1
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Mandahl N, Mertens F, Mitelman F. Gene amplification in neoplasia: A cytogenetic survey of 80 131 cases. Genes Chromosomes Cancer 2024; 63:e23214. [PMID: 38050922 DOI: 10.1002/gcc.23214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/02/2023] [Revised: 10/26/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
Gene amplification is a crucial process in cancer development, leading to the overexpression of oncogenes. It manifests cytogenetically as extrachromosomal double minutes (dmin), homogeneously staining regions (hsr), or ring chromosomes (r). This study investigates the prevalence and distribution of these amplification markers in a survey of 80 131 neoplasms spanning hematologic disorders, and benign and malignant solid tumors. The study reveals distinct variations in the frequency of dmin, hsr, and r among different tumor types. Rings were the most common (3.4%) sign of amplification, followed by dmin (1.3%), and hsr (0.8%). Rings were particularly frequent in malignant mesenchymal tumors, especially liposarcomas (47.5%) and osteosarcomas (23.4%), dmin were prevalent in neuroblastoma (30.9%) and pancreatic carcinoma (21.9%), and hsr frequencies were highest in head and neck carcinoma (14.0%) and neuroblastoma (9.0%). Combining all three amplification markers (dmin/hsr/r), malignant solid tumors consistently exhibited higher frequencies than hematologic disorders and benign solid tumors. The structural characteristics of these amplification markers and their potential role in tumorigenesis and tumor progression highlight the complex interplay between cancer-initiating gene-level alterations, for example, fusion genes, and subsequent amplification dynamics. Further research integrating cytogenetic and molecular approaches is warranted to better understand the underlying mechanisms of these amplifications, in particular, the enigmatic question of why certain malignancies display certain types of amplification. Comparing the present results with molecular genetic data proved challenging because of the diversity in definitions of amplification across studies. This study underscores the need for standardized definitions in future work.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, University Hospital, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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2
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Mandahl N, Mitelman F. Giemsa-negative chromosome bands preferentially recombine in cancer-associated translocations and gene fusions. Genes Chromosomes Cancer 2023; 62:61-74. [PMID: 36116030 PMCID: PMC10092824 DOI: 10.1002/gcc.23095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022] Open
Abstract
Chromosome abnormalities, in particular translocations, and gene fusions are hallmarks of neoplasia. Although both have been recognized as important drivers of cancer for decades, our knowledge of the characterizing features of the cytobands involved in recombinations is poorly understood. The present study, based on a comparative analysis of 10 442 translocation breakpoints and 30 762 gene fusions comprising 13 864 protein-coding genes, is the most comprehensive evaluation of the interactions of cytobands participating in the formation of such rearrangements in cancer. The major conclusion is that although large G-negative, gene-rich bands are most frequently involved, the greatest impact was seen for staining properties. Thus, 60% of the recombinations leading to the formation of both translocations and fusion genes take place between two G-negative bands whereas only about 10% involve two G-positive bands. There is compelling evidence that G-negative bands contain more genes than dark staining bands and it has previously been shown that breakpoints involved in structural chromosome rearrangements and in gene fusions preferentially affect gene-rich bands. The present study not only corroborates these findings but in addition demonstrates that the recombination processes favor the joining of two G-negative cytobands and that this feature may be a stronger factor than gene content. It is reasonable to assume that the formation of translocations and fusion genes in cancer cells, irrespective of whether they have a pathogenetically significant impact or not, may be mediated by some underlying mechanisms that either favor the origin or provide a selective advantage for recombinations of G-negative cytobands.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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3
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Wang J, Zheng J, Lee EE, Aguilar B, Phan J, Abdilleh K, Taylor RC, Longabaugh W, Johansson B, Mertens F, Mitelman F, Pot D, LaFramboise T. A cloud-based resource for genome coordinate-based exploration and large-scale analysis of chromosome aberrations and gene fusions in cancer. Genes Chromosomes Cancer 2023. [PMID: 36695636 DOI: 10.1002/gcc.23128] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023] Open
Abstract
