1
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Wei W, Schon KR, Elgar G, Orioli A, Tanguy M, Giess A, Tischkowitz M, Caulfield MJ, Chinnery PF. Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes. Nature 2022; 611:105-114. [PMID: 36198798 PMCID: PMC9630118 DOI: 10.1038/s41586-022-05288-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/29/2022] [Indexed: 02/02/2023]
Abstract
DNA transfer from cytoplasmic organelles to the cell nucleus is a legacy of the endosymbiotic event-the majority of nuclear-mitochondrial segments (NUMTs) are thought to be ancient, preceding human speciation1-3. Here we analyse whole-genome sequences from 66,083 people-including 12,509 people with cancer-and demonstrate the ongoing transfer of mitochondrial DNA into the nucleus, contributing to a complex NUMT landscape. More than 99% of individuals had at least one of 1,637 different NUMTs, with 1 in 8 individuals having an ultra-rare NUMT that is present in less than 0.1% of the population. More than 90% of the extant NUMTs that we evaluated inserted into the nuclear genome after humans diverged from apes. Once embedded, the sequences were no longer under the evolutionary constraint seen within the mitochondrion, and NUMT-specific mutations had a different mutational signature to mitochondrial DNA. De novo NUMTs were observed in the germline once in every 104 births and once in every 103 cancers. NUMTs preferentially involved non-coding mitochondrial DNA, linking transcription and replication to their origin, with nuclear insertion involving multiple mechanisms including double-strand break repair associated with PR domain zinc-finger protein 9 (PRDM9) binding. The frequency of tumour-specific NUMTs differed between cancers, including a probably causal insertion in a myxoid liposarcoma. We found evidence of selection against NUMTs on the basis of size and genomic location, shaping a highly heterogenous and dynamic human NUMT landscape.
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Affiliation(s)
- Wei Wei
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Katherine R Schon
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Marc Tischkowitz
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Patrick F Chinnery
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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2
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Ji F, Zhu X, Liao H, Ouyang L, Huang Y, Syeda MZ, Ying S. New Era of Mapping and Understanding Common Fragile Sites: An Updated Review on Origin of Chromosome Fragility. Front Genet 2022; 13:906957. [PMID: 35669181 PMCID: PMC9164283 DOI: 10.3389/fgene.2022.906957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic loci prone to forming gaps or breakages upon replication perturbation, which correlate well with chromosomal rearrangement and copy number variation. CFSs have been actively studied due to their important pathophysiological relevance in different diseases such as cancer and neurological disorders. The genetic locations and sequences of CFSs are crucial to understanding the origin of such unstable sites, which require reliable mapping and characterizing approaches. In this review, we will inspect the evolving techniques for CFSs mapping, especially genome-wide mapping and sequencing of CFSs based on current knowledge of CFSs. We will also revisit the well-established hypotheses on the origin of CFSs fragility, incorporating novel findings from the comprehensive analysis of finely mapped CFSs regarding their locations, sequences, and replication/transcription, etc. This review will present the most up-to-date picture of CFSs and, potentially, a new framework for future research of CFSs.
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Affiliation(s)
- Fang Ji
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinli Zhu
- Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Liao
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Liujian Ouyang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingfei Huang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Madiha Zahra Syeda
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
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3
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Ji F, Liao H, Pan S, Ouyang L, Jia F, Fu Z, Zhang F, Geng X, Wang X, Li T, Liu S, Syeda MZ, Chen H, Li W, Chen Z, Shen H, Ying S. Genome-wide high-resolution mapping of mitotic DNA synthesis sites and common fragile sites by direct sequencing. Cell Res 2020; 30:1009-1023. [PMID: 32561861 DOI: 10.1038/s41422-020-0357-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/31/2020] [Indexed: 01/13/2023] Open
Abstract
Common fragile sites (CFSs) are genomic loci prone to the formation of breaks or gaps on metaphase chromosomes. They are hotspots for chromosome rearrangements and structural variations, which have been extensively implicated in carcinogenesis, aging, and other pathological processes. Although many CFSs were identified decades ago, a consensus is still lacking for why they are particularly unstable and sensitive to replication perturbations. This is in part due to the lack of high-resolution mapping data for the vast majority of the CFSs, which has hindered mechanistic interrogations. Here, we seek to map human CFSs with high resolution on a genome-wide scale by sequencing the sites of mitotic DNA synthesis (MiDASeq) that are specific for CFSs. We generated a nucleotide-resolution atlas of MiDAS sites (MDSs) that covered most of the known CFSs, and comprehensively analyzed their sequence characteristics and genomic features. Our data on MDSs tallied well with long-standing hypotheses to explain CFS fragility while highlighting the contributions of late replication timing and large transcription units. Notably, the MDSs also encompassed most of the recurrent double-strand break clusters previously identified in mouse neural stem/progenitor cells, thus bridging evolutionarily conserved break points across species. Moreover, MiDAseq provides an important resource that can stimulate future research on CFSs to further unravel the mechanisms and biological relevance underlying these labile genomic regions.
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Affiliation(s)
- Fang Ji
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Hongwei Liao
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Sheng Pan
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Liujian Ouyang
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Fang Jia
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Zaiyang Fu
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Fengjiao Zhang
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Xinwei Geng
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Xinming Wang
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Tingting Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Shuangying Liu
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Madiha Zahra Syeda
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Haixia Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Zhihua Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China. .,State Key Laboratory of Respiratory Diseases, Guangzhou, Guangdong, 510120, China.
| | - Songmin Ying
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.
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4
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Guadarrama-Ponce R, Aranda-Anzaldo A. The epicenter of chromosomal fragility of Fra14A2, the mouse ortholog of human FRA3B common fragile site, is largely attached to the nuclear matrix in lymphocytes but not in other cell types that do not express such a fragility. J Cell Biochem 2019; 121:2209-2224. [PMID: 31646677 DOI: 10.1002/jcb.29444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/10/2019] [Indexed: 12/22/2022]
Abstract
Common fragile sites (CFSs) correspond to chromosomal regions susceptible to present breaks, discontinuities or constrictions in metaphase chromosomes from cells subjected to replication stress. They are considered as genomic regions intrinsically difficult to replicate and they are evolutionary conserved at least in mammals. However, the recent discovery that CFSs are cell-type specific indicates that DNA sequence by itself cannot account for CFS instability. Nevertheless, the large gene FHIT that includes FRA3B, the most highly expressed CFS in human lymphocytes, is commonly deleted in a variety of tumors suggesting a tumor suppressor role for its product. Here, we report that the epicenter of fragility of Fra14A2/Fhit, the mouse ortholog of human FRA3B/FHIT that like its human counterpart is the most highly expressed CFS in mouse lymphocytes, is largely attached to the nuclear matrix compartment in naive B lymphocytes but not in primary hepatocytes or cortical neurons that do not express such a CFS. Our results suggest a structural explanation for the difficult-to-replicate nature of such a region and so for its common fragility in lymphocytes, that is independent of the possible tumor suppressor role of the gene harboring such CFS.
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Affiliation(s)
- Rolando Guadarrama-Ponce
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Mexico
| | - Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Mexico
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5
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Druck T, Cheung DG, Park D, Trapasso F, Pichiorri F, Gaspari M, Palumbo T, Aqeilan RI, Gaudio E, Okumura H, Iuliano R, Raso C, Green K, Huebner K, Croce CM. Fhit-Fdxr interaction in the mitochondria: modulation of reactive oxygen species generation and apoptosis in cancer cells. Cell Death Dis 2019; 10:147. [PMID: 30770797 PMCID: PMC6377664 DOI: 10.1038/s41419-019-1414-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/08/2023]
Abstract
Fhit protein is lost in cancers of most, perhaps all, cancer types; when restored, it can induce apoptosis and suppress tumorigenicity, as shown in vitro and in mouse tumor models in vivo. Following protein cross-linking and proteomics analyses, we characterized a Fhit protein complex involved in triggering Fhit-mediated apoptosis. The complex includes the heat-shock chaperonin pair, HSP60/10, which is likely involved in importing Fhit into the mitochondria, where it interacts with ferredoxin reductase, responsible for transferring electrons from NADPH to cytochrome P450 via ferredoxin, in electron transport chain complex III. Overexpression of Fhit protein in Fhit-deficient cancer cells modulates the production of intracellular reactive oxygen species, causing increased ROS, following peroxide treatment, with subsequent increased apoptosis of lung cancer cells under oxidative stress conditions; conversely, Fhit-negative cells escape ROS overproduction and ROS-induced apoptosis, likely carrying oxidative damage. Thus, characterization of Fhit-interacting proteins has identified direct effectors of a Fhit-mediated apoptotic signal pathway that is lost in many cancers. This is of translational interest considering the very recent emphasis in a number of high-profile publications, concerning the role of oxidative phosphorylation in the treatment of human cancers, and especially cancer stem cells that rely upon oxidative phosphorylation for survival. Additionally, we have shown that cells from a Fhit-deficient lung cancer cell line, are sensitive to killing by exposure to atovaquone, thought to act as a selective oxidative phosphorylation inhibitor by targeting the CoQ10 dependence of the mitochondrial complex III, while the Fhit-expressing sister clone is resistant to this treatment.
