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Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, Barajas JM, Thomas ME, Walsh MP, Song G, Tian L, Liu Y, Chen X, Kolekar P, Tran Q, Foy SG, Maciaszek JL, Kleist AB, Leonti AR, Ju B, Easton J, Wu H, Valentine V, Valentine MB, Liu YC, Ries RE, Smith JL, Parganas E, Iacobucci I, Hiltenbrand R, Miller J, Myers JR, Rampersaud E, Rahbarinia D, Rusch M, Wu G, Inaba H, Wang YC, Alonzo TA, Downing JR, Mullighan CG, Pounds S, Babu MM, Zhang J, Rubnitz JE, Meshinchi S, Ma X, Klco JM. Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:194-207. [PMID: 35176137 PMCID: PMC9780084 DOI: 10.1158/2643-3230.bcd-21-0160] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 08/27/2021] [Accepted: 01/24/2022] [Indexed: 01/21/2023] Open
Abstract
The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in upstream binding transcription factor (UBTF) in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with cooccurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. In addition, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML. SIGNIFICANCE We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Benjamin J. Huang
- Department of Pediatrics, University of California, Benioff Children's Hospital, San Francisco, California
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juan M. Barajas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Melvin E. Thomas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael P. Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott G. Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew B. Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Bengsheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jenny L. Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan Parganas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan Miller
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Todd A. Alonzo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James R. Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - M. Madan Babu
- Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
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Montefiori LE, Bendig S, Gu Z, Chen X, Pölönen P, Ma X, Murison A, Zeng A, Garcia-Prat L, Dickerson K, Iacobucci I, Abdelhamed S, Hiltenbrand R, Mead PE, Mehr CM, Xu B, Cheng Z, Chang TC, Westover T, Ma J, Stengel A, Kimura S, Qu C, Valentine MB, Rashkovan M, Luger S, Litzow MR, Rowe JM, den Boer ML, Wang V, Yin J, Kornblau SM, Hunger SP, Loh ML, Pui CH, Yang W, Crews KR, Roberts KG, Yang JJ, Relling MV, Evans WE, Stock W, Paietta EM, Ferrando AA, Zhang J, Kern W, Haferlach T, Wu G, Dick JE, Klco JM, Haferlach C, Mullighan CG. Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia. Cancer Discov 2021; 11:2846-2867. [PMID: 34103329 PMCID: PMC8563395 DOI: 10.1158/2159-8290.cd-21-0145] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/27/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
Lineage-ambiguous leukemias are high-risk malignancies of poorly understood genetic basis. Here, we describe a distinct subgroup of acute leukemia with expression of myeloid, T lymphoid, and stem cell markers driven by aberrant allele-specific deregulation of BCL11B, a master transcription factor responsible for thymic T-lineage commitment and specification. Mechanistically, this deregulation was driven by chromosomal rearrangements that juxtapose BCL11B to superenhancers active in hematopoietic progenitors, or focal amplifications that generate a superenhancer from a noncoding element distal to BCL11B. Chromatin conformation analyses demonstrated long-range interactions of rearranged enhancers with the expressed BCL11B allele and association of BCL11B with activated hematopoietic progenitor cell cis-regulatory elements, suggesting BCL11B is aberrantly co-opted into a gene regulatory network that drives transformation by maintaining a progenitor state. These data support a role for ectopic BCL11B expression in primitive hematopoietic cells mediated by enhancer hijacking as an oncogenic driver of human lineage-ambiguous leukemia. SIGNIFICANCE: Lineage-ambiguous leukemias pose significant diagnostic and therapeutic challenges due to a poorly understood molecular and cellular basis. We identify oncogenic deregulation of BCL11B driven by diverse structural alterations, including de novo superenhancer generation, as the driving feature of a subset of lineage-ambiguous leukemias that transcend current diagnostic boundaries.This article is highlighted in the In This Issue feature, p. 2659.
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Affiliation(s)
- Lindsey E Montefiori
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alex Murison
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Andy Zeng
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Laura Garcia-Prat
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kirsten Dickerson
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Paul E Mead
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cyrus M Mehr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marcus B Valentine
- Cytogenetics Core Facility, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marissa Rashkovan
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jacob M Rowe
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Victoria Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jun Yin
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York
- Department of Pediatrics, Columbia University, New York, New York
- Department of Pathology and Cell Biology, Columbia University, New York, New York
- Department of Systems Biology, Columbia University, New York, New York
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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3
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Paulk NK, Pekrun K, Zhu E, Nygaard S, Li B, Xu J, Chu K, Leborgne C, Dane AP, Haft A, Zhang Y, Zhang F, Morton C, Valentine MB, Davidoff AM, Nathwani AC, Mingozzi F, Grompe M, Alexander IE, Lisowski L, Kay MA. Bioengineered AAV Capsids with Combined High Human Liver Transduction In Vivo and Unique Humoral Seroreactivity. Mol Ther 2018; 26:289-303. [PMID: 29055620 PMCID: PMC5763027 DOI: 10.1016/j.ymthe.2017.09.021] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 09/17/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023] Open
Abstract
Existing recombinant adeno-associated virus (rAAV) serotypes for delivering in vivo gene therapy treatments for human liver diseases have not yielded combined high-level human hepatocyte transduction and favorable humoral neutralization properties in diverse patient groups. Yet, these combined properties are important for therapeutic efficacy. To bioengineer capsids that exhibit both unique seroreactivity profiles and functionally transduce human hepatocytes at therapeutically relevant levels, we performed multiplexed sequential directed evolution screens using diverse capsid libraries in both primary human hepatocytes in vivo and with pooled human sera from thousands of patients. AAV libraries were subjected to five rounds of in vivo selection in xenografted mice with human livers to isolate an enriched human-hepatotropic library that was then used as input for a sequential on-bead screen against pooled human immunoglobulins. Evolved variants were vectorized and validated against existing hepatotropic serotypes. Two of the evolved AAV serotypes, NP40 and NP59, exhibited dramatically improved functional human hepatocyte transduction in vivo in xenografted mice with human livers, along with favorable human seroreactivity profiles, compared with existing serotypes. These novel capsids represent enhanced vector delivery systems for future human liver gene therapy applications.
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Affiliation(s)
- Nicole K Paulk
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Katja Pekrun
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erhua Zhu
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Sean Nygaard
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Bin Li
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jianpeng Xu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kirk Chu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Allison P Dane
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Annelise Haft
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Yue Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Chris Morton
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Marcus B Valentine
- Cytogenetic Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amit C Nathwani
- Department of Haematology, UCL Cancer Institute, London, UK; Department of Haematology and Katharine Dormandy Haemophilia Centre & Thrombosis Unit, Royal Free London NHS Foundation Trust Hospital, London, UK; National Health Services Blood and Transplant, Watford, UK
| | - Federico Mingozzi
- Genethon and INSERM U951, Evry, France; University Pierre and Marie Curie, Paris, France
| | - Markus Grompe
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ian E Alexander
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Leszek Lisowski
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia; Military Institute of Hygiene and Epidemiology (MIHE), Puławy, Poland
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA.
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4
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Lagutina IV, Valentine V, Picchione F, Harwood F, Valentine MB, Villarejo-Balcells B, Carvajal JJ, Grosveld GC. Modeling of the human alveolar rhabdomyosarcoma Pax3-Foxo1 chromosome translocation in mouse myoblasts using CRISPR-Cas9 nuclease. PLoS Genet 2015; 11:e1004951. [PMID: 25659124 PMCID: PMC4319822 DOI: 10.1371/journal.pgen.1004951] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 12/10/2014] [Indexed: 01/01/2023] Open
Abstract
Many recurrent chromosome translocations in cancer result in the generation of fusion genes that are directly implicated in the tumorigenic process. Precise modeling of the effects of cancer fusion genes in mice has been inaccurate, as constructs of fusion genes often completely or partially lack the correct regulatory sequences. The reciprocal t(2;13)(q36.1;q14.1) in human alveolar rhabdomyosarcoma (A-RMS) creates a pathognomonic PAX3-FOXO1 fusion gene. In vivo mimicking of this translocation in mice is complicated by the fact that Pax3 and Foxo1 are in opposite orientation on their respective chromosomes, precluding formation of a functional Pax3-Foxo1 fusion via a simple translocation. To circumvent this problem, we irreversibly inverted the orientation of a 4.9 Mb syntenic fragment on chromosome 3, encompassing Foxo1, by using Cre-mediated recombination of two pairs of unrelated oppositely oriented LoxP sites situated at the borders of the syntenic region. We tested if spatial proximity of the Pax3 and Foxo1 loci in myoblasts of mice homozygous for the inversion facilitated Pax3-Foxo1 fusion gene formation upon induction of targeted CRISPR-Cas9 nuclease-induced DNA double strand breaks in Pax3 and Foxo1. Fluorescent in situ hybridization indicated that fore limb myoblasts show a higher frequency of Pax3/Foxo1 co-localization than hind limb myoblasts. Indeed, more fusion genes were generated in fore limb myoblasts via a reciprocal t(1;3), which expressed correctly spliced Pax3-Foxo1 mRNA encoding Pax3-Foxo1 fusion protein. We conclude that locus proximity facilitates chromosome translocation upon induction of DNA double strand breaks. Given that the Pax3-Foxo1 fusion gene will contain all the regulatory sequences necessary for precise regulation of its expression, we propose that CRISPR-Cas9 provides a novel means to faithfully model human diseases caused by chromosome translocation in mice.
