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Sekerková G, Kilic S, Cheng YH, Fredrick N, Osmani A, Kim H, Opal P, Martina M. Phenotypical, genotypical and pathological characterization of the moonwalker mouse, a model of ataxia. Neurobiol Dis 2024; 195:106492. [PMID: 38575093 PMCID: PMC11089908 DOI: 10.1016/j.nbd.2024.106492] [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: 11/01/2023] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
We performed a comprehensive study of the morphological, functional, and genetic features of moonwalker (MWK) mice, a mouse model of spinocerebellar ataxia caused by a gain of function of the TRPC3 channel. These mice show numerous behavioral symptoms including tremor, altered gait, circling behavior, impaired motor coordination, impaired motor learning and decreased limb strength. Cerebellar pathology is characterized by early and almost complete loss of unipolar brush cells as well as slowly progressive, moderate loss of Purkinje cell (PCs). Structural damage also includes loss of synaptic contacts from parallel fibers, swollen ER structures, and degenerating axons. Interestingly, no obvious correlation was observed between PC loss and severity of the symptoms, as the phenotype stabilizes around 2 months of age, while the cerebellar pathology is progressive. This is probably due to the fact that PC function is severely impaired much earlier than the appearance of PC loss. Indeed, PC firing is already impaired in 3 weeks old mice. An interesting feature of the MWK pathology that still remains to be explained consists in a strong lobule selectivity of the PC loss, which is puzzling considering that TRPC is expressed in every PC. Intriguingly, genetic analysis of MWK cerebella shows, among other alterations, changes in the expression of both apoptosis inducing and resistance factors possibly suggesting that damaged PCs initiate specific cellular pathways that protect them from overt cell loss.
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Affiliation(s)
- Gabriella Sekerková
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA.
| | - Sumeyra Kilic
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Yen-Hsin Cheng
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Natalie Fredrick
- Department of Neurology, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Anne Osmani
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Haram Kim
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Puneet Opal
- Department of Neurology, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Marco Martina
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA.
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2
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Nazeen S, Wang X, Zielinski D, Lam I, Hallacli E, Xu P, Ethier E, Strom R, Zanella CA, Nithianandam V, Ritter D, Henderson A, Saurat N, Afroz J, Nutter-Upham A, Benyamini H, Copty J, Ravishankar S, Morrow A, Mitchel J, Neavin D, Gupta R, Farbehi N, Grundman J, Myers RH, Scherzer CR, Trojanowski JQ, Van Deerlin VM, Cooper AA, Lee EB, Erlich Y, Lindquist S, Peng J, Geschwind DH, Powell J, Studer L, Feany MB, Sunyaev SR, Khurana V. Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583145. [PMID: 38496508 PMCID: PMC10942362 DOI: 10.1101/2024.03.03.583145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Whether neurodegenerative diseases linked to misfolding of the same protein share genetic risk drivers or whether different protein-aggregation pathologies in neurodegeneration are mechanistically related remains uncertain. Conventional genetic analyses are underpowered to address these questions. Through careful selection of patients based on protein aggregation phenotype (rather than clinical diagnosis) we can increase statistical power to detect associated variants in a targeted set of genes that modify proteotoxicities. Genetic modifiers of alpha-synuclein (ɑS) and beta-amyloid (Aβ) cytotoxicity in yeast are enriched in risk factors for Parkinson's disease (PD) and Alzheimer's disease (AD), respectively. Here, along with known AD/PD risk genes, we deeply sequenced exomes of 430 ɑS/Aβ modifier genes in patients across alpha-synucleinopathies (PD, Lewy body dementia and multiple system atrophy). Beyond known PD genes GBA1 and LRRK2, rare variants AD genes (CD33, CR1 and PSEN2) and Aβ toxicity modifiers involved in RhoA/actin cytoskeleton regulation (ARGHEF1, ARHGEF28, MICAL3, PASK, PKN2, PSEN2) were shared risk factors across synucleinopathies. Actin pathology occurred in iPSC synucleinopathy models and RhoA downregulation exacerbated ɑS pathology. Even in sporadic PD, the expression of these genes was altered across CNS cell types. Genome-wide CRISPR screens revealed the essentiality of PSEN2 in both human cortical and dopaminergic neurons, and PSEN2 mutation carriers exhibited diffuse brainstem and cortical synucleinopathy independent of AD pathology. PSEN2 contributes to a common-risk signal in PD GWAS and regulates ɑS expression in neurons. Our results identify convergent mechanisms across synucleinopathies, some shared with AD.
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Affiliation(s)
- Sumaiya Nazeen
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Xinyuan Wang
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dina Zielinski
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Whitehead Institute of Biomedical Research, Cambridge, MA, USA
| | - Isabel Lam
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Erinc Hallacli
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ping Xu
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth Ethier
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ronya Strom
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Camila A Zanella
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vanitha Nithianandam
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dylan Ritter
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Alexander Henderson
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Nathalie Saurat
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Jalwa Afroz
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | | | - Hadar Benyamini
- Whitehead Institute of Biomedical Research, Cambridge, MA, USA
| | - Joseph Copty
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Autumn Morrow
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jonathan Mitchel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA
| | - Drew Neavin
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Renuka Gupta
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Nona Farbehi
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jennifer Grundman
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Clemens R Scherzer
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivianna M Van Deerlin
- Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Antony A Cooper
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Yaniv Erlich
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Susan Lindquist
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joseph Powell
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vikram Khurana
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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3
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El Badaoui L, Barr AJ. Analysis of Receptor-Type Protein Tyrosine Phosphatase Extracellular Regions with Insights from AlphaFold. Int J Mol Sci 2024; 25:820. [PMID: 38255894 PMCID: PMC10815196 DOI: 10.3390/ijms25020820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The receptor-type protein tyrosine phosphatases (RPTPs) are involved in a wide variety of physiological functions which are mediated via their diverse extracellular regions. They play key roles in cell-cell contacts, bind various ligands and are regulated by dimerization and other processes. Depending on the subgroup, they have been described as everything from 'rigid rods' to 'floppy tentacles'. Here, we review current experimental structural knowledge on the extracellular region of RPTPs and draw on AlphaFold structural predictions to provide further insights into structure and function of these cellular signalling molecules, which are often mutated in disease and are recognised as drug targets. In agreement with experimental data, AlphaFold predicted structures for extracellular regions of R1, and R2B subgroup RPTPs have an extended conformation, whereas R2B RPTPs are twisted, reflecting their high flexibility. For the R3 PTPs, AlphaFold predicts that members of this subgroup adopt an extended conformation while others are twisted, and that certain members, such as CD148, have one or more large, disordered loop regions in place of fibronectin type 3 domains suggested by sequence analysis.
