1
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Mihailovich M, Germain PL, Shyti R, Pozzi D, Noberini R, Liu Y, Aprile D, Tenderini E, Troglio F, Trattaro S, Fabris S, Ciptasari U, Rigoli MT, Caporale N, D’Agostino G, Mirabella F, Vitriolo A, Capocefalo D, Skaros A, Franchini AV, Ricciardi S, Biunno I, Neri A, Nadif Kasri N, Bonaldi T, Aebersold R, Matteoli M, Testa G. Multiscale modeling uncovers 7q11.23 copy number variation-dependent changes in ribosomal biogenesis and neuronal maturation and excitability. J Clin Invest 2024; 134:e168982. [PMID: 39007270 PMCID: PMC11245157 DOI: 10.1172/jci168982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/24/2024] [Indexed: 07/16/2024] Open
Abstract
Copy number variation (CNV) at 7q11.23 causes Williams-Beuren syndrome (WBS) and 7q microduplication syndrome (7Dup), neurodevelopmental disorders (NDDs) featuring intellectual disability accompanied by symmetrically opposite neurocognitive features. Although significant progress has been made in understanding the molecular mechanisms underlying 7q11.23-related pathophysiology, the propagation of CNV dosage across gene expression layers and their interplay remains elusive. Here we uncovered 7q11.23 dosage-dependent symmetrically opposite dynamics in neuronal differentiation and intrinsic excitability. By integrating transcriptomics, translatomics, and proteomics of patient-derived and isogenic induced neurons, we found that genes related to neuronal transmission follow 7q11.23 dosage and are transcriptionally controlled, while translational factors and ribosomal genes are posttranscriptionally buffered. Consistently, we found phosphorylated RPS6 (p-RPS6) downregulated in WBS and upregulated in 7Dup. Surprisingly, p-4EBP was changed in the opposite direction, reflecting dosage-specific changes in total 4EBP levels. This highlights different dosage-sensitive dyregulations of the mTOR pathway as well as distinct roles of p-RPS6 and p-4EBP during neurogenesis. Our work demonstrates the importance of multiscale disease modeling across molecular and functional layers, uncovers the pathophysiological relevance of ribosomal biogenesis in a paradigmatic pair of NDDs, and uncouples the roles of p-RPS6 and p-4EBP as mechanistically actionable relays in NDDs.
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Affiliation(s)
- Marija Mihailovich
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
| | - Pierre-Luc Germain
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Computational Neurogenomics, D-HEST Institute for Neuroscience, Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Reinald Shyti
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
| | - Davide Pozzi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | | | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Davide Aprile
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Flavia Troglio
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Sebastiano Trattaro
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Ummi Ciptasari
- Department of Cognitive Neurosciences, RadboudUmc, Donders Institute for Brain Cognition and Behaviour, Nijmegen, Netherlands
| | - Marco Tullio Rigoli
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicolò Caporale
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | | | - Alessandro Vitriolo
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Daniele Capocefalo
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Adrianos Skaros
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
| | | | - Sara Ricciardi
- Department of Biosciences, University of Milan, Milan, Italy
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Milan, Italy
| | - Ida Biunno
- Integrated Systems Engineering Srl, c/o OpenZone, Bresso, Milan, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Nael Nadif Kasri
- Department of Cognitive Neurosciences, RadboudUmc, Donders Institute for Brain Cognition and Behaviour, Nijmegen, Netherlands
| | - Tiziana Bonaldi
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Rudolf Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Michela Matteoli
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Giuseppe Testa
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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2
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Perycz M, Dabrowski MJ, Jardanowska-Kotuniak M, Roura AJ, Gielniewski B, Stepniak K, Dramiński M, Ciechomska IA, Kaminska B, Wojtas B. Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors. Acta Neuropathol Commun 2024; 12:72. [PMID: 38711090 PMCID: PMC11071216 DOI: 10.1186/s40478-024-01779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The RE1-silencing transcription factor (REST) acts either as a repressor or activator of transcription depending on the genomic and cellular context. REST is a key player in brain cell differentiation by inducing chromatin modifications, including DNA methylation, in a proximity of its binding sites. Its dysfunction may contribute to oncogenesis. Mutations in IDH1/2 significantly change the epigenome contributing to blockade of cell differentiation and glioma development. We aimed at defining how REST modulates gene activation and repression in the context of the IDH mutation-related phenotype in gliomas. We studied the effects of REST knockdown, genome wide occurrence of REST binding sites, and DNA methylation of REST motifs in IDH wild type and IDH mutant gliomas. We found that REST target genes, REST binding patterns, and TF motif occurrence proximal to REST binding sites differed in IDH wild-type and mutant gliomas. Among differentially expressed REST targets were genes involved in glial cell differentiation and extracellular matrix organization, some of which were differentially methylated at promoters or gene bodies. REST knockdown differently impacted invasion of the parental or IDH1 mutant glioma cells. The canonical REST-repressed gene targets showed significant correlation with the GBM NPC-like cellular state. Interestingly, results of REST or KAISO silencing suggested the interplay between these TFs in regulation of REST-activated and repressed targets. The identified gene regulatory networks and putative REST cooperativity with other TFs, such as KAISO, show distinct REST target regulatory networks in IDH-WT and IDH-MUT gliomas, without concomitant DNA methylation changes. We conclude that REST could be an important therapeutic target in gliomas.
