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Zhang N, Harbers L, Simonetti M, Diekmann C, Verron Q, Berrino E, Bellomo SE, Longo GMC, Ratz M, Schultz N, Tarish F, Su P, Han B, Wang W, Onorato S, Grassini D, Ballarino R, Giordano S, Yang Q, Sapino A, Frisén J, Alkass K, Druid H, Roukos V, Helleday T, Marchiò C, Bienko M, Crosetto N. High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue. Nat Commun 2024; 15:3475. [PMID: 38658552 PMCID: PMC11043350 DOI: 10.1038/s41467-024-47664-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.
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Affiliation(s)
- Ning Zhang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Michele Simonetti
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Quentin Verron
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sara E Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Oncology, University of Turin, Turin, Italy
| | | | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, 17177, Sweden
| | - Niklas Schultz
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | | | - Peng Su
- Department of Pathology, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Bo Han
- Department of Pathology, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Wanzhong Wang
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Sofia Onorato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Dora Grassini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Roberto Ballarino
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Silvia Giordano
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Oncology, University of Turin, Turin, Italy
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Anna Sapino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, 17177, Sweden
| | - Kanar Alkass
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, 17177, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Henrik Druid
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Vassilis Roukos
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
- Department of General Biology, Medical School, University of Patras, Patras, Greece
| | - Thomas Helleday
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Stockholm, 17177, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
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Camargo-Herrera V, Castellanos G, Rangel N, Jiménez-Tobón GA, Martínez-Agüero M, Rondón-Lagos M. Patterns of Chromosomal Instability and Clonal Heterogeneity in Luminal B Breast Cancer: A Pilot Study. Int J Mol Sci 2024; 25:4478. [PMID: 38674062 DOI: 10.3390/ijms25084478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 04/28/2024] Open
Abstract
Chromosomal instability (CIN), defined by variations in the number or structure of chromosomes from cell to cell, is recognized as a distinctive characteristic of cancer associated with the ability of tumors to adapt to challenging environments. CIN has been recognized as a source of genetic variation that leads to clonal heterogeneity (CH). Recent findings suggest a potential association between CIN and CH with the prognosis of BC patients, particularly in tumors expressing the epidermal growth factor receptor 2 (HER2+). In fact, information on the role of CIN in other BC subtypes, including luminal B BC, is limited. Additionally, it remains unknown whether CIN in luminal B BC tumors, above a specific threshold, could have a detrimental effect on the growth of human tumors or whether low or intermediate CIN levels could be linked to a more favorable BC patient prognosis when contrasted with elevated levels. Clarifying these relationships could have a substantial impact on risk stratification and the development of future therapeutic strategies aimed at targeting CIN in BC. This study aimed to assess CIN and CH in tumor tissue samples from ten patients with luminal B BC and compare them with established clinicopathological parameters. The results of this study reveal that luminal B BC patients exhibit intermediate CIN and stable aneuploidy, both of which correlate with lymphovascular invasion. Our results also provide valuable preliminary data that could contribute to the understanding of the implications of CIN and CH in risk stratification and the development of future therapeutic strategies in BC.
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Affiliation(s)
- Valentina Camargo-Herrera
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Giovanny Castellanos
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Nelson Rangel
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Guillermo Antonio Jiménez-Tobón
- Laboratorio de Patología, Hospital Universitario Mayor-Méderi, Bogotá 110311, Colombia
- Grupo BIOmedUR, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá 110231, Colombia
| | - María Martínez-Agüero
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 110231, Colombia
| | - Milena Rondón-Lagos
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
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Luke JJ, Davar D, Andtbacka RH, Bhardwaj N, Brody JD, Chesney J, Coffin R, de Baere T, de Gruijl TD, Fury M, Goldmacher G, Harrington KJ, Kaufman H, Kelly CM, Khilnani AD, Liu K, Loi S, Long GV, Melero I, Middleton M, Neyns B, Pinato DJ, Sheth RA, Solomon SB, Szapary P, Marabelle A. Society for Immunotherapy of Cancer (SITC) recommendations on intratumoral immunotherapy clinical trials (IICT): from premalignant to metastatic disease. J Immunother Cancer 2024; 12:e008378. [PMID: 38641350 PMCID: PMC11029323 DOI: 10.1136/jitc-2023-008378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Intratumorally delivered immunotherapies have the potential to favorably alter the local tumor microenvironment and may stimulate systemic host immunity, offering an alternative or adjunct to other local and systemic treatments. Despite their potential, these therapies have had limited success in late-phase trials for advanced cancer resulting in few formal approvals. The Society for Immunotherapy of Cancer (SITC) convened a panel of experts to determine how to design clinical trials with the greatest chance of demonstrating the benefits of intratumoral immunotherapy for patients with cancers across all stages of pathogenesis. METHODS An Intratumoral Immunotherapy Clinical Trials Expert Panel composed of international key stakeholders from academia and industry was assembled. A multiple choice/free response survey was distributed to the panel, and the results of this survey were discussed during a half-day consensus meeting. Key discussion points are summarized in the following manuscript. RESULTS The panel determined unique clinical trial designs tailored to different stages of cancer development-from premalignant to unresectable/metastatic-that can maximize the chance of capturing the effect of intratumoral immunotherapies. Design elements discussed included study type, patient stratification and exclusion criteria, indications of randomization, study arm determination, endpoints, biological sample collection, and response assessment with biomarkers and imaging. Populations to prioritize for the study of intratumoral immunotherapy, including stage, type of cancer and line of treatment, were also discussed along with common barriers to the development of these local treatments. CONCLUSIONS The SITC Intratumoral Immunotherapy Clinical Trials Expert Panel has identified key considerations for the design and implementation of studies that have the greatest potential to capture the effect of intratumorally delivered immunotherapies. With more effective and standardized trial designs, the potential of intratumoral immunotherapy can be realized and lead to regulatory approvals that will extend the benefit of these local treatments to the patients who need them the most.
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Affiliation(s)
- Jason J Luke
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Diwakar Davar
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | | | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joshua D Brody
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jason Chesney
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | | | - Thierry de Baere
- Center for Biotherapies In Situ (BIOTHERIS), INSERM CIC1428, Interventional Radiology Unit, Department of Medical Imaging, Gustave Roussy Cancer Center, University of Paris Saclay, Villejuif, France
| | - Tanja D de Gruijl
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, Netherlands
- Cancer Immunology, Amsterdam Institute for Infection and Immunology, Amsterdam, Netherlands
| | - Matthew Fury
- Oncology Clinical Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | | | - Kevin J Harrington
- The Institute of Cancer Research, The Royal Marsden National Institute for Health and Care Research Biomedical Research Centre, London, UK
| | - Howard Kaufman
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Ankyra Therapeutics, Boston, Massachusetts, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Ke Liu
- Marengo Therapeutics, Inc, Cambridge, Massachusetts, USA
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Georgina V Long
- Melanoma Institute Australia, University of Sydney, and Royal North Shore and Mater Hospitals, North Sydney, New South Wales, Australia
| | | | - Mark Middleton
- Department of Oncology, University of Oxford, Oxford, UK
| | - Bart Neyns
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Jette, Belgium
| | - David J Pinato
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
- Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Rahul A Sheth
- Department of Interventional Radiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stephen B Solomon
- Chief of Interventional Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Professor of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Philippe Szapary
- Interventional Oncology, Johnson & Johnson, New Brunswick, New Jersey, USA
| | - Aurelien Marabelle
- Center for Biotherapies In Situ (BIOTHERIS), INSERM CIC1428, Department for Therapeutic Innovation and Early Phase Trials (DITEP), Gustave Roussy Cancer Center, University of Paris Saclay, Villejuif, France
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Lv Y, Feng G, Yang L, Wu X, Wang C, Ye A, wang S, Xu C, Shi H. Differential whole-genome doubling based signatures for improvement on clinical outcomes and drug response in patients with breast cancer. Heliyon 2024; 10:e28586. [PMID: 38576569 PMCID: PMC10990872 DOI: 10.1016/j.heliyon.2024.e28586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
Whole genome doublings (WGD), a hallmark of human cancer, is pervasive in breast cancer patients. However, the molecular mechanism of the complete impact of WGD on survival and treatment response in breast cancer remains unclear. To address this, we performed a comprehensive and systematic analysis of WGD, aiming to identify distinct genetic alterations linked to WGD and highlight its improvement on clinical outcomes and treatment response for breast cancer. A linear regression model along with weighted gene co-expression network analysis (WGCNA) was applied on The Cancer Genome Atlas (TCGA) dataset to identify critical genes related to WGD. Further Cox regression models with random selection were used to optimize the most useful prognostic markers in the TCGA dataset. The clinical implication of the risk model was further assessed through prognostic impact evaluation, tumor stratification, functional analysis, genomic feature difference analysis, drug response analysis, and multiple independent datasets for validation. Our findings revealed a high aneuploidy burden, chromosomal instability (CIN), copy number variation (CNV), and mutation burden in breast tumors exhibiting WGD events. Moreover, 247 key genes associated with WGD were identified from the distinct genomic patterns in the TCGA dataset. A risk model consisting of 22 genes was optimized from the key genes. High-risk breast cancer patients were more prone to WGD and exhibited greater genomic diversity compared to low-risk patients. Some oncogenic signaling pathways were enriched in the high-risk group, while primary immune deficiency pathways were enriched in the low-risk group. We also identified a risk gene, ANLN (anillin), which displayed a strong positive correlation with two crucial WGD genes, KIF18A and CCNE2. Tumors with high expression of ANLN were more prone to WGD events and displayed worse clinical survival outcomes. Furthermore, the expression levels of these risk genes were significantly associated with the sensitivities of BRCA cell lines to multiple drugs, providing valuable insights for targeted therapies. These findings will be helpful for further improvement on clinical outcomes and contribution to drug development in breast cancer.
