1
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Scelfo A, Barra V, Abdennur N, Spracklin G, Busato F, Salinas-Luypaert C, Bonaiti E, Velasco G, Bonhomme F, Chipont A, Tijhuis AE, Spierings DC, Guérin C, Arimondo P, Francastel C, Foijer F, Tost J, Mirny L, Fachinetti D. Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization. J Cell Biol 2024; 223:e202307026. [PMID: 38376465 PMCID: PMC10876481 DOI: 10.1083/jcb.202307026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/20/2023] [Accepted: 01/15/2024] [Indexed: 02/21/2024] Open
Abstract
DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincides with a gradual reduction of cell fitness due to G1 arrest, with minor levels of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
| | - Viviana Barra
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Nezar Abdennur
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George Spracklin
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Florence Busato
- Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | | | - Elena Bonaiti
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
| | | | - Frédéric Bonhomme
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR n°3523 Chem4Life, Université Paris Cité, Paris, France
| | - Anna Chipont
- Cytometry Platform, Institut Curie, Paris, France
| | - Andréa E. Tijhuis
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Coralie Guérin
- Cytometry Platform, Institut Curie, Paris, France
- Université Paris Cité, INSERM, Paris, France
| | - Paola Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR n°3523 Chem4Life, Université Paris Cité, Paris, France
| | | | - Floris Foijer
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jӧrg Tost
- Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
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2
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Braun VZ, Karbon G, Schuler F, Schapfl MA, Weiss JG, Petermann PY, Spierings DC, Tijhuis AE, Foijer F, Labi V, Villunger A. Extra centrosomes delay DNA damage-driven tumorigenesis. SCIENCE ADVANCES 2024; 10:eadk0564. [PMID: 38552015 PMCID: PMC10980279 DOI: 10.1126/sciadv.adk0564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/23/2024] [Indexed: 04/01/2024]
Abstract
Deregulated centrosome numbers are frequently found in human cancer and can promote malignancies in model organisms. Current research aims to clarify if extra centrosomes are cause or consequence of malignant transformation, and if their biogenesis can be targeted for therapy. Here, we show that oncogene-driven blood cancer is inert to genetic manipulation of centrosome numbers, whereas the formation of DNA damage-induced malignancies is delayed. We provide first evidence that this unexpected phenomenon is connected to extra centrosomes eliciting a pro-death signal engaging the apoptotic machinery. Apoptosis induction requires the PIDDosome multi-protein complex, as it can be abrogated by loss of any of its three components, Caspase-2, Raidd/Cradd, or Pidd1. BCL2 overexpression equally blocks cell death, documenting for the first time induction of mitochondrial apoptosis downstream of extra centrosomes. Our findings demonstrate context-dependent effects of centrosome amplification during transformation and ask to adjust current belief that extra centrosomes are intrinsically pro-tumorigenic.
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Affiliation(s)
- Vincent Z. Braun
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerlinde Karbon
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Fabian Schuler
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Marina A. Schapfl
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes G. Weiss
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- Department of Paediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Paul Y. Petermann
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Andrea E. Tijhuis
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Verena Labi
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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3
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Gliech CR, Yeow ZY, Tapias-Gomez D, Yang Y, Huang Z, Tijhuis AE, Spierings DC, Foijer F, Chung G, Tamayo N, Bahrami-Nejad Z, Collins P, Nguyen TT, Plata Stapper A, Hughes PE, Payton M, Holland AJ. Weakened APC/C activity at mitotic exit drives cancer vulnerability to KIF18A inhibition. EMBO J 2024; 43:666-694. [PMID: 38279026 PMCID: PMC10907621 DOI: 10.1038/s44318-024-00031-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024] Open
Abstract
The efficacy of current antimitotic cancer drugs is limited by toxicity in highly proliferative healthy tissues. A cancer-specific dependency on the microtubule motor protein KIF18A therefore makes it an attractive therapeutic target. Not all cancers require KIF18A, however, and the determinants underlying this distinction remain unclear. Here, we show that KIF18A inhibition drives a modest and widespread increase in spindle assembly checkpoint (SAC) signaling from kinetochores which can result in lethal mitotic delays. Whether cells arrest in mitosis depends on the robustness of the metaphase-to-anaphase transition, and cells predisposed with weak basal anaphase-promoting complex/cyclosome (APC/C) activity and/or persistent SAC signaling through metaphase are uniquely sensitive to KIF18A inhibition. KIF18A-dependent cancer cells exhibit hallmarks of this SAC:APC/C imbalance, including a long metaphase-to-anaphase transition, and slow mitosis overall. Together, our data reveal vulnerabilities in the cell division apparatus of cancer cells that can be exploited for therapeutic benefit.