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Affiliation(s)
- Teresa Druck
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Douglas G Cheung
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Dongju Park
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Francesco Trapasso
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
| | - Flavia Pichiorri
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Marco Gaspari
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
| | - Tiziana Palumbo
- Dipartimento di Farmacologia Sperimentale Preclinica e Clinica, University of Catania, Catania, 95123, Italy
| | - Rami I Aqeilan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
- Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eugenio Gaudio
- Università della Svizzera italiana, Institute of Oncology Research, Bellinzona, Switzerland
| | - Hiroshi Okumura
- Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima, Japan
| | - Rodolfo Iuliano
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
| | - Cinzia Raso
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - Kari Green
- Department of Chemistry, Mass Spectrometry Research and Education Center, University of Florida, 126 Sisler Hall, Gainesville, FL, 32611-7200, USA
| | - Kay Huebner
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA.
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6
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Palumbo E, Russo A. Common fragile site instability in normal cells: Lessons and perspectives. Genes Chromosomes Cancer 2018; 58:260-269. [PMID: 30387295 DOI: 10.1002/gcc.22705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/26/2022] Open
Abstract
Mechanisms and events related to common fragile site (CFS) instability are well known in cancer cells. Here, we argue that normal cells remain an important experimental model to address questions related to CFS instability in the absence of alterations in cell cycle and DNA damage repair pathways, which are common features acquired in cancer. Furthermore, a major gap of knowledge concerns the stability of CFSs during gametogenesis. CFS instability in meiotic or postmeiotic stages of the germ cell line could generate chromosome deletions or large rearrangements. This in turn can lead to the functional loss of the several CFS-associated genes with tumor suppressor function. Our hypothesis is that such mutations can potentially result in genetic predisposition to develop cancer. Indirect evidence for CFS instability in human germ cells has been provided by genomic investigations in family pedigrees associated with genetic disease. The issue of CFS instability in the germ cell line should represent one of the future efforts, and may take advantage of the existence of sequence and functional conservation of CFSs between rodents and humans.
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Affiliation(s)
- Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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7
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Gaudio E, Paduano F, Ngankeu A, Ortuso F, Lovat F, Pinton S, D'Agostino S, Zanesi N, Aqeilan RI, Campiglia P, Novellino E, Alcaro S, Croce CM, Trapasso F. A Fhit-mimetic peptide suppresses annexin A4-mediated chemoresistance to paclitaxel in lung cancer cells. Oncotarget 2017; 7:29927-36. [PMID: 27166255 PMCID: PMC5058653 DOI: 10.18632/oncotarget.9179] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/11/2016] [Indexed: 01/04/2023] Open
Abstract
We recently reported that Fhit is in a molecular complex with annexin A4 (ANXA4); following to their binding, Fhit delocalizes ANXA4 from plasma membrane to cytosol in paclitaxel-resistant lung cancer cells, thus restoring their chemosensitivity to the drug. Here, we demonstrate that Fhit physically interacts with A4 through its N-terminus; molecular dynamics simulations were performed on a 3D Fhit model to rationalize its mechanism of action. This approach allowed for the identification of the QHLIKPS heptapeptide (position 7 to 13 of the wild-type Fhit protein) as the smallest Fhit sequence still able to preserve its ability to bind ANXA4. Interestingly, Fhit peptide also recapitulates the property of the native protein in inhibiting Annexin A4 translocation from cytosol to plasma membrane in A549 and Calu-2 lung cancer cells treated with paclitaxel. Finally, the combination of Tat-Fhit peptide and paclitaxel synergistically increases the apoptotic rate of cultured lung cancer cells and blocks in vivo tumor formation. Our findings address to the identification of chemically simplified Fhit derivatives that mimic Fhit tumor suppressor functions; intriguingly, this approach might lead to the generation of novel anticancer drugs to be used in combination with conventional therapies in Fhit-negative tumors to prevent or delay chemoresistance.
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Affiliation(s)
- Eugenio Gaudio
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA.,Lymphoma & Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland.,Dipartimento di Medicina Sperimentale e Clinica, University Magna Græcia, Campus "S. Venuta", Catanzaro, Italy
| | - Francesco Paduano
- Dipartimento di Medicina Sperimentale e Clinica, University Magna Græcia, Campus "S. Venuta", Catanzaro, Italy
| | - Apollinaire Ngankeu
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, University Magna Græcia, Campus "S. Venuta", Catanzaro, Italy
| | - Francesca Lovat
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Sandra Pinton
- Lymphoma & Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Sabrina D'Agostino
- Dipartimento di Medicina Sperimentale e Clinica, University Magna Græcia, Campus "S. Venuta", Catanzaro, Italy
| | - Nicola Zanesi
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Rami I Aqeilan
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA.,The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research, The Hebrew University, Jerusalem, Israel
| | - Pietro Campiglia
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, University Magna Græcia, Campus "S. Venuta", Catanzaro, Italy
| | - Carlo M Croce
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Francesco Trapasso
- Dipartimento di Medicina Sperimentale e Clinica, University Magna Græcia, Campus "S. Venuta", Catanzaro, Italy
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8
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The ubiquitous 'cancer mutational signature' 5 occurs specifically in cancers with deleted FHIT alleles. Oncotarget 2017; 8:102199-102211. [PMID: 29254236 PMCID: PMC5731946 DOI: 10.18632/oncotarget.22321] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/25/2017] [Indexed: 01/22/2023] Open
Abstract
The FHIT gene is located at the fragile FRA3B locus where activation by carcinogen-induced and endogenous replication stress causes FHIT deletions even in normal cells over a lifetime. Our lab has shown that loss of FHIT expression causes genome instability and provides single-strand DNA substrates for APOBEC3B hypermutation, in line with evidence that FHIT locus deletions occur in many cancers. Based on these biological features, we hypothesized that FHIT loss drives development of COSMIC mutational signature 5 and here provide evidence, including data mining of >6,500 TCGA samples, that FHIT is the cancer-associated gene with copy number alterations correlating most significantly with signature 5 mutation rate. In addition, tissues of Fhit-deficient mice exhibit a mutational signature strongly resembling signature 5 (cosine similarity value = 0.89). We conclude that FHIT loss is a molecular determinant for signature 5 mutations, which occur in all cancer types early in cancer development, are clock-like, and accelerated by carcinogen exposure. Loss of FHIT caretaker function may be a predictive and preventive marker for cancer development.
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9
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Gaudio E, Paduano F, Croce CM, Trapasso F. The Fhit protein: an opportunity to overcome chemoresistance. Aging (Albany NY) 2016; 8:3147-3150. [PMID: 27852977 PMCID: PMC5191891 DOI: 10.18632/aging.101123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 11/10/2016] [Indexed: 11/25/2022]
Affiliation(s)
- Eugenio Gaudio
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, OH, USA
- Lymphoma & Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
- Dipartimento di Medicina Sperimentale e Clinica, University , Catanzaro, Italy
| | - Francesco Paduano
- Dipartimento di Medicina Sperimentale e Clinica, University , Catanzaro, Italy
- Tecnologica Research Institute, Biomedical Section, Crotone, Italy
| | - Carlo M Croce
- Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, OH, USA
| | - Francesco Trapasso
- Dipartimento di Medicina Sperimentale e Clinica, University , Catanzaro, Italy
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10
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Gao G, Smith DI. Very large common fragile site genes and their potential role in cancer development. Cell Mol Life Sci 2014; 71:4601-15. [PMID: 25300511 PMCID: PMC11113612 DOI: 10.1007/s00018-014-1753-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
Abstract
Common fragile sites (CFSs) are large chromosomal regions that are hot-spots for alterations especially within cancer cells. The three most frequently expressed CFS regions (FRA3B, FRA16D and FRA6E) contain genes that span extremely large genomic regions (FHIT, WWOX and PARK2, respectively), and these genes were found to function as important tumor suppressors. Many other CFS regions contain extremely large genes that are also targets of alterations in multiple cancers, but none have yet been demonstrated to function as tumor suppressors. The loss of expression of just FHIT or WWOX has been found to be associated with a worse overall clinical outcome. Studies in different cancers have revealed that some cancers have decreased expression of multiple large CFS genes. This loss of expression could have a profound phenotypic effect on these cells. In this review, we will summarize the known large common fragile site genes and discuss their potential relationship to cancer development.
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Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - David I. Smith
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
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11
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Zainabadi K, Jain AV, Donovan FX, Elashoff D, Rao NP, Murty VV, Chandrasekharappa SC, Srivatsan ES. One in four individuals of African-American ancestry harbors a 5.5kb deletion at chromosome 11q13.1. Genomics 2014; 103:276-87. [PMID: 24412158 DOI: 10.1016/j.ygeno.2014.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 11/11/2013] [Accepted: 01/02/2014] [Indexed: 01/11/2023]
Abstract
Cloning and sequencing of 5.5 kb deletion at chromosome 11q13.1 from the HeLa cells, tumorigenic hybrids and two fibroblast cell lines have revealed homologous recombination between AluSx and AluY resulting in the deletion of intervening sequences. Long-range PCR of the 5.5 kb sequence in 494 normal lymphocyte samples showed heterozygous deletion in 28.3% of African-American ancestry samples but only in 4.8% of Caucasian samples (p<0.0001). This observation is strengthened by the copy number variation (CNV) data of the HapMap samples which showed that this deletion occurs in 27% of YRI (Yoruba--West African) population but none in non-African populations. The HapMap analysis further identified strong linkage disequilibrium between 5 single nucleotide polymorphisms and the 5.5 kb deletion in people of African ancestry. Computational analysis of 175 kb sequence surrounding the deletion site revealed enhanced flexibility, low thermodynamic stability, high repetitiveness, and stable stem-loop/hairpin secondary structures that are hallmarks of common fragile sites.
