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Chen CY. Chromothripsis in myeloid malignancies. Ann Hematol 2024:10.1007/s00277-024-05814-9. [PMID: 38814446 DOI: 10.1007/s00277-024-05814-9] [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: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Chromothripsis refers to massive genomic rearrangements developed during a catastrophic event. In total acute myeloid leukemia (AML), the incidence of chromothripsis ranges from 0 to 6.6%, in cases of complex karyotype AML, the incidence of chromothripsis ranges from 27.3 to 100%, whereas in cases of AML with TP53 mutations, the incidence ranges from 11.1 to 90%. For other types of malignancies, the incidence of chromothripsis also varies, from 0 to 10.5% in myelodysplastic syndrome to up to 61.5% in cases of myelodysplastic syndrome with TP53 mutations.Chromothripsis is typically associated with complex karyotypes and TP53 mutations, and monosomal karyotypes are associated with the condition. ERG amplifications are frequently noted in cases of chromothripsis, whereas MYC amplifications are not. Moreover, FLT3 and NPM1 mutations are negatively associated with chromothripsis. Chromothripsis typically occurs in older patients with AML with low leukocyte counts and bone marrow blast counts. Rare cases of patients with chromothripsis who received intensive induction chemotherapy revealed low response rates and poor overall prognosis. Signal pathways in chromothripsis typically involve copy number gain and upregulation of oncogene gene sets that promote cancer growth and a concomitant copy number loss and downregulation of gene sets associated with tumor suppression functions.Patients with chromothripsis showed a trend of lower complete remission rate and worse overall survival in myeloid malignancy. Large-scale studies are required to further elucidate the causes and treatments of the condition.
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Affiliation(s)
- Chien-Yuan Chen
- Department of Internal Medicine, Division of Hematology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan.
- Department of Pathology, Cytogenetic laboratory, National Taiwan University Hospital, Taipei, Taiwan.
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2
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Rengifo LY, Smits S, Boeckx N, Michaux L, Vandenberghe P, Dewaele B. Shallow whole-genome sequencing of bone marrow aspirates in myelodysplastic neoplasms: A retrospective comparison with cytogenetics. Genes Chromosomes Cancer 2023; 62:663-671. [PMID: 37293982 DOI: 10.1002/gcc.23183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Copy number alterations (CNA) are powerful prognostic markers in myelodysplastic neoplasms (MDS) and are routinely analyzed by conventional cytogenetic analysis (CCA) on bone marrow (BM). Although CCA is still the gold standard, it requires extensive hands-on time and highly trained staff for the analysis, making it a laborious technique. To reduce turn-around-time per case, shallow whole genome sequencing (sWGS) technologies offer new perspectives for the diagnostic work-up of this disorder. We compared sWGS with CCA for the detection of CNAs in 33 retrospective BM samples of patients with MDS. Using sWGS, CNAs were detected in all cases and additionally allowed the analysis of three cases for which CCA failed. The prognostic stratification (IPSS-R score) of 27 out of 30 patients was the same with both techniques. In the remaining cases, discrepancies were caused by the presence of balanced translocations escaping sWGS detection in two cases, a subclonal aberration reported with CCA that could not be confirmed by FISH or sWGS, and the presence of an isodicentric chromosome idic(17)(p11) missed by CCA. Since sWGS can almost entirely be automated, our findings indicate that sWGS is valuable in a routine setting validating it as a cost-efficient tool.
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Affiliation(s)
| | - Sanne Smits
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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3
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Marks JA, Wang X, Fenu EM, Bagg A, Lai C. TP53 in AML and MDS: The new (old) kid on the block. Blood Rev 2023; 60:101055. [PMID: 36841672 DOI: 10.1016/j.blre.2023.101055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
MDS and AML are clonal hematopoietic stem cell disorders of increasing incidence, having a variable prognosis based, among others, on co-occurring molecular abnormalities. TP53 mutations are frequently detected in these myeloid neoplasms and portend a poor prognosis with known therapeutic resistance. This article provides a timely review of the complexity of TP53 alterations, providing updates in diagnosis and prognosis based on new 2022 International Consensus Classification (ICC) and World Health Organization (WHO) guidelines. The article addresses optimal testing strategies and reviews current and arising therapeutic approaches. While the treatment landscape for this molecular subgroup is under active development, further exploration is needed to optimize the care of this group of patients with unmet needs.
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Affiliation(s)
- Jennifer A Marks
- Department of Medicine, Division of Hematology and Oncology, Georgetown University, 3800 Reservoir Road NW, Washington, D.C. 20007, USA.
| | - Xin Wang
- Department of Medicine, Division of Hematology and Oncology, Georgetown University, 3800 Reservoir Road NW, Washington, D.C. 20007, USA; Department of Medicine, Division of Hematology-Oncology, University of Pennsylvania, 12 South Pavilion, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
| | - Elena M Fenu
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA.
