 25240 Erzurum, Turkey
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4
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Santarpia L, Calin GA, Adam L, Ye L, Fusco A, Giunti S, Thaller C, Paladini L, Zhang X, Jimenez C, Trimarchi F, El-Naggar AK, Gagel RF. A miRNA signature associated with human metastatic medullary thyroid carcinoma. Endocr Relat Cancer 2013; 20:809-23. [PMID: 24127332 DOI: 10.1530/erc-13-0357] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
MicroRNAs (miRNAs) represent a class of small, non-coding RNAs that control gene expression by targeting mRNA and triggering either translational repression or RNA degradation. The objective of our study was to evaluate the involvement of miRNAs in human medullary thyroid carcinoma (MTC) and to identify the markers of metastatic cells and aggressive tumour behaviour. Using matched primary and metastatic tumour samples, we identified a subset of miRNAs aberrantly regulated in metastatic MTC. Deregulated miRNAs were confirmed by quantitative real-time PCR and validated by in situ hybridisation on a large independent set of primary and metastatic MTC samples. Our results uncovered ten miRNAs that were significantly expressed and deregulated in metastatic tumours: miR-10a, miR-200b/-200c, miR-7 and miR-29c were down-regulated and miR-130a, miR-138, miR-193a-3p, miR-373 and miR-498 were up-regulated. Bioinformatic approaches revealed potential miRNA targets and signals involved in metastatic MTC pathways. Migration, proliferation and invasion assays were performed in cell lines treated with miR-200 antagomirs to ascertain a direct role for this miRNA in MTC tumourigenesis. We show that the members of miR-200 family regulate the expression of E-cadherin by directly targeting ZEB1 and ZEB2 mRNA and through the enhanced expression of tumour growth factor β (TGFβ)-2 and TGFβ-1. Overall, the treated cells shifted to a mesenchymal phenotype, thereby acquiring an aggressive phenotype with increased motility and invasion. Our data identify a robust miRNA signature associated with metastatic MTC and distinct biological processes, e.g., TGFβ signalling pathway, providing new potential insights into the mechanisms of MTC metastasis.
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Affiliation(s)
- Libero Santarpia
- Departments of Endocrine Neoplasia and Hormonal Disorders Experimental Therapeutics Urology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA Department of Oncology, The University of Naples, Naples, Italy Department of Pathology, Centro Oncologico Fiorentino, Sesto Fiorentino, Florence, Italy Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine, Houston, Texas, USA Department of Oncology, Istituto Toscano Tumori, Hospital of Prato, Prato, Italy Department of Gynecologic Oncology, Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA Department of Endocrinology, University of Messina, Messina, Italy Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA Department of Internal Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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5
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Terzian T, Dumble M, Arbab F, Thaller C, Donehower LA, Lozano G, Justice MJ, Roop DR, Box NF. Rpl27a mutation in the sooty foot ataxia mouse phenocopies high p53 mouse models. J Pathol 2011; 224:540-52. [PMID: 21674502 DOI: 10.1002/path.2891] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/28/2011] [Accepted: 03/04/2011] [Indexed: 01/06/2023]
Abstract
Ribosomal stress is an important, yet poorly understood, mechanism that results in activation of the p53 tumour suppressor. We present a mutation in the ribosomal protein Rpl27a gene (sooty foot ataxia mice), isolated through a sensitized N-ethyl-N-nitrosourea (ENU) mutagenesis screen for p53 pathway defects, that shares striking phenotypic similarities with high p53 mouse models, including cerebellar ataxia, pancytopenia and epidermal hyperpigmentation. This phenocopy is rescued in a haploinsufficient p53 background. A detailed examination of the bone marrow in these mice identified reduced numbers of haematopoietic stem cells and a p53-dependent c-Kit down-regulation. These studies suggest that reduced Rpl27a increases p53 activity in vivo, further evident with a delay in tumorigenesis in mutant mice. Taken together, these data demonstrate that Rpl27a plays a crucial role in multiple tissues and that disruption of this ribosomal protein affects both development and transformation.
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Carson J, Ju T, Bello M, Thaller C, Warren J, Kakadiaris IA, Chiu W, Eichele G. Automated pipeline for atlas-based annotation of gene expression patterns: application to postnatal day 7 mouse brain. Methods 2010; 50:85-95. [PMID: 19698790 PMCID: PMC2818703 DOI: 10.1016/j.ymeth.2009.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 08/10/2009] [Accepted: 08/13/2009] [Indexed: 02/08/2023] Open
Abstract
Massive amounts of image data have been collected and continue to be generated for representing cellular gene expression throughout the mouse brain. Critical to exploiting this key effort of the post-genomic era is the ability to place these data into a common spatial reference that enables rapid interactive queries, analysis, data sharing, and visualization. In this paper, we present a set of automated protocols for generating and annotating gene expression patterns suitable for the establishment of a database. The steps include imaging tissue slices, detecting cellular gene expression levels, spatial registration with an atlas, and textual annotation. Using high-throughput in situ hybridization to generate serial sets of tissues displaying gene expression, this process was applied toward the establishment of a database representing over 200 genes in the postnatal day 7 mouse brain. These data using this protocol are now well-suited for interactive comparisons, analysis, queries, and visualization.
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Affiliation(s)
- James Carson
- Biological Monitoring and Modeling Group, Pacific Northwest National Laboratory, Richland, WA, USA
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7
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Rose MF, Ahmad KA, Thaller C, Zoghbi HY. Excitatory neurons of the proprioceptive, interoceptive, and arousal hindbrain networks share a developmental requirement for Math1. Proc Natl Acad Sci U S A 2009; 106:22462-7. [PMID: 20080794 PMCID: PMC2799716 DOI: 10.1073/pnas.0911579106] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Indexed: 11/18/2022] Open
Abstract
Hindbrain networks important for sensation and arousal contain diverse neuronal populations with distinct projections, yet share specific characteristics such as neurotransmitter expression. The relationship between the function of these neurons, their developmental origin, and the timing of their migration remains unclear. Mice lacking the proneural transcription factor Math1 (Atoh1) lose neurons essential for hearing, balance, and unconscious proprioception. By using a new, inducible Math1(Cre*PR) allele, we found that Math1 is also required for the conscious proprioceptive system, including excitatory projection neurons of the dorsal column nuclei and for vital components of the interoceptive system, such as Barrington's nucleus, that is closely associated with arousal. In addition to specific networks, Math1 lineages shared specific neurotransmitter expression, including glutamate, acetylcholine, somatostatin, corticotropin releasing hormone, and nitric oxide. These findings identify twenty novel Math1 lineages and indicate that the Math1 network functions partly as an interface for conscious (early-born) and unconscious (late-born) proprioceptive inputs to the cortex and cerebellum, respectively. In addition, these data provide previously unsuspected genetic and developmental links between proprioception, interoception, hearing, and arousal.
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Affiliation(s)
| | | | | | - Huda Y. Zoghbi
- Program in Developmental Biology
- Departments of Pediatrics
- Molecular and Human Genetics, and
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030
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Ben-Shachar S, Chahrour M, Thaller C, Shaw CA, Zoghbi HY. Mouse models of MeCP2 disorders share gene expression changes in the cerebellum and hypothalamus. Hum Mol Genet 2009; 18:2431-42. [PMID: 19369296 PMCID: PMC2694691 DOI: 10.1093/hmg/ddp181] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A group of post-natal neurodevelopmental disorders collectively referred to as MeCP2 disorders are caused by aberrations in the gene encoding methyl-CpG-binding protein 2 (MECP2). Loss of MeCP2 function causes Rett syndrome (RTT), whereas increased copy number of the gene causes MECP2 duplication or triplication syndromes. MeCP2 acts as a transcriptional repressor, however the gene expression changes observed in the hypothalamus of MeCP2 disorder mouse models suggest that MeCP2 can also upregulate gene expression, given that the majority of genes are downregulated upon loss of MeCP2 and upregulated in its presence. To determine if this dual role of MeCP2 extends beyond the hypothalamus, we studied gene expression patterns in the cerebellum of Mecp2-null and MECP2-Tg mice, modeling RTT and MECP2 duplication syndrome, respectively. We found that abnormal MeCP2 dosage causes alterations in the expression of hundreds of genes in the cerebellum. The majority of genes were upregulated in MECP2-Tg mice and downregulated in Mecp2-null mice, consistent with a role for MeCP2 as a modulator that can both increase and decrease gene expression. Interestingly, many of the genes altered in the cerebellum, particularly those increased by the presence of MeCP2 and decreased in its absence, were similarly altered in the hypothalamus. Our data suggest that either gain or loss of MeCP2 results in gene expression changes in multiple brain regions and that some of these changes are global. Further delineation of the expression pattern of MeCP2 target genes throughout the brain might identify subsets of genes that are more amenable to manipulation, and can thus be used to modulate some of the disease phenotypes.
