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Mitra S, Farswan A, Piccinelli P, Sydow S, Hesla A, Tsagkozis P, Vult von Steyern F, Almqvist M, Eriksson M, Magnusson L, Nilsson J, Pillay N, Mertens F. Transcriptomic profiles of myxofibrosarcoma and undifferentiated pleomorphic sarcoma correlate with clinical and genomic features. J Pathol 2024; 264:293-304. [PMID: 39258383 DOI: 10.1002/path.6347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/01/2024] [Accepted: 08/06/2024] [Indexed: 09/12/2024]
Abstract
Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) are two common and aggressive subtypes of soft tissue sarcoma. The aim of this study was to assess potential transcriptomic differences between MFS and UPS tumours and to evaluate the extent to which differences in gene expression profiles were associated with genomic and clinical features. The study included 162 patients with tumours diagnosed as MFS (N = 62) or UPS (N = 100). The patients had been diagnosed and treated at two Swedish sarcoma centres during a 30-year period. For gene expression profiling and gene fusion detection all tumours were analysed using RNA-sequencing and could be compared with data on clinical outcome (N = 155), global copy number profiles (N = 145), and gene mutations (N = 128). Gene expression profiling revealed three transcriptomic clusters (TCs) without any clear separation of MFS and UPS. One TC was associated with longer metastasis-free survival. These tumours had lower tumour mutation burden (TMB), were enriched for a copy number signature representative of focal LOH and chromosomal instability on a diploid background, and were relatively immune-depleted. MFS and UPS showed extensive genomic overlap, with whole genome doubling occurring more frequently among the latter. The results support the idea that MFS and UPS tumours have largely overlapping genomic and transcriptomic features, with UPS tumours showing more aggressive behaviour and more complex genomes. Independently of the tumour type, clinically relevant subgroups were revealed by gene expression analysis, and the finding of multiple genomic subgroups strongly suggest the existence of subgroups of relevance to treatment stratification. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Shamik Mitra
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Paul Piccinelli
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Saskia Sydow
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Asle Hesla
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Martin Almqvist
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Mikael Eriksson
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Nischalan Pillay
- University College London Cancer Institute, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, Lund, Sweden
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2
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Mertens F, Hofvander J, Mandahl N, Mitelman F. Aneuploidy in neoplasia: Single-cell data on 83,862 tumors. Int J Cancer 2024. [PMID: 39222304 DOI: 10.1002/ijc.35163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/05/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Chromosomal aneuploidy, that is, numerical chromosome aberrations, is one of the molecular hallmarks of cancer. However, when neoplasms are studied with sequencing- and array-based approaches, chromosome numbers and ploidy states are typically inferred from bulk DNA data. Furthermore, published molecular estimates of neoplasia-associated aneuploidy often also include genomic imbalances resulting from various types of structural rearrangement, which likely result from other mechanisms than numerical chromosome aberrations. We thus analyzed chromosome numbers using single-cell cytogenetic data from 83,862 tumors, and show that both benign and malignant tumors are highly heterogeneous with regard to deviations from the normal, diploid state. Focusing on the chromosome numbers in 112 specific tumor types, defined by both exact morphologic diagnosis and organ location and from which data from ≥50 cases were available, we found two major clusters: one predominated by near-diploid neoplasms and one by neoplasms with extensive aneuploidy and one or more whole genome doublings. The former cluster included most benign solid tumors, myeloid neoplasms, and malignant gene fusion-associated solid tumors, whereas the latter was predominated by malignant solid tumors and lymphomas. For 16 malignant tumor types, the distribution of chromosome numbers could be compared to TCGA ploidy level data. Cytogenetic and molecular data correlated well, but the former indicates a higher level of clonal heterogeneity. The results presented here suggest shared pathogenetic mechanisms in certain tumor types and provide a reference for molecular analyses.
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Affiliation(s)
- Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Division of Laboratory Medicine, Lund, Sweden
| | - Jakob Hofvander
- 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
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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3
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Ibstedt S, Piccinelli P, Sydow S, Köster J, Mertens F. Structural Variants in the SMC1A Gene Associated With Near-Haploidy in Undifferentiated Pleomorphic Sarcomas. Genes Chromosomes Cancer 2024; 63:e23255. [PMID: 39149945 DOI: 10.1002/gcc.23255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 08/17/2024] Open
Abstract
Near-haploidization, that is, loss of one copy of most chromosomes, is a relatively rare phenomenon in most tumors, but is enriched among certain soft tissue sarcomas, including undifferentiated pleomorphic sarcoma (UPS). Presumably, near-haploidization can arise through many mechanisms. This study aimed to identify gene rearrangements that could cause near-haploidization. We here present two UPS in which near-haploidization was an early event, identified through single nucleotide polymorphism (SNP) array analysis. One of the cases was studied further using whole genome and transcriptome sequencing, as well as cytogenetic and molecular cytogenetic methods. Both tumors had chromosomal rearrangements in the form of copy number shifts/structural variants affecting the SMC1A gene. These findings suggest that cohesin defects could contribute to mitotic errors resulting in massive loss of chromosomes. SMC1A encodes one of the components of the cohesin multiprotein complex, which is critical for proper alignment of the sister chromatids during S-phase and separation to opposite spindle poles. Further studies should explore the role of cohesin defects in near-haploidization in other sarcomas and to clarify its role in tumor development.
