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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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Høland M, Berg KCG, Eilertsen IA, Bjerkehagen B, Kolberg M, Boye K, Lingjærde OC, Guren TK, Mandahl N, van den Berg E, Palmerini E, Smeland S, Picci P, Mertens F, Sveen A, Lothe RA. Transcriptomic subtyping of malignant peripheral nerve sheath tumours highlights immune signatures, genomic profiles, patient survival and therapeutic targets. EBioMedicine 2023; 97:104829. [PMID: 37837931 PMCID: PMC10585232 DOI: 10.1016/j.ebiom.2023.104829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Malignant peripheral nerve sheath tumour (MPNST) is an aggressive orphan disease commonly affecting adolescents or young adults. Current knowledge of molecular tumour biology has been insufficient for development of rational treatment strategies. We aimed to discover molecular subtypes of potential clinical relevance. METHODS Fresh frozen samples of MPNSTs (n = 94) and benign neurofibromas (n = 28) from 115 patients in a European multicentre study were analysed by DNA copy number and/or transcriptomic profiling. Unsupervised transcriptomic subtyping was performed and the subtypes characterized for genomic aberrations, clinicopathological associations and patient survival. FINDINGS MPNSTs were classified into two transcriptomic subtypes defined primarily by immune signatures and proliferative processes. "Immune active" MPNSTs (44%) had sustained immune signals relative to neurofibromas, were more frequently low-grade (P = 0.01) and had favourable prognostic associations in a multivariable model of disease-specific survival with clinicopathological factors (hazard ratio 0.25, P = 0.003). "Immune deficient" MPNSTs were more aggressive and characterized by proliferative signatures, high genomic complexity, aberrant TP53 and PRC2 loss, as well as high relative expression of several potential actionable targets (EGFR, ERBB2, EZH2, KIF11, PLK1, RRM2). Integrated gene-wise analyses suggested a DNA copy number-basis for proliferative transcriptomic signatures in particular, and the tumour copy number burden further stratified the transcriptomic subtypes according to patient prognosis (P < 0.01). INTERPRETATION Approximately half of MPNSTs belong to an "immune deficient" transcriptomic subtype associated with an aggressive disease course, PRC2 loss and expression of several potential therapeutic targets, providing a rationale for molecularly-guided intervention trials. FUNDING Research grants from non-profit organizations, as stated in the Acknowledgements.
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Affiliation(s)
- Maren Høland
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway; Division of Laboratory Medicine, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Matthias Kolberg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kjetil Boye
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Tormod K Guren
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Eva van den Berg
- Department of Genetics, The University Medical Center Groningen, the Netherlands
| | - Emanuela Palmerini
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Sigbjørn Smeland
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway; Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Piero Picci
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
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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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Köster J, Arbajian E, Viklund B, Isaksson A, Hofvander J, Haglund F, Bauer H, Magnusson L, Mandahl N, Mertens F. Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development. Cancer Genet 2019; 241:34-41. [PMID: 31870844 DOI: 10.1016/j.cancergen.2019.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 06/20/2019] [Revised: 11/06/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
The dermatofibrosarcoma protuberans family of tumors (DPFT) comprises cutaneous soft tissue neoplasms associated with aberrant PDGFBR signaling, typically through a COL1A1-PDGFB fusion. The aim of the present study was to obtain a better understanding of the chromosomal origin of this fusion and to assess the spectrum of secondary mutations at the chromosome and nucleotide levels. We thus investigated 42 tumor samples from 35 patients using chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, and/or massively parallel sequencing (gene panel, whole exome and transcriptome sequencing) methods. We confirmed the age-associated differences in the origin of the COL1A1-PDGFB fusion and could show that it in most cases must arise after DNA synthesis, i.e., in the S or G2 phase of the cell cycle. Whereas there was a non-random pattern of secondary chromosomal rearrangements, single nucleotide variants seem to have little impact on tumor progression. No clear genomic differences between low-grade and high-grade DPFT were found, but the number of chromosomes and chromosomal imbalances as well as the frequency of 9p deletions all tended to be greater among the latter. Gene expression profiling of tumors with COL1A1-PDGFB fusions associated with unbalanced translocations or ring chromosomes identified several transcriptionally up-regulated genes in the amplified regions of chromosomes 17 and 22, including TBX2, PRKCA, MSI2, SOX9, SOX10, and PRAME.
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Affiliation(s)
- Jan Köster
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden.
| | - Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Björn Viklund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Haglund
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Bauer
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - 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; Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
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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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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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Høland M, Kolberg M, Danielsen SA, Bjerkehagen B, Eilertsen IA, Hektoen M, Mandahl N, van den Berg E, Smeland S, Mertens F, Sundby Hall K, Picci P, Sveen A, Lothe RA. Inferior survival for patients with malignant peripheral nerve sheath tumors defined by aberrant TP53. Mod Pathol 2018; 31:1694-1707. [PMID: 29946184 DOI: 10.1038/s41379-018-0074-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/22/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023]
Abstract
Malignant peripheral nerve sheath tumor is a rare and aggressive disease with poor treatment response, mainly affecting adolescents and young adults. Few molecular biomarkers are used in the management of this cancer type, and although TP53 is one of few recurrently mutated genes in malignant peripheral nerve sheath tumor, the mutation prevalence and the corresponding clinical value of the TP53 network remains unsettled. We present a multi-level molecular study focused on aberrations in the TP53 network in relation to patient outcome in a series of malignant peripheral nerve sheath tumors from 100 patients and 38 neurofibromas, including TP53 sequencing, high-resolution copy number analyses of TP53 and MDM2, and gene expression profiling. Point mutations in TP53 were accompanied by loss of heterozygosity, resulting in complete loss of protein function in 8.2% of the malignant peripheral nerve sheath tumors. Another 5.5% had MDM2 amplification. TP53 mutation and MDM2 amplification were mutually exclusive and patients with either type of aberration in their tumor had a worse prognosis, compared to those without (hazard ratio for 5-year disease-specific survival 3.5, 95% confidence interval 1.78-6.98). Both aberrations had similar consequences on the gene expression level, as analyzed by a TP53-associated gene signature, a property also shared with the copy number aberrations and/or loss of heterozygosity at the TP53 locus, suggesting a common "TP53-mutated phenotype" in as many as 60% of the tumors. This was a poor prognostic phenotype (hazard ratio = 4.1, confidence interval:1.7-9.8), thus revealing a TP53-non-aberrant patient subgroup with a favorable outcome. The frequency of the "TP53-mutated phenotype" warrants explorative studies of stratified treatment strategies in malignant peripheral nerve sheath tumor.
