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Trimbour R, Deutschmann IM, Cantini L. Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS. Bioinformatics 2024; 40:btae143. [PMID: 38460192 PMCID: PMC11065476 DOI: 10.1093/bioinformatics/btae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 03/11/2024] Open
Abstract
MOTIVATION The molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation. RESULTS Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation. We benchmarked HuMMuS with respect to the state-of-the-art on both paired and unpaired multi-omics datasets. Our results proved the improvements provided by HuMMuS in terms of transcription factor (TF) targets, TF binding motifs and regulatory regions prediction. Finally, once applied to snmC-seq, scATAC-seq and scRNA-seq data from mouse brain cortex, HuMMuS enabled to accurately cluster scRNA profiles and to identify potential driver TFs. AVAILABILITY AND IMPLEMENTATION HuMMuS is available at https://github.com/cantinilab/HuMMuS.
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Affiliation(s)
- Remi Trimbour
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Ina Maria Deutschmann
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Laura Cantini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
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2
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Qi H, Luo L, Lu C, Chen R, Zhou X, Zhang X, Jia Y. TCF7L2 acts as a molecular switch in midbrain to control mammal vocalization through its DNA binding domain but not transcription activation domain. Mol Psychiatry 2023; 28:1703-1717. [PMID: 36782064 DOI: 10.1038/s41380-023-01993-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 01/15/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Vocalization is an essential medium for social signaling in birds and mammals. Periaqueductal gray (PAG) a conserved midbrain structure is believed to be responsible for innate vocalizations, but its molecular regulation remains largely unknown. Here, through a mouse forward genetic screening we identified one of the key Wnt/β-catenin effectors TCF7L2/TCF4 controls ultrasonic vocalization (USV) production and syllable complexity during maternal deprivation and sexual encounter. Early developmental expression of TCF7L2 in PAG excitatory neurons is necessary for the complex trait, while TCF7L2 loss reduces neuronal gene expressions and synaptic transmission in PAG. TCF7L2-mediated vocal control is independent of its β-catenin-binding domain but dependent of its DNA binding ability. Patient mutations associated with developmental disorders, including autism spectrum disorders, disrupt the transcriptional repression effect of TCF7L2, while mice carrying those mutations display severe USV impairments. Therefore, we conclude that TCF7L2 orchestrates gene expression in midbrain to control vocal production through its DNA binding but not transcription activation domain.
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Affiliation(s)
- Huihui Qi
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,School of Medicine, Tsinghua University, Beijing, 100084, China.,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Li Luo
- Tsinghua Laboratory of Brain and Intelligence (THBI), Tsinghua University, Beijing, 100084, China
| | - Caijing Lu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runze Chen
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Xianyao Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, China
| | - Xiaohui Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Science, Beijing Normal University, Beijing, 100875, China
| | - Yichang Jia
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. .,School of Medicine, Tsinghua University, Beijing, 100084, China. .,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China. .,Tsinghua Laboratory of Brain and Intelligence (THBI), Tsinghua University, Beijing, 100084, China.
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3
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García-Corzo L, Calatayud-Baselga I, Casares-Crespo L, Mora-Martínez C, Julián Escribano-Saiz J, Hortigüela R, Asenjo-Martínez A, Jordán-Pla A, Ercoli S, Flames N, López-Alonso V, Vilar M, Mira H. The transcription factor LEF1 interacts with NFIX and switches isoforms during adult hippocampal neural stem cell quiescence. Front Cell Dev Biol 2022; 10:912319. [PMID: 35938168 PMCID: PMC9355129 DOI: 10.3389/fcell.2022.912319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
Stem cells in adult mammalian tissues are held in a reversible resting state, known as quiescence, for prolonged periods of time. Recent studies have greatly increased our understanding of the epigenetic and transcriptional landscapes that underlie stem cell quiescence. However, the transcription factor code that actively maintains the quiescence program remains poorly defined. Similarly, alternative splicing events affecting transcription factors in stem cell quiescence have been overlooked. Here we show that the transcription factor T-cell factor/lymphoid enhancer factor LEF1, a central player in canonical β-catenin-dependent Wnt signalling, undergoes alternative splicing and switches isoforms in quiescent neural stem cells. We found that active β-catenin and its partner LEF1 accumulated in quiescent hippocampal neural stem and progenitor cell (Q-NSPC) cultures. Accordingly, Q-NSPCs showed enhanced TCF/LEF1-driven transcription and a basal Wnt activity that conferred a functional advantage to the cultured cells in a Wnt-dependent assay. At a mechanistic level, we found a fine regulation of Lef1 gene expression. The coordinate upregulation of Lef1 transcription and retention of alternative spliced exon 6 (E6) led to the accumulation of a full-length protein isoform (LEF1-FL) that displayed increased stability in the quiescent state. Prospectively isolated GLAST + cells from the postnatal hippocampus also underwent E6 retention at the time quiescence is established in vivo. Interestingly, LEF1 motif was enriched in quiescence-associated enhancers of genes upregulated in Q-NSPCs and quiescence-related NFIX transcription factor motifs flanked the LEF1 binding sites. We further show that LEF1 interacts with NFIX and identify putative LEF1/NFIX targets. Together, our results uncover an unexpected role for LEF1 in gene regulation in quiescent NSPCs, and highlight alternative splicing as a post-transcriptional regulatory mechanism in the transition from stem cell activation to quiescence.
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Affiliation(s)
- Laura García-Corzo
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Isabel Calatayud-Baselga
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Lucía Casares-Crespo
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Carlos Mora-Martínez
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
- Evo-devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juan Julián Escribano-Saiz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | | | | | - Antonio Jordán-Pla
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Stefano Ercoli
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Nuria Flames
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | | | - Marçal Vilar
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Helena Mira
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
- *Correspondence: Helena Mira,
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4
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Dias C, Pfundt R, Kleefstra T, Shuurs-Hoeijmakers J, Boon EMJ, van Hagen JM, Zwijnenburg P, Weiss MM, Keren B, Mignot C, Isapof A, Weiss K, Hershkovitz T, Iascone M, Maitz S, Feichtinger RG, Kotzot D, Mayr JA, Ben-Omran T, Mahmoud L, Pais LS, Walsh CA, Shashi V, Sullivan JA, Stong N, Lecoquierre F, Guerrot AM, Charollais A, Rodan LH. De novo variants in TCF7L2 are associated with a syndromic neurodevelopmental disorder. Am J Med Genet A 2021; 185:2384-2390. [PMID: 34003604 DOI: 10.1002/ajmg.a.62254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/25/2021] [Accepted: 04/24/2021] [Indexed: 01/21/2023]
Abstract
TCF7L2 encodes transcription factor 7-like 2 (OMIM 602228), a key mediator of the evolutionary conserved canonical Wnt signaling pathway. Although several large-scale sequencing studies have implicated TCF7L2 in intellectual disability and autism, both the genetic mechanism and clinical phenotype have remained incompletely characterized. We present here a comprehensive genetic and phenotypic description of 11 individuals who have been identified to carry de novo variants in TCF7L2, both truncating and missense. Missense variation is clustered in or near a high mobility group box domain, involving this region in these variants' pathogenicity. All affected individuals present with developmental delays in childhood, but most ultimately achieved normal intelligence or had only mild intellectual disability. Myopia was present in approximately half of the individuals, and some individuals also possessed dysmorphic craniofacial features, orthopedic abnormalities, or neuropsychiatric comorbidities including autism and attention-deficit/hyperactivity disorder (ADHD). We thus present an initial clinical and genotypic spectrum associated with variation in TCF7L2, which will be important in informing both medical management and future research.
