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Liu S, Li W, Chen J, Li M, Geng Y, Liu Y, Wu W. The footprint of gut microbiota in gallbladder cancer: a mechanistic review. Front Cell Infect Microbiol 2024; 14:1374238. [PMID: 38774627 PMCID: PMC11106419 DOI: 10.3389/fcimb.2024.1374238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Gallbladder cancer (GBC) is the most common malignant tumor of the biliary system with the worst prognosis. Even after radical surgery, the majority of patients with GBC have difficulty achieving a clinical cure. The risk of tumor recurrence remains more than 65%, and the overall 5-year survival rate is less than 5%. The gut microbiota refers to a variety of microorganisms living in the human intestine, including bacteria, viruses and fungi, which profoundly affect the host state of general health, disease and even cancer. Over the past few decades, substantial evidence has supported that gut microbiota plays a critical role in promoting the progression of GBC. In this review, we summarize the functions, molecular mechanisms and recent advances of the intestinal microbiota in GBC. We focus on the driving role of bacteria in pivotal pathways, such as virulence factors, metabolites derived from intestinal bacteria, chronic inflammatory responses and ecological niche remodeling. Additionally, we emphasize the high level of correlation between viruses and fungi, especially EBV and Candida spp., with GBC. In general, this review not only provides a solid theoretical basis for the close relationship between gut microbiota and GBC but also highlights more potential research directions for further research in the future.
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Affiliation(s)
- Shujie Liu
- Joint Program of Nanchang University and Queen Mary University of London, Jiangxi Medical College of Nanchang University, Nanchang, Jiangxi, China
| | - Weijian Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Jun Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Maolan Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yajun Geng
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Wenguang Wu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
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Zhang Y, Shao Y, Ren J, Fang Y, Yang B, Lu S, Liu P. NCAPD3 exerts tumor-promoting effects in prostatic cancer via dual impact on miR-30a-5p by STAT3-MALAT1 and MYC. Cell Death Discov 2024; 10:159. [PMID: 38561330 PMCID: PMC10985108 DOI: 10.1038/s41420-024-01930-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Non-SMC condensin II complex subunit D3 (NCAPD3) is a subunit of the non-structural maintenance of chromosomes condensin II complex, which involves chromosome condensation and segregation during mitosis. NCAPD3 has recently been demonstrated as a crucial oncogenic factor. However, the underlying mechanism of NCAPD3 in prostate cancer (PCa) remains not completely clear. In this study, we confirmed that lncRNA MALAT1 was induced by NCAPD3-STAT3, and the expression of miR-30a-5p was controlled by NCAPD3 in PCa cells by miRNA-seq. Through quantitative real-time PCR, fluorescence in situ hybridization, western blotting, and immunohistochemistry assay, we demonstrated that miR-30a-5p was lowly expressed in PCa cells and tissues compared to the controls, which was contrary to NCAPD3 expression and markedly downregulated by NCAPD3. Then, MALAT1 was analyzed for the complementary sequence in the potential interaction with miR-30a-5p by using the predicted target module of public databases. Dual-luciferase reporter assay and RNA immunoprecipitation were carried out to verify that MALAT1 functioned as a sponge for miR-30a-5p to reduce miR-30a-5p expression. Meanwhile, MYC acted as a transcriptional repressor to directly bind the promoter of the miR-30a-5p located gene and repress the miR-30a-5p expression. Furthermore, the upregulation of NCAPD3 on cell viability and migration was significantly attenuated in PC-3 cells when miR-30a-5p was overexpressed. NCAPD3 overexpression also accelerated tumor growth in the xenograft mouse model and repressed miR-30-5p. In summary, this work elucidates NCAPD3 inhibits miR-30a-5p through two pathways: increasing STAT3-MALAT1 to sponge miR-30a-5p and increasing MYC to directly inhibit miR-30a-5p transcription, which could serve as potential therapeutic targets for prostate cancer.
