1
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Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles‐Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Maria Engler SS, Bishop DT, Newton‐Bishop J, Adams DJ. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol 2023; 259:56-68. [PMID: 36219477 PMCID: PMC10098817 DOI: 10.1002/path.6019] [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: 07/02/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Melanoma is a heterogenous malignancy with an unpredictable clinical course. Most patients who present in the clinic are diagnosed with primary melanoma, yet large-scale sequencing efforts have focused primarily on metastatic disease. In this study we sequence-profiled 524 American Joint Committee on Cancer Stage I-III primary tumours. Our analysis of these data reveals recurrent driver mutations, mutually exclusive genetic interactions, where two genes were never or rarely co-mutated, and an absence of co-occurring genetic events. Further, we intersected copy number calls from our primary melanoma data with whole-genome CRISPR screening data to identify the transcription factor interferon regulatory factor 4 (IRF4) as a melanoma-associated dependency. © 2022 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)
- Sofia Birkeälv
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Mark Harland
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Larissa Satiko Alcantara Sekimoto Matsuyama
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Mamun Rashid
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Ishan Mehta
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Jonathan P Laye
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | | | - Tracey Mell
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Vivek Iyer
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Carla Daniela Robles‐Espinoza
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de México, Campus JuriquillaSantiago de QuerétaroMexico
| | - Ultan McDermott
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | | | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Pathology and Leiden Center for Computational OncologyLeiden University Medical CenterLeidenthe Netherlands
| | - Patricia A Possik
- Division of Experimental and Translational ResearchBrazilian National Cancer InstituteRio de JaneiroBrazil
| | - Silvya Stuchi Maria Engler
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - D Timothy Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Julia Newton‐Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - David J Adams
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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2
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Antonarakis SE. Short arms of human acrocentric chromosomes and the completion of the human genome sequence. Genome Res 2022; 32:599-607. [PMID: 35361624 PMCID: PMC8997349 DOI: 10.1101/gr.275350.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The complete, ungapped sequence of the short arms of human acrocentric chromosomes (SAACs) is still unknown almost 20 years after the near completion of the Human Genome Project. Yet these short arms of Chromosomes 13, 14, 15, 21, and 22 contain the ribosomal DNA (rDNA) genes, which are of paramount importance for human biology. The sequences of SAACs show an extensive variation in the copy number of the various repetitive elements, the full extent of which is currently unknown. In addition, the full spectrum of repeated sequences, their organization, and the low copy number functional elements are also unknown. The Telomere-to-Telomere (T2T) Project using mainly long-read sequence technology has recently completed the assembly of the genome from a hydatidiform mole, CHM13, and has thus established a baseline reference for further studies on the organization, variation, functional annotation, and impact in human disorders of all the previously unknown genomic segments, including the SAACs. The publication of the initial results of the T2T Project will update and improve the reference genome for a better understanding of the evolution and function of the human genome.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, 1211 Geneva, Switzerland.,Foundation Campus Biotech, 1202 Geneva, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
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3
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Di J, Yang H, Jiang B, Wang Z, Ji J, Su X. Whole exome sequencing reveals intertumor heterogeneity and distinct genetic origins of sporadic synchronous colorectal cancer. Int J Cancer 2017; 142:927-939. [PMID: 29105743 DOI: 10.1002/ijc.31140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/26/2017] [Accepted: 10/16/2017] [Indexed: 12/24/2022]
Abstract
Sporadic synchronous colorectal cancer (CRC) refers to more than one primary tumor detected in a single patient at the time of the first diagnosis without predisposition of cancer development. Given the same genetic and microenvironment they raise, sporadic synchronous CRC is a unique model to study CRC tumorigenesis. We performed whole exome sequencing in 32 fresh frozen tumor lesions from 15 patients with sporadic synchronous CRC to compare their genetic alterations. This approach identified ubiquitously mutated genes in the range from 0.34% to 4.22% and from 0.8% to 7.0% in non-hypermutated tumors and hypermutated tumors, respectively, in a single patient. We show that both ubiquitously mutated genes and candidate cancer genes from different tumors in the same patient mutated at different sites. Consistently, obvious differences in somatic copy number variations (SCNV) were found in most patients with non-hypermutated tumor lesions, which had ubiquitous copy number amplification rates ranging from 0% to 8.8% and ubiquitous copy number deletion rates ranging from 0% to 8.2%. Hypermutated lesions were nearly diploid with 0% to 18.8% common copy number aberrations. Accordingly, clonal structures, altered signaling pathways and druggable genes in a single patient with synchronous CRC varied significantly. Taken together, the disparate SCNVs and mutations in synchronous CRC supported the field effect theory of tumorigenesis. Moreover, the intertumor heterogeneity of synchronous CRCs implies that analysis of all tumor lesions from the same patient is necessary for appropriate clinical treatment decisions.
