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Lynch AR, Bradford S, Zhou AS, Oxendine K, Henderson L, Horner VL, Weaver BA, Burkard ME. A survey of chromosomal instability measures across mechanistic models. Proc Natl Acad Sci U S A 2024; 121:e2309621121. [PMID: 38588415 PMCID: PMC11032477 DOI: 10.1073/pnas.2309621121] [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: 06/22/2023] [Accepted: 01/25/2024] [Indexed: 04/10/2024] Open
Abstract
Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, six-centromere FISH, bulk transcriptomics, and single-cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples significantly correlated (R = 0.72; P < 0.001) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also significantly correlate (R = 0.76; P < 0.001) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, scDNAseq detects CIN with high sensitivity, and significantly correlates with imaging methods (R = 0.82; P < 0.001). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate the comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division. This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.
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Affiliation(s)
- Andrew R. Lynch
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Shermineh Bradford
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Amber S. Zhou
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Kim Oxendine
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Les Henderson
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Vanessa L. Horner
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Beth A. Weaver
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI53705
| | - Mark E. Burkard
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
- Division of Hematology Oncology and Palliative Care, Department of Medicine University of Wisconsin–Madison, Madison, WI53705
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2
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Mallick S, Choi Y, Taylor AM, Cosper PF. Human Papillomavirus-Induced Chromosomal Instability and Aneuploidy in Squamous Cell Cancers. Viruses 2024; 16:501. [PMID: 38675844 PMCID: PMC11053578 DOI: 10.3390/v16040501] [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: 02/04/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Chromosomal instability (CIN) and aneuploidy are hallmarks of cancer. CIN is defined as a continuous rate of chromosome missegregation events over the course of multiple cell divisions. CIN causes aneuploidy, a state of abnormal chromosome content differing from a multiple of the haploid. Human papillomavirus (HPV) is a well-known cause of squamous cancers of the oropharynx, cervix, and anus. The HPV E6 and E7 oncogenes have well-known roles in carcinogenesis, but additional genomic events, such as CIN and aneuploidy, are often required for tumor formation. HPV+ squamous cancers have an increased frequency of specific types of CIN, including polar chromosomes. CIN leads to chromosome gains and losses (aneuploidies) specific to HPV+ cancers, which are distinct from HPV- cancers. HPV-specific CIN and aneuploidy may have implications for prognosis and therapeutic response and may provide insight into novel therapeutic vulnerabilities. Here, we review HPV-specific types of CIN and patterns of aneuploidy in squamous cancers, as well as how this impacts patient prognosis and treatment.
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Affiliation(s)
- Samyukta Mallick
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032, USA
| | - Yeseo Choi
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Cancer Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Alison M. Taylor
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Pippa F. Cosper
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
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3
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Schneider MP, Cullen AE, Pangonyte J, Skelton J, Major H, Van Oudenhove E, Garcia MJ, Chaves Urbano B, Piskorz AM, Brenton JD, Macintyre G, Markowetz F. scAbsolute: measuring single-cell ploidy and replication status. Genome Biol 2024; 25:62. [PMID: 38438920 PMCID: PMC10910719 DOI: 10.1186/s13059-024-03204-y] [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: 06/15/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information, scAbsolute achieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome duplications. We demonstrate scAbsolute's capabilities using experimental cell multiplets, a FUCCI cell cycle expression system, and a benchmark against state-of-the-art methods. scAbsolute provides a robust foundation for single-cell DNA sequencing analysis across different technologies and has the potential to enable improvements in a number of downstream analyses.
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Affiliation(s)
- Michael P Schneider
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Amy E Cullen
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Justina Pangonyte
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Jason Skelton
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Harvey Major
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Elke Van Oudenhove
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Maria J Garcia
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Anna M Piskorz
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - James D Brenton
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Geoff Macintyre
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Florian Markowetz
- University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK.
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4
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Lynch A, Bradford S, Burkard ME. The reckoning of chromosomal instability: past, present, future. Chromosome Res 2024; 32:2. [PMID: 38367036 DOI: 10.1007/s10577-024-09746-y] [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: 01/11/2024] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 02/19/2024]
Abstract
Quantitative measures of CIN are crucial to our understanding of its role in cancer. Technological advances have changed the way CIN is quantified, offering increased accuracy and insight. Here, we review measures of CIN through its rise as a field, discuss considerations for its measurement, and look forward to future quantification of CIN.
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Affiliation(s)
- Andrew Lynch
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Shermineh Bradford
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Mark E Burkard
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA.
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
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5
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Spoor JKH, den Braber M, Dirven CMF, Pennycuick A, Bartkova J, Bartek J, van Dis V, van den Bosch TPP, Leenstra S, Venkatesan S. Investigating chromosomal instability in long-term survivors with glioblastoma and grade 4 astrocytoma. Front Oncol 2024; 13:1218297. [PMID: 38260852 PMCID: PMC10800987 DOI: 10.3389/fonc.2023.1218297] [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: 05/06/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Background Only a small group of patients with glioblastoma multiforme (GBM) survives more than 36 months, so-called long-term survivors. Recent studies have shown that chromosomal instability (CIN) plays a prognostic and predictive role among different cancer types. Here, we compared histological (chromosome missegregation) and bioinformatic metrics (CIN signatures) of CIN in tumors of GBM typical survivors (≤36 months overall survival), GBM long-term survivors and isocitrate dehydrogenase (IDH)-mutant grade 4 astrocytomas. Methods Tumor sections of all gliomas were examined for anaphases and chromosome missegregation. Further CIN signature activity analysis in the The Cancer Genome Atlas (TCGA)-GBM cohort was performed. Results Our data show that chromosome missegregation is pervasive in high grade gliomas and is not different between the 3 groups. We find only limited evidence of altered CIN levels in tumors of GBM long-term survivors relative to the other groups, since a significant depletion in CIN signature 11 relative to GBM typical survivors was the only alteration detected. In contrast, within IDH-mutant grade 4 astrocytomas we detected a significant enrichment of CIN signature 5 and 10 activities and a depletion of CIN signature 1 activity relative to tumors of GBM typical survivors. Conclusions Our data suggest that CIN is pervasive in high grade gliomas, however this is unlikely to be a major contributor to the phenomenon of long-term survivorship in GBM. Nevertheless, further evaluation of specific types of CIN (signatures) could have prognostic value in patients suffering from grade 4 gliomas.
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Affiliation(s)
- Jochem K. H. Spoor
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Paediatric Neurosurgery, Erasmus Medical Center Sophia Children’s Hospital, Rotterdam, Netherlands
| | - May den Braber
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Clemens M. F. Dirven
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Adam Pennycuick
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Jirina Bartkova
- Genome Integrity Group, Danish Cancer Institute, Danish Cancer Society, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Danish Cancer Society, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Vera van Dis
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Sieger Leenstra
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Subramanian Venkatesan
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Oncology, University College London, London, United Kingdom
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Taluri S, Oza VH, Soelter TM, Fisher JL, Lasseigne BN. Inferring chromosomal instability from copy number aberrations as a measure of chromosomal instability across human cancers. Cancer Rep (Hoboken) 2023; 6:e1902. [PMID: 37680168 PMCID: PMC10728508 DOI: 10.1002/cnr2.1902] [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: 05/25/2023] [Revised: 08/16/2023] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Cancer is a complex disease that is the second leading cause of death in the United States. Despite research efforts, the ability to manage cancer and select optimal therapeutic responses for each patient remains elusive. Chromosomal instability (CIN) is primarily a product of segregation errors wherein one or many chromosomes, in part or whole, vary in number. CIN is an enabling characteristic of cancer, contributes to tumor-cell heterogeneity, and plays a crucial role in the multistep tumorigenesis process, especially in tumor growth and initiation and in response to treatment. AIMS Multiple studies have reported different metrics for analyzing copy number aberrations as surrogates of CIN from DNA copy number variation data. However, these metrics differ in how they are calculated with respect to the type of variation, the magnitude of change, and the inclusion of breakpoints. Here we compared metrics capturing CIN as either numerical aberrations, structural aberrations, or a combination of the two across 33 cancer data sets from The Cancer Genome Atlas (TCGA). METHODS AND RESULTS Using CIN inferred by methods in the CINmetrics R package, we evaluated how six copy number CIN surrogates compared across TCGA cohorts by assessing each across tumor types, as well as how they associate with tumor stage, metastasis, and nodal involvement, and with respect to patient sex. CONCLUSIONS We found that the tumor type impacts how well any two given CIN metrics correlate. While we also identified overlap between metrics regarding their association with clinical characteristics and patient sex, there was not complete agreement between metrics. We identified several cases where only one CIN metric was significantly associated with a clinical characteristic or patient sex for a given tumor type. Therefore, caution should be used when describing CIN based on a given metric or comparing it to other studies.
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Affiliation(s)
- Sasha Taluri
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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7
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Andrade JR, Gallagher AD, Maharaj J, McClelland SE. Disentangling the roles of aneuploidy, chromosomal instability and tumour heterogeneity in developing resistance to cancer therapies. Chromosome Res 2023; 31:28. [PMID: 37721639 PMCID: PMC10506951 DOI: 10.1007/s10577-023-09737-5] [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: 05/01/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Aneuploidy is defined as the cellular state of having a number of chromosomes that deviates from a multiple of the normal haploid chromosome number of a given organism. Aneuploidy can be present in a static state: Down syndrome individuals stably maintain an extra copy of chromosome 21 in their cells. In cancer cells, however, aneuploidy is usually present in combination with chromosomal instability (CIN) which leads to a continual generation of new chromosomal alterations and the development of intratumour heterogeneity (ITH). The prevalence of cells with specific chromosomal alterations is further shaped by evolutionary selection, for example, during the administration of cancer therapies. Aneuploidy, CIN and ITH have each been individually associated with poor prognosis in cancer, and a wealth of evidence suggests they contribute, either alone or in combination, to cancer therapy resistance by providing a reservoir of potential resistant states, or the ability to rapidly evolve resistance. A full understanding of the contribution and interplay between aneuploidy, CIN and ITH is required to tackle therapy resistance in cancer patients. However, these characteristics often co-occur and are intrinsically linked, presenting a major challenge to defining their individual contributions. Moreover, their accurate measurement in both experimental and clinical settings is a technical hurdle. Here, we attempt to deconstruct the contribution of the individual and combined roles of aneuploidy, CIN and ITH to therapy resistance in cancer, and outline emerging approaches to measure and disentangle their roles as a step towards integrating these principles into cancer therapeutic strategy.