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Affiliation(s)
- Yi Zhang
- College of Life Sciences, Nanjing Normal University, 210023, Nanjing, Jiangsu, P. R. China
| | - Yingying Shao
- College of Life Sciences, Nanjing Normal University, 210023, Nanjing, Jiangsu, P. R. China
| | - Jia Ren
- College of Life Sciences, Nanjing Normal University, 210023, Nanjing, Jiangsu, P. R. China
| | - Yuanyuan Fang
- College of Life Sciences, Nanjing Normal University, 210023, Nanjing, Jiangsu, P. R. China
| | - Bolin Yang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affliated Hospital of Nanjing University of Chinese Medicine, 210029, Nanjing, Jiangsu, P. R. China
| | - Shan Lu
- College of Life Sciences, Nanjing Normal University, 210023, Nanjing, Jiangsu, P. R. China.
| | - Ping Liu
- College of Life Sciences, Nanjing Normal University, 210023, Nanjing, Jiangsu, P. R. China.
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Mendiburu‐Eliçabe M, García‐Sancha N, Corchado‐Cobos R, Martínez‐López A, Chang H, Hua Mao J, Blanco‐Gómez A, García‐Casas A, Castellanos‐Martín A, Salvador N, Jiménez‐Navas A, Pérez‐Baena MJ, Sánchez‐Martín MA, Abad‐Hernández MDM, Carmen SD, Claros‐Ampuero J, Cruz‐Hernández JJ, Rodríguez‐Sánchez CA, García‐Cenador MB, García‐Criado FJ, Vicente RS, Castillo‐Lluva S, Pérez‐Losada J. NCAPH drives breast cancer progression and identifies a gene signature that predicts luminal a tumour recurrence. Clin Transl Med 2024; 14:e1554. [PMID: 38344872 PMCID: PMC10859882 DOI: 10.1002/ctm2.1554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/01/2024] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Luminal A tumours generally have a favourable prognosis but possess the highest 10-year recurrence risk among breast cancers. Additionally, a quarter of the recurrence cases occur within 5 years post-diagnosis. Identifying such patients is crucial as long-term relapsers could benefit from extended hormone therapy, while early relapsers might require more aggressive treatment. METHODS We conducted a study to explore non-structural chromosome maintenance condensin I complex subunit H's (NCAPH) role in luminal A breast cancer pathogenesis, both in vitro and in vivo, aiming to identify an intratumoural gene expression signature, with a focus on elevated NCAPH levels, as a potential marker for unfavourable progression. Our analysis included transgenic mouse models overexpressing NCAPH and a genetically diverse mouse cohort generated by backcrossing. A least absolute shrinkage and selection operator (LASSO) multivariate regression analysis was performed on transcripts associated with elevated intratumoural NCAPH levels. RESULTS We found that NCAPH contributes to adverse luminal A breast cancer progression. The intratumoural gene expression signature associated with elevated NCAPH levels emerged as a potential risk identifier. Transgenic mice overexpressing NCAPH developed breast tumours with extended latency, and in Mouse Mammary Tumor Virus (MMTV)-NCAPHErbB2 double-transgenic mice, luminal tumours showed increased aggressiveness. High intratumoural Ncaph levels correlated with worse breast cancer outcome and subpar chemotherapy response. A 10-gene risk score, termed Gene Signature for Luminal A 10 (GSLA10), was derived from the LASSO analysis, correlating with adverse luminal A breast cancer progression. CONCLUSIONS The GSLA10 signature outperformed the Oncotype DX signature in discerning tumours with unfavourable outcomes, previously categorised as luminal A by Prediction Analysis of Microarray 50 (PAM50) across three independent human cohorts. This new signature holds promise for identifying luminal A tumour patients with adverse prognosis, aiding in the development of personalised treatment strategies to significantly improve patient outcomes.