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Affiliation(s)
- Caroline Dias
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rolph Pfundt
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Tjitske Kleefstra
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | | | - Elles M J Boon
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Petra Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marjan M Weiss
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Boris Keren
- Département de Génétique, hôpital Pitié-Salpêtrière, APHP.Sorbonne Université, Paris, France
| | - Cyril Mignot
- Département de Génétique, hôpital Pitié-Salpêtrière, APHP.Sorbonne Université, Paris, France
| | - Arnaud Isapof
- Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tova Hershkovitz
- Genetics Institute, Rambam Health Care Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetic Unit, Pediatric Clinic, Fondazione MBBM, San Gerardo Hospital, Monza, Italy
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Dieter Kotzot
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Tawfeg Ben-Omran
- Department of Pediatrics, Sidra Medicine, Department of Medical Genetics, Hamad Medical Corporation, Weill Cornell Medical College, Doha, Qatar
| | - Laila Mahmoud
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Francois Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, Rouen, France
| | - Aude Charollais
- Reference Centre for Learning Disorders, Rouen University Hospital, F-76031 Rouen Cedex, Rouen, France.,Department of Neonatology and Paediatric Intensive Care, Rouen University Hospital, F-76031 Cedex, Rouen, France
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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5
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Puelles L, Diaz C, Stühmer T, Ferran JL, Martínez‐de la Torre M, Rubenstein JLR. LacZ-reporter mapping of Dlx5/6 expression and genoarchitectural analysis of the postnatal mouse prethalamus. J Comp Neurol 2021; 529:367-420. [PMID: 32420617 PMCID: PMC7671952 DOI: 10.1002/cne.24952] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022]
Abstract
We present here a thorough and complete analysis of mouse P0-P140 prethalamic histogenetic subdivisions and corresponding nuclear derivatives, in the context of local tract landmarks. The study used as fundamental material brains from a transgenic mouse line that expresses LacZ under the control of an intragenic enhancer of Dlx5 and Dlx6 (Dlx5/6-LacZ). Subtle shadings of LacZ signal, jointly with pan-DLX immunoreaction, and several other ancillary protein or RNA markers, including Calb2 and Nkx2.2 ISH (for the prethalamic eminence, and derivatives of the rostral zona limitans shell domain, respectively) were mapped across the prethalamus. The resulting model of the prethalamic region postulates tetrapartite rostrocaudal and dorsoventral subdivisions, as well as a tripartite radial stratification, each cell population showing a characteristic molecular profile. Some novel nuclei are proposed, and some instances of potential tangential cell migration were noted.
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Affiliation(s)
- Luis Puelles
- Department of Human Anatomy and Psychobiology and IMIB‐Arrixaca InstituteUniversity of MurciaMurciaSpain
| | - Carmen Diaz
- Department of Medical Sciences, School of Medicine and Institute for Research in Neurological DisabilitiesUniversity of Castilla‐La ManchaAlbaceteSpain
| | - Thorsten Stühmer
- Nina Ireland Laboratory of Developmental Neurobiology, Department of PsychiatryUCSF Medical SchoolSan FranciscoCaliforniaUSA
| | - José L. Ferran
- Department of Human Anatomy and Psychobiology and IMIB‐Arrixaca InstituteUniversity of MurciaMurciaSpain
| | | | - John L. R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of PsychiatryUCSF Medical SchoolSan FranciscoCaliforniaUSA
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6
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Karve K, Netherton S, Deng L, Bonni A, Bonni S. Regulation of epithelial-mesenchymal transition and organoid morphogenesis by a novel TGFβ-TCF7L2 isoform-specific signaling pathway. Cell Death Dis 2020; 11:704. [PMID: 32843642 PMCID: PMC7447769 DOI: 10.1038/s41419-020-02905-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/18/2022]
Abstract
Alternative splicing contributes to diversification of gene function, yet consequences of splicing on functions of specific gene products is poorly understood. The major transcription factor TCF7L2 undergoes alternative splicing but the biological significance of TCF7L2 isoforms has remained largely to be elucidated. Here, we find that the TCF7L2 E-isoforms maintain, whereas the M and S isoforms disrupt morphogenesis of 3D-epithelial cell-derived organoids via regulation of epithelial-mesenchymal transition (EMT). Remarkably, TCF7L2E2 antagonizes, whereas TCF7L2M2/S2 promotes EMT-like effects in epithelial cells induced by transforming growth factor beta (TGFβ) signaling. In addition, we find TGFβ signaling reduces the proportion of TCF7L2E to TCF7L2M/S protein in cells undergoing EMT. We also find that TCF7L2 operates via TGFβ-Smad3 signaling to regulate EMT. Collectively, our findings unveil novel isoform-specific functions for the major transcription factor TCF7L2 and provide novel links between TCF7L2 and TGFβ signaling in the control of EMT-like responses and epithelial tissue morphogenesis.
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Affiliation(s)
- Kunal Karve
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Stuart Netherton
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Lili Deng
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shirin Bonni
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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7
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Lipiec MA, Bem J, Koziński K, Chakraborty C, Urban-Ciećko J, Zajkowski T, Dąbrowski M, Szewczyk ŁM, Toval A, Ferran JL, Nagalski A, Wiśniewska MB. TCF7L2 regulates postmitotic differentiation programmes and excitability patterns in the thalamus. Development 2020; 147:dev.190181. [PMID: 32675279 PMCID: PMC7473649 DOI: 10.1242/dev.190181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022]
Abstract
Neuronal phenotypes are controlled by terminal selector transcription factors in invertebrates, but only a few examples of such regulators have been provided in vertebrates. We hypothesised that TCF7L2 regulates different stages of postmitotic differentiation in the thalamus, and functions as a thalamic terminal selector. To investigate this hypothesis, we used complete and conditional knockouts of Tcf7l2 in mice. The connectivity and clustering of neurons were disrupted in the thalamo-habenular region in Tcf7l2-/- embryos. The expression of subregional thalamic and habenular transcription factors was lost and region-specific cell migration and axon guidance genes were downregulated. In mice with a postnatal Tcf7l2 knockout, the induction of genes that confer thalamic terminal electrophysiological features was impaired. Many of these genes proved to be direct targets of TCF7L2. The role of TCF7L2 in terminal selection was functionally confirmed by impaired firing modes in thalamic neurons in the mutant mice. These data corroborate the existence of master regulators in the vertebrate brain that control stage-specific genetic programmes and regional subroutines, maintain regional transcriptional network during embryonic development, and induce terminal selection postnatally.