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Affiliation(s)
- Maren Høland
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Matthias Kolberg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Stine Aske Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Oral Biology, University of Oslo, Oslo, Norway.,Department of Pathology, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Eva van den Berg
- Department of Genetics, The University Medical Center Groningen, Groningen, The Netherlands
| | - Sigbjørn Smeland
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Kirsten Sundby Hall
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Piero Picci
- Laboratory of Experimental Oncology, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. .,Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
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Hofvander J, Viklund B, Isaksson A, Brosjö O, Vult von Steyern F, Rissler P, Mandahl N, Mertens F. Different patterns of clonal evolution among different sarcoma subtypes followed for up to 25 years. Nat Commun 2018; 9:3662. [PMID: 30201954 PMCID: PMC6131146 DOI: 10.1038/s41467-018-06098-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/14/2018] [Indexed: 02/08/2023] Open
Abstract
To compare clonal evolution in tumors arising through different mechanisms, we selected three types of sarcoma-amplicon-driven well-differentiated liposarcoma (WDLS), gene fusion-driven myxoid liposarcoma (MLS), and sarcomas with complex genomes (CXS)-and assessed the dynamics of chromosome and nucleotide level mutations by cytogenetics, SNP array analysis and whole-exome sequencing. Here we show that the extensive single-cell variation in WDLS has minor impact on clonal key amplicons in chromosome 12. In addition, only a few of the single nucleotide variants in WDLS were present in more than one lesion, suggesting that such mutations are of little significance in tumor development. MLS displays few mutations other than the FUS-DDIT3 fusion, and the primary tumor is genetically sometimes much more complex than its relapses, whereas CXS in general shows a gradual increase of both nucleotide- and chromosome-level mutations, similar to what has been described in carcinomas.
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Affiliation(s)
- Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.
| | - Björn Viklund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Otte Brosjö
- Department of Orthopedics, Karolinska Hospital, SE-171 76, Stockholm, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics, Clinical Sciences, Lund University and Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Pehr Rissler
- Department of Clinical Genetics and Pathology, University and Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
| | - Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.,Department of Clinical Genetics and Pathology, University and Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
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Mandahl N, Magnusson L, Nilsson J, Viklund B, Arbajian E, von Steyern FV, Isaksson A, Mertens F. Scattered genomic amplification in dedifferentiated liposarcoma. Mol Cytogenet 2017; 10:25. [PMID: 28652867 PMCID: PMC5483303 DOI: 10.1186/s13039-017-0325-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 04/13/2017] [Accepted: 06/08/2017] [Indexed: 01/07/2023] Open
Abstract
Background Atypical lipomatous tumor (ALT), well differentiated liposarcoma (WDLS) and dedifferentiated liposarcoma (DDLS) are cytogenetically characterized by near-diploid karyotypes with no or few other aberrations than supernumerary ring or giant marker chromosomes, although DDLS tend to have somewhat more complex rearrangements. In contrast, pleomorphic liposarcomas (PLS) have highly aberrant and heterogeneous karyotypes. The ring and giant marker chromosomes contain discontinuous amplicons, in particular including multiple copies of the target genes CDK4, HMGA2 and MDM2 from 12q, but often also sequences from other chromosomes. Results The present study presents a DDLS with an atypical hypertriploid karyotype without any ring or giant marker chromosomes. SNP array analyses revealed amplification of almost the entire 5p and discontinuous amplicons of 12q including the classical target genes, in particular CDK4. In addition, amplicons from 1q, 3q, 7p, 9p, 11q and 20q, covering from 2 to 14 Mb, were present. FISH analyses showed that sequences from 5p and 12q were scattered, separately or together, over more than 10 chromosomes of varying size. At RNA sequencing, significantly elevated expression, compared to myxoid liposarcomas, was seen for TRIO and AMACR in 5p and of CDK4, HMGA2 and MDM2 in 12q. Conclusions The observed pattern of scattered amplification does not show the characteristics of chromothripsis, but is novel and differs from the well known cytogenetic manifestations of amplification, i.e., double minutes, homogeneously staining regions and ring chromosomes. Possible explanations for this unusual distribution of amplified sequences might be the mechanism of alternative lengthening of telomeres that is frequently active in DDLS and events associated with telomere crisis. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0325-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Björn Viklund
- Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Anders Isaksson
- Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
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Walther C, Mayrhofer M, Nilsson J, Hofvander J, Jonson T, Mandahl N, Øra I, Gisselsson D, Mertens F. Genetic heterogeneity in rhabdomyosarcoma revealed by SNP array analysis. Genes Chromosomes Cancer 2015; 55:3-15. [DOI: 10.1002/gcc.22285] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/27/2015] [Indexed: 12/25/2022] Open
Affiliation(s)
- Charles Walther
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Markus Mayrhofer
- Array & Analysis Facility, Science for Life Laboratory, Uppsala University; Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Jakob Hofvander
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Tord Jonson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Nils Mandahl
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Ingrid Øra
- Department of Pediatric Oncology; Skåne University Hospital; Lund Sweden
| | - David Gisselsson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
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Hofvander J, Tayebwa J, Nilsson J, Magnusson L, Brosjö O, Larsson O, von Steyern FV, Domanski HA, Mandahl N, Mertens F. RNA sequencing of sarcomas with simple karyotypes: identification and enrichment of fusion transcripts. J Transl Med 2015; 95:603-9. [PMID: 25867764 DOI: 10.1038/labinvest.2015.50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 11/09/2022] Open
Abstract
Gene fusions are neoplasia-associated mutations arising from structural chromosomal rearrangements. They have a strong impact on tumor development and constitute important diagnostic markers. Malignant soft tissue tumors (sarcomas) constitute a heterogeneous group of neoplasms with >50 distinct subtypes, each of which is rare. In addition, there is considerable morphologic overlap between sarcomas and benign lesions. Several subtypes display distinct gene fusions, serving as excellent biomarkers. The development of methods for deep sequencing of the complete transcriptome (RNA-Seq) has substantially improved the possibilities for detecting gene fusions. With the aim of identifying new gene fusions of biological and clinical relevance, eight sarcomas with simple karyotypes, ie, only one or a few structural rearrangements, were subjected to massively parallel paired-end sequencing of mRNA. Three different algorithms were used to identify fusion transcripts from RNA-Seq data. Three novel (KIAA2026-NUDT11, CCBL1-ARL1, and AFF3-PHF1) and two previously known fusions (FUS-CREB3L2 and HAS2-PLAG1) were found and could be verified by other methods. These findings show that RNA-Seq is a powerful tool for detecting gene fusions in sarcomas but also suggest that it is advisable to use more than one algorithm to analyze the output data as only two of the confirmed fusions were reported by more than one of the gene fusion detection software programs. For all of the confirmed gene fusions, at least one of the genes mapped to a chromosome band implicated by the karyotype, suggesting that sarcomas with simple karyotypes constitute an excellent resource for identifying novel gene fusions.