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Affiliation(s)
- Irina V. Lagutina
- Departments of Genetics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Virginia Valentine
- Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Fabrizio Picchione
- Departments of Genetics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Frank Harwood
- Departments of Genetics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Marcus B. Valentine
- Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | | | - Jaime J. Carvajal
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Sevilla, Spain
| | - Gerard C. Grosveld
- Departments of Genetics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
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DeNardo BD, Holloway MP, Ji Q, Nguyen KT, Cheng Y, Valentine MB, Salomon A, Altura RA. Quantitative phosphoproteomic analysis identifies activation of the RET and IGF-1R/IR signaling pathways in neuroblastoma. PLoS One 2013; 8:e82513. [PMID: 24349301 PMCID: PMC3859635 DOI: 10.1371/journal.pone.0082513] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/24/2013] [Indexed: 12/20/2022] Open
Abstract
Neuroblastoma is an embryonal tumor of childhood with a heterogenous clinical presentation that reflects differences in activation of complex biological signaling pathways. Protein phosphorylation is a key component of cellular signal transduction and plays a critical role in processes that control cancer cell growth and survival. We used shotgun LC/MS to compare phosphorylation between a human MYCN amplified neuroblastoma cell line (NB10), modeling a resistant tumor, and a human neural precursor cell line (NPC), modeling a normal baseline neural crest cell. 2181 unique phosphorylation sites representing 1171 proteins and 2598 phosphopeptides were found. Protein kinases accounted for 6% of the proteome, with a predominance of tyrosine kinases, supporting their prominent role in oncogenic signaling pathways. Highly abundant receptor tyrosine kinase (RTK) phosphopeptides in the NB10 cell line relative to the NPC cell line included RET, insulin-like growth factor 1 receptor/insulin receptor (IGF-1R/IR), and fibroblast growth factor receptor 1 (FGFR1). Multiple phosphorylated peptides from downstream mediators of the PI3K/AKT/mTOR and RAS pathways were also highly abundant in NB10 relative to NPC. Our analysis highlights the importance of RET, IGF-1R/IR and FGFR1 as RTKs in neuroblastoma and suggests a methodology that can be used to identify potential novel biological therapeutic targets. Furthermore, application of this previously unexploited technology in the clinic opens the possibility of providing a new wide-scale molecular signature to assess disease progression and prognosis.
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Affiliation(s)
- Bradley D. DeNardo
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Michael P. Holloway
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Qinqin Ji
- Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
| | - Kevin T. Nguyen
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Yan Cheng
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Marcus B. Valentine
- St. Jude Comprehensive Cancer Center Cytogenetic Shared Resource, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Arthur Salomon
- Department of Molecular and Cellular Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Rachel A. Altura
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
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6
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Chen X, Stewart E, Shelat AA, Qu C, Bahrami A, Hatley M, Wu G, Bradley C, McEvoy J, Pappo A, Spunt S, Valentine MB, Valentine V, Krafcik F, Lang WH, Wierdl M, Tsurkan L, Tolleman V, Federico SM, Morton C, Lu C, Ding L, Easton J, Rusch M, Nagahawatte P, Wang J, Parker M, Wei L, Hedlund E, Finkelstein D, Edmonson M, Shurtleff S, Boggs K, Mulder H, Yergeau D, Skapek S, Hawkins DS, Ramirez N, Potter PM, Sandoval JA, Davidoff AM, Mardis ER, Wilson RK, Zhang J, Downing JR, Dyer MA. Targeting oxidative stress in embryonal rhabdomyosarcoma. Cancer Cell 2013; 24:710-24. [PMID: 24332040 PMCID: PMC3904731 DOI: 10.1016/j.ccr.2013.11.002] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/28/2013] [Accepted: 11/06/2013] [Indexed: 10/25/2022]
Abstract
Rhabdomyosarcoma is a soft-tissue sarcoma with molecular and cellular features of developing skeletal muscle. Rhabdomyosarcoma has two major histologic subtypes, embryonal and alveolar, each with distinct clinical, molecular, and genetic features. Genomic analysis shows that embryonal tumors have more structural and copy number variations than alveolar tumors. Mutations in the RAS/NF1 pathway are significantly associated with intermediate- and high-risk embryonal rhabdomyosarcomas (ERMS). In contrast, alveolar rhabdomyosarcomas (ARMS) have fewer genetic lesions overall and no known recurrently mutated cancer consensus genes. To identify therapeutics for ERMS, we developed and characterized orthotopic xenografts of tumors that were sequenced in our study. High-throughput screening of primary cultures derived from those xenografts identified oxidative stress as a pathway of therapeutic relevance for ERMS.
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Affiliation(s)
- Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunxu Qu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mark Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cori Bradley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Justina McEvoy
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alberto Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheri Spunt
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Marcus B Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Virginia Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Fred Krafcik
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walter H Lang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Monika Wierdl
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lyudmila Tsurkan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Viktor Tolleman
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sara M Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chris Morton
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles Lu
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Li Ding
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Panduka Nagahawatte
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jianmin Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erin Hedlund
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheila Shurtleff
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kristy Boggs
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Donald Yergeau
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steve Skapek
- Division of Pediatric Hematology-Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Douglas S Hawkins
- Division of Hematology-Oncology, Seattle Children's Hospital, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98105, USA
| | - Nilsa Ramirez
- Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John A Sandoval
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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7
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Teitz T, Inoue M, Valentine MB, Zhu K, Rehg JE, Zhao W, Finkelstein D, Wang YD, Johnson MD, Calabrese C, Rubinstein M, Hakem R, Weiss WA, Lahti JM. Th-MYCN mice with caspase-8 deficiency develop advanced neuroblastoma with bone marrow metastasis. Cancer Res 2013; 73:4086-97. [PMID: 23536557 DOI: 10.1158/0008-5472.can-12-2681] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Neuroblastoma, the most common extracranial pediatric solid tumor, is responsible for 15% of all childhood cancer deaths. Patients frequently present at diagnosis with metastatic disease, particularly to the bone marrow. Advances in therapy and understanding of the metastatic process have been limited due, in part, to the lack of animal models harboring bone marrow disease. The widely used transgenic model, the Th-MYCN mouse, exhibits limited metastasis to this site. Here, we establish the first genetic immunocompetent mouse model for metastatic neuroblastoma with enhanced secondary tumors in the bone marrow. This model recapitulates 2 frequent alterations in metastatic neuroblastoma, overexpression of MYCN and loss of caspase-8 expression. Mouse caspase-8 gene was deleted in neural crest lineage cells by crossing a Th-Cre transgenic mouse with a caspase-8 conditional knockout mouse. This mouse was then crossed with the neuroblastoma prone Th-MYCN mouse. Although overexpression of MYCN by itself rarely caused bone marrow metastasis, combining MYCN overexpression and caspase-8 deletion significantly enhanced bone marrow metastasis (37% incidence). Microarray expression studies of the primary tumors mRNAs and microRNAs revealed extracellular matrix structural changes, increased expression of genes involved in epithelial to mesenchymal transition, inflammation, and downregulation of miR-7a and miR-29b. These molecular changes have been shown to be associated with tumor progression and activation of the cytokine TGF-β pathway in various tumor models. Cytokine TGF-β can preferentially promote single cell motility and blood-borne metastasis and therefore activation of this pathway may explain the enhanced bone marrow metastasis observed in this animal model.
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Affiliation(s)
- Tal Teitz
- Departments of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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8
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Mattar CNZ, Nathwani AC, Waddington SN, Dighe N, Kaeppel C, Nowrouzi A, Mcintosh J, Johana NB, Ogden B, Fisk NM, Davidoff AM, David A, Peebles D, Valentine MB, Appelt JU, von Kalle C, Schmidt M, Biswas A, Choolani M, Chan JKY. Stable human FIX expression after 0.9G intrauterine gene transfer of self-complementary adeno-associated viral vector 5 and 8 in macaques. Mol Ther 2011; 19:1950-60. [PMID: 21629224 PMCID: PMC3222517 DOI: 10.1038/mt.2011.107] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/20/2011] [Indexed: 12/26/2022] Open
Abstract
Intrauterine gene transfer (IUGT) offers ontological advantages including immune naiveté mediating tolerance to the vector and transgenic products, and effecting a cure before development of irreversible pathology. Despite proof-of-principle in rodent models, expression efficacy with a therapeutic transgene has yet to be demonstrated in a preclinical nonhuman primate (NHP) model. We aimed to determine the efficacy of human Factor IX (hFIX) expression after adeno-associated-viral (AAV)-mediated IUGT in NHP. We injected 1.0-1.95 × 10(13) vector genomes (vg)/kg of self-complementary (sc) AAV5 and 8 with a LP1-driven hFIX transgene intravenously in 0.9G late gestation NHP fetuses, leading to widespread transduction with liver tropism. Liver-specific hFIX expression was stably maintained between 8 and 112% of normal activity in injected offspring followed up for 2-22 months. AAV8 induced higher hFIX expression (P = 0.005) and milder immune response than AAV5. Random hepatocellular integration was found with no hotspots. Transplacental spread led to low-level maternal tissue transduction, without evidence of immunotoxicity or germline transduction in maternal oocytes. A single intravenous injection of scAAV-LP1-hFIXco to NHP fetuses in late-gestation produced sustained clinically-relevant levels of hFIX with liver-specific expression and a non-neutralizing immune response. These data are encouraging for conditions where gene transfer has the potential to avert perinatal death and long-term irreversible sequelae.