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Affiliation(s)
| | - Alastair J. Barr
- School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK;
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4
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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5
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Nunes-Xavier CE, Zaldumbide L, Mosteiro L, López-Almaraz R, García de Andoin N, Aguirre P, Emaldi M, Torices L, López JI, Pulido R. Protein Tyrosine Phosphatases in Neuroblastoma: Emerging Roles as Biomarkers and Therapeutic Targets. Front Cell Dev Biol 2021; 9:811297. [PMID: 34957126 PMCID: PMC8692838 DOI: 10.3389/fcell.2021.811297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
Neuroblastoma is a type of cancer intimately related with early development and differentiation of neuroendocrine cells, and constitutes one of the pediatric cancers with higher incidence and mortality. Protein tyrosine phosphatases (PTPs) are key regulators of cell growth and differentiation by their direct effect on tyrosine dephosphorylation of specific protein substrates, exerting major functions in the modulation of intracellular signaling during neuron development in response to external cues driving cell proliferation, survival, and differentiation. We review here the current knowledge on the role of PTPs in neuroblastoma cell growth, survival, and differentiation. The potential of PTPs as biomarkers and molecular targets for inhibition in neuroblastoma therapies is discussed.
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Affiliation(s)
- Caroline E. Nunes-Xavier
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- *Correspondence: Caroline E. Nunes-Xavier, ; Rafael Pulido,
| | - Laura Zaldumbide
- Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | - Lorena Mosteiro
- Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | | | | | - Pablo Aguirre
- Department of Pathology, Donostia University Hospital, San Sebastian, Spain
| | - Maite Emaldi
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Leire Torices
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - José I. López
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- *Correspondence: Caroline E. Nunes-Xavier, ; Rafael Pulido,
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6
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Chapman RM, Tinsley CL, Hill MJ, Forrest MP, Tansey KE, Pardiñas AF, Rees E, Doyle AM, Wilkinson LS, Owen MJ, O’Donovan MC, Blake DJ. Convergent Evidence That ZNF804A Is a Regulator of Pre-messenger RNA Processing and Gene Expression. Schizophr Bull 2019; 45:1267-1278. [PMID: 30597088 PMCID: PMC6811834 DOI: 10.1093/schbul/sby183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies have linked common variation in ZNF804A with an increased risk of schizophrenia. However, little is known about the biology of ZNF804A and its role in schizophrenia. Here, we investigate the function of ZNF804A using a variety of complementary molecular techniques. We show that ZNF804A is a nuclear protein that interacts with neuronal RNA splicing factors and RNA-binding proteins including RBFOX1, which is also associated with schizophrenia, CELF3/4, components of the ubiquitin-proteasome system and the ZNF804A paralog, GPATCH8. GPATCH8 also interacts with splicing factors and is localized to nuclear speckles indicative of a role in pre-messenger RNA (mRNA) processing. Sequence analysis showed that GPATCH8 contains ultraconserved, alternatively spliced poison exons that are also regulated by RBFOX proteins. ZNF804A knockdown in SH-SY5Y cells resulted in robust changes in gene expression and pre-mRNA splicing converging on pathways associated with nervous system development, synaptic contact, and cell adhesion. We observed enrichment (P = 1.66 × 10-9) for differentially spliced genes in ZNF804A-depleted cells among genes that contain RBFOX-dependent alternatively spliced exons. Differentially spliced genes in ZNF804A-depleted cells were also enriched for genes harboring de novo loss of function mutations in autism spectrum disorder (P = 6.25 × 10-7, enrichment 2.16) and common variant alleles associated with schizophrenia (P = .014), bipolar disorder and schizophrenia (P = .003), and autism spectrum disorder (P = .005). These data suggest that ZNF804A and its paralogs may interact with neuronal-splicing factors and RNA-binding proteins to regulate the expression of a subset of synaptic and neurodevelopmental genes.
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Affiliation(s)
- Ria M Chapman
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Caroline L Tinsley
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Matthew J Hill
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Marc P Forrest
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,Present address: Department of Physiology, Feinberg School of Medicine, Northwestern University, Ward, Chicago, IL 60611
| | - Katherine E Tansey
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Antonio F Pardiñas
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Elliott Rees
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - A Michelle Doyle
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Lawrence S Wilkinson
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,School of Psychology, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael C O’Donovan
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Derek J Blake
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,To whom correspondence should be addressed; tel: 44(0)2920 688468, fax: +44(0)29 2068 7068, e-mail:
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7
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Reimer C, Rubin CJ, Sharifi AR, Ha NT, Weigend S, Waldmann KH, Distl O, Pant SD, Fredholm M, Schlather M, Simianer H. Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. BMC Genomics 2018; 19:687. [PMID: 30231878 PMCID: PMC6146782 DOI: 10.1186/s12864-018-5009-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022] Open
Abstract
Background Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in “SweepFinder”, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. Conclusion The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region. Electronic supplementary material The online version of this article (10.1186/s12864-018-5009-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany. .,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.