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA.
| | - Catherine Lai
- Department of Medicine, Division of Hematology-Oncology, University of Pennsylvania, 12 South Pavilion, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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4
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Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
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Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
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5
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Qin Y, Zhang H, Feng L, Wei H, Wu Y, Jiang C, Xu Z, Zhu H, Liu T. Combining metaphase cytogenetics with single nucleotide polymorphism arrays can improve the diagnostic yield and identify prognosis more precisely in myelodysplastic syndromes. Ann Med 2022; 54:2627-2636. [PMID: 36148999 PMCID: PMC9518301 DOI: 10.1080/07853890.2022.2125173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) encompass a group of heterogeneous haematopoietic stem cell malignancies characterised by ineffective haematopoiesis, cytological aberrations, and a propensity for progression to acute myeloid leukaemia. Diagnosis and disease prognostic stratification are much based on genomic abnormalities. The traditional metaphase cytogenetics analysis (MC) can detect about 40-60% aberrations. Single-nucleotide polymorphism arrays (SNP-A) karyotyping can detect copy number variations with a higher resolution and has a unique advantage in detection of copy number neutral loss of heterozygosity (CN-LOH). Combining these two methods may improve the diagnostic efficiency and accuracy for MDS. METHODS We retrospectively analysed the data of 110 MDS patients diagnosed from January 2012 to December 2019 to compare the detection yield of chromosomal abnormalities by MC with by SNP-A, and the relationship between chromosomal abnormalities and prognosis. RESULTS Our results showed that SNP-A improved the detection yield of chromosomal aberrations compared with MC (74.5 vs. 55.5%, p < .001). In addition, the positive yield could be further improved by combining MC with SNP-A to 77.3%, compared with MC alone. Univariate analysis showed that age >65 years, bone marrow blasts ≥5%, with acquired CN-LOH, new aberrations detected by SNP-A, TGA value > the median (81.435 Mb), higher risk by IPSS-R-MC, higher risk by IPSS-R-SNP-A all had poorer prognosis. More critically, multivariable analysis showed that age >65 years and higher risk by IPSS-R-SNP-A were independent predictors of inferior OS in MDS patients. CONCLUSION The combination of MC and SNP-A based karyotyping can further improve the diagnostic yield and provide more precise prognostic stratification in MDS patients. However, SNP-A may not completely replace MC because of its inability to detect balanced translocation and to detect different clones. From a practical point of view, we recommend the concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients on diagnosis and prognosis stratification.KEY MESSAGESSNP-A based karyotyping can further improve the MDS diagnostic yield and provide more precise prognostic stratification in MDS patients.Acquired CN-LOH is a characteristic chromosomal aberration of MDS, which should be integrated to the diagnostic project of MDS.The concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients can be recommended.
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Affiliation(s)
- Yao Qin
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Hang Zhang
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Lin Feng
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Haichen Wei
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yuling Wu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Chaoran Jiang
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Zhihong Xu
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Huanling Zhu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Ting Liu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
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Nguyen-Khac F, Bidet A, Daudignon A, Lafage-Pochitaloff M, Ameye G, Bilhou-Nabéra C, Chapiro E, Collonge-Rame MA, Cuccuini W, Douet-Guilbert N, Eclache V, Luquet I, Michaux L, Nadal N, Penther D, Quilichini B, Terre C, Lefebvre C, Troadec MB, Véronèse L. The complex karyotype in hematological malignancies: a comprehensive overview by the Francophone Group of Hematological Cytogenetics (GFCH). Leukemia 2022; 36:1451-1466. [DOI: 10.1038/s41375-022-01561-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/16/2022]
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Insight into the Molecular Basis Underlying Chromothripsis. Int J Mol Sci 2022; 23:ijms23063318. [PMID: 35328739 PMCID: PMC8948871 DOI: 10.3390/ijms23063318] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
Chromoanagenesis constitutes a group of events that arise from single cellular events during early development. This particular class of complex rearrangements is a newfound occurrence that may lead to chaotic and complex genomic realignments. By that, chromoanagenesis is thought to be a crucial factor regarding macroevolution of the genome, and consequently is affecting the karyotype revolution together with genomic plasticity. One of chromoanagenesis-type of events is chromothripsis. It is characterised by the breakage of the chromosomal structure and its reassembling in random order and orientation which results in the establishment of derivative forms of chromosomes. Molecular mechanisms that underlie this phenomenon are mostly related to chromosomal sequestration throughout the micronuclei formation process. Chromothripsis is linked both to congenital and cancer diseases, moreover, it might be detected in subjects characterised by a normal phenotype. Chromothripsis, as well as the other chromoanagenetic variations, may be confined to one or more chromosomes, which makes up a non-uniform variety of karyotypes among chromothriptic patients. The detection of chromothripsis is enabled via tools like microarray-based comparative genomic hybridisation, next generation sequencing or authorial protocols aimed for the recognition of structural variations.
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8
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Zavacka K, Plevova K. Chromothripsis in Chronic Lymphocytic Leukemia: A Driving Force of Genome Instability. Front Oncol 2021; 11:771664. [PMID: 34900721 PMCID: PMC8661134 DOI: 10.3389/fonc.2021.771664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
Chromothripsis represents a mechanism of massive chromosome shattering and reassembly leading to the formation of derivative chromosomes with abnormal functions and expression. It has been observed in many cancer types, importantly, including chronic lymphocytic leukemia (CLL). Due to the associated chromosomal rearrangements, it has a significant impact on the pathophysiology of the disease. Recent studies have suggested that chromothripsis may be more common than initially inferred, especially in CLL cases with adverse clinical outcome. Here, we review the main features of chromothripsis, the challenges of its assessment, and the potential benefit of its detection. We summarize recent findings of chromothripsis occurrence across hematological malignancies and address its causes and consequences in the context of CLL clinical features, as well as chromothripsis-related molecular abnormalities described in published CLL studies. Furthermore, we discuss the use of the current knowledge about genome functions associated with chromothripsis in the optimization of treatment strategies in CLL.