Cytogenetic analysis provides important information on the genetic mechanisms of cancer. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer (Mitelman DB) is the largest catalog of acquired chromosome aberrations, presently comprising >70 000 cases across multiple cancer types. Although this resource has enabled the identification of chromosome abnormalities leading to specific cancers and cancer mechanisms, a large-scale, systematic analysis of these aberrations and their downstream implications has been difficult due to the lack of a standard, automated mapping from aberrations to genomic coordinates. We previously introduced CytoConverter as a tool that automates such conversions. CytoConverter has now been updated with improved interpretation of karyotypes and has been integrated with the Mitelman DB, providing a comprehensive mapping of the 70 000+ cases to genomic coordinates, as well as visualization of the frequencies of chromosomal gains and losses. Importantly, all CytoConverter-generated genomic coordinates are publicly available in Google BigQuery, a cloud-based data warehouse, facilitating data exploration and integration with other datasets hosted by the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) Resource. We demonstrate the use of BigQuery for integrative analysis of Mitelman DB with other cancer datasets, including a comparison of the frequency of imbalances identified in Mitelman DB cases with those found in The Cancer Genome Atlas (TCGA) copy number datasets. This solution provides opportunities to leverage the power of cloud computing for low-cost, scalable, and integrated analysis of chromosome aberrations and gene fusions in cancer.
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Affiliation(s)
- Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jeanne Zheng
- School of Public Health, Brown University, Providence, Rhode Island, USA
| | - Elaine E Lee
- Institute for Systems Biology, Seattle, Washington, USA
| | - Boris Aguilar
- Institute for Systems Biology, Seattle, Washington, USA
| | - John Phan
- General Dynamics Information Technology, Rockville, Maryland, USA
| | - Kawther Abdilleh
- Pancreatic Cancer Action Network, Manhattan Beach, California, USA
| | - Ronald C Taylor
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | | | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - David Pot
- General Dynamics Information Technology, Rockville, Maryland, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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4
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Bruford EA, Antonescu CR, Carroll AJ, Chinnaiyan A, Cree IA, Cross NCP, Dalgleish R, Gale RP, Harrison CJ, Hastings RJ, Huret JL, Johansson B, Le Beau M, Mecucci C, Mertens F, Verhaak R, Mitelman F. HUGO Gene Nomenclature Committee (HGNC) recommendations for the designation of gene fusions. Leukemia 2021; 35:3040-3043. [PMID: 34615987 PMCID: PMC8550944 DOI: 10.1038/s41375-021-01436-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022]
Abstract
Gene fusions have been discussed in the scientific literature since they were first detected in cancer cells in the early 1980s. There is currently no standardized way to denote the genes involved in fusions, but in the majority of publications the gene symbols in question are listed either separated by a hyphen (-) or by a forward slash (/). Both types of designation suffer from important shortcomings. HGNC has worked with the scientific community to determine a new, instantly recognizable and unique separator-a double colon (::)-to be used in the description of fusion genes, and advocates its usage in all databases and articles describing gene fusions.
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Affiliation(s)
- Elspeth A Bruford
- HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Arul Chinnaiyan
- University of Michigan Medical School, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ian A Cree
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire, UK
| | - Raymond Dalgleish
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Robert Peter Gale
- Centre for Haematology Research, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Christine J Harrison
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Rosalind J Hastings
- The Women's Centre, John Radcliffe Hospital, Oxford University Hospitals Foundation Trust, Oxford, UK
| | | | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Michelle Le Beau
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
| | - Cristina Mecucci
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Roel Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T. Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia. Semin Cancer Biol 2021; 84:40-49. [PMID: 34606984 DOI: 10.1016/j.semcancer.2021.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
Transcriptional profiling of acute leukemia, specifically by RNA-sequencing or whole transcriptome sequencing (WTS), has provided fundamental insights into its underlying disease biology and allows unbiased detection of oncogenic gene fusions, as well as of gene expression signatures that can be used for improved disease classification. While used as a research tool for many years, RNA-sequencing is becoming increasingly used in clinical diagnostics. Here, we highlight key transcriptomic studies of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) that have improved our biological understanding of these heterogeneous malignant disorders and have paved the way for translation into clinical diagnostics. Recent single-cell transcriptomic studies of ALL and AML, which provide new insights into the cellular ecosystem of acute leukemia and point to future clinical utility, are also reviewed. Finally, we discuss current challenges that need to be overcome for a more wide-spread adoption of RNA-sequencing in clinical diagnostics and how this technology significantly can aid the identification of genetic alterations in current guidelines and of newly emerging disease entities, some of which are critical to identify because of the availability of targeted therapies, thereby paving the way for improved precision medicine of acute leukemia.