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Affiliation(s)
- Kayvan Zainabadi
- Division of General Surgery, Department of Surgery, VAGLAHS West Los Angeles, David Geffen School of Medicine at UCLA, Los Angeles, CA 90073, USA
| | - Anuja V Jain
- Division of General Surgery, Department of Surgery, VAGLAHS West Los Angeles, David Geffen School of Medicine at UCLA, Los Angeles, CA 90073, USA
| | - Frank X Donovan
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Elashoff
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90025, USA
| | - Nagesh P Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90025, USA
| | - Vundavalli V Murty
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Settara C Chandrasekharappa
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eri S Srivatsan
- Division of General Surgery, Department of Surgery, VAGLAHS West Los Angeles, David Geffen School of Medicine at UCLA, Los Angeles, CA 90073, USA.
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12
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Fhit delocalizes annexin a4 from plasma membrane to cytosol and sensitizes lung cancer cells to paclitaxel. PLoS One 2013; 8:e78610. [PMID: 24223161 PMCID: PMC3819369 DOI: 10.1371/journal.pone.0078610] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 09/14/2013] [Indexed: 11/29/2022] Open
Abstract
Fhit protein is lost or reduced in a large fraction of human tumors, and its restoration triggers apoptosis and suppresses tumor formation or progression in preclinical models. Here, we describe the identification of candidate Fhit-interacting proteins with cytosolic and plasma membrane localization. Among these, Annexin 4 (ANXA4) was validated by co-immunoprecipitation and confocal microscopy as a partner of this novel Fhit protein complex. Here we report that overexpression of Fhit prevents Annexin A4 translocation from cytosol to plasma membrane in A549 lung cancer cells treated with paclitaxel. Moreover, paclitaxel administration in combination with AdFHIT acts synergistically to increase the apoptotic rate of tumor cells both in vitro and in vivo experiments.
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13
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Ben-David U, Benvenisty N. High prevalence of evolutionarily conserved and species-specific genomic aberrations in mouse pluripotent stem cells. Stem Cells 2012; 30:612-22. [PMID: 22328490 DOI: 10.1002/stem.1057] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mouse pluripotent stem cells (PSCs) are the best studied pluripotent system and are regarded as the "gold standard" to which human PSCs are compared. However, while the genomic integrity of human PSCs has recently drawn much attention, mouse PSCs have not been systematically evaluated in this regard. The genomic stability of PSCs is a matter of profound significance, as it affects their pluripotency, differentiation, and tumorigenicity. We thus performed a thorough analysis of the genomic integrity of 325 samples of mouse PSCs, including 127 induced pluripotent stem cell (iPSC) samples. We found that genomic aberrations occur frequently in mouse embryonic stem cells of various mouse strains, add in mouse iPSCs of various cell origins and derivation techniques. Four hotspots of chromosomal aberrations were detected: full trisomy 11 (with a minimally recurrent gain in 11qE2), full trisomy 8, and deletions in chromosomes 10qB and 14qC-14qE. The most recurrent aberration in mouse PSCs, gain 11qE2, turned out to be fully syntenic to the common aberration 17q25 in human PSCs, while other recurrent aberrations were found to be species specific. Analysis of chromosomal aberrations in 74 samples of rhesus macaque PSCs revealed a gain in chromosome 16q, syntenic to the hotspot in human 17q. Importantly, these common aberrations jeopardize the interpretation of published comparisons of PSCs, which were unintentionally conducted between normal and aberrant cells. Therefore, this work emphasizes the need to carefully monitor genomic integrity of PSCs from all species, for their proper use in biomedical research.
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Affiliation(s)
- Uri Ben-David
- Stem Cell Unit, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
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14
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Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Res 2012; 22:993-1005. [PMID: 22456607 PMCID: PMC3371707 DOI: 10.1101/gr.134395.111] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Chromosomal common fragile sites (CFSs) are unstable genomic regions that break under replication stress and are involved in structural variation. They frequently are sites of chromosomal rearrangements in cancer and of viral integration. However, CFSs are undercharacterized at the molecular level and thus difficult to predict computationally. Newly available genome-wide profiling studies provide us with an unprecedented opportunity to associate CFSs with features of their local genomic contexts. Here, we contrasted the genomic landscape of cytogenetically defined aphidicolin-induced CFSs (aCFSs) to that of nonfragile sites, using multiple logistic regression. We also analyzed aCFS breakage frequencies as a function of their genomic landscape, using standard multiple regression. We show that local genomic features are effective predictors both of regions harboring aCFSs (explaining ∼77% of the deviance in logistic regression models) and of aCFS breakage frequencies (explaining ∼45% of the variance in standard regression models). In our optimal models (having highest explanatory power), aCFSs are predominantly located in G-negative chromosomal bands and away from centromeres, are enriched in Alu repeats, and have high DNA flexibility. In alternative models, CpG island density, transcription start site density, H3K4me1 coverage, and mononucleotide microsatellite coverage are significant predictors. Also, aCFSs have high fragility when colocated with evolutionarily conserved chromosomal breakpoints. Our models are predictive of the fragility of aCFSs mapped at a higher resolution. Importantly, the genomic features we identified here as significant predictors of fragility allow us to draw valuable inferences on the molecular mechanisms underlying aCFSs.
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Affiliation(s)
- Arkarachai Fungtammasan
- The Integrative Biosciences Graduate Program, Bioinformatics and Genomics Option, Pennsylvania State University, University Park, PA 16802, USA
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15
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Palakodeti A, Lucas I, Jiang Y, Young DJ, Fernald AA, Karrison T, Le Beau MM. Impaired replication dynamics at the FRA3B common fragile site. Hum Mol Genet 2010; 19:99-110. [PMID: 19815620 DOI: 10.1093/hmg/ddp470] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chromosomal common fragile sites (CFSs) are genetically unstable regions of the genome that are induced by conditions that impair DNA replication. In this report, we show that treatment with the DNA polymerase inhibitor, aphidicolin (APH), slows the replication rate throughout S phase. To investigate the unusual sensitivity of CFSs to APH-induced replication stress, we examined replication dynamics within a 50 kb region of the most frequently expressed CFS, FRA3B. We mapped four origins of replication, ori 1-4, using two independent methods. In untreated cells, we detected significantly less newly replicated DNA at FRA3B ori 1-3, as compared with three control origins located within non-fragile regions (NCFSs). In APH-treated cells, all FRA3B and control origins tested were active; however, there was a significant increase of nascent strand DNA at the control origins and, to a lesser extent, at the FRA3B ori 1-3. On the basis of these observations and the theoretical modeling of the nascent strand abundance assay developed in this study, we hypothesize that CFS origins may be less efficient, and that APH treatment slows replication fork movement near these origins to a greater extent, resulting in impaired DNA replication and, ultimately, leading to the genetic instability characteristic of CFSs.
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Affiliation(s)
- Aparna Palakodeti
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL 60637, USA
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16
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Hassan MI, Naiyer A, Ahmad F. Fragile histidine triad protein: structure, function, and its association with tumorogenesis. J Cancer Res Clin Oncol 2009; 136:333-50. [PMID: 20033706 DOI: 10.1007/s00432-009-0751-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 12/09/2009] [Indexed: 01/31/2023]
Abstract
BACKGROUND The human fragile histidine triad (FHIT) gene is a putative tumor suppressor gene, which is located at chromosome region 3p14.2. It was suggested that the loss of heterozygosity (LOH), homozygous deletions, and abnormal expression of the FHIT gene were involved in several types of human malignancies. MATERIALS AND METHODS To determine the role of FHIT in various cancers, we have performed structural and functional analysis of FHIT in detail. RESULTS AND DISCUSSION The protein FHIT catalyzes the Mg(2+) dependent hydrolysis of P1-5 cent-O-adenosine-P3-5 cent-O-adenosine triphosphate, Ap3A, to AMP, and ADP. The reaction is thought to follow a two-step mechanism. Histidine triad proteins, named for a motif related to the sequence H-cent-H-cent-H-cent-cent- (cent, a hydrophobic amino acid), belong to superfamily of nucleotide hydrolases and transferases. This enzyme acts on the R-phosphate of ribonucleotides, and contain a approximately 30-kDa domain that is typically a homodimer of approximately 15 kDa polypeptides with catalytic site. CONCLUSION Here we have gathered information is known about biological activities of FHIT, the structural and biochemical bases for their functions. Our approach may provide a comparative framework for further investigation of FHIT.
