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Simovic-Lorenz M, Ernst A. Chromothripsis in cancer. Nat Rev Cancer 2025; 25:79-92. [PMID: 39548283 DOI: 10.1038/s41568-024-00769-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/16/2024] [Indexed: 11/17/2024]
Abstract
Chromothripsis is a mutational phenomenon in which a single catastrophic event generates extensive rearrangements of one or a few chromosomes. This extreme form of genome instability has been detected in 30-50% of cancers. Studies conducted in the past few years have uncovered insights into how chromothripsis arises and deciphered some of the cellular and molecular consequences of chromosome shattering. This Review discusses the defining features of chromothripsis and describes its prevalence across different cancer types as indicated by the manifestations of chromothripsis detected in human cancer samples. The different mechanistic models of chromothripsis, derived from in vitro systems that enable causal inference through experimental manipulation, are discussed in detail. The contribution of chromothripsis to cancer development, the selective advantages that cancer cells might gain from chromothripsis, the evolutionary trajectories of chromothriptic tumours, and the potential vulnerabilities and therapeutic opportunities presented by chromothriptic cells are also highlighted.
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Affiliation(s)
- Milena Simovic-Lorenz
- Group Genome Instability in Tumors, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aurélie Ernst
- Group Genome Instability in Tumors, German Cancer Research Center, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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2
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Colombino M, Casula M, Paliogiannis P, Manca A, Sini MC, Pisano M, Santeufemia DA, Cossu A, Palmieri G. Heterogeneous pathogenesis of melanoma: BRAF mutations and beyond. Crit Rev Oncol Hematol 2024; 201:104435. [PMID: 38977143 DOI: 10.1016/j.critrevonc.2024.104435] [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: 01/31/2024] [Revised: 05/22/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024] Open
Abstract
Melanoma pathogenesis, conventionally perceived as a linear accumulation of molecular changes, discloses substantial heterogeneity driven by non-linear biological processes, including the direct transformation of melanocyte stem cells. This heterogeneity manifests in diverse biological phenotypes and developmental states, influencing variable responses to treatments. Unveiling the aberrant mechanisms steering melanoma initiation, progression, and metastasis is imperative. Beyond mutations in oncogenic and tumor suppressor genes, the involvement of distinct molecular pathways assumes a pivotal role in melanoma pathogenesis. Ultraviolet (UV) radiations, a principal factor in melanoma etiology, categorizes melanomas based on cumulative sun damage (CSD). The genomic landscape of lesions correlates with UV exposure, impacting mutational load and spectrum of mutations. The World Health Organization's 2018 classification underscores the interplay between sun exposure and genomic characteristics, distinguishing melanomas associated with CSD from those unrelated to CSD. The classification elucidates molecular features such as tumor mutational burden and copy number alterations associated with different melanoma subtypes. The significance of the mutated BRAF gene and its pathway, notably BRAFV600 variants, in melanoma is paramount. BRAF mutations, prevalent across diverse cancer types, present therapeutic avenues, with clinical trials validating the efficacy of targeted therapies and immunotherapy. Additional driver mutations in oncogenes further characterize specific melanoma pathways, impacting tumor behavior. While histopathological examination remains pivotal, challenges persist in molecularly classifying melanocytic tumors. In this review, we went through all molecular characterization that aid in discriminating common and ambiguous lesions. Integration of highly sensitive molecular diagnostic tests into the diagnostic workflow becomes indispensable, particularly in instances where histology alone fails to achieve a conclusive diagnosis. A diagnostic algorithm based on different molecular features inferred by the various studies is here proposed.
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Affiliation(s)
- Maria Colombino
- Unit of Cancer Genetics, Institute of Genetic Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy.
| | - Milena Casula
- Unit of Cancer Genetics, Institute of Genetic Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | | | - Antonella Manca
- Unit of Cancer Genetics, Institute of Genetic Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Maria Cristina Sini
- Unit of Cancer Genetics, Institute of Genetic Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Marina Pisano
- Unit of Cancer Genetics, Institute of Genetic Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | | | - Antonio Cossu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Genetic Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy; Immuno-Oncology & Targeted Cancer Biotherapies, University of Sassari, Sassari, Italy
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3
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Richardson TE, Walker JM, Hambardzumyan D, Brem S, Hatanpaa KJ, Viapiano MS, Pai B, Umphlett M, Becher OJ, Snuderl M, McBrayer SK, Abdullah KG, Tsankova NM. Genetic and epigenetic instability as an underlying driver of progression and aggressive behavior in IDH-mutant astrocytoma. Acta Neuropathol 2024; 148:5. [PMID: 39012509 PMCID: PMC11252228 DOI: 10.1007/s00401-024-02761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
In recent years, the classification of adult-type diffuse gliomas has undergone a revolution, wherein specific molecular features now represent defining diagnostic criteria of IDH-wild-type glioblastomas, IDH-mutant astrocytomas, and IDH-mutant 1p/19q-codeleted oligodendrogliomas. With the introduction of the 2021 WHO CNS classification, additional molecular alterations are now integrated into the grading of these tumors, given equal weight to traditional histologic features. However, there remains a great deal of heterogeneity in patient outcome even within these established tumor subclassifications that is unexplained by currently codified molecular alterations, particularly in the IDH-mutant astrocytoma category. There is also significant intercellular genetic and epigenetic heterogeneity and plasticity with resulting phenotypic heterogeneity, making these tumors remarkably adaptable and robust, and presenting a significant barrier to the design of effective therapeutics. Herein, we review the mechanisms and consequences of genetic and epigenetic instability, including chromosomal instability (CIN), microsatellite instability (MSI)/mismatch repair (MMR) deficits, and epigenetic instability, in the underlying biology, tumorigenesis, and progression of IDH-mutant astrocytomas. We also discuss the contribution of recent high-resolution transcriptomics studies toward defining tumor heterogeneity with single-cell resolution. While intratumoral heterogeneity is a well-known feature of diffuse gliomas, the contribution of these various processes has only recently been considered as a potential driver of tumor aggressiveness. CIN has an independent, adverse effect on patient survival, similar to the effect of histologic grade and homozygous CDKN2A deletion, while MMR mutation is only associated with poor overall survival in univariate analysis but is highly correlated with higher histologic/molecular grade and other aggressive features. These forms of genomic instability, which may significantly affect the natural progression of these tumors, response to therapy, and ultimately clinical outcome for patients, are potentially measurable features which could aid in diagnosis, grading, prognosis, and development of personalized therapeutics.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA.
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Neurosurgery, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Balagopal Pai
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
| | - Oren J Becher
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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Zhang M, He D, Zhang Y, Cheng K, Li H, Zhou Y, Long Q, Liu R, Liu J. Chromothripsis is a novel biomarker for prognosis and differentiation diagnosis of pancreatic neuroendocrine neoplasms. MedComm (Beijing) 2024; 5:e623. [PMID: 38988495 PMCID: PMC11234462 DOI: 10.1002/mco2.623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/22/2024] [Accepted: 05/20/2024] [Indexed: 07/12/2024] Open
Abstract
This study aimed to identify the role of chromothripsis as a novel biomarker in the prognosis and differentiation diagnosis of pancreatic neuroendocrine neoplasms (pNENs). We conducted next-generation gene sequencing in a cohort of 30 patients with high-grade (G3) pNENs. As a reference, a similar analysis was also performed on 25 patients with low-grade (G1/G2) pancreatic neuroendocrine tumors (pNETs). Chromothripsis and its relationship with clinicopathological features and prognosis were investigated. The results showed that DNA damage response and repair gene alteration and TP53 mutation were found in 29 and 11 patients, respectively. A total of 14 out of 55 patients had chromothripsis involving different chromosomes. Chromothripsis had a close relationship with TP53 alteration and higher grade. In the entire cohort, chromothripsis was associated with a higher risk of distant metastasis; both chromothripsis and metastasis (ENETS Stage IV) suggested a significantly shorter overall survival (OS). Importantly, in the high-grade pNENs group, chromothripsis was the only independent prognostic indicator significantly associated with a shorter OS, other than TP53 alteration or pathological pancreatic neuroendocrine carcinomas (pNECs) diagnosis. Chromothripsis can guide worse prognosis in pNENs, and help differentiate pNECs from high-grade (G3) pNETs.
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Affiliation(s)
- Ming‐Yi Zhang
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Du He
- Department of Pathology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yi Zhang
- Center of Life SciencesPeking UniversityBeijingChina
| | - Ke Cheng
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Hong‐Shuai Li
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yu‐Wen Zhou
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Qiong‐Xian Long
- Department of Pathology, Nan Chong Central Hospitalthe Second Affiliated Hospital of North Sichuan Medical CollegeNanchongSichuanChina
| | - Rui‐Zhi Liu
- School of Medical and Life SciencesChengdu University of Traditional Chinese MedicineChengduSichuanChina
| | - Ji‐Yan Liu
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
- Sichuan Clinical Research Center of BiotherapyChengduSichuanChina
- Department of OncologyThe First People's Hospital of ZiyangZiyangSichuanChina
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Takimoto N, Ishii Y, Mitsumoto T, Takasu S, Namiki M, Shibutani M, Ogawa K. Formation of hepatocyte cytoplasmic inclusions and their contribution to methylcarbamate-induced hepatocarcinogenesis in F344 rats. Toxicol Sci 2024; 198:40-49. [PMID: 38230821 DOI: 10.1093/toxsci/kfad131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Methylcarbamate (MC), a reaction product between dimethyl dicarbonate and ammonia or ammonium ion, is a potent hepatocarcinogen in F344 rats. Various genotoxicity tests have shown negative results for MC. Although previous studies have described the effects of MC on the liver, including the formation of characteristic basophilic cytoplasmic inclusions (CIs) in hepatocytes, the toxicological significance of CIs and their involvement in hepatocarcinogenesis remain unclear. In the current study, to elucidate the mechanisms of MC hepatocarcinogenesis, we examined hepatotoxicity and genotoxicity after 4 weeks of administration of MC using gpt delta rats with an F344 genetic background as a reporter gene transgenic animal model. Histopathologically, single-cell necrosis, karyomegaly, and the formation of CIs positive for Feulgen staining were observed in hepatocytes at the carcinogenic dose, demonstrating the hepatotoxicity of MC. CIs were also detected as large micronuclei in liver micronucleus tests but not in the bone marrow, suggesting that MC could cause chromosomal instability specifically in the livers of rats. Reporter gene mutation assays demonstrated that MC did not induce mutagenicity even in the liver. Immunofluorescence analyses revealed that CIs exhibited loss of nuclear envelope integrity, increased heterochromatinization, and accumulation of DNA damage. An increase in liver STING protein levels suggested an effect on the cyclic GMP-AMP synthase/stimulator of interferon genes innate immune pathway. Overall, these data demonstrated the possible occurrence of chromothripsis-like chromosomal rearrangements via CIs. Thus, the formation of CIs could be a crucial event in the early stage of MC-induced hepatocarcinogenesis in F344 rats.