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Affiliation(s)
- Jakob Hofvander
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Johnbosco Tayebwa
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Solna, Sweden
| | - Olle Larsson
- Department of Pathology, Karolinska University Hospital, Solna, Sweden
| | | | - Henryk A Domanski
- Department of Pathology, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
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12
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Kolberg M, Høland M, Lind GE, Ågesen TH, Skotheim RI, Hall KS, Mandahl N, Smeland S, Mertens F, Davidson B, Lothe RA. Protein expression of BIRC5, TK1, and TOP2A in malignant peripheral nerve sheath tumours--A prognostic test after surgical resection. Mol Oncol 2015; 9:1129-39. [PMID: 25769404 PMCID: PMC5528761 DOI: 10.1016/j.molonc.2015.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 09/02/2014] [Revised: 01/22/2015] [Accepted: 02/10/2015] [Indexed: 11/26/2022] Open
Abstract
No consensus treatment regime exists beyond surgery for malignant peripheral nerve sheath tumours (MPNST), and the purpose of the present study was to find new approaches to stratify patients with good and poor prognosis and to better guide therapeutic intervention for this aggressive soft tissue cancer. From a total of 67 MPNSTs from Scandinavian patients with and without neurofibromatosis type 1, 30 MPNSTs were investigated by genome‐wide RNA expression profiling and 63 MPNSTs by immunohistochemical (IHC) analysis, and selected genes were submitted to analyses of disease‐specific survival. The potential drug target genes survivin (BIRC5), thymidine kinase 1 (TK1), and topoisomerase 2‐alpha (TOP2A), all encoded on chromosome arm 17q, were up‐regulated in MPNST as compared to benign neurofibromas. Each of them was found to be independent prognostic markers on the gene expression level, as well as on the protein level. A prognostic profile was identified by combining the nuclear expression scores of the three proteins. For patients with completely resected tumours only 15% in the high risk group were alive after two years, as compared to 78% in the low risk group. In conclusion, we found a novel protein expression profile which identifies MPNST patients with inferior prognosis even after assumed curative surgery. The tested proteins are drug targets; therefore the expression profile may provide predictive information guiding the design of future clinical trials. Importantly, as the effect is seen on the protein level using IHC, the biomarker panel can be readily implemented in routine clinical testing.
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Affiliation(s)
- Matthias Kolberg
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maren Høland
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Trude H Ågesen
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kirsten Sundby Hall
- Department of Oncology, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Nils Mandahl
- Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden
| | - Sigbjørn Smeland
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Oncology, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Fredrik Mertens
- Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden
| | - Ben Davidson
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Pathology, Division of Diagnostics and Intervention, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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13
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Hofvander J, Tayebwa J, Nilsson J, Magnusson L, Brosjö O, Larsson O, Vult von Steyern F, Mandahl N, Fletcher CDM, Mertens F. Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma. Clin Cancer Res 2014; 21:864-9. [PMID: 25516889 DOI: 10.1158/1078-0432.ccr-14-2399] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Undifferentiated pleomorphic sarcoma (UPS) is defined as a sarcoma with cellular pleomorphism and no identifiable line of differentiation. It is typically a high-grade lesion with a metastatic rate of about one third. No tumor-specific rearrangement has been identified, and genetic markers that could be used for treatment stratification are lacking. We performed transcriptome sequencing (RNA-Seq) to search for novel gene fusions. EXPERIMENTAL DESIGN RNA-Seq, FISH, and/or various PCR methodologies were used to search for gene fusions and rearrangements of the PRDM10 gene in 84 soft tissue sarcomas. RESULTS Using RNA-Seq, two cases of UPS were found to display novel gene fusions, both involving the transcription factor PRDM10 as the 3' partner and either MED12 or CITED2 as the 5' partner gene. Further screening of 82 soft tissue sarcomas for rearrangements of the PRDM10 locus revealed one more UPS with a MED12/PRDM10 fusion. None of these genes has been implicated in neoplasia-associated gene fusions before. CONCLUSIONS Our results suggest that PRDM10 fusions are present in around 5% of UPS. Although the fusion-positive cases in our series showed the same nuclear pleomorphism and lack of differentiation as other UPS, it is noteworthy that all three were morphologically low grade and that none of the patients developed metastases. Thus, PRDM10 fusion-positive sarcomas may constitute a clinically important subset of UPS.
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Affiliation(s)
- Jakob Hofvander
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden.
| | - Johnbosco Tayebwa
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Solna, Sweden
| | - Olle Larsson
- Department of Pathology, Karolinska University Hospital, Solna, Sweden
| | | | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | | | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
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14
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Yan H, Killela PJ, Reitman ZJ, Jiao Y, Bettegowda C, Agrawal N, Diaz LA, Friedman AH, Friedman H, Gallia GL, Giovanella BC, Grollman AP, He TC, He Y, Hruban RH, Jallo GI, Mandahl N, Meeker AK, Mertens F, Netto GJ, Rasheed BA, Riggins GJ, Rosenquist TA, Schiffman M, Shih I, Theodorescu D, Torbenson MS, Velculescu VE, Wang TL, Wentzensen N, Wood LD, Zhang M, Healy P, Yang R, Diplas B, Wang ZH, Greer P, Zhu HS, Wang C, Carpenter A, Herndon JE, McLendon RE, Kinzler KW, Vogelstein B, Papadopoulos N, Bigner DD. TERT PROMOTER MUTATIONS OCCUR FREQUENTLY IN GLIOMAS AND A SUBSET OF TUMORS DERIVED FROM CELLS WITH LOW RATES OF SELF-RENEWAL. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou206.18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Płaszczyca A, Nilsson J, Magnusson L, Brosjö O, Larsson O, Vult von Steyern F, Domanski HA, Lilljebjörn H, Fioretos T, Tayebwa J, Mandahl N, Nord KH, Mertens F. Fusions involving protein kinase C and membrane-associated proteins in benign fibrous histiocytoma. Int J Biochem Cell Biol 2014; 53:475-81. [PMID: 24721208 DOI: 10.1016/j.biocel.2014.03.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 11/30/2022]
Abstract
Benign fibrous histiocytoma (BFH) is a mesenchymal tumor that most often occurs in the skin (so-called dermatofibroma), but may also appear in soft tissues (so-called deep BFH) and in the skeleton (so-called non-ossifying fibroma). The origin of BFH is unknown, and it has been questioned whether it is a true neoplasm. Chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, RNA sequencing, RT-PCR and quantitative real-time PCR were used to search for recurrent somatic mutations in a series of BFH. BFHs were found to harbor recurrent fusions of genes encoding membrane-associated proteins (podoplanin, CD63 and LAMTOR1) with genes encoding protein kinase C (PKC) isoforms PRKCB and PRKCD. PKCs are serine-threonine kinases that through their many phosphorylation targets are implicated in a variety of cellular processes, as well as tumor development. When inactive, the amino-terminal, regulatory domain of PKCs suppresses the activity of their catalytic domain. Upon activation, which requires several steps, they typically translocate to cell membranes, where they interact with different signaling pathways. The detected PDPN-PRKCB, CD63-PRKCD and LAMTOR1-PRKCD gene fusions are all predicted to result in chimeric proteins consisting of the membrane-binding part of PDPN, CD63 or LAMTOR1 and the entire catalytic domain of the PKC. This novel pathogenetic mechanism should result in constitutive kinase activity at an ectopic location. The results show that BFH indeed is a true neoplasm, and that distorted PKC activity is essential for tumorigenesis. The findings also provide means to differentiate BFH from other skin and soft tissue tumors. This article is part of a Directed Issue entitled: Rare cancers.