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Affiliation(s)
- Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
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17
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Sun J, Okumura H, Yearsley M, Frankel W, Fong LY, Druck T, Huebner K. Nit1 and Fhit tumor suppressor activities are additive. J Cell Biochem 2009; 107:1097-106. [PMID: 19479888 DOI: 10.1002/jcb.22207] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The fragile histidine triad gene (human FHIT, mouse Fhit) has been shown to act as a tumor suppressor gene. Nit1 and Fhit form a fusion protein, encoded by the NitFhit gene in flies and worms, suggesting that mammalian Nit1 and Fhit proteins, which are encoded by genes on different chromosomes in mammals, may function in the same signal pathway(s). A previous study showed that Nit1 deficiency in knockout mice confers a cancer prone phenotype, as does Fhit deficiency. We have now assessed the tumor susceptibility of Fhit(-/-)Nit1(-/-) mice and observed that double knockout mice develop more spontaneous and carcinogen-induced tumors than Fhit(-/-) mice, suggesting that the extent of tumor susceptibility due to Nit1 and Fhit deficiency is additive, and that Nit1 and Fhit affect distinct signal pathways in mammals. Nit1, like Fhit, is present in cytoplasm and mitochondria but not nuclei. Because Fhit deficiency affects responses to replicative and oxidative stress, we sought evidence for Nit1 function in response to such stresses in tissues and cultured cells: when treated with hydroxyurea, the normal kidney-derived double-deficient cells appear not to activate the pChk2 pathway and when treated with H(2)O(2), show little evidence of DNA damage, compared with wild type and Fhit(-/-) cells. The relevance of Nit1 deficiency to human cancers was examined in human esophageal cancer tissues, and loss of Nit1 expression was observed in 48% of esophageal adenocarcinomas.
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Affiliation(s)
- Jin Sun
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
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18
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McAvoy S, Zhu Y, Perez DS, James CD, Smith DI. Disabled-1 is a large common fragile site gene, inactivated in multiple cancers. Genes Chromosomes Cancer 2008; 47:165-74. [PMID: 18008369 DOI: 10.1002/gcc.20519] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Common fragile sites (CFS) are large, genomically unstable regions, which are hot-spots for deletions and other alterations, especially in cancer cells. Several have been shown to contain genes that span large genomic regions, such as FHIT (1.5 Mb), WWOX (1.0 Mb), GRID2 (1.36 Mb), PARK2 (1.3 Mb), and RORA (730 kb). These genes are frequently inactivated in multiple different cancers, and FHIT and WWOX are shown to function as tumor suppressors. The disabled-1 gene (DAB1) is one of the human homologs of the Drosophila disabled locus, which in mammals is involved in neuronal migration and lamination in the developing cerebral cortex. Mice DAB1 inactivation results in the neurological mutant Scrambler, having similarities to mice with the inactivation of PARK2 (Quaker), GRID2 (Lurcher), and RORA (Staggerer). We were interested in whether DAB1 was another large CFS gene that could have cancer development importance. We demonstrated here that the human DAB1 gene (spanning 1.25 Mb) mapped within FRA1B CFS region on chromosomal band 1p32.2. Real-time RT-PCR analysis revealed that the expression level of DAB1 was decreased in many human cancer samples, including primary tumor tissues and cancer-derived cell lines, from several different cancers, especially in brain and endometrial cancer. Additionally, the introduction of an over-expression DAB1 plasmid into two different cell lines, having insignificant endogenous DAB1 expression, resulted in decreased cell growth. In summary, DAB1 is another gene that resides within an unstable CFS region and might play a role in human tumorigenesis. These data may provide further linkage between neurological development and cancer.
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Affiliation(s)
- Sarah McAvoy
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
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19
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Pichiorri F, Ishii H, Okumura H, Trapasso F, Wang Y, Huebner K. Molecular parameters of genome instability: Roles of fragile genes at common fragile sites. J Cell Biochem 2008; 104:1525-33. [DOI: 10.1002/jcb.21560] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Trapasso F, Pichiorri F, Gaspari M, Palumbo T, Aqeilan RI, Gaudio E, Okumura H, Iuliano R, Di Leva G, Fabbri M, Birk DE, Raso C, Green-Church K, Spagnoli LG, Venuta S, Huebner K, Croce CM. Fhit interaction with ferredoxin reductase triggers generation of reactive oxygen species and apoptosis of cancer cells. J Biol Chem 2008; 283:13736-44. [PMID: 18319262 PMCID: PMC2376222 DOI: 10.1074/jbc.m709062200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 02/28/2008] [Indexed: 11/06/2022] Open
Abstract
Fhit protein is lost in most cancers, its restoration suppresses tumorigenicity, and virus-mediated FHIT gene therapy induces apoptosis and suppresses tumors in preclinical models. We have used protein cross-linking and proteomics methods to characterize a Fhit protein complex involved in triggering Fhit-mediated apoptosis. The complex includes Hsp60 and Hsp10 that mediate Fhit stability and may affect import into mitochondria, where it interacts with ferredoxin reductase, responsible for transferring electrons from NADPH to cytochrome P450 via ferredoxin. Viral-mediated Fhit restoration increases production of intracellular reactive oxygen species, followed by increased apoptosis of lung cancer cells under oxidative stress conditions; conversely, Fhit-negative cells escape apoptosis, carrying serious oxidative DNA damage that may contribute to an increased mutation rate. Characterization of Fhit interacting proteins has identified direct effectors of the Fhit-mediated apoptotic pathway that is lost in most cancers through loss of Fhit.
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Affiliation(s)
- Francesco Trapasso
- Ohio State University, Comprehensive Cancer Center, Columbus, Ohio 43210, USA
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21
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McCorkell KA, Mancini R, Siprashvili Z, Barnoski BL, Iliopoulos D, Siracusa LD, Zanesi N, Croce CM, Fong LYY, Druck T, Huebner K. Influence of a nonfragile FHIT transgene on murine tumor susceptibility. Cytogenet Genome Res 2007; 118:196-203. [PMID: 18000371 DOI: 10.1159/000108301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 09/11/2006] [Indexed: 11/19/2022] Open
Abstract
FHIT, at a constitutively active chromosome fragile site, is often a target of chromosomal aberrations and deletion in a large fraction of human tumors. Inactivation of murine Fhit allelessignificantly increases susceptibility of mice to spontaneous and carcinogen-induced tumorigenesis. In this study, transgenic mice, carrying a human FHIT cDNA under control of the endogenous promoter, were produced to determine the effect of Fhit expression, from a nonfragile cDNA transgene outside the fragile region, on carcinogen-induced tumor susceptibility of wildtype and Fhit heterozygous mice. Mice received sufficient oral doses of N-nitrosomethybenzylamine (NMBA) to cause forestomach tumors in >80% of nontransgenic control mice. Although the level of expression of the FHIT transgene in the recombinant mouse strains was much lower than the level of endogenous Fhit expression, the tumor burden in NMBA-treated male transgenic mice was significantly reduced, while female transgenic mice were not protected. To determine if the difference in protection could be due to differences in epigenetic changes at the transgene loci in male versus female mice, we examined expression, hypermethylation and induced re-expression of FHIT transgenes in male and female mice or cells derived from them. The transgene was methylated in male and female mice and in cell lines established from male and female transgenic kidneys, the FHIT locus was both hypermethylated and deacetylated. It is likely that the FHIT transgene is more tightly silenced in female transgenic mice, leading to a lack of protection from tumor induction.
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Affiliation(s)
- K A McCorkell
- Department of Microbiology and Immunology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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22
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Abstract
Chromosomal fragile sites are specific loci that preferentially exhibit gaps and breaks on metaphase chromosomes following partial inhibition of DNA synthesis. Their discovery has led to novel findings spanning a number of areas of genetics. Rare fragile sites are seen in a small proportion of individuals and are inherited in a Mendelian manner. Some, such as FRAXA in the FMR1 gene, are associated with human genetic disorders, and their study led to the identification of nucleotide-repeat expansion as a frequent mutational mechanism in humans. In contrast, common fragile sites are present in all individuals and represent the largest class of fragile sites. Long considered an intriguing component of chromosome structure, common fragile sites have taken on novel significance as regions of the genome that are particularly sensitive to replication stress and that are frequently rearranged in tumor cells. In recent years, much progress has been made toward understanding the genomic features of common fragile sites and the cellular processes that monitor and influence their stability. Their study has merged with that of cell cycle checkpoints and DNA repair, and common fragile sites have provided insight into understanding the consequences of replication stress on DNA damage and genome instability in cancer cells.
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Affiliation(s)
- Sandra G Durkin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-0618, USA.
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23
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Abstract
AIM: To screen out the differentially methylated DNA sequences between gastric primary tumor and metastatic lymph nodes, test the methylation difference of gene PTPRG between primary gastric tumor and metastatic lymph nodes, and test the regulatory function of 5-aza-2-deoxycytidine which is an agent with suppression on methylation and the level of methylation in gastric cancer cell line.