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Affiliation(s)
- Colin R Gliech
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Zhong Y Yeow
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Daniel Tapias-Gomez
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yuchen Yang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Zhaoyu Huang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Andréa E Tijhuis
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, AV, 9713, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, AV, 9713, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, AV, 9713, The Netherlands
| | - Grace Chung
- Oncology Research, Amgen Research, Thousand Oaks, CA, 91320, USA
| | - Nuria Tamayo
- Medicinal Chemistry, Amgen Research, Thousand Oaks, CA, 91320, USA
| | | | - Patrick Collins
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, 94084, USA
| | - Thong T Nguyen
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, 94084, USA
| | - Andres Plata Stapper
- Center for Research Acceleration by Digital Innovation, Amgen Research, South San Francisco, CA, 94084, USA
| | - Paul E Hughes
- Oncology Research, Amgen Research, Thousand Oaks, CA, 91320, USA
| | - Marc Payton
- Oncology Research, Amgen Research, Thousand Oaks, CA, 91320, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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4
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Saba KH, Difilippo V, Kovac M, Cornmark L, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Bidgoli M, Jonson T, Sumathi VP, Brosjö O, Staaf J, Foijer F, Styring E, Nathrath M, Baumhoer D, Nord KH. Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway. J Pathol 2024; 262:147-160. [PMID: 38010733 DOI: 10.1002/path.6219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 11/29/2023]
Abstract
TP53 is the most frequently mutated gene in human cancer. This gene shows not only loss-of-function mutations but also recurrent missense mutations with gain-of-function activity. We have studied the primary bone malignancy osteosarcoma, which harbours one of the most rearranged genomes of all cancers. This is odd since it primarily affects children and adolescents who have not lived the long life thought necessary to accumulate massive numbers of mutations. In osteosarcoma, TP53 is often disrupted by structural variants. Here, we show through combined whole-genome and transcriptome analyses of 148 osteosarcomas that TP53 structural variants commonly result in loss of coding parts of the gene while simultaneously preserving and relocating the promoter region. The transferred TP53 promoter region is fused to genes previously implicated in cancer development. Paradoxically, these erroneously upregulated genes are significantly associated with the TP53 signalling pathway itself. This suggests that while the classical tumour suppressor activities of TP53 are lost, certain parts of the TP53 signalling pathway that are necessary for cancer cell survival and proliferation are retained. In line with this, our data suggest that transposition of the TP53 promoter is an early event that allows for a new normal state of genome-wide rearrangements in osteosarcoma. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michal Kovac
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Louise Cornmark
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mahtab Bidgoli
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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5
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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] [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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6
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Tovini L, Johnson SC, Guscott MA, Andersen AM, Spierings DCJ, Wardenaar R, Foijer F, McClelland SE. Targeted assembly of ectopic kinetochores to induce chromosome-specific segmental aneuploidies. EMBO J 2023; 42:e111587. [PMID: 37063065 PMCID: PMC10183824 DOI: 10.15252/embj.2022111587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023] Open
Abstract
Cancer cells display persistent underlying chromosomal instability, with individual tumour types intriguingly exhibiting characteristic subsets of whole, and subchromosomal aneuploidies. Few methods to induce specific aneuploidies will exist, hampering investigation of functional consequences of recurrent aneuploidies, as well as the acute consequences of specific chromosome mis-segregation. We therefore investigated the possibility of sabotaging the mitotic segregation of specific chromosomes using nuclease-dead CRISPR-Cas9 (dCas9) as a cargo carrier to specific genomic loci. We recruited the kinetochore-nucleating domain of centromere protein CENP-T to assemble ectopic kinetochores either near the centromere of chromosome 9, or the telomere of chromosome 1. Ectopic kinetochore assembly led to increased chromosome instability and partial aneuploidy of the target chromosomes, providing the potential to induce specific chromosome mis-segregation events in a range of cell types. We also provide an analysis of putative endogenous repeats that could support ectopic kinetochore formation. Overall, our findings provide new insights into ectopic kinetochore biology and represent an important step towards investigating the role of specific aneuploidy and chromosome mis-segregation events in diseases associated with aneuploidy.