| | - C-J Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedicinska centrum BMC, Husargatan 3, 75237, Uppsala, Sweden
| | - A R Sharifi
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - N-T Ha
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - S Weigend
- Institute of Farm Animal Genetics of the Friedrich-Loeffler-Institut, Höltystraße 10, 31535, Neustadt-Mariensee, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - K-H Waldmann
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine - Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - O Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine - Foundation, Bünteweg 17p, 30559, Hannover, Germany
| | - S D Pant
- Graham Centre for Agricultural Innovation, School of Animal & Veterinary Sciences, Charles Sturt University, Locked Bag 588, Boorooma St., Wagga Wagga, NSW, Australia
| | - M Fredholm
- Department of Veterinary- and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
| | - M Schlather
- School of Business Informatics and Mathematics, University of Mannheim, A5 6, 68131, Mannheim, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - H Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
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8
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Pei J, Grishin NV. Expansion of divergent SEA domains in cell surface proteins and nucleoporin 54. Protein Sci 2017; 26:617-630. [PMID: 27977898 DOI: 10.1002/pro.3096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022]
Abstract
SEA (sea urchin sperm protein, enterokinase, agrin) domains, many of which possess autoproteolysis activity, have been found in a number of cell surface and secreted proteins. Despite high sequence divergence, SEA domains were also proposed to be present in dystroglycan based on a conserved autoproteolysis motif and receptor-type protein phosphatase IA-2 based on structural similarity. The presence of a SEA domain adjacent to the transmembrane segment appears to be a recurring theme in quite a number of type I transmembrane proteins on the cell surface, such as MUC1, dystroglycan, IA-2, and Notch receptors. By comparative sequence and structural analyses, we identified dystroglycan-like proteins with SEA domains in Capsaspora owczarzaki of the Filasterea group, one of the closest single-cell relatives of metazoans. We also detected novel and divergent SEA domains in a variety of cell surface proteins such as EpCAM, α/ε-sarcoglycan, PTPRR, collectrin/Tmem27, amnionless, CD34, KIAA0319, fibrocystin-like protein, and a number of cadherins. While these proteins are mostly from metazoans or their single cell relatives such as choanoflagellates and Filasterea, fibrocystin-like proteins with SEA domains were found in several other eukaryotic lineages including green algae, Alveolata, Euglenozoa, and Haptophyta, suggesting an ancient evolutionary origin. In addition, the intracellular protein Nucleoporin 54 (Nup54) acquired a divergent SEA domain in choanoflagellates and metazoans.
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Affiliation(s)
| | - Nick V Grishin
- Howard Hughes Medical Institute.,Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
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9
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Shah M, Smolko CM, Kinicki S, Chapman ZD, Brautigan DL, Janes KA. Profiling Subcellular Protein Phosphatase Responses to Coxsackievirus B3 Infection of Cardiomyocytes. Mol Cell Proteomics 2017; 16:S244-S262. [PMID: 28174228 DOI: 10.1074/mcp.o116.063487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/31/2017] [Indexed: 01/23/2023] Open
Abstract
Cellular responses to stimuli involve dynamic and localized changes in protein kinases and phosphatases. Here, we report a generalized functional assay for high-throughput profiling of multiple protein phosphatases with subcellular resolution and apply it to analyze coxsackievirus B3 (CVB3) infection counteracted by interferon signaling. Using on-plate cell fractionation optimized for adherent cells, we isolate protein extracts containing active endogenous phosphatases from cell membranes, the cytoplasm, and the nucleus. The extracts contain all major classes of protein phosphatases and catalyze dephosphorylation of plate-bound phosphosubstrates in a microtiter format, with cellular activity quantified at the end point by phosphospecific ELISA. The platform is optimized for six phosphosubstrates (ERK2, JNK1, p38α, MK2, CREB, and STAT1) and measures specific activities from extracts of fewer than 50,000 cells. The assay was exploited to examine viral and antiviral signaling in AC16 cardiomyocytes, which we show can be engineered to serve as susceptible and permissive hosts for CVB3. Phosphatase responses were profiled in these cells by completing a full-factorial experiment for CVB3 infection and type I/II interferon signaling. Over 850 functional measurements revealed several independent, subcellular changes in specific phosphatase activities. During CVB3 infection, we found that type I interferon signaling increases subcellular JNK1 phosphatase activity, inhibiting nuclear JNK1 activity that otherwise promotes viral protein synthesis in the infected host cell. Our assay provides a high-throughput way to capture perturbations in important negative regulators of intracellular signal-transduction networks.
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Affiliation(s)
- Millie Shah
- From the ‡Department of Biomedical Engineering
| | | | | | | | - David L Brautigan
- the ‖Center for Cell Signaling and Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22908
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10
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Lin HC, Huang CL, Huang YJ, Hsiao IL, Yang CW, Chuang CY. Transcriptomic gene-network analysis of exposure to silver nanoparticle reveals potentially neurodegenerative progression in mouse brain neural cells. Toxicol In Vitro 2016; 34:289-299. [PMID: 27131904 DOI: 10.1016/j.tiv.2016.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/30/2016] [Accepted: 04/24/2016] [Indexed: 10/21/2022]
Abstract
Silver nanoparticles (AgNPs) are commonly used in daily living products. AgNPs can induce inflammatory response in neuronal cells, and potentially develop neurological disorders. The gene networks in response to AgNPs-induced neurodegenerative progression have not been clarified in various brain neural cells. This study found that 3-5nm AgNPs were detectable to enter the nuclei of mouse neuronal cells after 24-h of exposure. The differentially expressed genes in mouse brain neural cells exposure to AgNPs were further identified using Phalanx Mouse OneArray® chip, and permitted to explore the gene network pathway regulating in neurodegenerative progression according to Cytoscape analysis. In focal adhesion pathway of ALT astrocytes, AgNPs induced the gene expression of RasGRF1 and reduced its downstream BCL2 gene for apoptosis. In cytosolic DNA sensing pathway of microglial BV2 cells, AgNPs reduced the gene expression of TREX1 and decreased IRF7 to release pro-inflammatory cytokines for inflammation and cellular activation. In MAPK pathway of neuronal N2a cells, AgNPs elevated GADD45α gene expression, and attenuated its downstream PTPRR gene to interfere with neuron growth and differentiation. Moreover, AgNPs induced beta amyloid deposition in N2a cells, and decreased PSEN1 and PSEN2, which may disrupt calcium homeostasis and presynaptic dysfunction for Alzheimer's disease development. These findings suggested that AgNPs exposure reveals the potency to induce the progression of neurodegenerative disorder.