METHODS: Methylated DNA sequences in genome were enriched with methylated CpG islands amplification (MCA) to undergo representational difference analysis (RDA), with MCA production of metastatic lymph nodes as tester and that of primary tumor as driver. The obtained differentially methylated fragments were cloned and sequenced to acquire the base sequence, which was analyzed with bioinformatics. With methylation-specific PCR (MSP) and RT-PCR, methylation difference of gene PTPRG was detected between primary tumor and metastatic lymph nodes in 36 cases of gastric cancer. Methylation of gene PTPRG and its regulated expression were observed in gastric cancer cell line before and after being treated with methylation-suppressive agent.
RESULTS: Nineteen differentially methylated sequences were obtained and located at 5’ end, exons, introns and 3’ end, in which KL59 was observed to be located at 9p21 as the first exon of gene p16 and KL22 to be located at promoter region of PRPRG. KL22, as the probes, was hybridized with driver, tester and 3-round RDA products respectively with all positive signals except with the driver. Significant difference was observed in both methylation rate of gene PTPRG and PTPRG mRNA expression rate between primary tumor and metastatic lymph nodes. Demethylation of gene PTPRG, with recovered expression of PTPRG mRNA, was observed after gastric cancer cell line being treated with methylation-suppressive agent.
CONCLUSION: Difference exists in DNA methylation between primary tumor and metastatic lymph nodes of gastric cancer, with MCA-RDA as one of the good analytical methods. Significant difference exists in methylation of gene PTPRG between primary tumor and metastatic lymph nodes of gastric cancer. Methylation level in gastric cancer cell line can be decreased by 5-aza-2’-deoxycytidine, which is the methylation-suppressive agent, with PTPRG expression being recovered.
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Ditzel Santos D, Ho AW, Tournilhac O, Hatjiharissi E, Leleu X, Xu L, Tassone P, Neri P, Hunter ZR, Chemaly MAZ, Branagan AR, Manning RJ, Patterson CJ, Moreau AS, Ciccarelli B, Adamia S, Kriangkum J, Kutok JL, Tai YT, Zhang J, Pilarski LM, Anderson KC, Munshi N, Treon SP. Establishment of BCWM.1 cell line for Waldenström's macroglobulinemia with productive in vivo engraftment in SCID-hu mice. Exp Hematol 2007; 35:1366-75. [PMID: 17761288 DOI: 10.1016/j.exphem.2007.05.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2007] [Revised: 05/23/2007] [Accepted: 05/31/2007] [Indexed: 10/22/2022]
Abstract
A significant impairment in understanding the biology and advancing therapeutics for Waldenstrom's macroglobulinemia (WM) has been the lack of a representative cell line and animal model. We, therefore, report on the establishment of the BCWM.1 cell line, which was derived from the long-term culture of CD19(+) selected bone marrow lymphoplasmacytic cells isolated from an untreated patient with WM. BCWM.1 cells morphologically resemble lymphoplasmacytic cells (LPC) and propagate in RPMI-1640 medium supplemented with 10% fetal bovine serum. Phenotypic characterization by flow cytometric analysis demonstrated typical WM LPC characteristics: CD5(-), CD10(-), CD19(+), CD20(+), CD23(+), CD27(-), CD38(+), CD138(+), CD40(+), CD52(+), CD70(+), CD117(+), cIgM(+), cIgG(-), cIgA(-), ckappa(-), clambda(+), as well as the survival proteins APRIL and BLYS, and their receptors TACI, BCMA and BAFF-R. Enzyme-linked immunosorbent assay studies demonstrated secretion of IgMlambda and soluble CD27. Karyotypic and multicolor fluorescence in situ hybridization studies did not demonstrate cytogenetic abnormalities. Molecular analysis of BCWM.1 cells confirmed clonality by determination of IgH rearrangements. Inoculation of BCWM.1 cells in human bone marrow chips implanted in severe combined immunodeficient-hu mice led to rapid engraftment of tumor cells and serum detection of human IgM, lambda, and soluble CD27. These studies support the use of BCWM.1 cells as an appropriate model for the study of WM, which in conjunction with the severe combined immunodeficient-hu mouse model may be used as a convenient model for studies focused on both WM pathogenesis and development of targeted therapies for WM.
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Affiliation(s)
- Daniel Ditzel Santos
- Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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25
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De Flora S, D'Agostini F, Izzotti A, Zanesi N, Croce CM, Balansky R. Molecular and cytogenetical alterations induced by environmental cigarette smoke in mice heterozygous for Fhit. Cancer Res 2007; 67:1001-6. [PMID: 17283132 DOI: 10.1158/0008-5472.can-06-3882] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Previous studies in humans and animal models provided evidence that the Fhit gene is an early target for cigarette smoke. We compared the induction of a variety of molecular and cytogenetical alterations in B6-129(F(1)) mice, either wild type or Fhit(+/-), after whole-body exposure to environmental cigarette smoke (ECS) for 15 consecutive days. Both mouse genotypes responded to ECS with a loss of Fhit protein in the bronchial epithelium, accompanied by induction of apoptosis and stimulation of cell proliferation. ECS induced formation of bulky DNA adducts in whole lung. In addition, ECS caused cytogenetical damage both in the respiratory tract and at a systemic level, as shown by a significant increase of micronucleus frequency in pulmonary alveolar macrophages, bone marrow polychromatic erythrocytes, and peripheral blood normochromatic erythrocytes of both wild-type and Fhit(+/-) mice. These results are compared with those generated in other species, strains, and genotypes of rodents exposed to ECS that we investigated previously. Although the loss of Fhit protein in the bronchial epithelium of ECS-exposed B6-129(F(1)) mice provides further evidence that the Fhit gene is an early molecular target for ECS, heterozygosity for Fhit does not seem to confer an increased susceptibility of mice in terms of the investigated early biomarkers.
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Affiliation(s)
- Silvio De Flora
- Department of Health Sciences, University of Genoa, via A. Pastore 1, I-16132 Genoa, Italy.
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26
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Smith DI, McAvoy S, Zhu Y, Perez DS. Large common fragile site genes and cancer. Semin Cancer Biol 2006; 17:31-41. [PMID: 17140807 DOI: 10.1016/j.semcancer.2006.10.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 09/07/2006] [Accepted: 10/17/2006] [Indexed: 12/01/2022]
Abstract
The common fragile sites are large regions of genomic instability that are found in all individuals and are hot spots for chromosomal rearrangements and deletions. A number of the common fragile sites have been found to span genes that are encoded by very large genomic regions. Two of these genes, FHIT and WWOX, have already been demonstrated to function as tumor suppressors. In this review we will discuss the large common fragile site genes that have been identified to date, and the role that these genes appear to play both in cellular responses to stress and in the development of cancer.
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Affiliation(s)
- David I Smith
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street, S.W., Rochester, MN 55905, United States.
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27
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Re A, Cora D, Puliti AM, Caselle M, Sbrana I. Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis. BMC Bioinformatics 2006; 7:413. [PMID: 16981993 PMCID: PMC1601973 DOI: 10.1186/1471-2105-7-413] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 09/18/2006] [Indexed: 01/26/2023] Open
Abstract
Background Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. Results Common fragile sites were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Moreover we showed how the internal organization of the graph in communities and even in very simple subgraphs can be a starting point for the identification of new factors of instability at common fragile sites. Conclusion We developed a computational method addressing the fundamental issue of studying the functional content of common fragile sites. Our analysis integrated two different approaches. First, data on common fragile site expression were analyzed in a complex networks framework. Second, outcomes of the network statistical description served as sources for the functional annotation of genes at common fragile sites by means of the Gene Ontology vocabulary. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression.
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Affiliation(s)
- Angela Re
- Dipartimento di Fisica Teorica dell'Università degli Studi di Torino e INFN, Via P. Giuria 1 – I 10125 Torino, Italy
| | - Davide Cora
- Dipartimento di Fisica Teorica dell'Università degli Studi di Torino e INFN, Via P. Giuria 1 – I 10125 Torino, Italy
- Centro Interdipartimentale Sistemi Complessi in Biologia e Medicina Molecolare, Via Accademia Albertina 13 – I 10123 Torino, Italy
| | - Alda Maria Puliti
- Dipartimento di Biologia dell'Università degli Studi di Pisa, Via San Giuseppe 22 – I 56126 Pisa, Italy
- Laboratorio di Genetica Molecolare, Istituto G.Gaslini, L.go Gaslini 5 – I 16147 Genova, Italy
| | - Michele Caselle
- Dipartimento di Fisica Teorica dell'Università degli Studi di Torino e INFN, Via P. Giuria 1 – I 10125 Torino, Italy
- Centro Interdipartimentale Sistemi Complessi in Biologia e Medicina Molecolare, Via Accademia Albertina 13 – I 10123 Torino, Italy
| | - Isabella Sbrana
- Dipartimento di Biologia dell'Università degli Studi di Pisa, Via San Giuseppe 22 – I 56126 Pisa, Italy
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Helmrich A, Stout-Weider K, Hermann K, Schrock E, Heiden T. Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes. Genome Res 2006; 16:1222-30. [PMID: 16954539 PMCID: PMC1581431 DOI: 10.1101/gr.5335506] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Common fragile sites (CFSs) are seen as chromosomal gaps and breaks brought about by inhibition of replication, and it is thought that they cluster with tumor breakpoints. This study presents a comprehensive analysis using conventional and molecular cytogenetic mapping of CFSs and their expression frequencies in two mouse strains, BALB/c and C57BL/6, and in human probands. Here we show that induced mouse CFSs relate to sites of spontaneous gaps and breaks and that CFS expression levels in chromosome bands are conserved between the two mouse strains and between syntenic mouse and human DNA segments. Furthermore, four additional mouse CFSs were found to be homologous to human CFSs on the molecular cytogenetic level (Fra2D-FRA2G, Fra4C2-FRA9E, Fra6A3.1-FRA7G, and Fra6B1-FRA7H), increasing the number of such CFSs already described in the literature to eight. Contrary to previous reports, DNA helix flexibility is not increased in the 15 human and eight mouse CFSs molecularly defined so far, compared to large nonfragile control regions. Our findings suggest that the mechanisms that provoke instability at CFSs are evolutionarily conserved. The role that large transcriptionally active genes may play in CFS expression is discussed.