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Affiliation(s)
- Kristyna Zavacka
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno & Faculty of Medicine, Masaryk University, Brno, Czechia.,Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno & Faculty of Medicine, Masaryk University, Brno, Czechia.,Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czechia.,Institute of Medical Genetics and Genomics, University Hospital Brno & Masaryk University, Brno, Czechia
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9
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Martín-Izquierdo M, Abáigar M, Hernández-Sánchez JM, Tamborero D, López-Cadenas F, Ramos F, Lumbreras E, Madinaveitia-Ochoa A, Megido M, Labrador J, Sánchez-Real J, Olivier C, Dávila J, Aguilar C, Rodríguez JN, Martín-Nuñez G, Santos-Mínguez S, Miguel-García C, Benito R, Díez-Campelo M, Hernández-Rivas JM. Co-occurrence of cohesin complex and Ras signaling mutations during progression from myelodysplastic syndromes to secondary acute myeloid leukemia. Haematologica 2021; 106:2215-2223. [PMID: 32675227 PMCID: PMC8327724 DOI: 10.3324/haematol.2020.248807] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/14/2020] [Indexed: 01/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are hematological disorders at high risk of progression to secondary acute myeloid leukemia (sAML). However, the mutational dynamics and clonal evolution underlying disease progression are poorly understood at present. To elucidate the mutational dynamics of pathways and genes occurring during the evolution to sAML, next generation sequencing was performed on 84 serially paired samples of MDS patients who developed sAML (discovery cohort) and 14 paired samples from MDS patients who did not progress to sAML during follow-up (control cohort). Results were validated in an independent series of 388 MDS patients (validation cohort). We used an integrative analysis to identify how mutations, alone or in combination, contribute to leukemic transformation. The study showed that MDS progression to sAML is characterized by greater genomic instability and the presence of several types of mutational dynamics, highlighting increasing (STAG2) and newly-acquired (NRAS and FLT3) mutations. Moreover, we observed cooperation between genes involved in the cohesin and Ras pathways in 15-20% of MDS patients who evolved to sAML, as well as a high proportion of newly acquired or increasing mutations in the chromatin-modifier genes in MDS patients receiving a disease-modifying therapy before their progression to sAML.
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Affiliation(s)
- Marta Martín-Izquierdo
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - María Abáigar
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Jesús M Hernández-Sánchez
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - David Tamborero
- Hospital del Mar Medical Research Institute (IMIM), Barcelona and Karolinska Institutet, Stockholm
| | - Félix López-Cadenas
- University of Salamanca, IBSAL, Hematology, Hospital Clinico Universitario, Salamanca, Spain
| | - Fernando Ramos
- Hematology, Hospital Universitario de León, Institute of Biomedicine (IBIOMED), Spain
| | - Eva Lumbreras
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | | | - Marta Megido
- Hematology, Hospital del Bierzo, Ponferrada, León, Spain
| | - Jorge Labrador
- Hematology, Hospital Universitario de Burgos, Burgos, Spain
| | - Javier Sánchez-Real
- Hematology, Hospital Universitario de León, Institute of Biomedicine (IBIOMED), Spain
| | | | - Julio Dávila
- Hematology, Hospital Nuestra Señora de Sónsoles, Ávila, Spain
| | | | | | | | - Sandra Santos-Mínguez
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Cristina Miguel-García
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Rocío Benito
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - María Díez-Campelo
- University of Salamanca, IBSAL, Hematology, Hospital Clínico Universitario, Salamanca, Spain
| | - Jesús M Hernández-Rivas
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
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10
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Chromothripsis-Explosion in Genetic Science. Cells 2021; 10:cells10051102. [PMID: 34064429 PMCID: PMC8147837 DOI: 10.3390/cells10051102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/27/2021] [Accepted: 05/01/2021] [Indexed: 12/13/2022] Open
Abstract
Chromothripsis has been defined as complex patterns of alternating genes copy number changes (normal, gain or loss) along the length of a chromosome or chromosome segment (International System for Human Cytogenomic Nomenclature 2020). The phenomenon of chromothripsis was discovered in 2011 and changed the concept of genome variability, mechanisms of oncogenic transformation, and hereditary diseases. This review describes the phenomenon of chromothripsis, its prevalence in genomes, the mechanisms underlying this phenomenon, and methods of its detection. Due to the fact that most often the phenomenon of chromothripsis occurs in cancer cells, in this review, we will separately discuss the issue of the contribution of chromothripsis to the process of oncogenesis.
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11
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BCOR gene alterations in hematological diseases. Blood 2021; 138:2455-2468. [PMID: 33945606 DOI: 10.1182/blood.2021010958] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
The BCL6 co-repressor (BCOR) is a transcription factor involved in the control of embryogenesis, mesenchymal stem cells function, hematopoiesis and lymphoid development. Recurrent somatic clonal mutations of the BCOR gene and its homologue BCORL1 have been detected in several hematological malignancies and aplastic anemia. They are scattered across the whole gene length and mostly represent frameshifts (deletions, insertions), nonsense and missence mutations. These disruptive events lead to the loss of full-length BCOR protein and to the lack or low expression of a truncated form of the protein, both consistent with the tumor suppressor role of BCOR. BCOR and BCORL1 mutations are similar to those causing two rare X-linked diseases: the oculo-facio-cardio-dental (OFCD) and the Shukla-Vernon syndromes, respectively. Here, we focus on the structure and function of normal BCOR and BCORL1 in normal hematopoietic and lymphoid tissues and review the frequency and clinical significance of the mutations of these genes in malignant and non-malignant hematological diseases. Moreover, we discuss the importance of mouse models to better understand the role of Bcor loss, alone and combined with alterations of other genes (e.g. Dnmt3a and Tet2), in promoting hematological malignancies and in providing a useful platform for the development of new targeted therapies.