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Affiliation(s)
- Malgorzata Perycz
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Michal J Dabrowski
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Jardanowska-Kotuniak
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
- Doctoral School of Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adria-Jaume Roura
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Stepniak
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dramiński
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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3
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Park SJ, Wang IH, Lee N, Jiang HC, Uemura T, Futai K, Kim D, Macosko E, Greer P. Combinatorial expression of neurexin genes regulates glomerular targeting by olfactory sensory neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587570. [PMID: 38617205 PMCID: PMC11014570 DOI: 10.1101/2024.04.01.587570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Precise connectivity between specific neurons is essential for the formation of the complex neural circuitry necessary for executing intricate motor behaviors and higher cognitive functions. While trans -interactions between synaptic membrane proteins have emerged as crucial elements in orchestrating the assembly of these neural circuits, the synaptic surface proteins involved in neuronal wiring remain largely unknown. Here, using unbiased single-cell transcriptomic and mouse genetic approaches, we uncover that the neurexin family of genes enables olfactory sensory neuron (OSNs) axons to form appropriate synaptic connections with their mitral and tufted (M/T) cell synaptic partners, within the mammalian olfactory system. Neurexin isoforms are differentially expressed within distinct populations of OSNs, resulting in unique pattern of neurexin expression that is specific to each OSN type, and synergistically cooperate to regulate axonal innervation, guiding OSN axons to their designated glomeruli. This process is facilitated through the interactions of neurexins with their postsynaptic partners, including neuroligins, which have distinct expression patterns in M/T cells. Our findings suggest a novel mechanism underpinning the precise assembly of olfactory neural circuits, driven by the trans -interaction between neurexins and their ligands.
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Lim B, Domsch K, Mall M, Lohmann I. Canalizing cell fate by transcriptional repression. Mol Syst Biol 2024; 20:144-161. [PMID: 38302581 PMCID: PMC10912439 DOI: 10.1038/s44320-024-00014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Precision in the establishment and maintenance of cellular identities is crucial for the development of multicellular organisms and requires tight regulation of gene expression. While extensive research has focused on understanding cell type-specific gene activation, the complex mechanisms underlying the transcriptional repression of alternative fates are not fully understood. Here, we provide an overview of the repressive mechanisms involved in cell fate regulation. We discuss the molecular machinery responsible for suppressing alternative fates and highlight the crucial role of sequence-specific transcription factors (TFs) in this process. Depletion of these TFs can result in unwanted gene expression and increased cellular plasticity. We suggest that these TFs recruit cell type-specific repressive complexes to their cis-regulatory elements, enabling them to modulate chromatin accessibility in a context-dependent manner. This modulation effectively suppresses master regulators of alternative fate programs and their downstream targets. The modularity and dynamic behavior of these repressive complexes enables a limited number of repressors to canalize and maintain major and minor cell fate decisions at different stages of development.
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Affiliation(s)
- Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany.