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Affiliation(s)
- Norifumi Takimoto
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yuji Ishii
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Tatsuya Mitsumoto
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachioji, Tokyo 192-0364, Japan
| | - Shinji Takasu
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Moeka Namiki
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Makoto Shibutani
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Kumiko Ogawa
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
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Sourty B, Basset L, Fontaine A, Garcion E, Rousseau A. Chromothripsis is rare in IDH-mutant gliomas compared to IDH-wild-type glioblastomas whereas whole-genome duplication is equally frequent in both tumor types. Neurooncol Adv 2024; 6:vdae059. [PMID: 38800696 PMCID: PMC11125406 DOI: 10.1093/noajnl/vdae059] [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] [Indexed: 05/29/2024] Open
Abstract
Background Adult-type diffuse gliomas comprise IDH (isocitrate dehydrogenase)-mutant astrocytomas, IDH-mutant 1p/19q-codeleted oligodendrogliomas (ODG), and IDH-wild-type glioblastomas (GBM). GBM displays genome instability, which may result from 2 genetic events leading to massive chromosome alterations: Chromothripsis (CT) and whole-genome duplication (WGD). These events are scarcely described in IDH-mutant gliomas. The better prognosis of the latter may be related to their genome stability compared to GBM. Methods Pangenomic profiles of 297 adult diffuse gliomas were analyzed at initial diagnosis using SNP arrays, including 192 GBM and 105 IDH-mutant gliomas (61 astrocytomas and 44 ODG). Tumor ploidy was assessed with Genome Alteration Print and CT events with CTLPScanner and through manual screening. Survival data were compared using the Kaplan-Meier method. Results At initial diagnosis, 37 GBM (18.7%) displayed CT versus 5 IDH-mutant gliomas (4.7%; P = .0008), the latter were all high-grade (grade 3 or 4) astrocytomas. WGD was detected at initial diagnosis in 18 GBM (9.3%) and 9 IDH-mutant gliomas (5 astrocytomas and 4 oligodendrogliomas, either low- or high-grade; 8.5%). Neither CT nor WGD was associated with overall survival in GBM or in IDH-mutant gliomas. Conclusions CT is less frequent in IDH-mutant gliomas compared to GBM. The absence of CT in ODG and grade 2 astrocytomas might, in part, explain their genome stability and better prognosis, while CT might underlie aggressive biological behavior in some high-grade astrocytomas. WGD is a rare and early event occurring equally in IDH-mutant gliomas and GBM.
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Affiliation(s)
- Baptiste Sourty
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Laëtitia Basset
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Alix Fontaine
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Emmanuel Garcion
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
| | - Audrey Rousseau
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
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Lanceta J, Tripodi J, Karp L, Shaham M, Mahmood N, Najfeld V, Edelman M, Cohen N. Chromothripsis in lipoblastoma: second reported case with complex PLAG1 rearrangement. Mol Cytogenet 2023; 16:32. [PMID: 38012697 PMCID: PMC10683218 DOI: 10.1186/s13039-023-00665-x] [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: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Lipoblastomas (LPBs) are rare benign neoplasms derived from embryonal adipose that occur predominantly in childhood. LPBs typically present with numeric or structural rearrangements of chromosome 8, the majority of which involve the pleomorphic adenoma gene 1 (PLAG1) proto-oncogene on chromosome 8q12. Here, we report on a LPB case on which showed evidence of chromothripsis. This is the second reported case of chromothripsis in LPB.
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Affiliation(s)
- Joel Lanceta
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA.
| | - Joseph Tripodi
- Tumor CytoGenomics, Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynne Karp
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
| | - Meira Shaham
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
| | - Nayyara Mahmood
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
| | - Vesna Najfeld
- Tumor CytoGenomics, Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Morris Edelman
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Pediatric Pathology, Cohen Children's Medical Center, New Hyde Park, NY, USA
| | - Ninette Cohen
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
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Yu J, Chen N, Zheng Z, Gao M, Liang N, Wong KC. Chromothripsis detection with multiple myeloma patients based on deep graph learning. Bioinformatics 2023; 39:btad422. [PMID: 37399092 PMCID: PMC10343948 DOI: 10.1093/bioinformatics/btad422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023] Open
Abstract
MOTIVATION Chromothripsis, associated with poor clinical outcomes, is prognostically vital in multiple myeloma. The catastrophic event is reported to be detectable prior to the progression of multiple myeloma. As a result, chromothripsis detection can contribute to risk estimation and early treatment guidelines for multiple myeloma patients. However, manual diagnosis remains the gold standard approach to detect chromothripsis events with the whole-genome sequencing technology to retrieve both copy number variation (CNV) and structural variation data. Meanwhile, CNV data are much easier to obtain than structural variation data. Hence, in order to reduce the reliance on human experts' efforts and structural variation data extraction, it is necessary to establish a reliable and accurate chromothripsis detection method based on CNV data. RESULTS To address those issues, we propose a method to detect chromothripsis solely based on CNV data. With the help of structure learning, the intrinsic relationship-directed acyclic graph of CNV features is inferred to derive a CNV embedding graph (i.e. CNV-DAG). Subsequently, a neural network based on Graph Transformer, local feature extraction, and non-linear feature interaction, is proposed with the embedding graph as the input to distinguish whether the chromothripsis event occurs. Ablation experiments, clustering, and feature importance analysis are also conducted to enable the proposed model to be explained by capturing mechanistic insights. AVAILABILITY AND IMPLEMENTATION The source code and data are freely available at https://github.com/luvyfdawnYu/CNV_chromothripsis.
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Affiliation(s)
- Jixiang Yu
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Nanjun Chen
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Zetian Zheng
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Ming Gao
- School of Management Science and Engineering, Dongbei University of Finance and Economics, Dalian 116025, China
| | - Ning Liang
- University of Michigan, Ann Arbor, MI 48105, United States
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Hong Kong Institute for Data Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
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9
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Seong G, Wu A, Kim C, Pathak N, Yakut E, Li Z, Chiu E. Metastatic Adrenocortical Carcinoma With Chromothripsis: A Case Report and Literature Review. Cureus 2023; 15:e41218. [PMID: 37397681 PMCID: PMC10313339 DOI: 10.7759/cureus.41218] [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] [Accepted: 06/30/2023] [Indexed: 07/04/2023] Open
Abstract
Metastatic adrenocortical carcinoma (ACC) often has a poor outcome, with a five-year survival of less than 25%. We report a rare case of metastatic ACC with a myxoid variant with chromothripsis. We review the histologic variants of ACC, including myxoid type, molecular drivers, and current and investigational therapies for adrenocortical carcinoma. We also discuss the mechanism of chromothripsis, chromothripsis in ACC tumorigenesis, and propose potential therapies targeting chromothripsis.
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Affiliation(s)
- Gyuhee Seong
- Department of Medicine, State University of New York (SUNY) Downstate Health Sciences University/Kings County Hospital Center, New York, USA
| | - Alexander Wu
- Department of Hematology and Oncology, State University of New York (SUNY) Downstate Health Sciences University/Kings County Hospital Center, New York, USA
| | - Charles Kim
- Department of Hematology and Oncology, State University of New York (SUNY) Downstate Health Sciences University/Kings County Hospital Center, New York, USA
| | - Nirmal Pathak
- Department of Hematology and Oncology, State University of New York (SUNY) Downstate Health Sciences University/Kings County Hospital Center, New York, USA
| | - Elif Yakut
- Department of Pathology, State University of New York (SUNY) Downstate Health Sciences University/Kings County Hospital Center, New York, USA
| | - Zhonghua Li
- Department of Pathology, State University of New York (SUNY) Downstate Health Sciences University/Kings County Hospital Center, New York, USA
| | - Edwin Chiu
- Department of Hematology and Oncology, State University of New York (SUNY) Downstate Health Sciences University/Kings County Hospital Center, New York, USA
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Huang Q, Baudis M. Candidate targets of copy number deletion events across 17 cancer types. Front Genet 2023; 13:1017657. [PMID: 36726722 PMCID: PMC9885371 DOI: 10.3389/fgene.2022.1017657] [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: 08/12/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Genome variation is the direct cause of cancer and driver of its clonal evolution. While the impact of many point mutations can be evaluated through their modification of individual genomic elements, even a single copy number aberration (CNA) may encompass hundreds of genes and therefore pose challenges to untangle potentially complex functional effects. However, consistent, recurring and disease-specific patterns in the genome-wide CNA landscape imply that particular CNA may promote cancer-type-specific characteristics. Discerning essential cancer-promoting alterations from the inherent co-dependency in CNA would improve the understanding of mechanisms of CNA and provide new insights into cancer biology and potential therapeutic targets. Here we implement a model using segmental breakpoints to discover non-random gene coverage by copy number deletion (CND). With a diverse set of cancer types from multiple resources, this model identified common and cancer-type-specific oncogenes and tumor suppressor genes as well as cancer-promoting functional pathways. Confirmed by differential expression analysis of data from corresponding cancer types, the results show that for most cancer types, despite dissimilarity of their CND landscapes, similar canonical pathways are affected. In 25 analyses of 17 cancer types, we have identified 19 to 169 significant genes by copy deletion, including RB1, PTEN and CDKN2A as the most significantly deleted genes among all cancer types. We have also shown a shared dependence on core pathways for cancer progression in different cancers as well as cancer type separation by genome-wide significance scores. While this work provides a reference for gene specific significance in many cancers, it chiefly contributes a general framework to derive genome-wide significance and molecular insights in CND profiles with a potential for the analysis of rare cancer types as well as non-coding regions.
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Affiliation(s)
- Qingyao Huang
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Michael Baudis
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
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11
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Reimann H, Stopper H, Hintzsche H. Fate of micronuclei and micronucleated cells after treatment of HeLa cells with different genotoxic agents. Arch Toxicol 2023; 97:875-889. [PMID: 36564592 PMCID: PMC9968706 DOI: 10.1007/s00204-022-03433-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Although micronuclei are well-known biomarkers of genotoxic damage, the biological consequences of micronucleus induction are only poorly understood. To further elucidate these consequences, HeLa cells stably expressing histone 2B coupled with green fluorescent protein were used for long-term live cell imaging to investigate the fate of micronuclei and micronucleated cells after treatment of cells with various genotoxic agents (doxorubicin (20, 30 and nM), tert-butyl hydroperoxide (tBHP, 50, 100 and 150 µM), radiation (0.5, 1 and 2 Gy), methyl methanesulfonate (MMS, 20, 25 and 30 µg/ml) and vinblastine (1, 2 and 3 nM)). Most micronuclei persist for multiple cell cycles or reincorporate while micronucleated cells were more prone to cell death, senescence and fatal mitotic errors compared to non-micronucleated cells, which is consistent with previous studies using etoposide. No clear substance-related effects on the fate of micronuclei and micronucleated cells were observed. To further investigate the fate of micronuclei, extrusion of micronuclei was studied with treatments reported as inducing the extrusion of micronuclei. Since extrusion was not observed in HeLa cells, the relevance of extrusion of micronuclei remains unclear. In addition, degradation of micronuclei was analysed via immunostaining of γH2AX, which demonstrated a high level of DNA damage in micronuclei compared to the main nuclei. Furthermore, transduction with two reporter genes (LC3B-dsRed and LaminB1-dsRed) was conducted followed by long-term live cell imaging. While autophagy marker LC3B was not associated with micronuclei, Lamin B1 was found in approximately 50% of all micronuclei. While degradation of micronuclei was not observed to be a frequent fate of micronuclei, the results show impaired stability of DNA and micronuclear envelope indicating rupture of micronuclei as a pre-step to chromothripsis.