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Affiliation(s)
- Joana Reis Andrade
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Annie Dinky Gallagher
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Jovanna Maharaj
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
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8
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Baba SA, Sun Q, Mugisha S, Labhsetwar S, Klemke R, Desgrosellier JS. Breast cancer stem cells tolerate chromosomal instability during tumor progression via c-Jun/AXL stress signaling. Heliyon 2023; 9:e20182. [PMID: 37809421 PMCID: PMC10559946 DOI: 10.1016/j.heliyon.2023.e20182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Chromosomal instability (CIN) is critical for tumor evolution, yet its relationship with stemness is unclear. Here, we describe CIN as a key stress induced during tumor initiation that is uniquely tolerated by breast cancer stem cells in an activated signaling state (aCSCs). While we noted elevated CIN specifically in tumors from aCSCs, this was not intrinsic to these cells, as baseline levels were similar to non-stem cell types. This suggests that CIN is induced during tumor initiation, and that aCSCs can better tolerate this stress. Further, this increased CIN may be transient, as it was only in low-burden aCSC tumors, with levels diminishing in more established disease. Phospho-array profiling revealed specific activation of c-Jun stress signaling in aCSCs, which we hypothesized could induce genes responsible for CIN tolerance. Indeed, we identified AXL as a c-Jun dependent gene enriched in aCSCs that enhances resistance to this stress. Thus, CIN tolerance mediated by c-Jun/AXL signaling may be a defining feature of stemness, contributing to breast cancer progression.
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Affiliation(s)
- Shahnawaz A. Baba
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California,San Diego, La Jolla, CA 92093, USA
| | - Qi Sun
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California,San Diego, La Jolla, CA 92093, USA
| | - Samson Mugisha
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California,San Diego, La Jolla, CA 92093, USA
| | - Shreyas Labhsetwar
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Richard Klemke
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California,San Diego, La Jolla, CA 92093, USA
| | - Jay S. Desgrosellier
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California,San Diego, La Jolla, CA 92093, USA
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9
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Taluri S, Oza VH, Soelter TM, Fisher JL, Lasseigne BN. Inferring chromosomal instability from copy number aberrations as a measure of chromosomal instability across human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542174. [PMID: 37292608 PMCID: PMC10245901 DOI: 10.1101/2023.05.24.542174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Cancer is a complex disease that is the second leading cause of death in the United States. Despite research efforts, the ability to manage cancer and select optimal therapeutic responses for each patient remains elusive. Chromosomal instability (CIN) is primarily a product of segregation errors wherein one or many chromosomes, in part or whole, vary in number. CIN is an enabling characteristic of cancer, contributes to tumor-cell heterogeneity, and plays a crucial role in the multistep tumorigenesis process, especially in tumor growth and initiation and in response to treatment. Aims Multiple studies have reported different metrics for analyzing copy number aberrations as surrogates of CIN from DNA copy number variation data. However, these metrics differ in how they are calculated with respect to the type of variation, the magnitude of change, and the inclusion of breakpoints. Here we compared metrics capturing CIN as either numerical aberrations, structural aberrations, or a combination of the two across 33 cancer data sets from The Cancer Genome Atlas (TCGA). Methods and results Using CIN inferred by methods in the CINmetrics R package, we evaluated how six copy number CIN surrogates compared across TCGA cohorts by assessing each across tumor types, as well as how they associate with tumor stage, metastasis, and nodal involvement, and with respect to patient sex. Conclusions We found that the tumor type impacts how well any two given CIN metrics correlate. While we also identified overlap between metrics regarding their association with clinical characteristics and patient sex, there was not complete agreement between metrics. We identified several cases where only one CIN metric was significantly associated with a clinical characteristic or patient sex for a given tumor type. Therefore, caution should be used when describing CIN based on a given metric or comparing it to other studies.
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Affiliation(s)
- Sasha Taluri
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Zhang X, Yao J, Li X, Niu N, Liu Y, Hajek RA, Peng G, Westin S, Sood AK, Liu J. Targeting polyploid giant cancer cells potentiates a therapeutic response and overcomes resistance to PARP inhibitors in ovarian cancer. SCIENCE ADVANCES 2023; 9:eadf7195. [PMID: 37478190 PMCID: PMC10361597 DOI: 10.1126/sciadv.adf7195] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
To understand the mechanism of acquired resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) olaparib, we induced the formation of polyploid giant cancer cells (PGCCs) in ovarian and breast cancer cell lines, high-grade serous cancer (HGSC)-derived organoids, and patient-derived xenografts (PDXs). Time-lapse tracking of ovarian cancer cells revealed that PGCCs primarily developed from endoreplication after exposure to sublethal concentrations of olaparib. PGCCs exhibited features of senescent cells but, after olaparib withdrawal, can escape senescence via restitutional multipolar endomitosis and other noncanonical modes of cell division to generate mitotically competent resistant daughter cells. The contraceptive drug mifepristone blocked PGCC formation and daughter cell formation. Mifepristone/olaparib combination therapy substantially reduced tumor growth in PDX models without previous olaparib exposure, while mifepristone alone decreased tumor growth in PDX models with acquired olaparib resistance. Thus, targeting PGCCs may represent a promising approach to potentiate the therapeutic response to PARPi and overcome PARPi-induced resistance.
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Affiliation(s)
- Xudong Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoran Li
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Na Niu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yan Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard A. Hajek
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shannon Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anil K. Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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11
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Cimini D. Twenty years of merotelic kinetochore attachments: a historical perspective. Chromosome Res 2023; 31:18. [PMID: 37466740 PMCID: PMC10411636 DOI: 10.1007/s10577-023-09727-7] [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: 05/01/2023] [Revised: 06/20/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Micronuclei, small DNA-containing structures separate from the main nucleus, were used for decades as an indicator of genotoxic damage. Micronuclei containing whole chromosomes were considered a biomarker of aneuploidy and were believed to form, upon mitotic exit, from chromosomes that lagged behind in anaphase as all other chromosomes segregated to the poles of the mitotic spindle. However, the mechanism responsible for inducing anaphase lagging chromosomes remained unknown until just over twenty years ago. Here, I summarize what preceded and what followed this discovery, highlighting some of the open questions and opportunities for future investigation.
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Affiliation(s)
- Daniela Cimini
- Department of Biological Sciences and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
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Lynch AR, Bradford S, Zhou AS, Oxendine K, Henderson L, Horner VL, Weaver BA, Burkard ME. A survey of CIN measures across mechanistic models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.544840. [PMID: 37398147 PMCID: PMC10312700 DOI: 10.1101/2023.06.15.544840] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, 6-centromere FISH, bulk transcriptomics, and single cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples correlated well (R=0.77; p<0.01) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also correlate well (R=0.77; p<0.01) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, single-cell DNA sequencing (scDNAseq) detects CIN with high sensitivity, and correlates very well with imaging methods (R=0.83; p<0.01). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division (MDD). This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.
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Affiliation(s)
- Andrew R. Lynch
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Shermineh Bradford
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Amber S. Zhou
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Kim Oxendine
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Les Henderson
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Vanessa L. Horner
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Beth A. Weaver
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, University of Wisconsin – Madison, Madison, WI, USA
| | - Mark E. Burkard
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
- Division of Hematology Oncology and Palliative Care, Department of Medicine, University of Wisconsin – Madison, Madison, WI, USA
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13
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Bakhoum SF. Targeting the undruggable. Science 2023; 380:47. [PMID: 37023189 DOI: 10.1126/science.adg7671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Journey through basic biology reveals a way to treat chromosomally unstable cancers.
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Affiliation(s)
- Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Department of Radiation Oncology, MSKCC, New York, NY, USA
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14
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Gordon MR, Zhu J, Sun G, Li R. Suppression of chromosome instability by targeting a DNA helicase in budding yeast. Mol Biol Cell 2022; 34:ar3. [PMID: 36350688 PMCID: PMC9816644 DOI: 10.1091/mbc.e22-09-0395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Chromosome instability (CIN) is an important driver of cancer initiation, progression, drug resistance, and aging. As such, genes whose inhibition suppresses CIN are potential therapeutic targets. We report here that deletion of an accessory DNA helicase, Rrm3, suppresses high CIN caused by a wide range of genetic or pharmacological perturbations in yeast. Although this helicase mutant has altered cell cycle dynamics, suppression of CIN by rrm3∆ is independent of the DNA damage and spindle assembly checkpoints. Instead, the rrm3∆ mutant may have increased kinetochore-microtubule error correction due to an altered localization of Aurora B kinase and associated phosphatase, PP2A-Rts1.
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Affiliation(s)
- Molly R. Gordon
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jin Zhu
- Mechanobiology Institute and
| | - Gordon Sun
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Department of Biomedical Engineering and
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Mechanobiology Institute and,Department of Biological Sciences, National University of Singapore, 117411,Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218,*Address correspondence to: Rong Li ()
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15
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Jiang XF, Zhang BM, Du FQ, Guo JN, Wang D, Li YE, Deng SH, Cui BB, Liu YL. Exploring biomarkers for prognosis and neoadjuvant chemosensitivity in rectal cancer: Multi-omics and ctDNA sequencing collaboration. Front Immunol 2022; 13:1013828. [PMID: 36569844 PMCID: PMC9780298 DOI: 10.3389/fimmu.2022.1013828] [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: 08/10/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction This study aimed to identified the key genes and sequencing metrics for predicting prognosis and efficacy of neoadjuvant chemotherapy (nCT) in rectal cancer (RC) based on genomic DNA sequencing in samples with different origin and multi-omics association database. Methods We collected 16 RC patients and obtained DNA sequencing data from cancer tissues and plasma cell-free DNA before and after nCT. Various gene variations were analyzed, including single nucleotide variants (SNV), copy number variation (CNV), tumor mutation burden (TMB), copy number instability (CNI) and mutant-allele tumor heterogeneity (MATH). We also identified genes by which CNV level can differentiate the response to nCT. The Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database were used to further evaluate the specific role of therapeutic relevant genes and screen out the key genes in multi-omics levels. After the intersection of the screened genes from differential expression analysis, survival analysis and principal components analysis dimensionality reduction cluster analysis, the key genes were finally identified. Results The genes CNV level of principal component genes in baseline blood and cancer tissues could significantly distinguish the two groups of patients. The CNV of HSP90AA1, EGFR, SRC, MTOR, etc. were relatively gained in the better group compared with the poor group in baseline blood. The CNI and TMB was significantly different between the two groups. The increased expression of HSP90AA1, EGFR, and SRC was associated with increased sensitivity to multiple chemotherapeutic drugs. The nCT predictive score obtained by therapeutic relevant genes could be a potential prognostic indicator, and the combination with TMB could further refine prognostic prediction for patients. After a series of analysis in multi-omics association database, EGFR and HSP90AA1 with significant differences in multiple aspects were identified as the key predictive genes related to prognosis and the sensitivity of nCT. Discussion This work revealed that effective combined application and analysis in multi-omics data are critical to search for predictive biomarkers. The key genes EGFR and HSP90AA1 could serve as an effective biomarker to predict prognose and neoadjuvant chemosensitivity.