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Affiliation(s)
- Anne Helmrich
- Institute of Clinical Genetics, Medical Faculty Carl Gustav Carus, University of Technology, 01307 Dresden, Germany.
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Arlt MF, Durkin SG, Ragland RL, Glover TW. Common fragile sites as targets for chromosome rearrangements. DNA Repair (Amst) 2006; 5:1126-35. [PMID: 16807141 DOI: 10.1016/j.dnarep.2006.05.010] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Common fragile sites are large chromosomal regions that preferentially exhibit gaps or breaks after DNA synthesis is partially perturbed. Fragile site instability in cultured cells is well documented and includes gaps and breaks on metaphase chromosomes, translocation and deletions breakpoints, and sister chromosome exchanges. In recent years, much has been learned about the genomic structure at fragile sites and the cellular mechanisms that monitor their stability. The study of fragile sites has merged with that of cell cycle checkpoints and DNA repair, with multiple proteins from these pathways implicated in fragile site stability, including ATR, BRCA1, CHK1, and RAD51. Since their discovery, fragile sites have been implicated in constitutional and cancer chromosome rearrangements in vivo and recent studies suggest that common fragile sites may serve as markers of chromosome damage caused by replication stress during early tumorigenesis. Here we review the relationship of fragile sites to chromosome rearrangements, particularly in tumor cells, and discuss the mechanisms that may be involved.
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Affiliation(s)
- Martin F Arlt
- Department of Human, Genetics University of Michigan, 4909 Buhl Box 0618, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
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Sbrana I, Veroni F, Nieri M, Puliti A, Barale R. Chromosomal fragile sites FRA3B and FRA16D show correlated expression and association with failure of apoptosis in lymphocytes from patients with thyroid cancer. Genes Chromosomes Cancer 2006; 45:429-36. [PMID: 16419058 DOI: 10.1002/gcc.20305] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
It has been suggested that common fragile sites (cFSs) are related to cancer development. This appears to be the case for FRA3B and FRA16D, localized in two tumor-suppressor genes (FHIT and WWOX, respectively) that are altered by deletions or loss of heterozygosity (LOH) in many cancers. The features responsible for fragility have not yet been identified. Furthermore, it is still unclear whether instability at these regions causes chance deletions and loss of function of the associated genes, or whether the gene function itself is related to the appearance of fragility. In this study, we analyzed cFS expression in lymphocytes from 20 healthy or thyroid cancer-affected subjects exposed to radiation after the Chernobyl accident. The same cells were examined for apoptosis, a principal function of both the FHIT and WWOX genes. Exceptionally elevated chromosome fragility was observed, particularly in cancer patients, affecting FRA3B, FRA16D, and a cluster of less highly expressed cFSs; levels of chromosome fragility were found to be correlated among these cFSs. Interestingly, most expressed cFSs were sites of LOH reported for thyroid tumors; moreover, cells with the highest fragility also had a reduced ability to undergo apoptosis. These findings reveal previously unknown genetic interactions affecting fragile loci, suggestive of a shared function inside mitotic cells. Attenuation of checkpoint control and apoptosis resistance seem to be the cell phenotypes associated with unusual chromosome fragility. We propose that breakage at specific cFS could derive from early epigenetic events at loci involved in radiation carcinogenesis. This article contains supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
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Affiliation(s)
- Isabella Sbrana
- Department of Human and Environmental Sciences, University of Pisa, Pisa, Italy.
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31
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Miller CT, Lin L, Casper AM, Lim J, Thomas DG, Orringer MB, Chang AC, Chambers AF, Giordano TJ, Glover TW, Beer DG. Genomic amplification of MET with boundaries within fragile site FRA7G and upregulation of MET pathways in esophageal adenocarcinoma. Oncogene 2006; 25:409-18. [PMID: 16186806 DOI: 10.1038/sj.onc.1209057] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Esophageal adenocarcinoma (EA) is characterized by a poor prognosis making the identification of clinically targetable proteins essential for improving patient outcome. We report the involvement of multiple alterations of the MET pathway in EA development and progression. Microarray analysis of Barrett's metaplasia, dysplasia, and EA revealed overexpression of the MET oncogene in EAs but only those with MET gene amplification. STS-amplification mapping revealed that the boundary of the MET amplicon in these EAs is defined by fragile site FRA7G. We also identified an amplicon at 11p13 that resulted in amplification and overexpression of CD44, a gene involved in MET autophosphorylation upon HGF stimulation. Tissue microarrays with phospho-MET-specific antibodies demonstrated a uniformly high abundance of MET activation in primary EA and cells metastatic to lymph nodes but to a lesser extent in a subset of metaplastic and dysplastic Barrett's samples. Increased expression of multiple genes in the MET pathway associated with invasive growth, for example, many MMPs and osteopontin, also was found in EAs. Treatment of EA-derived cell lines with geldanamycin, an inhibitor for tyrosine kinases including MET receptor kinase, reduced cell migration and induced EA cell apoptosis. The data indicate that upregulation of the MET pathway may contribute to the poor outcome of EA patients and that therapeutic agents targeting this pathway may help improve patient survival.
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Affiliation(s)
- C T Miller
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Zhu Y, McAvoy S, Kuhn R, Smith DI. RORA, a large common fragile site gene, is involved in cellular stress response. Oncogene 2006; 25:2901-8. [PMID: 16462772 DOI: 10.1038/sj.onc.1209314] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Common fragile sites (CFSs) are large genomic regions present in all individuals that are highly unstable and prone to breakage and rearrangement, especially in cancer cells with genomic instability. Eight of the 90 known CFSs have been precisely defined and five of these span genes that extend from 700 kb to over 1.5 Mb of genomic sequence. Although these genes reside within some of the most unstable chromosomal regions in the human genome, they are highly conserved evolutionarily. These genes are targets for large chromosomal deletions and rearrangements in cancer and are frequently inactivated in multiple tumor types. There is also an association between these genes and cellular responses to stress. Based upon the association between large genes and CFSs, we began to systematically test other large genes derived from chromosomal regions that were known to contain a CFS. In this study, we demonstrate that the 730 kb retinoic acid receptor-related orphan receptor alpha (RORA) gene is derived from the middle of the FRA15A (15q22.2) CFS. Although this gene is expressed in normal breast, prostate and ovarian epithelium, it is frequently inactivated in cancers that arise from these organs. RORA was previously shown to be involved in the cellular response to hypoxia and here we demonstrate changes in the amount of RORA message produced in cells exposed to a variety of different cellular stresses. Our results demonstrate that RORA is another very large CFS gene that is inactivated in multiple tumors. In addition, RORA appears to play a critical role in responses to cellular stress, lending further support to the idea that the large CFS genes function as part of a highly conserved stress response network that is uniquely susceptible to genomic instability in cancer cells.
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Affiliation(s)
- Y Zhu
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic College of Medicine, Rochester, MI, USA
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Abstract
Common fragile sites are regions showing site-specific gaps and breaks on metaphase chromosomes after partial inhibition of DNA synthesis. Common fragile sites are normally stable in somatic cells. However, following treatment of cultured cells with replication inhibitors, fragile sites display gaps, breaks, rearrangements and other features of unstable DNA. Studies showing that fragile sites and associated genes are frequently deleted or rearranged in many cancer cells have clearly demonstrated their importance in genome instability in cancer. Until recently, little was known about the molecular nature and mechanisms involved in fragile site instability. From studies conducted in many laboratories, it is now known that fragile sites extend over large regions, are associated with genes, exhibit delayed replication, and contain regions of high DNA flexibility. Recent findings from our laboratory showing that the key cell cycle checkpoint genes are important for genome stability at fragile sties have shed new light on these mechanisms and on the significance of these sites in cancer and normal chromosome structure. Since their discovery over two decades ago, much has been learned regarding their significance in chromosome structure and instability in cancer, but a number of key questions remain, including why these sites are 'fragile' and the impact of this instability on associated genes in cancer cells. These and other questions have been addressed by participants of this meeting, which highlighted instability at common fragile sites. This brief review is intended to provide background on common fragile sites that has led up to many of the studies presented in the accompanying reports in this volume and not to summarize the findings presented therein. Some aspects of this review were taken from Glover et al. (T.W. Glover, M.F. Arlt, A.M. Casper, S.G. Durkin, Mechanisms of common fragile site instability, Hum. Molec. Genet. 14 (in press). [1]).