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Affiliation(s)
- Hauke Reimann
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
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12
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Robert M, Crasta K. Breaking the vicious circle: Extrachromosomal circular DNA as an emerging player in tumour evolution. Semin Cell Dev Biol 2021; 123:140-150. [PMID: 34857471 DOI: 10.1016/j.semcdb.2021.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 12/16/2022]
Abstract
Extrachromosomal circular DNA (ecDNA) or double minutes have gained renewed interest since its discovery more than five decades ago, emerging as potent drivers of tumour evolution. This has largely been motivated by recent discovery that the tumour-exclusive ecDNA are highly prevalent in almost all cancers unlike previously thought. EcDNAs contribute to elevated oncogene expression, intratumoural heterogeneity, tumour adaptation and therapy resistance independently of canonical chromosomal alterations. Importantly, ecDNAs play a critical role in patient survival as ecDNA-based oncogene amplification adversely affects clinical outcome to a significantly greater extent than intrachromosomal amplification. Chromothripsis, a major driver of ecDNA biogenesis and gene amplification, is a mutational process characterised by chromosomal shattering and localised complex genome rearrangement. Chemotherapeutic drugs can lead to chromothriptic rearrangements and therapy resistance. In this review, we examine how ecDNAs mediate oncogene overexpression, facilitate accelerated tumour malignancy and enhance rapid adaptation independently of linear chromosomes. We delve into discoveries pertaining to mechanisms of biogenesis, distinctive features of ecDNA, gene regulation and topological interactions with active chromatin. We also discuss the critical role of chromothripsis in engendering ecDNA amplification and evolution. One envisions that insights into ecDNA biology not only hold importance for the cancer genome and tumour evolutionary dynamics, but could also inform prognostication and clinical intervention, particularly for cancers characterised by high oncogene amplification.
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Affiliation(s)
- Matius Robert
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, National University of Singapore, Singapore
| | - Karen Crasta
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, National University of Singapore, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Agency for Science, Technology & Research (A⁎STAR), Institute of Molecular and Cell Biology, Singapore.
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13
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Sepaniac LA, Martin W, Dionne LA, Stearns TM, Reinholdt LG, Stumpff J. Micronuclei in Kif18a mutant mice form stable micronuclear envelopes and do not promote tumorigenesis. J Cell Biol 2021; 220:212637. [PMID: 34515734 PMCID: PMC8441830 DOI: 10.1083/jcb.202101165] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/05/2021] [Accepted: 08/25/2021] [Indexed: 12/02/2022] Open
Abstract
Micronuclei, whole or fragmented chromosomes spatially separated from the main nucleus, are associated with genomic instability and have been identified as drivers of tumorigenesis. Paradoxically, Kif18a mutant mice produce micronuclei due to asynchronous segregation of unaligned chromosomes in vivo but do not develop spontaneous tumors. We report here that micronuclei in Kif18a mutant mice form stable nuclear envelopes. Challenging Kif18a mutant mice via deletion of the Trp53 gene led to formation of thymic lymphoma with elevated levels of micronuclei. However, loss of Kif18a had modest or no effect on survival of Trp53 homozygotes and heterozygotes, respectively. Micronuclei in cultured KIF18A KO cells form stable nuclear envelopes characterized by increased recruitment of nuclear envelope components and successful expansion of decondensing chromatin compared with those induced by nocodazole washout or radiation. Lagging chromosomes were also positioned closer to the main chromatin masses in KIF18A KO cells. These data suggest that not all micronuclei actively promote tumorigenesis.
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Affiliation(s)
- Leslie A Sepaniac
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT
| | | | | | | | | | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT
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14
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Kuisma H, Bramante S, Rajamäki K, Sipilä LJ, Kaasinen E, Kaukomaa J, Palin K, Mäkinen N, Sjöberg J, Sarvilinna N, Taipale J, Kauppi L, Tumiati M, Hassinen A, Pitkäniemi J, Jalkanen J, Heikkinen S, Pasanen A, Heikinheimo O, Bützow R, Välimäki N, Aaltonen LA. Parity associates with chromosomal damage in uterine leiomyomas. Nat Commun 2021; 12:5448. [PMID: 34521855 PMCID: PMC8440576 DOI: 10.1038/s41467-021-25806-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/30/2021] [Indexed: 12/16/2022] Open
Abstract
Mechanical forces in a constrained cellular environment were recently established as a facilitator of chromosomal damage. Whether this could contribute to tumorigenesis is not known. Uterine leiomyomas are common neoplasms that display relatively few chromosomal aberrations. We hypothesized that if mechanical forces contribute to chromosomal damage, signs of this could be seen in uterine leiomyomas from parous women. We examined the karyotypes of 1946 tumors, and found a striking overrepresentation of chromosomal damage associated with parity. We then subjected myometrial cells to physiological forces similar to those encountered during pregnancy, and found this to cause DNA breaks and a DNA repair response. While mechanical forces acting in constrained cellular environments may thus contribute to neoplastic degeneration, and genesis of uterine leiomyoma, further studies are needed to prove possible causality of the observed association. No evidence for progression to malignancy was found.
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Affiliation(s)
- Heli Kuisma
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Simona Bramante
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Lauri J Sipilä
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Eevi Kaasinen
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Jaana Kaukomaa
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Netta Mäkinen
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Jari Sjöberg
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nanna Sarvilinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Systems Oncology Research Program, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Liisa Kauppi
- Systems Oncology Research Program, University of Helsinki, Helsinki, Finland
| | - Manuela Tumiati
- Systems Oncology Research Program, University of Helsinki, Helsinki, Finland
| | - Antti Hassinen
- FIMM-HCA, Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Janne Pitkäniemi
- Institute for Statistical and Epidemiological Cancer Research, Finnish Cancer Registry, Helsinki, Finland
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jyrki Jalkanen
- Department of Obstetrics and Gynecology, Central Finland Central Hospital, Jyväskylä, Finland
| | - Sanna Heikkinen
- Institute for Statistical and Epidemiological Cancer Research, Finnish Cancer Registry, Helsinki, Finland
| | - Annukka Pasanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Oskari Heikinheimo
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ralf Bützow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland.
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15
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Giunta S. Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020. Cancer Metastasis Rev 2021; 40:909-924. [PMID: 34097189 PMCID: PMC8180541 DOI: 10.1007/s10555-021-09969-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022]
Abstract
Cancer is underlined by genetic changes. In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of over two thousand five hundred patients across 38 different cancer types, as well as the corresponding healthy tissue, with the aim of identifying genome-wide mutations exclusively found in cancer and uncovering new genetic changes that drive tumor formation. What set this project apart from earlier efforts is the use of whole genome sequencing (WGS) that enabled to explore alterations beyond the coding DNA, into cancer's non-coding genome. WGS of the entire cohort allowed to tease apart driving mutations that initiate and support carcinogenesis from passenger mutations that do not play an overt role in the disease. At least one causative mutation was found in 95% of all cancers, with many tumors showing an average of 5 driver mutations. The PCAWG Project also assessed the transcriptional output altered in cancer and rebuilt the evolutionary history of each tumor showing that initial driver mutations can occur years if not decades prior to a diagnosis. Here, I provide a concise review of the Pan-Cancer Project papers published on February 2020, along with key computational tools and the digital framework generated as part of the project. This represents an historic effort by hundreds of international collaborators, which provides a comprehensive understanding of cancer genetics, with publicly available data and resources representing a treasure trove of information to advance cancer research for years to come.
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Affiliation(s)
- Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology "Charles Darwin", University of Rome Sapienza, Rome, Italy.
- The Rockefeller University, 1230 York Avenue, New York, NY, USA.
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16
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Bolzán AD. Mutagen-induced telomere instability in human cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2021; 868-869:503387. [PMID: 34454696 DOI: 10.1016/j.mrgentox.2021.503387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 11/27/2022]
Abstract
Telomere instability is one of the main sources of genome instability and may result from chromosome end loss (due to chromosome breakage at one or both ends) or, more frequently, telomere dysfunction. Dysfunctional telomeres arise when they lose their end-capping function or become critically short, which causes chromosomal termini to behave like a DNA double-strand break. Telomere instability may occur at the chromosomal or at the molecular level, giving rise, respectively, to telomere-related chromosomal aberrations or the loss or modification of any of the components of the telomere (telomere DNA, telomere-associated proteins, or telomere RNA). Since telomeres play a fundamental role in maintaining genome stability, the study of telomere instability in cells exposed to mutagens is of great importance to understand the telomere-driven genomic instability present in those cells. In the present review, we will focus on the current knowledge about telomere instability induced by physical, chemical, and biological mutagens in human cells.
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Affiliation(s)
- Alejandro D Bolzán
- Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE, CONICET-CICPBA-UNLP), calle 526 y Camino General Belgrano, B1906APO La Plata, Buenos Aires, Argentina; Universidad Nacional de La Plata, Facultad de Ciencias Naturales y Museo, calle 60 y 122, La Plata, Buenos Aires, Argentina.