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Affiliation(s)
- Xiu-Feng Jiang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bo-Miao Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fen-Qi Du
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jun-Nan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dan Wang
- Department of Neurology, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, China
| | - Yi-En Li
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shen-Hui Deng
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bin-Bin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
| | - Yan-Long Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
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16
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Ma D, Ma Y, Ma Y, Liu J, Gu Y, Liu N, Xiang C, Liu H, Sang W. Molecular subtyping of CD5+ diffuse large B-cell lymphoma based on DNA-targeted sequencing and Lymph2Cx. Front Oncol 2022; 12:941347. [PMID: 36081566 PMCID: PMC9445310 DOI: 10.3389/fonc.2022.941347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundCD5-positive diffuse large B-cell lymphoma (CD5+ DLBCL) showed poor prognosis in the rituximab era, with limited research on its genetic characteristics and cell of origin (COO). We aimed to demonstrate the molecular characteristics of CD5+ DLBCL and to discover potential prognostic factors.MethodsWe included 24 cases of CD5+ DLBCL and 23 CD5-negative (CD5-) counterparts and collected their clinicopathological features. Targeted DNA sequencing of 475 lymphoma-related genes was performed, and all cases were assigned to distinct genetic subtypes using the LymphGen tool. The COO was determined by the Lymph2Cx assay. The Kaplan–Meier method and Cox proportional hazards model were applied to identify the possible prognostic factors.ResultsCompared with their CD5- counterparts, patients with CD5+ DLBCL tended to have a worse prognosis and a higher incidence of MYD88L265P and CD79B double mutation (MCD) subtype (54.17%, P = 0.005) and activated B cell-like (ABC) subtype (62.5%, P = 00017), as determined by next-generation sequencing and Lymph2Cx, respectively. Moreover, PIM1, MYD88, and KMT2D mutations were detected more frequently in CD5+ DLBCL cases (P < 0.05). According to multivariate analysis, MYC/BCL2 double expression and ABC subtype were correlated with unfavorable overall survival (OS). High mRNA expression of SERPINA9 and MME showed a significant correlation with a better OS, and high expression of MME showed a significant correlation with better progression-free survival in CD5+ DLBCL.ConclusionThe genetic profile of CD5+ DLBCL is characterized by PIM1, MYD88, and KMT2D mutations, with a higher incidence of MCD and ABC subtypes. MYC/BCL2 double expression, ABC subtype, and mRNA expression of SERPINA9 and MME are independently predictive of the prognosis of CD5+ DLBCL.
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Affiliation(s)
- Dongshen Ma
- Department of Pathology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yuhan Ma
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yuanyuan Ma
- Department of Pathology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jia Liu
- Department of Pathology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Ying Gu
- Department of Pathology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Nian Liu
- Department of Pathology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Chenxi Xiang
- Department of Pathology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Hui Liu
- Department of Pathology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Hui Liu, ; Wei Sang,
| | - Wei Sang
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Hui Liu, ; Wei Sang,
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Richardson TE, Walker JM, Abdullah KG, McBrayer SK, Viapiano MS, Mussa ZM, Tsankova NM, Snuderl M, Hatanpaa KJ. Chromosomal instability in adult-type diffuse gliomas. Acta Neuropathol Commun 2022; 10:115. [PMID: 35978439 PMCID: PMC9386991 DOI: 10.1186/s40478-022-01420-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Chromosomal instability (CIN) is a fundamental property of cancer and a key underlying mechanism of tumorigenesis and malignant progression, and has been documented in a wide variety of cancers, including colorectal carcinoma with mutations in genes such as APC. Recent reports have demonstrated that CIN, driven in part by mutations in genes maintaining overall genomic stability, is found in subsets of adult-type diffusely infiltrating gliomas of all histologic and molecular grades, with resulting elevated overall copy number burden, chromothripsis, and poor clinical outcome. Still, relatively few studies have examined the effect of this process, due in part to the difficulty of routinely measuring CIN clinically. Herein, we review the underlying mechanisms of CIN, the relationship between chromosomal instability and malignancy, the prognostic significance and treatment potential in various cancers, systemic disease, and more specifically, in diffusely infiltrating glioma subtypes. While still in the early stages of discovery compared to other solid tumor types in which CIN is a known driver of malignancy, the presence of CIN as an early factor in gliomas may in part explain the ability of these tumors to develop resistance to standard therapy, while also providing a potential molecular target for future therapies.
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Affiliation(s)
- Timothy E. Richardson
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Jamie M. Walker
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 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
| | - 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
| | - 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
| | - Zarmeen M. Mussa
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Nadejda M. Tsankova
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, NY 10016 USA
| | - Kimmo J. Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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18
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Li Z, Ma Z, Xue H, Shen R, Qin K, Zhang Y, Zheng X, Zhang G. Chromatin Separation Regulators Predict the Prognosis and Immune Microenvironment Estimation in Lung Adenocarcinoma. Front Genet 2022; 13:917150. [PMID: 35873497 PMCID: PMC9305311 DOI: 10.3389/fgene.2022.917150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Abnormal chromosome segregation is identified to be a common hallmark of cancer. However, the specific predictive value of it in lung adenocarcinoma (LUAD) is unclear. Method: The RNA sequencing and the clinical data of LUAD were acquired from The Cancer Genome Atlas (TACG) database, and the prognosis-related genes were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were carried out for functional enrichment analysis of the prognosis genes. The independent prognosis signature was determined to construct the nomogram Cox model. Unsupervised clustering analysis was performed to identify the distinguishing clusters in LUAD-samples based on the expression of chromosome segregation regulators (CSRs). The differentially expressed genes (DEGs) and the enriched biological processes and pathways between different clusters were identified. The immune environment estimation, including immune cell infiltration, HLA family genes, immune checkpoint genes, and tumor immune dysfunction and exclusion (TIDE), was assessed between the clusters. The potential small-molecular chemotherapeutics for the individual treatments were predicted via the connectivity map (CMap) database. Results: A total of 2,416 genes were determined as the prognosis-related genes in LUAD. Chromosome segregation is found to be the main bioprocess enriched by the prognostic genes. A total of 48 CSRs were found to be differentially expressed in LUAD samples and were correlated with the poor outcome in LUAD. Nine CSRs were identified as the independent prognostic signatures to construct the nomogram Cox model. The LUAD-samples were divided into two distinct clusters according to the expression of the 48 CSRs. Cell cycle and chromosome segregation regulated genes were enriched in cluster 1, while metabolism regulated genes were enriched in cluster 2. Patients in cluster 2 had a higher score of immune, stroma, and HLA family components, while those in cluster 1 had higher scores of TIDES and immune checkpoint genes. According to the hub genes highly expressed in cluster 1, 74 small-molecular chemotherapeutics were predicted to be effective for the patients at high risk. Conclusion: Our results indicate that the CSRs were correlated with the poor prognosis and the possible immunotherapy resistance in LUAD.
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Affiliation(s)
- Zhaoshui Li
- Qingdao Medical College, Qingdao University, Qingdao, China
- Cardiothoracic Surgery Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Zaiqi Ma
- Cardiothoracic Surgery Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Hong Xue
- Heart Center Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Ruxin Shen
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Kun Qin
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yu Zhang
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xin Zheng
- Cancer Center Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
- *Correspondence: Xin Zheng, ; Guodong Zhang,
| | - Guodong Zhang
- Thoracic Surgery Department, Shandong Cancer Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Xin Zheng, ; Guodong Zhang,
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19
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Overexpression of satellite RNAs in heterochromatin induces chromosomal instability and reflects drug sensitivity in mouse cancer cells. Sci Rep 2022; 12:10999. [PMID: 35768614 PMCID: PMC9243030 DOI: 10.1038/s41598-022-15071-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Overexpression of satellite RNAs in heterochromatin induces chromosomal instability (CIN) through the DNA damage response and cell cycle checkpoint activation. Although satellite RNAs may be therapeutic targets, the associated mechanisms underlying drug sensitivity are unknown. Here, we determined whether satellite RNAs reflect drug sensitivity to the topoisomerase I inhibitor camptothecin (CPT) via CIN induction. We constructed retroviral vectors expressing major satellite and control viruses, infected microsatellite stable mouse colon cancer cells (CT26) and MC38 cells harboring microsatellite instability, and assessed drug sensitivity after 48 h. Cells overexpressing satellite RNAs showed clear features of abnormal segregation, including micronuclei and anaphase bridging, and elevated levels of the DNA damage marker γH2AX relative to controls. Additionally, overexpression of satellite RNAs enhanced MC38 cell susceptibility to CPT [half-maximal inhibitory concentration: 0.814 μM (control) vs. 0.332 μM (MC38 cells with a major satellite), p = 0.003] but not that of CT26. These findings imply that MC38 cells, which are unlikely to harbor CIN, are more susceptible to CIN-induced CPT sensitivity than CT26 cells, which are characterized by CIN. Furthermore, CPT administration upregulated p53 levels but not those of p21, indicating that overexpression of major satellite transcripts likely induces CPT-responsive cell death rather than cellular senescence.
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20
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Al-Rawi DH, Bakhoum SF. Chromosomal instability as a source of genomic plasticity. Curr Opin Genet Dev 2022; 74:101913. [PMID: 35526333 DOI: 10.1016/j.gde.2022.101913] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/31/2022] [Indexed: 11/03/2022]
Abstract
Chromosomal instability (CIN) is a hallmark of the most aggressive malignancies. Features of these tumors include complex genomic rearrangements, the presence of mis-segregated chromosomes in micronuclei, and extrachromosomal DNA (ecDNA) formation. Here, we review the development of CIN, and examine CIN in the context of cancer evolution, tumor genomic evolution, and therapeutic resistance. We also discuss the role of whole-genome duplications, breakage-fusion-bridge cycles, ecDNA or double minutes in gene amplification promoting tumor evolution.
