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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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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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Lu J, Li J, Ren J, Ding S, Zeng Z, Huang T, Cai YD. Functional and embedding feature analysis for pan-cancer classification. Front Oncol 2022; 12:979336. [PMID: 36248961 PMCID: PMC9559388 DOI: 10.3389/fonc.2022.979336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
With the increasing number of people suffering from cancer, this illness has become a major health problem worldwide. Exploring the biological functions and signaling pathways of carcinogenesis is essential for cancer detection and research. In this study, a mutation dataset for eleven cancer types was first obtained from a web-based resource called cBioPortal for Cancer Genomics, followed by extracting 21,049 features from three aspects: relationship to GO and KEGG (enrichment features), mutated genes learned by word2vec (text features), and protein-protein interaction network analyzed by node2vec (network features). Irrelevant features were then excluded using the Boruta feature filtering method, and the retained relevant features were ranked by four feature selection methods (least absolute shrinkage and selection operator, minimum redundancy maximum relevance, Monte Carlo feature selection and light gradient boosting machine) to generate four feature-ranked lists. Incremental feature selection was used to determine the optimal number of features based on these feature lists to build the optimal classifiers and derive interpretable classification rules. The results of four feature-ranking methods were integrated to identify key functional pathways, such as olfactory transduction (hsa04740) and colorectal cancer (hsa05210), and the roles of these functional pathways in cancers were discussed in reference to literature. Overall, this machine learning-based study revealed the altered biological functions of cancers and provided a reference for the mechanisms of different cancers.
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Affiliation(s)
- Jian Lu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - JiaRui Li
- Advanced Research Computing, University of British Columbia, Vancouver, BC, Canada
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Shijian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
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