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5
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Vaz R, Edwards S, Dueñas-Rey A, Hofmeister W, Lindstrand A. Loss of ctnnd2b affects neuronal differentiation and behavior in zebrafish. Front Neurosci 2023; 17:1205653. [PMID: 37465584 PMCID: PMC10351287 DOI: 10.3389/fnins.2023.1205653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Delta-catenin (CTNND2) is an adhesive junction associated protein belonging to the family of p120 catenins. The human gene is located on the short arm of chromosome 5, the region deleted in Cri-du-chat syndrome (OMIM #123450). Heterozygous loss of CTNND2 has been linked to a wide spectrum of neurodevelopmental disorders such as autism, schizophrenia, and intellectual disability. Here we studied how heterozygous loss of ctnnd2b affects zebrafish embryonic development, and larvae and adult behavior. First, we observed a disorganization of neuronal subtypes in the developing forebrain, namely the presence of ectopic isl1-expressing cells and a local reduction of GABA-positive neurons in the optic recess region. Next, using time-lapse analysis, we found that the disorganized distribution of is1l-expressing forebrain neurons resulted from an increased specification of Isl1:GFP neurons. Finally, we studied the swimming patterns of both larval and adult heterozygous zebrafish and observed an increased activity compared to wildtype animals. Overall, this data suggests a role for ctnnd2b in the differentiation cascade of neuronal subtypes in specific regions of the vertebrate brain, with repercussions in the animal's behavior.
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Affiliation(s)
- Raquel Vaz
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Steven Edwards
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alfredo Dueñas-Rey
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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6
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Veverka P, Brom T, Janovič T, Stojaspal M, Pinkas M, Nováček J, Hofr C. Electron microscopy reveals toroidal shape of master neuronal cell differentiator REST - RE1-silencing transcription factor. Comput Struct Biotechnol J 2022; 21:731-741. [PMID: 36698979 PMCID: PMC9860152 DOI: 10.1016/j.csbj.2022.12.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The RE1-Silencing Transcription factor (REST) is essential for neuronal differentiation. Here, we report the first 18.5-angstrom electron microscopy structure of human REST. The refined electron map suggests that REST forms a torus that can accommodate DNA double-helix in the central hole. Additionally, we quantitatively described REST binding to the canonical DNA sequence of the neuron-restrictive silencer element. We developed protocols for the expression and purification of full-length REST and the shortened variant REST-N62 produced by alternative splicing. We tested the mutual interaction of full-length REST and the splicing variant REST-N62. Revealed structure-function relationships of master neuronal repressor REST will allow finding new biological ways of prevention and treatment of neurodegenerative disorders and diseases.
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Key Words
- CD, circular dichroism
- CoIP, coimmunoprecipitation
- DLS, dynamic light scattering
- Differentiation
- EM
- EM, electron microscopy
- Electron microscopy
- IDRs, intrinsically disordered regions
- NRSE, neuron-restrictive silencer element
- NRSF
- NRSF, neuron-restrictive silencer factor
- Neuron-restrictive silencer factor
- Neuronal
- PCNA, proliferating cell nuclear antigen
- RD1/2, repressor domain 1/2
- RE1, repressor element-1
- RE1-silencing transcription factor
- REST
- REST, RE1-silencing transcription factor
- REST-FL, full-length REST
- REST-N62
- REST-N62, splicing isoform of REST, also known as REST4 or REST4-S3
- REST4
- ZF, zinc finger
- aa, amino acid(s)
- bp, base pair(s)
- kDa, kilodaltons
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Affiliation(s)
- Pavel Veverka
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | - Tomáš Brom
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Tomáš Janovič
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Martin Stojaspal
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | | | - Jiří Nováček
- CEITEC, Masaryk University, Brno, Czech Republic
| | - Ctirad Hofr
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Corresponding author.
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7
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Kimura R, U Inoue Y, Kikkawa T, Tatehana M, Morimoto Y, Inada H, Oki S, Inoue T, Osumi N. Detection of REST expression in the testis using epitope-tag knock-in mice generated by genome editing. Dev Dyn 2021; 251:525-535. [PMID: 34542211 DOI: 10.1002/dvdy.417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/27/2021] [Accepted: 08/30/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Repressor element 1-silencing transcription factor (REST) is a master regulator that is highly expressed in multipotent stem cells to repress gene networks involving a wide range of biological processes. A recent study has suggested that REST might be involved in a misregulation of its target genes in the embryonic brain of offspring derived from aged fathers. However, detailed analyses of the REST function in spermatogenesis are lacking due to difficulty in the detection of REST protein in specific cell types. RESULTS To determine localization of REST, we generated an epitope tag knock-in (KI) mouse line with the C-terminus insertion of a podoplanin (PA)-tag at an endogenous Rest locus by the CRISPR/Cas9 system. Localization of the PA-tag was confirmed in neural stem cells marked with Pax6 in the embryonic brain. Moreover, PA-tagged REST was detected in undifferentiated and differentiating spermatogonia as well as Sertoli cells in both neonatal and adult testes. CONCLUSIONS We demonstrate that REST is expressed at the early step of spermatogenesis and suggest a possibility that REST may modulate the epigenetic state of male germline cells. Our KI mice may be useful for studying REST-associated molecular mechanisms of neurodevelopmental and age-related disorders.