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Affiliation(s)
- Sebastian Ibstedt
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Paul Piccinelli
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Saskia Sydow
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jan Köster
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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4
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Panuciak K, Nowicka E, Mastalerczyk A, Zawitkowska J, Niedźwiecki M, Lejman M. Overview on Aneuploidy in Childhood B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2023; 24:ijms24108764. [PMID: 37240110 DOI: 10.3390/ijms24108764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Recent years have brought significant progress in the treatment of B-cell acute lymphoblastic leukemia (ALL). This was influenced by both the improved schemes of conventionally used therapy, as well as the development of new forms of treatment. As a consequence, 5-year survival rates have increased and now exceed 90% in pediatric patients. For this reason, it would seem that everything has already been explored in the context of ALL. However, delving into its pathogenesis at the molecular level shows that there are many variations that still need to be analyzed in more detail. One of them is aneuploidy, which is among the most common genetic changes in B-cell ALL. It includes both hyperdiploidy and hypodiploidy. Knowledge of the genetic background is important already at the time of diagnosis, because the first of these forms of aneuploidy is characterized by a good prognosis, in contrast to the second, which is in favor of an unfavorable course. In our work, we will focus on summarizing the current state of knowledge on aneuploidy, along with an indication of all the consequences that may be correlated with it in the context of the treatment of patients with B-cell ALL.
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Affiliation(s)
- Kinga Panuciak
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Emilia Nowicka
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Angelika Mastalerczyk
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland
| | - Maciej Niedźwiecki
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Monika Lejman
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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Michal M, Kravtsov O, Ross JS, Skanderová D, Martínek P, Mosaieby E, Mata DA, Williams EA, Hung YP. Clear cell mesotheliomas with inactivating VHL mutations and near-haploid genomic features. Genes Chromosomes Cancer 2023; 62:267-274. [PMID: 36515470 DOI: 10.1002/gcc.23119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 12/15/2022] Open
Abstract
Clear cell mesothelioma is uncommon and shows predominance of clear cells with resemblance to clear cell carcinomas. Clinicopathologic and molecular descriptions of clear cell mesothelioma remained limited. In this study, we identified an index patient with clear cell mesothelioma, confirmed by immunohistochemical and ultrastructural studies. Targeted next-generation sequencing revealed the presence of an inactivating VHL mutation. We then systematically searched for VHL-mutant mesotheliomas in a comprehensive genomic profiling database of 1532 mesotheliomas. Collectively, we identified a cohort of four VHL-mutant clear cell mesotheliomas, including three peritoneal and one pleural tumors from three females and one male, with age range of 47-68 (median 63) years. Histologically, each tumor showed a microcystic to tubulopapillary architecture with prominent clear cells. By next-generation DNA sequencing, each of the four clear cell mesotheliomas harbored inactivating VHL mutations, while lacking other alterations typical of mesotheliomas such as BAP1, NF2, SETD2, CDKN2A, CDKN2B, TP53, and PTEN. By using low-pass whole genome sequencing on the index case and targeted next-generation sequencing on the remaining three cases, we identified extensive loss of heterozygosity throughout the genome but consistently sparing chromosomes 5, 7, and 20, characteristic of genomic near-haploidization. In summary, clear cell mesotheliomas were characterized by inactivating VHL mutations and genomic near-haploidization and appeared to represent a distinct clinicopathologic and molecular category of mesotheliomas. Our findings implicate VHL in the pathogenesis of a subset of mesotheliomas, particularly those with clear cell morphology.