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Affiliation(s)
- Jiabo Di
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Hong Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Beihai Jiang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Zaozao Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Jiafu Ji
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biobank, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Xiangqian Su
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
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4
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Kuemmel A, Simon P, Breitkreuz A, Röhlig J, Luxemburger U, Elsäßer A, Schmidt LH, Sebastian M, Sahin U, Türeci Ö, Buhl R. Humoral immune responses of lung cancer patients against the Transmembrane Phosphatase with TEnsin homology (TPTE). Lung Cancer 2015; 90:334-41. [PMID: 26350112 DOI: 10.1016/j.lungcan.2015.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/19/2015] [Accepted: 07/25/2015] [Indexed: 01/03/2023]
Abstract
OBJECTIVE The cancer/testis (C/T) antigen Transmembrane Phosphatase with TEnsin homology (TPTE) is aberrantly expressed in many tumors including lung cancer. In the present study, we analyzed TPTE-auto-antibodies in lung cancer patients. METHODS Using a crude-lysate ELISA, we analyzed a large cohort of 307 sera from lung cancer patients and 47 healthy donors for TPTE-specific autoantibodies. Sero-reactivity was correlated with clinical parameters and patients' survival. RESULTS TPTE-specific antibodies were detected in 41 of 307 (13.4%) sera from lung cancer patients. Based on an optimal cut-off value calculated by ROC curve analysis sensitivity for diagnosing lung cancer was 52% and specificity was 72%. TPTE sero-positivity was not associated with tumor stage, tumor histology, gender or age. Multivariate analysis indicated that TPTE sero-positivity is associated with prolonged survival in patients with lung cancer, but established prognostic factors for survival prediction such as stage and histology remain indispensable. CONCLUSION Autoantibodies against TPTE occur spontaneously in lung cancer patients. TPTE sero-reactivity has moderate sensitivity and specificity for diagnosing lung cancer and is a positive prognostic marker.
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Affiliation(s)
- Andreas Kuemmel
- Department of Hematology, Medical Oncology & Pneumology, University Medical Center Mainz, 55131 Mainz, Germany.
| | - Petra Simon
- Department of Hematology, Medical Oncology & Pneumology, University Medical Center Mainz, 55131 Mainz, Germany; TRON gGmbH, Translational Oncology at the University Medical Center, Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Andrea Breitkreuz
- Department of Hematology, Medical Oncology & Pneumology, University Medical Center Mainz, 55131 Mainz, Germany; TRON gGmbH, Translational Oncology at the University Medical Center, Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Julia Röhlig
- Department of Hematology, Medical Oncology & Pneumology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Ulrich Luxemburger
- Department of Hematology, Medical Oncology & Pneumology, University Medical Center Mainz, 55131 Mainz, Germany; TRON gGmbH, Translational Oncology at the University Medical Center, Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Amelie Elsäßer
- Institute of Medical Biostatistics, Epidemiology and Informatics, Johannes Gutenberg-University, 55101 Mainz, Germany
| | - Lars Henning Schmidt
- Department of Medicine A, University Medical Center Muenster, 48149 Muenster, Germany
| | - Martin Sebastian
- Department of Medicine III, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Ugur Sahin
- Department of Hematology, Medical Oncology & Pneumology, University Medical Center Mainz, 55131 Mainz, Germany; TRON gGmbH, Translational Oncology at the University Medical Center, Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Özlem Türeci
- Ganymed Pharmaceuticals AG, Freiligrathstr.12, 55131 Mainz, Germany
| | - Roland Buhl
- Department of Hematology, Medical Oncology & Pneumology, University Medical Center Mainz, 55131 Mainz, Germany
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5
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Abstract
The importance of PTEN in cellular function is underscored by the frequency of its deregulation in cancer. PTEN tumor-suppressor activity depends largely on its lipid phosphatase activity, which opposes PI3K/AKT activation. As such, PTEN regulates many cellular processes, including proliferation, survival, energy metabolism, cellular architecture, and motility. More than a decade of research has expanded our knowledge about how PTEN is controlled at the transcriptional level as well as by numerous posttranscriptional modifications that regulate its enzymatic activity, protein stability, and cellular location. Although the role of PTEN in cancers has long been appreciated, it is also emerging as an important factor in other diseases, such as diabetes and autism spectrum disorders. Our understanding of PTEN function and regulation will hopefully translate into improved prognosis and treatment for patients suffering from these ailments.