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Jiang H, Chan YW. Chromatin bridges: stochastic breakage or regulated resolution? Trends Genet 2024; 40:69-82. [PMID: 37891096 DOI: 10.1016/j.tig.2023.10.004] [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: 08/15/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
Genetic material is organized in the form of chromosomes, which need to be segregated accurately into two daughter cells in each cell cycle. However, chromosome fusion or the presence of unresolved interchromosomal linkages lead to the formation of chromatin bridges, which can induce DNA lesions and genome instability. Persistent chromatin bridges are trapped in the cleavage furrow and are broken at or after abscission, the final step of cytokinesis. In this review, we focus on recent progress in understanding the mechanism of bridge breakage and resolution. We discuss the molecular machinery and enzymes that have been implicated in the breakage and processing of bridge DNA. In addition, we outline both the immediate outcomes and genomic consequences induced by bridge breakage.
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Affiliation(s)
- Huadong Jiang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Ying Wai Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China.
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Mendiburu-Eliçabe M, García-Sancha N, Corchado-Cobos R, Martínez-López A, Chang H, Mao JH, Blanco-Gómez A, García-Casas A, Castellanos-Martín A, Salvador N, Jiménez-Navas A, Pérez-Baena MJ, Sánchez-Martín MA, Abad-Hernández MDM, Del Carmen S, Claros-Ampuero J, Cruz-Hernández JJ, Rodríguez-Sánchez CA, García-Cenador MB, García-Criado FJ, Vicente RS, Castillo-Lluva S, Pérez-Losada J. NCAPH Drives Breast Cancer Progression and Identifies a Gene Signature that Predicts Luminal A Tumor Recurrence. RESEARCH SQUARE 2023:rs.3.rs-3231230. [PMID: 37886490 PMCID: PMC10602143 DOI: 10.21203/rs.3.rs-3231230/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Despite their generally favorable prognosis, luminal A tumors paradoxically pose the highest ten-year recurrence risk among breast cancers. From those that relapse, a quarter of them do it within five years after diagnosis. Identifying such patients is crucial, as long-term relapsers could benefit from extended hormone therapy, whereas early relapsers may require aggressive treatment. In this study, we demonstrate that NCAPH plays a role in the pathogenesis of luminal A breast cancer, contributing to its adverse progression in vitro and in vivo. Furthermore, we reveal that a signature of intratumoral gene expression, associated with elevated levels of NCAPH, serves as a potential marker to identify patients facing unfavorable progression of luminal A breast cancer. Indeed, transgenic mice overexpressing NCAPH generated breast tumors with long latency, and in MMTV-NCAPH/ErbB2+ double-transgenic mice, the luminal tumors formed were more aggressive. In addition, high intratumoral levels of Ncaph were associated with worse breast cancer evolution and poor response to chemotherapy in a cohort of genetically heterogeneous transgenic mice generated by backcrossing. In this cohort of mice, we identified a series of transcripts associated with elevated intratumoral levels of NCAPH, which were linked to adverse progression of breast cancer in both mice and humans. Utilizing the Least Absolute Shrinkage and Selection Operator (LASSO) multivariate regression analysis on this series of transcripts, we derived a ten-gene risk score. This score is defined by a gene signature (termed Gene Signature for Luminal A 10 or GSLA10) that correlates with unfavorable progression of luminal A breast cancer. The GSLA10 signature surpassed the Oncotype DX signature in discerning tumors with unfavorable outcomes (previously categorized as Luminal A by PAM50) across three independent human cohorts. This GSLA10 signature aids in identifying patients with Luminal A tumors displaying adverse prognosis, who could potentially benefit from personalized treatment strategies.