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Affiliation(s)
- Ryuichi Kimura
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takako Kikkawa
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Misako Tatehana
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yuki Morimoto
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Hitoshi Inada
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Laboratory of Health and Sports Sciences, Division of Biomedical Engineering for Health and Welfare Tohoku University Graduate School of Biomedical Engineering, Sendai, Miyagi, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
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8
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Hol JA, Diets IJ, de Krijger RR, van den Heuvel-Eibrink MM, Jongmans MC, Kuiper RP. TRIM28 variants and Wilms' tumour predisposition. J Pathol 2021; 254:494-504. [PMID: 33565090 PMCID: PMC8252630 DOI: 10.1002/path.5639] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/22/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
TRIM28 was recently identified as a Wilms' tumour (WT) predisposition gene, with germline pathogenic variants identified in around 1% of isolated and 8% of familial WT cases. TRIM28 variants are associated with epithelial WT, but the presence of other tumour components or anaplasia does not exclude the presence of a germline or somatic TRIM28 variant. In children with WT, TRIM28 acts as a classical tumour suppressor gene, with both alleles generally disrupted in the tumour. Therefore, loss of TRIM28 (KAP1/TIF1beta) protein expression in tumour tissue by immunohistochemistry is an effective strategy to identify patients carrying pathogenic TRIM28 variants. TRIM28 is a ubiquitously expressed corepressor that binds transcription factors in a context‐, species‐, and cell‐type‐specific manner to control the expression of genes and transposable elements during embryogenesis and cellular differentiation. In this review, we describe the inheritance patterns, histopathological and clinical features of TRIM28‐associated WT, as well as potential underlying mechanisms of tumourigenesis during embryonic kidney development. Recognizing germline TRIM28 variants in patients with WT can enable counselling, genetic testing, and potential early detection of WT in other children in the family. A further exploration of TRIM28‐associated WT will help to unravel the diverse and complex mechanisms underlying WT development. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Janna A Hol
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Marjolijn Cj Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht/Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht/Wilhelmina Children's Hospital, Utrecht, The Netherlands
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9
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Garcia-Manteiga JM, D’Alessandro R, Meldolesi J. News about the Role of the Transcription Factor REST in Neurons: From Physiology to Pathology. Int J Mol Sci 2019; 21:E235. [PMID: 31905747 PMCID: PMC6982158 DOI: 10.3390/ijms21010235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
RE-1 silencing transcription factor (REST) (known also as NRSF) is a well-known transcription repressor whose strong decrease induces the distinction of neurons with respect to the other cells. Such distinction depends on the marked increased/decreased expression of specific genes, accompanied by parallel changes of the corresponding proteins. Many properties of REST had been identified in the past. Here we report those identified during the last 5 years. Among physiological discoveries are hundreds of genes governed directly/indirectly by REST, the mechanisms of its neuron/fibroblast conversions, and the cooperations with numerous distinct factors induced at the epigenetic level and essential for REST specific functions. New effects induced in neurons during brain diseases depend on the localization of REST, in the nucleus, where functions and toxicity occur, and in the cytoplasm. The effects of REST, including cell aggression or protection, are variable in neurodegenerative diseases in view of the distinct mechanisms of their pathology. Moreover, cooperations are among the mechanisms that govern the severity of brain cancers, glioblastomas, and medulloblastomas. Interestingly, the role in cancers is relevant also for therapeutic perspectives affecting the REST cooperations. In conclusion, part of the new REST knowledge in physiology and pathology appears promising for future developments in research and brain diseases.