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Affiliation(s)
- Citra N Z Mattar
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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9
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Lowy DR, Johnson MR, DeClue JE, Cen H, Zhang K, Papageorge AG, Vass WC, Willumsen BM, Valentine MB, Look AT. Cell transformation by ras and regulation of its protein product. Ciba Found Symp 2007; 176:67-80; discussion 80-4. [PMID: 8299427 DOI: 10.1002/9780470514450.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We are studying the biological activity and regulation of mammalian Ras protein in tumours and in physiological signalling. We have shown that GAP (the GTPase-activating protein) is a potent negative regulator of normal Ras in cells. Reduction or loss of the NF1 gene product neurofibromin, in association with genetic abnormalities of the NF1 locus, has been identified in schwannoma cell lines from patients with neurofibromatosis and in melanoma and neuroblastoma lines from patients without neurofibromatosis. Although loss of neurofibromin in the schwannoma lines was associated with a high proportion of normal Ras protein in the active GTP-bound state, Ras-GTP appeared to be appropriately regulated in the melanoma and neuroblastoma lines, which contain normal levels of GAP. Therefore the GTPase-activating activity of neurofibromin is not essential for negative regulation of Ras in some cell types and the putative tumour suppressor function of neurofibromin in such cell types is independent of its GTPase-activating activity. Mitogen activation of Ras in fibroblasts is mediated primarily by exchange factors, which probably interact with a region on the Ras protein distinct from the region required for interaction with GAP. Multiple full-length cDNAs have identified a mouse gene whose products are related to yeast CDC25 guanine nucleotide exchange factor.
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Affiliation(s)
- D R Lowy
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD
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10
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Inoue A, Li T, Roby SK, Valentine MB, Inoue M, Boyd K, Kidd VJ, Lahti JM. Loss of ChlR1 helicase in mouse causes lethality due to the accumulation of aneuploid cells generated by cohesion defects and placental malformation. Cell Cycle 2007; 6:1646-54. [PMID: 17611414 DOI: 10.4161/cc.6.13.4411] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human DDX11 and DDX12 are closely related genes encoding the helicases ChlR1 and ChlR2, which belong to the CHL1 DNA helicase family. Recently, it was shown that human ChlR1 interacts with components of the cohesin complex and is required for proper centromeric cohesion. To establish the function of ChlR1 in development we made a mutant mouse lacking Ddx11, the single mouse ChlR gene. The absence of Ddx11 resulted in embryonic lethality at E10.5. The mutant embryos were smaller in size, malformed and exhibited sparse cellularity in comparison to normal or heterozygous litter mates. Importantly, loss of Ddx11 resulted in the inability to form a proper placenta, indicating that ChlR1 is essential for placental formation. Detailed analysis of cells isolated from Ddx11-/- embryos revealed a G2/M cell cycle delay, an increased frequency of chromosome missegregation, decreased chromosome cohesion, and increased aneuploidy. To examine whether ChlR proteins are required for arm cohesion and for loading of the cohesin complex, further studies were preformed in ChlR1 siRNA treated cells. These studies revealed that ChlR1 is required for proper sister chromatid arm cohesion and that cohesin complexes bind more loosely to chromatin in the absence of ChlR1. Taken together, these studies provide the first data indicating that the ChlR1 helicase is essential for proper binding of the cohesin complex to both the centromere and the chromosome arms, and indicate that ChlR1 is essential for embryonic development and the prevention of aneuploidy in mammals.
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Affiliation(s)
- Akira Inoue
- Department Genetics and Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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11
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Yoon KJ, Danks MK, Ragsdale ST, Valentine MB, Valentine VA. Translocations of 17q21 approximately qter in neuroblastoma cell lines infrequently include the topoisomerase IIalpha gene. ACTA ACUST UNITED AC 2006; 167:92-4. [PMID: 16682295 DOI: 10.1016/j.cancergencyto.2005.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 10/24/2005] [Accepted: 11/01/2005] [Indexed: 11/15/2022]
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Abstract
PURPOSE Osteosarcoma is distinct from most cancers in that the majority of osteosarcomas lack telomerase expression and use the alternative lengthening of telomeres (ALT) mechanism to maintain telomeres. Laboratory studies suggest that compared with ALT, telomerase expression is associated with increased tumor aggressiveness. We evaluated the clinical significance of telomerase expression in human osteosarcoma. PATIENTS AND METHODS Fifty-six osteosarcomas from 51 patients treated at St Jude Children's Research Hospital between 1982 and 2003 were evaluated for telomerase enzyme activity, mRNA expression of the catalytic component of telomerase (TERT), and presence of the ALT pathway. RESULTS Outcome analysis was based on TERT mRNA expression in the primary tumor samples from 44 patients. Fourteen primary tumors expressed TERT mRNA (32%; eight TERT only, six TERT and ALT) and 30 did not express TERT mRNA (68%; 29 ALT, one no ALT). Progression-free survival (PFS) was inferior in the TERT-positive group compared with the TERT-negative group (3-year estimates, 21.4% +/- 9.5% v 63.7% +/- 11.1%; P =.014). Likewise, overall survival was inferior in the TERT-positive group compared with the TERT-negative group (3-year estimates, 42.9% +/- 12.2% v 70.0% +/- 9.9%; P =.031). Among 31 patients with nonmetastatic disease at diagnosis, PFS was lower in the TERT-positive group compared with the TERT-negative group (3-year estimates, 33.3% +/- 13.6% v 72.0% +/- 11.5%; P =.092). CONCLUSION Telomerase expression in primary tumor samples is associated with decreased PFS and OS in patients with osteosarcoma. Additional studies are warranted to better define the clinical utility of this molecular marker.
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Mathew P, Valentine MB, Bowman LC, Rowe ST, Nash MB, Valentine VA, Cohn SL, Castleberry RP, Brodeur GM, Look AT. Detection of MYCN gene amplification in neuroblastoma by fluorescence in situ hybridization: a pediatric oncology group study. Neoplasia 2001; 3:105-9. [PMID: 11420745 PMCID: PMC1505416 DOI: 10.1038/sj.neo.7900146] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2000] [Accepted: 10/02/2000] [Indexed: 11/09/2022] Open
Abstract
To assess the utility of fluorescence in situ hybridization (FISH) for analysis of MYCN gene amplification in neuroblastoma, we compared this assay with Southern blot analysis using tumor specimens collected from 232 patients with presenting characteristics typical of this disease. The FISH technique identified MYCN amplification in 47 cases, compared with 39 by Southern blotting, thus increasing the total number of positive cases by 21%. The major cause of discordancy was a low fraction of tumor cells (< or =30% replacement) in clinical specimens, which prevented an accurate estimate of MYCN copy number by Southern blotting. With FISH, by contrast, it was possible to analyze multiple interphase nuclei of tumor cells, regardless of the proportion of normal peripheral blood, bone marrow, or stromal cells in clinical samples. Thus, FISH could be performed accurately with very small numbers of tumor cells from touch preparations of needle biopsies. Moreover, this procedure allowed us to discern the heterogeneous pattern of MYCN amplification that is characteristic of neuroblastoma. We conclude that FISH improves the detection of MYCN gene amplification in childhood neuroblastomas in a clinical setting, thus facilitating therapeutic decisions based on the presence or absence of this prognostically important biologic marker.
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Affiliation(s)
- P Mathew
- Department of Experimental Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
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14
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Teitz T, Wei T, Valentine MB, Vanin EF, Grenet J, Valentine VA, Behm FG, Look AT, Lahti JM, Kidd VJ. Caspase 8 is deleted or silenced preferentially in childhood neuroblastomas with amplification of MYCN. Nat Med 2000; 6:529-35. [PMID: 10802708 DOI: 10.1038/75007] [Citation(s) in RCA: 551] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Caspase 8 is a cysteine protease regulated in both a death-receptor-dependent and -independent manner during apoptosis. Here, we report that the gene for caspase 8 is frequently inactivated in neuroblastoma, a childhood tumor of the peripheral nervous system. The gene is silenced through DNA methylation as well as through gene deletion. Complete inactivation of CASP8 occurred almost exclusively in neuroblastomas with amplification of the oncogene MYCN. Caspase 8-null neuroblastoma cells were resistant to death receptor- and doxorubicin-mediated apoptosis, deficits that were corrected by programmed expression of the enzyme. Thus, caspase 8 acts as a tumor suppressor in neuroblastomas with amplification of MYCN.
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Affiliation(s)
- T Teitz
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, Tennessee 38101, USA
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15
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Shearer PD, Valentine MB, Grundy P, DeCou JM, Banavali SD, Komuro H, Green DM, Beckwith JB, Look AT. Hemizygous deletions of chromosome band 16q24 in Wilms tumor: detection by fluorescence in situ hybridization. Cancer Genet Cytogenet 1999; 115:100-5. [PMID: 10598141 DOI: 10.1016/s0165-4608(99)00093-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Loss of heterozygosity (LOH) for markers on chromosome arm 16q in Wilms tumor has been linked to an increased risk of treatment failure. We therefore postulated that fluorescence in situ hybridization (FISH) with probes from this region might enhance current strategies for identifying high-risk patients at diagnosis. In a blinded comparative pilot study of 19 Wilms tumor samples from 18 patients with favorable histology, FISH and DNA polymorphism analysis yielded concordant results in 14 cases, either retention (n = 6) or loss (n = 8) of chromosome arm 16q markers. Discordant findings in 4 of the 5 remaining cases resulted from detection of LOH, but no loss by FISH. Two of these cases, directly comparable at marker D16S422, appeared to have tumor-specific uniparental disomy, in that 2 copies of D16S422 and the 16 centromere were evident, despite LOH. In 2 other cases, the discrepancies could be explained by LOH confined to loci distal to the D16S422 locus. In the fifth case, FISH detected 2 distinct populations of tumor cells, one characterized by normal diploidy and the other by monosomy 16, whereas DNA polymorphism analysis failed to indicate LOH altogether. Thus, FISH confirmed the presence of allelic loss (hence, the possible location of biologically important tumor suppressor genes) on the distal long arm of chromosome 16 in cases of favorable-histology Wilms tumor, with the advantages of technical simplicity, successful analysis of samples that were otherwise uninformative by analysis of DNA polymorphisms, and the addition of internal controls for chromosomal aneusomy. We suggest that combined analysis of the chromosome 16q region in Wilms tumor by FISH and DNA polymorphism analysis would improve evaluations to identify high-risk patients who might benefit from alternative therapy.