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Affiliation(s)
- Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Angélica Martínez-López
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Ana García-Casas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Andrés Castellanos-Martín
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Nélida Salvador
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Alejandro Jiménez-Navas
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Manuel Jesús Pérez-Baena
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Manuel Adolfo Sánchez-Martín
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Servicio de Transgénesis, Plataforma Nucleus, Universidad de Salamanca, Salamanca, Spain
| | - María Del Mar Abad-Hernández
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
- Servicio de Anatomía Patológica, Hospital Universitario de Salamanca, Spain
| | - Sofía Del Carmen
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
- Servicio de Anatomía Patológica, Hospital Universitario de Salamanca, Spain
| | - Juncal Claros-Ampuero
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Juan Jesús Cruz-Hernández
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - César Augusto Rodríguez-Sánchez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - María Begoña García-Cenador
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Javier García-Criado
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | | | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
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Dobbs OG, Wilson RHC, Newling K, Ainscough JFX, Coverley D. Epigenetic instability caused by absence of CIZ1 drives transformation during quiescence cycles. BMC Biol 2023; 21:175. [PMID: 37580709 PMCID: PMC10426085 DOI: 10.1186/s12915-023-01671-6] [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: 12/12/2022] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Cip1-interacting zinc finger protein 1 (CIZ1) forms RNA-dependent protein assemblies that stabilise epigenetic state, notable at the inactive X chromosome in females. CIZ1 has been linked with a range of human cancers and in mice genetic deletion of CIZ1 manifests as hyperproliferative lymphoid lineages in females. This suggests that its role in maintenance of epigenetic stability is linked with disease. RESULTS Here, we show that male and female CIZ1-null primary murine fibroblasts have reduced H4K20me1 and that this compromises nuclear condensation on entry to quiescence. Global transcriptional repression remains intact in condensation-deficient CIZ1-null cells; however, a subset of genes linked with chromatin condensation and homology-directed DNA repair are perturbed. Failure to condense is phenotypically mimicked by manipulation of the H4K20me1 methyltransferase, SET8, in WT cells and partially reverted in CIZ1-null cells upon re-expression of CIZ1. Crucially, during exit from quiescence, nuclear decondensation remains active, so that repeated entry and exit cycles give rise to expanded nuclei susceptible to mechanical stress, DNA damage checkpoint activation, and downstream emergence of transformed proliferative colonies. CONCLUSIONS Our results demonstrate a role for CIZ1 in chromatin condensation on entry to quiescence and explore the consequences of this defect in CIZ1-null cells. Together, the data show that CIZ1's protection of the epigenome guards against genome instability during quiescence cycles. This identifies loss of CIZ1 as a potentially devastating vulnerability in cells that undergo cycles of quiescence entry and exit.
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Affiliation(s)
- Olivia G Dobbs
- Department of Biology, University of York, York, YO10 5DD, UK.
- York Biomedical Research Institute, University of York, York, UK.
| | - Rosemary H C Wilson
- Department of Biology, University of York, York, YO10 5DD, UK
- Exact Sciences Innovation, The Sherard Building, Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Katherine Newling
- Department of Biology, University of York, York, YO10 5DD, UK
- Genomics and Bioinformatics Laboratory, Bioscience Technology Facility, University of York, York, YO10 5DD, UK
| | | | - Dawn Coverley
- Department of Biology, University of York, York, YO10 5DD, UK
- York Biomedical Research Institute, University of York, York, UK
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7
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Carlund O, Norberg A, Osterman P, Landfors M, Degerman S, Hultdin M. DNA methylation variations and epigenetic aging in telomere biology disorders. Sci Rep 2023; 13:7955. [PMID: 37193737 DOI: 10.1038/s41598-023-34922-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 05/18/2023] Open
Abstract
Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length and disease severity. Epigenetic alterations are also markers of aging and we aimed to evaluate whether DNA methylation (DNAm) could be part of the pathogenesis of TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed and the cases were grouped based on relative telomere length (RTL): short (S), with RTL close to normal controls, and extremely short (ES). TBD cases had increased epigenetic age and DNAm alterations were most prominent in the ES-RTL group. Thus, the differentially methylated (DM) CpG sites could be markers of short telomeres but could also be one of the mechanisms contributing to disease phenotype since DNAm alterations were observed in symptomatic, but not asymptomatic, cases with S-RTL. Furthermore, two or more DM-CpGs were identified in four genes previously linked to TBD or telomere length (PRDM8, SMC4, VARS, and WNT6) and in three genes that were novel in telomere biology (MAS1L, NAV2, and TM4FS1). The DM-CpGs in these genes could be markers of aging in hematological cells, but they could also be of relevance for the progression of TBD.