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Affiliation(s)
| | | | - Jacopo Meldolesi
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy;
- Department of Neuroscience, San Raffaele University, via Olgettina 58, 20132 Milan, Italy
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10
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Labrecque MP, Coleman IM, Brown LG, True LD, Kollath L, Lakely B, Nguyen HM, Yang YC, da Costa RMG, Kaipainen A, Coleman R, Higano CS, Yu EY, Cheng HH, Mostaghel EA, Montgomery B, Schweizer MT, Hsieh AC, Lin DW, Corey E, Nelson PS, Morrissey C. Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer. J Clin Invest 2019; 129:4492-4505. [PMID: 31361600 DOI: 10.1172/jci128212] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease with diverse drivers of disease progression and mechanisms of therapeutic resistance. We conducted deep phenotypic characterization of CRPC metastases and patient-derived xenograft (PDX) lines using whole genome RNA sequencing, gene set enrichment analysis and immunohistochemistry. Our analyses revealed five mCRPC phenotypes based on the expression of well-characterized androgen receptor (AR) or neuroendocrine (NE) genes: (i) AR-high tumors (ARPC), (ii) AR-low tumors (ARLPC), (iii) amphicrine tumors composed of cells co-expressing AR and NE genes (AMPC), (iv) double-negative tumors (i.e. AR-/NE-; DNPC) and (v) tumors with small cell or NE gene expression without AR activity (SCNPC). RE1-silencing transcription factor (REST) activity, which suppresses NE gene expression, was lost in AMPC and SCNPC PDX models. However, knockdown of REST in cell lines revealed that attenuated REST activity drives the AMPC phenotype but is not sufficient for SCNPC conversion. We also identified a subtype of DNPC tumors with squamous differentiation and generated an encompassing 26-gene transcriptional signature that distinguished the five mCRPC phenotypes. Together, our data highlight the central role of AR and REST in classifying treatment-resistant mCRPC phenotypes. These molecular classifications could potentially guide future therapeutic studies and clinical trial design.
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Affiliation(s)
- Mark P Labrecque
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Ilsa M Coleman
- Divison of Human Biology and.,Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lisha G Brown
- Department of Urology, University of Washington, Seattle, Washington, USA
| | | | - Lori Kollath
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Bryce Lakely
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Yu C Yang
- Divison of Human Biology and.,Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rui M Gil da Costa
- Divison of Human Biology and.,Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Arja Kaipainen
- Divison of Human Biology and.,Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Roger Coleman
- Divison of Human Biology and.,Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Celestia S Higano
- Department of Urology, University of Washington, Seattle, Washington, USA.,Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
| | - Evan Y Yu
- Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
| | - Heather H Cheng
- Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
| | - Elahe A Mostaghel
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA.,Geriatric Research, Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
| | - Bruce Montgomery
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA.,Geriatric Research, Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
| | - Michael T Schweizer
- Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
| | - Andrew C Hsieh
- Divison of Human Biology and.,Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
| | - Daniel W Lin
- Department of Urology, University of Washington, Seattle, Washington, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Peter S Nelson
- Divison of Human Biology and.,Divison of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington, USA
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11
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The interaction between RE1-silencing transcription factor (REST) and heat shock protein 90 as new therapeutic target against Huntington's disease. PLoS One 2019; 14:e0220393. [PMID: 31361762 PMCID: PMC6667143 DOI: 10.1371/journal.pone.0220393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/14/2019] [Indexed: 12/18/2022] Open
Abstract
The wild type huntingtin protein (Htt), supports the production of brain-derived neurotrophic factor (BDNF), a survival factor for striatal neurons, through cytoplasmic sequestering of RE-1silencing transcription factor (REST). In Huntington´s Disease an inherited degenerative disease, caused by a CAG expansion in the 5´coding region of the gene, the mutant huntingtin protein (mHtt), causes that REST enters pathologically into the nucleus of cells, resulting in the repression of neuronal genes including BDNF, resulting in the progressive neuronal death. It has been reported that Htt associates with Hsp90 and this interaction is involved in regulation of huntingtin aggregation. Discovering mechanisms to reduce the cellular levels of mutant huntingtin and REST provide promising strategies for treating Huntington disease. Here, we use the yeast two-hybrid system to show that N-terminus or REST interacts with the heat shock protein 90 (Hsp90) and identifies REST as an Hsp90 Client Protein. To assess the effects of Hsp90 we used antisense oligonucleotide, and evaluated the levels mHtt and REST levels. Our results show that direct knockdown of endogenous Hsp90 significantly reduces the levels of REST and mutant Huntingtin, decreased the percentage of cells with mHtt in nucleus and rescued cells from mHtt-induced cellular cytotoxicity. Additionally Hsp90–specific inhibitors geldanamicyn and PUH71 dramatically reduced mHtt and REST levels, thereby providing neuroprotective activity. Our data show that Hsp90 is necessary to maintain the levels of REST and mHtt, which suggests that the interactions between Hsp90-REST and Hsp90-Huntingtin could be potential therapeutic targets in Huntington's disease.