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Affiliation(s)
- Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anna Hagström-Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.
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6
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Persson H, Søkilde R, Häkkinen J, Vallon-Christersson J, Mitelman F, Borg Å, Höglund M, Rovira C. Analysis of fusion transcripts indicates widespread deregulation of snoRNAs and their host genes in breast cancer. Int J Cancer 2020; 146:3343-3353. [PMID: 32067223 DOI: 10.1002/ijc.32927] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/20/2022]
Abstract
Genomic rearrangements in cancer can join the sequences of two separate genes. Studies of such gene fusion events have mainly focused on identification of fusion proteins from the chimeric transcripts. We have previously investigated how fusions instead can affect the expression of intronic microRNA (miRNA) genes that are encoded within fusion gene partners. Here, we extend our analysis to small nucleolar RNAs (snoRNAs) that also are embedded within protein-coding or noncoding host genes. We found that snoRNA hosts are selectively enriched in fusion transcripts, like miRNA host genes, and that this enrichment is associated with all snoRNA classes. These structural changes may have functional consequences for the cell; proteins involved in the protein translation machinery are overrepresented among snoRNA host genes, a gene architecture assumed to be needed for closely coordinated expression of snoRNAs and host proteins. Our data indicate that this structure is frequently disrupted in cancer. We furthermore observed that snoRNA genes involved in fusions tend to associate with stronger promoters than the natural host, suggesting a mechanism that selects for snoRNA overexpression. In summary, we highlight a previously unexplored frequent structural change in cancer that affects important components of cellular physiology.
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Affiliation(s)
- Helena Persson
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden
| | - Rolf Søkilde
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Jari Häkkinen
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden
| | | | - Felix Mitelman
- Department of Laboratory Medicine, Clinical Genetics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Åke Borg
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden.,CREATE Health, Strategic Centre for Translational Cancer Research, Lund, Sweden
| | - Mattias Höglund
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden
| | - Carlos Rovira
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
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7
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Mitelman F. Farewell message from the Editor-in-Chief of Genes, Chromosomes & Cancer. Genes Chromosomes Cancer 2020; 59:3-4. [PMID: 31638293 DOI: 10.1002/gcc.22815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/03/2019] [Indexed: 01/24/2023] Open
Affiliation(s)
- Felix Mitelman
- Department of Clinical Genetics, Lund University, Lund, Sweden
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8
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Johansson B, Mertens F, Schyman T, Björk J, Mandahl N, Mitelman F. Most gene fusions in cancer are stochastic events. Genes Chromosomes Cancer 2019; 58:607-611. [PMID: 30807681 DOI: 10.1002/gcc.22745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/28/2022] Open
Abstract
Cancer-associated gene fusions resulting in chimeric proteins or aberrant expression of one or both partner genes are pathogenetically and clinically important in several hematologic malignancies and solid tumors. Since the advent of different types of massively parallel sequencing (MPS), the number of identified gene fusions has increased dramatically, prompting the question whether they all have a biologic impact. By ascertaining the chromosomal locations of 8934 genes involved in 10 861 gene fusions reported in the literature, we here show that there is a highly significant association between gene content of chromosomes and chromosome bands and number of genes involved in fusions. This strongly suggests that a clear majority of gene fusions detected by MPS are stochastic events associated with the number of genes available to participate in fusions and that most reported gene fusions are passengers without any pathogenetic importance.