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Affiliation(s)
- Michael Michal
- Department of Pathology, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic.,Department of Pathology, Bioptical Laboratory Ltd., Plzen, Czech Republic
| | - Oleksandr Kravtsov
- Department of Pathology, State University of New York Upstate Medical University, New York, New York, USA
| | - Jeffrey S Ross
- Department of Pathology, State University of New York Upstate Medical University, New York, New York, USA.,Department of Pathology, Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Daniela Skanderová
- Department of Clinical and Molecular Pathology, Institute of Translational and Molecular Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Petr Martínek
- Department of Pathology, Bioptical Laboratory Ltd., Plzen, Czech Republic
| | - Elaheh Mosaieby
- Department of Pathology, Bioptical Laboratory Ltd., Plzen, Czech Republic
| | - Douglas A Mata
- Department of Pathology, Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Erik A Williams
- Department of Pathology, Foundation Medicine, Inc., Cambridge, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, University of Miami, Miami, Florida, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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6
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Cross W, Lyskjær I, Lesluyes T, Hargreaves S, Strobl AC, Davies C, Waise S, Hames-Fathi S, Oukrif D, Ye H, Amary F, Tirabosco R, Gerrand C, Baker T, Barnes D, Steele C, Alexandrov L, Bond G, Cool P, Pillay N, Loo PV, Flanagan AM. A genetic model for central chondrosarcoma evolution correlates with patient outcome. Genome Med 2022; 14:99. [PMID: 36042521 PMCID: PMC9426036 DOI: 10.1186/s13073-022-01084-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Central conventional chondrosarcoma (CS) is the most common subtype of primary malignant bone tumour in adults. Treatment options are usually limited to surgery, and prognosis is challenging. These tumours are characterised by the presence and absence of IDH1 and IDH2 mutations, and recently, TERT promoter alterations have been reported in around 20% of cases. The effect of these mutations on clinical outcome remains unclear. The purpose of this study was to determine if prognostic accuracy can be improved by the addition of genomic data, and specifically by examination of IDH1, IDH2, and TERT mutations. METHODS In this study, we combined both archival samples and data sourced from the Genomics England 100,000 Genomes Project (n = 356). Mutations in IDH1, IDH2, and TERT were profiled using digital droplet PCR (n = 346), whole genome sequencing (n=68), or both (n = 64). Complex events and other genetic features were also examined, along with methylation array data (n = 84). We correlated clinical features and patient outcomes with our genetic findings. RESULTS IDH2-mutant tumours occur in older patients and commonly present with high-grade or dedifferentiated disease. Notably, TERT mutations occur most frequently in IDH2-mutant tumours, although have no effect on survival in this group. In contrast, TERT mutations are rarer in IDH1-mutant tumours, yet they are associated with a less favourable outcome in this group. We also found that methylation profiles distinguish IDH1- from IDH2-mutant tumours. IDH wild-type tumours rarely exhibit TERT mutations and tend to be diagnosed in a younger population than those with tumours harbouring IDH1 and IDH2 mutations. A major genetic feature of this group is haploidisation and subsequent genome doubling. These tumours evolve less frequently to dedifferentiated disease and therefore constitute a lower risk group. CONCLUSIONS Tumours with IDH1 or IDH2 mutations or those that are IDHwt have significantly different genetic pathways and outcomes in relation to TERT mutation. Diagnostic testing for IDH1, IDH2, and TERT mutations could therefore help to guide clinical monitoring and prognostication.
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Affiliation(s)
- William Cross
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Iben Lyskjær
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.83440.3b0000000121901201Medical Genomics Research Group, University College London, UCL Cancer Institute, London, UK
| | - Tom Lesluyes
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Steven Hargreaves
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Anna-Christina Strobl
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Christopher Davies
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Sara Waise
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5491.90000 0004 1936 9297Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Shadi Hames-Fathi
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Dahmane Oukrif
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Hongtao Ye
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Fernanda Amary
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Roberto Tirabosco
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Craig Gerrand
- grid.416177.20000 0004 0417 7890Bone Tumour Unit, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Toby Baker
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - David Barnes
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, Birmingham University, Birmingham, UK
| | - Christopher Steele
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Ludmil Alexandrov
- grid.266100.30000 0001 2107 4242University of California, San Diego, USA
| | - Gareth Bond
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, Birmingham University, Birmingham, UK
| | | | - Paul Cool
- grid.412943.90000 0001 0507 535XRobert Jones & Agnes Hunt Orthopaedic Hospital NHS Foundation Trust, Oswestry, UK ,grid.9757.c0000 0004 0415 6205Keele University, Keele, UK
| | - Nischalan Pillay
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Peter Van Loo
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Adrienne M. Flanagan
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
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Near-Haploidy and Low-Hypodiploidy in B-Cell Acute Lymphoblastic Leukemia: When Less Is Too Much. Cancers (Basel) 2021; 14:cancers14010032. [PMID: 35008193 PMCID: PMC8750410 DOI: 10.3390/cancers14010032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/17/2022] Open
Abstract
Hypodiploidy with less than 40 chromosomes is a rare genetic abnormality in B-cell acute lymphoblastic leukemia (B-ALL). This condition can be classified based on modal chromosome number as low-hypodiploidy (30–39 chromosomes) and near-haploidy (24–29 chromosomes), with unique cytogenetic and mutational landscapes. Hypodiploid B-ALL with <40 chromosomes has an extremely poor outcome, with 5-year overall survival rates below 50% and 20% in childhood and adult B-ALL, respectively. Accordingly, this genetic feature represents an adverse prognostic factor in B-ALL and is associated with early relapse and therapy refractoriness. Notably, half of all patients with hypodiploid B-ALL with <40 chromosomes cases ultimately exhibit chromosome doubling of the hypodiploid clone, resulting in clones with 50–78 chromosomes. Doubled clones are often the major clones at diagnosis, leading to “masked hypodiploidy”, which is clinically challenging as patients can be erroneously classified as hyperdiploid B-ALL. Here, we summarize the main cytogenetic and molecular features of hypodiploid B-ALL subtypes, and provide a brief overview of the diagnostic methods, standard-of-care treatments and overall clinical outcome. Finally, we discuss molecular mechanisms that may underlie the origin and leukemogenic impact of hypodiploidy and may open new therapeutic avenues to improve survival rates in these patients.