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12
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Kang HJ, Park H, Yoo EJ, Lee JH, Choi SY, Lee-Kwon W, Lee KY, Hur JH, Seo JK, Ra JS, Lee EA, Myung K, Kwon HM. TonEBP Regulates PCNA Polyubiquitination in Response to DNA Damage through Interaction with SHPRH and USP1. iScience 2019; 19:177-190. [PMID: 31376680 PMCID: PMC6677787 DOI: 10.1016/j.isci.2019.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/13/2019] [Accepted: 07/15/2019] [Indexed: 12/16/2022] Open
Abstract
Polyubiquitination of proliferating cell nuclear antigen (PCNA) regulates the error-free template-switching mechanism for the bypass of DNA lesions during DNA replication. PCNA polyubiquitination is critical for the maintenance of genomic integrity; however, the underlying mechanism is poorly understood. Here, we demonstrate that tonicity-responsive enhancer-binding protein (TonEBP) regulates PCNA polyubiquitination in response to DNA damage. TonEBP was recruited to DNA damage sites with bulky adducts and sequentially recruited E3 ubiquitin ligase SHPRH, followed by deubiquitinase USP1, to DNA damage sites, in correlation with the dynamics of PCNA polyubiquitination. Similarly, TonEBP was found to be required for replication fork protection in response to DNA damage. The Rel-homology domain of TonEBP, which encircles DNA, was essential for the interaction with SHPRH and USP1, PCNA polyubiquitination, and cell survival after DNA damage. The present findings suggest that TonEBP is an upstream regulator of PCNA polyubiquitination and of the DNA damage bypass pathway.
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Affiliation(s)
- Hyun Je Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyun Park
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eun Jin Yoo
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jun Ho Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Soo Youn Choi
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Whaseon Lee-Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Jin-Hoe Hur
- UNIST-Optical Biomed Imaging Center (UOBC), Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Eun-A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Hyug Moo Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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13
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Ning Z, Williams JM, Kumari R, Baranov PV, Moore T. Opposite Expression Patterns of Spry3 and p75NTR in Cerebellar Vermis Suggest a Male-Specific Mechanism of Autism Pathogenesis. Front Psychiatry 2019; 10:416. [PMID: 31275178 PMCID: PMC6591651 DOI: 10.3389/fpsyt.2019.00416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/24/2019] [Indexed: 12/22/2022] Open
Abstract
Autism is a genetically complex neurobehavioral disorder with a population prevalence of more than 1%. Cerebellar abnormalities, including Purkinje cell deficits in the vermis, are consistently reported, and rodent models of cerebellar dysfunction exhibit features analogous to human autism. We previously analyzed the regulation and expression of the pseudoautosomal region 2 gene SPRY3, which is adjacent to X chromosome-linked TMLHE, a known autism susceptibility gene. SPRY3 is a regulator of branching morphogenesis and is strongly expressed in Purkinje cells. We previously showed that mouse Spry3 is not expressed in cerebellar vermis lobules VI-VII and X, regions which exhibit significant Purkinje cell loss or abnormalities in autism. However, these lobules have relatively high expression of p75NTR, which encodes a neurotrophin receptor implicated in autism. We propose a mechanism whereby inappropriate SPRY3 expression in these lobules could interact with TrkB and p75NTR signaling pathways resulting in Purkinje cell pathology. We report preliminary characterization of X and Y chromosome-linked regulatory sequences upstream of SPRY3, which are polymorphic in the general population. We suggest that an OREG-annotated region on chromosome Yq12 ∼60 kb from SPRY3 acts as a silencer of Y-linked SPRY3 expression. Deletion of a β-satellite repeat, or alterations in chromatin structure in this region due to trans-acting factors, could affect the proposed silencing function, leading to reactivation and inappropriate expression of Y-linked SPRY3. This proposed male-specific mechanism could contribute to the male bias in autism prevalence.