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Affiliation(s)
- Marcin Andrzej Lipiec
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.,Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Joanna Bem
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Kamil Koziński
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Chaitali Chakraborty
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | | | - Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Michał Dąbrowski
- Nencki Institute of Experimental Biology, Pasteur 3, 02-093 Warsaw, Poland
| | | | - Angel Toval
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and IMIB-Arrixaca Institute, Campus de la Salud, 30120 El Palmar, Murcia, Spain
| | - José Luis Ferran
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and IMIB-Arrixaca Institute, Campus de la Salud, 30120 El Palmar, Murcia, Spain
| | - Andrzej Nagalski
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
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8
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Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW. Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Genome Res 2019; 29:2046-2055. [PMID: 31727681 PMCID: PMC6886501 DOI: 10.1101/gr.248435.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 09/16/2019] [Indexed: 02/05/2023]
Abstract
Alternative pre-mRNA splicing has long been proposed to contribute greatly to proteome complexity. However, the extent to which mature mRNA isoforms are successfully translated into protein remains controversial. Here, we used high-throughput RNA sequencing and mass spectrometry (MS)–based proteomics to better evaluate the translation of alternatively spliced mRNAs. To increase proteome coverage and improve protein quantitation, we optimized cell fractionation and sample processing steps at both the protein and peptide level. Furthermore, we generated a custom peptide database trained on analysis of RNA-seq data with MAJIQ, an algorithm optimized to detect and quantify differential and unannotated splice junction usage. We matched tandem mass spectra acquired by data-dependent acquisition (DDA) against our custom RNA-seq based database, as well as SWISS-PROT and RefSeq databases to improve identification of splicing-derived proteoforms by 28% compared with use of the SWISS-PROT database alone. Altogether, we identified peptide evidence for 554 alternate proteoforms corresponding to 274 genes. Our increased depth and detection of proteins also allowed us to track changes in the transcriptome and proteome induced by T-cell stimulation, as well as fluctuations in protein subcellular localization. In sum, our data here confirm that use of generic databases in proteomic studies underestimates the number of spliced mRNA isoforms that are translated into protein and provides a workflow that improves isoform detection in large-scale proteomic experiments.
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Affiliation(s)
- Laura M Agosto
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Caleb M Radens
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Genetics and Epigenetics, Cell & Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josue Baeza
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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9
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Ganmore I, Livny A, Ravona-Springer R, Cooper I, Alkelai A, Shelly S, Tsarfaty G, Heymann A, Schnaider Beeri M, Greenbaum L. TCF7L2 polymorphisms are associated with amygdalar volume in elderly individuals with Type 2 Diabetes. Sci Rep 2019; 9:15818. [PMID: 31676834 PMCID: PMC6825182 DOI: 10.1038/s41598-019-48899-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/08/2019] [Indexed: 02/06/2023] Open
Abstract
The association between several Single Nucleotide Polymorphisms (SNPs) within the transcription factor 7-like 2 (TCF7L2) gene and Type 2 Diabetes (T2D) as well as additional T2D-related traits is well established. Since alteration in total and regional brain volumes are consistent findings among T2D individuals, we studied the association of four T2D susceptibility SNPS within TCF7L2 (rs7901695, rs7903146, rs11196205, and rs12255372) with volumes of white matter hyperintensities (WMH), gray matter, and regional volumes of amygdala and hippocampus obtained from structural MRI among 191 T2D elderly Jewish individuals. Under recessive genetic model (controlling for age, sex and intracranial volume), we found that for all four SNPs, carriers of two copies of the T2D risk allele (homozygous genotype) had significantly smaller amygdalar volume: rs7901695- CC genotype vs. CT + TT genotypes, p = 0.002; rs7903146-TT vs. TC + CC, p = 0.003; rs11196205- CC vs. CG + GG, p = 0.0003; and rs12255372- TT vs. TG + GG, p = 0.003. Adjusting also for T2D-related covariates, body mass index (BMI), and ancestry did not change the results substantively (rs7901695, p = 0.003; rs7903146, p = 0.005; rs11196205, p = 0.001; and rs12255372, p = 0.005). Conditional analysis demonstrated that only rs11196205 was independently associated with amygdalar volume at a significant level. Separate analysis of left and right amygdala revealed stronger results for left amygdalar volume. Taken together, we report association of TCF7L2 SNPs with amygdalar volume among T2D elderly Jewish patients. Further studies in other populations are required to support these findings and reach more definitive conclusions.
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Affiliation(s)
- Ithamar Ganmore
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,Memory clinic, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Abigail Livny
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Memory clinic, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Itzik Cooper
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Shahar Shelly
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Galia Tsarfaty
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
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10
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Bem J, Brożko N, Chakraborty C, Lipiec MA, Koziński K, Nagalski A, Szewczyk ŁM, Wiśniewska MB. Wnt/β-catenin signaling in brain development and mental disorders: keeping TCF7L2 in mind. FEBS Lett 2019; 593:1654-1674. [PMID: 31218672 PMCID: PMC6772062 DOI: 10.1002/1873-3468.13502] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/12/2022]
Abstract
Canonical Wnt signaling, which is transduced by β-catenin and lymphoid enhancer factor 1/T cell-specific transcription factors (LEF1/TCFs), regulates many aspects of metazoan development and tissue renewal. Although much evidence has associated canonical Wnt/β-catenin signaling with mood disorders, the mechanistic links are still unknown. Many components of the canonical Wnt pathway are involved in cellular processes that are unrelated to classical canonical Wnt signaling, thus further blurring the picture. The present review critically evaluates the involvement of classical Wnt/β-catenin signaling in developmental processes that putatively underlie the pathology of mental illnesses. Particular attention is given to the roles of LEF1/TCFs, which have been discussed surprisingly rarely in this context. Highlighting recent discoveries, we propose that alterations in the activity of LEF1/TCFs, and particularly of transcription factor 7-like 2 (TCF7L2), result in defects previously associated with neuropsychiatric disorders, including imbalances in neurogenesis and oligodendrogenesis, the functional disruption of thalamocortical circuitry and dysfunction of the habenula.
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Affiliation(s)
- Joanna Bem
- Centre of New TechnologiesUniversity of WarsawPoland
| | - Nikola Brożko
- Centre of New TechnologiesUniversity of WarsawPoland
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11
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Bem J, Brożko N, Chakraborty C, Lipiec MA, Koziński K, Nagalski A, Szewczyk ŁM, Wiśniewska MB. Wnt/β-catenin signaling in brain development and mental disorders: keeping TCF7L2 in mind. FEBS Lett 2019. [PMID: 31218672 DOI: 10.1002/1873−3468.13502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Canonical Wnt signaling, which is transduced by β-catenin and lymphoid enhancer factor 1/T cell-specific transcription factors (LEF1/TCFs), regulates many aspects of metazoan development and tissue renewal. Although much evidence has associated canonical Wnt/β-catenin signaling with mood disorders, the mechanistic links are still unknown. Many components of the canonical Wnt pathway are involved in cellular processes that are unrelated to classical canonical Wnt signaling, thus further blurring the picture. The present review critically evaluates the involvement of classical Wnt/β-catenin signaling in developmental processes that putatively underlie the pathology of mental illnesses. Particular attention is given to the roles of LEF1/TCFs, which have been discussed surprisingly rarely in this context. Highlighting recent discoveries, we propose that alterations in the activity of LEF1/TCFs, and particularly of transcription factor 7-like 2 (TCF7L2), result in defects previously associated with neuropsychiatric disorders, including imbalances in neurogenesis and oligodendrogenesis, the functional disruption of thalamocortical circuitry and dysfunction of the habenula.