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Affiliation(s)
- Ho-Chen Lin
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chin-Lin Huang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Yuh-Jeen Huang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - I-Lun Hsiao
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chung-Wei Yang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chun-Yu Chuang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
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11
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Kobayashi Y, Ito K, Kanda A, Tomoda K, Miller-Larsson A, Barnes PJ, Mercado N. Protein tyrosine phosphatase PTP-RR regulates corticosteroid sensitivity. Respir Res 2016; 17:30. [PMID: 27013170 PMCID: PMC4806463 DOI: 10.1186/s12931-016-0349-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/17/2016] [Indexed: 12/30/2022] Open
Abstract
Background We have recently reported that protein phosphate 2A (PP2A) inactivation resulted in increased phosphorylation of the mitogen-activated protein kinase (MAPK) c-Jun N-terminal kinase 1 (JNK1) and glucocorticoid receptors (GR) at Ser226, thereby reducing GR nuclear translocation and causing corticosteroid insensitivity in severe asthmatics. Protein tyrosine phosphatases (PTPs) are also known to be critically involved in the regulation of MAPKs, such as JNK and therefore potentially associated with GR function. The aim of study was to elucidate the involvement of MAPK-PTPs (PTP-RR, PTP-N5 and PTP-N7), which can dephosphorylate MAPKs, in the regulation of corticosteroid sensitivity. Methods Corticosteroid sensitivity, GR nuclear translocation, phosphorylation levels of GR-Ser226, JNK1 and PP2A catalytic subunit (PP2AC)-Tyr307 and protein expression levels and activities of PTP-RR and PP2AC were evaluated in U937 cells and/or peripheral blood mononuclear cells (PBMCs). Knock-down effects of MAPK-PTPs using siRNA were also evaluated. Results Knock-down of PTP-RR, but not of PTP-N5 or PTP-N7 impaired corticosteroid sensitivity, induced GR-Ser226 phosphorylation and reduced GR nuclear translocation. Under IL-2/IL-4-induced corticosteroid insensitivity, PTP-RR expression, activity and associations with JNK1 and GR were reduced but PTP-RR activity was restored by formoterol. Also in PBMCs from severe asthmatic patients, PTP-RR and JNK1 expression were reduced and GR-Ser226 phosphorylation increased. Furthermore, PTP-RR was associated with PP2A. PTP-RR reduction enhanced PP2AC-Tyr307 phosphorylation leading to impairment of PP2A expression and activity. Conclusions We demonstrated that with corticosteroid insensitivity PTP-RR fails to reduce phosphorylation of JNK1 and GR-Ser226, resulting in down-regulation of GR nuclear translocation. Reduced PTP-RR may represent a novel cause of corticosteroid insensitivity in severe asthmatics. Electronic supplementary material The online version of this article (doi:10.1186/s12931-016-0349-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoshiki Kobayashi
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Royal Brompton Campus, Dovehouse Street, London, SW3 6LY, UK. .,Airway Medicine, Department of Otolaryngology, Kansai Medical University, Osaka, Japan.
| | - Kazuhiro Ito
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Royal Brompton Campus, Dovehouse Street, London, SW3 6LY, UK
| | - Akira Kanda
- Airway Medicine, Department of Otolaryngology, Kansai Medical University, Osaka, Japan
| | - Koich Tomoda
- Airway Medicine, Department of Otolaryngology, Kansai Medical University, Osaka, Japan
| | | | - Peter J Barnes
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Royal Brompton Campus, Dovehouse Street, London, SW3 6LY, UK
| | - Nicolas Mercado
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Royal Brompton Campus, Dovehouse Street, London, SW3 6LY, UK
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12
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Li X, Liu Z, Li W, Sun N, Xu Y, Xie Z, Zhang K. PTPRR regulates ERK dephosphorylation in depression mice model. J Affect Disord 2016; 193:233-41. [PMID: 26773914 DOI: 10.1016/j.jad.2015.12.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 12/16/2015] [Accepted: 12/26/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The Protein tyrosine phosphatase receptor type R (PTPRR), which regulates the dephosphorylation of the downstream mitogen-activated protein kinase (MAPK) steering cell proliferation, apoptosis and synaptic plasticity, may be involved in the pathogenesis of depression. METHODS Lentiviral vectors were utilized to express the PTPRR constitutively in the hippocampal dentate gyrus (DG) of mice before or after chronic mild stress. Behavior tests, MAPK levels, neuronal apoptosis and cell proliferation in the hippocampal DG were examined. RESULTS Without chronic mild stress (CMS), the lenti-shPTPRR mice showed shorter immobility time in the tail suspension test than controls, while the lenti-PTPRR mice exhibited significantly less sucrose intake and increased immobility time in the forced swim tests than control mice, indicating increased prodepressant-like effects of PTPRR in lenti-PTPRR mice. Similarly, under CMS, the lenti-shPTPRR mice had more sucrose intake, shorter immobility time in the forced swim test and tail suspension test compared to controls, and lenti-PTPRR mice had less sucrose intake and longer immobility time in forced swim test and tail suspension test, exhibiting increased susceptibility to depressive-like behaviors and greater sensitivity to CMS. Besides, the Phospho-ERK1/2(p-ERK) had significant lower phosphorylation in lenti-PTPRR group and higher expression in lenti-shPTPRR group, both without CMS. The Lenti-PTPRR mice exposed to CMS had significant lower p-ERK, and the lenti-shPTPRR mice exposed to CMS had significant higher p-ERK and lower p-P38. Moreover, there were more cells underwent apoptosis in lenti-PTPRR group ,with and without CMS. In cell proliferation, less BrdU positive cells were observed in lenti-PTPRR mice than controls. CONCLUSION The site-specific lentiviral injections resulted in the PTPRR over-expression in the hippocampal DG and subsequent increased ERK dephosphorylation, which leads to more neuron apoptosis, less cell proliferation, depression onset and increased sensitivity to CMS. PTPRR/ERK pathway could be potential target for depression therapy.