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Affiliation(s)
- Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| | - Tommy Schyman
- Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Jonas Björk
- Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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9
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Mitelman F, Johansson B, Mertens F, Schyman T, Mandahl N. Cancer chromosome breakpoints cluster in gene-rich genomic regions. Genes Chromosomes Cancer 2018; 58:149-154. [PMID: 30479017 PMCID: PMC6590459 DOI: 10.1002/gcc.22713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/23/2018] [Indexed: 11/11/2022] Open
Abstract
Cancer cells are characterized by chromosome abnormalities, of which some, in particular balanced rearrangements, are associated with distinct tumor entities and/or with specific gene rearrangements that represent important steps in the carcinogenic process. However, the vast majority of cytogenetically detectable structural aberrations in cancer cells have not been characterized at the nucleotide level; hence, their importance and functional consequences are unknown. By ascertaining the chromosomal breakpoints in 22 344 different clonal structural chromosome abnormalities identified in the karyotypes of 49 626 cases of neoplastic disorders we here show that the distribution of breakpoints is strongly associated (P < 0.0001) with gene content within the affected chromosomal bands. This association also remains highly significant in separate analyses of recurrent and nonrecurrent chromosome abnormalities as well as of specific subtypes of cancer (P < 0.0001 for all comparisons). In contrast, the impact of band length was negligible. The breakpoint distribution is thus not stochastic—gene‐rich regions are preferentially affected. Several genomic features relating to transcription, replication, and chromatin organization have been found to enhance chromosome breakage frequencies; this indicates that gene‐rich regions may be more break‐prone. The salient finding in the present study is that a substantial fraction of all structural chromosome abnormalities, not only those specifically associated with certain tumor types, may affect genes that are pathogenetically important. If this interpretation is correct, then the prevailing view that the great majority of cancer chromosome aberrations is cytogenetic noise can be seriously questioned.
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Affiliation(s)
- Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, Lund, Sweden
| | - Tommy Schyman
- Clinical Studies Sweden - Forum South, Skåne University Hospital, Lund, Sweden
| | - Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Lilljebjörn H, Henningsson R, Hyrenius-Wittsten A, Olsson L, Orsmark-Pietras C, von Palffy S, Askmyr M, Rissler M, Schrappe M, Cario G, Castor A, Pronk CJH, Behrendtz M, Mitelman F, Johansson B, Paulsson K, Andersson AK, Fontes M, Fioretos T. Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia. Nat Commun 2016; 7:11790. [PMID: 27265895 PMCID: PMC4897744 DOI: 10.1038/ncomms11790] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/11/2016] [Accepted: 04/28/2016] [Indexed: 12/16/2022] Open
Abstract
Fusion genes are potent driver mutations in cancer. In this study, we delineate the fusion gene landscape in a consecutive series of 195 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP ALL). Using RNA sequencing, we find in-frame fusion genes in 127 (65%) cases, including 27 novel fusions. We describe a subtype characterized by recurrent IGH-DUX4 or ERG-DUX4 fusions, representing 4% of cases, leading to overexpression of DUX4 and frequently co-occurring with intragenic ERG deletions. Furthermore, we identify a subtype characterized by an ETV6-RUNX1-like gene-expression profile and coexisting ETV6 and IKZF1 alterations. Thus, this study provides a detailed overview of fusion genes in paediatric BCP ALL and adds new pathogenetic insights, which may improve risk stratification and provide therapeutic options for this disease.