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics, 4909 Buhl, Box 0618, 1241 E. Catherine Street, University of Michigan, Ann Arbor, MI 48109-0618, USA.
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Myllykangas S, Knuutila S. Manifestation, mechanisms and mysteries of gene amplifications. Cancer Lett 2005; 232:79-89. [PMID: 16288831 DOI: 10.1016/j.canlet.2005.07.045] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2005] [Accepted: 07/30/2005] [Indexed: 12/31/2022]
Abstract
Gene amplifications are essential features of advanced cancers and have prognostic as well as therapeutic significance in clinical cancer treatment. Models explaining the amplification process, such as breakage-fusion-bridge cycle and excision and unequal segregation of extrachromosomal DNA fragments, predict that independent DNA double-stranded breaks must occur to induce amplification formation. Many cellular, tissue and environmental factors induce DNA damage and amplifications. Also labile DNA sequence features like fragile sites facilitate amplifications. Although, databases and data mining tools of various genomic attributes are already available, extra-large scale systems biology endeavors to decipher dynamics, interactions and dependencies between different factors contributing to amplification process fail, because current databases of DNA copy number aberrations and fragile sites comprise conventional cytogenetics results obtained at far too coarse chromosome band resolution. Array comparative genomic hybridization (aCGH) enables genome-wide gene copy number measurements and amplification detection at molecular genetic resolution. Similarly, cloning and sequencing of fragile sites produce mapping information of vastly improved resolution. In conclusion, databases of aCGH and sequenced fragile sites are needed to resolve the mechanisms of gene amplifications in systems biology configuration.
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Affiliation(s)
- Samuel Myllykangas
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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35
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Glover TW, Arlt MF, Casper AM, Durkin SG. Mechanisms of common fragile site instability. Hum Mol Genet 2005; 14 Spec No. 2:R197-205. [PMID: 16244318 DOI: 10.1093/hmg/ddi265] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The study of common fragile sites has its roots in the early cytogenetic investigations of the fragile X syndrome. Long considered an interesting component of chromosome structure, common fragile sites have taken on novel significance as regions of the genome that are particularly sensitive to certain forms of replication stress, which are frequently rearranged in cancer cells. In recent years, much has been learned about the genomic structure at fragile sites and the cellular checkpoint functions that monitor their stability. Recent findings suggest that common fragile sites may serve as markers of chromosome damage caused by replication stress during early stages of tumorigenesis. Thus, the study of common fragile sites can provide insight not only into the nature of fragile sites, but also into the broader consequences of replication stress on DNA damage and cancer. However, despite recent advances, many questions remain regarding the normal functional significance of these conserved regions and the basis of their fragility.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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36
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Smith DI, Zhu Y, McAvoy S, Kuhn R. Common fragile sites, extremely large genes, neural development and cancer. Cancer Lett 2005; 232:48-57. [PMID: 16221525 DOI: 10.1016/j.canlet.2005.06.049] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Accepted: 06/06/2005] [Indexed: 11/24/2022]
Abstract
Common fragile sites (CFSs) are large regions of profound genomic instability found in all individuals. They are biologically significant due to their role in a number of genomic alterations that are frequently found in many different types of cancer. The first CFS to be cloned and characterized was FRA3B, the most active CFS in the human genome. Instability within this region extends for over 4.0 Mbs and contained within the center of this CFS is the FHIT gene spanning 1.5 Mbs of genomic sequence. There are frequent deletions and other alterations within this gene in multiple tumor types and the protein encoded by this gene has been demonstrated to function as a tumor suppressor in vitro and in vivo. In spite of this, FHIT is not a traditional mutational target in cancer and many tumors have large intronic deletions without any exonic alterations. There are several other very large genes found within CFS regions including Parkin (1.37 Mbs in FRA6E), GRID2 (1.47 Mbs within 4q22.3), and WWOX (1.11 Mbs within FRA16D). These genes also appear to function as tumor suppressors but are not traditional mutational targets in cancer. Each of these genes is highly conserved and the regions spanning them are CFSs in mice. We have now examined lists of the largest human genes and found forty that span over one megabase. Many of these are derived from chromosomal bands containing CFSs. BACs within these genes are being utilized as FISH probes to determine if these are also CFS genes. Thus far we have identified the following as CFS genes: CNTNAP2 (2.3 Mbs in FRA7I), DMD (2.09 Mbs in FRAXC), LRP1B (1.9 Mbs in FRA2F), CTNNA3 (1.78 Mbs in FRA10D), DAB1 (1.55 Mbs in FRA1B), and IL1RAPL1 (1.36 Mbs in FRAXC). Although, these genes are also not traditional mutational targets in cancer they do exhibit loss of expression in multiple tumor types suggesting that they may also function as tumor suppressors. Many of the large CFS genes are involved in neurological development. Parkin is mutated in autosomal recessive juvenile Parkinsonism and deletions in mice are associated with the mouse mutant Quaking (viable). Spontaneous mouse mutants in GRID2 and DAB1 are associated with Lurcher and Reelin, respectively. In humans, alterations in IL1RAPL1 cause X-linked mental retardation and loss of WWOX is associated with Tau phosphorylation. We propose that the instability-induced alterations in these genes contribute to cancer development in a two-step process. Initial alterations will primarily occur within intronic regions, as these genes are greater than 99% intronic. These are not benign. Instead, they alter the repertoire of transcripts produced from these genes. As cancer progresses deletions will begin to encompass exons resulting in gene inactivation. These two types of alterations occurring in multiple large CFS genes may contribute significantly to the heterogeneity observed in cancer. There are also important potential linkages between normal neurological development and the development of cancer mediated by alterations in these genes.
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Affiliation(s)
- David I Smith
- Co-head of the Ovarian Cancer Program, Mayo Clinic Cancer Center, Mayo Clinic College of Medicine, Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Rochester, MN 55905, USA.
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Zanesi N, Pekarsky Y, Croce CM. A mouse model of the fragile gene FHIT: From carcinogenesis to gene therapy and cancer prevention. Mutat Res 2005; 591:103-9. [PMID: 16085127 DOI: 10.1016/j.mrfmmm.2005.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Revised: 05/09/2005] [Accepted: 05/09/2005] [Indexed: 11/26/2022]
Abstract
Mouse models of tumor suppressors are increasingly useful to investigate biomedical aspects of cancer genetics. Some tumor suppressor genes are located at common fragile sites that are specific chromosomal regions highly susceptible to DNA lesions. The tumor suppressor gene FHIT, at the fragile site FRA3B, is the first fragile gene with a developed and characterized mouse knockout model. The human gene FHIT is frequently deleted in cancers and cancer cell lines of many epithelial tissues, and Fhit protein is absent or reduced in most cancers. The mouse Fhit ortholog is also located at a common fragile site, Fra14A2 on murine chromosome 14, and sustains homozygous deletions in murine cancer cell lines. The Fhit knockout mouse is, therefore, an adequate model to study human FHIT function. To establish an animal model and to explore the role of FHIT in tumorigenesis, we have developed a mouse strain carrying one or two inactivated Fhit alleles. Insights into Fhit mouse genetics that have emerged in the last 7 years, and are reviewed in the present article, allowed for development of new tools in carcinogenesis and gene delivery studies.
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Affiliation(s)
- Nicola Zanesi
- Comprehensive Cancer Center, Ohio State University, 400 W. 12th Avenue, Columbus, OH, USA
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Zainabadi K, Benyamini P, Chakrabarti R, Veena MS, Chandrasekharappa SC, Gatti RA, Srivatsan ES. A 700-kb physical and transcription map of the cervical cancer tumor suppressor gene locus on chromosome 11q13. Genomics 2005; 85:704-14. [PMID: 15885497 DOI: 10.1016/j.ygeno.2005.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2004] [Revised: 02/11/2005] [Accepted: 02/25/2005] [Indexed: 11/18/2022]
Abstract
Nonrandom deletion of chromosome 11q13 sequences is a significant event in a number of human tumors. We have recently identified a 300-kb minimal area of deletion in primary cervical tumors that overlaps with deletions observed in endocrine and nasopharyngeal tumors. We have also observed a 5.7-kb homozygous deletion within this interval in HeLa cells (a cervical cancer cell line), HeLa cell-derived tumorigenic hybrids, and a primary cervical tumor, suggesting the presence of a tumor suppressor gene in this region. In the present investigation, we have constructed a 700-kb contig map encompassing the 300-kb deletion using the human genome sequence database and confirmed the map using various STS markers from the region. Our map also shows the overlap of a previously published rare, heritable fragile site, FRA11A, with the cervical cancer deletion locus. The mapped region contains highly repetitive GC-poor sequences. We have identified and characterized eight different polymorphic microsatellite markers from the sequences within and surrounding the deletion. Further, expression studies performed with 18 different ESTs localized adjacent to the homozygous deletion showed the presence of a transcript for only one of the ESTs, AA282789. This EST mapping within the homozygous deletion is also expressed in HeLa cells, thereby excluding the EST as the putative tumor suppressor gene. Additionally, analysis of four candidate genes (SF3B2, BRMS1, RIN1, and RAB1B) from the region showed expression of the expected size message in both the nontumorigenic and the tumorigenic HeLa cell hybrids, thereby excluding them as the putative tumor suppressor gene(s). However, Northern blot analysis with a fifth candidate gene, PACS1 (phosphofurin acidic cluster sorting protein), mapped to the deletion/FRA11A overlap region showed the expression of an 8-kb transcript in HeLa and five other tumor cell lines in addition to the expected 4.5-kb transcript. Since the gene shows abundant expression in normal tissues and an altered transcript is observed in tumor cell lines, we hypothesize that this gene could represent sequences of the putative tumor suppressor gene. Finally, we have observed a perfect 48-bp CAG/CCG repeat 99 kb proximal to D11S913, the marker linked to the neurodegenerative disorder spinocerebellar ataxia 5. The physical and transcription maps and the microsatellite markers of the 700-kb region of chromosome 11q13 should be helpful in the cloning of the cervical cancer tumor suppressor gene.