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Affiliation(s)
- Carolyn A Worby
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721;
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6
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Hobiger K, Friedrich T. Voltage sensitive phosphatases: emerging kinship to protein tyrosine phosphatases from structure-function research. Front Pharmacol 2015; 6:20. [PMID: 25713537 PMCID: PMC4322731 DOI: 10.3389/fphar.2015.00020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/21/2015] [Indexed: 02/03/2023] Open
Abstract
The transmembrane protein Ci-VSP from the ascidian Ciona intestinalis was described as first member of a fascinating family of enzymes, the voltage sensitive phosphatases (VSPs). Ci-VSP and its voltage-activated homologs from other species are stimulated by positive membrane potentials and dephosphorylate the head groups of negatively charged phosphoinositide phosphates (PIPs). In doing so, VSPs act as control centers at the cytosolic membrane surface, because they intervene in signaling cascades that are mediated by PIP lipids. The characteristic motif CX5RT/S in the active site classifies VSPs as members of the huge family of cysteine-based protein tyrosine phosphatases (PTPs). Although PTPs have already been well-characterized regarding both, structure and function, their relationship to VSPs has drawn only limited attention so far. Therefore, the intention of this review is to give a short overview about the extensive knowledge about PTPs in relation to the facts known about VSPs. Here, we concentrate on the structural features of the catalytic domain which are similar between both classes of phosphatases and their consequences for the enzymatic function. By discussing results obtained from crystal structures, molecular dynamics simulations, and mutagenesis studies, a possible mechanism for the catalytic cycle of VSPs is presented based on that one proposed for PTPs. In this way, we want to link the knowledge about the catalytic activity of VSPs and PTPs.
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Affiliation(s)
- Kirstin Hobiger
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-Universität Marburg Marburg, Germany
| | - Thomas Friedrich
- Max-Volmer-Laboratory of Biophysical Chemistry, Institute of Chemistry, Technische Universität Berlin Berlin, Germany
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7
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Abstract
Power-law distributions are the main functional form for the distribution of repeat size and repeat copy number in the human genome. When the genome is broken into fragments for sequencing, the limited size of fragments and reads may prevent an unique alignment of repeat sequences to the reference sequence. Repeats in the human genome can be as long as 104 bases, or 105 − 106 bases when allowing for mismatches between repeat units. Sequence reads from these regions are therefore unmappable when the read length is in the range of 103 bases. With a read length of 1000 bases, slightly more than 1% of the assembled genome, and slightly less than 1% of the 1 kb reads, are unmappable, excluding the unassembled portion of the human genome (8% in GRCh37/hg19). The slow decay (long tail) of the power-law function implies a diminishing return in converting unmappable regions/reads to become mappable with the increase of the read length, with the understanding that increasing read length will always move toward the direction of 100% mappability.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System Manhasset, NY, USA
| | - Jan Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System Manhasset, NY, USA
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8
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Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA. Using population admixture to help complete maps of the human genome. Nat Genet 2013; 45:406-14, 414e1-2. [PMID: 23435088 PMCID: PMC3683849 DOI: 10.1038/ng.2565] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 01/31/2013] [Indexed: 12/16/2022]
Abstract