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Affiliation(s)
- Duaa H Al-Rawi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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21
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Lynch AR, Arp NL, Zhou AS, Weaver BA, Burkard ME. Quantifying chromosomal instability from intratumoral karyotype diversity using agent-based modeling and Bayesian inference. eLife 2022; 11:e69799. [PMID: 35380536 PMCID: PMC9054132 DOI: 10.7554/elife.69799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/01/2022] [Indexed: 12/03/2022] Open
Abstract
Chromosomal instability (CIN)-persistent chromosome gain or loss through abnormal mitotic segregation-is a hallmark of cancer that drives aneuploidy. Intrinsic chromosome mis-segregation rate, a measure of CIN, can inform prognosis and is a promising biomarker for response to anti-microtubule agents. However, existing methodologies to measure this rate are labor intensive, indirect, and confounded by selection against aneuploid cells, which reduces observable diversity. We developed a framework to measure CIN, accounting for karyotype selection, using simulations with various levels of CIN and models of selection. To identify the model parameters that best fit karyotype data from single-cell sequencing, we used approximate Bayesian computation to infer mis-segregation rates and karyotype selection. Experimental validation confirmed the extensive chromosome mis-segregation rates caused by the chemotherapy paclitaxel (18.5 ± 0.5/division). Extending this approach to clinical samples revealed that inferred rates fell within direct observations of cancer cell lines. This work provides the necessary framework to quantify CIN in human tumors and develop it as a predictive biomarker.
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Affiliation(s)
- Andrew R Lynch
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
| | - Nicholas L Arp
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
| | - Amber S Zhou
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
| | - Beth A Weaver
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
- Department of Cell and Regenerative Biology, University of WisconsinMadisonUnited States
| | - Mark E Burkard
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
- Division of Hematology Medical Oncology and Palliative Care, Department of Medicine University of WisconsinMadisonUnited States
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22
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Distinct and Common Features of Numerical and Structural Chromosomal Instability across Different Cancer Types. Cancers (Basel) 2022; 14:cancers14061424. [PMID: 35326573 DOI: 10.3390/cancers14061424] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/27/2023] Open
Abstract
A large proportion of tumours is characterised by numerical or structural chromosomal instability (CIN), defined as an increased rate of gaining or losing whole chromosomes (W-CIN) or of accumulating structural aberrations (S-CIN). Both W-CIN and S-CIN are associated with tumourigenesis, cancer progression, treatment resistance and clinical outcome. Although W-CIN and S-CIN can co-occur, they are initiated by different molecular events. By analysing tumour genomic data from 33 cancer types, we show that the majority of tumours with high levels of W-CIN underwent whole genome doubling, whereas S-CIN levels are strongly associated with homologous recombination deficiency. Both CIN phenotypes are prognostic in several cancer types. Most drugs are less efficient in high-CIN cell lines, but we also report compounds and drugs which should be investigated as targets for W-CIN or S-CIN. By analysing associations between CIN and bio-molecular entities with pathway and gene expression levels, we complement gene signatures of CIN and report that the drug resistance gene CKS1B is strongly associated with S-CIN. Finally, we propose a potential copy number-dependent mechanism to activate the PI3K pathway in high-S-CIN tumours.
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23
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Kittai AS, Danilova OV, Lam V, Liu T, Bruss N, Best S, Fan G, Danilov AV. NEDD8-activating enzyme inhibition induces cell cycle arrest and anaphase catastrophe in malignant T-cells. Oncotarget 2021; 12:2068-2074. [PMID: 34611480 PMCID: PMC8487718 DOI: 10.18632/oncotarget.28063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is characterized by poor outcomes. We and others have shown that targeting the NEDD8-activating enzyme (NAE) with an investigational inhibitor pevonedistat deregulates cell cycle and mitosis in lymphoma and leukemia. Here, we report that PTCL is characterized by increased rate of chromosomal instability. NAE inhibition promotes cell cycle arrest and induces multipolar anaphases in T-cell lymphoma cell lines, resulting in apoptosis, also observed in primary malignant PTCL cells treated with pevonedistat. We identified p27Kip1 as a mediator of anaphase catastrophe in these cells. Targeting neddylation with pevonedistat may be a promising approach to treatment of PTCL.
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Affiliation(s)
- Adam S Kittai
- The Ohio State University, Columbus, OH 43210, USA.,These authors contributed equally to this work
| | - Olga V Danilova
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.,These authors contributed equally to this work
| | - Vi Lam
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Tingting Liu
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Nur Bruss
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Scott Best
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Guang Fan
- Oregon Health and Science University, Portland, OR 97239, USA
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Zhou L, Jilderda LJ, Foijer F. Exploiting aneuploidy-imposed stresses and coping mechanisms to battle cancer. Open Biol 2020; 10:200148. [PMID: 32873156 PMCID: PMC7536071 DOI: 10.1098/rsob.200148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023] Open
Abstract
Aneuploidy, an irregular number of chromosomes in cells, is a hallmark feature of cancer. Aneuploidy results from chromosomal instability (CIN) and occurs in almost 90% of all tumours. While many cancers display an ongoing CIN phenotype, cells can also be aneuploid without displaying CIN. CIN drives tumour evolution as ongoing chromosomal missegregation will yield a progeny of cells with variable aneuploid karyotypes. The resulting aneuploidy is initially toxic to cells because it leads to proteotoxic and metabolic stress, cell cycle arrest, cell death, immune cell activation and further genomic instability. In order to overcome these aneuploidy-imposed stresses and adopt a malignant fate, aneuploid cancer cells must develop aneuploidy-tolerating mechanisms to cope with CIN. Aneuploidy-coping mechanisms can thus be considered as promising therapeutic targets. However, before such therapies can make it into the clinic, we first need to better understand the molecular mechanisms that are activated upon aneuploidization and the coping mechanisms that are selected for in aneuploid cancer cells. In this review, we discuss the key biological responses to aneuploidization, some of the recently uncovered aneuploidy-coping mechanisms and some strategies to exploit these in cancer therapy.
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Affiliation(s)
| | | | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
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25
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Jin N, Lera RF, Yan RE, Guo F, Oxendine K, Horner VL, Hu Y, Wan J, Mattison RJ, Weaver BA, Burkard ME. Chromosomal instability upregulates interferon in acute myeloid leukemia. Genes Chromosomes Cancer 2020; 59:627-638. [PMID: 32557940 DOI: 10.1002/gcc.22880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 01/20/2023] Open
Abstract
Chromosome instability (CIN) generates genetic and karyotypic diversity that is common in hematological malignancies. Low to moderate levels of CIN are well tolerated and can promote cancer proliferation. However, high levels of CIN are lethal. Thus, CIN may serve both as a prognostic factor to predict clinical outcome and as a predictive biomarker. A retrospective study was performed to evaluate CIN in acute myeloid leukemia (AML). Chromosome mis-segregation frequency was correlated with clinical outcome in bone marrow core biopsy specimens from 17 AML cases. Additionally, we induced chromosome segregation errors in AML cell lines with AZ3146, an inhibitor of the Mps1 mitotic checkpoint kinase, to quantify the phenotypic effects of high CIN. We observed a broad distribution of chromosome mis-segregation frequency in AML bone marrow core specimens. High CIN correlated with complex karyotype in AML, as expected, although there was no clear survival effect. In addition to CIN, experimentally inducing chromosome segregation errors by Mps1 inhibition in AML cell lines causes DNA damage, micronuclei formation, and upregulation of interferon stimulated genes. High levels of CIN appear to be immunostimulatory, suggesting an opportunity to combine mitotic checkpoint inhibitors with immunotherapy in treatment of AML.
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Affiliation(s)
- Ning Jin
- Department of Medicine, Division of Hematology/Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.,Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA
| | - Robert F Lera
- Department of Medicine, Division of Hematology/Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.,Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA.,University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Rachel E Yan
- Department of Medicine, Division of Hematology/Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.,University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Fen Guo
- Department of Pathology and Laboratory Medicine, Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, Wisconsin, USA
| | - Kim Oxendine
- Department of Pathology and Laboratory Medicine, Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, Wisconsin, USA
| | - Vanessa L Horner
- Department of Pathology and Laboratory Medicine, Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, Wisconsin, USA
| | - Yang Hu
- Department of Medicine, Division of Hematology/Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.,Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA.,University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA.,Medical Scientist Training Program, University of Wisconsin, Madison, Wisconsin, USA
| | - Jun Wan
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA.,Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, USA.,Physiology Training Program, University of Wisconsin, Madison, Wisconsin, USA
| | - Ryan J Mattison
- Department of Medicine, Division of Hematology/Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.,Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA
| | - Beth A Weaver
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA.,University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA.,Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, USA
| | - Mark E Burkard
- Department of Medicine, Division of Hematology/Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.,Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA.,University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA
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26
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Exploiting Cancer's Tactics to Make Cancer a Manageable Chronic Disease. Cancers (Basel) 2020; 12:cancers12061649. [PMID: 32580319 PMCID: PMC7352192 DOI: 10.3390/cancers12061649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
The history of modern oncology started around eighty years ago with the introduction of cytotoxic agents such as nitrogen mustard into the clinic, followed by multi-agent chemotherapy protocols. Early success in radiation therapy in Hodgkin lymphoma gave birth to the introduction of radiation therapy into different cancer treatment protocols. Along with better understanding of cancer biology, we developed drugs targeting cancer-related cellular and genetic aberrancies. Discovery of the crucial role of vasculature in maintenance, survival, and growth of a tumor opened the way to the development of anti-angiogenic agents. A better understanding of T-cell regulatory pathways advanced immunotherapy. Awareness of stem-like cancer cells and their role in cancer metastasis and local recurrence led to the development of drugs targeting them. At the same time, sequential and rapidly accelerating advances in imaging and surgical technology have markedly increased our ability to safely remove ≥90% of tumor cells. While we have advanced our ability to kill cells from multiple directions, we have still failed to stop most types of cancer from recurring. Here we analyze the tactics employed in cancer evolution; namely, chromosomal instability (CIN), intra-tumoral heterogeneity (ITH), and cancer-specific metabolism. These tactics govern the resistance to current cancer therapeutics. It is time to focus on maximally delaying the time to recurrence, with drugs that target these fundamental tactics of cancer evolution. Understanding the control of CIN and the optimal state of ITH as the most important tactics in cancer evolution could facilitate the development of improved cancer therapeutic strategies designed to transform cancer into a manageable chronic disease.