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8
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Haas OA. Somatic Sex: On the Origin of Neoplasms With Chromosome Counts in Uneven Ploidy Ranges. Front Cell Dev Biol 2021; 9:631946. [PMID: 34422788 PMCID: PMC8373647 DOI: 10.3389/fcell.2021.631946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/22/2021] [Indexed: 01/09/2023] Open
Abstract
Stable aneuploid genomes with nonrandom numerical changes in uneven ploidy ranges define distinct subsets of hematologic malignancies and solid tumors. The idea put forward herein suggests that they emerge from interactions between diploid mitotic and G0/G1 cells, which can in a single step produce all combinations of mono-, di-, tri-, tetra- and pentasomic paternal/maternal homologue configurations that define such genomes. A nanotube-mediated influx of interphase cell cytoplasm into mitotic cells would thus be responsible for the critical nondisjunction and segregation errors by physically impeding the proper formation of the cell division machinery, whereas only a complete cell fusion can simultaneously generate pentasomies, uniparental trisomies as well as biclonal hypo- and hyperdiploid cell populations. The term "somatic sex" was devised to accentuate the similarities between germ cell and somatic cell fusions. A somatic cell fusion, in particular, recapitulates many processes that are also instrumental in the formation of an abnormal zygote that involves a diploid oocyte and a haploid sperm, which then may further develop into a digynic triploid embryo. Despite their somehow deceptive differences and consequences, the resemblance of these two routes may go far beyond of what has hitherto been appreciated. Based on the arguments put forward herein, I propose that embryonic malignancies of mesenchymal origin with these particular types of aneuploidies can thus be viewed as the kind of flawed somatic equivalent of a digynic triploid embryo.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Cancer Research Institute, Vienna, Austria
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9
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"Inflammatory Leiomyosarcoma" and "Histiocyte-rich Rhabdomyoblastic Tumor": a clinicopathological, immunohistochemical and genetic study of 13 cases, with a proposal for reclassification as "Inflammatory Rhabdomyoblastic Tumor". Mod Pathol 2021; 34:758-769. [PMID: 33318583 DOI: 10.1038/s41379-020-00703-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/08/2022]
Abstract
Inflammatory leiomyosarcoma (ILMS), defined as "a malignant neoplasm showing smooth muscle differentiation, a prominent inflammatory infiltrate, and near-haploidization", is a very rare soft tissue tumor with a generally favorable prognosis. The morphologic features of "histiocyte-rich rhabdomyoblastic tumor" (HRRMT) are similar to those of ILMS, although this lesion shows by definition a skeletal muscle phenotype. Recent gene expression profiling and immunohistochemical studies have also suggested that ILMS and HRRMT may be related. We studied the clinicopathologic, immunohistochemical and genetic features of four cases previously classified as ILMS and nine classified as HRRMT. Tumors from both groups tended to occur in the deep soft tissues of the extremities of young to middle-aged males and exhibited indolent behavior. Morphologically, all were well-circumscribed, often encapsulated, and showed a striking histiocyte-rich inflammatory infiltrate admixed with variably pleomorphic tumor cells showing spindled and epithelioid to rhabdoid morphology, eosinophilic cytoplasm, and prominent nucleoli, but few, if any, mitotic figures. Immunohistochemically, the tumor cells expressed desmin, alpha-smooth muscle actin, and the rhabdomyoblastic markers PAX7, MyoD1, and myogenin. H-caldesmon expression was absent in all cases, using the specific h-CD antibody. Karyotypic study (1 HRRMT) and genome-wide copy number analysis (7 HRRMT, OncoScan SNP assay), revealed near-haploidization in four cases, with subsequent genome doubling in one, an identical phenotype to that seen in ILMS. We propose reclassification of ILMS and HRRMT as "inflammatory rhabdomyoblastic tumor", a name which accurately describes the salient morphologic and immunohistochemical features of this distinctive tumor, as well as its intermediate (rarely metastasizing) clinical behavior.