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Affiliation(s)
- Joanna Bem
- Centre of New Technologies, University of Warsaw, Poland
| | - Nikola Brożko
- Centre of New Technologies, University of Warsaw, Poland
| | | | | | - Kamil Koziński
- Centre of New Technologies, University of Warsaw, Poland
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12
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Zhu D, Huang R, Chen L, Fu P, Luo L, He L, Li Y, Liao L, Zhu Z, Wang Y. Cloning and characterization of the LEF/TCF gene family in grass carp (Ctenopharyngodon idella) and their expression profiles in response to grass carp reovirus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 86:335-346. [PMID: 30500548 DOI: 10.1016/j.fsi.2018.11.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/05/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
T-cell factor/lymphoid enhancer-binding factor (TCF/LEF) proteins from the High Mobility Group (HMG) box family act as the main downstream effectors of the Wnt signaling pathway. HMGB proteins play multifaceted roles in the immune system of mammals. To clarify the immunological characteristics of LEF/TCF genes in grass carp (Ctenopharyngodon idella), five LEF/TCF genes (TCF7, LEF1, TCF7L1A, TCF7L1B, and TCF7L2) were identified and characterized. All five LEF/TCF proteins contained two characteristic domains: a HMG-BOX domain and a CTNNB1_binding region. Phylogenetic tree analysis revealed that the LEF/TCF proteins were represented different lineages. These results of subcellular localization showed that four of the LEF/TCF genes were localized exclusively within the nucleus, while TCF7L2 was localized in the cytoplasm and nucleus. The mRNA expression profiles of these LEF/TCF family genes differed across different tissues. The mRNA expression levels of TCF7, TCF7L1A, and TCF7L2 changed significantly in liver after grass carp reovirus (GCRV) challenge; TCF7 and TCF7L1A responded early while TCF7L2 responded late. This suggests that these genes may participate in GCRV-related immune responses. Moreover, TCF7 promoted Bcl6 transcription in response to the GCRV challenge. These findings further our understanding of the function of LEF/TCF genes in teleosts.
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Affiliation(s)
- Denghui Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Liangming Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peipei Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lifei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Libo He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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13
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Zhao L, Wang C, Lehman ML, He M, An J, Svingen T, Spiller CM, Ng ET, Nelson CC, Koopman P. Transcriptomic analysis of mRNA expression and alternative splicing during mouse sex determination. Mol Cell Endocrinol 2018; 478:84-96. [PMID: 30053582 DOI: 10.1016/j.mce.2018.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/23/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Mammalian sex determination hinges on sexually dimorphic transcriptional programs in developing fetal gonads. A comprehensive view of these programs is crucial for understanding the normal development of fetal testes and ovaries and the etiology of human disorders of sex development (DSDs), many of which remain unexplained. Using strand-specific RNA-sequencing, we characterized the mouse fetal gonadal transcriptome from 10.5 to 13.5 days post coitum, a key time window in sex determination and gonad development. Our dataset benefits from a greater sensitivity, accuracy and dynamic range compared to microarray studies, allows global dynamics and sex-specificity of gene expression to be assessed, and provides a window to non-transcriptional events such as alternative splicing. Spliceomic analysis uncovered female-specific regulation of Lef1 splicing, which may contribute to the enhanced WNT signaling activity in XX gonads. We provide a user-friendly visualization tool for the complete transcriptomic and spliceomic dataset as a resource for the field.
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Affiliation(s)
- Liang Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Chenwei Wang
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, 4102, Australia
| | - Melanie L Lehman
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, 4102, Australia
| | - Mingyu He
- Longsoft, Brisbane, Queensland, 4109, Australia
| | - Jiyuan An
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, 4102, Australia
| | - Terje Svingen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Cassy M Spiller
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Ee Ting Ng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, 4102, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia.
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14
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Liu Z, Zhang N, Zhang Y, Du Y, Zhang T, Li Z, Wu J, Wang X. Prioritized High-Confidence Risk Genes for Intellectual Disability Reveal Molecular Convergence During Brain Development. Front Genet 2018; 9:349. [PMID: 30279698 PMCID: PMC6153320 DOI: 10.3389/fgene.2018.00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 01/09/2023] Open
Abstract
Dissecting the genetic susceptibility to intellectual disability (ID) based on de novo mutations (DNMs) will aid our understanding of the neurobiological and genetic basis of ID. In this study, we identify 63 high-confidence ID genes with q-values < 0.1 based on four background DNM rates and coding DNM data sets from multiple sequencing cohorts. Bioinformatic annotations revealed a higher burden of these 63 ID genes in FMRP targets and CHD8 targets, and these genes show evolutionary constraint against functional genetic variation. Moreover, these ID risk genes were preferentially expressed in the cortical regions from the early fetal to late mid-fetal stages. In particular, a genome-wide weighted co-expression network analysis suggested that ID genes tightly converge onto two biological modules (M1 and M2) during human brain development. Functional annotations showed specific enrichment of chromatin modification and transcriptional regulation for M1 and synaptic function for M2, implying the divergent etiology of the two modules. In addition, we curated 12 additional strong ID risk genes whose molecular interconnectivity with known ID genes (q-values < 0.3) was greater than random. These findings further highlight the biological convergence of ID risk genes and help improve our understanding of the genetic architecture of ID.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yu Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yaoqiang Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaobing Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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15
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Schatton A, Mendoza E, Grube K, Scharff C. FoxP in bees: A comparative study on the developmental and adult expression pattern in three bee species considering isoforms and circuitry. J Comp Neurol 2018. [PMID: 29536541 DOI: 10.1002/cne.24430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mutations in the transcription factors FOXP1, FOXP2, and FOXP4 affect human cognition, including language. The FoxP gene locus is evolutionarily ancient and highly conserved in its DNA-binding domain. In Drosophila melanogaster FoxP has been implicated in courtship behavior, decision making, and specific types of motor-learning. Because honeybees (Apis mellifera, Am) excel at navigation and symbolic dance communication, they are a particularly suitable insect species to investigate a potential link between neural FoxP expression and cognition. We characterized two AmFoxP isoforms and mapped their expression in the brain during development and in adult foragers. Using a custom-made antiserum and in situ hybridization, we describe 11 AmFoxP expressing neuron populations. FoxP was expressed in equivalent patterns in two other representatives of Apidae; a closely related dwarf bee and a bumblebee species. Neural tracing revealed that the largest FoxP expressing neuron cluster in honeybees projects into a posterior tract that connects the optic lobe to the posterior lateral protocerebrum, predicting a function in visual processing. Our data provide an entry point for future experiments assessing the function of FoxP in eusocial Hymenoptera.
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Affiliation(s)
- Adriana Schatton
- Institute for Animal Behavior, Freie Universität Berlin, Berlin, 14195, Germany
| | - Ezequiel Mendoza
- Institute for Animal Behavior, Freie Universität Berlin, Berlin, 14195, Germany
| | - Kathrin Grube
- Institute for Animal Behavior, Freie Universität Berlin, Berlin, 14195, Germany
| | - Constance Scharff
- Institute for Animal Behavior, Freie Universität Berlin, Berlin, 14195, Germany
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16
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Wang Y, Huang A, Gan L, Bao Y, Zhu W, Hu Y, Ma L, Wei S, Lan Y. Screening of Potential Genes and Transcription Factors of Postoperative Cognitive Dysfunction via Bioinformatics Methods. Med Sci Monit 2018; 24:503-510. [PMID: 29374768 PMCID: PMC5791419 DOI: 10.12659/msm.907445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The aim of this study was to explore the potential genes and transcription factors involved in postoperative cognitive dysfunction (POCD) via bioinformatics analysis. Material/Methods GSE95070 miRNA expression profiles were downloaded from Gene Expression Omnibus database, which included five hippocampal tissues from POCD mice and controls. Moreover, the differentially expressed miRNAs (DEMs) between the two groups were identified. In addition, the target genes of DEMs were predicted using Targetscan 7.1, followed by protein-protein interaction (PPI) network construction, functional enrichment analysis, pathway analysis, and prediction of transcription factors (TFs) targeting the potential targets. Results A total of eight DEMs were obtained, and 823 target genes were predicted, including 170 POCD-associated genes. Furthermore, potential key genes in the network were remarkably enriched in focal adhesion, protein digestion and absorption, ECM-receptor interaction, and Wnt and MAPK signaling pathways. Conclusions Most potential target genes were involved in the regulation of TFs, including LEF1, SP1, and AP4, which may exert strong impact on the development of POCD.