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17
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Simovic M, Bolkestein M, Moustafa M, Wong JKL, Körber V, Benedetto S, Khalid U, Schreiber HS, Jugold M, Korshunov A, Hübschmann D, Mack N, Brons S, Wei PC, Breckwoldt MO, Heiland S, Bendszus M, Jürgen D, Höfer T, Zapatka M, Kool M, Pfister SM, Abdollahi A, Ernst A. Carbon ion radiotherapy eradicates medulloblastomas with chromothripsis in an orthotopic Li-Fraumeni patient-derived mouse model. Neuro Oncol 2021; 23:2028-2041. [PMID: 34049392 PMCID: PMC8643436 DOI: 10.1093/neuonc/noab127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Medulloblastomas with chromothripsis developing in children with Li-Fraumeni Syndrome (germline TP53 mutations) are highly aggressive brain tumors with dismal prognosis. Conventional photon radiotherapy and DNA-damaging chemotherapy are not successful for these patients and raise the risk of secondary malignancies. We hypothesized that the pronounced homologous recombination deficiency in these tumors might offer vulnerabilities that can be therapeutically utilized in combination with high linear energy transfer carbon ion radiotherapy. Methods We tested high-precision particle therapy with carbon ions and protons as well as topotecan with or without PARP inhibitor in orthotopic primary and matched relapsed patient-derived xenograft models. Tumor and normal tissue underwent longitudinal morphological MRI, cellular (markers of neurogenesis and DNA damage-repair), and molecular characterization (whole-genome sequencing). Results In the primary medulloblastoma model, carbon ions led to complete response in 79% of animals irrespective of PARP inhibitor within a follow-up period of 300 days postirradiation, as detected by MRI and histology. No sign of neurologic symptoms, impairment of neurogenesis or in-field carcinogenesis was detected in repair-deficient host mice. PARP inhibitors further enhanced the effect of proton irradiation. In the postradiotherapy relapsed tumor model, median survival was significantly increased after carbon ions (96 days) versus control (43 days, P < .0001). No major change in the clonal composition was detected in the relapsed model. Conclusion The high efficacy and favorable toxicity profile of carbon ions warrants further investigation in primary medulloblastomas with chromothripsis. Postradiotherapy relapsed medulloblastomas exhibit relative resistance compared to treatment-naïve tumors, calling for exploration of multimodal strategies.
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Affiliation(s)
- Milena Simovic
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ).,Faculty of Biosciences, Heidelberg University
| | - Michiel Bolkestein
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ)
| | - Mahmoud Moustafa
- Division of Molecular & Translational Radiation Oncology,Heidelberg Ion-Beam Therapy Center (HIT).,Heidelberg Institute for Radiation Oncology (HIRO).,National Center for Radiation Oncology (NCRO).,National Center for Tumor Diseases (NCT).,Heidelberg University Hospital (UKHD) and DKFZ.,German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Department of Clinical Pathology, Suez Canal University, Ismailia-Egypt
| | - John K L Wong
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Division of Molecular Genetics, DKFZ
| | | | | | - Umar Khalid
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ).,Faculty of Biosciences, Heidelberg University
| | - Hannah Sophia Schreiber
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ).,Faculty of Medicine, Heidelberg University
| | | | - Andrey Korshunov
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Clinical Cooperation Unit Neuropathology, DKFZ, Department of Neuropathology, UKHD
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ.,Heidelberg Institute for Stem cell Technology and Experimental Medicine.,Department of Pediatric Oncology, Hematology and Immunology, UKHD
| | - Norman Mack
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Division of Molecular Genetics, DKFZ.,Department of Pediatric Oncology, Hematology and Immunology, UKHD.,Hopp Children's Cancer Center, NCT Heidelberg (KiTZ).,Division of Pediatric Neurooncology, DKFZ
| | | | | | | | | | | | - Debus Jürgen
- Heidelberg Institute for Radiation Oncology (HIRO).,National Center for Tumor Diseases (NCT).,German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Department of Radiation Oncology, UKHD.,Department of Radiation Oncology, Eberhard-Karls-University Tuebingen.,Clinical Cooperation Unit Radiation Oncology, DKFZ
| | | | - Marc Zapatka
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Division of Molecular Genetics, DKFZ
| | - Marcel Kool
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Hopp Children's Cancer Center, NCT Heidelberg (KiTZ).,Division of Pediatric Neurooncology, DKFZ.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Stefan M Pfister
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Department of Pediatric Oncology, Hematology and Immunology, UKHD.,Hopp Children's Cancer Center, NCT Heidelberg (KiTZ).,Division of Pediatric Neurooncology, DKFZ
| | - Amir Abdollahi
- Division of Molecular & Translational Radiation Oncology,Heidelberg Ion-Beam Therapy Center (HIT).,Heidelberg Institute for Radiation Oncology (HIRO).,National Center for Radiation Oncology (NCRO).,National Center for Tumor Diseases (NCT).,Heidelberg University Hospital (UKHD) and DKFZ.,German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ
| | - Aurélie Ernst
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ)
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18
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Maura F, Boyle EM, Rustad EH, Ashby C, Kaminetzky D, Bruno B, Braunstein M, Bauer M, Blaney P, Wang Y, Ghamlouch H, Williams L, Stoeckle J, Davies FE, Walker BA, Maclachlan K, Diamond B, Landgren O, Morgan GJ. Chromothripsis as a pathogenic driver of multiple myeloma. Semin Cell Dev Biol 2021; 123:115-123. [PMID: 33958284 DOI: 10.1016/j.semcdb.2021.04.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 12/29/2022]
Abstract
Analysis of the genetic basis for multiple myeloma (MM) has informed many of our current concepts of the biology that underlies disease initiation and progression. Studying these events in further detail is predicted to deliver important insights into its pathogenesis, prognosis and treatment. Information from whole genome sequencing of structural variation is revealing the role of these events as drivers of MM. In particular, we discuss how the insights we have gained from studying chromothripsis suggest that it can be used to provide information on disease initiation and that, as a consequence, it can be used for the clinical classification of myeloma precursor diseases allowing for early intervention and prognostic determination. For newly diagnosed MM, the integration of information on the presence of chromothripsis has the potential to significantly enhance current risk prediction strategies and to better characterize patients with high-risk disease biology. In this article we summarize the genetic basis for MM and the role played by chromothripsis as a critical pathogenic factor active at early disease phases.
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Affiliation(s)
- Francesco Maura
- Myeloma Program, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Eileen M Boyle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Even H Rustad
- Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Benedetto Bruno
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Marc Braunstein
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Yubao Wang
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Louis Williams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - James Stoeckle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology Indiana University, Indianapolis, IN, USA
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ben Diamond
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ola Landgren
- Myeloma Program, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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19
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Shelke S, Das B. Radio-adaptive response and correlation of non-homologous end joining repair gene polymorphisms [XRRC5 (3R/2R/1R/0R), XRCC6(C/G) and XRCC7 (G/T)] in human peripheral blood mononuclear cells exposed to gamma radiation. Genes Environ 2021; 43:9. [PMID: 33685509 PMCID: PMC7938547 DOI: 10.1186/s41021-021-00176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 02/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Radio-adaptive response (RAR) is transient phenomena, where cells conditioned with a small dose (priming) of ionizing radiation shows significantly reduced DNA damage with a subsequent high challenging dose. The role of DNA double strand break repair gene polymorphism in RAR is not known. In the present study attempt was made to find out the influence of NHEJ repair gene polymorphisms [a VNTR; XRCC5 (3R/2R/1R/0R); two single nucleotide polymorphisms (SNPs); XRCC6 (C/G) and XRCC7 (G/T)] with DNA damage, repair and mRNA expression in human PBMCs in dose and adaptive response studies. Genomic DNA extracted from venous blood samples of 20 random healthy donors (16 adaptive and 4 non-adaptive) and genotyping of NHEJ repair genes was carried out using PCR amplified length polymorphism. RESULTS The dose response study revealed significant positive correlation of genotypes at XRRC5 (3R/2R/1R/0R), XRCC6(C/G) and XRCC7 (G/T) with DNA damage. Donors having genotypes with 2R allele at XRCC5 showed significant positive correlation with mRNA expression level (0R/2R: r = 0.846, P = 0.034; 1R/2R: r = 0.698, P = 0.0001 and 2R/2R: r = 0.831, P = 0.0001) for dose response. Genotypes C/C and C/G of XRCC6 showed a significant positive correlation (P = 0.0001), whereas, genotype T/T of XRCC7 showed significant negative correlation (r = - 0.376, P = 0.041) with mRNA expression. CONCLUSION Interestingly, adaptive donors having C/G genotype of XRCC6 showed significantly higher (P < 0.05) mRNA expression level in primed cells suggesting their role in RAR. In addition, NHEJ repair gene polymorphisms play crucial role with radio-sensitivity and RAR in human PBMCs.
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Affiliation(s)
- Shridevi Shelke
- Low Level Radiation Research Section, Radiation Biology & Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Birajalaxmi Das
- Low Level Radiation Research Section, Radiation Biology & Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India.
- Homi Bhabha National Institute (HBNI), Anushaktinagar, Mumbai, 400094, India.
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Dhillon VS, Deo P, Bonassi S, Fenech M. Lymphocyte micronuclei frequencies in skin, haematological, prostate, colorectal and esophageal cancer cases: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 787:108372. [PMID: 34083057 DOI: 10.1016/j.mrrev.2021.108372] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/17/2021] [Accepted: 01/31/2021] [Indexed: 01/07/2023]
Abstract
Micronucleus (MN) assay has been widely used as a biomarker of DNA damage, chromosomal instability, cancer risk and accelerated aging in many epidemiological studies. In this narrative review and meta-analysis we assessed the association between lymphocyte micronuclei (MNi) and cancers of the skin, blood, digestive tract, and prostate. The review identified nineteen studies with 717 disease subjects and 782 controls. Significant increases in MRi for MNi were observed in the following groups: subjects with blood cancer (MRi = 3.98; 95 % CI: 1.98-7.99; p = 0.000) and colorectal cancer (excluding IBD) (MRi = 2.69; 95 % CI: 1.82-3.98, p < 0.000). The results of this review suggest that lymphocyte MNi are a biomarker of DNA damage and chromosomal instability in people with haematological or colorectal cancers. However, the MRi for lymphocyte MNi in subjects with cancers of skin, prostate, esophagus was not significantly increased. More case-control and prospective studies are warranted to further verify the observed trends and to better understand the role of lymphocyte MNi as a biomarker of cancer risk in blood, skin, digestive tract and prostate.
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Affiliation(s)
- Varinderpal S Dhillon
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, 5000, Australia.
| | - Permal Deo
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, 5000, Australia
| | - Stefano Bonassi
- Department of Human Sciences and Quality of Life Promotion, San Raffaele University, Rome, Italy; Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, Rome, Italy
| | - Michael Fenech
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, 5000, Australia; Faculty of Health Sciences, National University of Malaysia, Kuala Lumpur, Malaysia
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21
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Reimann H, Ngo QA, Stopper H, Hintzsche H. Cytokinesis-block micronucleus assay of celecoxib and celecoxib derivatives. Toxicol Rep 2020; 7:1588-1591. [PMID: 33304828 PMCID: PMC7708851 DOI: 10.1016/j.toxrep.2020.11.004] [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: 07/13/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 11/19/2022] Open
Abstract
New derivatives of celecoxib can improve beneficial effects with better safety profile. DNA damage in form of micronuclei has not been observed after treatment with celecoxib or any derivative. Further development of celecoxib derivatives for chemoprevention may be promising.