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Affiliation(s)
- Xinrong Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhifen Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Wei Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Ning Sun
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yong Xu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhongchen Xie
- Animal center of Tsinghua university, Beijing, China
| | - Kerang Zhang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China.
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13
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Erkens M, Tanaka-Yamamoto K, Cheron G, Márquez-Ruiz J, Prigogine C, Schepens JT, Nadif Kasri N, Augustine GJ, Hendriks WJ. Protein tyrosine phosphatase receptor type R is required for Purkinje cell responsiveness in cerebellar long-term depression. Mol Brain 2015; 8:1. [PMID: 25571783 PMCID: PMC4304614 DOI: 10.1186/s13041-014-0092-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/19/2014] [Indexed: 01/24/2023] Open
Abstract
Background Regulation of synaptic connectivity, including long-term depression (LTD), allows proper tuning of cellular signalling processes within brain circuitry. In the cerebellum, a key centre for motor coordination, a positive feedback loop that includes mitogen-activated protein kinases (MAPKs) is required for proper temporal control of LTD at cerebellar Purkinje cell synapses. Here we report that the tyrosine-specific MAPK-phosphatase PTPRR plays a role in coordinating the activity of this regulatory loop. Results LTD in the cerebellum of Ptprr−/− mice is strongly impeded, in vitro and in vivo. Comparison of basal phospho-MAPK levels between wild-type and PTPRR deficient cerebellar slices revealed increased levels in mutants. This high basal phospho-MAPK level attenuated further increases in phospho-MAPK during chemical induction of LTD, essentially disrupting the positive feedback loop and preventing α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) phosphorylation and endocytosis. Conclusions Our findings indicate an important role for PTPRR in maintaining low basal MAPK activity in Purkinje cells. This creates an optimal ‘window’ to boost MAPK activity following signals that induce LTD, which can then propagate through feed-forward signals to cause AMPAR internalization and LTD.
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Affiliation(s)
- Mirthe Erkens
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, Nijmegen, 6500, HB, The Netherlands.
| | - Keiko Tanaka-Yamamoto
- Center for Functional Connectomics, Korea Institute of Science and Technology, 39-1 Hawolgokdong, Seongbukgu, Seoul, 136-791, Republic of Korea.
| | - Guy Cheron
- Laboratory of Electrophysiology, Université de Mons, Mons, 7000, Belgium. .,Laboratory of Neurophysiology and Movement Biomechanics, CP601, ULB Neurosciences Institut, Université Libre de Bruxelles, Brussels, 1070, Belgium.
| | - Javier Márquez-Ruiz
- División de Neurociencias, Universidad Pablo de Olavide, Sevilla, 41013, Spain. .,Department of Cognitive Neurosciences, Nijmegen, 6500, HB, The Netherlands.
| | - Cynthia Prigogine
- Laboratory of Electrophysiology, Université de Mons, Mons, 7000, Belgium. .,Laboratory of Neurophysiology and Movement Biomechanics, CP601, ULB Neurosciences Institut, Université Libre de Bruxelles, Brussels, 1070, Belgium.
| | - Jan Tg Schepens
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, Nijmegen, 6500, HB, The Netherlands.
| | - Nael Nadif Kasri
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, PO Box 9101, Nijmegen, HB, 6500, The Netherlands.
| | - George J Augustine
- Center for Functional Connectomics, Korea Institute of Science and Technology, 39-1 Hawolgokdong, Seongbukgu, Seoul, 136-791, Republic of Korea. .,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
| | - Wiljan Jaj Hendriks
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, Nijmegen, 6500, HB, The Netherlands.
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14
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Karasawa T, Lombroso PJ. Disruption of striatal-enriched protein tyrosine phosphatase (STEP) function in neuropsychiatric disorders. Neurosci Res 2014; 89:1-9. [PMID: 25218562 DOI: 10.1016/j.neures.2014.08.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 08/12/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
Striatal-enriched protein tyrosine phosphatase (STEP) is a brain-specific tyrosine phosphatase that plays a major role in the development of synaptic plasticity. Recent findings have implicated STEP in several psychiatric and neurological disorders, including Alzheimer's disease, schizophrenia, fragile X syndrome, Huntington's disease, stroke/ischemia, and stress-related psychiatric disorders. In these disorders, STEP protein expression levels and activity are dysregulated, contributing to the cognitive deficits that are present. In this review, we focus on the most recent findings on STEP, discuss how STEP expression and activity are maintained during normal cognitive function, and how disruptions in STEP activity contribute to a number of illnesses.