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The Phenoxyphenol Compound 4-HPPP Selectively Induces Antiproliferation Effects and Apoptosis in Human Lung Cancer Cells through Aneupolyploidization and ATR DNA Repair Signaling. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:5167292. [PMID: 32089770 PMCID: PMC7024103 DOI: 10.1155/2020/5167292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023]
Abstract
Lung cancer is a leading cause of cancer death worldwide, and non-small-cell lung cancer (NSCLC) accounts for 85% of lung cancer, which is highly metastatic, leading to the poor survival rate of patients. We recently reported that 4-[4-(4-hydroxyphenoxy)phenoxy]phenol (4-HPPP), a phenoxyphenol, exerts antihepatoma effects by inducing apoptosis and autophagy. In this study, we further examined the effect of 4-HPPP and its analogs on NSCLC cells. Colony formation assays showed that 4-HPPP exerts selective cytotoxicity against NSCLC H1299 cells; furthermore, the inhibitory effect of 4-HPPP on the proliferation and migration of NSCLC cells was validated using an in vivo zebrafish-based tumor xenograft assay. The flow cytometry-based dichlorofluorescein diacetate (DCF-DA) assays indicated that 4-HPPP caused an increase in reactive oxygen species (ROS) in NSCLC cells, and Western blot assays showed that the major ROS scavenging enzymes superoxide dismutases- (SODs-) 1/2 were upregulated, whereas peroxidase (PRX) was downregulated. Furthermore, 4-HPPP caused both aneuploidization and the accumulation of γH2AX, a sensor of DNA damage, as well as the activation of double-strand break (DSB) markers, especially Ataxia-telangiectasia-mutated and Rad3-related (ATR) in NSCLC cells. Our present work suggests that the antiproliferative effects of 4-HPPP on lung cancer cells could be due to its phenoxyphenol structure, and 4-HPPP could be a candidate molecule for treating NSCLC by modulating ROS levels and lowering the threshold of polyploidy-specific cell death in the future.
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de Jong MRW, Langendonk M, Reitsma B, Herbers P, Nijland M, Huls G, van den Berg A, Ammatuna E, Visser L, van Meerten T. WEE1 Inhibition Enhances Anti-Apoptotic Dependency as a Result of Premature Mitotic Entry and DNA Damage. Cancers (Basel) 2019; 11:cancers11111743. [PMID: 31703356 PMCID: PMC6895818 DOI: 10.3390/cancers11111743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Genomically unstable cancers are dependent on specific cell cycle checkpoints to maintain viability and prevent apoptosis. The cell cycle checkpoint protein WEE1 is highly expressed in genomically unstable cancers, including diffuse large B-cell lymphoma (DLBCL). Although WEE1 inhibition effectively induces apoptosis in cancer cells, the effect of WEE1 inhibition on anti-apoptotic dependency is not well understood. We show that inhibition of WEE1 by AZD1775 induces DNA damage and pre-mitotic entry in DLBCL, thereby enhancing dependency on BCL-2 and/or MCL-1. Combining AZD1775 with anti-apoptotic inhibitors such as venetoclax (BCL-2i) or S63845 (MCL-1i) enhanced sensitivity in a cell-specific manner. In addition, we demonstrate that both G2/M cell cycle arrest and DNA damage induction put a similar stress on DLBCL cells, thereby enhancing anti-apoptotic dependency. Therefore, genotoxic or cell cycle disrupting agents combined with specific anti-apoptotic inhibitors may be very effective in genomic unstable cancers such as DLBCL and therefore warrants further clinical evaluation.
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Affiliation(s)
- Mathilde Rikje Willemijn de Jong
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands; (A.v.d.B.); (L.V.)
| | - Myra Langendonk
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands; (A.v.d.B.); (L.V.)
| | - Bart Reitsma
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
| | - Pien Herbers
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
| | - Marcel Nijland
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
| | - Gerwin Huls
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands; (A.v.d.B.); (L.V.)
| | - Emanuele Ammatuna
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
| | - Lydia Visser
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands; (A.v.d.B.); (L.V.)
| | - Tom van Meerten
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands (M.L.); (B.R.); (P.H.); (M.N.); (G.H.); (E.A.)
- Correspondence: ; Tel.: +31-503-611-761
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Palmitelli M, Stanganelli C, Stella F, Krzywinski A, Bezares R, González Cid M, Slavutsky I. Analysis of basal chromosome instability in patients with chronic lymphocytic leukaemia. Mutagenesis 2019; 34:245-252. [PMID: 31037299 DOI: 10.1093/mutage/gez009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/22/2019] [Accepted: 04/15/2019] [Indexed: 01/25/2023] Open
Abstract
Genomic instability is a hallmark of cancer, contributing to tumour development and transformation, being chromosome instability (CIN) the most common form in human cancer. Chronic lymphocytic leukaemia (CLL) is the most frequent adult leukaemia in the Western world. In this study, we have evaluated basal CIN in untreated patients with CLL by measuring chromosome aberrations (CAs) and micronucleus (MN) frequency and their association with different prognostic factors. Seventy-two patients and 21 normal controls were analysed. Cytogenetic and fluorescence in situ hybridisation (FISH) studies were performed. IGHV (immunoglobulin heavy chain variable region) mutational status was evaluated by reverse transcription polymerase chain reaction and sequencing. An increased number of CA in patients compared with controls (P = 0.0001) was observed. Cases with abnormal karyotypes showed increased CA rate than those with normal karyotypes (P = 0.0026), with a particularly highest frequency in cases with complex karyotypes. Among FISH risk groups, a significant low frequency of CA was found in patients with no FISH alterations compared to those with del13q14 and ≥2 FISH alterations (P = 0.0074). When mean CA value (6.7%) was considered, significant differences in the distribution of low and high CA frequency between cases with normal and abnormal karyotypes (P = 0.002) were observed. By MN analysis, higher frequency in patients compared to controls (P = 0.0001) was also found, as well as between cases with ≥2 FISH abnormalities and those with no FISH alterations (P = 0.026). Similarly, significant differences were observed when patients were divided according to mean MN frequency (2.2%; P ≤ 0.04). Interestingly, patients with high MN frequency had shorter time to first treatment than those with low frequency (P = 0.024). Cases with mutated and unmutated IGHV status showed increased CA and MN frequencies compared to controls (P ≤ 0.0007), but no differences between both groups were found. Our results support the strong interaction between CIN and genomic complexity as well as their influence on poor outcome in this pathology.
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Affiliation(s)
- Micaela Palmitelli
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Carmen Stanganelli
- División Patología Molecular, Instituto de Investigaciones Hematológicas, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Flavia Stella
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Andrea Krzywinski
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Raimundo Bezares
- Servicio de Hematología, Hospital Teodoro Álvarez, Buenos Aires, Argentina
| | - Marcela González Cid
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Irma Slavutsky
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
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30
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Brás R, Sunkel CE, Resende LP. Tissue stem cells: the new actors in the aneuploidy field. Cell Cycle 2019; 18:1813-1823. [PMID: 31242809 DOI: 10.1080/15384101.2019.1635867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The development of multicellular organisms and the maintenance of its tissues relies on mitosis. However, this process represents a major challenge for genomic stability as each time a cell division occurs there are multiple steps where errors can lead to an abnormal chromosomal content in daughter cells - aneuploidy. Aneuploidy was first postulated to act as a tumour promoting agent over one century ago. Since then, we have learned to appreciate the complexity involving the cellular responses to aneuploidy and to value the importance of models where aneuploidy is induced in vivo and in a cell-type specific manner. Recent data suggests that stem cells evolved a distinct response to aneuploidy, being able to survive and proliferate as aneuploid. Since stem cells are the main cells responsible for tissue renewal, it is of the utmost importance to place the spotlight on stem cells within the aneuploidy field. Here, we briefly review some of the biological mechanisms implicated in aneuploidy, the relationship between aneuploidy and tissue pathologies, and summarize the most recent findings in Drosophila on how tissue stem cells respond to aneuploidy. Once we understand how stem cell behavior is impacted by aneuploidy, we might be able to better describe the complicated link between aneuploidy and tumourigenesis.
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Affiliation(s)
- Rita Brás
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,b IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal
| | - Claudio E Sunkel
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,c ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto , Porto , Portugal
| | - Luís Pedro Resende
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,b IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal
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Laucius CD, Orr B, Compton DA. Chromosomal instability suppresses the growth of K-Ras-induced lung adenomas. Cell Cycle 2019; 18:1702-1713. [PMID: 31179849 DOI: 10.1080/15384101.2019.1629790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Chromosomal instability (CIN) is defined as a high rate of whole chromosome loss or gain and is a hallmark of many aneuploid solid tumors. CIN positively correlates with poor patient prognosis and chemotherapeutic resistance. Despite this clinical importance, the role of CIN in tumor initiation, growth and/or progression remains poorly understood. To date, the only strategies developed to determine how CIN contributes to tumorigenesis have relied on transgenic mouse models that deliberately increase the rate of chromosomal mis-segregation. Here we develop a strain of transgenic mice that is designed to strategically decrease the rate of chromosome mis-segregation and suppress CIN. These animals modestly overexpress the kinesin-13 microtubule depolymerase Kif2b, a strategy proven successful in restoring faithful chromosome segregation to human cancer cells in culture. Using the LA2 K-Ras G12D-induced model for lung cancer, we show that Kif2b expression reduces the number of chromosome segregation defects but does not change the incidence of lung tumor lesions. However, pulmonary tumors were significantly larger in animals expressing Kif2b and those tumors exhibited elevated rates of Ki-67 positive cells relative to controls. Thus, in lung cancers driven by mutations in K-Ras, CIN has little impact on tumor initiation but suppresses tumor growth. These data support a model in which CIN imposes a burden on tumor cells, and that enhancement of mitotic fidelity results in accelerated tumor growth.