Tens of millions of base pairs of euchromatic human genome sequence, including many protein-coding genes, have no known location in the human genome. We describe an approach for localizing the human genome's missing pieces using the patterns of genome sequence variation created by population admixture. We mapped the locations of 70 scaffolds spanning 4 million base pairs of the human genome's unplaced euchromatic sequence, including more than a dozen protein-coding genes, and identified 8 new large interchromosomal segmental duplications. We find that most of these sequences are hidden in the genome's heterochromatin, particularly its pericentromeric regions. Many cryptic, pericentromeric genes are expressed at the RNA level and have been maintained intact for millions of years while their expression patterns diverged from those of paralogous genes elsewhere in the genome. We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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9
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Villalba-Galea CA. Voltage-Controlled Enzymes: The New JanusBifrons. Front Pharmacol 2012; 3:161. [PMID: 22993507 PMCID: PMC3440755 DOI: 10.3389/fphar.2012.00161] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 08/19/2012] [Indexed: 12/25/2022] Open
Abstract
The Ciona intestinalis voltage-sensitive phosphatase, Ci-VSP, was the first Voltage-controlled Enzyme (VEnz) proven to be under direct command of the membrane potential. The discovery of Ci-VSP conjugated voltage sensitivity and enzymatic activity in a single protein. These two facets of Ci-VSP activity have provided a unique model for studying how membrane potential is sensed by proteins and a novel mechanism for control of enzymatic activity. These facets make Ci-VSP a fascinating and versatile enzyme. Ci-VSP has a voltage sensing domain (VSD) that resembles those found in voltage-gated channels (VGC). The VSD resides in the N-terminus and is formed by four putative transmembrane segments. The fourth segment contains charged residues which are likely involved in voltage sensing. Ci-VSP produces sensing currents in response to changes in potential, within a defined range of voltages. Sensing currents are analogous to “gating” currents in VGC. As known, these latter proteins contain four VSDs which are entangled in a complex interaction with the pore domain – the effector domain in VGC. This complexity makes studying the basis of voltage sensing in VGC a difficult enterprise. In contrast, Ci-VSP is thought to be monomeric and its catalytic domain – the VSP’s effector domain – can be cleaved off without disrupting the basic electrical functioning of the VSD. For these reasons, VSPs are considered a great model for studying the activity of a VSD in isolation. Finally, VSPs are also phosphoinositide phosphatases. Phosphoinositides are signaling lipids found in eukaryotes and are involved in many processes, including modulation of VGC activity and regulation of cell proliferation. Understanding VSPs as enzymes has been the center of attention in recent years and several reviews has been dedicated to this area. Thus, this review will be focused instead on the other face of this true JanusBifrons and recapitulate what is known about VSPs as electrically active proteins.
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Affiliation(s)
- Carlos A Villalba-Galea
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine Richmond, VA, USA
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10
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New insights in the activity of voltage sensitive phosphatases. Cell Signal 2012; 24:1541-7. [PMID: 22481094 DOI: 10.1016/j.cellsig.2012.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/13/2012] [Accepted: 03/20/2012] [Indexed: 11/23/2022]
Abstract
The Ciona intestinalis voltage sensitive phosphatase (Ci-VSP) was the first proven enzyme to be under direct control of the membrane potential. Ci-VSP belongs to a family of proteins known as Protein Tyrosine Phosphatases (PTP), which are a group of enzymes that catalyze the removal of phosphate groups from phosphatidylinositides and phosphorylated tyrosine residues on proteins. What makes Ci-VSP and similar phosphatases unique is the presence of a Voltage Sensing Domain (VSD) in their N-terminus. The VSD of Ci-VSP shares high homology with those from voltage-gated channels and confers voltage sensitivity to these enzymes. The catalytic domain of Ci-VSP displays extraordinary structural and functional similarities to PTEN. This latter protein is encoded by the Phosphatase and Tensin homolog deleted from chromosome 10 gene, thus its name, and it is known as a tumor suppressor. The resemblance between these proteins has prompted the use of PTEN as a template for the study of Ci-VSP and produced a rapid advance in our understanding of the mechanism of activity of Ci-VSP. This review will be focused on discussing recent advances in the understanding of the activation mechanism for these molecules known as electrochemical coupling.
