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Lagunas-Rangel FA. Chromothripsis in hematologic malignancies. Exp Hematol 2024; 132:104172. [PMID: 38309572 DOI: 10.1016/j.exphem.2024.104172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Chromotrypsis, a phenomenon resulting from catastrophic mitotic errors and genomic instability, is defined by the occurrence of multiple DNA double-strand breaks in one or more chromosomes, subsequently subject to error-prone repair mechanisms. This unique process results in extensive rearrangements in the affected chromosomes, leading to loss of tumor suppressor function, the creation of fusion genes, and/or activation of oncogenes. The importance of chromothripsis in cancer, especially in the field of hematologic disorders, underscores the intricate interplay between genomic instability and the genesis of alterations that contribute to cancer. This accentuates the critical need to unravel these complex processes for the targeted development of specific therapeutic interventions. This review delves into the analysis of chromothripsis cases in various hematologic diseases, such as leukemia, lymphoma, and myeloma, with the aim of unveiling its profound impact on patient prognosis. Furthermore, the study explores the intricate molecular mechanisms underlying chromothripsis and investigates its consequences.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico.
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Kardian AS, Mack S. The Intersection of Epigenetic Alterations and Developmental State in Pediatric Ependymomas. Dev Neurosci 2024:000537694. [PMID: 38527429 DOI: 10.1159/000537694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/03/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Ependymomas are the third most common brain cancer in children and have no targeted therapies. They are divided into at least 9 major subtypes based on molecular characteristics and major drivers and have few genetic mutations compared to the adult form of this disease, leading to investigation of other mechanisms. SUMMARY Epigenetic alterations such as transcriptional programs activated by oncofusion proteins and alterations in histone modifications play an important role in development of this disease. Evidence suggests these alterations interact with the developmental epigenetic programs in the cell of origin to initiate neoplastic transformation and later disease progression, perhaps by keeping a portion of tumor cells in a developmental, proliferative state. KEY MESSAGES To better understand this disease, research on its developmental origins and associated epigenetic states needs to be further pursued. This could lead to better treatments, which are currently lacking due to the difficult-to-drug nature of known drivers such as fusion proteins. Epigenetic and developmental states characteristic of these tumors may not just be potential therapeutic targets, but used as a tool to find new avenues of treatment.
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Krupina K, Goginashvili A, Cleveland DW. Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements. Nat Rev Genet 2024; 25:196-210. [PMID: 37938738 PMCID: PMC10922386 DOI: 10.1038/s41576-023-00663-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 11/09/2023]
Abstract
Complex chromosome rearrangements, known as chromoanagenesis, are widespread in cancer. Based on large-scale DNA sequencing of human tumours, the most frequent type of complex chromosome rearrangement is chromothripsis, a massive, localized and clustered rearrangement of one (or a few) chromosomes seemingly acquired in a single event. Chromothripsis can be initiated by mitotic errors that produce a micronucleus encapsulating a single chromosome or chromosomal fragment. Rupture of the unstable micronuclear envelope exposes its chromatin to cytosolic nucleases and induces chromothriptic shattering. Found in up to half of tumours included in pan-cancer genomic analyses, chromothriptic rearrangements can contribute to tumorigenesis through inactivation of tumour suppressor genes, activation of proto-oncogenes, or gene amplification through the production of self-propagating extrachromosomal circular DNAs encoding oncogenes or genes conferring anticancer drug resistance. Here, we discuss what has been learned about the mechanisms that enable these complex genomic rearrangements and their consequences in cancer.