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Affiliation(s)
| | | | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xiaoliang Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Chengyi Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Aokun Ye
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Shuyuan wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
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Cosentini I, Condorelli DF, Locicero G, Ferro A, Pulvirenti A, Barresi V, Alaimo S. Measuring cancer driving force of chromosomal aberrations through multi-layer Boolean implication networks. PLoS One 2024; 19:e0301591. [PMID: 38593144 PMCID: PMC11003681 DOI: 10.1371/journal.pone.0301591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 04/11/2024] Open
Abstract
Multi-layer Complex networks are commonly used for modeling and analysing biological entities. This paper presents the advantage of using COMBO (Combining Multi Bio Omics) to suggest a new role of the chromosomal aberration as a cancer driver factor. Exploiting the heterogeneous multi-layer networks, COMBO integrates gene expression and DNA-methylation data in order to identify complex bilateral relationships between transcriptome and epigenome. We evaluated the multi-layer networks generated by COMBO on different TCGA cancer datasets (COAD, BLCA, BRCA, CESC, STAD) focusing on the effect of a specific chromosomal numerical aberration, broad gain in chromosome 20, on different cancer histotypes. In addition, the effect of chromosome 8q amplification was tested in the same TCGA cancer dataset. The results demonstrate the ability of COMBO to identify the chromosome 20 amplification cancer driver force in the different TCGA Pan Cancer project datasets.
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Affiliation(s)
- Ilaria Cosentini
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy
| | - Daniele Filippo Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, Italy
| | - Giorgio Locicero
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
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Feng Y, Tang D, Wang J. Emerging role and function of SPDL1 in human health and diseases. Open Med (Wars) 2024; 19:20240922. [PMID: 38623460 PMCID: PMC11017184 DOI: 10.1515/med-2024-0922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 04/17/2024] Open
Abstract
SPDL1 (spindle apparatus coiled-coil protein 1), also referred to as CCDC99, is a recently identified gene involved in cell cycle regulation. SPDL1 encodes a protein, hSpindly, which plays a critical role in the maintenance of spindle checkpoint silencing during mitosis. hSpindly coordinates microtubule attachment by promoting kinesin recruitment and mitotic checkpoint signaling. Moreover, the protein performs numerous biological functions in vivo and its aberrant expression is closely associated with abnormal neuronal development, pulmonary interstitial fibrosis, and malignant tumor development. In this review, we provide an overview of studies that reveal the characteristics of SPDL1 and of the protein encoded by it, as well as its biological and tumor-promoting functions.
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Affiliation(s)
- Yuejiao Feng
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, 200062, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, 230022, China
- Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Donghao Tang
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, 200062, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, 230022, China
- Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Jie Wang
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, 200062, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, 230022, China
- Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
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Guo X, Bian X, Li Y, Zhu X, Zhou X. The intricate dance of tumor evolution: Exploring immune escape, tumor migration, drug resistance, and treatment strategies. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167098. [PMID: 38412927 DOI: 10.1016/j.bbadis.2024.167098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/14/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
Recent research has unveiled fascinating insights into the intricate mechanisms governing tumor evolution. These studies have illuminated how tumors adapt and proliferate by exploiting various factors, including immune evasion, resistance to therapeutic drugs, genetic mutations, and their ability to adapt to different environments. Furthermore, investigations into tumor heterogeneity and chromosomal aberrations have revealed the profound complexity that underlies the evolution of cancer. Emerging findings have also underscored the role of viral influences in the development and progression of cancer, introducing an additional layer of complexity to the field of oncology. Tumor evolution is a dynamic and complex process influenced by various factors, including immune evasion, drug resistance, tumor heterogeneity, and viral influences. Understanding these elements is indispensable for developing more effective treatments and advancing cancer therapies. A holistic approach to studying and addressing tumor evolution is crucial in the ongoing battle against cancer. The main goal of this comprehensive review is to explore the intricate relationship between tumor evolution and critical aspects of cancer biology. By delving into this complex interplay, we aim to provide a profound understanding of how tumors evolve, adapt, and respond to treatment strategies. This review underscores the pivotal importance of comprehending tumor evolution in shaping effective approaches to cancer treatment.
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Affiliation(s)
- Xiaojun Guo
- Department of Immunology, School of Medicine, Nantong University, Nantong, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiaonan Bian
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Yitong Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China.
| | - Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, China.
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Hosea R, Hillary S, Naqvi S, Wu S, Kasim V. The two sides of chromosomal instability: drivers and brakes in cancer. Signal Transduct Target Ther 2024; 9:75. [PMID: 38553459 PMCID: PMC10980778 DOI: 10.1038/s41392-024-01767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and is associated with tumor cell malignancy. CIN triggers a chain reaction in cells leading to chromosomal abnormalities, including deviations from the normal chromosome number or structural changes in chromosomes. CIN arises from errors in DNA replication and chromosome segregation during cell division, leading to the formation of cells with abnormal number and/or structure of chromosomes. Errors in DNA replication result from abnormal replication licensing as well as replication stress, such as double-strand breaks and stalled replication forks; meanwhile, errors in chromosome segregation stem from defects in chromosome segregation machinery, including centrosome amplification, erroneous microtubule-kinetochore attachments, spindle assembly checkpoint, or defective sister chromatids cohesion. In normal cells, CIN is deleterious and is associated with DNA damage, proteotoxic stress, metabolic alteration, cell cycle arrest, and senescence. Paradoxically, despite these negative consequences, CIN is one of the hallmarks of cancer found in over 90% of solid tumors and in blood cancers. Furthermore, CIN could endow tumors with enhanced adaptation capabilities due to increased intratumor heterogeneity, thereby facilitating adaptive resistance to therapies; however, excessive CIN could induce tumor cells death, leading to the "just-right" model for CIN in tumors. Elucidating the complex nature of CIN is crucial for understanding the dynamics of tumorigenesis and for developing effective anti-tumor treatments. This review provides an overview of causes and consequences of CIN, as well as the paradox of CIN, a phenomenon that continues to perplex researchers. Finally, this review explores the potential of CIN-based anti-tumor therapy.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sumera Naqvi
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
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9
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Di Tommaso E, Giunta S. Dynamic interplay between human alpha-satellite DNA structure and centromere functions. Semin Cell Dev Biol 2024; 156:130-140. [PMID: 37926668 DOI: 10.1016/j.semcdb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.
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Affiliation(s)
- Elena Di Tommaso
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy.
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10
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Darmasaputra GS, van Rijnberk LM, Galli M. Functional consequences of somatic polyploidy in development. Development 2024; 151:dev202392. [PMID: 38415794 PMCID: PMC10946441 DOI: 10.1242/dev.202392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Polyploid cells contain multiple genome copies and arise in many animal tissues as a regulated part of development. However, polyploid cells can also arise due to cell division failure, DNA damage or tissue damage. Although polyploidization is crucial for the integrity and function of many tissues, the cellular and tissue-wide consequences of polyploidy can be very diverse. Nonetheless, many polyploid cell types and tissues share a remarkable similarity in function, providing important information about the possible contribution of polyploidy to cell and tissue function. Here, we review studies on polyploid cells in development, underlining parallel functions between different polyploid cell types, as well as differences between developmentally-programmed and stress-induced polyploidy.
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Affiliation(s)
- Gabriella S. Darmasaputra
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Lotte M. van Rijnberk
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Matilde Galli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
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11
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Wu M, Dong H, Xu C, Sun M, Gao H, Bu F, Chen J. The Wnt-dependent and Wnt-independent functions of BCL9 in development, tumorigenesis, and immunity: Implications in therapeutic opportunities. Genes Dis 2024; 11:701-710. [PMID: 37692512 PMCID: PMC10491870 DOI: 10.1016/j.gendis.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/27/2023] [Accepted: 03/05/2023] [Indexed: 09/12/2023] Open
Abstract
B-cell CLL/lymphoma 9 (BCL9) is considered a key developmental regulator and a well-established oncogenic driver in multiple cancer types, mainly through potentiating the Wnt/β-catenin signaling. However, increasing evidences indicate that BCL9 also plays multiple Wnt-independent roles. Herein, we summarized the updates of the canonical and non-canonical functions of BCL9 in cellular, physiological, or pathological processes. Moreover, we also concluded that the targeted inhibitors disrupt the interaction of β-catenin with BCL9 reported recently.
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Affiliation(s)
- Minjie Wu
- College of Pharmacy and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Heng Dong
- College of Pharmacy and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Chao Xu
- College of Pharmacy and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Mengqing Sun
- College of Pharmacy and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Haojin Gao
- College of Pharmacy and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Fangtian Bu
- College of Pharmacy and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Jianxiang Chen
- College of Pharmacy and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
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12
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Reeves MQ, Balmain A. Mutations, Bottlenecks, and Clonal Sweeps: How Environmental Carcinogens and Genomic Changes Shape Clonal Evolution during Tumor Progression. Cold Spring Harb Perspect Med 2024; 14:a041388. [PMID: 38052482 PMCID: PMC10910358 DOI: 10.1101/cshperspect.a041388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The transition from a single, initiated cell to a full-blown malignant tumor involves significant genomic evolution. Exposure to carcinogens-whether directly mutagenic or not-can drive progression toward malignancy, as can stochastic acquisition of cancer-promoting genetic events. Mouse models using both carcinogens and germline genetic manipulations have enabled precise inquiry into the evolutionary dynamics that take place as a tumor progresses from benign to malignant to metastatic stages. Tumor progression is characterized by changes in somatic point mutations and copy-number alterations, even though any single tumor can itself have a high or low burden of genomic alterations. Further, lineage-tracing, single-cell analyses and CRISPR barcoding have revealed the distinct clonal dynamics within benign and malignant tumors. Application of these tools in a range of mouse models can shed unique light on the patterns of clonal evolution that take place in both mouse and human tumors.