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Affiliation(s)
- Olivia Carlund
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Anna Norberg
- Department of Medical Biosciences, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
| | - Pia Osterman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden.
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8
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Balaji AK, Saha S, Deshpande S, Poola D, Sengupta K. Nuclear envelope, chromatin organizers, histones, and DNA: The many achilles heels exploited across cancers. Front Cell Dev Biol 2022; 10:1068347. [PMID: 36589746 PMCID: PMC9800887 DOI: 10.3389/fcell.2022.1068347] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
In eukaryotic cells, the genome is organized in the form of chromatin composed of DNA and histones that organize and regulate gene expression. The dysregulation of chromatin remodeling, including the aberrant incorporation of histone variants and their consequent post-translational modifications, is prevalent across cancers. Additionally, nuclear envelope proteins are often deregulated in cancers, which impacts the 3D organization of the genome. Altered nuclear morphology, genome organization, and gene expression are defining features of cancers. With advances in single-cell sequencing, imaging technologies, and high-end data mining approaches, we are now at the forefront of designing appropriate small molecules to selectively inhibit the growth and proliferation of cancer cells in a genome- and epigenome-specific manner. Here, we review recent advances and the emerging significance of aberrations in nuclear envelope proteins, histone variants, and oncohistones in deregulating chromatin organization and gene expression in oncogenesis.
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9
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Feng Z, Zhang L, Liu Y, Zhang W. NCAPG2 contributes to the progression of malignant melanoma through regulating proliferation and metastasis. Biochem Cell Biol 2022; 100:473-484. [PMID: 36265182 DOI: 10.1139/bcb-2022-0048] [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: 12/14/2022] Open
Abstract
Malignant melanoma is a highly aggressive cutaneous neoplasm with increasing incidence worldwide. Non-SMC condensin II complex subunit G2 (NCAPG2) exerts import biological function in the pathogenesis of several tumors. In this study, the functional roles of NCAPG2 knockdown in malignant melanoma were revealed in in vitro and in vivo experiments. In vitro study demonstrated that NCAPG2 depletion could inhibit proliferation and migration and promote apoptosis of malignant melanoma cells. Our in vivo date further confirmed that NCAPG2 knockdown attenuated tumor growth of malignant melanoma. Interestingly, NCAPG2 drove tumor development of malignant melanoma through activating the signal transducer and activator of transcription 3 (STAT3). In conclusion, this study elaborated the tumor-promoting effects of NCAPG2 on malignant melanoma, and NCAPG2 may be a potential therapeutic target for malignant melanoma therapy.
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Affiliation(s)
- Zhang Feng
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong 250021, China
| | - Linfeng Zhang
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong 250021, China
| | - Yanxin Liu
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong 250021, China
| | - Wei Zhang
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong 250021, China
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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11
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Gönenc II, Wolff A, Schmidt J, Zibat A, Müller C, Cyganek L, Argyriou L, Räschle M, Yigit G, Wollnik B. OUP accepted manuscript. Hum Mol Genet 2022; 31:2185-2193. [PMID: 35099000 PMCID: PMC9262399 DOI: 10.1093/hmg/ddab373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/02/2021] [Accepted: 12/27/2021] [Indexed: 11/12/2022] Open
Abstract
Bloom syndrome (BS) is an autosomal recessive disease clinically characterized by primary microcephaly, growth deficiency, immunodeficiency and predisposition to cancer. It is mainly caused by biallelic loss-of-function mutations in the BLM gene, which encodes the BLM helicase, acting in DNA replication and repair processes. Here, we describe the gene expression profiles of three BS fibroblast cell lines harboring causative, biallelic truncating mutations obtained by single-cell (sc) transcriptome analysis. We compared the scRNA transcription profiles from three BS patient cell lines to two age-matched wild-type controls and observed specific deregulation of gene sets related to the molecular processes characteristically affected in BS, such as mitosis, chromosome segregation, cell cycle regulation and genomic instability. We also found specific upregulation of genes of the Fanconi anemia pathway, in particular FANCM, FANCD2 and FANCI, which encode known interaction partners of BLM. The significant deregulation of genes associated with inherited forms of primary microcephaly observed in our study might explain in part the molecular pathogenesis of microcephaly in BS, one of the main clinical characteristics in patients. Finally, our data provide first evidence of a novel link between BLM dysfunction and transcriptional changes in condensin complex I and II genes. Overall, our study provides novel insights into gene expression profiles in BS on an sc level, linking specific genes and pathways to BLM dysfunction.