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Affiliation(s)
- P D Shearer
- Department of Hematology/Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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16
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Komuro H, Valentine MB, Rubnitz JE, Saito M, Raimondi SC, Carroll AJ, Yi T, Sherr CJ, Look AT. p27KIP1 deletions in childhood acute lymphoblastic leukemia. Neoplasia 1999; 1:253-61. [PMID: 10935480 PMCID: PMC1508076 DOI: 10.1038/sj.neo.7900033] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/1999] [Accepted: 06/09/1999] [Indexed: 11/08/2022]
Abstract
The p27KIP1 gene, which encodes a cyclin-dependent kinase (CDK) inhibitor, has been assigned to chromosome band 12p12, a region often affected by cytogenetically apparent deletions or translocations in childhood acute lymphoblastic leukemia (ALL). As described here, fluorescence in situ hybridization (FISH) analysis of 35 primary ALL samples with cytogenetic evidence of 12p abnormalities revealed hemizygous deletions of p27KIP1 in 29 cases. Further analysis of 19 of these cases with two additional gene-specific probes from the 12p region (hematopoietic cell phosphatase, HCP and cyclin D2, CCND2) showed that p27KIP1 is located more proximally on the short arm of chromosome 12 and is deleted more frequently than either HCP or CCND2. Of 16 of these cases with hemizygous deletion of p27KIP1, only eight showed loss of HCP or CCND2, whereas loss of either of the latter two loci was uniformly associated with loss of p27KIP1. Missense mutations or mutations leading to premature termination codons were not detected in the coding sequences of the retained p27KIP1 alleles in any of the 16 ALL cases examined, indicating a lack of homozygous inactivation. By Southern blot analysis, one case of primary T-cell ALL had hemizygous loss of a single p27KIP1 allele and a 34.5-kb deletion, including the second coding exon of the other allele. Despite homozygous inactivation of p27KP1 in this case, our data suggest that haploinsufficiency for p27KIP1 is the primary consequence of 12p chromosomal deletions in childhood ALL. The oncogenic role of reduced, but not absent, levels of p27KIP1 is supported by recent studies in murine models and evidence that this protein not only inhibits the activity of complexes containing CDK2 and cyclin E, but also promotes the assembly and catalytic activity of CDK4 or CDK6 in complexes with cyclin D.
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Affiliation(s)
- H Komuro
- Department of Experimental Oncology, Howard Hughes Medical Institute, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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17
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Kong XT, Valentine VA, Rowe ST, Valentine MB, Ragsdale ST, Jones BG, Wilkinson DA, Brodeur GM, Cohn SL, Look AT. Lack of homozygously inactivated p73 in single-copy MYCN primary neuroblastomas and neuroblastoma cell lines. Neoplasia 1999; 1:80-9. [PMID: 10935473 PMCID: PMC1716055 DOI: 10.1038/sj.neo.7900010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We examined 18 neuroblastoma cell lines and 32 primary single-copy MYCN tumor specimens to determine whether mutations of p73, a novel p53-related gene located in chromosome band 1p36.33, contribute to the genesis or progression of childhood neuroblastoma. By fluorescence in situ hybridization, 16 of the 18 cell lines, but only 3 of the 32 primary tumors, had evidence of a deleted p73 allele. Sequence analysis of the p73 coding region in the mRNAs expressed by these cell lines and tumors did not reveal inactivating mutations, suggesting that p73 is not homozygously inactivated in neuroblastoma. However, several novel splice forms of p73 mRNAs were identified, including one without exon 11 that predominated in multiple MYCN-amplified cell lines. Its encoded p73 protein differed from other splice forms in that the C-terminus was derived from an alternative reading frame. Further study of the functional properties of the protein encoded by this splice form of p73 will be needed to determine whether it contributes to the pathogenesis of childhood neuroblastoma with MYCN gene amplification.
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Affiliation(s)
- X T Kong
- Department of Experimental Oncology, St Jude Children's Research Hospital, Memphis, TN 38105-2794, USA
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18
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Bodner SM, Naeve CW, Rakestraw KM, Jones BG, Valentine VA, Valentine MB, Luthardt FW, Willman CL, Raimondi SC, Downing JR, Roussel MF, Sherr CJ, Look AT. Cloning and chromosomal localization of the gene encoding human cyclin D-binding Myb-like protein (hDMP1). Gene 1999; 229:223-8. [PMID: 10095122 DOI: 10.1016/s0378-1119(98)00591-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The murine transcription factor murine cyclin D-binding Myb-like protein (mDmp1) arrests the cell cycle in G1 phase, through an activity that can be overridden by direct interaction with the D-type cyclins. Here, we describe the identification, sequence, chromosomal localization, and expression of the human cognate, hDMP1. The hDMP1 cDNA contains a 2280bp open reading frame that shares a high degree of identity with the mDmp1 coding region. The 4.4kb hDMP1 messenger RNA is ubiquitously expressed in normal human tissues, with highest levels in testis and substructures within the brain. By use of fluorescence in situ hybridization with a human genomic P1 probe, we assigned hDMP1 to chromosome 7, band q21. This chromosomal region is frequently deleted as part of the 7q-minus and monosomy 7 abnormalities of human acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). We analyzed hDMP1 copy number by fluorescence in situ hybridization in leukemic blasts from nine patients with abnormalities of the long arm of chromosome 7, and in each case one allele of the hDMP1 gene was deleted. Functional analysis of the mDmp1 protein has shown that it negatively regulates cell proliferation, which suggests that this gene is a candidate suppressor of malignant transformation. Further study will be needed to determine whether gene-specific mutations implicate hDMP1 as a tumor suppressor in acute leukemias with deletions of the long arm of chromosome 7 or in other types of human malignancy.
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Affiliation(s)
- S M Bodner
- Department of Pathology and Laboratory Medicine, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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19
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Nichols KE, Harkin DP, Levitz S, Krainer M, Kolquist KA, Genovese C, Bernard A, Ferguson M, Zuo L, Snyder E, Buckler AJ, Wise C, Ashley J, Lovett M, Valentine MB, Look AT, Gerald W, Housman DE, Haber DA. Inactivating mutations in an SH2 domain-encoding gene in X-linked lymphoproliferative syndrome. Proc Natl Acad Sci U S A 1998; 95:13765-70. [PMID: 9811875 PMCID: PMC24894 DOI: 10.1073/pnas.95.23.13765] [Citation(s) in RCA: 402] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/1998] [Indexed: 12/18/2022] Open
Abstract
X-linked lymphoproliferative syndrome (XLP) is an inherited immunodeficiency characterized by increased susceptibility to Epstein-Barr virus (EBV). In affected males, primary EBV infection leads to the uncontrolled proliferation of virus-containing B cells and reactive cytotoxic T cells, often culminating in the development of high-grade lymphoma. The XLP gene has been mapped to chromosome band Xq25 through linkage analysis and the discovery of patients harboring large constitutional genomic deletions. We describe here the presence of small deletions and intragenic mutations that specifically disrupt a gene named DSHP in 6 of 10 unrelated patients with XLP. This gene encodes a predicted protein of 128 amino acids composing a single SH2 domain with extensive homology to the SH2 domain of SHIP, an inositol polyphosphate 5-phosphatase that functions as a negative regulator of lymphocyte activation. DSHP is expressed in transformed T cell lines and is induced following in vitro activation of peripheral blood T lymphocytes. Expression of DSHP is restricted in vivo to lymphoid tissues, and RNA in situ hybridization demonstrates DSHP expression in activated T and B cell regions of reactive lymph nodes and in both T and B cell neoplasms. These observations confirm the identity of DSHP as the gene responsible for XLP, and suggest a role in the regulation of lymphocyte activation and proliferation. Induction of DSHP may sustain the immune response by interfering with SHIP-mediated inhibition of lymphocyte activation, while its inactivation in XLP patients results in a selective immunodeficiency to EBV.
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Affiliation(s)
- K E Nichols
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
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20
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Komuro H, Valentine MB, Rowe ST, Kidd VJ, Makino S, Brodeur GM, Cohn SL, Look AT. Fluorescence in situ hybridization analysis of chromosome 1p36 deletions in human MYCN amplified neuroblastoma. J Pediatr Surg 1998; 33:1695-8. [PMID: 9856898 DOI: 10.1016/s0022-3468(98)90612-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND/PURPOSE Deletion of the short arm of chromosome 1 (1p) is one of the poor prognostic factors in human neuroblastomas. Recent studies have suggested that one or more of the neuroblastoma tumor suppressor genes reside in this region and have identified the shortest region of overlap (SRO) on 1p36. The purpose of this study was to examine deletions of 1p in human neuroblastomas by fluorescence in situ hybridization (FISH). METHODS Two-color FISH analysis was performed to detect chromosome 1p36 abnormalities in 42 MYCN-amplified neuroblastomas. Four different probes from the 1p36 region, the E2F2, NPPA, D1S160, and CDC2L1 loci were used for detection of 1p abnormalities. A repeat sequence probe, which is specific for the heterochromatic region of chromosome 1 (pUC1.77), was used as a control. RESULTS Large deletions of 1p36 were observed in 31 (73.8%) of 42 tumors, whereas the remaining 11 (26.2%) showed no deletion. In these 11 tumors, a translocation of 1p was found in one and a duplication of 1p was detected in another. CONCLUSIONS A strong correlation between 1p abnormalities and MYCN amplification was found in this study. MYCN-amplified neuroblastomas were found to show large deletions of 1p encompassing the SRO. FISH provided a rapid and reliable method to detect hemizygous deletions of 1p.