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Affiliation(s)
- Anna Płaszczyca
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Linda Magnusson
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, SE-171 76 Solna, Sweden
| | - Olle Larsson
- Department of Pathology, Karolinska University Hospital, SE-171 76 Solna, Sweden
| | | | - Henryk A Domanski
- Department of Pathology, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Henrik Lilljebjörn
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Johnbosco Tayebwa
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Karolin H Nord
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden.
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16
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Macchia G, Nord KH, D'Alessandro G, Nilsson J, Magnusson L, Mandahl N, Storlazzi CT, Mertens F. Rearrangements of chromosome bands 15q12-q21 are secondary to HMGA2 deregulation in conventional lipoma. Oncol Rep 2013; 31:807-11. [PMID: 24297246 DOI: 10.3892/or.2013.2889] [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] [Received: 09/18/2013] [Accepted: 10/25/2013] [Indexed: 11/05/2022] Open
Abstract
Rearrangements of chromosome arm 15q are rare but recurrent in conventional lipomas, a tumor type often showing deregulated expression of the HMGA2 gene. In order to assess whether 15q rearrangements could constitute a distinct pathogenetic mechanism, we studied seven cases of conventional lipoma that at G-banding analysis had various rearrangements of 15q12-q21. The breakpoints in 15q were mapped by fluorescence in situ hybridization (FISH) and single nucleotide polymorphism array analyses, and the status of the HMGA2 gene was evaluated by FISH and/or quantitative PCR. We found an overlapping deletion on 15q in two cases, but no recurring breakpoint among the other cases. In addition, all cases displayed rearrangement of HMGA2 at the genomic or the transcriptional level. Although 15q rearrangements sometimes are noted as the sole aberration at cytogenetic analysis of conventional lipomas, they are secondary to HMGA2 deregulation.
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Affiliation(s)
- Gemma Macchia
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, SE-221 85 Lund, Sweden
| | - Karolin H Nord
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, SE-221 85 Lund, Sweden
| | | | - Jenny Nilsson
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, SE-221 85 Lund, Sweden
| | - Linda Magnusson
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, SE-221 85 Lund, Sweden
| | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, SE-221 85 Lund, Sweden
| | | | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, SE-221 85 Lund, Sweden
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17
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Joseph CG, Hwang H, Jiao Y, Wood LD, Kinde I, Wu J, Mandahl N, Luo J, Hruban RH, Diaz LA, He TC, Vogelstein B, Kinzler KW, Mertens F, Papadopoulos N. Exomic analysis of myxoid liposarcomas, synovial sarcomas, and osteosarcomas. Genes Chromosomes Cancer 2013; 53:15-24. [PMID: 24190505 DOI: 10.1002/gcc.22114] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 02/03/2023] Open
Abstract
Bone and soft tissue sarcomas are a group of histologically heterogeneous and relatively uncommon tumors. To explore their genetic origins, we sequenced the exomes of 13 osteosarcomas, eight myxoid liposarcomas (MLPS), and seven synovial sarcomas (SYN). These tumors had few genetic alterations (median of 10.8). Nevertheless, clear examples of driver gene mutations were observed, including canonical mutations in TP53, PIK3CA, SETD2, AKT1, and subclonal mutation in FBXW7. Of particular interest were mutations in H3F3A, encoding the variant histone H3.3. Mutations in this gene have only been previously observed in gliomas. Loss of heterozygosity of exomic regions was extensive in osteosarcomas but rare in SYN and MLPS. These results provide intriguing nucleotide-level information on these relatively uncommon neoplasms and highlight pathways that help explain their pathogenesis.
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Affiliation(s)
- Christine G Joseph
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Heejung Hwang
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Yuchen Jiao
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Laura D Wood
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Isaac Kinde
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Jian Wu
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-22185 Lund, Sweden
| | - Jinyong Luo
- Ministry of Educations Key Laboratory of Clinical Diagnostic Medicine, Chongqinq 400046, China
| | - Ralph H Hruban
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Luis A Diaz
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Tong-Chuan He
- The University of Chicago Medical Center, Chicago, IL 60637
| | - Bert Vogelstein
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W Kinzler
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-22185 Lund, Sweden
| | - Nickolas Papadopoulos
- Ludwig Center, the Howard Hughes Medical Institutions, and the Departmentof Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
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18
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Nord KH, Macchia G, Tayebwa J, Nilsson J, Vult von Steyern F, Brosjö O, Mandahl N, Mertens F. Integrative genome and transcriptome analyses reveal two distinct types of ring chromosome in soft tissue sarcomas. Hum Mol Genet 2013; 23:878-88. [PMID: 24070870 DOI: 10.1093/hmg/ddt479] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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
Gene amplification is a common phenomenon in malignant neoplasms of all types. One mechanism behind increased gene copy number is the formation of ring chromosomes. Such structures are mitotically unstable and during tumor progression they accumulate material from many different parts of the genome. Hence, their content varies considerably between and within tumors. Partly due to this extensive variation, the genetic content of many ring-containing tumors remains poorly characterized. Ring chromosomes are particularly prevalent in specific subtypes of sarcoma. Here, we have combined fluorescence in situ hybridization (FISH), global genomic copy number and gene expression data on ring-containing soft tissue sarcomas and show that they harbor two fundamentally different types of ring chromosome: MDM2-positive and MDM2-negative rings. While the former are often found in an otherwise normal chromosome complement, the latter seem to arise in the context of general chromosomal instability. In line with this, sarcomas with MDM2-negative rings commonly show complete loss of either CDKN2A or RB1 -both known to be important for genome integrity. Sarcomas with MDM2-positive rings instead show co-amplification of a variety of potential driver oncogenes. More than 100 different genes were found to be involved, many of which are known to induce cell growth, promote proliferation or inhibit apoptosis. Several of the amplified and overexpressed genes constitute potential drug targets.