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Affiliation(s)
- Melissa Q Reeves
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
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13
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Watson EV, Lee JJK, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet 2024:10.1038/s41588-024-01665-2. [PMID: 38388848 DOI: 10.1038/s41588-024-01665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
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Affiliation(s)
- Emma V Watson
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rayna Y Magesh
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Abdulrazak Frederick
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kunitoshi Chiba
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric C Wooten
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Kamila Naxerova
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Mengoni M, Braun AD, Seedarala S, Bonifatius S, Kostenis E, Schanze D, Zenker M, Tüting T, Gaffal E. Transactivation of Met signaling by oncogenic Gnaq drives the evolution of melanoma in Hgf-Cdk4 mice. Cancer Gene Ther 2024:10.1038/s41417-024-00744-0. [PMID: 38360887 DOI: 10.1038/s41417-024-00744-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Recent pan-cancer genomic analyses have identified numerous oncogenic driver mutations that occur in a cell-type and tissue-specific distribution. For example, oncogenic mutations in Braf and Nras genes arise predominantly in melanocytic neoplasms of the epidermis, while oncogenic mutations in Gnaq/11 genes arise mostly in melanocytic lesions of the dermis or the uvea. The mechanisms promoting cell-type and tissue-specific oncogenic events currently remain poorly understood. Here, we report that Gnaq/11 hotspot mutations occur as early oncogenic drivers during the evolution of primary melanomas in Hgf-Cdk4 mice. Additional single base substitutions in the Trp53 gene and structural chromosomal aberrations favoring amplifications of the chromosomal region containing the Met receptor gene accumulate during serial tumor transplantation and in cell lines established in vitro. Mechanistically, we found that the GnaqQ209L mutation transactivates the Met receptor. Overexpression of oncogenic GnaqQ209L in the immortalized melanocyte cell line promoted in vivo growth that was enhanced by transgenic Hgf expression in the tumor microenvironment. This cross-signaling mechanism explains the selection of oncogenic Gnaq/11 in primary Hgf-Cdk4 melanomas and provides an example of how oncogenic driver mutations, intracellular signaling cascades, and microenvironmental cues cooperate to drive cancer development in a tissue-specific fashion.
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Affiliation(s)
- Miriam Mengoni
- Laboratory for Experimental Dermatology, Department of Dermatology, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Andreas Dominik Braun
- Laboratory for Experimental Dermatology, Department of Dermatology, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Sahithi Seedarala
- Laboratory for Experimental Dermatology, Department of Dermatology, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Susanne Bonifatius
- Laboratory for Experimental Dermatology, Department of Dermatology, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Thomas Tüting
- Laboratory for Experimental Dermatology, Department of Dermatology, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Evelyn Gaffal
- Laboratory for Experimental Dermatology, Department of Dermatology, University Hospital Magdeburg, 39120, Magdeburg, Germany.
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16
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Carceles-Cordon M, Orme JJ, Domingo-Domenech J, Rodriguez-Bravo V. The yin and yang of chromosomal instability in prostate cancer. Nat Rev Urol 2024:10.1038/s41585-023-00845-9. [PMID: 38307951 DOI: 10.1038/s41585-023-00845-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2023] [Indexed: 02/04/2024]
Abstract
Metastatic prostate cancer remains an incurable lethal disease. Studies indicate that prostate cancer accumulates genomic changes during disease progression and displays the highest levels of chromosomal instability (CIN) across all types of metastatic tumours. CIN, which refers to ongoing chromosomal DNA gain or loss during mitosis, and derived aneuploidy, are known to be associated with increased tumour heterogeneity, metastasis and therapy resistance in many tumour types. Paradoxically, high CIN levels are also proposed to be detrimental to tumour cell survival, suggesting that cancer cells must develop adaptive mechanisms to ensure their survival. In the context of prostate cancer, studies indicate that CIN has a key role in disease progression and might also offer a therapeutic vulnerability that can be pharmacologically targeted. Thus, a comprehensive evaluation of the causes and consequences of CIN in prostate cancer, its contribution to aggressive advanced disease and a better understanding of the acquired CIN tolerance mechanisms can translate into new tumour classifications, biomarker development and therapeutic strategies.
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Affiliation(s)
| | - Jacob J Orme
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Josep Domingo-Domenech
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
| | - Veronica Rodriguez-Bravo
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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17
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Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. Nat Cancer 2024; 5:228-239. [PMID: 38286829 DOI: 10.1038/s43018-023-00711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Mutational processes that alter large genomic regions occur frequently in developing tumors. They range from simple copy number gains and losses to the shattering and reassembly of entire chromosomes. These catastrophic events, such as chromothripsis, chromoplexy and the formation of extrachromosomal DNA, affect the expression of many genes and therefore have a substantial effect on the fitness of the cells in which they arise. In this review, we cover large genomic alterations, the mechanisms that cause them and their effect on tumor development and evolution.
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Affiliation(s)
- Toby M Baker
- The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Waise
- The Francis Crick Institute, London, UK
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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18
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Antonello A, Bergamin R, Calonaci N, Househam J, Milite S, Williams MJ, Anselmi F, d'Onofrio A, Sundaram V, Sosinsky A, Cross WCH, Caravagna G. Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome Biol 2024; 25:38. [PMID: 38297376 PMCID: PMC10832148 DOI: 10.1186/s13059-024-03170-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.
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Affiliation(s)
- Alice Antonello
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Riccardo Bergamin
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Nicola Calonaci
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Jacob Househam
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Salvatore Milite
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
- Centre for Computational Biology, Human Technopole, Milan, Italy
| | - Marc J Williams
- Department of Computational Oncology, Memorial Sloan Kettering, New York, USA
| | - Fabio Anselmi
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Alberto d'Onofrio
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | | | | | - William C H Cross
- Department of Research Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy.
- Evolutionary Genomics and Modelling Team, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
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19
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Feng D, Tuo Z, Wang J, Ye L, Li D, Wu R, Wei W, Yang Y, Zhang C. Establishment of novel ferroptosis-related prognostic subtypes correlating with immune dysfunction in prostate cancer patients. Heliyon 2024; 10:e23495. [PMID: 38187257 PMCID: PMC10770465 DOI: 10.1016/j.heliyon.2023.e23495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/19/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Background We aimed to identify two new prognostic subtypes and create a predictive index for prostate cancer (PCa) patients based on ferroptosis database. Methods The nonnegative matrix factorization approach was used to identify molecular subtypes. We investigate the differences between cluster 1 and cluster 2 in terms of clinical features, functional pathways, tumour stemness, tumour heterogeneity, gene mutation and tumour immune microenvironment score after identifying the two molecular subtypes. Colony formation assay and flow cytometry assay were performed. Results The stratification of two clusters was closely connected to BCR-free survival using the nonnegative matrix factorization method, which was validated in the other three datasets. Furthermore, multivariate Cox regression analysis revealed that this classification was an independent risk factor for patients with PCa. Ribosome, aminoacyl tRNA production, oxidative phosphorylation, and Parkinson's disease-related pathways were shown to be highly enriched in cluster 1. In comparison to cluster 2, patients in cluster 1 exhibited significantly reduced CD4+ T cells, CD8+ T cells, neutrophils, dendritic cells and tumor immune microenvironment scores. Only HHLA2 was more abundant in cluster 1. Moreover, we found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of C4-2B and DU145 cell lines. Conclusions We discovered two new prognostic subtypes associated with immunological dysfunction in PCa patients based on ferroptosis-related genes and found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of PCa cell lines.
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Affiliation(s)
- Dechao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Zhouting Tuo
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Luxia Ye
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Dengxiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ruicheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yubo Yang
- Department of Urology, Three Gorges Hospital, Chongqing University, Wanzhou, Chongqing, 404000, China
| | - Chi Zhang
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
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20
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Sun Y, Wu P, Zhang Z, Wang Z, Zhou K, Song M, Ji Y, Zang F, Lou L, Rao K, Wang P, Gu Y, Gu J, Lu B, Chen L, Pan X, Zhao X, Peng L, Liu D, Chen X, Wu K, Lin P, Wu L, Su Y, Du M, Hou Y, Yang X, Qiu S, Shi Y, Sun H, Zhou J, Huang X, Peng DH, Zhang L, Fan J. Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinoma. Cancer Cell 2024; 42:135-156.e17. [PMID: 38101410 DOI: 10.1016/j.ccell.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 09/27/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Comprehensive molecular analyses of metastatic hepatocellular carcinoma (HCC) are lacking. Here, we generate multi-omic profiling of 257 primary and 176 metastatic regions from 182 HCC patients. Primary tumors rich in hypoxia signatures facilitated polyclonal dissemination. Genomic divergence between primary and metastatic HCC is high, and early dissemination is prevalent. The remarkable neoantigen intratumor heterogeneity observed in metastases is associated with decreased T cell reactivity, resulting from disruptions to neoantigen presentation. We identify somatic copy number alterations as highly selected events driving metastasis. Subclones without Wnt mutations show a stronger selective advantage for metastasis than those with Wnt mutations and are characterized by a microenvironment rich in activated fibroblasts favoring a pro-metastatic phenotype. Finally, metastases without Wnt mutations exhibit higher enrichment of immunosuppressive B cells that mediate terminal exhaustion of CD8+ T cells via HLA-E:CD94-NKG2A checkpoint axis. Collectively, our results provide a multi-dimensional dissection of the complex evolutionary process of metastasis.