Celecoxib is used widely for the acute treatment of pain and for pain relief in various diseases. Furthermore, it shows potential in chemoprevention, although chronic treatment with celecoxib could lead to adverse effects like cardiovascular events. New derivatives of celecoxib were synthesised that may be suitable as chemopreventive agent without inducing adverse effects. Critical endpoint for a safe use of pharmaceuticals is genotoxicity after application. A standard test for the assessment of genotoxicity is the cytokinesis-block micronucleus assay, that evaluates the number micronuclei after treatment of cells with a test compound as biomarker for DNA damage. Various promising derivatives of celecoxib have been assessed with the cytokinesis-block micronucleus assay in HeLa-H2B-GFP cells. It could be demonstrated, that neither celecoxib nor its derivatives were genotoxic in this assay and therefore celecoxib derivatives could be developed further for a safe use as chemopreventive agent.
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Affiliation(s)
- Hauke Reimann
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078 Würzburg, Germany
| | - Quoc Anh Ngo
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, CauGiay, Hanoi, Viet Nam
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078 Würzburg, Germany
| | - Henning Hintzsche
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078 Würzburg, Germany
- Bavarian Health and Food Safety Authority, Eggenreuther Weg 43, 91058 Erlangen, Germany
- Corresponding author at: Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078 Würzburg, Germany.
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22
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Gonzalez Curto G, Der Vartanian A, Frarma YEM, Manceau L, Baldi L, Prisco S, Elarouci N, Causeret F, Korenkov D, Rigolet M, Aurade F, De Reynies A, Contremoulins V, Relaix F, Faklaris O, Briscoe J, Gilardi-Hebenstreit P, Ribes V. The PAX-FOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition. PLoS Genet 2020; 16:e1009164. [PMID: 33175861 PMCID: PMC7682867 DOI: 10.1371/journal.pgen.1009164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/23/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
The chromosome translocations generating PAX3-FOXO1 and PAX7-FOXO1 chimeric proteins are the primary hallmarks of the paediatric fusion-positive alveolar subtype of Rhabdomyosarcoma (FP-RMS). Despite the ability of these transcription factors to remodel chromatin landscapes and promote the expression of tumour driver genes, they only inefficiently promote malignant transformation in vivo. The reason for this is unclear. To address this, we developed an in ovo model to follow the response of spinal cord progenitors to PAX-FOXO1s. Our data demonstrate that PAX-FOXO1s, but not wild-type PAX3 or PAX7, trigger the trans-differentiation of neural cells into FP-RMS-like cells with myogenic characteristics. In parallel, PAX-FOXO1s remodel the neural pseudo-stratified epithelium into a cohesive mesenchyme capable of tissue invasion. Surprisingly, expression of PAX-FOXO1s, similar to wild-type PAX3/7, reduce the levels of CDK-CYCLIN activity and increase the fraction of cells in G1. Introduction of CYCLIN D1 or MYCN overcomes this PAX-FOXO1-mediated cell cycle inhibition and promotes tumour growth. Together, our findings reveal a mechanism that can explain the apparent limited oncogenicity of PAX-FOXO1 fusion transcription factors. They are also consistent with certain clinical reports indicative of a neural origin of FP-RMS.
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Affiliation(s)
| | | | | | - Line Manceau
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Lorenzo Baldi
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Selene Prisco
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Frédéric Causeret
- Université de Paris, Imagine Institute, Team Genetics and Development of the Cerebral Cortex, Paris, France
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Paris, France
| | - Daniil Korenkov
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Muriel Rigolet
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
| | - Frédéric Aurade
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
- Sorbonne Université, INSERM, UMRS974, Center for Research in Myology, Paris, France
| | - Aurélien De Reynies
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Vincent Contremoulins
- ImagoSeine core facility of Institut Jacques Monod and member of France-BioImaging, France
| | - Frédéric Relaix
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
| | - Orestis Faklaris
- ImagoSeine core facility of Institut Jacques Monod and member of France-BioImaging, France
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
| | | | - Vanessa Ribes
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
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23
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DNA Associated with Circulating Exosomes as a Biomarker for Glioma. Genes (Basel) 2020; 11:genes11111276. [PMID: 33137926 PMCID: PMC7692052 DOI: 10.3390/genes11111276] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Cancerous and non-cancerous cells secrete exosomes, a type of nanovesicle known to carry the molecular signature of the parent for intercellular communications. Exosomes secreted by tumor cells carry abnormal DNA, RNA, and protein molecules that reflect the cancerous status. DNA is the master molecule that ultimately affects the function of RNA and proteins. Aberrations in DNA can potentially lead a cell to malignancy. Deviant quantities and the differential sequences of exosomal DNA are useful characteristics as cancer biomarkers. Since these alterations are either associated with specific stages of cancer or caused due to a clinical treatment, exosomal DNA is valuable as a diagnostic, prognostic, predictive, and therapeutic-intervention response biomarker. Notably, the exosomes can cross an intact blood–brain barrier and anatomical compartments by transcytosis. As such, the cancer-specific trademark molecules can be detected in systemic blood circulation and other body fluids, including cerebrospinal fluid, with non-invasive or minimally invasive procedures. This comprehensive review highlights the cancer-specific modulations of DNA associated with circulating exosomes that are beneficial as glioma biomarkers.
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24
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Albertini RJ, Kaden DA. Mutagenicity monitoring in humans: Global versus specific origin of mutations. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108341. [PMID: 33339577 DOI: 10.1016/j.mrrev.2020.108341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 01/19/2023]
Abstract
An underappreciated aspect of human mutagenicity biomonitoring is tissue specificity reflected in different assays, especially those that measure events that can only occur in developing bone marrow (BM) cells. Reviewed here are 9 currently-employed human mutagenicity biomonitoring assays. Several assays measure chromosome-level events in circulating T-lymphocytes (T-cells), i.e., traditional analyses of aberrations, translocation studies involving chromosome painting and fluorescence in situ hybridization (FISH) and determinations of micronuclei (MN). Other T-cell assays measure gene mutations. i.e., hypoxanthine-guanine phosphoriboslytransferase (HPRT) and phosphoribosylinositol glycan class A (PIGA). In addition to the T-cell assays, also reviewed are those assays that measure events in peripheral blood cells that necessarily arose in BM cells, i.e., MN in reticulocytes; glycophorin A (GPA) gene mutations in red blood cells (RBCs), and PIGA gene mutations in RBC or granulocytes. This review considers only cell culture- or cytometry-based assays to describe endpoints measured, methods, optimal sampling times, and sample summaries of typical quantitative and qualitative results. However, to achieve its intended focus on the target cells where events occur, kinetics of the cells of peripheral blood that derive at some point from precursor cells are reviewed to identify body sites and tissues where the genotoxic events originate. Kinetics indicate that in normal adults, measured events in T-cells afford global assessments of in vivo mutagenicity but are not specific for BM effects. Therefore, an agent's capacity for inducing mutations in BM cells cannot be reliably inferred from T-cell assays as the magnitude of effect in BM, if any, is unknown. By contrast, chromosome or gene level mutations measured in RBCs/reticulocytes or granulocytes must originate in BM cells, i.e. in RBC or granulocyte precursors, thereby making them specific indicators for effects in BM. Assays of mutations arising directly in BM cells may quantitatively reflect the mutagenicity of potential leukemogenic agents.
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Affiliation(s)
- Richard J Albertini
- University of Vermont, 111 Colchester Avenue, Burlington, VT 05401, United States
| | - Debra A Kaden
- Ramboll US Consulting, Inc., 101 Federal Street, Suite 1900, Boston, MA 02110, United States.
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25
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Faldoni FLC, Villacis RAR, Canto LM, Fonseca-Alves CE, Cury SS, Larsen SJ, Aagaard MM, Souza CP, Scapulatempo-Neto C, Osório CABT, Baumbach J, Marchi FA, Rogatto SR. Inflammatory Breast Cancer: Clinical Implications of Genomic Alterations and Mutational Profiling. Cancers (Basel) 2020; 12:2816. [PMID: 33007869 PMCID: PMC7650681 DOI: 10.3390/cancers12102816] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory breast cancer (IBC) is a rare and aggressive type of breast cancer whose molecular basis is poorly understood. We performed a comprehensive molecular analysis of 24 IBC biopsies naïve of treatment, using a high-resolution microarray platform and targeted next-generation sequencing (105 cancer-related genes). The genes more frequently affected by gains were MYC (75%) and MDM4 (71%), while frequent losses encompassed TP53 (71%) and RB1 (58%). Increased MYC and MDM4 protein expression levels were detected in 18 cases. These genes have been related to IBC aggressiveness, and MDM4 is a potential therapeutic target in IBC. Functional enrichment analysis revealed genes associated with inflammatory regulation and immune response. High homologous recombination (HR) deficiency scores were detected in triple-negative and metastatic IBC cases. A high telomeric allelic imbalance score was found in patients having worse overall survival (OS). The mutational profiling was compared with non-IBC (TCGA, n = 250) and IBC (n = 118) from four datasets, validating our findings. Higher frequency of TP53 and BRCA2 variants were detected compared to non-IBC, while PIKC3A showed similar frequency. Variants in mismatch repair and HR genes were associated with worse OS. Our study provided a framework for improved diagnosis and therapeutic alternatives for this aggressive tumor type.
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Affiliation(s)
- Flávia L. C. Faldoni
- International Research Center, A.C.Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.L.C.F.); (F.A.M.)
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
| | - Rolando A. R. Villacis
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília-UnB, Brasília 70910-900, Brazil;
| | - Luisa M. Canto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
| | - Carlos E. Fonseca-Alves
- Department of Veterinary Surgery and Anesthesiology, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu 18618-681, Brazil;
| | - Sarah S. Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University-UNESP, Botucatu 18618-689, Brazil;
| | - Simon J. Larsen
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark; (S.J.L.); (J.B.)
| | - Mads M. Aagaard
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
| | - Cristiano P. Souza
- Department of Breast and Gynecologic Oncology, Barretos Cancer Hospital, Pio XII Foundation, Barretos 14784-390, Brazil;
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos SP 14784-400, Brazil;
- Diagnósticos da América (DASA), Barueri 01525-001, Brazil
| | | | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark; (S.J.L.); (J.B.)