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Affiliation(s)
- Takatoshi Karasawa
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi 480-0392, Japan.
| | - Paul J Lombroso
- Departments of Neurobiology, Psychiatry and Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
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15
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Kayakabe M, Kakizaki T, Kaneko R, Sasaki A, Nakazato Y, Shibasaki K, Ishizaki Y, Saito H, Suzuki N, Furuya N, Yanagawa Y. Motor dysfunction in cerebellar Purkinje cell-specific vesicular GABA transporter knockout mice. Front Cell Neurosci 2014; 7:286. [PMID: 24474904 PMCID: PMC3893617 DOI: 10.3389/fncel.2013.00286] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 12/20/2013] [Indexed: 01/24/2023] Open
Abstract
γ-Aminobutyric acid (GABA) is a major inhibitory neurotransmitter in the adult mammalian central nervous system and plays modulatory roles in neural development. The vesicular GABA transporter (VGAT) is an essential molecule for GABAergic neurotransmission due to its role in vesicular GABA release. Cerebellar Purkinje cells (PCs) are GABAergic projection neurons that are indispensable for cerebellar function. To elucidate the significance of VGAT in cerebellar PCs, we generated and characterized PC-specific VGAT knockout (L7-VGAT) mice. VGAT mRNAs and proteins were specifically absent in the 40-week-old L7-VGAT PCs. The morphological characteristics, such as lamination and foliation of the cerebellar cortex, of the L7-VGAT mice were similar to those of the control littermate mice. Moreover, the protein expression levels and patterns of pre- (calbindin and parvalbumin) and postsynaptic (GABA-A receptor α1 subunit and gephyrin) molecules between the L7-VGAT and control mice were similar in the deep cerebellar nuclei that receive PC projections. However, the L7-VGAT mice performed poorly in the accelerating rotarod test and displayed ataxic gait in the footprint test. The L7-VGAT mice also exhibited severer ataxia as VGAT deficits progressed. These results suggest that VGAT in cerebellar PCs is not essential for the rough maintenance of cerebellar structure, but does play an important role in motor coordination. The L7-VGAT mice are a novel model of ataxia without PC degeneration, and would also be useful for studying the role of PCs in cognition and emotion.
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Affiliation(s)
- Mikiko Kayakabe
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine Maebashi, Japan ; Japan Science and Technology Agency CREST, Tokyo, Japan ; Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Toshikazu Kakizaki
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine Maebashi, Japan ; Japan Science and Technology Agency CREST, Tokyo, Japan
| | - Ryosuke Kaneko
- Japan Science and Technology Agency CREST, Tokyo, Japan ; Institute of Experimental Animal Research, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Atsushi Sasaki
- Department of Pathology, Saitama Medical University Moroyama, Japan
| | - Yoichi Nakazato
- Department of Human Pathology, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Koji Shibasaki
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Yasuki Ishizaki
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Hiromitsu Saito
- Department of Animal Genomics, Functional Genomics Institute, Mie University Life Science Research Center Tsu, Japan
| | - Noboru Suzuki
- Department of Animal Genomics, Functional Genomics Institute, Mie University Life Science Research Center Tsu, Japan
| | - Nobuhiko Furuya
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Yuchio Yanagawa
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine Maebashi, Japan ; Japan Science and Technology Agency CREST, Tokyo, Japan
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16
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Li R, Xie DD, Dong JH, Li H, Li KS, Su J, Chen LZ, Xu YF, Wang HM, Gong Z, Cui GY, Yu X, Wang K, Yao W, Xin T, Li MY, Xiao KH, An XF, Huo Y, Xu ZG, Sun JP, Pang Q. Molecular mechanism of ERK dephosphorylation by striatal-enriched protein tyrosine phosphatase. J Neurochem 2013; 128:315-329. [PMID: 24117863 DOI: 10.1111/jnc.12463] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 12/26/2022]
Abstract
Striatal-enriched tyrosine phosphatase (STEP) is an important regulator of neuronal synaptic plasticity, and its abnormal level or activity contributes to cognitive disorders. One crucial downstream effector and direct substrate of STEP is extracellular signal-regulated protein kinase (ERK), which has important functions in spine stabilisation and action potential transmission. The inhibition of STEP activity toward phospho-ERK has the potential to treat neuronal diseases, but the detailed mechanism underlying the dephosphorylation of phospho-ERK by STEP is not known. Therefore, we examined STEP activity toward para-nitrophenyl phosphate, phospho-tyrosine-containing peptides, and the full-length phospho-ERK protein using STEP mutants with different structural features. STEP was found to be a highly efficient ERK tyrosine phosphatase that required both its N-terminal regulatory region and key residues in its active site. Specifically, both kinase interaction motif (KIM) and kinase-specific sequence of STEP were required for ERK interaction. In addition to the N-terminal kinase-specific sequence region, S245, hydrophobic residues L249/L251, and basic residues R242/R243 located in the KIM region were important in controlling STEP activity toward phospho-ERK. Further kinetic experiments revealed subtle structural differences between STEP and HePTP that affected the interactions of their KIMs with ERK. Moreover, STEP recognised specific positions of a phospho-ERK peptide sequence through its active site, and the contact of STEP F311 with phospho-ERK V205 and T207 were crucial interactions. Taken together, our results not only provide the information for interactions between ERK and STEP, but will also help in the development of specific strategies to target STEP-ERK recognition, which could serve as a potential therapy for neurological disorders. Regulation of phospho-ERK by STEP underlies important neuronal activities. A detailed enzymologic characterisation and cellular studies of STEP revealed that specific residues in KIM and active site mediated ERK recognition. Structural differences between the KIM-ERK interfaces and the active site among different ERK phosphatases could be targeted to develop specific STEP inhibitor, which has therapeutic potential for neurological disorders. PKA, protein kinase A & NGF, nerve growth factor.