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Affiliation(s)
- Yunfan Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.
| | - Pin Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China
| | - Zefan Zhang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Zejian Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiqian Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Minfang Song
- Research Center for Intelligent Computing Platforms, Zhejiang Lab, Hangzhou, Zhejiang 311121, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Fenglin Zang
- Department of Pathology, Liver Cancer Research Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Limu Lou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Keqiang Rao
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Pengxiang Wang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Yutong Gu
- Department of Orthopaedic Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Binbin Lu
- Dunwill Med-Tech, Shanghai 200032, China
| | | | - Xiuqi Pan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Lihua Peng
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Dongbing Liu
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Xiaofang Chen
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Kui Wu
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Penghui Lin
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Liang Wu
- BGI Research, Shenzhen 518083, China
| | - Yulin Su
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Min Du
- Department of Pathology, Huadong Hospital, Fudan University, Shanghai 200032, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xinrong Yang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Shuangjian Qiu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Yinghong Shi
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Huichuan Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Xingxu Huang
- Research Center for Intelligent Computing Platforms, Zhejiang Lab, Hangzhou, Zhejiang 311121, China
| | | | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
| | - Jia Fan
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.
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Mandahl N, Mertens F, Mitelman F. Gene amplification in neoplasia: A cytogenetic survey of 80 131 cases. Genes Chromosomes Cancer 2024; 63:e23214. [PMID: 38050922 DOI: 10.1002/gcc.23214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/26/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
Gene amplification is a crucial process in cancer development, leading to the overexpression of oncogenes. It manifests cytogenetically as extrachromosomal double minutes (dmin), homogeneously staining regions (hsr), or ring chromosomes (r). This study investigates the prevalence and distribution of these amplification markers in a survey of 80 131 neoplasms spanning hematologic disorders, and benign and malignant solid tumors. The study reveals distinct variations in the frequency of dmin, hsr, and r among different tumor types. Rings were the most common (3.4%) sign of amplification, followed by dmin (1.3%), and hsr (0.8%). Rings were particularly frequent in malignant mesenchymal tumors, especially liposarcomas (47.5%) and osteosarcomas (23.4%), dmin were prevalent in neuroblastoma (30.9%) and pancreatic carcinoma (21.9%), and hsr frequencies were highest in head and neck carcinoma (14.0%) and neuroblastoma (9.0%). Combining all three amplification markers (dmin/hsr/r), malignant solid tumors consistently exhibited higher frequencies than hematologic disorders and benign solid tumors. The structural characteristics of these amplification markers and their potential role in tumorigenesis and tumor progression highlight the complex interplay between cancer-initiating gene-level alterations, for example, fusion genes, and subsequent amplification dynamics. Further research integrating cytogenetic and molecular approaches is warranted to better understand the underlying mechanisms of these amplifications, in particular, the enigmatic question of why certain malignancies display certain types of amplification. Comparing the present results with molecular genetic data proved challenging because of the diversity in definitions of amplification across studies. This study underscores the need for standardized definitions in future work.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, University Hospital, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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22
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Kandala S, Ramos M, Voith von Voithenberg L, Diaz-Jimenez A, Chocarro S, Keding J, Brors B, Imbusch CD, Sotillo R. Chronic chromosome instability induced by Plk1 results in immune suppression in breast cancer. Cell Rep 2023; 42:113266. [PMID: 37979172 DOI: 10.1016/j.celrep.2023.113266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/28/2023] [Accepted: 09/28/2023] [Indexed: 11/20/2023] Open
Abstract
Chromosome instability (CIN) contributes to resistance to therapies and tumor evolution. Although natural killer (NK) cells can eliminate cells with complex karyotypes, high-CIN human tumors have an immunosuppressive phenotype. To understand which CIN-associated molecular features alter immune recognition during tumor evolution, we overexpress Polo-like kinase 1 (Plk1) in a Her2+ breast cancer model. These high-CIN tumors activate a senescence-associated secretory phenotype (SASP), upregulate PD-L1 and CD206, and induce non-cell-autonomous nuclear factor κB (NF-κβ) signaling, facilitating immune evasion. Single-cell RNA sequencing from pre-neoplastic mammary glands unveiled the presence of Arg1+ macrophages, NK cells with reduced effector functions, and increased resting regulatory T cell infiltration. We further show that high PLK1-expressing human breast tumors display gene expression patterns associated with SASP, NF-κβ signaling, and immune suppression. These findings underscore the need to understand the immune landscape in CIN tumors to identify more effective therapies, potentially combining immune checkpoint or NF-κβ inhibitors with current treatments.
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Affiliation(s)
- Sridhar Kandala
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Maria Ramos
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lena Voith von Voithenberg
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Alberto Diaz-Jimenez
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Johanna Keding
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany.
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Lakhani AA, Thompson SL, Sheltzer JM. Aneuploidy in human cancer: new tools and perspectives. Trends Genet 2023; 39:968-980. [PMID: 37778926 PMCID: PMC10715718 DOI: 10.1016/j.tig.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Chromosome copy number imbalances, otherwise known as aneuploidies, are a common but poorly understood feature of cancer. Here, we describe recent advances in both detecting and manipulating aneuploidies that have greatly advanced our ability to study their role in tumorigenesis. In particular, new clustered regularly interspaced short palindromic repeats (CRISPR)-based techniques have been developed that allow the creation of isogenic cell lines with specific chromosomal changes, thereby facilitating experiments in genetically controlled backgrounds to uncover the consequences of aneuploidy. These approaches provide increasing evidence that aneuploidy is a key driver of cancer development and enable the identification of multiple dosage-sensitive genes encoded on aneuploid chromosomes. Consequently, measuring aneuploidy may inform clinical prognosis, while treatment strategies that target aneuploidy could represent a novel method to counter malignant growth.
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Affiliation(s)
- Asad A Lakhani
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring, Harbor, NY 11724, USA
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25
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Guo L, Li F, Liu H, Kong D, Chen C, Sun S. SIX1 amplification modulates stemness and tumorigenesis in breast cancer. J Transl Med 2023; 21:866. [PMID: 38031089 PMCID: PMC10685563 DOI: 10.1186/s12967-023-04679-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/29/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Sine oculis homeobox homolog 1 (SIX1) is a transcription factor that has recently been identified as a crucial regulator of embryonic development and tumorigenesis. SIX1 is upregulated in different types of tumors, including breast cancer. However, the role and mechanism of SIX1 upregulation in breast cancer carcinogenesis remains uncertain. METHODS In this study, we utilized various databases such as UALCAN, TCGA, STRING, and Kaplan-Meier Plotter to investigate the mRNA expression, prognosis, transcriptional profile changes, signal pathway rewiring, and interaction with cancer stem cells of SIX1 in breast cancer. We also conducted both in vitro and in vivo experiments to validate its positive regulation effect on breast cancer stem cells. RESULTS Our findings demonstrated that the expression of SIX1 varies among different subtypes of breast cancer and that it upregulates breast cancer grading and lymph node metastasis. Besides, SIX1 participates in the rewiring of several cancer signaling pathways, including estrogen, WNT, MAPK, and other pathways, and interacts with cancer stem cells. SIX1 showed a significant positive correlation with breast cancer stem cell markers such as ALDH1A1, EPCAM, ITGB1, and SOX2. Moreover, our in vitro and in vivo experiments confirmed that SIX1 can promote the increase in the proportion of stem cells and tumor progression. CONCLUSIONS Altogether, our results suggest that SIX1 plays an essential regulatory role in breast cancer's occurrence, and its amplification can be utilized as a diagnostic and prognostic predictor. The interaction between SIX1 and cancer stem cells may play a critical role in regulating breast cancer's initiation and metastasis.
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Affiliation(s)
- Liantao Guo
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Faminzi Li
- Reproductive Medical Center, Renmin Hospital of Wuhan University and Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Hanqing Liu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Deguang Kong
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
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26
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Kinnaman MD, Zaccaria S, Makohon-Moore A, Arnold B, Levine MF, Gundem G, Arango Ossa JE, Glodzik D, Rodríguez-Sánchez MI, Bouvier N, Li S, Stockfisch E, Dunigan M, Cobbs C, Bhanot UK, You D, Mullen K, Melchor JP, Ortiz MV, O'Donohue TJ, Slotkin EK, Wexler LH, Dela Cruz FS, Hameed MR, Glade Bender JL, Tap WD, Meyers PA, Papaemmanuil E, Kung AL, Iacobuzio-Donahue CA. Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma. Cancer Res 2023; 83:3796-3812. [PMID: 37812025 PMCID: PMC10646480 DOI: 10.1158/0008-5472.can-23-0385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023]
Abstract
Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. We conducted longitudinal whole-genome sequencing of 37 tumor samples from 8 patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and a metastatic or relapse site. Subclonal copy-number alterations were identified in all patients except one. In 5 patients, subclones from the primary tumor emerged and dominated at subsequent relapses. MYC gain/amplification was enriched in the treatment-resistant clones in 6 of 7 patients with multiple clones. Amplifications in other potential driver genes, such as CCNE1, RAD21, VEGFA, and IGF1R, were also observed in the resistant copy-number clones. A chromosomal duplication timing analysis revealed that complex genomic rearrangements typically occurred prior to diagnosis, supporting a macroevolutionary model of evolution, where a large number of genomic aberrations are acquired over a short period of time followed by clonal selection, as opposed to ongoing evolution. A mutational signature analysis of recurrent tumors revealed that homologous repair deficiency (HRD)-related SBS3 increases at each time point in patients with recurrent disease, suggesting that HRD continues to be an active mutagenic process after diagnosis. Overall, by examining the clonal relationships between temporally and spatially separated samples from patients with relapsed/refractory osteosarcoma, this study sheds light on the intratumor heterogeneity and potential drivers of treatment resistance in this disease. SIGNIFICANCE The chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.