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Fabio A. Marchi
- International Research Center, A.C.Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.L.C.F.); (F.A.M.)
| | - Silvia R. Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
- Institute of Regional Health Research, University of Southern Denmark, 500 Odense, Denmark
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26
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Using telomeric chromosomal aberrations to evaluate clastogen-induced genomic instability in mammalian cells. Chromosome Res 2020; 28:259-276. [DOI: 10.1007/s10577-020-09641-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/06/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022]
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27
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Reimann H, Stopper H, Hintzsche H. Long-term fate of etoposide-induced micronuclei and micronucleated cells in Hela-H2B-GFP cells. Arch Toxicol 2020; 94:3553-3561. [PMID: 32681187 PMCID: PMC7502055 DOI: 10.1007/s00204-020-02840-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Micronuclei are small nuclear cellular structures containing whole chromosomes or chromosomal fragments. While there is a lot of information available about the origin and formation of micronuclei, less is known about the fate of micronuclei and micronucleated cells. Possible fates include extrusion, degradation, reincorporation and persistence. Live cell imaging was performed to quantitatively analyse the fates of micronuclei and micronucleated cells occurring in vitro. Imaging was conducted for up to 96 h in HeLa-H2B-GFP cells treated with 0.5, 1 and 2 µg/ml etoposide. While a minority of micronuclei was reincorporated into the main nucleus during mitosis, the majority of micronuclei persisted without any alterations. Degradation and extrusion were observed rarely or never. The presence of micronuclei affected the proliferation of the daughter cells and also had an influence on cell death rates. Mitotic errors were found to be clearly increased in micronucleus-containing cells. The results show that micronuclei and micronucleated cells can, although delayed in cell cycle, sustain for multiple divisions.
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Affiliation(s)
- Hauke Reimann
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Henning Hintzsche
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany. .,Bavarian Health and Food Safety Authority, Eggenreuther Weg 43, 91058, Erlangen, Germany.
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28
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Chakravarty D, Nair SS, Hammouda N, Ratnani P, Gharib Y, Wagaskar V, Mohamed N, Lundon D, Dovey Z, Kyprianou N, Tewari AK. Sex differences in SARS-CoV-2 infection rates and the potential link to prostate cancer. Commun Biol 2020; 3:374. [PMID: 32641750 PMCID: PMC7343823 DOI: 10.1038/s42003-020-1088-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 01/08/2023] Open
Abstract
The recent outbreak of infections and the pandemic caused by SARS-CoV-2 represent one of the most severe threats to human health in more than a century. Emerging data from the United States and elsewhere suggest that the disease is more severe in men. Knowledge gained, and lessons learned, from studies of the biological interactions and molecular links that may explain the reasons for the greater severity of disease in men, and specifically in the age group at risk for prostate cancer, will lead to better management of COVID-19 in prostate cancer patients. Such information will be indispensable in the current and post-pandemic scenarios.
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Affiliation(s)
- Dimple Chakravarty
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Sujit S Nair
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nada Hammouda
- Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Parita Ratnani
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yasmine Gharib
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vinayak Wagaskar
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nihal Mohamed
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dara Lundon
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zachary Dovey
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Natasha Kyprianou
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ashutosh K Tewari
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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29
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Brás A, Rodrigues AS, Rueff J. Copy number variations and constitutional chromothripsis (Review). Biomed Rep 2020; 13:11. [PMID: 32765850 PMCID: PMC7391299 DOI: 10.3892/br.2020.1318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Both copy number variations (CNVs) and chromothripsis are phenomena that involve complex genomic rearrangements. Chromothripsis results in CNVs and other structural changes. CNVs are frequently observed in the human genome. Studies on CNVs have been increasing exponentially; the Database of Genomic Variants shows an increase in the number of data published on structural variations added to the database in the last 15 years. CNVs may be a result of replicative and non-replicative mechanisms, and are hypothesized to serve important roles in human health and disease. Chromothripsis is a phenomena of chromosomal rearrangement following chromosomal breaks at multiple locations and involves impaired DNA repair. In 2011, Stephens et al coined the term chromothripsis for this type of fragmenting event. Several proposed mechanisms have been suggested to underlie chromothripsis, such as p53 inactivation, micronuclei formation, abortive apoptosis and telomere fusions in telomere crisis. Chromothripsis gives rise to normal or abnormal phenotypes. In this review, constitutional chromothripsis, which may coexist with multiple de novo CNVs are described and discussed. This reviews aims to summarize recent advances in our understanding of CNVs and chromothripsis, and describe the effects of these phenomena on human health and birth defects.
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Affiliation(s)
- Aldina Brás
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - António Sebastião Rodrigues
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - José Rueff
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
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30
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Miller ET, You S, Cadaneanu RM, Kim M, Yoon J, Liu ST, Li X, Kwan L, Hodge J, Quist MJ, Grasso CS, Lewis MS, Knudsen BS, Freeman MR, Garraway IP. Chromosomal instability in untreated primary prostate cancer as an indicator of metastatic potential. BMC Cancer 2020; 20:398. [PMID: 32380981 PMCID: PMC7204307 DOI: 10.1186/s12885-020-06817-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022] Open
Abstract
Background Metastatic prostate cancer (PC) is highly lethal. The ability to identify primary tumors capable of dissemination is an unmet need in the quest to understand lethal biology and improve patient outcomes. Previous studies have linked chromosomal instability (CIN), which generates aneuploidy following chromosomal missegregation during mitosis, to PC progression. Evidence of CIN includes broad copy number alterations (CNAs) spanning > 300 base pairs of DNA, which may also be measured via RNA expression signatures associated with CNA frequency. Signatures of CIN in metastatic PC, however, have not been interrogated or well defined. We examined a published 70-gene CIN signature (CIN70) in untreated and castration-resistant prostate cancer (CRPC) cohorts from The Cancer Genome Atlas (TCGA) and previously published reports. We also performed transcriptome and CNA analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases to determine if CIN was linked to clinical stage and outcome. Methods PNBX were collected from 99 patients treated in the VA Greater Los Angeles (GLA-VA) Healthcare System between 2000 and 2016. Total RNA was extracted from high-grade cancer areas in PNBX cores, followed by RNA sequencing and/or copy number analysis using OncoScan. Multivariate logistic regression analyses permitted calculation of odds ratios for CIN status (high versus low) in an expanded GLA-VA PNBX cohort (n = 121). Results The CIN70 signature was significantly enriched in primary tumors and CRPC metastases from M1 PC cases. An intersection of gene signatures comprised of differentially expressed genes (DEGs) generated through comparison of M1 versus M0 PNBX and primary CRPC tumors versus metastases revealed a 157-gene “metastasis” signature that was further distilled to 7-genes (PC-CIN) regulating centrosomes, chromosomal segregation, and mitotic spindle assembly. High PC-CIN scores correlated with CRPC, PC-death and all-cause mortality in the expanded GLA-VA PNBX cohort. Interestingly, approximately 1/3 of M1 PNBX cases exhibited low CIN, illuminating differential pathways of lethal PC progression. Conclusions Measuring CIN in PNBX by transcriptome profiling is feasible, and the PC-CIN signature may identify patients with a high risk of lethal progression at the time of diagnosis.
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Affiliation(s)
- Eric T Miller
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Sungyong You
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Radu M Cadaneanu
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Minhyung Kim
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Junhee Yoon
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Sandy T Liu
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA.,Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Xinmin Li
- Department of Pathology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Lorna Kwan
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Jennelle Hodge
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael J Quist
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Catherine S Grasso
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael S Lewis
- Department of Pathology, Greater Los Angeles Veterans Affairs Health System, California, Los Angeles, USA
| | - Beatrice S Knudsen
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael R Freeman
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Isla P Garraway
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA. .,Division of Urology, Greater Los Angeles Veterans Affairs Healthcare Center, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA.
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31
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Ain Q, Schmeer C, Wengerodt D, Witte OW, Kretz A. Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration. Int J Mol Sci 2020; 21:E2477. [PMID: 32252492 PMCID: PMC7177960 DOI: 10.3390/ijms21072477] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Still unresolved is the question of how a lifetime accumulation of somatic gene copy number alterations impact organ functionality and aging and age-related pathologies. Such an issue appears particularly relevant in the broadly post-mitotic central nervous system (CNS), where non-replicative neurons are restricted in DNA-repair choices and are prone to accumulate DNA damage, as they remain unreplaced over a lifetime. Both DNA injuries and consecutive DNA-repair strategies are processes that can evoke extrachromosomal circular DNA species, apparently from either part of the genome. Due to their capacity to amplify gene copies and related transcripts, the individual cellular load of extrachromosomal circular DNAs will contribute to a dynamic pool of additional coding and regulatory chromatin elements. Analogous to tumor tissues, where the mosaicism of circular DNAs plays a well-characterized role in oncogene plasticity and drug resistance, we suggest involvement of the "circulome" also in the CNS. Accordingly, we summarize current knowledge on the molecular biogenesis, homeostasis and gene regulatory impacts of circular extrachromosomal DNA and propose, in light of recent discoveries, a critical role in CNS aging and neurodegeneration. Future studies will elucidate the influence of individual extrachromosomal DNA species according to their sequence complexity and regional distribution or cell-type-specific abundance.
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Affiliation(s)
- Quratul Ain
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
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32
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Du M, Tian Y, Tan W, Wang L, Wang L, Kilari D, Huang CC, Wang L, Kohli M. Plasma cell-free DNA-based predictors of response to abiraterone acetate/prednisone and prognostic factors in metastatic castration-resistant prostate cancer. Prostate Cancer Prostatic Dis 2020; 23:705-713. [PMID: 32203070 PMCID: PMC7501185 DOI: 10.1038/s41391-020-0224-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 11/24/2022]
Abstract
Background: The combination of abiraterone acetate and prednisone (AA/P) is used to treat metastatic prostate cancer, but molecular predictors of treatment response are not well elucidated. We evaluated plasma circulating tumor DNA– (ctDNA-) based copy number alterations (CNAs) to determine treatment-related predictive and prognostic biomarkers for metastatic castration-resistant prostate cancer (mCRPC). Methods: Serial plasma specimens were prospectively collected from 88 chemotherapy-naive mCRPC patients before and after 12 weeks of AA/P treatment. Sequencing-based CNA analyses were performed on 174 specimens. We evaluated CNA-associated 12-week responses for primary resistance, time to treatment change (TTTC) for secondary resistance, and overall survival for prognosis (P < .05). Associations with primary resistance were analyzed using the Fisher exact test. Kaplan–Meier survival curves and Cox regression analyses were used to determine the associations of CNAs with acquired resistance and overall survival. Results: ctDNA reduced by 3.89% in responders and increased by 0.94% in nonresponders (P = .0043). Thirty-one prostate cancer–related genes from whole genome CNAs were tested. AR and AR enhancer amplification were associated with primary resistance (P = .0039) and shorter TTTC (P = .0003). ZFHX3 deletion and PIK3CA amplification were associated with primary resistance (P = .026 and P = .017, respectively), shorter TTTC (P = .0008 and P= .0016, respectively), and poor survival (P = .0025 and P = .0022, respectively). CNA-based risk scores combining selected significant associations (AR, NKX3.1, and PIK3CA) at the univariate level with TTTC were predictive of secondary resistance (P = .0002). and established prognoses for survival based on CNAs in ZFHX3, RB1, PIK3CA, and OPHN1 (P = .002). Multigene risk scores were more predictive than individual genes or clinical risk factors (P < .05). Conclusion: Plasma ctDNA CNAs and risk scores can predict mCRPC-state treatment and survival outcomes.