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Affiliation(s)
- Shay Ben-Shachar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Miesegaes GR, Klisch TJ, Thaller C, Ahmad KA, Atkinson RC, Zoghbi HY. Identification and subclassification of new Atoh1 derived cell populations during mouse spinal cord development. Dev Biol 2008; 327:339-51. [PMID: 19135992 DOI: 10.1016/j.ydbio.2008.12.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 12/10/2008] [Accepted: 12/10/2008] [Indexed: 01/06/2023]
Abstract
At spinal levels, sensory information pertaining to body positioning (proprioception) is relayed to the cerebellum by the spinocerebellar tracts (SCTs). In the past we revealed the basic helix-loop-helix transcription factor Atoh1 (Math1) to be important for establishing Dorsal Progenitor 1 (DP1) commissural interneurons, which comprise a subset of proprioceptive interneurons. Given there exists multiple subdivisions of the SCT we asked whether Atoh1 may also play a role in specifying other cell types in the spinal cord. Here, we reveal the generation of at least three DP1 derived interneuron populations that reside at spatially restricted positions along the rostral-caudal axis. Each of these cell populations expresses distinct markers and anatomically coincides with the cell bodies of the various subdivisions of the SCT. In addition, we found that as development proceeds (e.g. by E13.5) Atoh1 expression becomes apparent in the dorsal midline in the region of the roof plate (RP). Interestingly, we find that cells derived from Atoh1 expressing RP progenitors express SSEA-1, and in the absence of Atoh1 these progenitors become SOX9 positive. Altogether we reveal the existence of multiple Atoh1 dependent cell types in the spinal cord, and uncover a novel progenitor domain that arises late in development.
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Affiliation(s)
- George R Miesegaes
- Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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10
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Abstract
Previous studies have demonstrated that ribbon synapses in the retina do not contain the t-SNARE (target-soluble N-ethylmaleimide-sensitive factor attachment protein receptor) syntaxin 1A that is found in conventional synapses of the nervous system. In contrast, ribbon synapses of the retina contain the related isoform syntaxin 3. In addition to its localization in ribbon synapses, syntaxin 3 is also found in nonneuronal cells, where it has been implicated in the trafficking of transport vesicles to the apical plasma membrane of polarized cells. The syntaxin 3 gene codes for four different splice forms, syntaxins 3A, 3B, 3C, and 3D. We demonstrate here by using analysis of EST databases, RT-PCR, in situ hybridization, and Northern blot analysis that cells in the mouse retina express only syntaxin 3B. In contrast, nonneuronal tissues, such as kidney, express only syntaxin 3A. The two major syntaxin isoforms (3A and 3B) have an identical N-terminal domain but differ in the C-terminal half of the SNARE domain and the C-terminal transmembrane domain. These two domains are thought to be directly involved in synaptic vesicle fusion. The interaction of syntaxin 1A and syntaxin 3B with other synaptic proteins was examined. We found that both proteins bind Munc18/N-sec1 with similar affinity. In contrast, syntaxin 3B had a much lower binding affinity for the t-SNARE SNAP25 compared with syntaxin 1A. By using an in vitro fusion assay, we could demonstrate that vesicles containing syntaxin 3B and SNAP25 could fuse with vesicles containing synaptobrevin2/VAMP2, demonstrating that syntaxin 3B can function as a t-SNARE.
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Affiliation(s)
- Leigh B Curtis
- Department of Neurobiology and Anatomy, The University of Texas Medical School, Houston, Texas 77030, USA
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Lee Y, Samaco RC, Gatchel JR, Thaller C, Orr HT, Zoghbi HY. miR-19, miR-101 and miR-130 co-regulate ATXN1 levels to potentially modulate SCA1 pathogenesis. Nat Neurosci 2008; 11:1137-9. [PMID: 18758459 PMCID: PMC2574629 DOI: 10.1038/nn.2183] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/08/2008] [Indexed: 11/09/2022]
Abstract
Spinocerebellar ataxia type 1 is caused by expansion of a translated CAG repeat in ataxin1 (ATXN1). The level of the polyglutamine-expanded protein is one of the factors that contributes to disease severity. Here we found that miR-19, miR-101 and miR-130 co-regulate ataxin1 levels and that their inhibition enhanced the cytotoxicity of polyglutamine-expanded ATXN1 in human cells. We provide a new candidate mechanism for modulating the pathogenesis of neurodegenerative diseases sensitive to protein dosage.
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Affiliation(s)
- Yoontae Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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12
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Flora A, Garcia JJ, Thaller C, Zoghbi HY. The E-protein Tcf4 interacts with Math1 to regulate differentiation of a specific subset of neuronal progenitors. Proc Natl Acad Sci U S A 2007; 104:15382-7. [PMID: 17878293 PMCID: PMC1978485 DOI: 10.1073/pnas.0707456104] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proneural factors represent <10 transcriptional regulators required for specifying all of the different neurons of the mammalian nervous system. The mechanisms by which such a small number of factors creates this diversity are still unknown. We propose that proteins interacting with proneural factors confer such specificity. To test this hypothesis we isolated proteins that interact with Math1, a proneural transcription factor essential for the establishment of a neural progenitor population (rhombic lip) that gives rise to multiple hindbrain structures and identified the E-protein Tcf4. Interestingly, haploinsufficiency of TCF4 causes the Pitt-Hopkins mental retardation syndrome, underscoring the important role for this protein in neural development. To investigate the functional relevance of the Math1/Tcf4 interaction in vivo, we studied Tcf4(-/-) mice and found that they have disrupted pontine nucleus development. Surprisingly, this selective deficit occurs without affecting other rhombic lip-derived nuclei, despite expression of Math1 and Tcf4 throughout the rhombic lip. Importantly, deletion of any of the other E-protein-encoding genes does not have detectable effects on Math1-dependent neurons, suggesting a specialized role for Tcf4 in distinct neural progenitors. Our findings provide the first in vivo evidence for an exclusive function of dimers formed between a proneural basic helix-loop-helix factor and a specific E-protein, offering insight about the mechanisms underlying transcriptional programs that regulate development of the mammalian nervous system.
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Affiliation(s)
- Adriano Flora
- *Howard Hughes Medical Institute
- Departments of Molecular and Human Genetics
- To whom correspondence may be addressed. E-mail: or
| | - Jesus J. Garcia
- *Howard Hughes Medical Institute
- Departments of Molecular and Human Genetics
| | | | - Huda Y. Zoghbi
- *Howard Hughes Medical Institute
- Departments of Molecular and Human Genetics
- Neuroscience, and
- Pediatrics, and
- **Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030
- To whom correspondence may be addressed. E-mail: or
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Carson JP, Ju T, Thaller C, Warren J, Bello M, Kakadiaris I, Chiu W, Eichele G. Automated characterization of gene expression patterns with an atlas of the mouse brain. Conf Proc IEEE Eng Med Biol Soc 2007; 2004:2917-20. [PMID: 17270888 DOI: 10.1109/iembs.2004.1403829] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A spatio-temporal map of gene activity in the brain would be an important contribution to the understanding of brain development, disease, and function. Such a resource is now possible using high-throughput in situ hybridization, a method for transcriptome-wide acquisition of cellular resolution gene expression patterns in serial tissue sections. However, querying an enormous quantity of image data requires computational methods for describing and organizing gene expression patterns in a consistent manner. In addressing this, we have developed procedures for automated annotation of gene expression patterns in the postnatal mouse brain.