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11
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Mishra RR, Chaudhary JK, Bajaj GD, Rath PC. A novel human TPIP splice-variant (TPIP-C2) mRNA, expressed in human and mouse tissues, strongly inhibits cell growth in HeLa cells. PLoS One 2011; 6:e28433. [PMID: 22164291 PMCID: PMC3229583 DOI: 10.1371/journal.pone.0028433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/08/2011] [Indexed: 11/23/2022] Open
Abstract
Alternative splicing of mRNAs is known to involve a major regulation of gene expression at RNA level in mammalian cells. The PTEN (Phosphatase and TENsin homologue deleted from the human chromosome 10), TPTE (Transmembrane Phosphatase with TEnsin homology) and TPIP (TPTE and PTEN homologous Inositol lipid Phosphatase) belong to a family of dual-specific lipid and protein phosphatases. PTEN is a well characterized tumor suppressor, which plays crucial role in cell survival, cell cycle regulation, cell proliferation as well as adhesion, motility and migration of cells. The C2-domain of PTEN is essential for PTEN-functions. We have isolated a novel 1019 bp human TPIP cDNA (TPIP-C2) from a human testis cDNA library. In silico analysis of the cDNA revealed that it is produced from the TPIP-locus on the human chromosome 13 by alternative RNA-splicing. It has a unique 5′-Alu sequence, a LINE sequence followed by a 582 bp Open Reading Frame (ORF) encoding a 193 aa polypeptide with a partial phosphatase domain and a C2-domain. TPIP-C2 mRNA is expressed in human testis and in mouse tissues. Mouse testis and brain showed higher levels of TPIP-C2 mRNA in comparison to the heart, liver and kidney under normal physiological conditions. TPIP-C2 mRNAs from human and mouse testes show extensive sequence identity. Over-expression of TPIP-C2 cDNA in HeLa cells strongly (up to 85%) inhibited cell growth/proliferation and caused apoptosis in a caspase 3-dependent manner. These findings suggest for the first time that a TPIP splice-variant mRNA with a partial phosphatase domain and a C2-domain is expressed in cells and tissues of human and murine origins under normal physiological conditions. Inhibition of cell growth/proliferation and induction of apoptosis by overexpression of TPIP-C2 mRNA in HeLa cells suggest that it may be involved in negative regulation of cell growth/proliferation.
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Affiliation(s)
- Rasmi Rekha Mishra
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jitendra Kumar Chaudhary
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gagan Deep Bajaj
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pramod C. Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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12
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Eichler EE, Clark RA, She X. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat Rev Genet 2004; 5:345-54. [PMID: 15143317 DOI: 10.1038/nrg1322] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Evan E Eichler
- Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, BRB720, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
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13
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Tapparel C, Reymond A, Girardet C, Guillou L, Lyle R, Lamon C, Hutter P, Antonarakis SE. The TPTE gene family: cellular expression, subcellular localization and alternative splicing. Gene 2003; 323:189-99. [PMID: 14659893 DOI: 10.1016/j.gene.2003.09.038] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The human TPTE (Transmembrane Phosphatase with TEnsin homology) gene family encodes a PTEN-related tyrosine phosphatase with four potential transmembrane domains. Chromosomal mapping revealed multiple copies of the TPTE gene on chromosomes 13, 15, 21, 22 and Y. Human chromosomes 13 and 21 copies encode two functional proteins, TPIP (TPTE and PTEN homologous Inositol lipid Phosphatase) and TPTE, respectively, whereas only one copy of the gene exists in the mouse genome. In the present study, we show that TPTE and TPIP proteins are expressed in secondary spermatocytes and/or prespermatids. In addition, we report the existence of several novel alternatively spliced isoforms of these two proteins with variable number of transmembrane domains. The latter has no influence on the subcellular localization of these different peptides as shown by co-immunofluorescence experiments. Finally, we identify another expressed TPTE copy, mapping to human chromosome 22, whose transcription appears to be under the control of the LTR of human endogenous retrovirus RTVL-H3.
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Affiliation(s)
- Caroline Tapparel
- Division of Medical Genetics, Centre Medical Universitaire, University of Geneva Medical School, 1, Rue Michel Servet CH-1211, Geneva, Switzerland
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14
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Brun ME, Ruault M, Ventura M, Roizès G, De Sario A. Juxtacentromeric region of human chromosome 21: a boundary between centromeric heterochromatin and euchromatic chromosome arms. Gene 2003; 312:41-50. [PMID: 12909339 DOI: 10.1016/s0378-1119(03)00530-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have analysed the genomic structure and transcriptional activity of a 2.3-Mb genomic sequence in the juxtacentromeric region of human chromosome 21. Our work shows that this region comprises two different chromosome domains. The 1.5-Mb proximal domain: (i) is a patchwork of chromosome duplications; (ii) shares sequence similarity with several chromosomes; (iii) contains several gene fragments (truncated genes having an intron/exon structure) intermingled with retrotransposed pseudogenes; and (iv) harbours two genes (TPTE and BAGE2) that belong to gene families and have a cancer and/or testis expression profile. The TPTE gene family was generated before the branching of Old World monkeys from the great ape lineage, by intra- and interchromosome duplications of the ancestral TPTE gene mapping to phylogenetic chromosome XIII. By contrast, the 0.8-Mb distal domain: (i) is devoid of chromosome duplications; (ii) has a chromosome 21-specific sequence; (iii) contains no gene fragments and only one retrotransposed pseudogene; and (iv) harbours six genes including housekeeping genes. G-rich sequences commonly associated with duplication termini cluster at the boundary between the two chromosome domains. These structural and transcriptional features lead us to suggest that the proximal domain has heterochromatic properties, whereas the distal domain has euchromatic properties.