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Affiliation(s)
- Michael D. Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, United Kingdom
| | - Alvin Makohon-Moore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian Arnold
- Department of Computer Science, Princeton University, Princeton, New Jersey
- Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey
| | - Max F. Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juan E. Arango Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dominik Glodzik
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shanita Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marisa Dunigan
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cassidy Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh K. Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katelyn Mullen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York
| | - Jerry P. Melchor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael V. Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tara J. O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily K. Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard H. Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Filemon S. Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera R. Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julia L. Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D. Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul A. Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine A. Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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27
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Kreuzaler P, Inglese P, Ghanate A, Gjelaj E, Wu V, Panina Y, Mendez-Lucas A, MacLachlan C, Patani N, Hubert CB, Huang H, Greenidge G, Rueda OM, Taylor AJ, Karali E, Kazanc E, Spicer A, Dexter A, Lin W, Thompson D, Silva Dos Santos M, Calvani E, Legrave N, Ellis JK, Greenwood W, Green M, Nye E, Still E, Barry S, Goodwin RJA, Bruna A, Caldas C, MacRae J, de Carvalho LPS, Poulogiannis G, McMahon G, Takats Z, Bunch J, Yuneva M. Vitamin B 5 supports MYC oncogenic metabolism and tumor progression in breast cancer. Nat Metab 2023; 5:1870-1886. [PMID: 37946084 PMCID: PMC10663155 DOI: 10.1038/s42255-023-00915-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023]
Abstract
Tumors are intrinsically heterogeneous and it is well established that this directs their evolution, hinders their classification and frustrates therapy1-3. Consequently, spatially resolved omics-level analyses are gaining traction4-9. Despite considerable therapeutic interest, tumor metabolism has been lagging behind this development and there is a paucity of data regarding its spatial organization. To address this shortcoming, we set out to study the local metabolic effects of the oncogene c-MYC, a pleiotropic transcription factor that accumulates with tumor progression and influences metabolism10,11. Through correlative mass spectrometry imaging, we show that pantothenic acid (vitamin B5) associates with MYC-high areas within both human and murine mammary tumors, where its conversion to coenzyme A fuels Krebs cycle activity. Mechanistically, we show that this is accomplished by MYC-mediated upregulation of its multivitamin transporter SLC5A6. Notably, we show that SLC5A6 over-expression alone can induce increased cell growth and a shift toward biosynthesis, whereas conversely, dietary restriction of pantothenic acid leads to a reversal of many MYC-mediated metabolic changes and results in hampered tumor growth. Our work thus establishes the availability of vitamins and cofactors as a potential bottleneck in tumor progression, which can be exploited therapeutically. Overall, we show that a spatial understanding of local metabolism facilitates the identification of clinically relevant, tractable metabolic targets.
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Affiliation(s)
- Peter Kreuzaler
- The Francis Crick Institute, London, UK.
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
| | - Paolo Inglese
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | | | | | - Vincen Wu
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | | | - Andres Mendez-Lucas
- The Francis Crick Institute, London, UK
- Department of Physiological Sciences, University of Barcelona, Barcelona, Spain
| | | | | | | | - Helen Huang
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | | | - Oscar M Rueda
- University of Cambridge, MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Evdoxia Karali
- Signalling and Cancer Metabolism Team, Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Emine Kazanc
- Signalling and Cancer Metabolism Team, Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | | | - Alex Dexter
- The National Physical Laboratory, Teddington, UK
| | - Wei Lin
- The Francis Crick Institute, London, UK
| | | | | | | | | | | | - Wendy Greenwood
- University of Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | | | - Emma Nye
- The Francis Crick Institute, London, UK
| | | | - Simon Barry
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Richard J A Goodwin
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Alejandra Bruna
- Modelling of Paediatric Cancer Evolution, Centre for Paediatric Oncology, Experimental Medicine, Centre for Cancer Evolution: Molecular Pathology Division, The Institute of Cancer Research, Belmont, Sutton, London, UK
| | - Carlos Caldas
- University of Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | | | | | - George Poulogiannis
- Signalling and Cancer Metabolism Team, Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Greg McMahon
- The National Physical Laboratory, Teddington, UK
| | - Zoltan Takats
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | - Josephine Bunch
- The National Physical Laboratory, Teddington, UK
- The Rosalind Franklin Institute, Harwell Campus, Didcot, UK
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28
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Marques JF, Kops GJPL. Permission to pass: on the role of p53 as a gatekeeper for aneuploidy. Chromosome Res 2023; 31:31. [PMID: 37864038 PMCID: PMC10589155 DOI: 10.1007/s10577-023-09741-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023]
Abstract
Aneuploidy-the karyotype state in which the number of chromosomes deviates from a multiple of the haploid chromosome set-is common in cancer, where it is thought to facilitate tumor initiation and progression. However, it is poorly tolerated in healthy cells: during development and tissue homeostasis, aneuploid cells are efficiently cleared from the population. It is still largely unknown how cancer cells become, and adapt to being, aneuploid. P53, the gatekeeper of the genome, has been proposed to guard against aneuploidy. Aneuploidy in cancer genomes strongly correlates with mutations in TP53, and p53 is thought to prevent the propagation of aneuploid cells. Whether p53 also participates in preventing the mistakes in cell division that lead to aneuploidy is still under debate. In this review, we summarize the current understanding of the role of p53 in protecting cells from aneuploidy, and we explore the consequences of functional p53 loss for the propagation of aneuploidy in cancer.
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Affiliation(s)
- Joana F Marques
- Royal Netherlands Academy of Arts and Sciences (KNAW), Hubrecht Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
- University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521AL, Utrecht, the Netherlands
| | - Geert J P L Kops
- Royal Netherlands Academy of Arts and Sciences (KNAW), Hubrecht Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands.
- University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, the Netherlands.
- Oncode Institute, Jaarbeursplein 6, 3521AL, Utrecht, the Netherlands.
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29
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Wang X, Lin M, Zhu L, Ye Z. GAS-STING: a classical DNA recognition pathways to tumor therapy. Front Immunol 2023; 14:1200245. [PMID: 37920470 PMCID: PMC10618366 DOI: 10.3389/fimmu.2023.1200245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/28/2023] [Indexed: 11/04/2023] Open
Abstract
Cyclic GMP-AMP synthetase (cGAS), recognized as the primary DNA sensor within cells, possesses the capability to identify foreign DNA molecules along with free DNA fragments. This identification process facilitates the production of type I IFNs through the activator of the interferon gene (STING) which induces the phosphorylation of downstream transcription factors. This action characterizes the most archetypal biological functionality of the cGAS-STING pathway. When treated with anti-tumor agents, cells experience DNA damage that triggers activation of the cGAS-STING pathway, culminating in the expression of type I IFNs and associated downstream interferon-stimulated genes. cGAS-STING is one of the important innate immune pathways,the role of type I IFNs in the articulation between innate immunity and T-cell antitumour immunity.type I IFNs promote the recruitment and activation of inflammatory cells (including NK cells) at the tumor site.Type I IFNs also can promote the activation and maturation of dendritic cel(DC), improve the antigen presentation of CD4+T lymphocytes, and enhance the cross-presentation of CD8+T lymphocytes to upregulating anti-tumor responses. This review discussed the cGAS-STING signaling and its mechanism and biological function in traditional tumor therapy and immunotherapy.
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Affiliation(s)
- Xinrui Wang
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Meijia Lin
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Liping Zhu
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Zhoujie Ye
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
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30
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Ghorani E, Swanton C, Quezada SA. Cancer cell-intrinsic mechanisms driving acquired immune tolerance. Immunity 2023; 56:2270-2295. [PMID: 37820584 DOI: 10.1016/j.immuni.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
Immune evasion is a hallmark of cancer, enabling tumors to survive contact with the host immune system and evade the cycle of immune recognition and destruction. Here, we review the current understanding of the cancer cell-intrinsic factors driving immune evasion. We focus on T cells as key effectors of anti-cancer immunity and argue that cancer cells evade immune destruction by gaining control over pathways that usually serve to maintain physiological tolerance to self. Using this framework, we place recent mechanistic advances in the understanding of cancer immune evasion into broad categories of control over T cell localization, antigen recognition, and acquisition of optimal effector function. We discuss the redundancy in the pathways involved and identify knowledge gaps that must be overcome to better target immune evasion, including the need for better, routinely available tools that incorporate the growing understanding of evasion mechanisms to stratify patients for therapy and trials.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology and Immunotherapy Unit, Department of Surgery and Cancer, Imperial College London, London, UK; Department of Medical Oncology, Imperial College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London, UK.
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31
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Shi Y, Shen H. DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma. Front Genet 2023; 14:1231415. [PMID: 37867602 PMCID: PMC10587545 DOI: 10.3389/fgene.2023.1231415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/05/2023] [Indexed: 10/24/2023] Open
Abstract
Stomach Adenocarcinoma (STAD) is a leading cause of death worldwide. Somatic Copy Number Alterations (SCNAs), which result in Homologous recombination (HR) deficiency in double-strand break repair, are associated with the progression of STAD. However, the landscape of frequent breakpoints of SCNAs (hotspots) and their functional impacts remain poorly understood. In this study, we aimed to explore the frequency and impact of these hotspots in 332 STAD patients and 1,043 cancer cells using data from the Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE). We studied the rates of DSB (Double-Strand Breaks) loci in STAD patients by employing the Non-Homogeneous Poisson Distribution (λ), based on which we identified 145 DSB-hotspots with genes affected. We further verified DNA cytosine deamination as a critical process underlying the burden of DSB in STAD. Finally, we illustrated the clinical impact of the significant biological processes. Our findings highlighted the relationship between DNA cytosine deamination and SCNA in cancer was associated with recurrent Somatic Copy Number Alterations in STAD.