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Affiliation(s)
- J P Carson
- Graduate Program in Struct. & Comput. Biol. & Molecular Biophys., Nat. Center for Macromolecular Imaging, Houston, TX, USA
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Wang X, Reid Sutton V, Omar Peraza-Llanes J, Yu Z, Rosetta R, Kou YC, Eble TN, Patel A, Thaller C, Fang P, Van den Veyver IB. Mutations in X-linked PORCN, a putative regulator of Wnt signaling, cause focal dermal hypoplasia. Nat Genet 2007; 39:836-8. [PMID: 17546030 DOI: 10.1038/ng2057] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 04/30/2007] [Indexed: 02/07/2023]
Abstract
Focal dermal hypoplasia is an X-linked dominant disorder characterized by patchy hypoplastic skin and digital, ocular and dental malformations. We used array comparative genomic hybridization to identify a 219-kb deletion in Xp11.23 in two affected females. We sequenced genes in this region and found heterozygous and mosaic mutations in PORCN in other affected females and males, respectively. PORCN encodes the human homolog of Drosophila melanogaster porcupine, an endoplasmic reticulum protein involved in secretion of Wnt proteins.
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Affiliation(s)
- Xiaoling Wang
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas 77030, USA
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15
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Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, Jones AR. Genome-wide atlas of gene expression in the adult mouse brain. Nature 2006; 445:168-76. [PMID: 17151600 DOI: 10.1038/nature05453] [Citation(s) in RCA: 3830] [Impact Index Per Article: 212.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 11/15/2006] [Indexed: 11/09/2022]
Abstract
Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of approximately 20,000 genes in the adult mouse brain. Data were generated using automated high-throughput procedures for in situ hybridization and data acquisition, and are publicly accessible online. Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes. Unbiased fine-resolution analysis has identified highly specific cellular markers as well as extensive evidence of cellular heterogeneity not evident in classical neuroanatomical atlases. This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function.
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Affiliation(s)
- Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98103, USA.
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16
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Yaylaoglu MB, Agbemafle BM, Oesterreicher TJ, Finegold MJ, Thaller C, Henning SJ. Diverse patterns of cell-specific gene expression in response to glucocorticoid in the developing small intestine. Am J Physiol Gastrointest Liver Physiol 2006; 291:G1041-50. [PMID: 16825705 DOI: 10.1152/ajpgi.00139.2006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although glucocorticoids are known to elicit functional maturation of the gastrointestinal tract, the molecular mechanisms of glucocorticoid action on the developing intestine have not been fully elucidated. Our previous microarray studies identified 66 transcripts as being rapidly induced in the jejunum following dexamethasone (Dex) administration to suckling mice. Now we report the specific cellular location of a subset of these transcripts. Mouse pups at P8 received Dex or vehicle and intestinal segments were collected 3-4 h later. Robotic-based in situ hybridization (ISH) was performed with digoxygenin-labeled riboprobes. Transcripts studied included Ndrg1, Sgk1, Fos, and two unknown genes (Gene 9 and Gene 36). As predicted, ISH revealed marked diversity of cellular expression. In small intestinal segments, Sgk1 mRNA was in all epithelial cells; Fos mRNA was confined to epithelial cells at the villus tip; and Ndrg1 and Gene 36 mRNAs were localized to epithelial cells of the upper crypt and villus base. The remaining transcript (Gene 9) was induced modestly in villus stroma and strongly in the muscle layers. In the colon, Ndrg1, Sgk1, and Gene 36 were induced in all epithelial cells; Gene 9 was in muscle layers only; and Fos was not detectable. For jejunal segments, quantitation of ISH signals in tissue from Dex-treated and vehicle-treated mice demonstrated mRNA increases very similar to those measured by Northern blotting. We conclude that glucocorticoid action in the intestine reflects diverse molecular mechanisms operating in different cell types and that quantitative ISH is a valuable tool for studying hormone action in this tissue.
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Affiliation(s)
- Murat B Yaylaoglu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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17
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McGill BE, Bundle SF, Yaylaoglu MB, Carson JP, Thaller C, Zoghbi HY. Enhanced anxiety and stress-induced corticosterone release are associated with increased Crh expression in a mouse model of Rett syndrome. Proc Natl Acad Sci U S A 2006; 103:18267-72. [PMID: 17108082 PMCID: PMC1636379 DOI: 10.1073/pnas.0608702103] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rett syndrome (RTT), a postnatal neurodevelopmental disorder, is caused by mutations in the methyl-CpG-binding protein 2 (MECP2) gene. Children with RTT display cognitive and motor abnormalities as well as autistic features. We studied mice bearing a truncated Mecp2 allele (Mecp2(308/Y) mice) and found evidence of increased anxiety-like behavior and an abnormal stress response as evidenced by elevated serum corticosterone levels. We found increased corticotropin-releasing hormone (Crh) gene expression in the paraventricular nucleus of the hypothalamus, the central amygdala, and the bed nucleus of the stria terminalis. Finally, we discovered that MeCP2 binds the Crh promoter, which is enriched for methylated CpG dinucleotides. In contrast, the MeCP2(308) protein was not detected at the Crh promoter. This study identifies Crh as a target of MeCP2 and implicates Crh overexpression in the development of specific features of the Mecp2(308/Y) mouse, thereby providing opportunities for clinical investigation and therapeutic intervention in RTT.
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Affiliation(s)
- Bryan E. McGill
- *Department of Neuroscience
- Medical Scientist Training Program
| | | | | | - James P. Carson
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology
- National Center for Macromolecular Imaging
| | - Christina Thaller
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology
| | - Huda Y. Zoghbi
- *Department of Neuroscience
- Department of Molecular and Human Genetics
- Department of Neurology
- **Department of Pediatrics, and
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030
- To whom correspondence should be addressed. E-mail:
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18
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Bello M, Ju T, Warren J, Carson J, Chiu W, Thaller C, Eichele G, Kakadiaris IA. Hybrid segmentation framework for tissue images containing gene expression data. ACTA ACUST UNITED AC 2006; 8:254-61. [PMID: 16685853 DOI: 10.1007/11566465_32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Associating specific gene activity with functional locations in the brain results in a greater understanding of the role of the gene. To perform such an association for the over 20,000 genes in the mammalian genome, reliable automated methods that characterize the distribution of gene expression in relation to a standard anatomical model are required. In this work, we propose a new automatic method that results in the segmentation of gene expression images into distinct anatomical regions in which the expression can be quantified and compared with other images. Our method utilizes shape models from training images, texture differentiation at region boundaries, and features of anatomical landmarks, to deform a subdivision mesh-based atlas to fit gene expression images. The subdivision mesh provides a common coordinate system for internal brain data through which gene expression patterns can be compared across images. The automated large-scale annotation will help scientists interpret gene expression patterns at cellular resolution more efficiently.
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Affiliation(s)
- Musodiq Bello
- Computational Biomedicine Lab, Dept. of Computer Science, University of Houston, Houston TX, USA
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19
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Ju T, Warren J, Carson J, Bello M, Kakadiaris I, Chiu W, Thaller C, Eichele G. 3D volume reconstruction of a mouse brain from histological sections using warp filtering. J Neurosci Methods 2006; 156:84-100. [PMID: 16580732 DOI: 10.1016/j.jneumeth.2006.02.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 02/13/2006] [Accepted: 02/13/2006] [Indexed: 10/24/2022]
Abstract
Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.
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Affiliation(s)
- Tao Ju
- Washington University, St. Louis, MO, USA.
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20
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Yaylaoglu MB, Titmus A, Visel A, Alvarez-Bolado G, Thaller C, Eichele G. Comprehensive expression atlas of fibroblast growth factors and their receptors generated by a novel robotic in situ hybridization platform. Dev Dyn 2006; 234:371-86. [PMID: 16123981 DOI: 10.1002/dvdy.20441] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
A recently developed robotic platform termed "Genepaint" can carry out large-scale nonradioactive in situ hybridization (ISH) on tissue sections. We report a series of experiments that validate this novel platform. Signal-to-noise ratio and mRNA detection limits were comparable to traditional ISH procedures, and hybridization was transcript-specific, even in cases in which probes could have hybridized to several transcripts of a multigene family. We established an atlas of expression patterns of fibroblast growth factors (Fgfs) and their receptors (Fgfrs) for the embryonic day 14.5 mouse embryo. This atlas provides a comprehensive overview of previously known as well as novel sites of expression for this important family of signaling molecules. The Fgf/Fgfr atlas was integrated into the transcriptome database (www.genepaint.org), where individual Fgf and Fgfr expression patterns can be interactively viewed at cellular resolution and where sites of expressions can be retrieved using an anatomy-based search.