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Affiliation(s)
- Ksenia Krupina
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Alexander Goginashvili
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
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Lestringant V, Guermouche-Flament H, Jimenez-Pocquet M, Gaillard JB, Penther D. Cytogenetics in the management of hematological malignancies: An overview of alternative technologies for cytogenetic characterization. Curr Res Transl Med 2024; 72:103440. [PMID: 38447270 DOI: 10.1016/j.retram.2024.103440] [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: 07/10/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Genomic characterization is an essential part of the clinical management of hematological malignancies for diagnostic, prognostic and therapeutic purposes. Although CBA and FISH are still the gold standard in hematology for the detection of CNA and SV, some alternative technologies are intended to complement their deficiencies or even replace them in the more or less near future. In this article, we provide a technological overview of these alternatives. CMA is the historical and well established technique for the high-resolution detection of CNA. For SV detection, there are emerging techniques based on the study of chromatin conformation and more established ones such as RTMLPA for the detection of fusion transcripts and RNA-seq to reveal the molecular consequences of SV. Comprehensive techniques that detect both CNA and SV are the most interesting because they provide all the information in a single examination. Among these, OGM is a promising emerging higher-solution technique that offers a complete solution at a contained cost, at the expense of a relatively low throughput per machine. WGS remains the most adaptable solution, with long-read approaches enabling very high-resolution detection of CAs, but requiring a heavy bioinformatics installation and at a still high cost. However, the development of high-resolution genome-wide detection techniques for CAs allows for a much better description of chromoanagenesis. Therefore, we have included in this review an update on the various existing mechanisms and their consequences and implications, especially prognostic, in hematological malignancies.
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Affiliation(s)
| | | | | | - Jean-Baptiste Gaillard
- Unité de Génétique Chromosomique, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Montpellier, France
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Zheng R, Fuda F, Gagan JR, Weinberg OK, Koduru P, Cantu M, Ludwig K, Truscott JM, Collins R, Chung S, Madanat YF, Chen W. Genomic heterogeneity within B/T mixed phenotype acute leukemia in a context of an immunophenotype. Leuk Res Rep 2023; 21:100410. [PMID: 38273970 PMCID: PMC10808966 DOI: 10.1016/j.lrr.2023.100410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/19/2023] [Accepted: 12/29/2023] [Indexed: 01/27/2024] Open
Abstract
B/T mixed phenotype acute leukemia (MPAL) is a rare aggressive leukemia. Three cases of B/T MPAL were identified with comprehensive immunophenotypic, cytogenetic, and molecular studies. T-lineage predominant B/T MPAL shares a genetic signature with T-ALL whereas B/T lineage co-dominant B/T MPAL lacks such a T-ALL signature. All three patients were treated with lineage-matched-ALL therapy and alive at the last follow-up. Our study is the first to demonstrate molecular heterogeneity within B/T MPAL in a context of an immunophenotype of T-lineage versus B-lineage predominance. The implication of such a phenotype-genotype association on diagnostic classification is briefly discussed.
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Affiliation(s)
- Ruifang Zheng
- Departments of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Franklin Fuda
- Departments of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey R. Gagan
- Departments of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Olga K. Weinberg
- Departments of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prasad Koduru
- Departments of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miguel Cantu
- Departments of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kathleen Ludwig
- Departments of Pediatrics (Hematology and Oncology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jamie M. Truscott
- Departments of Pediatrics (Hematology and Oncology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert Collins
- Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stephen Chung
- Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yazan F. Madanat
- Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Weina Chen
- Departments of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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De Bie J, Quessada J, Tueur G, Lefebvre C, Luquet I, Toujani S, Cuccuini W, Lafage-Pochitaloff M, Michaux L. Cytogenetics in the management of T-cell acute lymphoblastic leukemia (T-ALL): Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103431. [PMID: 38016418 DOI: 10.1016/j.retram.2023.103431] [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: 07/03/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Molecular analysis is the hallmark of T-cell acute lymphoblastic leukemia (T-ALL) categorization. Several T-ALL sub-groups are well recognized based on the aberrant expression of specific transcription factors. This recently resulted in the implementation of eight provisional T-ALL entities into the novel 2022 International Consensus Classification, albeit not into the updated World Health Organization classification system. Despite this extensive molecular characterization, cytogenetic analysis remains the backbone of T-ALL diagnosis in many countries as chromosome banding analysis and fluorescence in situ hybridization are relatively inexpensive techniques to obtain results of diagnostic, prognostic and therapeutic interest. Here, we provide an overview of recurrent chromosomal abnormalities detectable in T-ALL patients and propose guidelines regarding their detection. By referring in parallel to the more general molecular classification approach, we hope to offer a diagnostic framework useful in a broad clinical genetic setting.
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Affiliation(s)
- Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Saloua Toujani
- Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, Rennes 35033, France
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium.
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