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Affiliation(s)
- Kayvan Zainabadi
- Department of Surgery 10H2, VAGLAHS West Los Angeles, David Geffen School of Medicine, University of California at Los Angeles, Building 304, Room E2-218, 11301 Wiltshire Boulevard, West Los Angeles, CA 90073, USA
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Kameoka Y, Tagawa H, Tsuzuki S, Karnan S, Ota A, Suguro M, Suzuki R, Yamaguchi M, Morishima Y, Nakamura S, Seto M. Contig array CGH at 3p14.2 points to the FRA3B/FHIT common fragile region as the target gene in diffuse large B-cell lymphoma. Oncogene 2005; 23:9148-54. [PMID: 15480422 DOI: 10.1038/sj.onc.1208136] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Deletions of the 3p arm have been detected in various solid tumors, but no study to date has investigated this deletion in diffuse large B-cell lymphoma (DLBCL). Recently, we demonstrated that 3p14.2 was deleted in approximately 30% of DLBCL cases by use of a genome-wide array-comparative genomic hybridization (CGH). For a more detailed examination of the genomic losses at 3p14.2, here we made use of contig BAC array for 3p14.2, and found that 12 DLBCL samples displayed losses. All of the deleted regions were located within the fragile histidine triad (FHIT) gene, and the most frequent region of loss was mapped to 0.4 Mbp of the region encompassing the introns 4 and 5 and exon 5 of the FHIT gene. Concomitant analysis of transcripts showed that the FHIT gene was aberrantly transcribed in 31% of the DLBCL samples examined and that the lost exons of the aberrant transcripts were correlated with genomic deletions. These findings indicate that (1) loss of genomic material at 3q14.2 is responsible for exon losses of the FHIT gene, and (2) genomic loss of the FHIT gene is one of the causes of the generation of aberrant transcripts.
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Affiliation(s)
- Yoshihiro Kameoka
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Aichi, Japan
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Ishii H, Mimori K, Inageta T, Murakumo Y, Vecchione A, Mori M, Furukawa Y. Components of DNA Damage Checkpoint Pathway Regulate UV Exposure–Dependent Alterations of Gene Expression of FHIT and WWOX at Chromosome Fragile Sites. Mol Cancer Res 2005; 3:130-8. [PMID: 15798093 DOI: 10.1158/1541-7786.mcr-04-0209] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Common chromosome fragile sites are highly recombinogenic and susceptible to deletions during the development of environmental carcinogen-induced epithelial tumors. Previous studies showed that not only genetic but also epigenetic alterations in cancerous cells are involved in inactivation of the genes FHIT and WWOX at chromosome fragile sites, reported to be potential tumor suppressor genes. Here we investigated the effect of UV light on the gene expression. After exposure to UV, the mRNA and protein of the two genes in murine embryonic fibroblasts (MEF) were unstable, apparently at the G1-S phase of the cell cycle, which was consistent with nuclear run-on assay. A study of MEFs synchronized via a double thymidine block indicated that, after the exposure, the expression of Fhit and Wwox was reduced in E2f-1-deficient cells and markedly in wild-type cells, whereas the reduction was partially inhibited in Trp53-deficient cells; cells at the S phase seemed to be sensitive to exogenous FHIT, suggesting a role of the checkpoint at the G1-S phase in the stability of gene expression and a possible involvement of FHIT function at the S phase. The transfection experiment showed that the UV-induced decrease in expression was partially inhibited by transfection of kinase-dead Atr (ataxia telangiectasia mutated and Rad3 related), which is a sensor of UV-induced damage. Taken together, the present study showed that UV-induced alterations of the fragile site gene expression are involved at least partially in the checkpoint function, suggesting the role in the process of carcinogenesis after exposure to UV.
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Affiliation(s)
- Hideshi Ishii
- Center for Molecular Medicine, Jichi Medical School, Tochigi 329-0498, Japan.
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Zhou Y, Mishra B. Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling. Proc Natl Acad Sci U S A 2005; 102:4051-6. [PMID: 15741274 PMCID: PMC554802 DOI: 10.1073/pnas.0407957102] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Indexed: 01/07/2023] Open
Abstract
A large number of the segmental duplications in mammalian genomes have been cataloged by genome-wide sequence analyses. The molecular mechanisms involved in these duplications mostly remain a matter of speculation. To uncover, test, and further quantify the hypotheses on the mechanisms for the recent duplications in the mammalian genomes, we have performed a series of statistical analyses on the sequences flanking the duplicated segments and proposed a dynamic model for the duplication process. The model, when applied to the human duplication data, indicates that approximately 30% of the recent human segmental duplications were caused by a recombination-like mechanism, among which 12% were mediated by the most recently active repeat, Alu. But a significant proportion of the duplications are caused by some mechanism independent of the repeat distribution. A less sure but similar picture is found in the rodent genomes. A further analysis on the physical features of the flanking sequences suggests that one of the uncharacterized duplication mechanisms shared by the mammalian genomes is surprisingly well correlated with the physical instability in the DNA sequences.
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Affiliation(s)
- Yi Zhou
- Department of Biology, New York University, New York, NY 10003, USA
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Arlt MF, Xu B, Durkin SG, Casper AM, Kastan MB, Glover TW. BRCA1 is required for common-fragile-site stability via its G2/M checkpoint function. Mol Cell Biol 2004; 24:6701-9. [PMID: 15254237 PMCID: PMC444841 DOI: 10.1128/mcb.24.15.6701-6709.2004] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 03/04/2004] [Accepted: 05/04/2004] [Indexed: 01/26/2023] Open
Abstract
Common fragile sites are loci that form chromosome gaps or breaks when DNA synthesis is partially inhibited. Fragile sites are prone to deletions, translocations, and other rearrangements that can cause the inactivation of associated tumor suppressor genes in cancer cells. It was previously shown that ATR is critical to fragile-site stability and that ATR-deficient cells have greatly elevated fragile-site expression (A. M. Casper, P. Nghiem, M. F. Arlt, and T. W. Glover, Cell 111:779-789, 2002). Here we demonstrate that mouse and human cells deficient for BRCA1, due to mutation or knockdown by RNA interference, also have elevated fragile-site expression. We further show that BRCA1 functions in the induction of the G(2)/M checkpoint after aphidicolin-induced replication stalling and that this checkpoint function is involved in fragile-site stability. These data indicate that BRCA1 is important in fragile-site stability and that fragile sites are recognized by the G(2)/M checkpoint pathway, in which BRCA1 plays a key role. Furthermore, they suggest that mutations in BRCA1 or interacting proteins could lead to rearrangements at fragile sites in cancer cells.
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Affiliation(s)
- Martin F Arlt
- Department of Human Genetics, 4909 Buhl, Box 0618, 1241 E. Catherine Street, University of Michigan, Ann Arbor, MI 48109-0618, USA
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Pekarsky Y, Garrison PN, Palamarchuk A, Zanesi N, Aqeilan RI, Huebner K, Barnes LD, Croce CM. Fhit is a physiological target of the protein kinase Src. Proc Natl Acad Sci U S A 2004; 101:3775-9. [PMID: 15007172 PMCID: PMC374320 DOI: 10.1073/pnas.0400481101] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The FHIT gene is a tumor suppressor that is frequently inactivated by genomic alterations at chromosomal region 3p14.2. In the last few years, a considerable amount of data describing inactivation of FHIT in a variety of human malignancies and demonstrating the tumor suppressor potential of Fhit have been reported. Despite the demonstration that FHIT functions as a tumor suppressor, the pathway through which Fhit induces apoptosis and inhibits growth of cancer cells is not known. Our data demonstrate that Fhit is a target of tyrosine phosphorylation by the Src protein kinase. We show that Src phosphorylates Y114 of Fhit in vitro and in vivo, providing insight into a biochemical pathway involved in Fhit signaling.
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Affiliation(s)
- Yuri Pekarsky
- Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
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