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12
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A Single-Run Next-Generation Sequencing (NGS) Assay for the Simultaneous Detection of Both Gene Mutations and Large Chromosomal Abnormalities in Patients with Myelodysplastic Syndromes (MDS) and Related Myeloid Neoplasms. Cancers (Basel) 2021; 13:cancers13081947. [PMID: 33919541 PMCID: PMC8072643 DOI: 10.3390/cancers13081947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Chromosomal abnormalities and somatic mutations are found in patients with myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) in around 50–80% of cases. The identification of these alterations is important for the accurate diagnosis and prognostic classification of these patients. Often, an apparently normal or failed karyotype might lead to an inadequate estimation of the prognostic risk, and several strategies should be combined to solve these cases. The aim of this study was to introduce a novel next-generation sequencing (NGS)-based strategy for the simultaneous detection of all the clinically relevant genetic alterations associated with these disorders. We validated this approach on a large cohort of patients by comparing our findings with those obtained with standard-of-care methods (i.e., karyotype and SNP-arrays). We show that our platform represents a significant improvement on current strategies in defining diagnosis and risk stratification of patients with MDS and myeloid-related disorders. Abstract Myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms are clonal disorders that share most of their cytogenetic and molecular alterations. Despite the increased knowledge of the prognostic importance of genetics in these malignancies, next-generation sequencing (NGS) has not been incorporated into clinical practice in a validated manner, and the conventional karyotype remains mandatory in the evaluation of suspected cases. However, non-informative cytogenetics might lead to an inadequate estimation of the prognostic risk. Here, we present a novel targeted NGS-based assay for the simultaneous detection of all the clinically relevant genetic alterations associated with these disorders. We validated this platform in a large cohort of patients by performing a one-to-one comparison with the lesions from karyotype and single-nucleotide polymorphism (SNP) arrays. Our strategy demonstrated an approximately 97% concordance with standard clinical assays, showing sensitivity at least equivalent to that of SNP arrays and higher than that of conventional cytogenetics. In addition, this NGS assay was able to identify both copy-neutral loss of heterozygosity events distributed genome-wide and copy number alterations, as well as somatic mutations within significant driver genes. In summary, we show a novel NGS platform that represents a significant improvement to current strategies in defining diagnosis and risk stratification of patients with MDS and myeloid-related disorders.
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13
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Ah-Pine F, Casas D, Menei P, Boisselier B, Garcion E, Rousseau A. RNA-sequencing of IDH-wild-type glioblastoma with chromothripsis identifies novel gene fusions with potential oncogenic properties. Transl Oncol 2021; 14:100884. [PMID: 33074125 PMCID: PMC7569239 DOI: 10.1016/j.tranon.2020.100884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most frequent and most aggressive form of glioma. It is characterized by marked genomic instability, which suggests that chromothripsis (CT) might be involved in GBM initiation. Recently, CT has emerged as an alternative mechanism of cancer development, involving massive chromosome rearrangements in a one-step catastrophic event. The aim of the study was to detect CT in GBM and identify novel gene fusions in CT regions. One hundred and seventy IDH-wild-type GBM were screened for CT patterns using whole-genome single nucleotide polymorphism (SNP) arrays. RNA sequencing was performed in 52 GBM with CT features to identify gene fusions within CT regions. Forty tumors (40/52, 77%) harbored at least one gene fusion within CT regions. We identified 120 candidate gene fusions, 30 of which with potential oncogenic activities. We validated 11 gene fusions, which involved the most recurrent fusion partners (EGFR, SEPT14, VOPP1 and CPM), by RT-PCR and Sanger sequencing. The occurrence of CT points to underlying gene fusions in IDH-wild-type GBM. CT provides exciting new research avenues in this highly aggressive cancer.
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Key Words
- baf, b-allele frequency
- chr, chromosome
- cna, copy number alteration
- cns, central nervous system
- ct, chromothripsis
- fpkm, fragments per kilobase of exon per million fragments mapped
- gbm, glioblastoma multiform
- hd, homozygous deletion
- loh, loss of heterozygosity
- rna-seq, rna sequencing
- rt-pcr, reverse transcriptase – polymerase chain reaction
- snp, single nucleotide polymorphism
- who, world health organization
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Affiliation(s)
- Franck Ah-Pine
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, 4 rue Larrey, 49100 Angers, France
| | - Déborah Casas
- CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France.
| | - Philippe Menei
- Département de Neurochirurgie, CHU Angers, 4 rue Larrey, 49100 Angers, France.
| | - Blandine Boisselier
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, 4 rue Larrey, 49100 Angers, France; CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France
| | - Emmanuel Garcion
- CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France.
| | - Audrey Rousseau
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, 4 rue Larrey, 49100 Angers, France; CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France.
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14
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Cumbo C, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. TP53 in Myelodysplastic Syndromes: Recent Biological and Clinical Findings. Int J Mol Sci 2020; 21:E3432. [PMID: 32414002 PMCID: PMC7279310 DOI: 10.3390/ijms21103432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
TP53 dysregulation plays a pivotal role in the molecular pathogenesis of myelodysplastic syndromes (MDS), identifying a subgroup of patients with peculiar features. In this review we report the recent biological and clinical findings of TP53-mutated MDS, focusing on the molecular pathways activation and on its impact on the cellular physiology. In MDS, TP53 mutational status is deeply associated with del(5q) syndrome and its dysregulation impacts on cell cycle, DNA repair and apoptosis inducing chromosomal instability and the clonal evolution of disease. TP53 defects influence adversely the MDS clinical outcome and the treatment response rate, thus new therapeutic approaches are being developed for these patients. TP53 allelic state characterization and the mutational burden evaluation can therefore predict prognosis and identify the subgroup of patients eligible for targeted therapy. For these reasons, in the era of precision medicine, the MDS diagnostic workup cannot do without the complete assessment of TP53 mutational profile.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy; (C.C.); (G.T.); (L.A.); (A.Z.); (G.S.)