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Affiliation(s)
- Meijun Du
- Department of the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yijun Tian
- Department of the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Winston Tan
- Department of Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Liguo Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Deepak Kilari
- Department of Medicine, Medical College of Wisconsin and Milwaukee VA Medical Center, Milwaukee, WI, USA
| | - Chiang-Ching Huang
- Department of Biostatistics, University of Wisconsin, Milwaukee, WI, USA
| | - Liang Wang
- Department of the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - Manish Kohli
- Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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Fucic A, Druzhinin V, Aghajanyan A, Slijepcevic P, Bakanova M, Baranova E, Minina V, Golovina T, Kourdakov K, Timofeeva A, Titov V. Rogue versus chromothriptic cell as biomarker of cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108299. [PMID: 32430100 DOI: 10.1016/j.mrrev.2020.108299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 11/30/2022]
Abstract
New molecular cytogenetic biomarkers may significantly contribute to biodosimetry, whose application is still globally diverse and not fully standardized. In 2011, a new term, chromothripsis, was introduced raising great interest among researchers and soon motivating further investigations of the phenomenon. Chromothripsis is described as a single event in which one or more chromosomes go through severe DNA damage very much resembling rogue cells (RC) described more than 50 years ago. In this review, we for the first time compare these two multi-aberrant cells types, RC versus chromothriptic cells, giving insight into the similarities of the mechanisms involved in their etiology. In order to make a better comparison, data on RC in 3366 subjects from studies on cancer patients, Chernobyl liquidators, child victims of the Chernobyl nuclear plant accident, residentially and occupationally exposed population have been summarized for the first time. Results of experimental and epidemiological analysis show that chromothriptic cells and RC may be caused by exposure to high LET ionizing radiation. Experience and knowledge collected on RC may be used in future for further investigations of chromothripsis, introducing a new class of cells which include both chromothriptic and RC, and better insight into the frequency of chromothriptic cell per subject, which is currently absent. Both cell types are relevant in investigations of cancer etiology, biomonitoring of accidentally exposed population to ionizing radiation and biomonitoring of astronauts due to their exposure to high LET ionizing radiation during interplanetary voyages.
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Affiliation(s)
- Aleksandra Fucic
- Institute for Medical Research and Occupational Health, Zagreb, Croatia.
| | | | - Anna Aghajanyan
- Medical Institute Peoples' Friendship University of Russia (RUDN University), Moscow, Russia Federation
| | - Predrag Slijepcevic
- Brunel University London, Department of Life Sciences, College of Health and Life Sciences, Uxbridge, UK
| | | | | | | | | | | | | | - Victor Titov
- Kemerovo Regional Oncology Center, Kemerovo, Russian Federation
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34
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Thompson LL, Baergen AK, Lichtensztejn Z, McManus KJ. Reduced SKP1 Expression Induces Chromosome Instability through Aberrant Cyclin E1 Protein Turnover. Cancers (Basel) 2020; 12:E531. [PMID: 32106628 PMCID: PMC7139525 DOI: 10.3390/cancers12030531] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
Chromosome instability (CIN), or progressive changes in chromosome numbers, is an enabling feature of many cancers; however, the mechanisms giving rise to CIN remain poorly understood. To expand our mechanistic understanding of the molecular determinants of CIN in humans, we employed a cross-species approach to identify 164 human candidates to screen. Using quantitative imaging microscopy (QuantIM), we show that silencing 148 genes resulted in significant changes in CIN-associated phenotypes in two distinct cellular contexts. Ten genes were prioritized for validation based on cancer patient datasets revealing frequent gene copy number losses and associations with worse patient outcomes. QuantIM determined silencing of each gene-induced CIN, identifying novel roles for each as chromosome stability genes. SKP1 was selected for in-depth analyses as it forms part of SCF (SKP1, CUL1, FBox) complex, an E3 ubiquitin ligase that targets proteins for proteolytic degradation. Remarkably, SKP1 silencing induced increases in replication stress, DNA double strand breaks and chromothriptic events that were ascribed to aberrant increases in Cyclin E1 levels arising from reduced SKP1 expression. Collectively, these data reveal a high degree of evolutionary conservation between human and budding yeast CIN genes and further identify aberrant mechanisms associated with increases in chromothriptic events.
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Affiliation(s)
- Laura L. Thompson
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Allison K. Baergen
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Kirk J. McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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35
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Abstract
In this review, Slade provides an overview of the molecular mechanisms and cellular consequences of PARP and PARG inhibition. The author also highlights the clinical performance of four PARP inhibitors used in cancer therapy (olaparib, rucaparib, niraparib, and talazoparib) and discusses the predictive biomarkers of inhibitor sensitivity and mechanisms of resistance as well as the means of overcoming them through combination therapy. Oxidative and replication stress underlie genomic instability of cancer cells. Amplifying genomic instability through radiotherapy and chemotherapy has been a powerful but nonselective means of killing cancer cells. Precision medicine has revolutionized cancer therapy by putting forth the concept of selective targeting of cancer cells. Poly(ADP-ribose) polymerase (PARP) inhibitors represent a successful example of precision medicine as the first drugs targeting DNA damage response to have entered the clinic. PARP inhibitors act through synthetic lethality with mutations in DNA repair genes and were approved for the treatment of BRCA mutated ovarian and breast cancer. PARP inhibitors destabilize replication forks through PARP DNA entrapment and induce cell death through replication stress-induced mitotic catastrophe. Inhibitors of poly(ADP-ribose) glycohydrolase (PARG) exploit and exacerbate replication deficiencies of cancer cells and may complement PARP inhibitors in targeting a broad range of cancer types with different sources of genomic instability. Here I provide an overview of the molecular mechanisms and cellular consequences of PARP and PARG inhibition. I highlight clinical performance of four PARP inhibitors used in cancer therapy (olaparib, rucaparib, niraparib, and talazoparib) and discuss the predictive biomarkers of inhibitor sensitivity, mechanisms of resistance as well as the means of overcoming them through combination therapy.
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Affiliation(s)
- Dea Slade
- Department of Biochemistry, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, 1030 Vienna, Austria
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36
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Anderson KJ, Tan AC, Parkinson J, Back M, Kastelan M, Newey A, Brewer J, Wheeler H, Hudson AL, Amin SB, Johnson KC, Barthel FP, Verhaak RGW, Khasraw M. Molecular and clonal evolution in recurrent metastatic gliosarcoma. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004671. [PMID: 31896544 PMCID: PMC6996521 DOI: 10.1101/mcs.a004671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/01/2019] [Indexed: 01/25/2023] Open
Abstract
We discuss the molecular evolution of gliosarcoma, a mesenchymal type of glioblastoma (GBM), using the case of a 37-yr-old woman who developed two recurrences and an extracranial metastasis. She was initially diagnosed with isocitrate dehydrogenase (IDH) wild-type gliosarcoma in the frontal lobe and treated with surgery followed by concurrent radiotherapy with temozolomide. Five months later the tumor recurred in the left frontal lobe, outside the initially resected area, and was treated with further surgery and radiotherapy. Six months later the patient developed a second left frontal recurrence and was again treated with surgery and radiotherapy. Six weeks later, further recurrence was observed in the brain and bone, and biopsy confirmed metastases in the pelvic bones. To understand the clonal relationships between the four tumor instances and the origin of metastasis, we performed whole-genome sequencing of the intracranial tumors and the tumor located in the right iliac bone. We compared their mutational and copy-number profiles and inferred the clonal phylogeny. The tumors harbored shared alterations in GBM driver genes, including mutations in TP53, NF1, and RB1, and CDKN2A deletion. Whole-genome doubling was identified in the first recurrence and the extracranial metastasis. Comparisons of the metastatic to intracranial tumors highlighted a high similarity in molecular profile but contrasting evidence regarding the origin of the metastasis. Subclonal reconstruction suggested a parallel evolution of the recurrent tumors, and that the metastatic tumor was largely derived from the first recurrence. We conclude that metastasis in glioma can be a late event in tumorigenesis.
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Affiliation(s)
- Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06085, USA
| | - Aaron C Tan
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia.,National Cancer Centre Singapore, Singapore, 169610 Singapore
| | - Jonathon Parkinson
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia.,The Brain Cancer Group, North Shore Private Hospital, St Leonards, New South Wales 2065, Australia.,The NHMRC Clinical Trials Centre, the University of Sydney, Camperdown, New South Wales 2066, Australia
| | - Michael Back
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia.,The Brain Cancer Group, North Shore Private Hospital, St Leonards, New South Wales 2065, Australia.,The NHMRC Clinical Trials Centre, the University of Sydney, Camperdown, New South Wales 2066, Australia
| | - Marina Kastelan
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia.,The Brain Cancer Group, North Shore Private Hospital, St Leonards, New South Wales 2065, Australia
| | - Allison Newey
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia
| | - Janice Brewer
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia
| | - Helen Wheeler
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia.,The Brain Cancer Group, North Shore Private Hospital, St Leonards, New South Wales 2065, Australia.,The NHMRC Clinical Trials Centre, the University of Sydney, Camperdown, New South Wales 2066, Australia.,Bill Walsh Translational Cancer Research Laboratory, Kolling Institute of Medical Research, St Leonards, New South Wales 2065, Australia
| | - Amanda L Hudson
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia.,The Brain Cancer Group, North Shore Private Hospital, St Leonards, New South Wales 2065, Australia.,The NHMRC Clinical Trials Centre, the University of Sydney, Camperdown, New South Wales 2066, Australia.,Bill Walsh Translational Cancer Research Laboratory, Kolling Institute of Medical Research, St Leonards, New South Wales 2065, Australia
| | - Samirkumar B Amin
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06085, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06085, USA
| | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06085, USA.,Department of Pathology, VU University Medical Center/Brain Tumor Center Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06085, USA
| | - Mustafa Khasraw
- Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales 2065, Australia.,The Brain Cancer Group, North Shore Private Hospital, St Leonards, New South Wales 2065, Australia.,The NHMRC Clinical Trials Centre, the University of Sydney, Camperdown, New South Wales 2066, Australia
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37
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Dewhurst SM. Chromothripsis and telomere crisis: engines of genome instability. Curr Opin Genet Dev 2020; 60:41-47. [PMID: 32151946 PMCID: PMC7230029 DOI: 10.1016/j.gde.2020.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 12/14/2022]
Abstract
In the early stages of carcinogenesis cells confront two key suppressive checkpoints; senescence and telomere crisis. Telomere crisis is characterized by massive chromosomal instability and cell death. The genetic instability initiated during crisis leaves detectable scars on cancer genomes, the full scope of which is only just beginning to be appreciated. In particular, the dramatic genome reshuffling phenomenon chromothripsis has been mechanistically linked to the resolution of DNA bridges formed by dicentric chromosomes, and by the shattering of DNA inside micronuclei. Furthermore, an intriguing connection to innate immune signaling has begun to position telomere crisis as a crucial stage not only in the evolution of the cancer genome, but also in the interaction between the genome and the immune system.