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10
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Hung YP, Dong F, Dubuc AM, Dal Cin P, Bueno R, Chirieac LR. Molecular characterization of localized pleural mesothelioma. Mod Pathol 2020; 33:271-280. [PMID: 31371807 PMCID: PMC7359734 DOI: 10.1038/s41379-019-0330-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/31/2022]
Abstract
Localized pleural mesothelioma is a rare solitary circumscribed pleural tumor that is microscopically similar to diffuse malignant pleural mesothelioma. However, the molecular characteristics and nosologic relationship with its diffuse counterpart remain unknown. In a consecutive cohort of 1110 patients with pleural mesotheliomas diagnosed in 2005-2018, we identified six (0.5%) patients diagnosed with localized pleural mesotheliomas. We gathered clinical history, evaluated the histopathology, and in select cases performed karyotypic analysis and targeted next-generation sequencing. The cohort included three women and three men (median age 63; range 28-76), often presenting incidentally during radiologic evaluation for unrelated conditions. Neoadjuvant chemotherapy was administered in two patients. All tumors (median size 5.0 cm; range 2.7-13.5 cm) demonstrated gross circumscription (with microscopic invasion into lung, soft tissue, and/or rib in four cases), mesothelioma histology (four biphasic and two epithelioid types), and mesothelial immunophenotype. Of four patients with at least 6-month follow-up, three were alive (up to 8.9 years). Genomic characterization identified several subgroups: (1) BAP1 mutations with deletions of CDKN2A and NF2 in two tumors; (2) TRAF7 mutations in two tumors, including one harboring trisomies of chromosomes 3, 5, 7, and X; and (3) genomic near-haploidization, characterized by extensive loss of heterozygosity sparing chromosomes 5 and 7. Localized pleural mesotheliomas appear genetically heterogeneous and include BAP1-mutated, TRAF7-mutated, and near-haploid subgroups. While the BAP1-mutated subgroup is similar to diffuse malignant pleural mesotheliomas, the TRAF7-mutated subgroup overlaps genetically with adenomatoid tumors and well-differentiated papillary mesotheliomas, in which recurrent TRAF7 mutations have been described. Genomic near-haploidization, identified recently in a subset of diffuse malignant pleural mesotheliomas, suggests a novel mechanism in the pathogenesis of both localized pleural mesothelioma and diffuse malignant pleural mesothelioma. Our findings describe distinctive genetic features of localized pleural mesothelioma, with both similarities to and differences from diffuse malignant pleural mesothelioma.
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Affiliation(s)
- Yin P. Hung
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Fei Dong
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Raphael Bueno
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lucian R. Chirieac
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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11
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Hyperhaploid plasma cell myeloma characterized by poor outcome and monosomy 17 with frequently co-occurring TP53 mutations. Blood Cancer J 2019; 9:20. [PMID: 30783078 PMCID: PMC6381150 DOI: 10.1038/s41408-019-0182-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/18/2019] [Accepted: 01/30/2019] [Indexed: 01/20/2023] Open
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12
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Ashby C, Tytarenko RG, Wang Y, Weinhold N, Johnson SK, Bauer M, Wardell CP, Schinke C, Thanendrarajan S, Zangari M, van Rhee F, Davies FE, Sawyer JR, Morgan GJ, Walker BA. Poor overall survival in hyperhaploid multiple myeloma is defined by double-hit bi-allelic inactivation of TP53. Oncotarget 2019; 10:732-737. [PMID: 30774775 PMCID: PMC6366829 DOI: 10.18632/oncotarget.26589] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 12/29/2018] [Indexed: 11/25/2022] Open
Abstract
Hyperhaploid multiple myeloma is a rare numerical aberration group defined by a range of 24-34 chromosomes, which is associated with a poor prognosis with a 5-year survival rate of 23%. Hyperhaploid patient samples (n=8) were sequenced and copy number and mutations identified. Samples had a median of 13 monosomies (range 12-14), which in general were those not associated with trisomies in hyperdiploid samples. The chromosomes traditionally trisomic in hyperdiploid myeloma were disomic in hyperhaploid myeloma with retention of heterodisomy. We examined the hyperhaploid samples for frequently mutated genes and found that 8/8 (100%) hyperhaploid samples had a mutation in TP53, exceeding the overall rate of mutation in newly diagnosed patients (5.5%), indicating an oncogenic dependency in this group. All samples with TP53 mutation also had monosomy of chromosome 17, indicating bi-allelic inactivation of TP53. As such, this high risk group is part of double-hit myeloma.
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Affiliation(s)
- Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruslana G Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yan Wang
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Niels Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah K Johnson
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Mauricio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Faith E Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jeffrey R Sawyer
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gareth J Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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13
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Arbajian E, Köster J, Vult von Steyern F, Mertens F. Inflammatory leiomyosarcoma is a distinct tumor characterized by near-haploidization, few somatic mutations, and a primitive myogenic gene expression signature. Mod Pathol 2018; 31:93-100. [PMID: 28884746 DOI: 10.1038/modpathol.2017.113] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 12/28/2022]
Abstract
Inflammatory leiomyosarcoma is a soft-tissue tumor resembling conventional leiomyosarcoma, but with a prominent intrinsic inflammatory component. Previous studies have suggested that inflammatory leiomyosarcoma differs genetically from leiomyosarcoma, but in-depth analyses are lacking. Here we provide a comprehensive picture of the genome and transcriptome of inflammatory leiomyosarcoma by combining cytogenetic, single-nucleotide polymorphism array, mRNA-sequencing, and whole-exome sequencing data. The results show that inflammatory leiomyosarcoma has a specific genetic profile characterized by near-haploidization with or without subsequent whole-genome doubling. Consistently, both parental copies of chromosomes 5 and 22 are preserved. Apart from recurrent mutation of the NF1 gene, additional somatic events that could serve as driver mutations were not found at either the nucleotide or the genome level. Furthermore, no fusion transcripts were identified. Global gene expression profiling revealed particularly prominent differential expression of genes, including ITGA7, MYF5, MYF6, MYOD1, MYOG, and PAX7, involved in muscle development and function, providing strong argument for grouping inflammatory leiomyosarcoma with myogenic sarcomas, rather than with myofibroblastic lesions. Combined with previously published data, there are now 10 cases of inflammatory leiomyosarcoma with confirmed near-haploid genotype. These patients differ from leiomyosarcoma patients in being younger (median 41 years), showing a male predominance (9:1), and few relapses (1 of 8 informative patients). Thus, the clinical, morphological, and genetic data provide compelling support for inflammatory leiomyosarcoma being a distinct subtype of myogenic tumors.