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Affiliation(s)
- Yafeng Wang
- Department of Anesthesiology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Ailan Huang
- Department of Anesthesiology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Lixia Gan
- Department of Anesthesiology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Yanli Bao
- Department of Anesthesiology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Weilin Zhu
- Department of Anesthesiology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Yanyan Hu
- Department of Anesthesiology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Li Ma
- Department of Anesthesiology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Shiyang Wei
- Department of Gynecology, People’s Hospital of Guangxi Zhuang Autonomous
Region, Nanning, Guangxi, P.R. China
| | - Yuyan Lan
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical
University, Nanning, Guangxi, P.R. China
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17
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Palluzzi F, Ferrari R, Graziano F, Novelli V, Rossi G, Galimberti D, Rainero I, Benussi L, Nacmias B, Bruni AC, Cusi D, Salvi E, Borroni B, Grassi M. A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PLoS One 2017; 12:e0185797. [PMID: 29020091 PMCID: PMC5636111 DOI: 10.1371/journal.pone.0185797] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 09/19/2017] [Indexed: 01/04/2023] Open
Abstract
Frontotemporal Dementia (FTD) is the form of neurodegenerative dementia with the highest prevalence after Alzheimer’s disease, equally distributed in men and women. It includes several variants, generally characterized by behavioural instability and language impairments. Although few mendelian genes (MAPT, GRN, and C9orf72) have been associated to the FTD phenotype, in most cases there is only evidence of multiple risk loci with relatively small effect size. To date, there are no comprehensive studies describing FTD at molecular level, highlighting possible genetic interactions and signalling pathways at the origin FTD-associated neurodegeneration. In this study, we designed a broad FTD genetic interaction map of the Italian population, through a novel network-based approach modelled on the concepts of disease-relevance and interaction perturbation, combining Steiner tree search and Structural Equation Model (SEM) analysis. Our results show a strong connection between Calcium/cAMP metabolism, oxidative stress-induced Serine/Threonine kinases activation, and postsynaptic membrane potentiation, suggesting a possible combination of neuronal damage and loss of neuroprotection, leading to cell death. In our model, Calcium/cAMP homeostasis and energetic metabolism impairments are primary causes of loss of neuroprotection and neural cell damage, respectively. Secondly, the altered postsynaptic membrane potentiation, due to the activation of stress-induced Serine/Threonine kinases, leads to neurodegeneration. Our study investigates the molecular underpinnings of these processes, evidencing key genes and gene interactions that may account for a significant fraction of unexplained FTD aetiology. We emphasized the key molecular actors in these processes, proposing them as novel FTD biomarkers that could be crucial for further epidemiological and molecular studies.
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Affiliation(s)
- Fernando Palluzzi
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
- * E-mail:
| | - Raffaele Ferrari
- Department of Molecular Neuroscience, Institute of Neurology, University College London (UCL), London, United Kingdom
| | - Francesca Graziano
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
| | - Valeria Novelli
- Department of Genetics, Fondazione Policlinico A. Gemelli, Roma, Italy
| | - Giacomina Rossi
- Division of Neurology V and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Daniela Galimberti
- Department of Neurological Sciences, Dino Ferrari Institute, University of Milan, Milano, Italy
| | - Innocenzo Rainero
- Department of Neuroscience, Neurology I, University of Torino and Città della Salute e della Scienza di Torino, Torino, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Firenze, Italy
| | - Amalia C. Bruni
- Neurogenetic Regional Centre ASPCZ Lamezia Terme, Lamezia Terme (CZ), Italy
| | - Daniele Cusi
- Department of Health Sciences, University of Milan at San Paolo Hospital, Milano, Italy
- Institute of Biomedical Technologies, Italian National Research Council, Milano, Italy
| | - Erika Salvi
- Institute of Biomedical Technologies, Italian National Research Council, Milano, Italy
| | - Barbara Borroni
- Department of Medical Sciences, Neurology Clinic, University of Brescia, Brescia, Italy
| | - Mario Grassi
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
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18
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Yao L, Liu Y, Qiu Z, Kumar S, Curran JE, Blangero J, Chen Y, Lehman DM. Molecular Profiling of Human Induced Pluripotent Stem Cell-Derived Hypothalamic Neurones Provides Developmental Insights into Genetic Loci for Body Weight Regulation. J Neuroendocrinol 2017; 29:10.1111/jne.12455. [PMID: 28071834 PMCID: PMC5328859 DOI: 10.1111/jne.12455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 01/04/2017] [Accepted: 01/06/2017] [Indexed: 01/16/2023]
Abstract
Recent data suggest that common genetic risks for metabolic disorders such as obesity may be human-specific and exert effects via the central nervous system. To overcome the limitation of human tissue access for study, we have generated induced human pluripotent stem cell (hiPSC)-derived neuronal cultures that recapture many features of hypothalamic neurones within the arcuate nucleus. In the present study, we have comprehensively characterised this model across development, benchmarked these neurones to in vivo events, and demonstrate a link between obesity risk variants and hypothalamic development. The dynamic transcriptome across neuronal maturation was examined using microarray and RNA sequencing methods at nine time points. K-means clustering of the longitudinal data was conducted to identify co-regulation and microRNA control of biological processes. The transcriptomes were compared with those of 103 samples from 13 brain regions reported in the Genotype-Tissue Expression database (GTEx) using principal components analysis. Genes with proximity to body mass index (BMI)-associated genetic variants were mapped to the developmentally expressed genesets, and enrichment significance was assessed with Fisher's exact test. The human neuronal cultures have a transcriptional and physiological profile of neuropeptide Y/agouti-related peptide arcuate nucleus neurones. The neuronal transcriptomes were highly correlated with adult hypothalamus compared to any other brain region from the GTEx. Also, approximately 25% of the transcripts showed substantial changes in expression across neuronal development and potential co-regulation of biological processes that mirror neuronal development in vivo. These developmentally expressed genes were significantly enriched for genes in proximity to BMI-associated variants. We confirmed the utility of this in vitro human model for studying the development of key hypothalamic neurones involved in energy balance and show that genes at loci associated with body weight regulation may share a pattern of developmental regulation. These data support the need to investigate early development to elucidate the human-specific central nervous system pathophysiology underlying obesity susceptibility.