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Affiliation(s)
- Yilin Shi
- The College of Letters & Science, University of Wisconsin–Madison, Madison, WI, United States
| | - Huangxuan Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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32
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Bao C, Tourdot RW, Brunette GJ, Stewart C, Sun L, Baba H, Watanabe M, Agoston AT, Jajoo K, Davison JM, Nason KS, Getz G, Wang KK, Imamura Y, Odze R, Bass AJ, Stachler MD, Zhang CZ. Genomic signatures of past and present chromosomal instability in Barrett's esophagus and early esophageal adenocarcinoma. Nat Commun 2023; 14:6203. [PMID: 37794034 PMCID: PMC10550953 DOI: 10.1038/s41467-023-41805-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.
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Affiliation(s)
- Chunyang Bao
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Richard W Tourdot
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Gregory J Brunette
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Chip Stewart
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Lili Sun
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 2 Chome-40-1 Kurokami, Chuo Ward, Kumamoto, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kunal Jajoo
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Jon M Davison
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Katie S Nason
- Department of Surgery, Baystate Medical Center, University of Massachusetts Medical School, 759 Chestnut St, Springfield, MA, 01107, USA
| | - Gad Getz
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Department of Pathology and Lab Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Matthew D Stachler
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Department of Pathology, University of California, San Francisco. 513 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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33
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Watkins TBK, Colliver EC, Huska MR, Kaufmann TL, Lim EL, Duncan CB, Haase K, Van Loo P, Swanton C, McGranahan N, Schwarz RF. Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity. PLoS Comput Biol 2023; 19:e1011379. [PMID: 37871126 PMCID: PMC10621967 DOI: 10.1371/journal.pcbi.1011379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 11/02/2023] [Accepted: 07/22/2023] [Indexed: 10/25/2023] Open
Abstract
Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.
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Affiliation(s)
- Thomas B. K. Watkins
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Matthew R. Huska
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
| | - Tom L. Kaufmann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Emilia L. Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Cody B. Duncan
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kerstin Haase
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Van Loo
- The Francis Crick Institute, London, United Kingdom
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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34
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Zhang H, Chen S, Xu S, Li X. COTE1 Facilitates Intrahepatic Cholangiocarcinoma Progression via Beclin1-Dependent Autophagy Inhibition. Biomed Res Int 2023; 2023:5491682. [PMID: 37780485 PMCID: PMC10541304 DOI: 10.1155/2023/5491682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/26/2023] [Accepted: 07/17/2023] [Indexed: 10/03/2023]
Abstract
COTE1 was recently described as an oncogene in hepatocellular carcinoma and gastric cancer. However, the roles of COTE1 in intrahepatic cholangiocarcinoma (ICC) are little known. Our study is aimed at clarifying novel functions of COTE1 in ICC progression, including proliferation, invasion, and autophagy. By using quantitative real-time PCR, immunohistochemistry staining, and western blotting, we found that COTE1 expression was frequently upregulated in ICC tissues, compared to paracarcinoma tissues. High COTE1 expression was significantly correlated with aggressive clinical features and predicted poor prognosis of ICC patients. Functional experiments revealed that ectopic COTE1 expression promoted ICC cell proliferation, colony formation, cellular invasion, migration, and in vivo tumorigenicity; in contrast, COTE1 knockdown resulted in the opposite effects. At molecular mechanism in vitro and vivo, our study revealed that COTE1 overexpression suppressed autophagy via Beclin1 transcription inhibition; conversely, COTE1 silencing facilitated autophagy through promoting Beclin1 expression. Furthermore, the suppression of COTE1 knockdown on cellular growth and invasion was rescued/aggravated by Beclin1 inhibition/accumulation. Our data, for the first time, illustrate that COTE1 is an oncogene in ICC pathogenesis, and the ectopic COTE1 expression promotes ICC proliferation and invasion via Beclin1-dependent autophagy inhibition.
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Affiliation(s)
- Hai Zhang
- Key Laboratory on Living Donor Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Shu Chen
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Sanrong Xu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Xiangcheng Li
- Key Laboratory on Living Donor Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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35
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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36
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Borgsmüller N, Valecha M, Kuipers J, Beerenwinkel N, Posada D. Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues. Cell Genom 2023; 3:100380. [PMID: 37719146 PMCID: PMC10504633 DOI: 10.1016/j.xgen.2023.100380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 09/19/2023]
Abstract
Cell lineages accumulate somatic mutations during organismal development, potentially leading to pathological states. The rate of somatic evolution within a cell population can vary due to multiple factors, including selection, a change in the mutation rate, or differences in the microenvironment. Here, we developed a statistical test called the Poisson Tree (PT) test to detect varying evolutionary rates among cell lineages, leveraging the phylogenetic signal of single-cell DNA sequencing (scDNA-seq) data. We applied the PT test to 24 healthy and cancer samples, rejecting a constant evolutionary rate in 11 out of 15 cancer and five out of nine healthy scDNA-seq datasets. In six cancer datasets, we identified subclonal mutations in known driver genes that could explain the rate accelerations of particular cancer lineages. Our findings demonstrate the efficacy of scDNA-seq for studying somatic evolution and suggest that cell lineages often evolve at different rates within cancer and healthy tissues.
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Affiliation(s)
- Nico Borgsmüller
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Monica Valecha
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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37
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Lee JE, Kim KT, Shin SJ, Cheong JH, Choi YY. Genomic and evolutionary characteristics of metastatic gastric cancer by routes. Br J Cancer 2023; 129:672-682. [PMID: 37422528 PMCID: PMC10421927 DOI: 10.1038/s41416-023-02338-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND In gastric cancer (GC) patients, metastatic progression through the lymphatic, hematogenous, peritoneal, and ovarian routes, is the ultimate cause of death. However, the genomic and evolutionary characteristics of metastatic GC have not been widely evaluated. METHODS Whole-exome sequencing data were analyzed for 99 primary and paired metastatic gastric cancers from 15 patients who underwent gastrectomy and metastasectomy. RESULTS Hematogenous metastatic tumors were associated with increased chromosomal instability and de novo gain/amplification in cancer driver genes, whereas peritoneal/ovarian metastasis was linked to sustained chromosomal stability and de novo somatic mutations in driver genes. The genomic distance of the hematogenous and peritoneal metastatic tumors was found to be closer to the primary tumors than lymph node (LN) metastasis, while ovarian metastasis was closer to LN and peritoneal metastasis than the primary tumor. Two migration patterns for metastatic GCs were identified; branched and diaspora. Both molecular subtypes of the metastatic tumors, rather than the primary tumor, and their migration patterns were related to patient survival. CONCLUSIONS Genomic characteristics of metastatic gastric cancer is distinctive by routes and associated with patients' prognosis along with genomic evolution pattenrs, indicating that both primary and metastatic gastric cancers require genomic evaluation.
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Affiliation(s)
- Jae Eun Lee
- Portrai Inc., Seoul, Korea
- Department of Surgery, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Ki Tae Kim
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry, Seoul National University, Seoul, South Korea
- Dental Research Institute and Dental Multi-omics Center, Seoul National University, Seoul, South Korea
| | - Su-Jin Shin
- Department of Pathology, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea.
| | - Yoon Young Choi
- Department of Surgery, Soonchunhyang Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, South Korea.
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38
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Luo X, Zhang L, Cui J, An Q, Li H, Zhang Z, Sun G, Huang W, Li Y, Li C, Jia W, Zou L, Zhao G, Xiao F. Small extrachromosomal circular DNAs as biomarkers for multi-cancer diagnosis and monitoring. Clin Transl Med 2023; 13:e1393. [PMID: 37649244 PMCID: PMC10468585 DOI: 10.1002/ctm2.1393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Small extrachromosomal circular DNAs (eccDNAs) have the potential to be cancer biomarkers. However, the formation mechanisms and functions of small eccDNAs selected in carcinogenesis are not clear, and whether the small eccDNA profile in the plasma of cancer patients represents that in cancer tissues remains to be elucidated. METHODS A novel sequencing workflow based on the nanopore sequencing platform was used to sequence naturally existing full-length small eccDNAs in tissues and plasma collected from 25 cancer patients (including prostate cancer, hepatocellular carcinoma and colorectal cancer), and from an independent validation cohort (including 7 cancer plasma and 14 healthy plasma). RESULTS Compared with those in non-cancer tissues, small eccDNAs detected in cancer tissues had a significantly larger number and size (P = 0.040 and 2.2e-16, respectively), along with more even distribution and different formation mechanisms. Although small eccDNAs had different general characteristics and genomic annotation between cancer tissues and the paired plasma, they had similar formation mechanisms and cancer-related functions. Small eccDNAs originated from some specific genes had great multi-cancer diagnostic value in tissues (AUC ≥ 0.8) and plasma (AUC > 0.9), especially increasing the accuracy of multi-cancer prediction of CEA/CA19-9 levels. The high multi-cancer diagnostic value of small eccDNAs originated from ALK&ETV6 could be extrapolated from tissues (AUC = 0.804) to plasma and showed high positive predictive value (100%) and negative predictive value (82.35%) in a validation cohort. CONCLUSIONS As independent and stable circular DNA molecules, small eccDNAs in both tissues and plasma can be used as ideal biomarkers for cost-effective multi-cancer diagnosis and monitoring.