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Affiliation(s)
- Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jan Köster
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics and Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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14
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Near-haploid and low-hypodiploid acute lymphoblastic leukemia: two distinct subtypes with consistently poor prognosis. Blood 2016; 129:420-423. [PMID: 27903530 DOI: 10.1182/blood-2016-10-743765] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/22/2016] [Indexed: 11/20/2022] Open
Abstract
Hypodiploidy <40 chromosomes is an uncommon genetic feature of acute lymphoblastic leukemia (ALL) in both children and adults. It has long been clear by cytogenetic analyses, and recently confirmed by mutational profiling, that these cases may be further subdivided into 2 subtypes: near-haploid ALL with 24 to 30 chromosomes and low-hypodiploid ALL with 31 to 39 chromosomes. Both groups are associated with a very poor prognosis, and these patients are among those who could benefit most from novel treatments.
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15
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Safavi S, Olsson L, Biloglav A, Veerla S, Blendberg M, Tayebwa J, Behrendtz M, Castor A, Hansson M, Johansson B, Paulsson K. Genetic and epigenetic characterization of hypodiploid acute lymphoblastic leukemia. Oncotarget 2016; 6:42793-802. [PMID: 26544893 PMCID: PMC4767471 DOI: 10.18632/oncotarget.6000] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/17/2015] [Indexed: 01/23/2023] Open
Abstract
Purpose To investigate the genetic and epigenetic landscape of hypodiploid (<45 chromosomes) acute lymphoblastic leukemia (ALL). Methods Single nucleotide polymorphism array, whole exome sequencing, RNA sequencing, and methylation array analyses were performed on eleven hypodiploid ALL cases. Results In line with previous studies, mutations in IKZF3 and FLT3 were detected in near-haploid (25–30 chromosomes) cases. Low hypodiploidy (31–39 chromosomes) was associated with somatic TP53 mutations. Notably, mutations of this gene were also found in 3/3 high hypodiploid (40–44 chromosomes) cases, suggesting that the mutational patterns are similar in low hypodiploid and high hypodiploid ALL. The high hypodiploid ALLs frequently displayed substantial cell-to-cell variability in chromosomal content, indicative of chromosomal instability; a rare phenomenon in ALL. Gene expression analysis showed that genes on heterodisomic chromosomes were more highly expressed in hypodiploid cases. Cases clustered according to hypodiploid subtype in the unsupervised methylation analyses, but there was no association between chromosomal copy number and methylation levels. A comparison between samples obtained at diagnosis and relapse showed that the relapse did not arise from the major diagnostic clone in 3/4 cases. Conclusion Taken together, our data support the conclusion that near-haploid and low hypodiploid ALL are different with regard to mutational profiles and also suggest that ALL cases with high hypodiploidy may harbor chromosomal instability.
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Affiliation(s)
- Setareh Safavi
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Olsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics, University and Regional Laboratories, Region Skåne, Lund, Sweden
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Srinivas Veerla
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Molly Blendberg
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johnbosco Tayebwa
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Mikael Behrendtz
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund, Sweden
| | - Markus Hansson
- Division of Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics, University and Regional Laboratories, Region Skåne, Lund, Sweden
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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16
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Hyperhaploidy is a novel high-risk cytogenetic subgroup in multiple myeloma. Leukemia 2016; 31:637-644. [PMID: 27694925 DOI: 10.1038/leu.2016.253] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 07/20/2016] [Accepted: 08/19/2016] [Indexed: 12/13/2022]
Abstract
Hyperhaploid clones (24-34 chromosomes) were identified in 33 patients with multiple myeloma (MM), demonstrating a novel numerical cytogenetic subgroup. Strikingly, all hyperhaploid karyotypes were found to harbor monosomy 17p, the single most important risk stratification lesion in MM. A catastrophic loss of nearly a haploid set of chromosomes results in disomies of chromosomes 3, 5, 7, 9, 11, 15, 18, 19 and 21, the same basic set of odd-numbered chromosomes found in trisomy in hyperdiploid myeloma. All other autosomes are found in monosomy, resulting in additional clinically relevant monosomies of 1p, 6q, 13q and 16q. Hypotriploid subclones (58-68 chromosomes) were also identified in 11 of the 33 patients and represent a duplication of the hyperhaploid clone. Analysis of clones utilizing interphase fluorescence in situ hybridization (iFISH), metaphase FISH and spectral karyotyping identified either monosomy 17 or del17p in all patients. Amplification of 1q21 was identified in eight patients, demonstrating an additional high-risk marker. Importantly, our findings indicate that current iFISH strategies may be uninformative or ambiguous in the detection of these clones, suggesting this patient subgroup maybe underreported. Overall survival for patients with hyperhaploid clones was poor, with a 5-year survival rate of 23.1%. These findings identify a distinct numerical subgroup with cytogenetically defined high-risk disease.