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Affiliation(s)
- Karolin H Nord
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, 221 84 Lund, Sweden
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19
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Walther C, Nilsson J, von Steyern FV, Wiebe T, Bauer HCF, Nord KH, Gisselsson D, Domanski HA, Mandahl N, Mertens F. Cytogenetic and single nucleotide polymorphism array findings in soft tissue tumors in infants. Cancer Genet 2013; 206:299-303. [PMID: 23938179 DOI: 10.1016/j.cancergen.2013.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 12/25/2022]
Abstract
Soft tissue tumors in children under one year of age (infants) are rare. The etiology is usually unknown, with external factors or congenital birth defects and hereditary syndromes being recognized in only a small proportion of the cases. We ascertained the cytogenetic findings in 16 infants from whom tumor tissue had been obtained during a 25-year period. In eight of them, single nucleotide polymorphism (SNP) array analyses could also be performed. No constitutional chromosome aberrations were detected, and assessment of clinical files did not reveal any congenital or later anatomical defects. Three tumors--one infantile fibrosarcoma, one embryonal rhabdomyosarcoma, and one angiomatoid fibrous histiocytoma (AFH)--had abnormal karyotypes. As the AFH had an exchange between chromosome arms 12p and 15q, additional fluorescence in situ hybridization and reverse transcription-polymerase chain reaction analyses were performed, unexpectedly revealing an ETV6/NTRK3 fusion. Three of the eight tumors, including the AFH with an abnormal karyotype, analyzed by SNP array showed aberrations (loss of heterozygosity or imbalances). The present series suggests that the addition of array-based technologies is valuable for detecting underlying pathogenetic mechanisms.
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Affiliation(s)
- Charles Walther
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden; Department of Pathology, University and Regional Laboratories, Skåne University Hospital, Lund, Sweden.
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20
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Mohajeri A, Tayebwa J, Collin A, Nilsson J, Magnusson L, von Steyern FV, Brosjö O, Domanski HA, Larsson O, Sciot R, Debiec-Rychter M, Hornick JL, Mandahl N, Nord KH, Mertens F. Comprehensive genetic analysis identifies a pathognomonicNAB2/STAT6fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor. Genes Chromosomes Cancer 2013; 52:873-86. [DOI: 10.1002/gcc.22083] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/12/2022] Open
Affiliation(s)
- Arezoo Mohajeri
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
| | - Johnbosco Tayebwa
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
| | - Anna Collin
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
| | - Linda Magnusson
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
| | | | - Otte Brosjö
- Department of Orthopedics; Karolinska University Hospital; Solna; Sweden
| | - Henryk A. Domanski
- Department of Pathology; University and Regional Laboratories; Lund University; Lund; Sweden
| | - Olle Larsson
- Department of Pathology; Karolinska University Hospital; Solna; Sweden
| | - Raf Sciot
- Department of Pathology; KU Leuven and University Hospitals; Leuven; Belgium
| | | | - Jason L. Hornick
- Department of Pathology; Brigham and Women's Hospital, Harvard Medical School; Boston; USA
| | - Nils Mandahl
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
| | - Karolin H. Nord
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics; University and Regional Laboratories, Lund University; Lund; Sweden
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21
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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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Abstract
Three pediatric germ cell tumors (GCT) were cytogenetically analyzed. A mediastinal mature teratoma in a 15-year-old girl had a balanced t(8;22)(p21;q12) as the sole clonal aberration, an intrathoracic immature teratoma in a 2-year-old girl had the complex karyotype 46,XX,der(6) ins(6;2)(q15;q11q23),de1(8)(q22),-1O,der(12)t(10;12),(q22;q22- 23),der(16)t(1;16)(q12;q11),+mar and a congenital presacral endodermal sinus tumor was characterized by the karyotype 47,XY,add(11)(p15),der(13)t(1;13)(q21;p13),add(14)(p13),d e1(15)(q24),+der(?)t(?;11)(?;q13). The present three tumors had no chromosome aberration in common, nor has any specific change been detected in the 13 previously reported cytogenetically aberrant pediatric GCT. The karyotypic picture comes across as far more heterogeneous than that of GCT of adults. Whereas gain of 12p material, in the vast majority through i(12)(p10) formation, dominates in the adult setting, the most common cytogenetic abnormalities in pediatric GCT seem to be unbalanced recombinations leading to gain of 1q. Other recurrent changes include, in decreasing order of frequency, numerical and structural aberrations leading to gain of 8q and 12p, loss of distal 1p, +3, loss of 7q22-32, -10, -13 and -18.
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Affiliation(s)
- F Mertens
- UNIV LUND HOSP,DEPT CLIN PATHOL,S-22185 LUND,SWEDEN. UNIV LUND HOSP,DEPT PEDIAT SURG,S-22185 LUND,SWEDEN. NORWEGIAN RADIUM HOSP,DEPT GENET,OSLO,NORWAY. INST CANC RES,N-0310 OSLO,NORWAY
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Mertens F, Brosjö O, von Steyern FV, Nord KH, Mandahl N. The MDM2 SNP309 G allele is not preferentially amplified in bone and soft tissue tumors. Cancer Genet 2012; 205:470-3. [PMID: 22939400 DOI: 10.1016/j.cancergen.2012.06.001] [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] [Received: 05/21/2012] [Revised: 06/07/2012] [Accepted: 06/07/2012] [Indexed: 11/25/2022]
Abstract
The transcriptional enhancer region in intron 1 of the proto-oncogene MDM2 contains a polymorphic site (SNP309) that may harbor a G or a T nucleotide. Previous studies have shown that the G allele confers a higher affinity for the Sp1 transcription factor, resulting in an increased transcriptional activity of MDM2. A constitutional G allele has also been associated with earlier onset of various cancer types, and studies of sarcomas have shown an enrichment of the G allele in tumors with MDM2 amplification, notably atypical lipomatous tumor (also known as well-differentiated liposarcoma). In the present study, we analyzed the SNP309 genotype in blood samples and tumor tissue from 57 patients with bone or soft tissue tumors showing amplification of MDM2. We did not observe any constitutional enrichment of the G allele. More importantly, there was no preferential amplification of the G allele in tumor tissue from TG heterozygotes. The expression levels of MDM2 messenger RNA were not higher in tumors with amplification of the G allele than in tumors with amplification of the T allele. Thus, we could not find any evidence for a selective advantage of the SNP309 G allele in bone and soft tissue tumors with MDM2 amplification.