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Affiliation(s)
- Li Yao
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Yuanhang Liu
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Zhifang Qiu
- Department of Microbiology and Immunology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, Brownsville, TX, USA
| | - Joanne E. Curran
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, Brownsville, TX, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, Brownsville, TX, USA
| | - Yidong Chen
- Department of Epidemiology and Biostatistics, and Greehey Children’s Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Donna M. Lehman
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
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Misztal K, Brozko N, Nagalski A, Szewczyk LM, Krolak M, Brzozowska K, Kuznicki J, Wisniewska MB. TCF7L2 mediates the cellular and behavioral response to chronic lithium treatment in animal models. Neuropharmacology 2016; 113:490-501. [PMID: 27793772 DOI: 10.1016/j.neuropharm.2016.10.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 11/15/2022]
Abstract
The mechanism of lithium's therapeutic action remains obscure, hindering the discovery of safer treatments for bipolar disorder. Lithium can act as an inhibitor of the kinase GSK3α/β, which in turn negatively regulates β-catenin, a co-activator of LEF1/TCF transcription factors. However, unclear is whether therapeutic levels of lithium activate β-catenin in the brain, and whether this activation could have a therapeutic significance. To address this issue we chronically treated mice with lithium. Although the level of non-phospho-β-catenin increased in all of the brain areas examined, β-catenin translocated into cellular nuclei only in the thalamus. Similar results were obtained when thalamic and cortical neurons were treated with a therapeutically relevant concentration of lithium in vitro. We tested if TCF7L2, a member of LEF1/TCF family that is highly expressed in the thalamus, facilitated the activation of β-catenin. Silencing of Tcf7l2 in thalamic neurons prevented β-catenin from entering the nucleus, even when the cells were treated with lithium. Conversely, when Tcf7l2 was ectopically expressed in cortical neurons, β-catenin shifted to the nucleus, and lithium augmented this process. Lastly, we silenced tcf7l2 in zebrafish and exposed them to lithium for 3 days, to evaluate whether TCF7L2 is involved in the behavioral response. Lithium decreased the dark-induced activity of control zebrafish, whereas the activity of zebrafish with tcf7l2 knockdown was unaltered. We conclude that therapeutic levels of lithium activate β-catenin selectively in thalamic neurons. This effect is determined by the presence of TCF7L2, and potentially contributes to the therapeutic response.
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Affiliation(s)
- Katarzyna Misztal
- International Institute of Molecular and Cell Biology, Laboratory of Neurodegeneration, Warsaw, Poland
| | - Nikola Brozko
- International Institute of Molecular and Cell Biology, Laboratory of Neurodegeneration, Warsaw, Poland; University of Warsaw, Centre of New Technologies, Laboratory of Molecular Neurobiology, Poland; Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Andrzej Nagalski
- International Institute of Molecular and Cell Biology, Laboratory of Neurodegeneration, Warsaw, Poland; University of Warsaw, Centre of New Technologies, Laboratory of Molecular Neurobiology, Poland
| | - Lukasz M Szewczyk
- International Institute of Molecular and Cell Biology, Laboratory of Neurodegeneration, Warsaw, Poland; Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Marta Krolak
- University of Warsaw, College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Poland
| | - Katarzyna Brzozowska
- International Institute of Molecular and Cell Biology, Laboratory of Neurodegeneration, Warsaw, Poland; University of Warsaw, Centre of New Technologies, Laboratory of Molecular Neurobiology, Poland; Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Jacek Kuznicki
- International Institute of Molecular and Cell Biology, Laboratory of Neurodegeneration, Warsaw, Poland
| | - Marta B Wisniewska
- International Institute of Molecular and Cell Biology, Laboratory of Neurodegeneration, Warsaw, Poland; University of Warsaw, Centre of New Technologies, Laboratory of Molecular Neurobiology, Poland.
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Nagalski A, Kozinski K, Wisniewska MB. Metabolic pathways in the periphery and brain: Contribution to mental disorders? Int J Biochem Cell Biol 2016; 80:19-30. [PMID: 27644152 DOI: 10.1016/j.biocel.2016.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022]
Abstract
The association between mental disorders and diabetes has a long history. Recent large-scale, well-controlled epidemiological studies confirmed a link between diabetes and psychiatric illnesses. The scope of this review is to summarize our current understanding of this relationship from a molecular perspective. We first discuss the potential contribution of diabetes-associated metabolic impairments to the etiology of mental conditions. Then, we focus on possible shared molecular risk factors and mechanisms. Simple comorbidity, shared susceptibility loci, and common pathophysiological processes in diabetes and mental illnesses have changed our traditional way of thinking about mental illness. We conclude that schizophrenia and affective disorders are not limited to an imbalance in dopaminergic and serotoninergic neurotransmission in the brain. They are also systemic disorders that can be considered, to some extent, as metabolic disorders.
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Affiliation(s)
- Andrzej Nagalski
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Kamil Kozinski
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marta B Wisniewska
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
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21
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Wang K, Li N, Yeung CH, Cooper TG, Liu XX, Liu J, Wang WT, Li Y, Shi H, Liu FJ. Comparison of gene expression of the oncogenic Wnt/β-catenin signaling pathway components in the mouse and human epididymis. Asian J Androl 2016; 17:1006-11. [PMID: 26228040 PMCID: PMC4814947 DOI: 10.4103/1008-682x.157396] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
β-catenin is an integral part of the Wnt signaling pathway and has been linked to tumorigenesis and multiple developmental processes. The high β-catenin expression with low tumor incidence in the human epididymis is thus intriguing. In the present study, the β-catenin gene and protein was found to be highly expressed in the murine caput epididymidis, and the protein mainly localized along the lateral plasma membranes of adjacent epithelial cells throughout both human and mouse epididymides. Furthermore, the adult mouse epididymis was found to express almost all the Wnt/β-catenin signaling pathway genes that were determined previously by our group in the human organ. Despite the differences in epididymal structure, the similar location of β-catenin and the high concordance of this pathway's components’ gene expression in both the adult human and mouse epididymides make the mouse a suitable animal model for studying the anti-tumor mechanism of the epididymis. In addition, both the mRNA and protein expression of β-catenin shared a similar spatial expression as the mRNA of Ros1, a proto-oncogene and a key developmental regulator of the initial segment of the mouse epididymis. The observations on the parallel temporal expression of β-catenin and Ros1 during postnatal development raise the possibility that the canonical Wnt signaling pathway has an additional role in the postnatal development of mouse epididymis.
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Affiliation(s)
- Kai Wang
- School of Agriculture, Ludong University; Central Laboratory, Yantai Yuhuangding Hospital, Yantai, Shandong, China
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22
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Nagalski A, Puelles L, Dabrowski M, Wegierski T, Kuznicki J, Wisniewska MB. Molecular anatomy of the thalamic complex and the underlying transcription factors. Brain Struct Funct 2016; 221:2493-510. [PMID: 25963709 PMCID: PMC4884203 DOI: 10.1007/s00429-015-1052-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 04/27/2015] [Indexed: 01/19/2023]
Abstract
Thalamocortical loops have been implicated in the control of higher-order cognitive functions, but advances in our understanding of the molecular underpinnings of neocortical organization have not been accompanied by similar analyses in the thalamus. Using expression-based correlation maps and the manual mapping of mouse and human datasets available in the Allen Brain Atlas, we identified a few individual regions and several sets of molecularly related nuclei that partially overlap with the classic grouping that is based on topographical localization and thalamocortical connections. These new molecular divisions of the adult thalamic complex are defined by the combinatorial expression of Tcf7l2, Lef1, Gbx2, Prox1, Pou4f1, Esrrg, and Six3 transcription factor genes. Further in silico and experimental analyses provided the evidence that TCF7L2 might be a pan-thalamic specifier. These results provide substantial insights into the "molecular logic" that underlies organization of the thalamic complex.
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Affiliation(s)
- Andrzej Nagalski
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, Warsaw, 00-927, Poland
| | - Luis Puelles
- Department of Human Anatomy, University of Murcia and IMIB, Murcia, 30071, Spain
| | - Michal Dabrowski
- Laboratory of Bioinformatics, Center of Neurobiology, Nencki Institute of Experimental Biology, Warsaw, 02-093, Poland
| | - Tomasz Wegierski
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Jacek Kuznicki
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Marta B Wisniewska
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland.
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, Warsaw, 00-927, Poland.