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Affiliation(s)
- Rong Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Di-Dong Xie
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Jun-Hong Dong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China.,Weifang Medical University,Weifang, Shandong, 261042, China
| | - Hui Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Kang-Shuai Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Jing Su
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Lai-Zhong Chen
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Yun-Fei Xu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Hong-Mei Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Zheng Gong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Weihai campus, Shandong University, Weihai, Shandong, 264209, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Guo-Ying Cui
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Kai Wang
- Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Wei Yao
- Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Tao Xin
- Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Min-Yong Li
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Kun-Hong Xiao
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiao-Fei An
- Drug Discovery Center, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055
| | - Yuqing Huo
- Vascular Biology Center, Department of Cellular Biology and Anatomy, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912
| | - Zhi-Gang Xu
- Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China.,Shandong University, School of Life Sciences, Jinan, Shandong, 250021, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Qi Pang
- Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
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Hendriks WJAJ, Pulido R. Protein tyrosine phosphatase variants in human hereditary disorders and disease susceptibilities. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1673-96. [PMID: 23707412 DOI: 10.1016/j.bbadis.2013.05.022] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/18/2022]
Abstract
Reversible tyrosine phosphorylation of proteins is a key regulatory mechanism to steer normal development and physiological functioning of multicellular organisms. Phosphotyrosine dephosphorylation is exerted by members of the super-family of protein tyrosine phosphatase (PTP) enzymes and many play such essential roles that a wide variety of hereditary disorders and disease susceptibilities in man are caused by PTP alleles. More than two decades of PTP research has resulted in a collection of PTP genetic variants with corresponding consequences at the molecular, cellular and physiological level. Here we present a comprehensive overview of these PTP gene variants that have been linked to disease states in man. Although the findings have direct bearing for disease diagnostics and for research on disease etiology, more work is necessary to translate this into therapies that alleviate the burden of these hereditary disorders and disease susceptibilities in man.
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Affiliation(s)
- Wiljan J A J Hendriks
- Department of Cell Biology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Hawthorne F, Feng S, Metlapally R, Li YJ, Tran-Viet KN, Guggenheim JA, Malecaze F, Calvas P, Rosenberg T, Mackey DA, Venturini C, Hysi PG, Hammond CJ, Young TL. Association mapping of the high-grade myopia MYP3 locus reveals novel candidates UHRF1BP1L, PTPRR, and PPFIA2. Invest Ophthalmol Vis Sci 2013; 54:2076-86. [PMID: 23422819 DOI: 10.1167/iovs.12-11102] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Myopia, or nearsightedness, is a common ocular genetic disease for which over 20 candidate genomic loci have been identified. The high-grade myopia locus, MYP3, has been reported on chromosome 12q21-23 by four independent linkage studies. METHODS We performed a genetic association study of the MYP3 locus in a family-based high-grade myopia cohort (n = 82) by genotyping 768 single-nucleotide polymorphisms (SNPs) within the linkage region. Qualitative testing for high-grade myopia (sphere ≤ -5 D affected, > -0.5 D unaffected) and quantitative testing on the average dioptric sphere were performed. RESULTS Several genetic markers were nominally significantly associated with high-grade myopia in qualitative testing, including rs3803036, a missense mutation in PTPRR (P = 9.1 × 10(-4)) and rs4764971, an intronic SNP in UHRF1BP1L (P = 6.1 × 10(-4)). Quantitative testing determined statistically significant SNPs rs4764971, also found by qualitative testing (P = 3.1 × 10(-6)); rs7134216, in the 3' untranslated region (UTR) of DEPDC4 (P = 5.4 × 10(-7)); and rs17306116, an intronic SNP within PPFIA2 (P < 9 × 10(-4)). Independently conducted whole genome expression array analyses identified protein tyrosine phosphatase genes PTPRR and PPFIA2, which are in the same gene family, as differentially expressed in normal rapidly growing fetal relative to normal adult ocular tissue (confirmed by RT-qPCR). CONCLUSIONS In an independent high-grade myopia cohort, an intronic SNP in UHRF1BP1L, rs4764971, was validated for quantitative association, and SNPs within PTPRR (quantitative) and PPFIA2 (qualitative and quantitative) approached significance. Three genes identified by our association study and supported by ocular expression and/or replication, UHRF1BP1L, PTPRR, and PPFIA2, are novel candidates for myopic development within the MYP3 locus that should be further studied.
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Affiliation(s)
- Felicia Hawthorne
- Duke Center for Human Genetics, Duke University, Durham, NC 27710, USA
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Receptor type protein tyrosine phosphatases (RPTPs) - roles in signal transduction and human disease. J Cell Commun Signal 2012; 6:125-38. [PMID: 22851429 DOI: 10.1007/s12079-012-0171-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 07/12/2012] [Indexed: 01/06/2023] Open
Abstract
Protein tyrosine phosphorylation is a fundamental regulatory mechanism controlling cell proliferation, differentiation, communication, and adhesion. Disruption of this key regulatory mechanism contributes to a variety of human diseases including cancer, diabetes, and auto-immune diseases. Net protein tyrosine phosphorylation is determined by the dynamic balance of the activity of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). Mammals express many distinct PTKs and PTPs. Both of these families can be sub-divided into non-receptor and receptor subtypes. Receptor protein tyrosine kinases (RPTKs) comprise a large family of cell surface proteins that initiate intracellular tyrosine phosphorylation-dependent signal transduction in response to binding of extracellular ligands, such as growth factors and cytokines. Receptor-type protein tyrosine phosphatases (RPTPs) are enzymatic and functional counterparts of RPTKs. RPTPs are a family of integral cell surface proteins that possess intracellular PTP activity, and extracellular domains that have sequence homology to cell adhesion molecules. In comparison to extensively studied RPTKs, much less is known about RPTPs, especially regarding their substrate specificities, regulatory mechanisms, biological functions, and their roles in human diseases. Based on the structure of their extracellular domains, the RPTP family can be grouped into eight sub-families. This article will review one representative member from each RPTP sub-family.