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Affiliation(s)
- Christopher D Laucius
- a Department of Biochemistry , Geisel School of Medicine at Dartmouth , Hanover , NH , USA.,b Norris Cotton Cancer Center , Lebanon , NH , USA
| | - Bernardo Orr
- a Department of Biochemistry , Geisel School of Medicine at Dartmouth , Hanover , NH , USA.,b Norris Cotton Cancer Center , Lebanon , NH , USA
| | - Duane A Compton
- a Department of Biochemistry , Geisel School of Medicine at Dartmouth , Hanover , NH , USA.,b Norris Cotton Cancer Center , Lebanon , NH , USA
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Zhao Y, Carter R, Natarajan S, Varn FS, Compton DA, Gawad C, Cheng C, Godek KM. Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells. BMC Med Genomics 2019; 12:79. [PMID: 31151460 PMCID: PMC6545015 DOI: 10.1186/s12920-019-0532-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Background Intra-tumor heterogeneity stems from genetic, epigenetic, functional, and environmental differences among tumor cells. A major source of genetic heterogeneity comes from DNA sequence differences and/or whole chromosome and focal copy number variations (CNVs). Whole chromosome CNVs are caused by chromosomal instability (CIN) that is defined by a persistently high rate of chromosome mis-segregation. Accordingly, CIN causes constantly changing karyotypes that result in extensive cell-to-cell genetic heterogeneity. How the genetic heterogeneity caused by CIN influences gene expression in individual cells remains unknown. Methods We performed single-cell RNA sequencing on a chromosomally unstable glioblastoma cancer stem cell (CSC) line and a control normal, diploid neural stem cell (NSC) line to investigate the impact of CNV due to CIN on gene expression. From the gene expression data, we computationally inferred large-scale CNVs in single cells. Also, we performed copy number adjusted differential gene expression analysis between NSCs and glioblastoma CSCs to identify copy number dependent and independent differentially expressed genes. Results Here, we demonstrate that gene expression across large genomic regions scales proportionally to whole chromosome copy number in chromosomally unstable CSCs. Also, we show that the differential expression of most genes between normal NSCs and glioblastoma CSCs is largely accounted for by copy number alterations. However, we identify 269 genes whose differential expression in glioblastoma CSCs relative to normal NSCs is independent of copy number. Moreover, a gene signature derived from the subset of genes that are differential expressed independent of copy number in glioblastoma CSCs correlates with tumor grade and is prognostic for patient survival. Conclusions These results demonstrate that CIN is directly responsible for gene expression changes and contributes to both genetic and transcriptional heterogeneity among glioblastoma CSCs. These results also demonstrate that the expression of some genes is buffered against changes in copy number, thus preserving some consistency in gene expression levels from cell-to-cell despite the continuous change in karyotype driven by CIN. Importantly, a gene signature derived from the subset of genes whose expression is buffered against copy number alterations correlates with tumor grade and is prognostic for patient survival that could facilitate patient diagnosis and treatment. Electronic supplementary material The online version of this article (10.1186/s12920-019-0532-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanding Zhao
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Robert Carter
- Departments of Oncology and Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraman Natarajan
- Departments of Oncology and Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Frederick S Varn
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Present Address: Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Duane A Compton
- Department of Biochemistry and Cell Biology, HB7200, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Charles Gawad
- Departments of Oncology and Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chao Cheng
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA. .,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA. .,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA. .,Present Address: Baylor College of Medicine, Houston, TX, USA.
| | - Kristina M Godek
- Department of Biochemistry and Cell Biology, HB7200, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA. .,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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Elizalde S, Laughney AM, Bakhoum SF. A Markov chain for numerical chromosomal instability in clonally expanding populations. PLoS Comput Biol 2018; 14:e1006447. [PMID: 30204765 PMCID: PMC6150543 DOI: 10.1371/journal.pcbi.1006447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 09/21/2018] [Accepted: 08/18/2018] [Indexed: 01/17/2023] Open
Abstract
Cancer cells frequently undergo chromosome missegregation events during mitosis, whereby the copies of a given chromosome are not distributed evenly among the two daughter cells, thus creating cells with heterogeneous karyotypes. A stochastic model tracing cellular karyotypes derived from clonal populations over hundreds of generations was recently developed and experimentally validated, and it was capable of predicting favorable karyotypes frequently observed in cancer. Here, we construct and study a Markov chain that precisely describes karyotypic evolution during clonally expanding cancer cell populations. The Markov chain allows us to directly predict the distribution of karyotypes and the expected size of the tumor after many cell divisions without resorting to computationally expensive simulations. We determine the limiting karyotype distribution of an evolving tumor population, and quantify its dependency on several key parameters including the initial karyotype of the founder cell, the rate of whole chromosome missegregation, and chromosome-specific cell viability. Using this model, we confirm the existence of an optimal rate of chromosome missegregation probabilities that maximizes karyotypic heterogeneity, while minimizing the occurrence of nullisomy. Interestingly, karyotypic heterogeneity is significantly more dependent on chromosome missegregation probabilities rather than the number of cell divisions, so that maximal heterogeneity can be reached rapidly (within a few hundred generations of cell division) at chromosome missegregation rates commonly observed in cancer cell lines. Conversely, at low missegregation rates, heterogeneity is constrained even after thousands of cell division events. This leads us to conclude that chromosome copy number heterogeneity is primarily constrained by chromosome missegregation rates and the risk for nullisomy and less so by the age of the tumor. This model enables direct integration of karyotype information into existing models of tumor evolution based on somatic mutations. Chromosomal instability (CIN) is a hallmark of cancer and it results from persistent chromosome segregation errors during cell division. CIN has been shown to play a key role in drug resistance and tumor metastasis. While our understanding of CIN on the cellular level has grown over the past decade, our ability to predict the behavior of tumors containing billions of cells remains limited due to the paucity of adequate mathematical models. Here, we develop a Markov-chain model that is capable of providing exact solutions for long-term chromosome copy number distributions during tumor growth. Using this model we confirm the presence of optimal chromosome missegregation rates that balance genomic heterogeneity required for tumor evolution and survival. Interestingly, we show that chromosome copy number heterogeneity is primarily influenced by the rate of chromosome segregation errors rather than the age of the tumor. At chromosome missegregation rates frequently observed in cancer, tumors can acquire maximal genomic heterogeneity after a few hundred cell divisions. This model enables the integration of selection imparted by CIN into existing models of tumor evolution based on somatic mutations to explore their mutual effects.
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Affiliation(s)
- Sergi Elizalde
- Department of Mathematics, Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
| | - Ashley M. Laughney
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Samuel F. Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
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35
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Bakhoum SF, Cantley LC. The Multifaceted Role of Chromosomal Instability in Cancer and Its Microenvironment. Cell 2018; 174:1347-1360. [PMID: 30193109 PMCID: PMC6136429 DOI: 10.1016/j.cell.2018.08.027] [Citation(s) in RCA: 371] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/03/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Chromosomal instability (CIN) is a hallmark of human cancer, and it is associated with poor prognosis, metastasis, and therapeutic resistance. CIN results from errors in chromosome segregation during mitosis, leading to structural and numerical chromosomal abnormalities. In addition to generating genomic heterogeneity that acts as a substrate for natural selection, CIN promotes inflammatory signaling by introducing double-stranded DNA into the cytosol, engaging the cGAS-STING anti-viral pathway. These multipronged effects distinguish CIN as a central driver of tumor evolution and as a genomic source for the crosstalk between the tumor and its microenvironment, in the course of immune editing and evasion.
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Affiliation(s)
- Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Lewis C Cantley
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
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36
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Kawakami M, Liu X, Dmitrovsky E. New Cell Cycle Inhibitors Target Aneuploidy in Cancer Therapy. Annu Rev Pharmacol Toxicol 2018; 59:361-377. [PMID: 30110577 DOI: 10.1146/annurev-pharmtox-010818-021649] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aneuploidy is a hallmark of cancer. Defects in chromosome segregation result in aneuploidy. Multiple pathways are engaged in this process, including errors in kinetochore-microtubule attachments, supernumerary centrosomes, spindle assembly checkpoint (SAC) defects, and chromosome cohesion defects. Although aneuploidy provides an adaptation and proliferative advantage in affected cells, excessive aneuploidy beyond a critical level can be lethal to cancer cells. Given this, enhanced chromosome missegregation is hypothesized to limit survival of aneuploid cancer cells, especially when compared to diploid cells. Based on this concept, proteins and pathways engaged in chromosome segregation are being exploited as candidate therapeutic targets for aneuploid cancers. Agents that induce chromosome missegregation and aneuploidy now exist, including SAC inhibitors, those that alter centrosome fidelity and others that are under active study in preclinical and clinical contexts. This review explores the therapeutic potentials of such new agents, including the benefits of combining them with other antineoplastic agents.
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Affiliation(s)
- Masanori Kawakami
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, Texas 77030, USA
| | - Xi Liu
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, Texas 77030, USA
| | - Ethan Dmitrovsky
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, Texas 77030, USA.,Department of Cancer Biology, MD Anderson Cancer Center, The University of Texas, Houston, Texas 77030, USA.,Current affiliation: Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA;
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37
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Abstract
This review by Levine and Holland reviews the sources of mitotic errors in human tumors and their effect on cell fitness and transformation. They discuss new findings that suggest that chromosome missegregation can produce a proinflammatory environment and impact tumor responsiveness to immunotherapy and survey the vulnerabilities exposed by cell division errors and how they can be exploited therapeutically. Mitosis is a delicate event that must be executed with high fidelity to ensure genomic stability. Recent work has provided insight into how mitotic errors shape cancer genomes by driving both numerical and structural alterations in chromosomes that contribute to tumor initiation and progression. Here, we review the sources of mitotic errors in human tumors and their effect on cell fitness and transformation. We discuss new findings that suggest that chromosome missegregation can produce a proinflammatory environment and impact tumor responsiveness to immunotherapy. Finally, we survey the vulnerabilities exposed by cell division errors and how they can be exploited therapeutically.
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Affiliation(s)
- Michelle S Levine
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Godek KM, Compton DA. Quantitative methods to measure aneuploidy and chromosomal instability. Methods Cell Biol 2018; 144:15-32. [PMID: 29804667 DOI: 10.1016/bs.mcb.2018.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cell viability requires accurate chromosome segregation during meiosis and mitosis so that the daughter cells produced have the correct chromosome complement. In contrast, chromosome segregation errors lead to aneuploidy, a state of abnormal chromosome numbers. Furthermore, a persistently high rate of chromosome segregation errors causes the related phenomenon of whole chromosomal instability (w-CIN). Aneuploidy and w-CIN are common characteristics of several human conditions and diseases including birth defects and cancers. Thus, methods to measure aneuploidy and w-CIN have important research applications in many areas of cell biology. In this chapter, we describe methods to measure chromosome missegregation rates and aneuploid cell survival with a focus on cells grown in culture; however, we also highlight methods that are amenable to primary tissue samples. Together, these methods provide a comprehensive approach to determining the frequency of aneuploidy and w-CIN in cells.