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Affiliation(s)
- Sally M Dewhurst
- Laboratory of Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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38
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Pellestor F, Gatinois V. Chromoanagenesis: a piece of the macroevolution scenario. Mol Cytogenet 2020; 13:3. [PMID: 32010222 PMCID: PMC6988253 DOI: 10.1186/s13039-020-0470-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/05/2020] [Indexed: 01/04/2023] Open
Abstract
Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution. Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms. In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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39
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Hernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez J, Ochoa S. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. Genes (Basel) 2019; 10:E865. [PMID: 31671657 PMCID: PMC6896122 DOI: 10.3390/genes10110865] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the characterization of the disease. More important though is the understanding of their causes, prognosis, and therapeutics. There is a multitude of factors associated with anomalous control of gene expression in cancer. Many of these factors are now amenable to be studied comprehensively by means of experiments based on diverse omic technologies. However, characterizing each dimension of the phenomenon individually has proven to fall short in presenting a clear picture of expression regulation as a whole. In this review article, we discuss some of the more relevant factors affecting gene expression control both, under normal conditions and in tumor settings. We describe the different omic approaches that we can use as well as the computational genomic analysis needed to track down these factors. Then we present theoretical and computational frameworks developed to integrate the amount of diverse information provided by such single-omic analyses. We contextualize this within a systems biology-based multi-omic regulation setting, aimed at better understanding the complex interplay of gene expression deregulation in cancer.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Helena Reyes-Gopar
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
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40
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Ben-David U, Amon A. Context is everything: aneuploidy in cancer. Nat Rev Genet 2019; 21:44-62. [DOI: 10.1038/s41576-019-0171-x] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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41
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Pantelias A, Karachristou I, Georgakilas AG, Terzoudi GI. Interphase Cytogenetic Analysis of Micronucleated and Multinucleated Cells Supports the Premature Chromosome Condensation Hypothesis as the Mechanistic Origin of Chromothripsis. Cancers (Basel) 2019; 11:E1123. [PMID: 31390832 PMCID: PMC6721583 DOI: 10.3390/cancers11081123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 08/03/2019] [Indexed: 12/19/2022] Open
Abstract
The discovery of chromothripsis in cancer genomes challenges the long-standing concept of carcinogenesis as the result of progressive genetic events. Despite recent advances in describing chromothripsis, its mechanistic origin remains elusive. The prevailing conception is that it arises from a massive accumulation of fragmented DNA inside micronuclei (MN), whose defective nuclear envelope ruptures or leads to aberrant DNA replication, before main nuclei enter mitosis. An alternative hypothesis is that the premature chromosome condensation (PCC) dynamics in asynchronous micronucleated cells underlie chromosome shattering in a single catastrophic event, a hallmark of chromothripsis. Specifically, when main nuclei enter mitosis, premature chromatin condensation provokes the shattering of chromosomes entrapped inside MN, if they are still undergoing DNA replication. To test this hypothesis, the agent RO-3306, a selective ATP-competitive inhibitor of CDK1 that promotes cell cycle arrest at the G2/M boundary, was used in this study to control the degree of cell cycle asynchrony between main nuclei and MN. By delaying the entrance of main nuclei into mitosis, additional time was allowed for the completion of DNA replication and duplication of chromosomes inside MN. We performed interphase cytogenetic analysis using asynchronous micronucleated cells generated by exposure of human lymphocytes to γ-rays, and heterophasic multinucleated Chinese hamster ovary (CHO) cells generated by cell fusion procedures. Our results demonstrate that the PCC dynamics during asynchronous mitosis in micronucleated or multinucleated cells are an important determinant of chromosome shattering and may underlie the mechanistic origin of chromothripsis.
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Affiliation(s)
- Antonio Pantelias
- Laboratory of Health Physics, Radiobiology & Cytogenetics, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Centre for Scientific Research "Demokritos", 15341 Agia Paraskevi, Greece.
- DNA Damage Laboratory, Physics Department, School of Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780 Zografou, Greece.
| | - Ioanna Karachristou
- Laboratory of Health Physics, Radiobiology & Cytogenetics, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Centre for Scientific Research "Demokritos", 15341 Agia Paraskevi, Greece
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780 Zografou, Greece
| | - Georgia I Terzoudi
- Laboratory of Health Physics, Radiobiology & Cytogenetics, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Centre for Scientific Research "Demokritos", 15341 Agia Paraskevi, Greece.
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Baltus C, Toffoli S, London F, Delrée P, Gilliard C, Gustin T. Chromothripsis in an Early Recurrent Chordoid Meningioma. World Neurosurg 2019; 130:380-385. [PMID: 31295612 DOI: 10.1016/j.wneu.2019.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 01/21/2023]
Abstract
BACKGROUND Chromothripsis is characterized by a multitude of chromosomal rearrangements during a unique cataclysmic event in a cell life. Disintegration of one or several chromosomes is followed by a chaotic rearrangement of generated fragments. It might play a role in oncogenesis and tumor progression. It is observed in 2%-3% of cancers and is rarely reported in benign tumors. We report a case of massive chromothripsis in a fast growing chordoid meningioma. CASE DESCRIPTION A 55-year-old woman was admitted for a meningeal mass developing in the right parietal parasagittal area. She underwent subtotal resection of the tumor. Histologic analysis revealed a chordoid meningioma (World Health Organization grade II). Six months later, magnetic resonance imaging showed a large bilateral tumor recurrence. After a second surgery, the patient received radiotherapy. Thereafter, the clinical course was uneventful. Comparative genomic hybridization showed only a monosomy X in the primary tumor. In the recurrent meningioma, this anomaly was associated with a massive chromothripsis including more than 370 chromosomal abnormalities affecting chromosomes 1-22. CONCLUSIONS Chromothripsis is rarely described in benign tumors and especially in meningiomas. In the presented case, the high number of chromosomal rearrangements and the onset of this phenomenon at a later stage of tumor progression are very unusual. The role of surgical stress on the emergence of chromothripsis and its relation with tumor aggressiveness are discussed.
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Affiliation(s)
- Cédric Baltus
- Department of Neurosurgery, CHU UcL Namur, Yvoir, Belgium.
| | | | | | - Paul Delrée
- Pathology and Genetics Institute, Gosselies, Belgium
| | | | - Thierry Gustin
- Department of Neurosurgery, CHU UcL Namur, Yvoir, Belgium
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Huguet F, Flynn S, Vagnarelli P. The Role of Phosphatases in Nuclear Envelope Disassembly and Reassembly and Their Relevance to Pathologies. Cells 2019; 8:cells8070687. [PMID: 31284660 PMCID: PMC6678589 DOI: 10.3390/cells8070687] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 12/20/2022] Open
Abstract
The role of kinases in the regulation of cell cycle transitions is very well established, however, over the past decade, studies have identified the ever-growing importance of phosphatases in these processes. It is well-known that an intact or otherwise non-deformed nuclear envelope (NE) is essential for maintaining healthy cells and any deviation from this can result in pathological conditions. This review aims at assessing the current understanding of how phosphatases contribute to the remodelling of the nuclear envelope during its disassembling and reformation after cell division and how errors in this process may lead to the development of diseases.
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Affiliation(s)
- Florentin Huguet
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Shane Flynn
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK.
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Biermann J, Langen B, Nemes S, Holmberg E, Parris TZ, Werner Rönnerman E, Engqvist H, Kovács A, Helou K, Karlsson P. Radiation-induced genomic instability in breast carcinomas of the Swedish hemangioma cohort. Genes Chromosomes Cancer 2019; 58:627-635. [PMID: 30938900 DOI: 10.1002/gcc.22757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Radiation-induced genomic instability (GI) is hypothesized to persist after exposure and ultimately promote carcinogenesis. Based on the absorbed dose to the breast, an increased risk of developing breast cancer was shown in the Swedish hemangioma cohort that was treated with radium-226 for skin hemangioma as infants. Here, we screened 31 primary breast carcinomas for genetic alterations using the OncoScan CNV Plus Assay to assess GI and chromothripsis-like patterns associated with the absorbed dose to the breast. Higher absorbed doses were associated with increased numbers of copy number alterations in the tumor genome and thus a more unstable genome. Hence, the observed dose-dependent GI in the tumor genome is a measurable manifestation of the long-term effects of irradiation. We developed a highly predictive Cox regression model for overall survival based on the interaction between absorbed dose and GI. The Swedish hemangioma cohort is a valuable cohort to investigate the biological relationship between absorbed dose and GI in irradiated humans. This work gives a biological basis for improved risk assessment to minimize carcinogenesis as a secondary disease after radiation therapy.
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Affiliation(s)
- Jana Biermann
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Britta Langen
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Szilárd Nemes
- Department of Orthopedics, Swedish Hip Arthroplasty Register, Gothenburg, Sweden
| | - Erik Holmberg
- Department of Oncology, Regional Cancer Center Western Sweden, Gothenburg, Sweden
| | - Toshima Z Parris
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Hanna Engqvist
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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Abstract
Abstract
Chromosomes were discovered more than 130 years ago. The implementation of chromosomal investigations in clinical diagnostics was fueled by determining the correct number of human chromosomes to be 46 and the development of specific banding techniques. Subsequent technical improvements in the field of genetic diagnostics, such as fluorescence in situ hybridization (FISH), chromosomal microarrays (CMA, array CGH) or next-generation sequencing (NGS) techniques, partially succeeded in overcoming limitations of banding cytogenetics. Consequently, nowadays, higher diagnostic yields can be achieved if new approaches such as NGS, CMA or FISH are applied in combination with cytogenetics. Nonetheless, high-resolution DNA-focused techniques have dominated clinical diagnostics more recently, rather than a “chromosomic view,” including banding cytogenetics as a precondition for the application of higher resolution methods. Currently, there is a renaissance of this “chromosomic view” in research, understanding chromosomes to be an essential feature of genomic architecture, owing to the discovery of (i) higher order chromosomal sub-compartments, (ii) chromosomal features that influence genomic architecture, gene expression, and evolution, and (iii) 3D and 4D chromatin organization within the nucleus, including the complex way in which chromosomes interact with each other. Interestingly, in many instances research was triggered by specific clinical diagnostic cases or diseases that contributed to new and fascinating insights, not only into disease mechanisms but also into basic principles of chromosome biology. Here we review the role, the intrinsic value, and the perspectives of chromosomes in a molecular genetics-dominated human genetics diagnostic era and make comparison with basic research, where these benefits are well-recognized.
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