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17
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Rommel B, Holzmann C, Bullerdiek J. Malignant mesenchymal tumors of the uterus - time to advocate a genetic classification. Expert Rev Anticancer Ther 2016; 16:1155-1166. [PMID: 27602604 DOI: 10.1080/14737140.2016.1233817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Sarcomas are rare uterine tumors with leiomyosarcomas and endometrial stromal sarcomas constituting the predominant entities often making their first appearance in young and middle-aged women. By histology combined with immunostaining alone some of these tumors can offer diagnostic challenges e.g. for the differential diagnosis between leiomyosarcomas and smooth muscle tumors of uncertain malignant potential (STUMP). Areas covered: Recent advances in the genetic classification and subclassification, respectively, have shown that genetic markers can offer a valuable adjunct to conventional diagnostic tools. Herein, we will review these recent data from the literature also referring to genetic alterations found in STUMP, endometrial stromal nodules, and leiomyomas including their variants. Expert commentary: For the future, we consider genetic classification as a necessary step in the clinical management of these tumors which will help not only to improve the diagnosis but also the therapy of these malignancies often associated with a worse prognosis.
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Affiliation(s)
- Birgit Rommel
- a Center for Human Genetics , University of Bremen , Bremen , Germany
| | - Carsten Holzmann
- b Institute of Medical Genetics , University Rostock Medical Center , Rostock , Germany
| | - Jörn Bullerdiek
- b Institute of Medical Genetics , University Rostock Medical Center , Rostock , Germany
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18
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Holzmann C, Löning T, Bullerdiek J. Hyperhaploid uterine mesenchymal tumors-a novel genetic subgroup? Cancer Genet 2016; 209:278-81. [PMID: 27397601 DOI: 10.1016/j.cancergen.2016.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 11/18/2022]
Abstract
Hyperhaploid karyotypes have been described to occur in subsets of various solid tumors and leukemias. In these cases, monosomy is noted for most of the chromosomes while a few chromosomes still remain disomic. Evidence has emerged that at least in some tumor entities these remaining chromosomes are non-randomly selected. In addition, structural alterations can accompany the reduced chromosome number and secondary duplication of the chromosome complement is also a frequent finding. In this report, we describe hyperhaploidy in a case of an endometrial stromal nodule of a 50 year old woman who underwent hysterectomy because of symptomatic uterine fibroids. In addition, we review two other recently described cases of uterine mesenchymal tumors with that type of genetic alteration. Despite some histologic differences, striking similarities between these three cases exist with respect to the chromosomes were retained as disomic. Thus, the question arises if hyperhaploidy defines a novel genetic subgroup of uterine mesenchymal tumors.
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Affiliation(s)
- Carsten Holzmann
- Institute of Medical Genetics, University Rostock Medical Center, Rostock, Germany
| | - Thomas Löning
- Pathology Department, Albertinen-Hospital, Hamburg, Germany
| | - Jörn Bullerdiek
- Institute of Medical Genetics, University Rostock Medical Center, Rostock, Germany; Center of Human Genetics, University of Bremen, Bremen, Germany.
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19
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Hofvander J, Jo VY, Ghanei I, Gisselsson D, Mårtensson E, Mertens F. Comprehensive genetic analysis of a paediatric pleomorphic myxoid liposarcoma reveals near-haploidization and loss of theRB1gene. Histopathology 2016; 69:141-147. [DOI: 10.1111/his.12913] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jakob Hofvander
- Department of Clinical Genetics; University and Regional Laboratories; Skåne University Hospital; Lund University; Lund Sweden
| | - Vickie Y Jo
- Department of Pathology; Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Iman Ghanei
- Department of Orthopedics; Skåne University Hospital; Lund University; Lund Sweden
| | - David Gisselsson
- Department of Clinical Genetics; University and Regional Laboratories; Skåne University Hospital; Lund University; Lund Sweden
| | - Emma Mårtensson
- 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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20
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Array-based comparative genomic hybridization detects copy number variations with prognostic relevance in 80% of ALL with normal karyotype or failed chromosome analysis. Leukemia 2015; 30:318-24. [PMID: 26449660 DOI: 10.1038/leu.2015.276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/09/2015] [Accepted: 09/30/2015] [Indexed: 11/08/2022]
Abstract
Pretreatment cytogenetics is an important parameter for risk stratification and therapy approach in acute lymphoblastic leukemia (ALL). However, in up to 30% of cases, chromosome banding analysis (CBA) fails or reveals a normal karyotype. To characterize the subset of ALL with normal karyotype or failed CBA, we performed fluorescence in situ hybridization (FISH) or PCR for BCR-ABL1 and MLL rearrangements as well as array comparative genomic hybridization (aCGH) in 186 adult patients. We further carried out FISH for MYC in cases with Burkitt leukemia phenotype. FISH or PCR revealed one of the respective rearrangements in 22% of patients. In 80% of cases, copy number variations (CNV) were identified by aCGH. In 22% of cases, all CNV were below the resolution of CBA. On the basis of results of FISH, RT-PCR and aCGH, patients were categorized into three groups. The novel subset of patients with submicroscopic CNV only showed an overall survival at 3 years of 84% compared with 64% for patients classified as adverse abnormalities and 77% for cases with other aberrations (P=0.046). Thus, ALL with non-informative CBA can be further classified by FISH and aCGH providing prognostic information, which may be useful for a more individualized therapy.