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Affiliation(s)
- H Komuro
- Department of Experimental Oncology, St Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
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21
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Reardon DA, Michalkiewicz E, Boyett JM, Sublett JE, Entrekin RE, Ragsdale ST, Valentine MB, Behm FG, Li H, Heideman RL, Kun LE, Shapiro DN, Look AT. Extensive genomic abnormalities in childhood medulloblastoma by comparative genomic hybridization. Cancer Res 1997; 57:4042-7. [PMID: 9307291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We analyzed 27 samples of primary medulloblastoma, using comparative genomic hybridization and a novel statistical approach to evaluate chromosomal regions for significant gain or loss of genomic DNA. An array of nonrandom changes was found in most samples. Two discrete regions of high-level DNA amplification of chromosome bands 5p15.3 and 11q22.3 were observed in 3 of 27 tumors. Nonrandom genomic losses were most frequent in regions on chromosomes 10q (41% of samples), 11 (41%), 16q (37%), 17p (37%), and 8p (33%). Regions of DNA gain most often involved chromosomes 17q (48%) and 7 (44%). These findings suggest a greater degree of genomic imbalance in medulloblastoma than has been recognized previously and highlight chromosomal loci likely to contain oncogenes or tumor suppressor genes that may contribute to the molecular pathogenesis of this tumor.
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Affiliation(s)
- D A Reardon
- Department of Hematology-Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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22
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Perlman EJ, Valentine MB, Griffin CA, Look AT. Deletion of 1p36 in childhood endodermal sinus tumors by two-color fluorescence in situ hybridization: a pediatric oncology group study. Genes Chromosomes Cancer 1996; 16:15-20. [PMID: 9162192 DOI: 10.1002/(sici)1098-2264(199605)16:1<15::aid-gcc2>3.0.co;2-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Childhood endodermal sinus tumors (CESTs) are a unique category of germ cell tumors involving the testis and extragonadal region in children less than 4 years of age. Recent studies of CEST have shown recurrent cytogenetic abnormalities involving the short arm of chromosome 1, most commonly, a deletion of distal 1p. Experience with neuroblastomas has shown that cytogenetic analyses may underestimate the frequency of 1p deletion. To determine the frequency of deletion of Ip in CEST and to verify that 1p is, in fact, deleted and not translocated, we analyzed ten tumors by two-color fluorescence in situ hybridization on single-cell suspensions of interphase nuclei by using a cosmid probe from the PITSLRE kinase (p58) locus (previously mapped to 1p36) cohybridized with plasmid probe pUC1.77 (which recognizes the 1q heterochromatic region) to determine the copy number of chromosome 1. Eight of the ten tumors examined showed evidence of deletion of 1p36. Five of the eight tumors exhibited multiple subdones, and all subdones showed deletion of at least one copy of 1p36, indicating that the deletion probably occurred before the development of chromosome 1 aneusomy. We conclude that deletions of the short arm of chromosome 1, specifically 1p36, do occur in CEST and probably occur at a, higher incidence than that found in neuroblastoma Further studies are needed to determine the degree of overlap of the common area of deletion in CEST with that of neuroblastoma and to determine whether 1p deletion in CEST has prognostic significance.
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Affiliation(s)
- E J Perlman
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
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23
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Yoneda-Kato N, Look AT, Kirstein MN, Valentine MB, Raimondi SC, Cohen KJ, Carroll AJ, Morris SW. The t(3;5)(q25.1;q34) of myelodysplastic syndrome and acute myeloid leukemia produces a novel fusion gene, NPM-MLF1. Oncogene 1996; 12:265-75. [PMID: 8570204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A t(3;5)(q25.1;q34) chromosomal translocation associated with myelodysplastic syndrome and acute myeloid leukemia (AML) was found to rearrange part of the nucleophosmin (NPM) gene on chromosome 5 with sequences from a novel gene on chromosome 3. Chimeric transcripts expressed by these cells contain 5' NPM coding sequences fused in-frame to those of the new gene, which we named myelodysplasia/myeloid leukemia factor 1 (MLF1). RNA-based polymerase chain reaction analysis revealed identical NPM-MLF1 mRNA fusions in each of the three t(3;5)-positive cases of AML examined. The predicted MLF1 amino acid sequence lacked homology to previously characterized proteins and did not contain known functional motifs. Normal MLF1 transcripts were expressed in a variety of tissues, most abundantly in testis, ovary, skeletal muscle, heart, kidney and colon. Anti-MLF1 antibodies detected the wild-type 31 kDa protein in K562 and HEL erythroleukemia cell lines, but not in HL-60, U937 or KG-1 myeloid leukemia lines. By contrast, t(3;5)-positive leukemia cells expressed a 54 kDa NPM-MLF1 protein, but not normal MLF1. Immunostaining experiments indicated that MLF1 is normally located in the cytoplasm, whereas NPM-MLF1 is targeted to the nucleus, with highest levels in the nucleolus. The nuclear/nucleolar localization of NPM-MLF1 mirrors that of NPM, indicating that NPM trafficking signals direct MLF1 to an inappropriate cellular compartment in myeloid leukemia cells.
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Affiliation(s)
- N Yoneda-Kato
- Department of Experimental Oncology, St. Jude Children's Research Hospital
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24
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White PS, Maris JM, Beltinger C, Sulman E, Marshall HN, Fujimori M, Kaufman BA, Biegel JA, Allen C, Hilliard C, Valentine MB, Look AT, Enomoto H, Sakiyama S, Brodeur GM. A region of consistent deletion in neuroblastoma maps within human chromosome 1p36.2-36.3. Proc Natl Acad Sci U S A 1995; 92:5520-4. [PMID: 7777541 PMCID: PMC41727 DOI: 10.1073/pnas.92.12.5520] [Citation(s) in RCA: 195] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Deletion of the short arm of human chromosome 1 is the most common cytogenetic abnormality observed in neuroblastoma. To characterize the region of consistent deletion, we performed loss of heterozygosity (LOH) studies on 122 neuroblastoma tumor samples with 30 distal chromosome 1p polymorphisms. LOH was detected in 32 of the 122 tumors (26%). A single region of LOH, marked distally by D1Z2 and proximally by D1S228, was detected in all tumors demonstrating loss. Also, cells from a patient with a constitutional deletion of 1p36, and from a neuroblastoma cell line with a small 1p36 deletion, were analyzed by fluorescence in situ hybridization. Cells from both sources had interstitial deletions of 1p36.2-36.3 which overlapped the consensus region of LOH defined by the tumors. Interstitial deletion in the constitutional case was confirmed by allelic loss studies using the panel of polymorphic markers. Four proposed candidate genes--DAN, ID3 (heir-1), CDC2L1 (p58), and TNFR2--were shown to lie outside of the consensus region of allelic loss, as defined by the above deletions. These results more precisely define the location of a neuroblastoma suppressor gene within 1p36.2-36.3, eliminating 33 centimorgans of proximal 1p36 from consideration. Furthermore, a consensus region of loss, which excludes the four leading candidate genes, was found in all tumors with 1p36 LOH.
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Affiliation(s)
- P S White
- Division of Oncology, Children's Hospital of Philadelphia, PA 19104, USA
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25
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Okuda T, Shurtleff SA, Valentine MB, Raimondi SC, Head DR, Behm F, Curcio-Brint AM, Liu Q, Pui CH, Sherr CJ. Frequent deletion of p16INK4a/MTS1 and p15INK4b/MTS2 in pediatric acute lymphoblastic leukemia. Blood 1995; 85:2321-30. [PMID: 7727766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The tandemly linked p16INK4aMTS1 and p15INK4b/MTS2 genes on chromosome 9, band p21 encode proteins that function as specific inhibitors of the cyclin D-dependent kinases CDK4 and CDK6. This locus undergoes frequent bi-allelic deletion in human cancer cell lines, suggesting that the encoded proteins may function as tumor suppressors. However, more recent analysis of primary tumor samples has shown a much lower frequency of abnormalities affecting this region, raising doubt over the importance of these proteins in human malignancies. Hemizygous deletions and rearrangements of chromosome 9, band p21, are among the most frequent cytogenetic abnormalities detected in pediatric acute lymphoblastic leukemia (ALL), occurring in approximately 10% of cases. To determine if the p16INK4a/p15INK4b locus might be the target of these chromosomal lesions, we analyzed both genes in primary clinical samples from 43 pediatric ALL patients using interphase fluorescence in situ hybridization, Southern blot analysis, and the polymerase chain reaction. Deletions of p16INK4a/p15INK4b were identified in 18 of 20 cases with cytogenetically observed abnormalities of 9p and 5 of 23 with apparently normal chromosomes 9p, with the majority containing bi-allelic deletions (16 homozygous/7 hemizygous). Although most homozygous deletions involved both genes, Southern blot analysis showed an interstitial deletion in a single case that was confined to p16INK4a, suggesting that p15INK4b was not the critical target gene in this case. Sequence analysis of both p16INK4a and p15INK4b in all seven cases with hemizygous deletions failed to show mutations within the coding regions of the retained alleles. In this select group of patients, deletion of p16INK4a/p15INK4b was associated with T-cell phenotype, nonhyperdiploid karyotype (< 50 chromosomes), and poor event-free survival. These findings indicate that deletion of the p16INK4a/p15INK4b locus is one of the most common genetic abnormalities so far detected in pediatric ALL, and that loss of one or more of these cell cycle kinase inhibitors is important in leukemogenesis.