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21
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Lalani SR, Safiullah AM, Fernbach SD, Harutyunyan KG, Thaller C, Peterson LE, McPherson JD, Gibbs RA, White LD, Hefner M, Davenport SLH, Graham JM, Bacino CA, Glass NL, Towbin JA, Craigen WJ, Neish SR, Lin AE, Belmont JW. Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation. Am J Hum Genet 2006; 78:303-14. [PMID: 16400610 PMCID: PMC1380237 DOI: 10.1086/500273] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 11/28/2005] [Indexed: 11/03/2022] Open
Abstract
CHARGE syndrome is a well-established multiple-malformation syndrome with distinctive consensus diagnostic criteria. Characteristic associated anomalies include ocular coloboma, choanal atresia, cranial nerve defects, distinctive external and inner ear abnormalities, hearing loss, cardiovascular malformations, urogenital anomalies, and growth retardation. Recently, mutations of the chromodomain helicase DNA-binding protein gene CHD7 were reported to be a major cause of CHARGE syndrome. We sequenced the CHD7 gene in 110 individuals who had received the clinical diagnosis of CHARGE syndrome, and we detected mutations in 64 (58%). Mutations were distributed throughout the coding exons and conserved splice sites of CHD7. Of the 64 mutations, 47 (73%) predicted premature truncation of the protein. These included nonsense and frameshift mutations, which most likely lead to haploinsufficiency. Phenotypically, the mutation-positive group was more likely to exhibit cardiovascular malformations (54 of 59 in the mutation-positive group vs. 30 of 42 in the mutation-negative group; P=.014), coloboma of the eye (55 of 62 in the mutation-positive group vs. 30 of 43 in the mutation-negative group; P=.022), and facial asymmetry, often caused by seventh cranial nerve abnormalities (36 of 56 in the mutation-positive group vs. 13 of 39 in the mutation-negative group; P=.004). Mouse embryo whole-mount and section in situ hybridization showed the expression of Chd7 in the outflow tract of the heart, optic vesicle, facio-acoustic preganglion complex, brain, olfactory pit, and mandibular component of the first branchial arch. Microarray gene-expression analysis showed a signature pattern of gene-expression differences that distinguished the individuals with CHARGE syndrome with CHD7 mutation from the controls. We conclude that cardiovascular malformations, coloboma, and facial asymmetry are common findings in CHARGE syndrome caused by CHD7 mutation.
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Affiliation(s)
- Seema R. Lalani
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Arsalan M. Safiullah
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Susan D. Fernbach
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Karine G. Harutyunyan
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Christina Thaller
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Leif E. Peterson
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - John D. McPherson
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Richard A. Gibbs
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Lisa D. White
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Margaret Hefner
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Sandra L. H. Davenport
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - John M. Graham
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Carlos A. Bacino
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Nancy L. Glass
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Jeffrey A. Towbin
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - William J. Craigen
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Steven R. Neish
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - Angela E. Lin
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
| | - John W. Belmont
- Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Medicine, and Pediatrics, Baylor College of Medicine, Houston; Department of Pediatrics, Saint Louis University, St. Louis; Sensory Genetics/Neuro-Development, Bloomington, MN; Medical Genetics Institute, Department of Pediatrics, Cedar-Sinai Medical Center, David Geffen School of Medicine at University of California–Los Angeles, Los Angeles; and Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston
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Visel A, Alvarez-Bolado G, Thaller C, Eichele G. Comprehensive analysis of the expression patterns of the adenylate cyclase gene family in the developing and adult mouse brain. J Comp Neurol 2006; 496:684-97. [PMID: 16615126 DOI: 10.1002/cne.20953] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Adenylate cyclases (Adcys) are components of several developmentally, neurophysiologically, and pharmacologically relevant signaling pathways. A prominent feature of Adcys is their ability to integrate multiple signaling pathways into a single second messenger pathway, the production of cAMP. Nine isoforms of membrane-bound Adcys are known, each encoded by a distinct gene. These isoforms differ in their response to regulatory upstream pathways as well as in their distribution in the brain and elsewhere. Use of various detection methods and animal species has, however, hampered a direct comparison of expression patterns, so the potential contribution of single isoforms to Adcy activity in different brain regions remains unclear. We have determined the expression patterns of all nine Adcy genes in the embryonic, postnatal day 7, and adult mouse brain by nonradioactive robotic in situ hybridization (ISH). Here we describe the salient features of these patterns. Regional colocalization of Adcy transcripts encoding isoforms with different regulatory properties was detected in the cortex, subregions of the hippocampus, olfactory bulb, thalamus, and striatum. Hence, our expression data support models for modulation of cAMP signaling by combinatorial action of multiple Adcy isoforms. However, in several instances, the expression domains of genes encoding isoforms with similar regulatory properties spatially exclude each other, which is most evident in not previously described expression domains of the embryonic midbrain roof. This is suggestive of functional specialization.
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Affiliation(s)
- Axel Visel
- Max Planck Institute of Experimental Endocrinology, Hannover, Germany
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23
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Carson JP, Ju T, Lu HC, Thaller C, Xu M, Pallas SL, Crair MC, Warren J, Chiu W, Eichele G. A digital atlas to characterize the mouse brain transcriptome. PLoS Comput Biol 2005; 1:e41. [PMID: 16184189 PMCID: PMC1215388 DOI: 10.1371/journal.pcbi.0010041] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Accepted: 08/16/2005] [Indexed: 01/03/2023] Open
Abstract
Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson disease by using the expression of a dopamine transporter in the substantia nigra as a search query pattern. In addition, we discover that transcription factor Rorb is down-regulated in the barrelless mutant relative to control mice by quantitative comparison of expression patterns in layer IV somatosensory cortex. The semi-automated annotation method developed here is applicable to a broad spectrum of complex tissues and data modalities. The mammalian brain is a complex organ with hundreds of functional parts. Describing when and where genes are expressed in the brain is thus a potentially powerful method for understanding the function of gene products. In recent years, several mammalian genomes including those of human and mouse have been characterized. There are now efforts around the world that aim to determine the expression patterns for all genes in the mouse brain. To search these expression data readily, they must be placed into an atlas. The authors propose a new method for bringing such genetic data into a common spatial framework so that one can perform spatial searches and comparisons of gene expression patterns. To create this atlas, the authors developed a series of maps of the brain using a graphical modeling method called subdivision. These maps were deformed to match the shape of tissue sections, and genetic activity information was associated with the appropriate coordinates on the map. After placing 200 genes into the context of this atlas, the authors illustrate its application in discovering genes potentially involved in diseases and brain development.
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Affiliation(s)
- James P Carson
- Program in Structural and Computational Biology and Molecular Biophysics, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, Texas, United States of America.
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Senechal KR, Thaller C, Noebels JL. ADPEAF mutations reduce levels of secreted LGI1, a putative tumor suppressor protein linked to epilepsy. Hum Mol Genet 2005; 14:1613-20. [PMID: 15857855 DOI: 10.1093/hmg/ddi169] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations in LGI1 have been linked to autosomal dominant partial epilepsy with auditory features (ADPEAF), an unusual inherited human partial epilepsy phenotype. In addition, decreases in LGI1 expression are observed in glioblastoma patient samples and glioblastoma cell lines. LGI1, one member of the LGI gene family, encodes a approximately 63 kDa protein, with strong regional expression in neurons within the temporal lobe. Although the function of LGI proteins remains unknown, structural analyses suggest that LGI1 could be either localized to the membrane or secreted. Here, we show that LGI1-4 exhibit overlapping patterns of diffuse mRNA expression in the adult mouse brain, with some areas of specific localization characteristic of each family member. We find robust secretion of mouse LGI1 protein following transfection into 293T cells. LGI family members, LGI3, LGI4 and a newly identified splice form of LGI2, LGI2B, are also secreted in culture, indicating that secretion is a conserved feature of this protein family. Introduction of mutations in LGI1, including those identified in ADPEAF pedigrees, reveals that the mutant proteins either are not secreted or are unstable. These results demonstrate loss-of-function as a pathogenic basis for LGI1-mediated ADPEAF.