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Affiliation(s)
- Xuanmei Luo
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Lili Zhang
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Jian Cui
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Qi An
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Hexin Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Zaifeng Zhang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gaoyuan Sun
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Wei Huang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Yifei Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Chang Li
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Wenzhuo Jia
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Lihui Zou
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gang Zhao
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Fei Xiao
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
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39
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Hasan AMM, Cremaschi P, Wetterskog D, Jayaram A, Wong SQ, Williams S, Pasam A, Trigos A, Trujillo B, Grist E, Friedrich S, Vainauskas O, Parry M, Ismail M, Devlies W, Wingate A, Linch M, Naceur-Lombardelli C, Swanton C, Jamal-Hanjani M, Lise S, Sandhu S, Attard G. Copy number architectures define treatment-mediated selection of lethal prostate cancer clones. Nat Commun 2023; 14:4823. [PMID: 37563129 PMCID: PMC10415299 DOI: 10.1038/s41467-023-40315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Despite initial responses to hormone treatment, metastatic prostate cancer invariably evolves to a lethal state. To characterize the intra-patient evolutionary relationships of metastases that evade treatment, we perform genome-wide copy number profiling and bespoke approaches targeting the androgen receptor (AR) on 167 metastatic regions from 11 organs harvested post-mortem from 10 men who died from prostate cancer. We identify diverse and patient-unique alterations clustering around the AR in metastases from every patient with evidence of independent acquisition of related genomic changes within an individual and, in some patients, the co-existence of AR-neutral clones. Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin across metastases and diagnostic biopsies, and identified in individual patients, clusters of metastases occupied by dominant clones with diverged autosomal copy number alterations. These autosome-defined clusters are characterized by cluster-specific AR gene architectures, and in two index cases are topologically more congruent than by chance (p-values 3.07 × 10-8 and 6.4 × 10-4). Integration with anatomical sites suggests patterns of spread and points of genomic divergence. Here, we show that copy number boundaries identify treatment-selected clones with putatively distinct lethal trajectories.
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Affiliation(s)
| | | | | | - Anuradha Jayaram
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Scott Williams
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Anupama Pasam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna Trigos
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Blanca Trujillo
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Emily Grist
- University College London Cancer Institute, London, UK
| | | | | | - Marina Parry
- University College London Cancer Institute, London, UK
| | | | - Wout Devlies
- University College London Cancer Institute, London, UK
| | - Anna Wingate
- University College London Cancer Institute, London, UK
| | - Mark Linch
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Stefano Lise
- University College London Cancer Institute, London, UK
| | | | - Gerhardt Attard
- University College London Cancer Institute, London, UK.
- University College London Hospitals, London, UK.
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41
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Li J, Hubisz MJ, Earlie EM, Duran MA, Hong C, Varela AA, Lettera E, Deyell M, Tavora B, Havel JJ, Phyu SM, Amin AD, Budre K, Kamiya E, Cavallo JA, Garris C, Powell S, Reis-Filho JS, Wen H, Bettigole S, Khan AJ, Izar B, Parkes EE, Laughney AM, Bakhoum SF. Non-cell-autonomous cancer progression from chromosomal instability. Nature 2023; 620:1080-1088. [PMID: 37612508 PMCID: PMC10468402 DOI: 10.1038/s41586-023-06464-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/20/2023] [Indexed: 08/25/2023]
Abstract
Chromosomal instability (CIN) is a driver of cancer metastasis1-4, yet the extent to which this effect depends on the immune system remains unknown. Using ContactTracing-a newly developed, validated and benchmarked tool to infer the nature and conditional dependence of cell-cell interactions from single-cell transcriptomic data-we show that CIN-induced chronic activation of the cGAS-STING pathway promotes downstream signal re-wiring in cancer cells, leading to a pro-metastatic tumour microenvironment. This re-wiring is manifested by type I interferon tachyphylaxis selectively downstream of STING and a corresponding increase in cancer cell-derived endoplasmic reticulum (ER) stress response. Reversal of CIN, depletion of cancer cell STING or inhibition of ER stress response signalling abrogates CIN-dependent effects on the tumour microenvironment and suppresses metastasis in immune competent, but not severely immune compromised, settings. Treatment with STING inhibitors reduces CIN-driven metastasis in melanoma, breast and colorectal cancers in a manner dependent on tumour cell-intrinsic STING. Finally, we show that CIN and pervasive cGAS activation in micronuclei are associated with ER stress signalling, immune suppression and metastasis in human triple-negative breast cancer, highlighting a viable strategy to identify and therapeutically intervene in tumours spurred by CIN-induced inflammation.
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Affiliation(s)
- Jun Li
- 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
| | - Melissa J Hubisz
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Ethan M Earlie
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Mercedes A Duran
- 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
| | - Christy Hong
- 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
| | - Austin A Varela
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Emanuele Lettera
- 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
| | - Matthew Deyell
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Su M Phyu
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Amit Dipak Amin
- Columbia Center for Translational Immunology, New York, NY, USA
- Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Karolina Budre
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Erina Kamiya
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Julie-Ann Cavallo
- 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
| | - Christopher Garris
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Simon Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Atif J Khan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Izar
- Columbia Center for Translational Immunology, New York, NY, USA
- Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Eileen E Parkes
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Ashley M Laughney
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, 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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Myers MA, Arnold BJ, Bansal V, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. bioRxiv 2023:2023.07.13.548855. [PMID: 37502835 PMCID: PMC10370020 DOI: 10.1101/2023.07.13.548855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different numbers of copies of parental haplotypes in different tumor clones. HATCHet2 also has high accuracy in identifying focal CNAs and extends the earlier HATCHet method in several directions. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 50 prostate cancer samples from 10 patients reveals previously-unreported mirrored-subclonal CNAs affecting cancer genes.
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Affiliation(s)
- Matthew A. Myers
- Department of Computer Science, Princeton University, Princeton, USA
| | - Brian J. Arnold
- Center for Statistics and Machine Learning, Princeton University, Princeton, USA
| | - Vineet Bansal
- Princeton Research Computing, Princeton University, Princeton, NJ, USA
| | - Katelyn M. Mullen
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
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43
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Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature 2023; 619:176-183. [PMID: 37286593 PMCID: PMC10322720 DOI: 10.1038/s41586-023-06084-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/14/2023] [Indexed: 06/09/2023]
Abstract
Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.
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Affiliation(s)
- Albert S Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Duaa 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
| | - Bhargavi Dameracharla
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Bailey S C L Jones
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Lorenzo Scipioni
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Jens Luebeck
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Melody Di Bona
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Danguole Norkunaite
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Tri-institutional MD-PhD Program, New York, NY, USA
| | - Mercedes Duran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seongmin Choi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shira Yomtoubian
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eléonore Toufektchan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristina Keuper
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Paul S Mischel
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vivek Mittal
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Maciejowski
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zuzana Storchova
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Enrico Gratton
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dan Landau
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Mathieu F Bakhoum
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-institutional PhD Program in Chemical Biology, 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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44
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Li M, Sun J, Shi G. Application of CRISPR screen in mechanistic studies of tumor development, tumor drug resistance, and tumor immunotherapy. Front Cell Dev Biol 2023; 11:1220376. [PMID: 37427373 PMCID: PMC10326906 DOI: 10.3389/fcell.2023.1220376] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Tumor is one of the biggest threats to human health. Though tumor therapy has been dramatically advanced by the progress of technology and research in recent decades, it is still far from expectations. Thus, it is of great significance to explore the mechanisms of tumor growth, metastasis, and resistance. Screen based on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein (Cas) 9 gene editing technology are powerful tools for exploring the abovementioned facets. This review summarizes the recent screen performed in cancer cells and immune cells in the tumor microenvironment. The screens in cancer cells mainly focus on exploring the mechanisms underlying cancer cells' growth, metastasis, and how cancer cells escape from the FDA approved drugs or immunotherapy. And the studies in tumor-associated immune cells are primarily aimed at identifying signaling pathways that can enhance the anti-tumor function of cytotoxic T lymphocytes (CTLs), CAR-T cells, and macrophages. Moreover, we discuss the limitations, merits of the CRISPR screen, and further its future application in tumor studies. Importantly, recent advances in high throughput tumor related CRISPR screen have deeply contributed to new concepts and mechanisms underlying tumor development, tumor drug resistance, and tumor immune therapy, all of which will eventually potentiate the clinical therapy for tumor patients.
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Affiliation(s)
- Min Li
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, Shanghai, China
| | - Jin Sun
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Shanghai, China
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45
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Lu B, Curtius K, Graham TA, Yang Z, Barnes CP. CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples. Genome Biol 2023; 24:144. [PMID: 37340508 DOI: 10.1186/s13059-023-02983-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.
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Affiliation(s)
- Bingxin Lu
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Kit Curtius
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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Liu L, Wang Y, Chang J, Zhang P, Xiong S, Liu H. A correlation graph attention network for classifying chromosomal instabilities from histopathology whole-slide images. iScience 2023; 26:106874. [PMID: 37260749 PMCID: PMC10227422 DOI: 10.1016/j.isci.2023.106874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/23/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
The chromosome instability (CIN) is one of the hallmarks of cancer and is closely related to tumor metastasis. However, the sheer size and resolution of histopathology whole-slide images (WSIs) already challenges the capabilities of computational pathology. In this study, we propose a correlation graph attention network (MLP-GAT) that can construct graphs for classifying multi-type CINs from the WSIs of breast cancer. We construct a WSIs dataset of breast cancer from the Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA). Extensive experiments show that MLP-GAT far outperforms accepted state-of-the-art methods and demonstrate the advantages of the constructed graph networks for analyzing WSI data. The visualization shows the difference among the tiles in a WSI. Furthermore, the generalization performance of the proposed method was verified on the stomach cancer. This study provides guidance for studying the relationship between CIN and cancer from the perspective of image phenotype.