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15
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Berry NK, Scott RJ, Rowlings P, Enjeti AK. Clinical use of SNP-microarrays for the detection of genome-wide changes in haematological malignancies. Crit Rev Oncol Hematol 2019; 142:58-67. [PMID: 31377433 DOI: 10.1016/j.critrevonc.2019.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
Single nucleotide polymorphism (SNP) microarrays are commonly used for the clinical investigation of constitutional genomic disorders; however, their adoption for investigating somatic changes is being recognised. With increasing importance being placed on defining the cancer genome, a shift in technology is imperative at a clinical level. Microarray platforms have the potential to become frontline testing, replacing or complementing standard investigations such as FISH or karyotype. This 'molecular karyotype approach' exemplified by SNP-microarrays has distinct advantages in the investigation of several haematological malignancies. A growing body of literature, including guidelines, has shown support for the use of SNP-microarrays in the clinical laboratory to aid in a more accurate definition of the cancer genome. Understanding the benefits of this technology along with discussing the barriers to its implementation is necessary for the development and incorporation of SNP-microarrays in a clinical laboratory for the investigation of haematological malignancies.
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Affiliation(s)
- Nadine K Berry
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia.
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia
| | - Philip Rowlings
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
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16
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Abstract
BCOR is a gene that encodes for an epigenetic regulator involved in the specification of cell differentiation and body structure development and takes part in the noncanonical polycomb repressive complex 1. This review provides a comprehensive summary of BCOR’s involvement in oncology, illustrating that various BCOR aberrations, such as the internal tandem duplications of the PCGF Ub-like fold discriminator domain and different gene fusions (mainly BCOR–CCNB3, BCOR–MAML3 and ZC3H7B–BCOR), represent driver elements of various sarcomas such as clear cell sarcoma of the kidney, primitive mesenchymal myxoid tumor of infancy, small round blue cell sarcoma, endometrial stromal sarcoma and histologically heterogeneous CNS neoplasms group with similar genomic methylation patterns known as CNS-HGNET-BCOR. Furthermore, other BCOR alterations (often loss of function mutations) recur in a large variety of mesenchymal, epithelial, neural and hematological tumors, suggesting a central role in cancer evolution.
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Affiliation(s)
- Annalisa Astolfi
- 'Giorgio Prodi' Cancer Research Center, University of Bologna, 40138 Bologna, Italy
| | - Michele Fiore
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Fraia Melchionda
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Valentina Indio
- 'Giorgio Prodi' Cancer Research Center, University of Bologna, 40138 Bologna, Italy
| | - Salvatore N Bertuccio
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Andrea Pession
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy.,Department of Medical & Surgical Sciences, University of Bologna, S Orsola-Malpighi Hospital, 40138 Bologna, Italy
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17
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Iacobucci I, Wen J, Meggendorfer M, Choi JK, Shi L, Pounds SB, Carmichael CL, Masih KE, Morris SM, Lindsley RC, Janke LJ, Alexander TB, Song G, Qu C, Li Y, Payne-Turner D, Tomizawa D, Kiyokawa N, Valentine M, Valentine V, Basso G, Locatelli F, Enemark EJ, Kham SKY, Yeoh AEJ, Ma X, Zhou X, Sioson E, Rusch M, Ries RE, Stieglitz E, Hunger SP, Wei AH, To LB, Lewis ID, D'Andrea RJ, Kile BT, Brown AL, Scott HS, Hahn CN, Marlton P, Pei D, Cheng C, Loh ML, Ebert BL, Meshinchi S, Haferlach T, Mullighan CG. Genomic subtyping and therapeutic targeting of acute erythroleukemia. Nat Genet 2019; 51:694-704. [PMID: 30926971 PMCID: PMC6828160 DOI: 10.1038/s41588-019-0375-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
Acute erythroid leukemia (AEL) is a high-risk leukemia of poorly understood genetic basis, with controversy regarding diagnosis in the spectrum of myelodysplasia and myeloid leukemia. We compared genomic features of 159 childhood and adult AEL cases with non-AEL myeloid disorders and defined five age-related subgroups with distinct transcriptional profiles: adult, TP53 mutated; NPM1 mutated; KMT2A mutated/rearranged; adult, DDX41 mutated; and pediatric, NUP98 rearranged. Genomic features influenced outcome, with NPM1 mutations and HOXB9 overexpression being associated with a favorable prognosis and TP53, FLT3 or RB1 alterations associated with poor survival. Targetable signaling mutations were present in 45% of cases and included recurrent mutations of ALK and NTRK1, the latter of which drives erythroid leukemogenesis sensitive to TRK inhibition. This genomic landscape of AEL provides the framework for accurate diagnosis and risk stratification of this disease, and the rationale for testing targeted therapies in this high-risk leukemia.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - John K Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Catherine L Carmichael
- The Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Katherine E Masih
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sarah M Morris
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Virginia Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Giuseppe Basso
- Clinic of Paediatric Haematology and Oncology, Department for Children's and Women's Health, University of Padua, Padua, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Franco Locatelli
- Department of Gynecology/Obstetrics and Pediatrics, Sapienza University of Rome, Rome, Italy
- Department of Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Eric J Enemark
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shirley K Y Kham
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Allen E J Yeoh
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rhonda E Ries
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew H Wei
- The Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Haematology, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - L Bik To
- Departments of Haematology, SA Pathology and Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ian D Lewis
- Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Richard J D'Andrea
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Benjamin T Kile
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Anna L Brown