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Affiliation(s)
- Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
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Gebre-Medhin S, Nord KH, Möller E, Mandahl N, Magnusson L, Nilsson J, Jo VY, Vult von Steyern F, Brosjö O, Larsson O, Domanski HA, Sciot R, Debiec-Rychter M, Fletcher CD, Mertens F. Recurrent Rearrangement of the PHF1 Gene in Ossifying Fibromyxoid Tumors. The American Journal of Pathology 2012; 181:1069-77. [DOI: 10.1016/j.ajpath.2012.05.030] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/21/2012] [Accepted: 05/30/2012] [Indexed: 11/26/2022]
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Trombetta D, Macchia G, Mandahl N, Nord KH, Mertens F. Molecular genetic characterization of the 11q13 breakpoint in a desmoplastic fibroma of bone. Cancer Genet 2012; 205:410-3. [DOI: 10.1016/j.cancergen.2012.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/02/2012] [Accepted: 05/02/2012] [Indexed: 11/16/2022]
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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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Jin Y, Möller E, Nord KH, Mandahl N, Von Steyern FV, Domanski HA, Mariño-Enríquez A, Magnusson L, Nilsson J, Sciot R, Fletcher CDM, Debiec-Rychter M, Mertens F. Fusion of the AHRR and NCOA2 genes through a recurrent translocation t(5;8)(p15;q13) in soft tissue angiofibroma results in upregulation of aryl hydrocarbon receptor target genes. Genes Chromosomes Cancer 2012; 51:510-20. [DOI: 10.1002/gcc.21939] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 11/09/2022] Open
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Mertens F, Romeo S, Bovée JV, Tirabosco R, Athanasou N, Alberghini M, Hogendoorn PC, Dei Tos AP, Sciot R, Domanski HA, Aström K, Mandahl N, Debiec-Rychter M. Reclassification and subtyping of so-called malignant fibrous histiocytoma of bone: comparison with cytogenetic features. Clin Sarcoma Res 2011; 1:10. [PMID: 22588017 PMCID: PMC3351725 DOI: 10.1186/2045-3329-1-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 10/13/2011] [Indexed: 11/10/2022] Open
Abstract
Background The diagnostic entity malignant fibrous histiocytoma (MFH) of bone is, like its soft tissue counterpart, likely to be a misnomer, encompassing a variety of poorly differentiated sarcomas. When reviewing a series of 57 so-called MFH of bone within the framework of the EuroBoNeT consortium according to up-to-date criteria and ancillary immunohistochemistry, a fourth of all tumors were reclassified and subtyped. Methods In the present study, the cytogenetic data on 11 of these tumors (three myoepithelioma-like sarcomas, two leiomyosarcomas, one undifferentiated pleomorphic sarcoma with incomplete myogenic differentiation, two undifferentiated pleomorphic sarcomas, one osteosarcoma, one spindle cell sarcoma, and one unclassifiable biphasic sarcoma) are presented. Results All tumors were high-grade lesions and showed very complex karyotypes. Neither the overall pattern (ploidy level, degree of complexity) nor specific cytogenetic features distinguished any of the subtypes. The subgroup of myoepithelioma-like sarcomas was further investigated with regard to the status of the EWSR1 and FUS loci; however, no rearrangement was found. Nor was any particular aberration that could differentiate any of the subtypes from osteosarcomas detected. Conclusions chromosome banding analysis is unlikely to reveal potential genotype-phenotype correlations between morphologic subtypes among so-called MFH of bone.
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Affiliation(s)
- Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
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Mandahl N, Bartuma H, Magnusson L, Isaksson M, Macchia G, Mertens F. HMGA2 and MDM2 expression in lipomatous tumors with partial, low-level amplification of sequences from the long arm of chromosome 12. Cancer Genet 2011; 204:550-6. [DOI: 10.1016/j.cancergen.2011.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/12/2011] [Accepted: 09/29/2011] [Indexed: 12/15/2022]
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Bartuma H, Nord KH, Macchia G, Isaksson M, Nilsson J, Domanski HA, Mandahl N, Mertens F. Gene expression and single nucleotide polymorphism array analyses of spindle cell lipomas and conventional lipomas with 13q14 deletion. Genes Chromosomes Cancer 2011; 50:619-32. [DOI: 10.1002/gcc.20884] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/24/2011] [Accepted: 03/24/2011] [Indexed: 01/07/2023] Open
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Walther C, Domanski HA, von Steyern FV, Mandahl N, Mertens F. Chromosome banding analysis of cells from fine-needle aspiration biopsy samples from soft tissue and bone tumors: is it clinically meaningful? Cancer Genet 2011; 204:203-6. [DOI: 10.1016/j.cancergen.2011.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/08/2011] [Accepted: 01/21/2011] [Indexed: 02/08/2023]
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Mertens F, Möller E, Mandahl N, Picci P, Perez-Atayde AR, Samson I, Sciot R, Debiec-Rychter M. The t(X;6) in subungual exostosis results in transcriptional deregulation of the gene for insulin receptor substrate 4. Int J Cancer 2010; 128:487-91. [DOI: 10.1002/ijc.25353] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Brekke HR, Ribeiro FR, Kolberg M, Agesen TH, Lind GE, Eknaes M, Hall KS, Bjerkehagen B, van den Berg E, Teixeira MR, Mandahl N, Smeland S, Mertens F, Skotheim RI, Lothe RA. Genomic changes in chromosomes 10, 16, and X in malignant peripheral nerve sheath tumors identify a high-risk patient group. J Clin Oncol 2010; 28:1573-82. [PMID: 20159821 DOI: 10.1200/jco.2009.24.8989] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The purpose of this study was to identify genetic aberrations contributing to clinical aggressiveness of malignant peripheral nerve sheath tumors (MPNSTs). PATIENTS AND METHODS Samples from 48 MPNSTs and 10 neurofibromas were collected from 51 patients with (n = 31) or without (n = 20) neurofibromatosis type 1 (NF1). Genome-wide DNA copy number changes were assessed by chromosomal and array-based comparative genomic hybridization (CGH) and examined for prognostic significance. For a subset of 20 samples, RNA microarray data were integrated with the genome data to identify potential target genes. RESULTS Forty-four (92%) MPNSTs displayed DNA copy number changes (median, 18 changes per tumor; range, 2 to 35 changes). Known frequent chromosomal gains at chromosome arms 8q (69%), 17q (67%), and 7p (52%) and losses from 9p (50%), 11q (48%), and 17p (44%) were confirmed. Additionally, gains at 16p or losses from 10q or Xq identified a high-risk group with only 11% 10-year disease-specific survival (P = .00005). Multivariate analyses including NF1 status, tumor location, size, grade, sex, complete remission, and initial metastatic status showed that the genomic high-risk group was the most significant predictor of poor survival. Several genes whose expression was affected by the DNA copy number aberrations were identified. CONCLUSION The presence of specific genetic aberrations was strongly associated with poor survival independent of known clinical risk factors. Conversely, within the total patient cohort with 34% 10-year disease-specific survival, a low-risk group was identified: without changes at chromosomes 10q, 16p, or Xq in their MPNSTs, the patients had 74% 10-year survival.