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Affiliation(s)
| | - Sarah C Johnson
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Molly A Guscott
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Alexander M Andersen
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Diana Carolina Johanna Spierings
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Sarah E McClelland
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
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7
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Rutten MGS, Lei Y, Hoogerland JH, Bloks VW, Yang H, Bos T, Krishnamurthy KA, Bleeker A, Koster MH, Thomas RE, Wolters JC, van den Bos H, Mithieux G, Rajas F, Mardinoglu A, Spierings DCJ, de Bruin A, van de Sluis B, Oosterveer MH. Normalization of hepatic ChREBP activity does not protect against liver disease progression in a mouse model for Glycogen Storage Disease type Ia. Cancer Metab 2023; 11:5. [PMID: 37085901 PMCID: PMC10122297 DOI: 10.1186/s40170-023-00305-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/21/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Glycogen storage disease type 1a (GSD Ia) is an inborn error of metabolism caused by a defect in glucose-6-phosphatase (G6PC1) activity, which induces severe hepatomegaly and increases the risk for liver cancer. Hepatic GSD Ia is characterized by constitutive activation of Carbohydrate Response Element Binding Protein (ChREBP), a glucose-sensitive transcription factor. Previously, we showed that ChREBP activation limits non-alcoholic fatty liver disease (NAFLD) in hepatic GSD Ia. As ChREBP has been proposed as a pro-oncogenic molecular switch that supports tumour progression, we hypothesized that ChREBP normalization protects against liver disease progression in hepatic GSD Ia. METHODS Hepatocyte-specific G6pc knockout (L-G6pc-/-) mice were treated with AAV-shChREBP to normalize hepatic ChREBP activity. RESULTS Hepatic ChREBP normalization in GSD Ia mice induced dysplastic liver growth, massively increased hepatocyte size, and was associated with increased hepatic inflammation. Furthermore, nuclear levels of the oncoprotein Yes Associated Protein (YAP) were increased and its transcriptional targets were induced in ChREBP-normalized GSD Ia mice. Hepatic ChREBP normalization furthermore induced DNA damage and mitotic activity in GSD Ia mice, while gene signatures of chromosomal instability, the cytosolic DNA-sensing cGAS-STING pathway, senescence, and hepatocyte dedifferentiation emerged. CONCLUSIONS In conclusion, our findings indicate that ChREBP activity limits hepatomegaly while decelerating liver disease progression and protecting against chromosomal instability in hepatic GSD Ia. These results disqualify ChREBP as a therapeutic target for treatment of liver disease in GSD Ia. In addition, they underline the importance of establishing the context-specific roles of hepatic ChREBP to define its therapeutic potential to prevent or treat advanced liver disease.