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Christopher N Hahn
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Paula Marlton
- Princess Alexandra Hospital and University of Queensland School of Clinical Medicine, Brisbane, Queensland, Australia
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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18
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Feurstein S, Thomay K, Hofmann W, Buesche G, Kreipe H, Thol F, Heuser M, Ganser A, Schlegelberger B, Göhring G. Routes of Clonal Evolution into Complex Karyotypes in Myelodysplastic Syndrome Patients with 5q Deletion. Int J Mol Sci 2018; 19:ijms19103269. [PMID: 30347879 PMCID: PMC6214088 DOI: 10.3390/ijms19103269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/01/2023] Open
Abstract
Myelodysplastic syndrome (MDS) can easily transform into acute myeloid leukemia (AML), a process which is often associated with clonal evolution and development of complex karyotypes. Deletion of 5q (del(5q)) is the most frequent aberration in complex karyotypes. This prompted us to analyze clonal evolution in MDS patients with del(5q). There were 1684 patients with low and intermediate-risk MDS and del(5q) with or without one additional cytogenetic abnormality, who were investigated cytogenetically in our department, involving standard karyotyping, fluorescence in situ hybridization (FISH) and multicolor FISH. We identified 134 patients (8%) with aspects of clonal evolution. There are two main routes of cytogenetic clonal evolution: a stepwise accumulation of cytogenetic events over time and a catastrophic event, which we defined as the occurrence of two or more aberrations present at the same time, leading to a sudden development of highly complex clones. Of the 134 patients, 61% underwent a stepwise accumulation of events whereas 39% displayed a catastrophic event. Patients with isolated del(5q) showed significantly more often a stepwise accumulation of events rather than a catastrophic event. The most frequent aberrations in the group of stepwise accumulation were trisomy 8 and trisomy 21 which were significantly more frequent in this group compared to the catastrophic event group. In the group with catastrophic events, del(7q)/-7 and del(17p)/-17 were the most common aberrations. A loss of 17p, containing the tumor suppressor gene TP53, was found significantly more frequent in this group compared to the group of stepwise accumulation. This leads to the assumption that the loss of TP53 is the driving force in patients with del(5q) who undergo a sudden catastrophic event and evolve into complex karyotypes.
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Affiliation(s)
- Simone Feurstein
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 900 E 57th street, Chicago, IL 60637, USA.
| | - Kathrin Thomay
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Guntram Buesche
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Brigitte Schlegelberger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
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19
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Elevated expression of p53 in early colon polyps in a pig model of human familial adenomatous polyposis. J Appl Genet 2018; 59:485-491. [PMID: 30145695 DOI: 10.1007/s13353-018-0461-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 01/02/2023]
Abstract
Familial adenomatous polyposis (FAP) is a hereditary predisposition to formation of colon polyps that can progress to colorectal cancer (CRC). The severity of polyposis varies substantially within families bearing the same germline mutation in the adenomatous polyposis coli (APC) tumour suppressor gene. The progressive step-wise accumulation of genetic events in tumour suppressor genes and oncogenes leads to oncogenic transformation, with driver alterations in the tumour protein p53 (TP53) gene playing a key role in advanced stage CRC. We analysed groups of pigs carrying a truncating mutation in APC (APC1311/+; orthologous to human APC1309/+) to study the influence of TP53 polymorphisms and expression on the frequency of polyp formation and polyp progression in early-stage FAP. Five generations of APC1311/+ pigs were examined by colonoscopy for polyposis severity and development. A total of 19 polymorphisms were found in 5'-flanking, coding, and 3' untranslated regions of TP53. The distribution of TP53 genotypes did not differ between APC1311/+ pigs with low (LP) and high (HP) number of colon polyps. p53 mRNA expression was analysed in distally located normal mucosa samples of wild-type pigs, APC1311/+ LP and HP pigs, and also in distally located polyp samples histologically classified as low-grade (LG-IEN) and high-grade intraepithelial dysplastic (HG-IEN) from APC1311/+ pigs. p53 mRNA expression was found to be significantly elevated in HG-IEN compared to LG-IEN samples (p = 0.012), suggesting a role for p53 in the early precancerous stages of polyp development.
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20
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van Poppelen NM, Yavuzyigitoglu S, Smit KN, Vaarwater J, Eussen B, Brands T, Paridaens D, Kiliç E, de Klein A. Chromosomal rearrangements in uveal melanoma: Chromothripsis. Genes Chromosomes Cancer 2018; 57:452-458. [PMID: 29726589 PMCID: PMC6175119 DOI: 10.1002/gcc.4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 12/22/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in the Western world. Recurrent mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, EIF1AX, and SF3B1 are described as well as non-random chromosomal aberrations. Chromothripsis is a rare event in which chromosomes are shattered and rearranged and has been reported in a variety of cancers including UM. SNP arrays of 249 UM from patients who underwent enucleation, biopsy or endoresection were reviewed for the presence of chromothripsis. Chromothripsis was defined as ten or more breakpoints per chromosome involved. Genetic analysis of GNAQ, GNA11, BAP1, SF3B1, and EIF1AX was conducted using Sanger and next-generation sequencing. In addition, immunohistochemistry for BAP1 was performed. Chromothripsis was detected in 7 out of 249 tumors and the affected chromosomes were chromosomes 3, 5, 6, 8, 12, and 13. The mean total of fragments per chromosome was 39.8 (range 12-116). In 1 UM, chromothripsis was present in 2 different chromosomes. GNAQ, GNA11 or CYSLTR2 mutations were present in 6 of these tumors and 5 tumors harbored a BAP1 mutation and/or lacked BAP1 protein expression by immunohistochemistry. Four of these tumors metastasized and for the fifth only short follow-up data are available. One of these metastatic tumors harbored an SF3B1 mutation. No EIF1AX mutations were detected in any of the tumors. To conclude, chromothripsis is a rare event in UM, occurring in 2.8% of samples and without significant association with mutations in any of the common UM driver genes.