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Affiliation(s)
- Helge R Brekke
- Department of Cancer Prevention, Institute for Cancer Research, The Norwegian Radium Hospital, Rikshospitalet, Oslo University Hospital, Oslo, Norway
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Trombetta D, Mertens F, Lonoce A, D'Addabbo P, Rennstam K, Mandahl N, Storlazzi CT. Characterization of a hotspot region on chromosome 12 for amplification in ring chromosomes in atypical lipomatous tumors. Genes Chromosomes Cancer 2010; 48:993-1001. [PMID: 19691106 DOI: 10.1002/gcc.20700] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ring chromosomes are cytogenetic hallmarks of genomic amplification in several bone and soft tissue tumors, in particular atypical lipomatous tumors (ALT). In ALT, the ring chromosomes invariably contain amplified material from the central part of the long arm of chromosome 12, mainly 12q12-->15, but often also segments from other chromosomes are involved. Previous studies have shown that one of the recurrent amplicons in ALT, located in 12q13.3-14.1 and harboring the candidate target genes TSPAN31 and CDK4, often has a sharp centromeric border. To characterize this breakpoint region in more detail, 12 cases of ALT with ring chromosomes were analyzed by array comparative genomic hybridization and fluorescence in situ hybridization. In the seven cases showing a sharply delineated amplicon in 12q13.3-14.1, the breakpoint region was further investigated by real time quantitative polymerase chain reaction and Vectorette PCR. The breakpoints clustered to a 146-kb region containing 11 genes. Whereas there was no indication that the breakpoints gave rise to fusion genes, in silico analysis revealed that the breakpoint region was enriched for repeated elements that could be important for ring chromosome formation in ALT.
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Affiliation(s)
- Domenico Trombetta
- Department of Genetics and Microbiology, University of Bari, Bari, Italy.
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Gorunova L, Vult von Steyern F, Storlazzi CT, Bjerkehagen B, Follerås G, Heim S, Mandahl N, Mertens F. Cytogenetic analysis of 101 giant cell tumors of bone: nonrandom patterns of telomeric associations and other structural aberrations. Genes Chromosomes Cancer 2009; 48:583-602. [PMID: 19396867 DOI: 10.1002/gcc.20667] [Citation(s) in RCA: 40] [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: 11/08/2022] Open
Abstract
Giant cell tumor of bone (GCTB) is a benign but locally aggressive tumor with metastatic potential. We performed cytogenetic analysis on 101 GCTB from 92 patients. Karyotypes were obtained from 95 tumors, 47 of which had clonal aberrations. The majority of the cytogenetically abnormal GCTB had multiple, up to 28 per tumor, clones. Clonal telomeric associations (tas) and other structural and numerical changes were found in about 70, 60, and 30%, respectively, of clonally abnormal tumors. Forty-seven aberrations were recurrent, of which 35 are novel. The vast majority of the recurrent aberrations were tas, confirming the important role of telomeric fusions in the development of GCTB. The frequency of tas in GCTB cultures increased with passaging, suggesting a selective advantage of tas-positive cells in vitro. The termini most frequently involved in tas were 22p, 13p, 15p, 21p, 14p, 19q, 1q, 12p, 11p, and 20q. The frequency of tas (irrespective of their clonality) was significantly higher in tumors carrying clonal changes, indicating that tas are precursors of other types of aberrations. In line with this assumption, the chromosomes preferentially involved in tas in a given tumor were also the ones most often affected by other rearrangements. We did not find the previously reported amplicon in 20q11.1, assessed by fluorescence in situ hybridization in 10 tumors. Nor did we find any association between cytogenetic features and adverse clinical outcome. Thus, local recurrences probably depend more on the adequacy of surgical treatment than on the intrinsic biology of the tumors.
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Affiliation(s)
- Ludmila Gorunova
- Department of Medical Genetics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
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Affiliation(s)
- N Mandahl
- Dept of Clinical Genetics, Lund University Hospital, Lund, Sweden.
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Bartuma H, Panagopoulos I, Collin A, Trombetta D, Domanski HA, Mandahl N, Mertens F. Expression levels of HMGA2 in adipocytic tumors correlate with morphologic and cytogenetic subgroups. Mol Cancer 2009; 8:36. [PMID: 19508721 PMCID: PMC2702300 DOI: 10.1186/1476-4598-8-36] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 06/09/2009] [Indexed: 11/21/2022] Open
Abstract
Background The HMGA2 gene encodes a protein that alters chromatin structure. Deregulation, typically through chromosomal rearrangements, of HMGA2 has an important role in the development of several mesenchymal neoplasms. These rearrangements result in the expression of a truncated protein lacking the acidic C-terminus, a fusion protein consisting of the AT-hook domains encoded by exons 1–3 and parts from another gene, or a full-length protein; loss of binding sites for regulatory microRNA molecules from the 3' untranslated region (UTR) of HMGA2 has been suggested to be a common denominator. Methods Seventy adipocytic tumors, representing different morphologic and cytogenetic subgroups, were analyzed by qRT-PCR to study the expression status of HMGA2; 18 of these tumors were further examined by PCR to search for mutations or deletions in the 3'UTR. Results Type (full-length or truncated) and level of expression varied with morphology and karyotype, with the highest levels in atypical lipomatous tumors and lipomas with rearrangements of 12q13-15 and the lowest in lipomas with 6p- or 13q-rearrangements, hibernomas, spindle cell lipomas and myxoid liposarcomas. All 18 examined tumors showed reduced or absent expression of the entire, or parts of, the 3'UTR, which was not due to mutations at the DNA level. Conclusion In adipocytic tumors with deregulated HMGA2 expression, the 3'UTR is consistently lost, either due to physical disruption of HMGA2 or a shift to production of shorter 3'UTR.