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Affiliation(s)
| | | | | | | | - Tom Moore
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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14
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Wang R, Wang Y, Zhang X, Zhang Y, Du X, Fang Y, Li G. Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. BMC Genomics 2019; 20:296. [PMID: 32039697 PMCID: PMC7226942 DOI: 10.1186/s12864-019-5535-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and promoters in linear DNA (1D). Enhancers and promoters are fundamental non-coding elements enriched with transcription factors (TFs) to form chromatin loops. However, the specific cooperation of TFs involved in forming chromatin loops is not fully understood. Results Here, we proposed a method for investigating the cooperation of TFs in four cell lines by the integrative analysis of DNA sequences, ChIP-Seq and ChIA-PET data. Results demonstrate that the interaction of enhancers and promoters is a hierarchical and dynamic complex process with cooperative interactions of different TFs synergistically regulating gene expression and chromatin structure. The TF cooperation involved in maintaining and regulating the chromatin loop of cells can be regulated by epigenetic factors, such as other TFs and DNA methylation. Conclusions Such cooperation among TFs provides the potential features that can affect chromatin’s 3D architecture in cells. The regulation of chromatin 3D organization and gene expression is a complex process associated with the hierarchical and dynamic prosperities of TFs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5535-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruimin Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Yunlong Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Xueying Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Yaliang Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Xiaoyong Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China.,Huazhong Agricultural University, Wuhan, 430070, China
| | - Yaping Fang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China. .,Huazhong Agricultural University, Wuhan, 430070, China. .,College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China. .,Huazhong Agricultural University, Wuhan, 430070, China. .,College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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15
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Diets IJ, Hoyer J, Ekici AB, Popp B, Hoogerbrugge N, van Reijmersdal SV, Bhaskaran R, Hadjihannas M, Vasileiou G, Thiel CT, Seven D, Uebe S, Ilencikova D, Waanders E, Mavinkurve-Groothuis AMC, Roeleveld N, de Krijger RR, Wegert J, Graf N, Vokuhl C, Agaimy A, Gessler M, Reis A, Kuiper RP, Jongmans MCJ, Metzler M. TRIM28 haploinsufficiency predisposes to Wilms tumor. Int J Cancer 2019; 145:941-951. [PMID: 30694527 DOI: 10.1002/ijc.32167] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/08/2018] [Accepted: 01/15/2019] [Indexed: 12/21/2022]
Abstract
Two percent of patients with Wilms tumors have a positive family history. In many of these cases the genetic cause remains unresolved. By applying germline exome sequencing in two families with two affected individuals with Wilms tumors, we identified truncating mutations in TRIM28. Subsequent mutational screening of germline and tumor DNA of 269 children affected by Wilms tumor was performed, and revealed seven additional individuals with germline truncating mutations, and one individual with a somatic truncating mutation in TRIM28. TRIM28 encodes a complex scaffold protein involved in many different processes, including gene silencing, DNA repair and maintenance of genomic integrity. Expression studies on mRNA and protein level showed reduction of TRIM28, confirming a loss-of-function effect of the mutations identified. The tumors showed an epithelial-type histology that stained negative for TRIM28 by immunohistochemistry. The tumors were bilateral in six patients, and 10/11 tumors are accompanied by perilobar nephrogenic rests. Exome sequencing on eight tumor DNA samples from six individuals showed loss-of-heterozygosity (LOH) of the TRIM28-locus by mitotic recombination in seven tumors, suggesting that TRIM28 functions as a tumor suppressor gene in Wilms tumor development. Additionally, the tumors showed very few mutations in known Wilms tumor driver genes, suggesting that loss of TRIM28 is the main driver of tumorigenesis. In conclusion, we identified heterozygous germline truncating mutations in TRIM28 in 11 children with mainly epithelial-type Wilms tumors, which become homozygous in tumor tissue. These data establish TRIM28 as a novel Wilms tumor predisposition gene, acting as a tumor suppressor gene by LOH.