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Stankiewicz AM, Goscik J, Dyr W, Juszczak GR, Ryglewicz D, Swiergiel AH, Wieczorek M, Stefanski R. Novel candidate genes for alcoholism--transcriptomic analysis of prefrontal medial cortex, hippocampus and nucleus accumbens of Warsaw alcohol-preferring and non-preferring rats. Pharmacol Biochem Behav 2015; 139:27-38. [PMID: 26455281 DOI: 10.1016/j.pbb.2015.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Animal models provide opportunity to study neurobiological aspects of human alcoholism. Changes in gene expression have been implicated in mediating brain functions, including reward system and addiction. The current study aimed to identify genes that may underlie differential ethanol preference in Warsaw High Preferring (WHP) and Warsaw Low Preferring (WLP) rats. METHODS Microarray analysis comparing gene expression in nucleus accumbens (NAc), hippocampus (HP) and medial prefrontal cortex (mPFC) was performed in male WHP and WLP rats bred for differences in ethanol preference. RESULTS Differential and stable between biological repeats expression of 345, 254 and 129 transcripts in NAc, HP and mPFC was detected. Identified genes and processes included known mediators of ethanol response (Mx2, Fam111a, Itpr1, Gabra4, Agtr1a, LTP/LTD, renin-angiotensin signaling pathway), toxicity (Sult1c2a, Ces1, inflammatory response), as well as genes involved in regulation of important addiction-related brain systems such as dopamine, tachykinin or acetylcholine (Gng7, Tac4, Slc5a7). CONCLUSIONS The identified candidate genes may underlie differential ethanol preference in an animal model of alcoholism. COMMENT Names of genes are written in italics, while names of proteins are written in standard font. Names of human genes/proteins are written in all capital letters. Names of rodent genes/proteins are written in capital letter followed by small letters.
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Affiliation(s)
- Adrian M Stankiewicz
- Department of Animal Behaviour, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, 05-552 Jastrzebiec, Poland
| | - Joanna Goscik
- Software Department, Faculty of Computer Science, Bialystok University of Technology, 15-351 Bialystok, Poland
| | - Wanda Dyr
- Department of Pharmacology and Physiology of the Nervous System, Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland
| | - Grzegorz R Juszczak
- Department of Animal Behaviour, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, 05-552 Jastrzebiec, Poland
| | - Danuta Ryglewicz
- First Department of Neurology, Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland
| | - Artur H Swiergiel
- Department of Animal and Human Physiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; Department of Pharmacology, Toxicology and Neuroscience, Louisiana State University Health Sciences Center, Shreveport, LA71130, USA.
| | - Marek Wieczorek
- Department of Neurobiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
| | - Roman Stefanski
- Department of Pharmacology and Physiology of the Nervous System, Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland
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24
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The Wnt effector transcription factor 7-like 2 positively regulates oligodendrocyte differentiation in a manner independent of Wnt/β-catenin signaling. J Neurosci 2015; 35:5007-22. [PMID: 25810530 DOI: 10.1523/jneurosci.4787-14.2015] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genetic or pharmacological activation of canonical Wnt/β-catenin signaling inhibits oligodendrocyte differentiation. Transcription factor 7-like 2 (TCF7l2), also known as TCF4, is a Wnt effector induced transiently in the oligodendroglial lineage. A well accepted dogma is that TCF7l2 inhibits oligodendrocyte differentiation through activation of Wnt/β-catenin signaling. We report that TCF7l2 is upregulated transiently in postmitotic, newly differentiated oligodendrocytes. Using in vivo gene conditional ablation, we found surprisingly that TCF7l2 positively regulates neonatal and postnatal mouse oligodendrocyte differentiation during developmental myelination and remyelination in a manner independent of the Wnt/β-catenin signaling pathway. We also reveal a novel role of TCF7l2 in repressing a bone morphogenetic protein signaling pathway that is known to inhibit oligodendrocyte differentiation. Thus, our study provides novel data justifying therapeutic attempts to enhance, rather than inhibit, TCF7l2 signaling to overcome arrested oligodendroglial differentiation in multiple sclerosis and other demyelinating diseases.
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25
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Okamura-Oho Y, Shimokawa K, Nishimura M, Takemoto S, Sato A, Furuichi T, Yokota H. Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain. Sci Rep 2014; 4:6969. [PMID: 25382412 PMCID: PMC4225549 DOI: 10.1038/srep06969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/07/2014] [Indexed: 12/12/2022] Open
Abstract
Using a recently invented technique for gene expression mapping in the whole-anatomy context, termed transcriptome tomography, we have generated a dataset of 36,000 maps of overall gene expression in the adult-mouse brain. Here, using an informatics approach, we identified a broad co-expression network that follows an inverse power law and is rich in functional interaction and gene-ontology terms. Our framework for the integrated analysis of expression maps and graphs of co-expression networks revealed that groups of combinatorially expressed genes, which regulate cell differentiation during development, were present in the adult brain and each of these groups was associated with a discrete cell types. These groups included non-coding genes of unknown function. We found that these genes specifically linked developmentally conserved groups in the network. A previously unrecognized robust expression pattern covering the whole brain was related to the molecular anatomy of key biological processes occurring in particular areas.
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Affiliation(s)
- Yuko Okamura-Oho
- Brain Research Network (BReNt), 2-2-41 Sakurayama, Zushi-shi, Kanagawa, 249-0005, Japan
- Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan
| | - Kazuro Shimokawa
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-chou Aoba-ku Sendai-shi Miyagi, 980-8573, Japan
| | - Masaomi Nishimura
- Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan
| | - Satoko Takemoto
- Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan
| | - Akira Sato
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan
| | - Teiichi Furuichi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan
| | - Hideo Yokota
- Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan
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26
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Abellán A, Desfilis E, Medina L. Combinatorial expression of Lef1, Lhx2, Lhx5, Lhx9, Lmo3, Lmo4, and Prox1 helps to identify comparable subdivisions in the developing hippocampal formation of mouse and chicken. Front Neuroanat 2014; 8:59. [PMID: 25071464 PMCID: PMC4082316 DOI: 10.3389/fnana.2014.00059] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 06/12/2014] [Indexed: 11/23/2022] Open
Abstract
We carried out a study of the expression patterns of seven developmental regulatory genes (Lef1, Lhx2, Lhx9, Lhx5, Lmo3, Lmo4, and Prox1), in combination with topological position, to identify the medial pallial derivatives, define its major subdivisions, and compare them between mouse and chicken. In both species, the medial pallium is defined as a pallial sector adjacent to the cortical hem and roof plate/choroid tela, showing moderate to strong ventricular zone expression of Lef1, Lhx2, and Lhx9, but not Lhx5. Based on this, the hippocampal formation (indusium griseum, dentate gyrus, Ammon's horn fields, and subiculum), the medial entorhinal cortex, and part of the amygdalo-hippocampal transition area of mouse appeared to derive from the medial pallium. In the chicken, based on the same position and gene expression profile, we propose that the hippocampus (including the V-shaped area), the parahippocampal area (including its caudolateral part), the entorhinal cortex, and the amygdalo-hippocampal transition area are medial pallial derivatives. Moreover, the combinatorial expression of Lef1, Prox1, Lmo4, and Lmo3 allowed the identification of dentate gyrus/CA3-like, CA1/subicular-like, and medial entorhinal-like comparable sectors in mouse and chicken, and point to the existence of mostly conserved molecular networks involved in hippocampal complex development. Notably, while the mouse medial entorhinal cortex derives from the medial pallium (similarly to the hippocampal formation, both being involved in spatial navigation and spatial memory), the lateral entorhinal cortex (involved in processing non-spatial, contextual information) appears to derive from a distinct dorsolateral caudal pallial sector.