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Affiliation(s)
- Liangliang Liu
- College of Information and Management Science, Henan Agricultural University, Zhengzhou, Henan 450046, P.R. China
| | - Ying Wang
- College of Information and Management Science, Henan Agricultural University, Zhengzhou, Henan 450046, P.R. China
| | - Jing Chang
- College of Information and Management Science, Henan Agricultural University, Zhengzhou, Henan 450046, P.R. China
| | - Pei Zhang
- College of Information and Management Science, Henan Agricultural University, Zhengzhou, Henan 450046, P.R. China
| | - Shufeng Xiong
- College of Information and Management Science, Henan Agricultural University, Zhengzhou, Henan 450046, P.R. China
| | - Hebing Liu
- College of Information and Management Science, Henan Agricultural University, Zhengzhou, Henan 450046, P.R. China
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Spain L, Coulton A, Lobon I, Rowan A, Schnidrig D, Shepherd ST, Shum B, Byrne F, Goicoechea M, Piperni E, Au L, Edmonds K, Carlyle E, Hunter N, Renn A, Messiou C, Hughes P, Nobbs J, Foijer F, van den Bos H, Wardenaar R, Spierings DC, Spencer C, Schmitt AM, Tippu Z, Lingard K, Grostate L, Peat K, Kelly K, Sarker S, Vaughan S, Mangwende M, Terry L, Kelly D, Biano J, Murra A, Korteweg J, Lewis C, O'Flaherty M, Cattin AL, Emmerich M, Gerard CL, Pallikonda HA, Lynch J, Mason R, Rogiers A, Xu H, Huebner A, McGranahan N, Al Bakir M, Murai J, Naceur-Lombardelli C, Borg E, Mitchison M, Moore DA, Falzon M, Proctor I, Stamp GW, Nye EL, Young K, Furness AJ, Pickering L, Stewart R, Mahadeva U, Green A, Larkin J, Litchfield K, Swanton C, Jamal-Hanjani M, Turajlic S. Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways. Cancer Discov 2023; 13:1364-1385. [PMID: 36977461 PMCID: PMC10236155 DOI: 10.1158/2159-8290.cd-22-1427] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Understanding the evolutionary pathways to metastasis and resistance to immune-checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here, we present the most comprehensive intrapatient metastatic melanoma dataset assembled to date as part of the Posthumous Evaluation of Advanced Cancer Environment (PEACE) research autopsy program, including 222 exome sequencing, 493 panel-sequenced, 161 RNA sequencing, and 22 single-cell whole-genome sequencing samples from 14 ICI-treated patients. We observed frequent whole-genome doubling and widespread loss of heterozygosity, often involving antigen-presentation machinery. We found KIT extrachromosomal DNA may have contributed to the lack of response to KIT inhibitors of a KIT-driven melanoma. At the lesion-level, MYC amplifications were enriched in ICI nonresponders. Single-cell sequencing revealed polyclonal seeding of metastases originating from clones with different ploidy in one patient. Finally, we observed that brain metastases that diverged early in molecular evolution emerge late in disease. Overall, our study illustrates the diverse evolutionary landscape of advanced melanoma. SIGNIFICANCE Despite treatment advances, melanoma remains a deadly disease at stage IV. Through research autopsy and dense sampling of metastases combined with extensive multiomic profiling, our study elucidates the many mechanisms that melanomas use to evade treatment and the immune system, whether through mutations, widespread copy-number alterations, or extrachromosomal DNA. See related commentary by Shain, p. 1294. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Lavinia Spain
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Alexander Coulton
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
| | - Irene Lobon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Desiree Schnidrig
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Scott T.C. Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria Goicoechea
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Elisa Piperni
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Kim Edmonds
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Nikki Hunter
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Christina Messiou
- The Royal Marsden Hospital, London, United Kingdom
- The Institute of Cancer Research, Kensington and Chelsea, United Kingdom
| | - Peta Hughes
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jaime Nobbs
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Rene Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Charlotte Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Kema Peat
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Sarah Sarker
- The Royal Marsden Hospital, London, United Kingdom
| | | | | | - Lauren Terry
- The Royal Marsden Hospital, London, United Kingdom
| | - Denise Kelly
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Aida Murra
- The Royal Marsden Hospital, London, United Kingdom
| | | | | | | | - Anne-Laure Cattin
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Max Emmerich
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- St. John's Institute of Dermatology, Guy's and St Thomas’ Hospital NHS Foundation Trust, London, United Kingdom
| | - Camille L. Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Precision Oncology Center, Oncology Department, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Joanna Lynch
- The Royal Marsden Hospital, London, United Kingdom
| | - Robert Mason
- Gold Coast University Hospital, Queensland, Australia
| | - Aljosja Rogiers
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Hang Xu
- The Francis Crick Institute, London, United Kingdom
| | - Ariana Huebner
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Jun Murai
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
- Drug Discovery Technology Laboratories, Ono Pharmaceutical Co., Ltd. Osaka, Japan
| | | | - Elaine Borg
- University College London Hospital, London, United Kingdom
| | | | - David A. Moore
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Mary Falzon
- University College London Hospital, London, United Kingdom
| | - Ian Proctor
- University College London Hospital, London, United Kingdom
| | | | - Emma L. Nye
- The Francis Crick Institute, London, United Kingdom
| | - Kate Young
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Andrew J.S. Furness
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- The Institute of Cancer Research, Kensington and Chelsea, United Kingdom
| | | | - Ruby Stewart
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Ula Mahadeva
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Anna Green
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - James Larkin
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | | | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
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Zeng J, Chen J, Li M, Zhong C, Liu Z, Wang Y, Li Y, Jiang F, Fang S, Zhong W. Integrated high-throughput analysis identifies super enhancers in metastatic castration-resistant prostate cancer. Front Pharmacol 2023; 14:1191129. [PMID: 37292153 PMCID: PMC10244677 DOI: 10.3389/fphar.2023.1191129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/25/2023] [Indexed: 06/10/2023] Open
Abstract
Background: Metastatic castration-resistant prostate cancer (mCRPC) is a highly aggressive stage of prostate cancer, and non-mutational epigenetic reprogramming plays a critical role in its progression. Super enhancers (SE), epigenetic elements, are involved in multiple tumor-promoting signaling pathways. However, the SE-mediated mechanism in mCRPC remains unclear. Methods: SE-associated genes and transcription factors were identified from a cell line (C4-2B) of mCRPC by the CUT&Tag assay. Differentially expressed genes (DEGs) between mCRPC and primary prostate cancer (PCa) samples in the GSE35988 dataset were identified. What's more, a recurrence risk prediction model was constructed based on the overlapping genes (termed SE-associated DEGs). To confirm the key SE-associated DEGs, BET inhibitor JQ1 was applied to cells to block SE-mediated transcription. Finally, single-cell analysis was performed to visualize cell subpopulations expressing the key SE-associated DEGs. Results: Nine human TFs, 867 SE-associated genes and 5417 DEGs were identified. 142 overlapping SE-associated DEGs showed excellent performance in recurrence prediction. Time-dependent receiver operating characteristic (ROC) curve analysis showed strong predictive power at 1 year (0.80), 3 years (0.85), and 5 years (0.88). The efficacy of his performance has also been validated in external datasets. In addition, FKBP5 activity was significantly inhibited by JQ1. Conclusion: We present a landscape of SE and their associated genes in mCPRC, and discuss the potential clinical implications of these findings in terms of their translation to the clinic.
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Affiliation(s)
- Jie Zeng
- Department of Urology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiahong Chen
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, Guangdong, China
| | - Maozhang Li
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, Guangdong, China
| | - Chuanfan Zhong
- Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zezhen Liu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, and Guangdong Key Laboratory of Urology, Guangzhou, Guangdong, China
| | - Yan Wang
- Department of Urology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Yuejiao Li
- Department of Urology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Funeng Jiang
- Department of Urology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Shumin Fang
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, Guangdong, China
| | - Weide Zhong
- Department of Urology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. Biology (Basel) 2023; 12:biology12050671. [PMID: 37237485 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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50
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Bosco N, Goldberg A, Zhao X, Mays JC, Cheng P, Johnson AF, Bianchi JJ, Toscani C, Di Tommaso E, Katsnelson L, Annuar D, Mei S, Faitelson RE, Pesselev IY, Mohamed KS, Mermerian A, Camacho-Hernandez EM, Gionco CA, Manikas J, Tseng YS, Sun Z, Fani S, Keegan S, Lippman SM, Fenyö D, Giunta S, Santaguida S, Davoli T. KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres. Cell 2023; 186:1985-2001.e19. [PMID: 37075754 PMCID: PMC10676289 DOI: 10.1016/j.cell.2023.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/17/2022] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer. Here, we describe KaryoCreate (karyotype CRISPR-engineered aneuploidy technology), a system that enables the generation of chromosome-specific aneuploidies by co-expression of an sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to mutant KNL1. We design unique and highly specific sgRNAs for 19 of the 24 chromosomes. Expression of these constructs leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny, with an average efficiency of 8% for gains and 12% for losses (up to 20%) validated across 10 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, frequent in gastrointestinal cancers, promotes resistance to TGF-β, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe an innovative technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.
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Affiliation(s)
- Nazario Bosco
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleah Goldberg
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Xin Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joseph C Mays
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Pan Cheng
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Adam F Johnson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joy J Bianchi
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Cecilia Toscani
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Elena Di Tommaso
- Department of Biology and Biotechnology Charles Darwin, University of Rome "La Sapienza", 00185 Rome, Italy
| | - Lizabeth Katsnelson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Dania Annuar
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sally Mei
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Roni E Faitelson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Ilan Y Pesselev
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Kareem S Mohamed
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Angela Mermerian
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Elaine M Camacho-Hernandez
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Courtney A Gionco
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Julie Manikas
- Department of Cell Biology, NYU Langone Health, New York, NY, USA
| | - Yi-Shuan Tseng
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Zhengxi Sun
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Somayeh Fani
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Scott M Lippman
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Simona Giunta
- Department of Biology and Biotechnology Charles Darwin, University of Rome "La Sapienza", 00185 Rome, Italy
| | - Stefano Santaguida
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Teresa Davoli
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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