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Affiliation(s)
- Kristina M Godek
- Geisel School of Medicine, Hanover, NH, United States; Norris Cotton Cancer Center, Lebanon, NH, United States
| | - Duane A Compton
- Geisel School of Medicine, Hanover, NH, United States; Norris Cotton Cancer Center, Lebanon, NH, United States.
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Mizuno Y, Tsukamoto T, Kawata E, Uoshima N, Uchiyama H, Yokota I, Maegawa S, Takimoto T, Tanba K, Matsumura-Kimoto Y, Kuwahara-Ota S, Fujibayashi Y, Yamamoto-Sugitani M, Chinen Y, Shimura Y, Horiike S, Taniwaki M, Kobayashi T, Kuroda J. Chromosomal abnormality variation detected by G-banding is associated with prognosis of diffuse large B-cell lymphoma treated by R-CHOP-based therapy. Cancer Med 2018; 7:655-664. [PMID: 29473332 PMCID: PMC5852349 DOI: 10.1002/cam4.1342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/02/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL), which is the most prevalent disease subtype of non-Hodgkin lymphoma, is highly heterogeneous in terms of cytogenetic and molecular features. This study retrospectively investigated the clinical impact of G-banding-defined chromosomal abnormality on treatment outcomes of DLBCL in the era of rituximab-containing immunochemotherapy. Of 181 patients who were diagnosed with DLBCL and treated with R-CHOP or an R-CHOP-like regimen between January 2006 and April 2014, metaphase spreads were evaluable for G-banding in 120. In these 120 patients, 40 were found to harbor a single chromosomal aberration type; 63 showed chromosomal abnormality variations (CAVs), which are defined by the presence of different types of chromosomal abnormalities in G-banding, including 19 with two CAVs and 44 with ≥3 CAVs; and 17 had normal karyotypes. No specific chromosomal break point or numerical abnormality was associated with overall survival (OS) or progression-free survival (PFS), but the presence of ≥3 CAVs was significantly associated with inferior OS rates (hazard ratio (HR): 2.222, 95% confidence interval (CI): 1.056-4.677, P = 0.031) and tended to be associated with shorter PFS (HR: 1.796, 95% CI: 0.965-3.344, P = 0.061). In addition, ≥3 CAVs more frequently accumulated in high-risk patients, as defined by several conventional prognostic indices, such as the revised International Prognostic Index. In conclusion, our results suggest that the emergence of more CAVs, especially ≥3, based on chromosomal instability underlies the development of high-risk disease features and a poor prognosis in DLBCL.
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Affiliation(s)
- Yoshimi Mizuno
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eri Kawata
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Nobuhiko Uoshima
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Hitoji Uchiyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Isao Yokota
- Department of Biostatistics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Saori Maegawa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoko Takimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuna Tanba
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Saeko Kuwahara-Ota
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mio Yamamoto-Sugitani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Bakhoum SF, Ngo B, Laughney AM, Cavallo JA, Murphy CJ, Ly P, Shah P, Sriram RK, Watkins TBK, Taunk NK, Duran M, Pauli C, Shaw C, Chadalavada K, Rajasekhar VK, Genovese G, Venkatesan S, Birkbak NJ, McGranahan N, Lundquist M, LaPlant Q, Healey JH, Elemento O, Chung CH, Lee NY, Imielenski M, Nanjangud G, Pe’er D, Cleveland DW, Powell SN, Lammerding J, Swanton C, Cantley LC. Chromosomal instability drives metastasis through a cytosolic DNA response. Nature 2018; 553:467-472. [PMID: 29342134 PMCID: PMC5785464 DOI: 10.1038/nature25432] [Citation(s) in RCA: 906] [Impact Index Per Article: 151.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 12/06/2017] [Indexed: 12/14/2022]
Abstract
Chromosomal instability is a hallmark of cancer that results from ongoing errors in chromosome segregation during mitosis. Although chromosomal instability is a major driver of tumour evolution, its role in metastasis has not been established. Here we show that chromosomal instability promotes metastasis by sustaining a tumour cell-autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signalling. Genetic suppression of chromosomal instability markedly delays metastasis even in highly aneuploid tumour models, whereas continuous chromosome segregation errors promote cellular invasion and metastasis in a STING-dependent manner. By subverting lethal epithelial responses to cytosolic DNA, chromosomally unstable tumour cells co-opt chronic activation of innate immune pathways to spread to distant organs.
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Affiliation(s)
- Samuel F. Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Bryan Ngo
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Ashley M. Laughney
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Julie-Ann Cavallo
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Charles J. Murphy
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Peter Ly
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, California 92093, USA
| | - Pragya Shah
- Nancy E. and Peter C. Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14850, USA
| | - Roshan K Sriram
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | | | - Neil K. Taunk
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Mercedes Duran
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Chantal Pauli
- Institute for Pathology and Molecular Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Christine Shaw
- Molecular Cytogenetics Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Kalyani Chadalavada
- Molecular Cytogenetics Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Vinagolu K. Rajasekhar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Giulio Genovese
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | | | - Nicolai J. Birkbak
- The Francis Crick Institute, London NW1 1AT, UK
- UCL Cancer Institute, London WC1E 6BT, UK
| | - Nicholas McGranahan
- The Francis Crick Institute, London NW1 1AT, UK
- UCL Cancer Institute, London WC1E 6BT, UK
| | - Mark Lundquist
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Quincey LaPlant
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - John H. Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Olivier Elemento
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | | | - Nancy Y. Lee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Marcin Imielenski
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Gouri Nanjangud
- Molecular Cytogenetics Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Dana Pe’er
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Don W. Cleveland
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, California 92093, USA
| | - Simon N. Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jan Lammerding
- Nancy E. and Peter C. Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14850, USA
| | - Charles Swanton
- The Francis Crick Institute, London NW1 1AT, UK
- UCL Cancer Institute, London WC1E 6BT, UK
| | - Lewis C. Cantley
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
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41
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Adaptive Resistance to an Inhibitor of Chromosomal Instability in Human Cancer Cells. Cell Rep 2017; 17:1755-1763. [PMID: 27829147 DOI: 10.1016/j.celrep.2016.10.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/05/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023] Open
Abstract
Karyotype diversity is a hallmark of solid tumors that contributes to intratumor heterogeneity. This diversity is generated by persistent chromosome mis-segregation associated with chromosomal instability (CIN). CIN correlates with tumor relapse and is thought to promote drug resistance by creating a vast genomic landscape through which karyotypically unique clones survive lethal drug selection. We explore this proposition using a small molecule (UMK57) that suppresses chromosome mis-segregation in CIN cancer cells by potentiating the activity of the kinesin-13 protein MCAK. Sublethal doses of UMK57 destabilize kinetochore-microtubule (k-MT) attachments during mitosis to increase chromosome segregation fidelity. Surprisingly, chromosome mis-segregation rebounds in UMK57-treated cancer cells within a few days. This rapid relapse is driven by alterations in the Aurora B signaling pathway that hyper-stabilize k-MT attachments and is reversible following UMK57 removal. Thus, cancer cells display adaptive resistance to therapies targeting CIN through rapid and reversible changes to mitotic signaling networks.
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42
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McClelland SE. Role of chromosomal instability in cancer progression. Endocr Relat Cancer 2017; 24:T23-T31. [PMID: 28696210 DOI: 10.1530/erc-17-0187] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022]
Abstract
Cancer cells often display chromosomal instability (CIN), a defect that involves loss or rearrangement of the cell's genetic material - chromosomes - during cell division. This process results in the generation of aneuploidy, a deviation from the haploid number of chromosomes, and structural alterations of chromosomes in over 90% of solid tumours and many haematological cancers. This trait is unique to cancer cells as normal cells in the body generally strictly maintain the correct number and structure of chromosomes. This key difference between cancer and normal cells has led to two important hypotheses: (i) cancer cells have had to overcome inherent barriers to changes in chromosomes that are not tolerated in non-cancer cells and (ii) CIN represents a cancer-specific target to allow the specific elimination of cancer cells from the body. To exploit these hypotheses and design novel approaches to treat cancer, a full understanding of the mechanisms driving CIN and how CIN contributes to cancer progression is required. Here, we will discuss the possible mechanisms driving chromosomal instability, how CIN may contribute to the progression at multiple stages of tumour evolution and possible future therapeutic directions based on targeting cancer chromosomal instability.
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43
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Santaguida S, Richardson A, Iyer DR, M'Saad O, Zasadil L, Knouse KA, Wong YL, Rhind N, Desai A, Amon A. Chromosome Mis-segregation Generates Cell-Cycle-Arrested Cells with Complex Karyotypes that Are Eliminated by the Immune System. Dev Cell 2017; 41:638-651.e5. [PMID: 28633018 PMCID: PMC5536848 DOI: 10.1016/j.devcel.2017.05.022] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 03/07/2017] [Accepted: 05/23/2017] [Indexed: 01/14/2023]
Abstract
Aneuploidy, a state of karyotype imbalance, is a hallmark of cancer. Changes in chromosome copy number have been proposed to drive disease by modulating the dosage of cancer driver genes and by promoting cancer genome evolution. Given the potential of cells with abnormal karyotypes to become cancerous, do pathways that limit the prevalence of such cells exist? By investigating the immediate consequences of aneuploidy on cell physiology, we identified mechanisms that eliminate aneuploid cells. We find that chromosome mis-segregation leads to further genomic instability that ultimately causes cell-cycle arrest. We further show that cells with complex karyotypes exhibit features of senescence and produce pro-inflammatory signals that promote their clearance by the immune system. We propose that cells with abnormal karyotypes generate a signal for their own elimination that may serve as a means for cancer cell immunosurveillance.
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Affiliation(s)
- Stefano Santaguida
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA.
| | - Amelia Richardson
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Divya Ramalingam Iyer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Ons M'Saad
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA
| | - Lauren Zasadil
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA
| | - Kristin A Knouse
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA; Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Yao Liang Wong
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Arshad Desai
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelika Amon
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA.