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Affiliation(s)
- Kristen R Senechal
- Developmental Neurogenetics Laboratory, Department of Neurology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Belizaire R, Komanduri C, Wooten K, Chen M, Thaller C, Janz R. Characterization of synaptogyrin 3 as a new synaptic vesicle protein. J Comp Neurol 2004; 470:266-81. [PMID: 14755516 DOI: 10.1002/cne.20008] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Synaptogyrins comprise a family of tyrosine-phosphorylated proteins with two neuronal (synaptogyrins 1 and 3) and one ubiquitous (cellugyrin) isoform. Previous studies have indicated that synaptogyrins are involved in the regulation of neurotransmitter release. Synaptogyrin 1 is a synaptic vesicle protein; cellugyrin, by contrast, is absent from synaptic vesicles. In an effort to further characterize the synaptogyrin family, we studied the distribution of the synaptogyrin 3 protein in the nervous system. Subcellular fractionation and immunoprecipitation of synaptic vesicles from mouse brain showed that synaptogyrin 3 is associated with synaptic vesicles and that synaptogyrins 1 and 3 can reside on the same synaptic vesicle. Immunofluorescent staining of cultured hippocampal neurons confirmed the synaptic localization of synaptogyrin 3. Analysis of the relative distributions of synaptogyrins 1 and 3 in mouse brain revealed a more restricted expression pattern for synaptogyrin 3 compared to the ubiquitous distribution of synaptogyrin 1. Strong synaptogyrin 3 labeling was observed in the mossy fiber region of the hippocampus, substantia nigra pars reticulata, pallidum, and deep cerebellar nuclei. By comparison, the striatum and reticular and ventral posterolateral thalamic nuclei, which all showed synaptogyrin 1 labeling, contained significantly less synaptogyrin 3. Finally, we used in situ hybridization experiments to correlate synaptogyrin 3 mRNA in cell bodies with synaptogyrin 3 protein at synapses. Altogether, our data indicate that neuronal synaptogyrins are differentially expressed protein isoforms that may represent functionally distinct populations of synapses and/or synaptic vesicles.
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Affiliation(s)
- Roger Belizaire
- W.M. Keck Center for Learning and Memory, Department of Neurobiology and Anatomy, University of Texas-Houston Medical School, Houston, Texas, 77030, USA.
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Abstract
High-throughput instruments were recently developed to determine gene expression patterns on tissue sections by RNA in situ hybridization. The resulting images of gene expression patterns, chiefly of E14.5 mouse embryos, are accessible to the public at http://www.genepaint.org. This relational database is searchable for gene identifiers and RNA probe sequences. Moreover, patterns and intensity of expression in approximately 100 different embryonic tissues are annotated and can be searched using a standardized catalog of anatomical structures. A virtual microscope tool, the Zoom Image Server, was implemented in GenePaint.org and permits interactive zooming and panning across approximately 15,000 high-resolution images.
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Affiliation(s)
- Axel Visel
- Max Planck Institute of Experimental Endocrinology, Feodor-Lynen-Strasse 7, D-30625 Hannover, Germany
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Ju T, Warren J, Eichele G, Thaller C, Chiu W, Carson J. A geometric database for gene expression data. Symp Geom Process 2003; 2003:166-176. [PMID: 20631855 PMCID: PMC2903551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
As the logical next step after sequencing the mouse genome, biologists have developed laboratory methods for rapidly determining where each of the 30K genes in the mouse genome is synthesizing protein. Applying these methods to the mouse brain, biologists are currently generating large numbers of 2D cross-sectional images that record the expression pattern for each gene in the mouse genome. In this paper, we describe the structure of a geometric database for the mouse brain that allows biologists to organize and search this gene expression data. The central component of this database is an atlas that explicitly partitions the mouse brain into key anatomical regions. This atlas is represented as a Catmull-Clark subdivision mesh with anatomical regions separated by a network of B-spline crease curves. New gene expression images are added to the database by deforming this atlas onto each image using techniques developed for fitting subdivision surfaces to scatter data. Due to this partitioning of the subdivision mesh, user queries comparing expression data between various genes can be restricted to anatomical regions without difficulty while the multi-resolution structure of the subdivision mesh allows these queries to be processed efficiently.
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Affiliation(s)
- Tao Ju
- Rice University, Houston, USA
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Moeller C, Yaylaoglu MB, Alvarez-Bolado G, Thaller C, Eichele G. Murine Lix1, a novel marker for substantia nigra, cortical layer 5, and hindbrain structures. Gene Expr Patterns 2002; 1:199-203. [PMID: 12638132 DOI: 10.1016/s1567-133x(02)00018-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the expression of Lix1 in the mouse. Starting at E8, transcripts are present in a regionalized fashion and persist throughout development. mLix1 is expressed in the cortical plate, subventricular zone, layer 5 of the postnatal cortex, the substantia nigra, dorsal root ganglia, specific nuclei of the brain stem and in spinal cord. Limb buds and facial primordia show transient expression. The prominent expression of mLix1 in the developing cerebral cortex and in the substantia nigra pars compacta makes this novel gene a candidate marker for both of these tissues.
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Affiliation(s)
- Carsten Moeller
- Max Planck Institute of Experimental Endocrinology, Hanover 30625, Germany
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Abstract
A genome-wide expression atlas of the nervous system at cellular resolution would be a valuable resource for neurobiology, genetics, developmental biology and medicine. Progress in automation of in situ hybridization makes such an atlas possible. Standardized and computerized annotation of expression patterns will be critical for producing a searchable atlas database that can be accessed through the internet.
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Affiliation(s)
- James P Carson
- Program in Structural and Computational Biology and Molecular Biophysics and National Center for Macromolecular Imaging, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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Herzig U, Cadenas C, Sieckmann F, Sierralta W, Thaller C, Visel A, Eichele G. Development of high-throughput tools to unravel the complexity of gene expression patterns in the mammalian brain. Novartis Found Symp 2002; 239:129-46; discussion 146-59. [PMID: 11529308 DOI: 10.1002/0470846674.ch11] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Genomes of animals contain between 15000 (e.g. Drosophila) and 50000 (human, mouse) genes, many of which encode proteins involved in regulatory processes. The availability of sequence data for many of these genes opens up opportunities to study complex genetic and protein interactions that underlie biological regulation. Many examples demonstrate that an understanding of regulatory networks consisting of multiple components is significantly advanced by a detailed knowledge of the spatiotemporal expression pattern of each of the components. Gene expression patterns can readily be determined by RNA in situ hybridization. The unique challenge emerging from the knowledge of the sequence of entire genomes is that assignment of biological functions to genes needs to be carried out on an appropriately large scale. In terms of gene expression analysis by RNA in situ hybridization, efficient technologies need to be developed that permit determination and representation of expression patterns of thousands of genes within an acceptable time-scale. We set out to determine the spatial expression pattern of several thousand genes encoding putative regulatory proteins. To achieve this goal we have developed high-throughput technologies that allow the determination and visualization of gene expression patterns by RNA in situ hybridization on tissue sections at cellular resolution. In particular, we have invented instrumentation for robotic in situ hybridization capable of carrying out in a fully automated fashion, all steps required for detecting sites of gene expression in tissue sections. In addition, we have put together hardware and software for automated microscopic scanning of gene expression data that are produced by RNA in situ hybridization. The potential and limitations of these techniques and our efforts to build a Web-based database of gene expression patterns are discussed.
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Affiliation(s)
- U Herzig
- Max-Planck-Institute of Experimental Endocrinology, Hannover, Germany
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Abstract
Limb Expression 1 (Lix1), a founding member of a novel gene family, was identified in a screen for genes transiently and locally expressed during early chicken limb development. Most prominently, Lix1 is transiently expressed in the nascent hindlimb bud between Hamburger-Hamilton stages 15 and 19. Chicken Lix1 transcripts are also found in the basal plate of rhombomeres 3 and 5, in pharyngeal and in foregut mesenchyme and in all facial primordia except for the mandibular arches. Homologs of chick Lix1 exist in human, mouse and Drosophila.