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21
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Corver WE, van Wezel T, Molenaar K, Schrumpf M, van den Akker B, van Eijk R, Ruano Neto D, Oosting J, Morreau H. Near-haploidization significantly associates with oncocytic adrenocortical, thyroid, and parathyroid tumors but not with mitochondrial DNA mutations. Genes Chromosomes Cancer 2014; 53:833-44. [DOI: 10.1002/gcc.22194] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 05/28/2014] [Indexed: 01/06/2023] Open
Affiliation(s)
- Willem E. Corver
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Tom van Wezel
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Kees Molenaar
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Melanie Schrumpf
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Brendy van den Akker
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Ronald van Eijk
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Dina Ruano Neto
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Jan Oosting
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Hans Morreau
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
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22
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Mühlbacher V, Zenger M, Schnittger S, Weissmann S, Kunze F, Kohlmann A, Bellos F, Kern W, Haferlach T, Haferlach C. Acute lymphoblastic leukemia with low hypodiploid/near triploid karyotype is a specific clinical entity and exhibits a very highTP53mutation frequency of 93%. Genes Chromosomes Cancer 2014; 53:524-36. [DOI: 10.1002/gcc.22163] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/26/2014] [Accepted: 02/26/2014] [Indexed: 12/24/2022] Open
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23
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Walen KH. Haploidization of Human Diploid Metaphase Cells: Is This Genome Reductive Mechanism Opperational in Near-Haploid Leukemia? ACTA ACUST UNITED AC 2014. [DOI: 10.4236/jct.2014.51013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Walen KH. Neoplastic-Like CELL Changes of Normal Fibroblast Cells Associated with Evolutionary Conserved Maternal and Paternal Genomic Autonomous Behavior (Gonomery). ACTA ACUST UNITED AC 2014. [DOI: 10.4236/jct.2014.59094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Retained heterodisomy is associated with high gene expression in hyperhaploid inflammatory leiomyosarcoma. Neoplasia 2013; 14:807-12. [PMID: 23019412 DOI: 10.1593/neo.12930] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/02/2012] [Accepted: 08/03/2012] [Indexed: 02/03/2023] Open
Abstract
Inflammatory leiomyosarcoma (ILMS) is a soft tissue tumor that morphologically resembles conventional leiomyosarcoma (LMS) admixed with a prominent inflammatory infiltrate. Genetic data on ILMS are still limited but have suggested that this entity is characterized by hyperhaploidy (24-34 chromosomes). This low chromosome number is otherwise uncommon in neoplasia and has been found only in 0.2% to 0.3% of cytogenetically investigated tumors. Here, three ILMS were investigated using cytogenetic, single-nucleotide polymorphism (SNP) array, and global gene expression analyses. All cases displayed a hyperhaploid origin. Combined with previously reported cases, hyperhaploidy has been found in six of seven cytogenetically investigated ILMS. The copy number distribution of individual chromosomes is clearly nonrandom; the hyperhaploid clones of all six cases displayed disomy for chromosomes 5 and 20, and two copies of chromosomes 18, 21, and 22 were also common. All chromosomes identified as disomic showed a biparental origin by SNP array analysis; whether this is of pathogenetic importance is not known. Compared with conventional LMS, ILMS had a distinct gene expression signature. Furthermore, the number of chromosome copies correlated well with gene expression levels; disomic chromosomes showed higher gene expression levels than monosomic chromosomes, a finding that has not previously been reported for hyperhaploid tumors. Taken together, our findings suggest that disomy for some chromosomes, notably 5 and 20, as well as distorted gene expression achieved through massive loss of other chromosomes are essential features of ILMS.
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Safavi S, Forestier E, Golovleva I, Barbany G, Nord KH, Moorman AV, Harrison CJ, Johansson B, Paulsson K. Loss of chromosomes is the primary event in near-haploid and low-hypodiploid acute lymphoblastic leukemia. Leukemia 2012; 27:248-50. [PMID: 22889820 DOI: 10.1038/leu.2012.227] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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