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MESH Headings
- ATP-Binding Cassette Transporters/genetics
- Adaptor Proteins, Vesicular Transport/genetics
- Alternative Splicing
- Animals
- Antigens, Neoplasm/genetics
- Base Composition
- Blotting, Northern
- Cell Line
- Centromere/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 21/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Databases, Nucleic Acid
- Euchromatin/genetics
- Female
- Gene Duplication
- Gene Expression
- Heterochromatin/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Membrane Proteins/genetics
- Molecular Sequence Data
- PTEN Phosphohydrolase
- Phosphoric Monoester Hydrolases
- Protein Tyrosine Phosphatases/genetics
- Pseudogenes/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/genetics
- Repetitive Sequences, Nucleic Acid
- Retroelements/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Marie-Elisabeth Brun
- Institut de Génétique Humaine, CNRS UPR 1142, 141, rue de la Cardonille, 34396 Montpellier, France
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15
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Ruault M, Ventura M, Galtier N, Brun ME, Archidiacono N, Roizès G, De Sario A. BAGE genes generated by juxtacentromeric reshuffling in the Hominidae lineage are under selective pressure. Genomics 2003; 81:391-9. [PMID: 12676563 DOI: 10.1016/s0888-7543(03)00025-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this paper, we show that the BAGE (B melanoma antigen) gene family was generated by chromosome rearrangements that occurred during the evolution of hominoids. An 84-kb DNA fragment derived from the phylogenetic 7q36 region was duplicated in the juxtacentromeric region of either chromosome 13 or chromosome 21. The duplicated region contained a fragment of the MLL3 gene, which, after juxtacentromeric reshuffling, generated the ancestral BAGE gene. Then, this ancestral gene gave rise to several independent genes through successive rounds of inter- and intrachromosome duplications. Comparison of synonymous and nonsynonymous mutations in putative coding regions shows that BAGE genes, but not the BAGE gene fragments, are under selective pressure. Our data strongly suggest that BAGE proteins have a function and that juxtacentromeric regions, whose plasticity is now largely proved, are not a simple junkyard of gene fragments, but may be the birth site of novel genes.
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MESH Headings
- Animals
- Antigens, Neoplasm/genetics
- Centromere/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 7/genetics
- Cluster Analysis
- DNA Primers
- Electrophoresis, Gel, Pulsed-Field
- Gene Duplication
- Gene Rearrangement/genetics
- Hominidae/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Phylogeny
- Selection, Genetic
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Affiliation(s)
- Myriam Ruault
- Institut de Génétique Humaine, CNRS UPR 1142, 141, Rue de la Cardonille, 34396 Montpellier, France
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16
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Abstract
This review considers the role of the sperm in fertilization, addressing areas of misunderstanding and unfounded assumptions and taking particular advantage of the large body of data resulting from work with rodent species in vitro. Considerable attention is given to the appropriate use and interpretation of assays for capacitation, acrosomal exocytosis, hyperactivation, and sperm protein phosphorylation, as well as tests for sperm-zona and sperm-oocyte membrane interactions. The lack of general agreement on the means of sperm adhesion to and penetration of the zona pellucida is addressed, and the need for new approaches to this problem is pointed out. Some molecular advances in our understanding of specific steps in the process of fertilization are discussed in the context of intact cell-matrix and cell-cell interaction. This review should provide practical information for researchers just beginning the study of fertilization and interesting but not widely known observations to stimulate new ideas in experienced scientists.