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Affiliation(s)
| | | | - Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Arne Zibat
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Christian Müller
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Lukas Cyganek
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Loukas Argyriou
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Markus Räschle
- Department of Molecular Genetics, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Bernd Wollnik
- To whom correspondence should be addressed at: Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany. Tel: +49 5513960606; Fax: +49 5513969303;
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12
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Guo C, Zhou J, Ma B, Wang R, Ge Y, Wang Z, Ji B, Wang W, Zhang J, Wang Z. A Somatic Mutation-Derived LncRNA Signature of Genomic Instability Predicts Prognosis for Patients With Liver Cancer. Front Surg 2021; 8:724792. [PMID: 34504866 PMCID: PMC8421795 DOI: 10.3389/fsurg.2021.724792] [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: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
Background: Genomic instability is considered as one of the hallmarks of hepatocellular carcinoma (HCC) and poses a significant challenge to the clinical treatment. The emerging evidence has revealed the roles of long non-coding RNAs (lncRNAs) in the maintenance of genomic instability. This study is aimed to develop a genomic instability-related lncRNA signature for determining HCC prognosis and the suitability of patients for immunotherapy. Methods: In this study, data related to transcriptome profiling, clinical features, and the somatic mutations of patients with HCC were downloaded from The Cancer Genomic Atlas (TCGA). Bioinformatics analysis was performed to identify and construct a somatic mutation-derived genomic instability-associated lncRNA signature (GILncSig). Single-sample gene set enrichment analysis (ssGSEA) was applied to estimate the levels of immune cell infiltration. A nomogram was constructed, and calibration was performed to assess the effectiveness of the model. Results: In the study, seven genomic instability-related lncRNAs were identified and used to define a prognostic signature. Patients with HCC were stratified into high- and low-risk groups with significant differences in the survival (median survival time = 1.489, 1.748 year; p = 0.006) based on the optimal cutoff value (risk score = 1.010) of the risk score in the training group. In addition, GILncSig was demonstrated to be an independent risk factor for the patients with HCC when compared to the clinical parameters (p < 0.001). According to the receiver operating characteristic (ROC) curve, nomogram, and calibration plot, the signature could predict the survival rate for the patients with HCC in the 1st, 3rd, and 5th years. Furthermore, ssGSEA revealed the potential of the signature in guiding decisions for administering clinical treatment. Conclusions: In this study, we developed a novel prognostic model based on the somatic mutation-derived lncRNAs and validated it using an internal dataset. The independence of the GILncSig was estimated using univariate and follow-up multivariate analyses. Immunologic analysis was used to evaluate the complex factors involved in the HCC progression.
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Affiliation(s)
- Cheng Guo
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Zhou
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Boyu Ma
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rui Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yanli Ge
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhe Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bing Ji
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junjie Zhang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhirong Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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13
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Lee JH, Hong J, Zhang Z, de la Peña Avalos B, Proietti CJ, Deamicis AR, Guzmán G P, Lam HM, Garcia J, Roudier MP, Sisk AE, De La Rosa R, Vu K, Yang M, Liao Y, Scheirer J, Pechacek D, Yadav P, Rao MK, Zheng S, Johnson-Pais TL, Leach RJ, Elizalde PV, Dray E, Xu K. Regulation of telomere homeostasis and genomic stability in cancer by N 6-adenosine methylation (m 6A). SCIENCE ADVANCES 2021; 7:7/31/eabg7073. [PMID: 34321211 PMCID: PMC8318370 DOI: 10.1126/sciadv.abg7073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/11/2021] [Indexed: 05/04/2023]
Abstract
The role of RNA methylation on N 6-adenosine (m6A) in cancer has been acknowledged, but the underlying mechanisms remain obscure. Here, we identified homeobox containing 1 (HMBOX1) as an authentic target mRNA of m6A machinery, which is highly methylated in malignant cells compared to the normal counterparts and subject to expedited degradation upon the modification. m6A-mediated down-regulation of HMBOX1 causes telomere dysfunction and inactivation of p53 signaling, which leads to chromosome abnormalities and aggressive phenotypes. CRISPR-based, m6A-editing tools further prove that the methyl groups on HMBOX1 per se contribute to the generation of altered cancer genome. In multiple types of human cancers, expression of the RNA methyltransferase METTL3 is negatively correlated with the telomere length but favorably with fractions of altered cancer genome, whereas HMBOX1 mRNA levels show the opposite patterns. Our work suggests that the cancer-driving genomic alterations may potentially be fixed by rectifying particular epitranscriptomic program.