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Affiliation(s)
- Illja J Diets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Juliane Hoyer
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Arif B Ekici
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Bernt Popp
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Simon V van Reijmersdal
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Rajith Bhaskaran
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Michel Hadjihannas
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Georgia Vasileiou
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Christian T Thiel
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Didem Seven
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany.,Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Steffen Uebe
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Denisa Ilencikova
- Department of Pediatrics, Children's University Hospital, Comenius University, Bratislava, Slovakia
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.,Department of Pediatrics, Radboudumc Amalia's Children's Hospital, Nijmegen, The Netherlands
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Norbert Graf
- Department of Pediatric Hematology and Oncology, Saarland University, Medical Center Homburg/Saar, Homburg, Germany
| | - Christian Vokuhl
- Kiel Pediatric Tumor Registry, Section of Pediatric Pathology, Department of Pathology, Christian Albrechts University, Kiel, Germany
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - André Reis
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Markus Metzler
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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16
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Halliday BJ, Fukuzawa R, Markie DM, Grundy RG, Ludgate JL, Black MA, Skeen JE, Weeks RJ, Catchpoole DR, Roberts AGK, Reeve AE, Morison IM. Germline mutations and somatic inactivation of TRIM28 in Wilms tumour. PLoS Genet 2018; 14:e1007399. [PMID: 29912901 PMCID: PMC6005459 DOI: 10.1371/journal.pgen.1007399] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
Wilms tumour is a childhood tumour that arises as a consequence of somatic and rare germline mutations, the characterisation of which has refined our understanding of nephrogenesis and carcinogenesis. Here we report that germline loss of function mutations in TRIM28 predispose children to Wilms tumour. Loss of function of this transcriptional co-repressor, which has a role in nephrogenesis, has not previously been associated with cancer. Inactivation of TRIM28, either germline or somatic, occurred through inactivating mutations, loss of heterozygosity or epigenetic silencing. TRIM28-mutated tumours had a monomorphic epithelial histology that is uncommon for Wilms tumour. Critically, these tumours were negative for TRIM28 immunohistochemical staining whereas the epithelial component in normal tissue and other Wilms tumours stained positively. These data, together with a characteristic gene expression profile, suggest that inactivation of TRIM28 provides the molecular basis for defining a previously described subtype of Wilms tumour, that has early age of onset and excellent prognosis. The germline and somatic molecular events associated with Wilms tumour, a childhood kidney cancer, have been progressively defined over the past three decades. Among the uncharacterised tumours are a group of tumours that have monomorphic epithelial histology, familial association, distinctively clustered gene-expression patterns, early age of diagnosis, and excellent prognosis. Here, we describe germline mutations and loss of function of TRIM28 in familial Wilms tumours, along with somatic loss of function in a non-familial Wilms tumour. All TRIM28-mutant tumours showed the rare monomorphic epithelial histology, suggesting that loss of TRIM28 expression could be a useful marker to define a group of tumours with excellent prognosis. Future studies could lead to identification and reassurance of families that carry TRIM28 mutations, and to the use of reduced intensity of treatment for children who develop TRIM28-null tumours.
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Affiliation(s)
- Benjamin J. Halliday
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Ryuji Fukuzawa
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Department of Pathology, International University of Health and Welfare, School of Medicine, Narita, Japan
| | - David M. Markie
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Richard G. Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Jackie L. Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael A. Black
- Cancer Genetics Laboratory, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Robert J. Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Daniel R. Catchpoole
- Tumour Bank, Children’s Cancer Research Unit, The Children’s Hospital at Westmead, Westmead, NSW, Australia
| | - Aedan G. K. Roberts
- Tumour Bank, Children’s Cancer Research Unit, The Children’s Hospital at Westmead, Westmead, NSW, Australia
| | - Anthony E. Reeve
- Cancer Genetics Laboratory, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ian M. Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- * E-mail:
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17
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Mozzi A, Guerini FR, Forni D, Costa AS, Nemni R, Baglio F, Cabinio M, Riva S, Pontremoli C, Clerici M, Sironi M, Cagliani R. REST, a master regulator of neurogenesis, evolved under strong positive selection in humans and in non human primates. Sci Rep 2017; 7:9530. [PMID: 28842657 PMCID: PMC5573535 DOI: 10.1038/s41598-017-10245-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/07/2017] [Indexed: 12/03/2022] Open
Abstract
The transcriptional repressor REST regulates many neuronal genes by binding RE1 motifs. About one third of human RE1s are recently evolved and specific to primates. As changes in the activity of a transcription factor reverberate on its downstream targets, we assessed whether REST displays fast evolutionary rates in primates. We show that REST was targeted by very strong positive selection during primate evolution. Positive selection was also evident in the human lineage, with six selected sites located in a region that surrounds a VNTR in exon 4. Analysis of expression data indicated that REST brain expression peaks during aging in humans but not in other primates. Because a REST coding variant (rs3796529) was previously associated with protection from hippocampal atrophy in elderly subjects with mild cognitive impairment (MCI), we analyzed a cohort of Alzheimer disease (AD) continuum patients. Genotyping of two coding variants (rs3796529 and rs2227902) located in the region surrounding the VNTR indicated a role for rs2227902 in modulation of hippocampal volume loss, indirectly confirming a role for REST in neuroprotection. Experimental studies will be instrumental to determine the functional effect of positively selected sites in REST and the role of REST variants in neuropreservation/neurodegeneration.
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Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | | | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | | | | | | | - Monia Cabinio
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20148, Milan, Italy
| | - Stefania Riva
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Mario Clerici
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20148, Milan, Italy.,Department of Physiopathology and Transplantation, University of Milan, 20090, Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy.
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