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Goebel-Goody SM, Baum M, Paspalas CD, Fernandez SM, Carty NC, Kurup P, Lombroso PJ. Therapeutic implications for striatal-enriched protein tyrosine phosphatase (STEP) in neuropsychiatric disorders. Pharmacol Rev 2011; 64:65-87. [PMID: 22090472 DOI: 10.1124/pr.110.003053] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Striatal-enriched protein tyrosine phosphatase (STEP) is a brain-specific phosphatase that modulates key signaling molecules involved in synaptic plasticity and neuronal function. Targets include extracellular-regulated kinase 1 and 2 (ERK1/2), stress-activated protein kinase p38 (p38), the Src family tyrosine kinase Fyn, N-methyl-D-aspartate receptors (NMDARs), and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs). STEP-mediated dephosphorylation of ERK1/2, p38, and Fyn leads to inactivation of these enzymes, whereas STEP-mediated dephosphorylation of surface NMDARs and AMPARs promotes their endocytosis. Accordingly, the current model of STEP function posits that it opposes long-term potentiation and promotes long-term depression. Phosphorylation, cleavage, dimerization, ubiquitination, and local translation all converge to maintain an appropriate balance of STEP in the central nervous system. Accumulating evidence over the past decade indicates that STEP dysregulation contributes to the pathophysiology of several neuropsychiatric disorders, including Alzheimer's disease, schizophrenia, fragile X syndrome, epileptogenesis, alcohol-induced memory loss, Huntington's disease, drug abuse, stroke/ischemia, and inflammatory pain. This comprehensive review discusses STEP expression and regulation and highlights how disrupted STEP function contributes to the pathophysiology of diverse neuropsychiatric disorders.
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Affiliation(s)
- Susan M Goebel-Goody
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA
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Chesini IM, Debyser G, Croes H, Ten Dam GB, Devreese B, Stoker AW, Hendriks WJAJ. PTPBR7 binding proteins in myelinating neurons of the mouse brain. Int J Biol Sci 2011; 7:978-91. [PMID: 21850207 PMCID: PMC3157272 DOI: 10.7150/ijbs.7.978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 07/21/2011] [Indexed: 12/29/2022] Open
Abstract
Mouse protein tyrosine phosphatase PTPBR7 is a receptor-like, transmembrane protein that is localized on the surface of neuronal cells. Its protein phosphatase activity is reduced upon multimerization, and PTPBR7-deficient mice display motor coordination defects. Extracellular molecules that may influence PTPBR7 activity, however, remain to be determined. We here show that the PTPBR7 extracellular domain binds to highly myelinated regions in mouse brain, in particular the white matter tracks in cerebellum. PTPBR7 deficiency does not alter this binding pattern, as witnessed by RAP in situ staining of Ptprr-/- mouse brain sections. Additional in situ and in vitro experiments also suggest that sugar moieties of heparan sulphate and chondroitin sulphate glycosaminoglycans are not critical for PTPBR7 binding. Candidate binding proteins were affinity-purified exploiting the PTPBR7 extracellular domain and identified by mass spectrometric means. Results support the suggested link between PTPRR isoforms and cerebellar calcium ion homeostasis, and suggest an additional role in the process of cell-cell adhesion.
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Affiliation(s)
- Irene M Chesini
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
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Vergult S, Krgovic D, Loeys B, Lyonnet S, Liedén A, Anderlid BM, Sharkey F, Joss S, Mortier G, Menten B. Nasal speech and hypothyroidism are common hallmarks of 12q15 microdeletions. Eur J Hum Genet 2011; 19:1032-7. [PMID: 21505450 DOI: 10.1038/ejhg.2011.67] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The introduction of array CGH in clinical diagnostics has led to the discovery of many new microdeletion/microduplication syndromes. Most of them are rare and often present with a variable range of clinical anomalies. In this study we report three patients with a de novo overlapping microdeletion of chromosome bands 12q15q21.1. The deletions are ∼2.5 Mb in size, with a 1.34-Mb common deleted region containing six RefSeq genes. All three patients present with learning disability or developmental delay, nasal speech and hypothyroidism. In this paper we will further elaborate on the genotype-phenotype correlation associated with this deletion and compare our patients with previously reported cases.
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Affiliation(s)
- Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Menigatti M, Cattaneo E, Sabates-Bellver J, Ilinsky VV, Went P, Buffoli F, Marquez VE, Jiricny J, Marra G. The protein tyrosine phosphatase receptor type R gene is an early and frequent target of silencing in human colorectal tumorigenesis. Mol Cancer 2009; 8:124. [PMID: 20015382 PMCID: PMC2801661 DOI: 10.1186/1476-4598-8-124] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 12/16/2009] [Indexed: 12/19/2022] Open
Abstract
Background Tumor development in the human colon is commonly accompanied by epigenetic changes, such as DNA methylation and chromatin modifications. These alterations result in significant, inheritable changes in gene expression that contribute to the selection of tumor cells with enhanced survival potential. Results A recent high-throughput gene expression analysis conducted by our group identified numerous genes whose transcription was markedly diminished in colorectal tumors. One of these, the protein-tyrosine phosphatase receptor type R (PTPRR) gene, was dramatically downregulated from the earliest stages of cellular transformation. Here, we show that levels of both major PTPRR transcript variants are markedly decreased (compared with normal mucosal levels) in precancerous and cancerous colorectal tumors, as well in colorectal cancer cell lines. The expression of the PTPRR-1 isoform was inactivated in colorectal cancer cells as a result of de novo CpG island methylation and enrichment of transcription-repressive histone-tail marks, mainly H3K27me3. De novo methylation of the PTPRR-1 transcription start site was demonstrated in 29/36 (80%) colorectal adenomas, 42/44 (95%) colorectal adenocarcinomas, and 8/8 (100%) liver metastases associated with the latter tumors. Conclusions Epigenetic downregulation of PTPRR seems to be an early alteration in colorectal cell transformation, which is maintained during the clonal selection associated with tumor progression. It may represent a preliminary step in the constitutive activation of the RAS/RAF/MAPK/ERK signalling, an effect that will later be consolidated by mutations in genes encoding key components of this pathway.
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Affiliation(s)
- Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Switzerland.
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