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Affiliation(s)
- Henrik Lilljebjörn
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | | | - Axel Hyrenius-Wittsten
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Linda Olsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Christina Orsmark-Pietras
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Sofia von Palffy
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Maria Askmyr
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Marianne Rissler
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund 22185, Sweden
| | - Cornelis J. H. Pronk
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund 22185, Sweden
| | - Mikael Behrendtz
- Department of Pediatrics, Linköping University Hospital, Linköping 58185, Sweden
| | - Felix Mitelman
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Bertil Johansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
- Department of Clinical Genetics, University and Regional Laboratories Region Skåne, Lund 22185, Sweden
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Anna K. Andersson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Magnus Fontes
- Centre for Mathematical Sciences, Lund University, Lund 22362, Sweden
| | - Thoas Fioretos
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
- Department of Clinical Genetics, University and Regional Laboratories Region Skåne, Lund 22185, Sweden
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11
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Mertens F, Antonescu CR, Mitelman F. Gene fusions in soft tissue tumors: Recurrent and overlapping pathogenetic themes. Genes Chromosomes Cancer 2015; 55:291-310. [PMID: 26684580 DOI: 10.1002/gcc.22335] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/01/2015] [Accepted: 11/01/2015] [Indexed: 12/21/2022] Open
Abstract
Gene fusions have been described in approximately one-third of soft tissue tumors (STT); of the 142 different fusions that have been reported, more than half are recurrent in the same histologic subtype. These gene fusions constitute pivotal driver mutations, and detailed studies of their cellular effects have provided important knowledge about pathogenetic mechanisms in STT. Furthermore, most fusions are strongly associated with a particular histotype, serving as ideal molecular diagnostic markers. In recent years, it has also become apparent that some chimeric proteins, directly or indirectly, constitute excellent treatment targets, making the detection of gene fusions in STT ever more important. Indeed, pharmacological treatment of STT displaying fusions that activate protein kinases, such as ALK and ROS1, or growth factors, such as PDGFB, is already in clinical use. However, the vast majority (52/78) of recurrent gene fusions create structurally altered and/or deregulated transcription factors, and a small but growing subset develops through rearranged chromatin regulators. The present review provides an overview of the spectrum of currently recognized gene fusions in STT, and, on the basis of the protein class involved, the mechanisms by which they exert their oncogenic effect are discussed.
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Affiliation(s)
- Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | | | - Felix Mitelman
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
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12
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Abstract
Structural chromosome rearrangements may result in the exchange of coding or regulatory DNA sequences between genes. Many such gene fusions are strong driver mutations in neoplasia and have provided fundamental insights into the disease mechanisms that are involved in tumorigenesis. The close association between the type of gene fusion and the tumour phenotype makes gene fusions ideal for diagnostic purposes, enabling the subclassification of otherwise seemingly identical disease entities. In addition, many gene fusions add important information for risk stratification, and increasing numbers of chimeric proteins encoded by the gene fusions serve as specific targets for treatment, resulting in dramatically improved patient outcomes. In this Timeline article, we describe the spectrum of gene fusions in cancer and how the methods to identify them have evolved, and also discuss conceptual implications of current, sequencing-based approaches for detection.
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Affiliation(s)
- Fredrik Mertens
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Bertil Johansson
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Felix Mitelman
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
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Olsson H, Berger R, Bernheim A, Kristoffersson U, Mitelman F. C-Band Heteromorphism in Breast Cancer Patients. Fam Cancer 2015. [DOI: 10.1159/000412527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Olsson H, Kristoffersson U, Berger R, Bernheim A, �kerman M, Mitelman F. C-Band Polymorphism in Non-Hodgkin�s Lymphoma. Fam Cancer 2015. [DOI: 10.1159/000412563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Petersson C, Johansson B, Pandis N, Gorunova L, Ingvar C, Idvall I, Mandahl N, Mitelman F. Clonal chromosome-aberrations in fibrocystic breast disease-associated with increased risk of cancer. Int J Oncol 2012; 5:1207-10. [PMID: 21559699 DOI: 10.3892/ijo.5.6.1207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Short-term cultures of 29 samples of fibrocystic breast disease were cytogenetically analyzed. Clonal chromosome aberrations were found in six specimens, whereas the remaining 23 had a normal karyotype. Three of the abnormal samples displayed karyotypic anomalies previously associated with breast cancer, i.e., gain of Iq, trisomy 18 and cytogenetic multiclonality. Furthermore, all cytogenetically aberrant specimens had either proliferative disease without atypia or atypical hyperplasia, features of fibrocystic disease considered risk factors for subsequent breast cancer development. The cytogenetic similarities between breast carcinomas and proliferative fibrocystic breast disease add further support for classifying certain types of fibrocystic disease as a premalignant condition. Whether cytogenetically abnormal fibrocystic lesions are the ones that subsequently progress to cancer remains to be elucidated.