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Affiliation(s)
- Natasha M van Poppelen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Serdar Yavuzyigitoglu
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kyra N Smit
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bert Eussen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tom Brands
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Emine Kiliç
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
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21
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Singh ZN, Richards S, El Chaer F, Duong VH, Gudipati MA, Waters EO, Koon S, Webley M, Pitel B, Hoppman NL, Baer MR, Zou YS. Cryptic ETV6–PDGFRB fusion in a highly complex rearrangement of chromosomes 1, 5, and 12 due to a chromothripsis-like event in a myelodysplastic syndrome/myeloproliferative neoplasm. Leuk Lymphoma 2018; 60:1304-1307. [DOI: 10.1080/10428194.2018.1480774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Zeba N. Singh
- Department of Pathology, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Stephanie Richards
- Department of Pathology, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Firas El Chaer
- Department of Medicine, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Vu H. Duong
- Department of Medicine, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Mary A. Gudipati
- Department of Pathology, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Elizabeth O. Waters
- Department of Pathology, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Sarah Koon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew Webley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Beth Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L. Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Maria R. Baer
- Department of Medicine, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Ying S. Zou
- Department of Pathology, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
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22
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Luijten MNH, Lee JXT, Crasta KC. Mutational game changer: Chromothripsis and its emerging relevance to cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:29-51. [PMID: 30115429 DOI: 10.1016/j.mrrev.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022]
Abstract
In recent years, the paradigm that genomic abnormalities in cancer cells arise through progressive accumulation of mutational events has been challenged by the discovery of single catastrophic events. One such phenomenon termed chromothripsis, involving massive chromosomal rearrangements arising all at once, has emerged as a major mutational game changer. The strong interest in this process stems from its widespread association with a range of cancer types and its potential as a mutational driver. In this review, we first describe chromothripsis detection and incidence in cancers. We then explore recently proposed underlying mechanistic origins, which explain the curious observations of the highly localised nature of the rearrangements on chromothriptic chromosomes. Detection of chromothriptic patterns following incorporation of single chromosomes into micronuclei or following telomere attrition have greatly contributed to our understanding of the reasons behind this chromosomal restriction. These underlying cellular events have been found to be participants in the tumourigenic process, strongly suggesting a potential role for chromothripsis in cancer development. Thus, we discuss potential implications of chromothripsis for cancer progression and therapy.
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Affiliation(s)
| | - Jeannie Xue Ting Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.
| | - Karen Carmelina Crasta
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, 61 Biopolis Drive, 138673, Singapore; Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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23
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Sequential immunotherapy in a patient with primary refractory Hodgkin lymphoma and novel mutations. Oncotarget 2018; 9:20928-20940. [PMID: 29755699 PMCID: PMC5945535 DOI: 10.18632/oncotarget.25037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Primary resistant Hodgkin lymphoma is an aggressive disease with few treatment options and short survival. Neoplastic cells of classical Hodgkin lymphoma are heavily dependent on microenvironmental stimuli, regularly express PD-L1, and a relevant proportion of relapsed patients is sensitive to blocking of the PD1/PD-L1 axis. However, response duration is limited and further treatment options are unknown but urgently needed. We report a case of a patient without relevant response to five subsequent chemotherapy regimens who immediately and dramatically responded to an anti-PD1 mab. During the following two years she responded to the anti-CTLA-4 mab ipilimumab, the Jak2 inhibitor ruxolitinib, and a combination of lenalidomide plus cyclophosphamide given in subsequent relapses. A thorough genomic analysis demonstrated seven genomic alterations with six of them not previously described in this disease (i.e. BRIP1 G212fs*62, KRAS L19F, KDM5A R1239W, MYC A59T, ARIDA1A E1683fs*15 and TP53 277Y). Three alterations were considered actionable and one of them drugable. The number of mutations increased over time and the BRIP1 mutation was found to be a germline mutation.
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24
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Marcozzi A, Pellestor F, Kloosterman WP. The Genomic Characteristics and Origin of Chromothripsis. Methods Mol Biol 2018; 1769:3-19. [PMID: 29564814 DOI: 10.1007/978-1-4939-7780-2_1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In 2011 a phenomenon involving complex chromosomal rearrangements was discovered in cancer genomes. This phenomenon has been termed chromothripsis, on the basis of its chromosomal hallmarks, which point to an underlying process involving chromosome (chromo) shattering (thripsis). The prevailing hypothesis of cancer genome evolution as a gradual process of mutation and selection was challenged by the discovery of chromothripsis, because its patterns of chromosome rearrangement rather indicated an one-off catastrophic burst of genome rearrangement. The initial discovery of chromothripsis has led to many more examples of chromothripsis both in cancer genomes as well as in patients with congenital diseases and in the genomes of healthy individuals. Since then, a burning topic has been the study of the molecular mechanism that leads to chromothripsis. Cumulating evidence has shown that chromothripsis may result from lagging chromosomes encapsulated in micronuclei, as well as from telomere fusions followed by chromosome bridge formation. In this chapter, we will outline the genomic characteristics of chromothripsis, and we present genomic methodologies that enable the detection of chromothripsis. Furthermore, we will give an overview of recent insights into the mechanisms underlying chromothripsis.