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Affiliation(s)
- E C Swindell
- Max Planck Institute for Experimental Endocrinology, Foedor-Lynen Strasse 7, 30625, Hannover, Germany
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White J, Grütter M, Wilson E, Thaller C, Ford G, Smit J, Jansonius J, Kirschner K. Crystallization and preliminary X-ray crystallographic data of the bifunctional enzyme phosphoribosyl-anthranilate isomerase-indole-3-glycerol-phosphate synthase fromEscherichia coli. FEBS Lett 2001. [DOI: 10.1016/0014-5793(82)81248-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lu HC, Swindell EC, Sierralta WD, Eichele G, Thaller C. Evidence for a role of protein kinase C in FGF signal transduction in the developing chick limb bud. Development 2001; 128:2451-60. [PMID: 11493562 DOI: 10.1242/dev.128.13.2451] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In developing limbs, numerous signaling molecules have been identified but less is known about the mechanisms by which such signals direct patterning. We have explored signal transduction pathways in the chicken limb bud. A cDNA encoding RACK1, a protein that binds and stabilizes activated protein kinase C (PKC), was isolated in a screen for genes induced by retinoic acid (RA) in the chick wing bud. Fibroblast growth factor (FGF) also induced RACK1 and such induction of RACK1 expression was accompanied by a significant augmentation in the number of active PKC molecules and an elevation of PKC enzymatic activity. This suggests that PKCs mediate signal transduction in the limb bud. Application of chelerythrine, a potent PKC inhibitor, to the presumptive wing region resulted in buds that did not express sonic hedgehog (Shh) and developed into wings that were severely truncated. This observation suggests that the expression of Shh depends on PKCs. Providing ectopic SHH protein, RA or ZPA grafts overcome the effects of blocking PKC with chelerythrine and resulted in a rescue of the wing morphology. Taken together, these findings suggest that the responsiveness of Shh to FGF is mediated, at least in part, by PKCs.
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Affiliation(s)
- H C Lu
- Developmental Biology Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Thaller C, Shalev M, Frolov A, Eichele G, Thompson TC, Williams RH, Dillioglugil O, Kadmon D. Fenretinide therapy in prostate cancer: effects on tissue and serum retinoid concentration. J Clin Oncol 2000; 18:3804-8. [PMID: 11078493 DOI: 10.1200/jco.2000.18.22.3804] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE To examine the feasibility of using fenretinide (4-HPR) for the prevention and treatment of prostate cancer. MATERIALS AND METHODS We measured the impact of 4-HPR therapy on retinoid concentrations in vivo, in a mouse model of prostate cancer and clinically, in patients with prostate cancer who were given oral 4-HPR (200 mg/d) or placebo for 4 weeks before undergoing a radical prostatectomy. RESULTS Prostate tumors in mice treated with 4-HPR contained high levels of 4-HPR and of all-trans-retinoic acid (RA) and reduced levels of retinol (ROH). Patients given 4-HPR were found to have significantly higher concentrations of 4-HPR in the cancerous prostate as compared with the serum levels (463 nmol/L v 326 nmol/L; P =.049), but they were only 1/10 the levels found in mice and were far below the concentrations reported in human breast tissue. Serum and tissue ROH levels were reduced to less than half the concentrations found in untreated controls. RA concentrations in human serum and in cancerous prostates were not significantly affected by 4-HPR treatment, in contrast with the findings in mice. CONCLUSION The standard oral dose of 4-HPR proposed for breast cancer (200 mg/d) achieved only modest drug levels in the prostate and is unlikely to be effective for prostate cancer prevention or treatment. Higher doses need to be explored.
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Affiliation(s)
- C Thaller
- Department of Biochemistry, Matsunaga-Conte Prostate Cancer Research Center, Baylor College of Medicine, Houston, TX 77030, USA
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Swindell EC, Thaller C, Sockanathan S, Petkovich M, Jessell TM, Eichele G. Complementary domains of retinoic acid production and degradation in the early chick embryo. Dev Biol 1999; 216:282-96. [PMID: 10588879 DOI: 10.1006/dbio.1999.9487] [Citation(s) in RCA: 211] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Excess retinoids as well as retinoid deprivation cause abnormal development, suggesting that retinoid homeostasis is critical for proper morphogenesis. RALDH-2 and CYP26, two key enzymes that carry out retinoic acid (RA) synthesis and degradation, respectively, were cloned from the chick and show significant homology with their orthologs in other vertebrates. Expression patterns of RALDH-2 and CYP26 genes were determined in the early chick embryo by in situ hybridization. During gastrulation and neurulation RALDH-2 and CYP26 were expressed in nonoverlapping regions, with RALDH-2 transcripts localized to the presumptive presomitic and lateral plate mesoderm and CYP26 mRNA to the presumptive mid- and forebrain. The two domains of expression were separated by an approximately 300-micrometer-wide gap, encompassing the presumptive hindbrain. In the limb region, a similar spatial segregation of RALDH-2 and CYP26 expression was found at stages 14 and 15. Limb region mesoderm expressed RALDH-2, whereas the overlying limb ectoderm expressed CYP26. RA-synthesizing and -degrading enzymatic activities were measured biochemically in regions expressing RALDH-2 or CYP26. Regions expressing RALDH-2 generated RA efficiently from precursor retinal but degraded RA only inefficiently. Conversely, tissue expressing CYP26 efficiently degraded but did not synthesize RA. Localized regions of RA synthesis and degradation mediated by these two enzymes may therefore provide a mechanism to regulate RA homeostasis spatially in vertebrate embryos.
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Affiliation(s)
- E C Swindell
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas, 77030, USA
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36
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Abstract
Both retinoid receptor null mutants and classic nutritional deficiency studies have demonstrated that retinoids are essential for the normal development of diverse embryonic structures (e.g. eye, heart, nervous system, urogenital tract). Detailed analysis of retinoid-modulated events is hampered by several limitations of these models, including that deficiency or null mutation is present throughout gestation, making it difficult to isolate primary effects, and preventing analysis beyond embryolethality. We developed a mammalian model in which retinoid-dependent events are documented during distinct targeted windows of embryogenesis. This was accomplished through the production of vitamin A-depleted (VAD) female rats maintained on sufficient oral retinoic acid (RA) for growth and fertility. After mating to normal males, these RA-sufficient/VAD females were given oral RA doses which allowed for gestation in an RA-sufficient state; embryogenesis proceeded normally until retinoids were withdrawn dietarily to produce a sudden, acute retinoid deficiency during a selected gestational window. In this trial, final RA doses were administered on E11.5, vehicle at E12.5, and embryos analyzed on E13.5; during this 48 hour window, the last RA dose was metabolized and embryos progressed in a retinoid-deficient state. RA-sufficient embryos were normal. Retinoid-depleted embryos exhibited specific malformations of the face, neural crest, eyes, heart, and nervous system. Some defects were phenocopies of those seen in null mutant mice for RXR alpha(−/−), RXR alpha(−/−)/RAR alpha(−/−), and RAR alpha(−/−)/RAR gamma(−/−), confirming that RA transactivation of its nuclear receptors is essential for normal embryogenesis. Other defects were unique to this deficiency model, showing that complete ligand ‘knock-out’ is required to see those retinoid-dependent events previously concealed by receptor functional redundancy, and reinforcing that retinoid receptors have separate yet overlapping contributions in the embryo. This model allows for precise targeting of retinoid form and deficiency to specific developmental windows, and will facilitate studies of distinct temporal events.
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Affiliation(s)
- E D Dickman
- Department of Nutritional Sciences, University of Wisconsin-Madison, 53706, USA
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Helms JA, Kim CH, Hu D, Minkoff R, Thaller C, Eichele G. Sonic hedgehog participates in craniofacial morphogenesis and is down-regulated by teratogenic doses of retinoic acid. Dev Biol 1997; 187:25-35. [PMID: 9224671 DOI: 10.1006/dbio.1997.8589] [Citation(s) in RCA: 210] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The face is one of the most intricately patterned structures in human and yet little is known of the mechanisms by which the tissues are instructed to grow, fuse, and differentiate. We undertook a study to determine if the craniofacial primordia used the same molecular cues that mediate growth and patterning in other embryonic tissues such as the neural tube and the limb. Here we provide evidence for the presence of organizer-like tissues in the craniofacial primordia. These candidate organizers express the polarizing signal sonic hedghog (shh) and its putative receptor, patched, as well as fibroblast growth factor 8 and bone morphogeneic protein 2. Shh-expressing epithelial grafts functioned as organizing tissues in a limb bud assay system, where they evoked duplications of the digit pattern. High doses of retinoic acid, which are known to truncate the growth of the frontonasal and maxillary processes and thus produce bilateral clefting of the lip and palate, inhibited the expression of shh and patched but not fgf8, in the craniofacial primordia, and abolished polarizing activity of these tissues. From these studies we conclude that the embryonic face contains signaling centers in the epithelium that participate in craniofacial growth and patterning. In addition, we discuss a novel mechanism whereby retinoids can exert a teratogenic effect on craniofacial morphogenesis independent of its effects on Hox gene expression or neural crest cell migration.