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Affiliation(s)
- T Okuda
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
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26
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Cohn SL, Look AT, Joshi VV, Holbrook T, Salwen H, Chagnovich D, Chesler L, Rowe ST, Valentine MB, Komuro H. Lack of correlation of N-myc gene amplification with prognosis in localized neuroblastoma: a Pediatric Oncology Group study. Cancer Res 1995; 55:721-6. [PMID: 7850780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Multiple copies of N-myc proto-oncogene are only rarely detected in localized neuroblastomas (NBs), and the prognostic relevance of amplification in this subset of patients is not clear. We analyzed a series of 850 children with NB admitted to a Pediatric Oncology Group NB Biology Study and identified six patients with localized NBs harboring N-myc gene amplification. Three patients whose tumors showed favorable histology by Shimada classification and low-risk histological features according to the Joshi classification have remained disease-free, whereas two of three patients with unfavorable histology tumors have developed recurrent disease. Although earlier studies have indicated that N-myc amplification is associated with diploid DNA content, flow cytometric analysis revealed that only two of the localized tumors contained stem lines with diploid DNA content. Loss of chromosome 1p was not detected by fluorescence in situ hybridization in the two tumors examined. N-myc protein was detected by immunohistochemical studies in four of the five NBs analyzed. However, N-myc protein was not visualized in one of the tumors with stroma-rich histology, and Western blot analysis revealed only low levels of N-myc protein expression in another NB with favorable histology. These studies indicate that the presence of N-myc amplification in localized NBs does not necessarily portend an adverse outcome. Furthermore, the biological features of this subset of N-myc-amplified NBs appear to differ from those of more advanced N-myc-amplified tumors.
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Affiliation(s)
- S L Cohn
- Department of Pediatrics, Northwestern University, Chicago, Illinois
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27
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Morris SW, Kirstein MN, Valentine MB, Dittmer K, Shapiro DN, Look AT, Saltman DL. Fusion of a kinase gene, ALK, to a nucleolar protein gene, NPM, in non-Hodgkin's lymphoma. Science 1995; 267:316-7. [PMID: 7824924 DOI: 10.1126/science.267.5196.316-b] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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28
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Saito M, Helin K, Valentine MB, Griffith BB, Willman CL, Harlow E, Look AT. Amplification of the E2F1 transcription factor gene in the HEL erythroleukemia cell line. Genomics 1995; 25:130-8. [PMID: 7774910 DOI: 10.1016/0888-7543(95)80118-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The E2F transcription factor plays an important regulatory role in cell proliferation, mediating the expression of genes whose products are essential for inducing resting cells to enter the cell cycle and synthesize DNA. To investigate the possible involvement of E2F in hematopoietic malignancies, we isolated genomic clones encompassing the human E2F1 gene. We then used fluorescence in situ hybridization to localize E2F1 to human chromosome 20q11, telomeric to the p107 locus, a gene whose product is related to the retinoblastoma gene product (pRb). This finding contrasts with the 1p36 and 6q22 chromosomal locations previously assigned E2F2 and E2F3, two additional members of the E2F family. Although deletions or structural rearrangements of E2F1 were not detected in 14 primary acute leukemia or myelodysplasia samples with structural abnormalities of chromosome 20q11, the gene was amplified and overexpressed in HEL erythroleukemia cells and translocated to other chromosomes in several established human leukemia cell lines. This study provides the first evidence of gene amplification involving a member of the E2F family of transcription factors. We propose that E2F1 overexpression in erythroid progenitors may stimulate abnormal cell proliferation by overriding negative regulatory signals mediated by tumor suppressor proteins such as pRb.
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MESH Headings
- Animals
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Carrier Proteins
- Cell Cycle Proteins
- Cell Division
- Cell Line
- Chromosome Mapping
- Chromosomes, Human, Pair 20
- Cloning, Molecular
- Cricetinae
- DNA-Binding Proteins
- E2F Transcription Factors
- E2F1 Transcription Factor
- E2F2 Transcription Factor
- E2F3 Transcription Factor
- Gene Amplification
- Gene Expression
- Genes, Tumor Suppressor
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/metabolism
- Humans
- Hybrid Cells
- In Situ Hybridization, Fluorescence
- Leukemia, Erythroblastic, Acute/genetics
- Leukemia, Erythroblastic, Acute/metabolism
- Molecular Sequence Data
- Multigene Family
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- Retinoblastoma-Binding Protein 1
- Telomere
- Transcription Factor DP1
- Transcription Factors/biosynthesis
- Transcription Factors/genetics
- Tumor Cells, Cultured
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Affiliation(s)
- M Saito
- Department of Experimental Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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29
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Cerretti DP, Hollingsworth LT, Kozlosky CJ, Valentine MB, Shapiro DN, Morris SW, Nelson N. Molecular characterization of the gene for human interleukin-1 beta converting enzyme (IL1BC). Genomics 1994; 20:468-73. [PMID: 8034320 DOI: 10.1006/geno.1994.1202] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Interleukin-1 beta (IL-1 beta) mediates a wide range of immune and inflammatory responses. The active cytokine is generated by proteolytic cleavage of an inactive precursor by a protease called the IL-1 beta converting enzyme (ICE). A cDNA encoding this protease was recently isolated. A human genomic clone containing the ICE gene (IL1BC) was isolated using the cDNA as a probe. The gene consists of 10 exons spanning at least 10.6 kb. 5'-anchored polymerase chain reaction indicated a single transcription start site approximately 33 bp upstream of the initiator Met codon. The 5'-flanking region does not have an apparent TATA box but may contain an initiator (Inr) promoter element. However, transcriptional activity could not be detected with a fusion gene containing the 5'-flanking region linked to the bacterial chloramphenicol acetyltransferase gene (CAT) when transfected into the human acute monocytic leukemia cell line THP-1. Using the genomic IL1BC clone, we have confirmed the localization of the gene to chromosome 11 band q22.2-q22.3 by fluorescence in situ hybridization.
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30
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Morris SW, Kirstein MN, Valentine MB, Dittmer KG, Shapiro DN, Saltman DL, Look AT. Fusion of a kinase gene, ALK, to a nucleolar protein gene, NPM, in non-Hodgkin's lymphoma. Science 1994; 263:1281-4. [PMID: 8122112 DOI: 10.1126/science.8122112] [Citation(s) in RCA: 1650] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The 2;5 chromosomal translocation occurs in most anaplastic large-cell non-Hodgkin's lymphomas arising from activated T lymphocytes. This rearrangement was shown to fuse the NPM nucleolar phosphoprotein gene on chromosome 5q35 to a previously unidentified protein tyrosine kinase gene, ALK, on chromosome 2p23. In the predicted hybrid protein, the amino terminus of nucleophosmin (NPM) is linked to the catalytic domain of anaplastic lymphoma kinase (ALK). Expressed in the small intestine, testis, and brain but not in normal lymphoid cells, ALK shows greatest sequence similarity to the insulin receptor subfamily of kinases. Unscheduled expression of the truncated ALK may contribute to malignant transformation in these lymphomas.
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MESH Headings
- Amino Acid Sequence
- Anaplastic Lymphoma Kinase
- Base Sequence
- Brain/enzymology
- Cell Transformation, Neoplastic
- Chromosome Walking
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 5
- Cloning, Molecular
- Gene Expression Regulation, Neoplastic
- Humans
- Intestine, Small/enzymology
- Lymphoma, Large-Cell, Anaplastic/chemistry
- Lymphoma, Large-Cell, Anaplastic/enzymology
- Lymphoma, Large-Cell, Anaplastic/genetics
- Male
- Molecular Sequence Data
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Nucleophosmin
- Phosphoproteins/chemistry
- Phosphoproteins/genetics
- Promoter Regions, Genetic
- Protein-Tyrosine Kinases/chemistry
- Protein-Tyrosine Kinases/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor Protein-Tyrosine Kinases
- Sequence Alignment
- Signal Transduction
- Testis/enzymology
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- S W Morris
- Department of Experimental Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
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31
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Shapiro DN, Sublett JE, Li B, Valentine MB, Morris SW, Noll M. The gene for PAX7, a member of the paired-box-containing genes, is localized on human chromosome arm 1p36. Genomics 1993; 17:767-9. [PMID: 7902328 DOI: 10.1006/geno.1993.1404] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The murine Pax-7 gene and the cognate human gene, formerly designated HuP1, are members of the multigene paired-box-containing class of developmental regulatory genes first identified in Drosophila. By analysis of somatic cell hybrids segregating human chromosomes, the gene encoding PAX7 was localized to human chromosome 1. Fluorescence in situ hybridization confirmed this assignment and allowed mapping of the gene to the terminal region of the short arm (1p36) of the chromosome. Additionally, these results confirm the extensive homology between human chromosome 1p and the distal segment of mouse chromosome 4, extending from bands C5 through E2.