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Affiliation(s)
- Alessio Marcozzi
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franck Pellestor
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France.,INSERM Unit Plasticity of the Genome and Aging, Institute of Functional Genomics, Montpellier, France
| | - Wigard P Kloosterman
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
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25
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Berry NK, Dixon-McIver A, Scott RJ, Rowlings P, Enjeti AK. Detection of complex genomic signatures associated with risk in plasma cell disorders. Cancer Genet 2017; 218-219:1-9. [PMID: 29153091 DOI: 10.1016/j.cancergen.2017.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/30/2017] [Accepted: 08/06/2017] [Indexed: 01/10/2023]
Abstract
Plasma cell disorders (PCD) range from benign to highly malignant disease. The ability to detect risk-stratifying aberrations based on cytogenetic and molecular genetic assays plays an increasing role in therapeutic decision making. In this study, 58 patients were chosen for screening by comparative genomic hybridisation microarray (aCGH) to identify the new high-risk prognostic markers of chromothripsis and chromoanasynthesis. All patients had an unequivocal clinical diagnosis of a plasma cell disorder (plasma cell myeloma (PCM)(n = 51) or monoclonal gammopathy of undetermined significance (MGUS)(n = 7)) and an abnormal FISH result. There were a total of 17 complex genomic events identified across 9 patient samples, which were selected for further investigation by high definition single nucleotide polymorphism (HD-SNP) microarray. Each event was analysed and characterised for chromothripsis, chromoanasynthesis or a complex step-wise chromosomal event. We describe an effective method to identify the new high-risk prognostic markers of chromothripsis and chromoanasynthesis in plasma cell disorders.
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Affiliation(s)
- Nadine K Berry
- Department of Hematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.
| | | | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia; Department of Molecular Medicine, Pathology North Newcastle, Rankin Park, New South Wales, Australia
| | - Philip Rowlings
- Department of Hematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Hematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
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26
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New Insights in the Cytogenetic Practice: Karyotypic Chaos, Non-Clonal Chromosomal Alterations and Chromosomal Instability in Human Cancer and Therapy Response. Genes (Basel) 2017; 8:genes8060155. [PMID: 28587191 PMCID: PMC5485519 DOI: 10.3390/genes8060155] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022] Open
Abstract
Recently, non-clonal chromosomal alterations previously unappreciated are being proposed to be included in cytogenetic practice. The aim of this inclusion is to obtain a greater understanding of chromosomal instability (CIN) and tumor heterogeneity and their role in cancer evolution and therapy response. Although several genetic assays have allowed the evaluation of the variation in a population of cancer cells, these assays do not provide information at the level of individual cells, therefore limiting the information of the genomic diversity within tumors (heterogeneity). The karyotype is one of the few available cytogenetic techniques that allow us not only to identify the chromosomal alterations present within a single cell, but also allows us to profile both clonal (CCA) and non-clonal chromosomal alterations (NCCAs). A greater understanding of CIN and tumor heterogeneity in cancer could not only improve existing therapeutic regimens but could also be used as targets for the design of new therapeutic approaches. In this review we indicate the importance and significance of karyotypic chaos, NCCAs and CIN in the prognosis of human cancers.
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27
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Song Q, Peng M, Chu Y, Huang S. Techniques for detecting chromosomal aberrations in myelodysplastic syndromes. Oncotarget 2017; 8:62716-62729. [PMID: 28977983 PMCID: PMC5617543 DOI: 10.18632/oncotarget.17698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/19/2017] [Indexed: 11/25/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic diseases. Chromosomal aberrations are important for the initiation, development, and progression of MDS. Detection of chromosomal abnormalities in MDS is important for categorization, risk stratification, therapeutic selection, and prognosis evaluation of the disease. Recent progress of multiple techniques has brought powerful molecular cytogenetic information to reveal copy number variation, uniparental disomy, and complex chromosomal aberrations in MDS. In this review, we will introduce some common chromosomal aberrations in MDS and their clinical significance. Then we will explain the application, advantages, and limitations of different techniques for detecting chromosomal abnormalities in MDS. The information in this review may be helpful for clinicians to select appropriate methods in patient-related decision making.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar Global, Wuhan, China
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28
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Richter-Pechańska P, Kunz JB, Hof J, Zimmermann M, Rausch T, Bandapalli OR, Orlova E, Scapinello G, Sagi JC, Stanulla M, Schrappe M, Cario G, Kirschner-Schwabe R, Eckert C, Benes V, Korbel JO, Muckenthaler MU, Kulozik AE. Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia. Blood Cancer J 2017; 7:e523. [PMID: 28157215 PMCID: PMC5386337 DOI: 10.1038/bcj.2017.3] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
In the search for genes that define critical steps of relapse in pediatric T-cell acute lymphoblastic leukemia (T-ALL) and can serve as prognostic markers, we performed targeted sequencing of 313 leukemia-related genes in 214 patients: 67 samples collected at the time of relapse and 147 at initial diagnosis. As relapse-specific genetic events, we identified activating mutations in NT5C2 (P=0.0001, Fisher's exact test), inactivation of TP53 (P=0.0007, Fisher's exact test) and duplication of chr17:q11.2-24.3 (P=0.0068, Fisher's exact test) in 32/67 of T-ALL relapse samples. Alterations of TP53 were frequently homozygous events, which significantly correlated with higher rates of copy number alterations in other genes compared with wild-type TP53 (P=0.0004, Mann–Whitney's test). We subsequently focused on mutations with prognostic impact and identified genes governing DNA integrity (TP53, n=8; USP7, n=4; MSH6, n=4), having key roles in the RAS signaling pathway (KRAS, NRAS, n=8), as well as IL7R (n=4) and CNOT3 (n=4) to be exclusively mutated in fatal relapses. These markers recognize 24/49 patients with a second event. In 17 of these patients with mostly refractory relapse and dire need for efficient treatment, we identified candidate targets for personalized therapy with p53 reactivating compounds, MEK inhibitors or JAK/STAT-inhibitors that may be incorporated in future treatment strategies.
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Affiliation(s)
- P Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - J B Kunz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - J Hof
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - M Zimmermann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - T Rausch
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - O R Bandapalli
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - E Orlova
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - G Scapinello
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,University of Padua, Padua, Italy
| | - J C Sagi
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - M Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - M Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - G Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - R Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - C Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - V Benes
- European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - J O Korbel
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - M U Muckenthaler
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - A E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
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