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Affiliation(s)
- Ji Hoon Lee
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Juyeong Hong
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Bárbara de la Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
| | - Cecilia J Proietti
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Agustina Roldán Deamicis
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Pablo Guzmán G
- Departamento de Anatomía Patológica (BIOREN), Universidad de La Frontera, Temuco Casilla 54-D, Chile
| | - Hung-Ming Lam
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Jose Garcia
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Martine P Roudier
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Anthony E Sisk
- Department of Pathology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Richard De La Rosa
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kevin Vu
- Department of Medical Education, Joe R. and Teresa Lozano Long School of Medicine, San Antonio, TX 78229, USA
| | - Mei Yang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yiji Liao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jessica Scheirer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Douglas Pechacek
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Pooja Yadav
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Manjeet K Rao
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Teresa L Johnson-Pais
- Department of Urology, University of Texas Health Sciences Center at San Antonio, San Antonio, TX 78229, USA
| | - Robin J Leach
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Patricia V Elizalde
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Eloïse Dray
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
| | - Kexin Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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14
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Weyburne E, Bosco G. Cancer-associated mutations in the condensin II subunit CAPH2 cause genomic instability through telomere dysfunction and anaphase chromosome bridges. J Cell Physiol 2020; 236:3579-3598. [PMID: 33078399 PMCID: PMC7983937 DOI: 10.1002/jcp.30113] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 01/10/2023]
Abstract
Genome instability in cancer drives tumor heterogeneity, undermines the success of therapies, and leads to metastasis and recurrence. Condensins are conserved chromatin‐binding proteins that promote genomic stability, mainly by ensuring proper condensation of chromatin and mitotic chromosome segregation. Condensin mutations are found in human tumors, but it is not known how or even if such mutations promote cancer progression. In this study, we focus on condensin II subunit CAPH2 and specific CAPH2 mutations reported to be enriched in human cancer patients, and we test how CAPH2 cancer‐specific mutations may lead to condensin II complex dysfunction and contribute to genome instability. We find that R551P, R551S, and S556F mutations in CAPH2 cause genomic instability by causing DNA damage, anaphase defects, micronuclei, and chromosomal instability. DNA damage and anaphase defects are caused primarily by ataxia telangiectasia and Rad3‐related‐dependent telomere dysfunction, as anaphase bridges are enriched for telomeric repeat sequences. We also show that these mutations decrease the binding of CAPH2 to the ATPase subunit SMC4 as well as the rest of the condensin II complex, and decrease the amount of CAPH2 protein bound to chromatin. Thus, in vivo the R551P, R551S, and S556F cancer‐specific CAPH2 mutant proteins are likely to impair condensin II complex formation, impede condensin II activity during mitosis and interphase, and promote genetic heterogeneity in cell populations that can lead to clonal outgrowth of cancer cells with highly diverse genotypes.
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Affiliation(s)
- Emily Weyburne
- Department of Molecular and Systems Biology, Dartmouth College, Hanover, New Hampshire, USA
| | - Giovanni Bosco
- Department of Molecular and Systems Biology, Dartmouth College, Hanover, New Hampshire, USA
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