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44
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Funk LC, Zasadil LM, Weaver BA. Living in CIN: Mitotic Infidelity and Its Consequences for Tumor Promotion and Suppression. Dev Cell 2017; 39:638-652. [PMID: 27997823 DOI: 10.1016/j.devcel.2016.10.023] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Errors in chromosome segregation during mitosis have been recognized as a hallmark of tumor cells since the late 1800s, resulting in the long-standing hypothesis that mitotic abnormalities drive tumorigenesis. Recent work has shown that mitotic defects can promote tumors, suppress them, or do neither, depending on the rate of chromosome missegregation. Here we discuss the causes of chromosome missegregation, their effects on tumor initiation and progression, and the evidence that increasing the rate of chromosome missegregation may be an effective chemotherapeutic strategy.
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Affiliation(s)
- Laura C Funk
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Lauren M Zasadil
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Beth A Weaver
- Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, 6109 WIMR I, Madison, WI 53705-2275, USA.
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45
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New Insights in the Cytogenetic Practice: Karyotypic Chaos, Non-Clonal Chromosomal Alterations and Chromosomal Instability in Human Cancer and Therapy Response. Genes (Basel) 2017; 8:genes8060155. [PMID: 28587191 PMCID: PMC5485519 DOI: 10.3390/genes8060155] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022] Open
Abstract
Recently, non-clonal chromosomal alterations previously unappreciated are being proposed to be included in cytogenetic practice. The aim of this inclusion is to obtain a greater understanding of chromosomal instability (CIN) and tumor heterogeneity and their role in cancer evolution and therapy response. Although several genetic assays have allowed the evaluation of the variation in a population of cancer cells, these assays do not provide information at the level of individual cells, therefore limiting the information of the genomic diversity within tumors (heterogeneity). The karyotype is one of the few available cytogenetic techniques that allow us not only to identify the chromosomal alterations present within a single cell, but also allows us to profile both clonal (CCA) and non-clonal chromosomal alterations (NCCAs). A greater understanding of CIN and tumor heterogeneity in cancer could not only improve existing therapeutic regimens but could also be used as targets for the design of new therapeutic approaches. In this review we indicate the importance and significance of karyotypic chaos, NCCAs and CIN in the prognosis of human cancers.
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46
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Bakhoum SF, Landau DA. Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a029611. [PMID: 28213433 DOI: 10.1101/cshperspect.a029611] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Large-scale, massively parallel sequencing of human cancer samples has revealed tremendous genetic heterogeneity within individual tumors. Indeed, tumors are composed of an admixture of diverse subpopulations-subclones-that vary in space and time. Here, we discuss a principal driver of clonal diversification in cancer known as chromosomal instability (CIN), which complements other modes of genetic diversification creating the multilayered genomic instability often seen in human cancer. Cancer cells have evolved to fine-tune chromosome missegregation rates to balance the acquisition of heterogeneity while preserving favorable genotypes, a dependence that can be exploited for a therapeutic benefit. We discuss how whole-genome doubling events accelerate clonal evolution in a subset of tumors by providing a viable path toward favorable near-triploid karyotypes and present evidence for CIN-induced clonal speciation that can overcome the dependence on truncal initiating events.
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Affiliation(s)
- Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065
| | - Dan Avi Landau
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065.,Division of Hematology and Medical Oncology and the Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10021.,Core member of the New York Genome Center, New York, New York 10013
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Salomon-Perzyński A, Salomon-Perzyńska M, Michalski B, Skrzypulec-Plinta V. High-grade serous ovarian cancer: the clone wars. Arch Gynecol Obstet 2017; 295:569-576. [PMID: 28154920 PMCID: PMC5315707 DOI: 10.1007/s00404-017-4292-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND The last 5 years' studies using next-generation sequencing provided evidences that many types of solid tumors present spatial and temporal genetic heterogeneity and are composed of multiple populations of genetically distinct subclones that evolve over time following a pattern of branched evolution. The evolutionary nature of cancer has been proposed as the major contributor to drug resistance and treatment failure. In this review, we present the current state of knowledge about the clonal evolution of high-grade serous ovarian cancer and discuss the challenge that clonal evolution poses for efforts to achieve an optimal cancer control. METHODS A systemic search of peer-reviewed articles published between August 2007 and October 2016 was performed using PUBMED and Google Scholar database. RESULTS AND CONCLUSIONS Recent studies using next-generation sequencing have allowed us to look inside the evolutionary nature of high-grade serous ovarian cancer, which in the light of current evidence can explain the relapsing course of the disease frequently observed in the clinical practice. Since only minimal improvement in the survival of patients treated with standard therapy has been observed in the last decade, novel molecular targeted therapies are of great interest in high-grade serous ovarian cancer. However, both spatial and temporal intratumoral genetic heterogeneity is a major challenge for personalized medicine, and greater knowledge of the molecular rules that drive tumor evolution through space and time is required to achieve a long-term clinical benefit from personalized therapy.
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Affiliation(s)
- Aleksander Salomon-Perzyński
- Department of Internal Medicine and Oncological Chemotherapy, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Magdalena Salomon-Perzyńska
- Department of Gynaecology Oncological, School of Health Sciences in Katowice, Medical University of Silesia, Katowice, Poland.
| | - Bogdan Michalski
- Department of Gynaecology Oncological, School of Health Sciences in Katowice, Medical University of Silesia, Katowice, Poland
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48
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Impaired haematopoietic stem cell differentiation and enhanced skewing towards myeloid progenitors in aged caspase-2-deficient mice. Cell Death Dis 2016; 7:e2509. [PMID: 27906175 PMCID: PMC5260989 DOI: 10.1038/cddis.2016.406] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/26/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022]
Abstract
The apoptotic cysteine protease caspase-2 has been shown to suppress tumourigenesis in mice and its reduced expression correlates with poor prognosis in some human malignancies. Caspase-2-deficient mice develop normally but show ageing-related traits and, when challenged by oncogenic stimuli or certain stress, show enhanced tumour development, often accompanied by extensive aneuploidy. As stem cells are susceptible to acquiring age-related functional defects because of their self-renewal and proliferative capacity, we examined whether loss of caspase-2 promotes such defects with age. Using young and aged Casp2−/− mice, we demonstrate that deficiency of caspase-2 results in enhanced aneuploidy and DNA damage in bone marrow (BM) cells with ageing. Furthermore, we demonstrate for the first time that caspase-2 loss results in significant increase in immunophenotypically defined short-term haematopoietic stem cells (HSCs) and multipotent progenitors fractions in BM with a skewed differentiation towards myeloid progenitors with ageing. Caspase-2 deficiency leads to enhanced granulocyte macrophage and erythroid progenitors in aged mice. Colony-forming assays and long-term culture-initiating assay further recapitulated these results. Our results provide the first evidence of caspase-2 in regulating HSC and progenitor differentiation, as well as aneuploidy, in vivo.
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Jemaà M, Manic G, Lledo G, Lissa D, Reynes C, Morin N, Chibon F, Sistigu A, Castedo M, Vitale I, Kroemer G, Abrieu A. Whole-genome duplication increases tumor cell sensitivity to MPS1 inhibition. Oncotarget 2016; 7:885-901. [PMID: 26637805 PMCID: PMC4808040 DOI: 10.18632/oncotarget.6432] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/18/2015] [Indexed: 12/31/2022] Open
Abstract
Several lines of evidence indicate that whole-genome duplication resulting in tetraploidy facilitates carcinogenesis by providing an intermediate and metastable state more prone to generate oncogenic aneuploidy. Here, we report a novel strategy to preferentially kill tetraploid cells based on the abrogation of the spindle assembly checkpoint (SAC) via the targeting of TTK protein kinase (better known as monopolar spindle 1, MPS1). The pharmacological inhibition as well as the knockdown of MPS1 kills more efficiently tetraploid cells than their diploid counterparts. By using time-lapse videomicroscopy, we show that tetraploid cells do not survive the aborted mitosis due to SAC abrogation upon MPS1 depletion. On the contrary diploid cells are able to survive up to at least two more cell cycles upon the same treatment. This effect might reflect the enhanced difficulty of cells with whole-genome doubling to tolerate a further increase in ploidy and/or an elevated level of chromosome instability in the absence of SAC functions. We further show that MPS1-inhibited tetraploid cells promote mitotic catastrophe executed by the intrinsic pathway of apoptosis, as indicated by the loss of mitochondrial potential, the release of the pro-apoptotic cytochrome c from mitochondria, and the activation of caspases. Altogether, our results suggest that MPS1 inhibition could be used as a therapeutic strategy for targeting tetraploid cancer cells.
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Affiliation(s)
- Mohamed Jemaà
- CRBM, CNRS UMR5237, Université de Montpellier, Montpellier, France
| | | | - Gwendaline Lledo
- CRBM, CNRS UMR5237, Université de Montpellier, Montpellier, France
| | - Delphine Lissa
- Université Paris-Sud/Paris XI, Le Kremlin-Bicêtre, France.,INSERM, UMRS1138, Paris, France.,Equipe 11 Labelisée par la Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France
| | - Christelle Reynes
- EA 2415, Laboratoire de Biostatistique, d'Epidémiologie et de Recherche Clinique, Université de Montpellier, Montpellier, France
| | - Nathalie Morin
- CRBM, CNRS UMR5237, Université de Montpellier, Montpellier, France
| | - Frédéric Chibon
- Department of Biopathology, Institut Bergonié, Comprehensive Cancer Centre, Bordeaux, France.,INSERM U916, Bordeaux, France
| | | | - Maria Castedo
- Université Paris-Sud/Paris XI, Le Kremlin-Bicêtre, France.,INSERM, UMRS1138, Paris, France.,Equipe 11 Labelisée par la Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France
| | - Ilio Vitale
- Regina Elena National Cancer Institute, Rome, Italy.,Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Guido Kroemer
- INSERM, UMRS1138, Paris, France.,Equipe 11 Labelisée par la Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Université Pierre et Marie Curie/Paris VI, Paris, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Ariane Abrieu
- CRBM, CNRS UMR5237, Université de Montpellier, Montpellier, France
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Abstract
It is now clear that functional p53 is critical to protect the genome from alterations that lead to tumorigenesis. However, with the myriad of cellular stresses and pathways linked to p53 activation, much remains unknown about how p53 maintains genome stability and the proteins involved. The current understanding of the multiple ways p53 contributes to genome stability and how two of its negative regulators, Mdm2 and Mdmx, induce genome instability will be described.
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Affiliation(s)
- Christine M Eischen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212
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