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Affiliation(s)
- Patricia Olds-Clarke
- Department of Anatomy and Cell Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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17
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Ruault M, van der Bruggen P, Brun ME, Boyle S, Roizès G, De Sario A. New BAGE (B melanoma antigen) genes mapping to the juxtacentromeric regions of human chromosomes 13 and 21 have a cancer/testis expression profile. Eur J Hum Genet 2002; 10:833-40. [PMID: 12461691 DOI: 10.1038/sj.ejhg.5200891] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2002] [Revised: 07/30/2002] [Accepted: 07/31/2002] [Indexed: 11/09/2022] Open
Abstract
A first BAGE (B melanoma antigen) gene, BAGE1, was identified because it encodes a human tumour antigen recognised by a cytolytic T lymphocyte. Here, we characterised five new BAGE genes mapping to the juxtacentromeric regions of human chromosomes 13 and 21 and nine BAGE gene fragments mapping to the juxtacentromeric regions of chromosomes 9, 13, 18, and 21. Genes and gene fragments share extensive regions of 90-99% nucleotide identity. We analysed the expression of BAGE genes on 215 tumours of various histological types and on nine normal tissues. Similar to BAGE1, the new BAGE genes are expressed in melanomas, bladder and lung carcinomas and in a few tumours of other histological types. All the normal tissues were negative, with the exception of testis. Our results show that human juxtacentromeric regions harbour genes, which are transcribed and translated, in addition to gene fragments that are generally not expressed. We suggest that the pattern of expression restricted to cancer/testis is a feature of the few genes mapping to juxtacentromeric regions.
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Affiliation(s)
- Myriam Ruault
- Institut de Génétique Humaine, CNRS UPR 1142, 141, rue de la Cardonille, 34396 Montpellier, France
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18
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Abstract
The six-transmembrane channels are thought to be composed of two modules: pore and sensor. Whereas the modular design of the pore has been established, the modularity of the sensor remains hypothetical. As a first step toward establishing the modularity of this region, we searched for genes where the sensor is found independent of the pore and have identified new members of the sensor superfamily. Analysis of these sensors reveals a motif shared among not only these newly discovered members and voltage-gated, transient receptor potential, and polycystin channel sensors, but also MscL, a bacterial mechanosensitive channel. Mutational analyses presented here and in previous studies demonstrate that highly conserved residues within this motif are required for normal channel activity; mutations of residues within this motif in different subfamilies lead to consistent channel phenotypes. Previous studies have demonstrated that peptides containing this motif and the adjacent conserved transmembrane domain elicit channel activities when reconstituted into lipid membranes. These data provide evidence for the modularity of the sensor, imply a model for its evolution, suggest a common origin for mechano- and voltage-sensing, and may offer a glimpse of the properties of the first sensor/channel.
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Affiliation(s)
- Attila Kumánovics
- Center for Immunology and, Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
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19
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Abstract
The PTEN (phosphatase and tensin homologue deleted on chromosome 10) tumour suppressor is a phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P(3)] 3-phosphatase that plays a critical role in regulating many cellular processes by antagonizing the phosphoinositide 3-kinase signalling pathway. We have identified and characterized two human homologues of PTEN, which differ with respect to their subcellular localization and lipid phosphatase activities. The previously cloned, but uncharacterized, TPTE (transmembrane phosphatase with tensin homology) is localized to the plasma membrane, but lacks detectable phosphoinositide 3-phosphatase activity. TPIP (TPTE and PTEN homologous inositol lipid phosphatase) is a novel phosphatase that occurs in several differentially spliced forms of which two, TPIP alpha and TPIP beta, appear to be functionally distinct. TPIP alpha displays similar phosphoinositide 3-phosphatase activity compared with PTEN against PtdIns(3,4,5)P(3), PtdIns(3,5)P(2), PtdIns(3,4)P(2) and PtdIns(3)P, has N-terminal transmembrane domains and appears to be localized on the endoplasmic reticulum. This is unusual as most signalling-lipid-metabolizing enzymes are not integral membrane proteins. TPIP beta, however, lacks detectable phosphatase activity and is cytosolic. TPIP has a wider tissue distribution than the testis-specific TPTE, with specific splice variants being expressed in testis, brain and stomach. TPTE and TPIP do not appear to be functional orthologues of the Golgi-localized and more distantly related murine PTEN2. We suggest that TPIP alpha plays a role in regulating phosphoinositide signalling on the endoplasmic reticulum, and might also represent a tumour suppressor and functional homologue of PTEN in some tissues.
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Affiliation(s)
- S M Walker
- Division of Cell Signalling, School of Life Sciences, University of Dundee, MSI/WTB Complex, Dow Street, Dundee DD1 5EH, Scotland, UK
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