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Affiliation(s)
- D N Shapiro
- Department of Experimental Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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32
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Johnson MR, Look AT, DeClue JE, Valentine MB, Lowy DR. Inactivation of the NF1 gene in human melanoma and neuroblastoma cell lines without impaired regulation of GTP.Ras. Proc Natl Acad Sci U S A 1993; 90:5539-43. [PMID: 8516298 PMCID: PMC46756 DOI: 10.1073/pnas.90.12.5539] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The NF1 gene, which is altered in patients with type 1 neurofibromatosis, encodes neurofibromin, a protein whose GTPase-activating function can negatively regulate GTP-Ras by accelerating its conversion to inactive GDP-Ras. In schwannoma cell lines from patients with neurofibromatosis, loss of neurofibromin was previously shown to be associated with impaired regulation of GTP-Ras. Our analysis of other neural crest-derived tumor cell lines has shown that some melanoma and neuroblastoma cell lines established from tumors occurring in patients without neurofibromatosis contain reduced or undetectable levels of neurofibromin, with concomitant genetic abnormalities of the NF1 locus. In contrast to the schwannoma cell lines, GTP-Ras was appropriately regulated in the melanoma and neuroblastoma lines that were deficient in neurofibromin, even when c-H-ras was overexpressed in the lines. These results demonstrate that some neural crest tumors not associated with neurofibromatosis have acquired somatically inactivated NF1 genes and suggest a tumor-suppressor function for neurofibromin that is independent of Ras GTPase activation.
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MESH Headings
- Blotting, Northern
- Blotting, Southern
- DNA, Neoplasm/genetics
- DNA, Neoplasm/isolation & purification
- GTPase-Activating Proteins
- Gene Expression
- Gene Expression Regulation, Neoplastic
- Genes, Neurofibromatosis 1
- Genes, ras
- Guanine Nucleotides/metabolism
- Humans
- In Situ Hybridization, Fluorescence
- Kinetics
- Melanoma
- Neuroblastoma
- Neurofibromin 1
- Phosphates/metabolism
- Protein Biosynthesis
- Proteins/genetics
- RNA, Messenger/isolation & purification
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Tumor Cells, Cultured
- ras GTPase-Activating Proteins
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Affiliation(s)
- M R Johnson
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892
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33
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Shapiro DN, Valentine MB, Rowe ST, Sinclair AE, Sublett JE, Roberts WM, Look AT. Detection of N-myc gene amplification by fluorescence in situ hybridization. Diagnostic utility for neuroblastoma. Am J Pathol 1993; 142:1339-46. [PMID: 7684192 PMCID: PMC1886925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We assessed fluorescence in situ hybridization (FISH) as an alternative to Southern blot analysis for determination of N-myc gene amplification in neuroblastoma. In the 44 pediatric solid tumor cell lines examined (20 neuroblastomas), the mean number of N-myc copies determined by FISH correlated closely with Southern blot results. There was wide intercellular variability in gene copy number in tumors that had evidence of amplification; however, tumors judged to be non-amplified completely lacked any cells with high N-myc copy number. FISH provided reliable estimates of N-myc amplification in 12 clinical samples even when the percentage of tumor was low. The other advantages of FISH over Southern blot analysis were speed and technical simplicity, ability to discern heterogeneous gene amplification among tumor cells in the same specimen, and capacity to determine the source of the amplified N-myc signal, whether extrachromosomal double-minute chromosomes, expanded intrachromosomal regions, or chromosome 2 aneuploidy. We conclude that FISH would refine the analysis of N-myc amplification in neuroblastoma and thus improve the assignment of patients to prognostic groups based on this unfavorable risk factor.
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Affiliation(s)
- D N Shapiro
- Department of Experimental Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
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Abstract
The human ARH9 gene (originally rhoC), a member of the RAS gene superfamily, was initially isolated on the basis of cross-hybridization with a RAS-related cDNA from the marine snail Aplysia. The ARH9 gene locus was previously assigned to the telomeric region of chromosome 5q by isotopic chromosomal in situ hybridization and Southern analysis of somatic cell hybrid DNAs; the gene was noted to cosegregate with the CSF1 gene locus in human-rodent somatic cell hybrids carrying partial chromosomes 5, together with other human chromosomes. With the recent reassignment of the human CSF1 locus to chromosome 1, region p13-p21, it seemed important to reexamine the localization of the ARH9 gene, since it segregates 100% concordantly with the CSF1 locus in hybrid cells. Results of our investigation demonstrate that the ARH9 locus is also present in hybrids retaining chromosome 1, but not 5. Using hybrids carrying partial 1p, we mapped the ARH9 locus relative to other 1p loci, localizing the gene to the region 1p13-p31. Fluorescence in situ hybridization to metaphase chromosomes with a genomic ARH9 clone refined the gene's localization to chromosome 1, bands p13-p21.
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Affiliation(s)
- S W Morris
- Department of Hematology-Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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Morris SW, Nelson N, Valentine MB, Shapiro DN, Look AT, Kozlosky CJ, Beckmann MP, Cerretti DP. Assignment of the genes encoding human interleukin-8 receptor types 1 and 2 and an interleukin-8 receptor pseudogene to chromosome 2q35. Genomics 1992; 14:685-91. [PMID: 1427896 DOI: 10.1016/s0888-7543(05)80169-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two human cDNA clones that encode different interleukin-8 (IL8) receptors have recently been isolated. The interleukin-8 receptor type 1 (IL8R1) binds IL8 only, whereas the interleukin-8 receptor type 2 (IL8R2) (previously designated IL8RA) also binds growth regulated gene (GRO), and neutrophil activating protein-2 (NAP-2) with high affinity. In the process of screening a genomic library with these cDNAs to obtain large clones for use in chromosomal localization studies, we isolated an interleukin-8 receptor pseudogene (IL8RP) that bears greatest similarity to IL8R2. Using Southern hybridization analysis of human x rodent somatic cell hybrid DNAs with cDNA probes for IL8R1 and IL8R2 and probes from the IL8RP locus, we assigned the three loci to chromosome 2; fluorescence in situ hybridization (FISH) to metaphase chromosome preparations using genomic clones from each locus refined this localization to chromosome 2, band q35, for all three. By virtue of their chromosomal location, IL8R1 and IL8R2 may be considered candidate genes for several human disorders in which the involved locus has been mapped to distal 2q or that are associated with structural abnormalities of this segment, including van der Woude syndrome and the neoplastic diseases rhabdomyosarcoma and uterine leiomyomata. In addition, because this region of chromosome 2q is homologous to proximal mouse chromosome 1 in the segment containing the Lsh-Ity-Bcg locus involved in mediating host resistance to infection with intracellular pathogens, examination for abnormalities of the murine homologues of the IL8R genes should be considered in mice affected by mutations of this locus.
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Affiliation(s)
- S W Morris
- Department of Hematology-Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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Morris SW, Foust JT, Valentine MB, Roberts WM, Shapiro DN, Look AT. Sublocalization of the chromosome 5 breakpoint of the 3;5 translocation in myelodysplastic syndromes and acute myeloid leukemia. Genes Chromosomes Cancer 1992; 5:385-91. [PMID: 1283327 DOI: 10.1002/gcc.2870050414] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A t(3;5)(q25.1;q34) reciprocal translocation identifies a subset of cases of myelodysplastic syndrome or acute myeloid leukemia (AML) that are characterized by increased numbers of megakaryocytes and severe trilineage dysplasia. As a first step in characterizing the t(3;5) breakpoints, we asked whether the translocation involves the CSFIR/PDGFRB locus at 5q33-q35. Pulsed-field gel electrophoretic analysis of a region extending 580 kb 5' to the PDGFRB gene and 120 kb 3' to the CSFIR gene did not reveal aberrant restriction fragments in leukemic cell DNA, confirming that the breakpoint does not occur in the vicinity of these genes. To sublocalize the breakpoint, we performed Southern blot hybridizations using DNA from human x hamster somatic cell hybrids containing the normal 3, the normal 5, the derivative 3, or the derivative 5 human chromosome. Using a series of polymorphic DNA probes from the long arm of chromosome 5, which have been linked by genetic recombination, we bracketed the breakpoint to within a region that spans approximately 13 centimorgans (sex average) and is flanked by the q34-qter markers cKK5.19 and L1200 (D5S62). This analysis places the chromosome 5 breakpoint of the t(3;5) considerably telomeric to the CSFIR/PDGFRB locus, confirming our studies with pulsed-field electrophoresis. Future efforts to identify the genes affected by the t(3;5) should focus on the 5q segment described in this study.
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MESH Headings
- Animals
- Blotting, Southern
- Chromosomes, Human, Pair 3/ultrastructure
- Chromosomes, Human, Pair 5/ultrastructure
- Cricetinae
- Cricetulus
- DNA Probes
- DNA, Neoplasm/analysis
- Electrophoresis, Gel, Pulsed-Field
- Genetic Markers
- Humans
- Hybrid Cells
- Leukemia, Myeloid, Acute/genetics
- Myelodysplastic Syndromes/genetics
- Polymorphism, Restriction Fragment Length
- Receptor, Macrophage Colony-Stimulating Factor/genetics
- Receptors, Platelet-Derived Growth Factor/genetics
- Translocation, Genetic
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Affiliation(s)
- S W Morris
- Department of Hematology-Oncology, St Jude Children's Research Hospital, Memphis, TN 38105
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Morishita K, Parganas E, William CL, Whittaker MH, Drabkin H, Oval J, Taetle R, Valentine MB, Ihle JN. Activation of EVI1 gene expression in human acute myelogenous leukemias by translocations spanning 300-400 kilobases on chromosome band 3q26. Proc Natl Acad Sci U S A 1992; 89:3937-41. [PMID: 1570317 PMCID: PMC525606 DOI: 10.1073/pnas.89.9.3937] [Citation(s) in RCA: 222] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Retroviral activation of Evi-1 gene expression is one of the most common transforming events in murine myeloid leukemias. To evaluate the role of the EVI1 gene in human acute myelogenous leukemia (AML), leukemic blasts or cell lines from 116 patients were examined. In eight patients the EVI1 gene was expressed and all but one had cytogenetically detectable translocations of chromosome 3q26 where the EVI1 gene has been localized. To identify breakpoints, a restriction map that spans 1700 kilobases (kb) of the EVI1 locus was developed by pulsed-field gel electrophoresis. In one case, t(3;3)(q21;q26), a rearrangement was localized to 170-330 kb 5' of the gene. In a second case, t(3;3)(q21;q26), there was a rearrangement 13 kb 5' of the gene. This rearrangement was cloned and shown to be due to the fusion of sequences from 3q21-22 with the EVI1 locus. In the third case, ins(3)-(q21q25q27), there was a rearrangement that mapped 150 kb downstream from the 5' end of the gene.