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Affiliation(s)
- C Petersson
- UNIV LUND HOSP,DEPT SURG,S-22185 LUND,SWEDEN. UNIV LUND HOSP,DEPT CLIN PATHOL,S-22185 LUND,SWEDEN
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Mandahl N, Mertens F, Aman P, Rydholm A, Brosjo O, Willen H, Mitelman F. Nonrandom secondary chromosome-aberrations in liposarcomas with t(12, 16). Int J Oncol 2012; 4:307-10. [PMID: 21566924 DOI: 10.3892/ijo.4.2.307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ten liposarcomas were analyzed cytogenetically after short-term culturing. Eight tumors had a t(12;16) (q13;p11) and two tumors had complex translocations involving chromosomes 7, 12, and 16 and 2, 9, 12, 16 and 20, respectively. Among the secondary aberrations seen in five tumors, +8 was found in two tumors and i(7)(q10) in four tumors. Trisomy 8 has previously been described as a nonrandom secondary aberration in myxoid liposarcoma, but i(7q) has only been reported in a single case before. All recurrent chromosome aberrations reported in liposarcomas with recombination between 12q13 and 16p11 (42 cases) were surveyed and compared with their frequencies in liposarcomas without this recombination (33 cases). Trisomy 5 and 8 were found in both tumor groups, whereas +19, t(3;15)(p23;q15), del(6)(q21), i(7q), and rearrangements of 1p11 and 2q35 were found exclusively in tumors with 12q13 and 16p11 aberrations.
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Affiliation(s)
- N Mandahl
- UNIV LUND HOSP,DEPT ORTHOPED SURG,S-22185 LUND,SWEDEN. UNIV LUND HOSP,DEPT CLIN PATHOL,S-22185 LUND,SWEDEN. KAROLINSKA HOSP,DEPT ORTHOPED,TUMOR SERV,S-10401 STOCKHOLM 60,SWEDEN
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Mandahl N, Johansson B, Mertens F, Mitelman F. Disease-associated patterns of disomic chromosomes in hyperhaploid neoplasms. Genes Chromosomes Cancer 2012; 51:536-44. [PMID: 22334476 DOI: 10.1002/gcc.21947] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/16/2012] [Indexed: 01/09/2023] Open
Abstract
The chromosome number of human tumors varies widely, from near-haploidy to more than decaploidy. Overt hyperhaploid (24-34 chromosomes) tumors constitute a small minority (0.2-0.3% of cytogenetically investigated lesions), but occur in many different disease entities. In these karyotypes, most chromosomes are present in one copy; one or a few chromosomes are disomic. Published reports on 141 strictly hyperhaploid tumors, supplemented with nine previously unpublished cases, were used for evaluating the pattern of disomic chromosomes. Only one tumor type, acute lymphoblastic leukemia (ALL), was sufficiently common (n = 75) to allow proper evaluation; other neoplasms were lumped together in as reasonably logical groups as possible, including 10 myeloid leukemias (ML), nine plasma cell neoplasms (PCN), 13 chondrosarcomas (CS), 11 soft tissue tumors (STT), nine adeno- or squamous cell carcinomas (ASC), and eight tumors of the nervous system (TNS); the remaining 15 tumors could not be grouped. It was evident that the pattern of disomies is nonrandom. Moreover, unique signatures for each tumor group were detected. Among ALL, most disomies were independent of age and gender, except for disomy 10, which was overrepresented in females. Chromosome 21 was invariably disomic, whereas chromosome 17 was always monosomic. The most frequent disomies were two gonosomes in ML, chromosomes 7, 9, 11, 3, 18, and 19 in PCN, 7, 5, 20, 19, and 21 in CS, 20 in STT, 7 in ASC, and 1, 7, and 9 in TNS. Chromosome 1 was often partially disomic, due to unbalanced structural rearrangements, with segment 1q21-31 in common. Doubling of the hyperhaploid clone was found in at least one-third of the cases, apart from in ML where only one of 10 cases showed chromosome doubling. The present findings indicate that retention of disomy for some chromosomes is pathogenetically important and that the chromosome(s) maintained in two copies is related to cell type or histological context.