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Affiliation(s)
- Antonio Abellán
- Laboratory of Brain Development and Evolution, Department of Experimental Medicine, Institute of Biomedical Research of Lleida, University of Lleida Lleida, Spain
| | - Ester Desfilis
- Laboratory of Brain Development and Evolution, Department of Experimental Medicine, Institute of Biomedical Research of Lleida, University of Lleida Lleida, Spain
| | - Loreta Medina
- Laboratory of Brain Development and Evolution, Department of Experimental Medicine, Institute of Biomedical Research of Lleida, University of Lleida Lleida, Spain
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Murine Joubert syndrome reveals Hedgehog signaling defects as a potential therapeutic target for nephronophthisis. Proc Natl Acad Sci U S A 2014; 111:9893-8. [PMID: 24946806 DOI: 10.1073/pnas.1322373111] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nephronophthisis (NPHP) is the major cause of pediatric renal failure, yet the disease remains poorly understood, partly due to the lack of appropriate animal models. Joubert syndrome (JBTS) is an inherited ciliopathy giving rise to NPHP with cerebellar vermis aplasia and retinal degeneration. Among patients with JBTS and a cerebello-oculo-renal phenotype, mutations in CEP290 (NPHP6) are the most common genetic lesion. We present a Cep290 gene trap mouse model of JBTS that displays the kidney, eye, and brain abnormalities that define the syndrome. Mutant mice present with cystic kidney disease as neonates. Newborn kidneys contain normal amounts of lymphoid enhancer-binding factor 1 (Lef1) and transcription factor 1 (Tcf1) protein, indicating normal function of the Wnt signaling pathway; however, an increase in the protein Gli3 repressor reveals abnormal Hedgehog (Hh) signaling evident in newborn kidneys. Collecting duct cells from mutant mice have abnormal primary cilia and are unable to form spheroid structures in vitro. Treatment of mutant cells with the Hh agonist purmorphamine restored normal spheroid formation. Renal epithelial cells from a JBTS patient with CEP290 mutations showed similar impairments to spheroid formation that could also be partially rescued by exogenous stimulation of Hh signaling. These data implicate abnormal Hh signaling as the cause of NPHP and suggest that Hh agonists may be exploited therapeutically.
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Chen C, Han S, Meng L, Li Z, Zhang X, Wu A. TERT promoter mutations lead to high transcriptional activity under hypoxia and temozolomide treatment and predict poor prognosis in gliomas. PLoS One 2014; 9:e100297. [PMID: 24937153 PMCID: PMC4061075 DOI: 10.1371/journal.pone.0100297] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/22/2014] [Indexed: 02/07/2023] Open
Abstract
Objective This study explored the effects of telomerase reverse transcriptase (TERT) promoter mutations on transcriptional activity of the TERT gene under hypoxic and temozolomide (TMZ) treatment conditions, and investigated the status and prognostic value of these mutations in gliomas. Methods The effect of TERT promoter mutations on the transcriptional activity of the TERT gene under hypoxic and TMZ treatment conditions was investigated in glioma cells using the luciferase assay. TERT promoter mutations were detected in 101 glioma samples (grades I–IV) and 49 other brain tumors by sequencing. TERT mRNA expression in gliomas was examined by real-time PCR. Hazard ratios from survival analysis of glioma patients were determined relative to the presence of TERT promoter mutations. Results Mutations in the TERT promoter enhanced gene transcription even under hypoxic and TMZ treatment conditions, inducing upregulation of TERT mRNA expression. Mutations were detected in gliomas, but not in meningiomas, pituitary adenomas, cavernomas, intracranial metastases, normal brain tissues, or peripheral blood of glioma patients. Patients with TERT promoter mutations had lower survival rates, even after adjusting for other known or potential risk factors, and the incidence of mutation was correlated with patient age. Conclusion TERT promoter mutations were specific to gliomas. TERT promoter mutations maintained its ability of inducing high transcriptional activity even under hypoxic and TMZ treatment conditions, and the presence of mutations was associated with poor prognosis in glioma patients. These findings demonstrate that TERT promoter mutations are novel prognostic markers for gliomas that can inform prospective therapeutic strategies.
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Affiliation(s)
- Chen Chen
- Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, China
| | - Sheng Han
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lingxuan Meng
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhonghua Li
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xue Zhang
- Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, China
- Department of Medical Genetics, Peking Union Medical University, Peking, China
| | - Anhua Wu
- Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, China
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
- * E-mail:
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Ren H, Yan S, Zhang B, Lu TY, Arancio O, Accili D. Glut4 expression defines an insulin-sensitive hypothalamic neuronal population. Mol Metab 2014; 3:452-9. [PMID: 24944904 PMCID: PMC4060214 DOI: 10.1016/j.molmet.2014.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 04/10/2014] [Indexed: 11/19/2022] Open
Abstract
Insulin signaling in the CNS modulates satiety and glucose metabolism, but insulin target neurons are poorly defined. We have previously shown that ablation of insulin receptors (InsR) in Glut4-expressing tissues results in systemic abnormalities of insulin action. We propose that Glut4 neurons constitute an insulin-sensitive neuronal subset. We determined their gene expression profiles using flow-sorted hypothalamic Glut4 neurons. Gene ontology analyses demonstrated that Glut4 neurons are enriched in olfacto-sensory receptors, M2 acetylcholine receptors, and pathways required for the acquisition of insulin sensitivity. Following genetic ablation of InsR, transcriptome profiling of Glut4 neurons demonstrated impairment of the insulin, peptide hormone, and cAMP signaling pathways, with a striking upregulation of anion homeostasis pathway. Accordingly, hypothalamic InsR-deficient Glut4 neurons showed reduced firing activity. The molecular signature of Glut4 neurons is consistent with a role for this neural population in the integration of olfacto-sensory cues with hormone signaling to regulate peripheral metabolism.
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Affiliation(s)
- Hongxia Ren
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians & Surgeons, New York, NY 10032, USA
| | - Shijun Yan
- Department of Pathology and Cell Biology, Columbia University College of Physicians & Surgeons, New York, NY 10032, USA
| | - Baifang Zhang
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians & Surgeons, New York, NY 10032, USA
| | - Taylor Y. Lu
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians & Surgeons, New York, NY 10032, USA
| | - Ottavio Arancio
- Department of Pathology and Cell Biology, Columbia University College of Physicians & Surgeons, New York, NY 10032, USA
| | - Domenico Accili
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians & Surgeons, New York, NY 10032, USA
- Corresponding author.
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30
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Wisniewska MB. Physiological role of β-catenin/TCF signaling in neurons of the adult brain. Neurochem Res 2013; 38:1144-55. [PMID: 23377854 PMCID: PMC3653035 DOI: 10.1007/s11064-013-0980-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 12/21/2012] [Accepted: 01/19/2013] [Indexed: 12/21/2022]
Abstract
Wnt/β-catenin pathway, the effectors of which are transcription factors of the LEF1/TCF family, is primarily associated with development. Strikingly, however, some of the genes of the pathway are schizophrenia susceptibility genes, and the proteins that are often mutated in neurodegenerative diseases have the ability to regulate β-catenin levels. If impairment of this pathway indeed leads to these pathologies, then it likely plays a physiological role in the adult brain. This review provides an overview of the current knowledge on this subject. The involvement of β-catenin and LEF1/TCF factors in adult neurogenesis, synaptic plasticity, and the function of thalamic neurons are discussed. The data are still very preliminary and often based on circumstantial or indirect evidence. Further research might help to understand the etiology of the aforementioned pathologies.
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Affiliation(s)
- Marta B Wisniewska
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.
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