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Affiliation(s)
- K Morishita
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, TN 38105
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Shapiro DN, Valentine MB, Sublett JE, Sinclair AE, Tereba AM, Scheffer H, Buys CH, Look AT. Chromosomal sublocalization of the 2;13 translocation breakpoint in alveolar rhabdomyosarcoma. Genes Chromosomes Cancer 1992; 4:241-9. [PMID: 1382566 DOI: 10.1002/gcc.2870040309] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A characteristic balanced reciprocal chromosomal translocation [t(2;13)(q35;q14)] has been identified in more than 50% of alveolar rhabdomyosarcomas. As the first step in characterization of the genes involved in this translocation, we constructed somatic cell hybrids that retained either the derivative chromosome 2 or the derivative chromosome 13 without a normal chromosome 13 homologue. Ten linked DNA probes known to be located within bands 13q13-q14 were mapped relative to the breakpoint on chromosome 13, allowing localization of the breakpoint region between two loci separated by 5.5 cM. A long-range restriction map extending approximately 2,300 kb around these loci failed to provide evidence of rearrangement. Additionally, we confirmed that the FMS-like tyrosine kinase gene (FLT), previously localized to 13q12 by in situ hybridization, is located proximal to the breakpoint, and we demonstrated that FLT is not a target for disruption by this tumor-specific translocation.
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Affiliation(s)
- D N Shapiro
- Department of Hematology-Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
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Natarajan AT, Vermeulen S, Darroudi F, Valentine MB, Brent TP, Mitra S, Tano K. Chromosomal localization of human O6-methylguanine-DNA methyltransferase (MGMT) gene by in situ hybridization. Mutagenesis 1992; 7:83-5. [PMID: 1635460 DOI: 10.1093/mutage/7.1.83] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recombinant lambda phage DNA containing segments of human O6-methylguanine-DNA transferase gene was employed to localize this gene among the human chromosomes using non-radioactive in situ hybridization technique. This gene was found to be present at the telomeric end, 26q, of the long arm of the chromosome 10.
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Affiliation(s)
- A T Natarajan
- MGC Department of Radiation Genetics and Chemical Mutagenesis, State University of Leiden, The Netherlands
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40
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Askew DS, Bartholomew C, Buchberg AM, Valentine MB, Jenkins NA, Copeland NG, Ihle JN. His-1 and His-2: identification and chromosomal mapping of two commonly rearranged sites of viral integration in a myeloid leukemia. Oncogene 1991; 6:2041-7. [PMID: 1682866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To identify genes that contribute to myeloid leukemogenesis we have cloned viral integration sites from a CasBrM-MuLV-induced interleukin 3-independent myeloid leukemia cell line. Genomic probes derived from cellular sequences flanking two integrated proviruses were used to screen restriction digests of DNAs from a panel of 52 hematopoietic cell lines, 30 of which were established from CasBrM-MuLV- or MoMuLV-induced mouse leukemias. Probes from one integration site (His-1) defined a region that was rearranged in 3/52 cell lines, and probes from a second integration site (His-2) identified a rearrangement in 2/52 cell lines. Both cases of His-2 rearrangements occurred in concert with viral insertions in the His-1 locus. Genetic mapping of these loci using interspecific backcross analysis assigned the His-1 locus to mouse chromosome 2 and the His-2 locus to mouse chromosome 19. In situ hybridization with a probe from the human homologous region mapped the His-1 locus to human chromosome 2q14-q21. No recombinants were observed between His-2 and Gin-1, a common site of provirus integration in Gross passage A MuLV-induced T-cell leukemias, in 131 backcross animals, suggesting that these loci are tightly linked. The His-1 locus maps to mouse chromosome 2 distinct from any known oncogene or common site of integration but near the proximal breakpoint for a deletion that is observed in over 90% of radiation-induced leukemias.
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Affiliation(s)
- D S Askew
- Department of Biochemistry, St Jude Children's Research Hospital, Memphis, Tennessee 38105
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Morris SW, Valentine MB, Shapiro DN, Sublett JE, Deaven LL, Foust JT, Roberts WM, Cerretti DP, Look AT. Reassignment of the human CSF1 gene to chromosome 1p13-p21. Blood 1991; 78:2013-20. [PMID: 1912583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Human macrophage colony-stimulating factor (CSF-1 or M-CSF) is encoded by a single gene that was previously assigned to the long arm of chromosome 5, band q33.1, in a region adjacent to the gene encoding its receptor (Pettenati MJ, et al, Proc Natl Acad Sci USA 84:2970, 1987). Using fluorescence in situ hybridization with genomic probes to examine normal metaphase chromosomes, we reassigned the human CSF1 gene to the short arm of chromosome 1, bands p13-p21. We confirmed this result by hybridizing a CSF1 cDNA probe to filters containing flow-sorted chromosomes and by identifying CSF1 sequences in DNAs extracted from human x rodent somatic cell hybrids that contained human chromosome 1 but not human chromosome 5. Our findings are consistent with studies that have shown tight linkage between the murine CSF1 and amylase genes, as part of a conserved linkage group between mouse chromosome 3 and the short arm of human chromosome 1, which also includes the genes encoding the beta subunits of thyrotropin and nerve growth factor. Assignment of the CSF1 gene to chromosome 1 at bands p13-p21 raises the possibility that it may be altered by certain nonrandom chromosomal abnormalities arising in human hematopoietic malignancies and solid tumors.
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Affiliation(s)
- S W Morris
- Department of Hematology-Oncology, St Jude Children's Research Hospital, Memphis, TN 38105
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42
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Valentine MB, Giuffrida D. The right to appoint a representative. Can J Psychiatry 1991; 36:313-4. [PMID: 1868431 DOI: 10.1177/070674379103600426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Abstract
The bifunctional enzyme uridine monophosphate (UMP) synthase catalyzes the last two steps in de novo pyrimidine biosynthesis. A genetic deficiency in the activity of this enzyme causes the inherited human disease orotic aciduria. We used a human cDNA probe to localize the gene for UMP synthase to human chromosome region 3q13 by the technique of in situ hybridization.
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Affiliation(s)
- M B Qumsiyeh
- Department of Biochemical and Clinical Pharmacology, St. Jude Children's Research Hospital, Memphis 38101
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Valentine MB, Capponi P. Mental health consumer participation on boards and committees: barriers and strategies. Can Ment Health 1989; 37:8-12. [PMID: 10294601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The article provides an overview of factors related to the participation of consumers of mental health services on boards and committees. Six primary barriers to effective consumer participation are addressed: incongruency between stated values and actual practice, tokenism, lack of representativeness, role strain, poor communication and economic factors. Strategies are proposed to increase the potential for effective implementation of consumer participation. The article concludes with a broad statement affirming interdependence and the potential for increasing the effectiveness of boards and committees and exerting a positive influence on the system.
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Valentine MB, Turner T. Political awareness of psychiatric patients. CMAJ 1989; 140:498. [PMID: 2917294 PMCID: PMC1268704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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46
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Raimondi SC, Dubé ID, Valentine MB, Mirro J, Watt HJ, Larson RA, Bitter MA, Le Beau MM, Rowley JD. Clinicopathologic manifestations and breakpoints of the t(3;5) in patients with acute nonlymphocytic leukemia. Leukemia 1989; 3:42-7. [PMID: 2642576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Acquired chromosomal rearrangements in acute nonlymphocytic leukemia (ANLL) have been linked to specific clinicopathologic features that suggest new disease subtypes. In this collaborative study, we report five patients with ANLL and a t(3;5) in their leukemic cells. At diagnosis, four of the patients had a t(3;5) as their sole karyotypic anomaly; the remaining patient had additional structural and numerical abnormalities. Careful cytogenetic analysis indicated that the breakpoints of this rearrangement are 3q25.1 and 5q34, in contrast to the various breakpoints reported in earlier studies (3q21----3q25 and 5q31----5q35). The karyotypic, morphologic, and clinical characteristics of this group, as well as those of 14 previously reported patients with the t(3;5), were compared to identify any features that might warrant consideration of a specific syndrome. The available information indicates a worldwide distribution and a nearly equal male:female ratio for patients with this translocation. The median age of the group, 37 years, was younger than that of all patients with ANLL, 49 years. A preceding myelodysplastic syndrome was observed in three patients. The limited numbers of observations on leukocyte count, hemoglobin level, and platelet count precluded meaningful comparison with data for ANLL patients in general. Although each FAB morphologic subtype, except M3, occurred in patients with a t(3;5), the frequency of M6 was much greater than expected. Bone marrows from each of the five patients we report showed increased numbers of megakaryocytes; trilineage dysplasia was observed in the marrow of each of the four patients for whom it could be assessed. Taken together, these findings suggest that the t(3;5) may affect cells capable of differentiation into multiple lineages.
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Affiliation(s)
- S C Raimondi
- Department of Pathology and Laboratory Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee 38101
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