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Affiliation(s)
- Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
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Lilljebjörn H, Rissler M, Lassen C, Heldrup J, Behrendtz M, Mitelman F, Johansson B, Fioretos T. Whole-exome sequencing of pediatric acute lymphoblastic leukemia. Leukemia 2011; 26:1602-7. [PMID: 22094584 DOI: 10.1038/leu.2011.333] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Acute lymphoblastic leukemia (ALL), the most common malignant disorder in childhood, is typically associated with numerical chromosomal aberrations, fusion genes or small focal deletions, thought to represent important pathogenetic events in the development of the leukemia. Mutations, such as single nucleotide changes, have also been reported in childhood ALL, but these have only been studied by sequencing a small number of candidate genes. Herein, we report the first unbiased sequencing of the whole exome of two cases of pediatric ALL carrying the ETV6/RUNX1 (TEL/AML1) fusion gene (the most common genetic subtype) and corresponding normal samples. A total of 14 somatic mutations were identified, including four and seven protein-altering nucleotide substitutions in each ALL. Twelve mutations (86%) occurred in genes previously described to be mutated in other types of cancer, but none was found to be recurrent in an extended series of 29 ETV6/RUNX1-positive ALLs. The number of single nucleotide mutations was similar to the number of copy number alterations as detected by single nucleotide polymorphism arrays. Although the true pathogenetic significance of the mutations must await future functional evaluations, this study provides a first estimate of the mutational burden at the genetic level of t(12;21)-positive childhood ALL.
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Affiliation(s)
- H Lilljebjörn
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
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Lilljebjörn H, Soneson C, Andersson A, Heldrup J, Behrendtz M, Kawamata N, Ogawa S, Koeffler HP, Mitelman F, Johansson B, Fontes M, Fioretos T. The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias. Hum Mol Genet 2010; 19:3150-8. [PMID: 20513752 DOI: 10.1093/hmg/ddq224] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ETV6/RUNX1 fusion gene, present in 25% of B-lineage childhood acute lymphoblastic leukemia (ALL), is thought to represent an initiating event, which requires additional genetic changes for leukemia development. To identify additional genetic alterations, 24 ETV6/RUNX1-positive ALLs were analyzed using 500K single nucleotide polymorphism arrays. The results were combined with previously published data sets, allowing us to ascertain genomic copy number aberrations (CNAs) in 164 cases. In total, 45 recurrent CNAs were identified with an average number of 3.5 recurrent changes per case (range 0-13). Twenty-six percent of cases displayed a set of recurrent CNAs identical to that of other cases in the data set. The majority (74%), however, displayed a unique pattern of recurrent CNAs, indicating a large heterogeneity within this ALL subtype. As previously demonstrated, alterations targeting genes involved in B-cell development were common (present in 28% of cases). However, the combined analysis also identified alterations affecting nuclear hormone response (24%) to be a characteristic feature of ETV6/RUNX1-positive ALL. Studying the correlation pattern of the CNAs allowed us to highlight significant positive and negative correlations between specific aberrations. Furthermore, oncogenetic tree models identified ETV6, CDKN2A/B, PAX5, del(6q) and +16 as possible early events in the leukemogenic process.