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Affiliation(s)
- J A Helms
- Department of Orthopaedic Surgery, University of California at San Francisco, 94143, USA.
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Lu HC, Revelli JP, Goering L, Thaller C, Eichele G. Retinoid signaling is required for the establishment of a ZPA and for the expression of Hoxb-8, a mediator of ZPA formation. Development 1997; 124:1643-51. [PMID: 9165113 DOI: 10.1242/dev.124.9.1643] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We show that retinoid receptor antagonists applied to the presumptive wing region block the formation of a zone of polarizing activity (ZPA). This suggests a direct relationship between retinoid signaling and the establishment of the ZPA. We provide evidence that the Hox gene, Hoxb-8, is a direct target of retinoid signaling since exogenously applied RA rapidly induces this gene in the absence of protein synthesis and, moreover, retinoid receptor antagonists down-regulate Hoxb-8 expression. In addition, we find that, in the lateral plate mesoderm, the domains of Hoxb-8 expression and of polarizing activity are coextensive. Taken together, these findings support the hypothesis that retinoids are required for the establishment of a ZPA, and that retinoids act, at least in part, through Hoxb-8, a gene associated with ZPA formation (Charite et al., 1994).
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Affiliation(s)
- H C Lu
- Developmental Biology Program, and V. and M. McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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Abstract
Retinoids regulate various aspects of vertebrate development through the action of two types of receptors, the retinoic acid receptors (RARs) and the retinoid-X-receptors (RXRs). Although RXRs bind 9-cis-retinoic acid (9cRA) with high affinity, in vitro experiments suggest that RXRs are for the most part not liganded, but serve as auxiliary factors forming heterodimers with liganded partner receptors such as RAR. Here we have used RXR- and RAR-specific ligands 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-napthyl)ethenyl]b enzoic acid (LG69) and (E)-4-[2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-2-naphthalenyl)-1-prope nyl]benzoic acid (TTNPB), and show that, in the context of an embryo, liganded RXR can mediate retinoid signal transduction. This conclusion emerges from examining the induction of several retinoid-responsive genes in the limb bud (Hoxb-6/-8, RARbeta) and in the developing central nervous system (Hoxb-1, otx-2). RARbeta and Hoxb-1 genes were most effectively activated by a combination of TTNPB and LG69, suggesting that the activation of these genes benefits from the presence of ligand-bound RAR and ligand-bound RXR. Hoxb-6/-8 genes were most efficiently induced by LG69, suggesting that liganded RXR can activate these genes. The regulation of the expression of the otx-2 gene was complex; expression was repressed by TTNPB, but such repression was relieved when LG69 was provided together with TTNPB, suggesting that ligand-bound RXR can overcome repression of transcription exerted by liganded RAR. Based on these findings, we propose that in our experimental system in which ligands are provided exogenously, transcriptional regulation of several genes involves liganded RXR.
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Affiliation(s)
- H C Lu
- V. and M. McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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40
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Affiliation(s)
- C Thaller
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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41
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Abstract
Vitamin A (retinol) and its derivatives, the retinoids, have been implicated as chemopreventive and differentiating agents in a variety of cancers, including that of the prostate. Very little is known about the physiological role of retinoids in the prostate. Here we show that normal prostate, benign prostate hyperplasia (BPH), and prostate carcinoma tissues contain endogenous retinol and its biologically active metabolite retinoic acid. In our studies, the concentration of retinol was 2-fold elevated in BPH compared with the other two tissues. In contrast, prostate carcinoma tissue contained five to eight times less retinoic acid than normal prostate or BPH. Moreover, we found that prostate tissue expresses dehydrogenases capable of converting retinol to retinoic acid through retinaldehyde as an intermediate. Formation of retinal from retinol takes place in microsomes, and the conversion of retinal to retinoic acid occurs in the cytosol. Furthermore, we found that the nuclear retinoic acid receptors alpha, beta, and gamma are expressed in normal and tumor samples. These studies establish a role for retinoids in the physiology of the prostate and possibly also in the pathophysiology of prostate cancer.
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Affiliation(s)
- D Pasquali
- V. and M. McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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42
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Abstract
In the chick limb bud, the zone of polarizing activity controls limb patterning along the anteroposterior and proximodistal axes. Since retinoic acid can induce ectopic polarizing activity, we examined whether this molecule plays a role in the establishment of the endogenous zone of polarizing activity. Grafts of wing bud mesenchyme treated with physiologic doses of retinoic acid had weak polarizing activity but inclusion of a retinoic acid-exposed apical ectodermal ridge or of prospective wing bud ectoderm evoked strong polarizing activity. Likewise, polarizing activity of prospective wing mesenchyme was markedly enhanced by co-grafting either a retinoic acid-exposed apical ectodermal ridge or ectoderm from the wing region. This equivalence of ectoderm-mesenchyme interactions required for the establishment of polarizing activity in retinoic acid-treated wing buds and in prospective wing tissue, suggests a role of retinoic acid in the establishment of the zone of polarizing activity. We found that prospective wing bud tissue is a high-point of retinoic acid synthesis. Furthermore, retinoid receptor-specific antagonists blocked limb morphogenesis and down-regulated a polarizing signal, sonic hedgehog. Limb agenesis was reversed when antagonist-exposed wing buds were treated with retinoic acid. Our results demonstrate a role of retinoic acid in the establishment of the endogenous zone of polarizing activity.
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Affiliation(s)
- J A Helms
- Department of Otorhinolaryngology, Baylor College of Medicine, Houston TX 77030, USA
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43
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Abstract
Local application of all-trans-retinoic acid (RA) to the anterior margin of chick limb buds results in pattern duplications reminescent of those that develop after grafting cells from the zone of polarizing activity (ZPA). RA may act directly by conferring positional information to limb bud cells, or it may act indirectly by creating a polarizing region in the tissue distal to the RA source. Here we demonstrate that tissue distal to an RA-releasing bead acquires polarizing activity in a dose-dependent manner. Treatments with pharmacological (beads soaked in 330 micrograms/ml) and physiological (beads soaked in 10 micrograms/ml) doses of RA are equally capable of inducing digit pattern duplication. Additionally, both treatments induce sonic hedgehog (shh; also known as vertebrate hedgehog-1, vhh-1), a putative ZPA morphogen and Hoxd-11, a gene induced by the polarizing signal. However, tissue transplantation assays reveal that pharmacological, but not physiological, doses create a polarizing region. This differential response could be explained if physiological doses induced less shh than pharmacological doses. However, our in situ hybridization analyses demonstrate that both treatments result in similar amounts of mRNA encoding this candidate ZPA morphogen. We outline a model describing the apparently disparate effects of pharmacologic and physiological doses RA on limb bud tissue.
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Affiliation(s)
- J Helms
- Department of Otorhinolaryngology, Baylor College of Medicine, Houston, Texas 77030
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44
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Abstract
In response to external stimuli, steroid receptors are directly influenced to transactivate gene expression. Assuming they exist, identification of ligands for orphan steroid receptors is a key to understanding their physiology. In the orphan subgroup of the steroid receptor superfamily, the putative carboxyl terminal ligand-binding domain (LBD) is well conserved among members of the superfamily, which suggests a role in ligand binding. A consequence of ligand binding is the induction of a significant conformational change within the LBD which is necessary for the transactivation function. This characteristic conformational change can be detected by partial proteolytic digestion and has been localized by mutational analysis and epitopic mapping of the LBD using monoclonal antibodies. Based on this finding, a sensitive in vitro assay was developed for the rapid screening and identification of potential ligands for orphan receptors. We examined the patterns of conformational changes in the androgen receptor, glucocorticoid receptor, and progesterone receptor induced by binding of their cognate agonists and antagonists. We demonstrated that the conformational changes induced by ligands can serve as characteristic and reliable markers to distinguish between the ligand-bound and apoprotein states of a receptor. The sensitivity and feasibility of employing this assay to detect new endogenous ligands using fractionated cellular extracts were also tested. The results strongly suggest that unknown compounds can be defined as potential ligands for orphan receptors using this approach.