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Affiliation(s)
- Hammurabi Bartuma
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
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Gebre-Medhin S, Broberg K, Jonson T, Gorunova L, von Steyern FV, Brosjö O, Jin Y, Gisselsson D, Panagopoulos I, Mandahl N, Mertens F. Telomeric associations correlate with telomere length reduction and clonal chromosome aberrations in giant cell tumor of bone. Cytogenet Genome Res 2009; 124:121-7. [PMID: 19420923 DOI: 10.1159/000207516] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2008] [Indexed: 11/19/2022] Open
Abstract
Giant cell tumor of bone (GCTB) is characterized cytogenetically by frequent telomeric associations (tas). To explore the mechanisms behind the formation of tas in GCTB and to investigate their karyotypic consequences, the frequencies of tas and clonal aberrations other than tas in 20 GCTBs were compared to telomere length and status, as assessed by quantitative PCR, fluorescence in situ hybridization (FISH), and expression levels of four genes involved in telomere maintenance. Based on the G-banding results, the tumors were divided into two groups, one with a high frequency of tas and one with a low frequency. Clonal aberrations were found to be restricted to the group with a high level of tas, and the same group showed a significantly larger reduction in telomere length in tumor cells compared to peripheral blood cells. Furthermore, 65 out of 66 tas analyzed by FISH were negative for telomeric sequences. The expression levels of TERT, TERF1, TERF2, and POT1 did not correlate with telomere length or the frequency of tas. Thus, the present findings provide strong support for the notion that decreased telomere length is a prerequisite for tas in GCTBs and that the clonal changes occurring in GCTBs are derived from tas.
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Affiliation(s)
- S Gebre-Medhin
- Department of Clinical Genetics, University Hospital, Lund, Sweden.
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Abstract
A case of Ullrich-Noonan syndrome with pulmonary stenosis, epicanthus, ptosis, small stature, curved tibia, positive sex chromatin, and a diploid chromosome number is presented. A detailed chromosomal banding analysis with the G-staining, C-staining and Ag-I-staining techniques revealed no significant anomalies. The literature is reviewed and the criteria for diagnosing Ullrich-Noonan syndrome are presented.
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Hallor KH, Staaf J, Bovée JVMG, Hogendoorn PCW, Cleton-Jansen AM, Knuutila S, Savola S, Niini T, Brosjö O, Bauer HCF, Vult von Steyern F, Jonsson K, Skorpil M, Mandahl N, Mertens F. Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors. Clin Cancer Res 2009; 15:2685-94. [PMID: 19336518 DOI: 10.1158/1078-0432.ccr-08-2330] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Histologic grade is currently the best predictor of clinical course in chondrosarcoma patients. Grading suffers, however, from extensive interobserver variability and new objective markers are needed. Hence, we have investigated DNA copy numbers in chondrosarcomas with the purpose of identifying markers useful for prognosis and subclassification. EXPERIMENTAL DESIGN The overall pattern of genomic imbalances was assessed in a series of 67 chondrosarcomas using array comparative genomic hybridization. Statistical analyses were applied to evaluate the significance of alterations detected in subgroups based on clinical data, morphology, grade, tumor size, and karyotypic features. Also, the global gene expression profiles were obtained in a subset of the tumors. RESULTS Genomic imbalances, in most tumors affecting large regions of the genome, were found in 90% of the cases. Several apparently distinctive aberrations affecting conventional central and peripheral tumors, respectively, were identified. Although rare, recurrent amplifications were found at 8q24.21-q24.22 and 11q22.1-q22.3, and homozygous deletions of loci previously implicated in chondrosarcoma development affected the CDKN2A, EXT1, and EXT2 genes. The chromosomal imbalances in two distinct groups of predominantly near-haploid and near-triploid tumors, respectively, support the notion that polyploidization of an initially hyperhaploid/hypodiploid cell population is a common mechanism of chondrosarcoma progression. Increasing patient age as well as tumor grade were associated with adverse outcome, but no copy number imbalance affected metastasis development or tumor-associated death. CONCLUSION Despite similarities in the overall genomic patterns, the present findings suggest that some regions are specifically altered in conventional central and peripheral tumors, respectively.
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Affiliation(s)
- Karolin H Hallor
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
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Möller E, Mandahl N, Iliszko M, Mertens F, Panagopoulos I. Bidirectionality and transcriptional activity of the EWSR1 promoter region. Oncol Rep 2009; 21:641-648. [PMID: 19212622] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
EWSR1 is involved in chimeric proteins which play crucial roles in the development of a variety of bone and soft tissue tumors. Many of the chimeric genes involving EWSR1 have been extensively studied, whereas less is known about the wild-type (wt) gene and its regulation. As the expression of the chimeric gene is driven by the EWSR1 promoter, it is of importance to study the mechanisms regulating wt EWSR1 expression. We estimated the transcriptional activity of the EWSR1 promoter through deletion fragments driving reporter gene expression. This assay identified the 100-bp region immediately downstream of the EWSR1 transcriptional start site (+1) and the downstream region from +100 to +300 as important regions for transcriptional regulation. We also found that EWSR1 and RHBDD3, a gene located directly upstream of EWSR1 that is likely to share regulatory elements with EWSR1, were co-expressed in the tissue panels, Ewing tumor biopsies and cell lines. Thus, our results show that the EWSR1 promoter functions in a bidirectional manner, thereby regulating also RHBDD3, and identifies specific regions that strongly influence promoter activity.
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Affiliation(s)
- Emely Möller
- Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden.
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Levan G, Mandahl N, Bengtsson BO, Levan A. Experimental elimination and recovery of double minute chromosomes in malignant cell populations. Hereditas 2009; 86:75-90. [PMID: 903253 DOI: 10.1111/j.1601-5223.1977.tb01214.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Mandahl N, Fredga K. A comparative chromosome study by means of G-, C-, and NOR-bandings of the weasel, the pygmy weasel and the stoat (Mustela, Carnivora, Mammalia). Hereditas 2009; 93:75-83. [PMID: 6160121 DOI: 10.1111/j.1601-5223.1980.tb01045.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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