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Affiliation(s)
- Henrik Lilljebjörn
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
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Mitelman F. Predetermined sequential chromosome changes in serial transplantation of Rous rat sarcomas. Acta Pathol Microbiol Scand A 2009; 80:313-28. [PMID: 4114666 DOI: 10.1111/j.1699-0463.1972.tb00286.x] [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: 01/08/2023]
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Mitelman F, Levan G, Mark J. The origin of double-minutes in a Rous rat sarcoma. Acta Pathol Microbiol Scand A 2009; 80:428-9. [PMID: 4339872 DOI: 10.1111/j.1699-0463.1972.tb00300.x] [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: 01/10/2023]
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26
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Mark J, Mitelman F, Levan G. On the specificity of the G abnormality in human meningomas studied by the fluorescence technique. Acta Pathol Microbiol Scand A 2009; 80:812-20. [PMID: 4676208 DOI: 10.1111/j.1699-0463.1972.tb00352.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Sjögren U, Brandt L, Mitelman F. Relation between life expectancy and composition of the bone marrow at diagnosis of chronic myeloid leukaemia. Scand J Haematol 2009; 12:369-73. [PMID: 4527963 DOI: 10.1111/j.1600-0609.1974.tb00223.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Mitelman F, Brandt L, Nilsson PG. Cytogenetic evidence for splenic origin of blastic transformation in chronic myeloid leukaemia. Scand J Haematol 2009; 13:87-92. [PMID: 4529166 DOI: 10.1111/j.1600-0609.1974.tb00240.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Brandt L, Levan G, Mitelman F, Olsson I, Sjögren U. Trisomy G-21 in adult myelomonocytic leukaemia. An abnormality common to granulocytic and monocytic cells. Scand J Haematol 2009; 12:117-22. [PMID: 4133853 DOI: 10.1111/j.1600-0609.1974.tb00190.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Brandt L, Emanuelsson H, Mitelman F, Stenstam M, Söderström N. Pronounced deficiency in T-cells and lymphocyte chromosomal aberrations in a patient with sarcoidosis, myelofibrosis and acute leukaemia following thorotrast angiography. Acta Med Scand 2009; 201:487-9. [PMID: 302634 DOI: 10.1111/j.0954-6820.1977.tb15734.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A patient exposed to thorotrast angiography developed sarcoidosis 21 years after the injection and myelofibrosis 13 years later. On the latter occasion an extreme deficiency in circulating lymphocytes forming rosettes with sheep erythrocytes (T-cells) was observed and a large fraction of the cells had chromosomal aberrations. Acute leukaemia developed 1 year later. The multiple clinical symptoms may be related to radiation-induced destruction of bone marrow tissue, mutations in haemopoietic cells and depression of cell-mediated immunity.
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Pero RW, Bryngelsson T, Mitelman F, Levan G. Changes in the deoxyadenylate regions of rat DNA in sarcomas induced by 7,12-dimethylbenz(alpha)anthracene and Rous sarcoma virus. Hereditas 2009; 80:153-5. [PMID: 166964 DOI: 10.1111/j.1601-5223.1975.tb01512.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Högstedt B, Gullberg B, Mark-Vendel E, Mitelman F, Skerfving S. Micronuclei and chromosome aberrations in bone marrow cells and lymphocytes of humans exposed mainly to petroleum vapors. Hereditas 2009; 94:179-87. [PMID: 7298351 DOI: 10.1111/j.1601-5223.1981.tb01751.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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37
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Högstedt B, Mitelman F. The interrelations of micronuclei, chromosomal instability, and mutational activity in acute non-lymphocytic leukemia--a hypothesis. Hereditas 2009; 95:165-7. [PMID: 7333870 DOI: 10.1111/j.1601-5223.1981.tb01336.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Levan G, Mitelman F. G-banding in Rous rat sarcomas during serial transfer: significant chromosome aberrations and incidence of stromal mitoses. Hereditas 2009; 84:1-14. [PMID: 188790 DOI: 10.1111/j.1601-5223.1976.tb01190.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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