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Affiliation(s)
- Z Zeng
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030
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45
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Abstract
The effects of retinoids are mediated by two types of receptors, the retinoic acid receptors (RARs) and the retinoid-X-receptors (RXRs). The physiological ligand of the RARs is all-trans-retinoic acid whereas RXRs have high affinity for 9-cis-retinoic acid, a naturally occurring retinoid isomer. RXRs are broadly expressed in embryonic and adult tissues, and they are capable of forming homodimers as well as heterodimers with RARs and other nuclear hormone receptors. The role of 9-cis-retinoic acid in regulating the activity of RXR homodimers and RXR-containing heterodimers is poorly understood in vivo. To begin to explore the function of 9-cis-retinoic acid in morphogenesis, we have examined the activity of this isomer in the chick wing. Using reverse transcriptase polymerase chain reaction analyses, we show that RXR gamma is expressed in stage 20 wing buds. Similar to all-trans-retinoic acid, the 9-cis-isomer induces pattern duplications when locally applied to chick wing buds, but the 9-cis isomer is about 25 times more potent than the all-trans form. Furthermore, applied all-trans-retinoic acid is converted to the 9-cis isomer in the wing bud. The ratio of 9-cis to all-trans-retinoic acid established in the tissue is approximately 1:25. This quantitative agreement between the degree of conversion and the 25-fold higher efficacy of the 9-cis isomer, raises the possibility that, at least in part, the effects of all-trans-retinoic acid on the wing pattern result from a conversion to the 9-cis isomer.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- C Thaller
- V. and M. McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030
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46
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Abstract
Hensen's node of amniotes, like the Spemann organizer of amphibians, can induce a second body axis when grafted into a host embryo. The avian node, as well as several midline structures originating from it (notochord, floor plate), can also induce digit pattern duplications when grafted into the chick wing bud. We report here that the equivalent of Hensen's node from mouse is an effective inducer of digits in the chick wing bud. Tissues anterior and posterior to the node also evoke pattern duplications, but with a significantly lower efficiency. The finding that the murine node operates in an avian wing bud suggests that the same inducing agent(s) function in both primary and secondary embryonic fields and have been conserved during vertebrate evolution. Digit pattern duplications are also evoked by local administration of all-trans-retinoic acid. This similarity raises the possibility that Hensen's node is a source of retinoic acid. The mouse node is capable of synthesizing retinoic acid from its biosynthetic precursor all-trans-retinol at a substantially higher rate than either anterior or posterior tissues.
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Affiliation(s)
- B L Hogan
- Department of Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2175
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47
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Abstract
All-trans retinoic acid (RA) has previously been shown to modulate the transcriptional properties of the retinoic acid receptor (RAR) and retinoid X receptor (RXR). The inability of all-trans RA to bind to RXR suggests that it may be metabolized to a more active high affinity ligand. We report here an experimental approach that has identified 9-cis RA as an RXR ligand. It is up to 40-fold more potent than all-trans RA in transfection assays and binds with high affinity. The production of 9-cis RA in cultured cells and the identification of this molecule in liver and kidney demonstrates the existence of this molecule in living organisms. The discovery of this novel hormone points to the key role retinoid metabolism may have in generating new signaling pathways.
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Affiliation(s)
- R A Heyman
- Ligand Pharmaceuticals, Inc., San Diego, California 92121
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48
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Picot D, Sandmeier E, Thaller C, Vincent MG, Christen P, Jansonius JN. The open/closed conformational equilibrium of aspartate aminotransferase. Studies in the crystalline state and with a fluorescent probe in solution. Eur J Biochem 1991; 196:329-41. [PMID: 2007402 DOI: 10.1111/j.1432-1033.1991.tb15821.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aspartate aminotransferase undergoes major shifts in the conformational equilibrium of the protein matrix during transamination. The present study defines the two conformational states of the enzyme by crystallographic analysis, examines the conditions under which the enzyme crystallizes in each of these conformations, and correlates these conditions with the conformational behaviour of the enzyme in solution, as monitored by a fluorescent reporter group. Cocrystallization of chicken mitochondrial aspartate aminotransferase with inhibitors and covalent coenzymesubstrate adducts yields three different crystal forms. Unliganded enzyme forms triclinic crystals of the open conformation, the structure of which has been solved (space group P1) [Ford, G. C., Eichele, G. & Jansonius, J. N. (1980) Proc. Natl Acad. Sci. USA 77, 2559-2563; Kirsch, J. F., Eichele, G., Ford, G. C., Vincent, M. G., Jansonius, J. N., Gehring, H. & Christen, P. (1984) J. Mol. Biol. 174, 487-525]. Complexes of the enzyme with dicarboxylate ligands form monoclinic or orthorhombic crystals of the closed conformation. The results of structure determinations of the latter two crystal forms at 0.44 nm resolution are described here. In the closed conformation, the small domain has undergone a rigid-body rotation of 12-14 which closes the active-site pocket. Shifts in the conformational equilibrium of aspartate aminotransferase in solution, as induced by substrates, substrate analogues and specific dicarboxylic inhibitors, can be monitored by changes in the relative fluoresence yield of the enzyme labelled at Cys166 with monobromotrimethylammoniobimane. The pyridoxal and pyridoxamine forms of the labelled enzyme show the same fluorescence properties, whereas in the apoenzyme the fluorescence intensity is reduced by 30%. All active-site ligands, if added to the labelled pyridoxal enzyme at saturating concentrations, cause a decrease in the fluorescence intensity by 40-70% and a blue shift of maximally 5 nm. Comparison of the fluorescence properties of the enzyme in various functional states with the crystallographic data shows that both techniques probe the same conformational equilibrium. The conformational change that closes the active site seems to be ligand-induced in the reaction of the pyridoxal form of the enzyme and syncatalytic in the reverse reaction with the pyridoxamine enzyme.
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Affiliation(s)
- D Picot
- Abteilung Strukturbiologie, Biozentrum der Univeristät Basel, Switzerland
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49
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Abstract
There is increasing evidence that retinoic acid is a morphogen involved in vertebrate development. This evidence comes in part from studies of the chick wing bud, in which local application of all-trans-retinoic acid results in a duplication of the digit pattern along the anteroposterior axis. Retinoic acid may be only one of several morphogenetic signalling compounds required for limb pattern formation. To identify novel morphogenetically active compounds, fractionated extracts of whole chick embryos were tested for their ability to induce digit pattern duplications. We describe here the isolation of a new activity present in the limb bud, which we have identified as all-trans-3,4-didehydroretinoic acid. The 3,4-didehydroretinoic acid is generated in situ from retinol through a 3,4-didehydroretinol intermediate. We show that 3,4-didehydroretinoic acid and retinoic acid are equipotent in evoking digit duplications. These findings suggest that there are at least two endogenous retinoids with morphogenetic properties in the chick limb.
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Affiliation(s)
- C Thaller
- Department of Cellular and Molecular Physiology, Harvard Medical School, Boston, Massachusetts 02115
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50
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Abstract
In many developing organisms the establishment of axial polarity and the patterning of cells depend on local signals that derive from restricted regions of the embryo. In vertebrate embryos, the origins of tissue polarity have been examined extensively in the developing limb. The anteroposterior pattern of the chick limb seems to be controlled by a morphogen, possibly retinoic acid, that is enriched in a region of the limb known as the zone of polarizing activity (ZPA). Certain tissues other than the ZPA have also shown polarizing activity experimentally in the chick limb, raising the possibility that signalling molecules involved in pattern formation in different embryonic tissues are conserved. Here we provide evidence that a similar polarizing activity is also present in a restricted region of the developing central nervous system (CNS). We show that a specialized group of neural cells termed the floor plate, but not other regions of the CNS, mimics the ZPA in respecifying the digit pattern in the developing chick limb. In addition, using an in vitro biochemical assay, we show that the floor plate can synthesize retinoic acid and 3,4-didehydroretinol, the precursor of a second morphogenetically active retinoid, 3,4-didehydroretinoic acid. These results show that the floor plate is a local source of a ZPA-like polarizing signal, possibly a retinoid, which may regulate the pattern of cell differentiation in the developing CNS.
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Affiliation(s)
- M Wagner
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
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