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Affiliation(s)
- Martijn G S Rutten
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yu Lei
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Joanne H Hoogerland
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hong Yang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Trijnie Bos
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kishore A Krishnamurthy
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Aycha Bleeker
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mirjam H Koster
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rachel E Thomas
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Justina C Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gilles Mithieux
- Institut National de La Santé Et de La Recherche Médicale, U1213, Lyon, France
- Université de Lyon, Lyon, France
- Université Lyon 1, Villeurbanne, France
| | - Fabienne Rajas
- Institut National de La Santé Et de La Recherche Médicale, U1213, Lyon, France
- Université de Lyon, Lyon, France
- Université Lyon 1, Villeurbanne, France
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alain de Bruin
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bart van de Sluis
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maaike H Oosterveer
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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8
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Woodward EL, Yang M, Moura-Castro LH, van den Bos H, Gunnarsson R, Olsson-Arvidsson L, Spierings DCJ, Castor A, Duployez N, Zaliova M, Zuna J, Johansson B, Foijer F, Paulsson K. Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia. Nat Commun 2023; 14:1658. [PMID: 36966135 PMCID: PMC10039905 DOI: 10.1038/s41467-023-37356-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
High hyperdiploid acute lymphoblastic leukemia (HeH ALL), one of the most common childhood malignancies, is driven by nonrandom aneuploidy (abnormal chromosome numbers) mainly comprising chromosomal gains. In this study, we investigate how aneuploidy in HeH ALL arises. Single cell whole genome sequencing of 2847 cells from nine primary cases and one normal bone marrow reveals that HeH ALL generally display low chromosomal heterogeneity, indicating that they are not characterized by chromosomal instability and showing that aneuploidy-driven malignancies are not necessarily chromosomally heterogeneous. Furthermore, most chromosomal gains are present in all leukemic cells, suggesting that they arose early during leukemogenesis. Copy number data from 577 primary cases reveals selective pressures that were used for in silico modeling of aneuploidy development. This shows that the aneuploidy in HeH ALL likely arises by an initial tripolar mitosis in a diploid cell followed by clonal evolution, in line with a punctuated evolution model.
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Affiliation(s)
- Eleanor L Woodward
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Minjun Yang
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Larissa H Moura-Castro
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rebeqa Gunnarsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Olsson-Arvidsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund, Sweden
| | - Nicolas Duployez
- Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France
- Unité Mixte de Recherche en Santé (UMR-S) 1172, INSERM/University of Lille, Lille, France
| | - Marketa Zaliova
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Jan Zuna
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Bertil Johansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.
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9
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Garribba L, De Feudis G, Martis V, Galli M, Dumont M, Eliezer Y, Wardenaar R, Ippolito MR, Iyer DR, Tijhuis AE, Spierings DCJ, Schubert M, Taglietti S, Soriani C, Gemble S, Basto R, Rhind N, Foijer F, Ben-David U, Fachinetti D, Doksani Y, Santaguida S. Short-term molecular consequences of chromosome mis-segregation for genome stability. Nat Commun 2023; 14:1353. [PMID: 36906648 PMCID: PMC10008630 DOI: 10.1038/s41467-023-37095-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/01/2023] [Indexed: 03/13/2023] Open
Abstract
Chromosome instability (CIN) is the most common form of genome instability and is a hallmark of cancer. CIN invariably leads to aneuploidy, a state of karyotype imbalance. Here, we show that aneuploidy can also trigger CIN. We found that aneuploid cells experience DNA replication stress in their first S-phase and precipitate in a state of continuous CIN. This generates a repertoire of genetically diverse cells with structural chromosomal abnormalities that can either continue proliferating or stop dividing. Cycling aneuploid cells display lower karyotype complexity compared to the arrested ones and increased expression of DNA repair signatures. Interestingly, the same signatures are upregulated in highly-proliferative cancer cells, which might enable them to proliferate despite the disadvantage conferred by aneuploidy-induced CIN. Altogether, our study reveals the short-term origins of CIN following aneuploidy and indicates the aneuploid state of cancer cells as a point mutation-independent source of genome instability, providing an explanation for aneuploidy occurrence in tumors.
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Affiliation(s)
- Lorenza Garribba
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Giuseppina De Feudis
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Valentino Martis
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Martina Galli
- IFOM ETS - The AIRC Institute of Molecular Oncology, via Adamello 16, 20139, Milan, Italy
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Yonatan Eliezer
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Marica Rosaria Ippolito
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Divya Ramalingam Iyer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
| | - Andréa E Tijhuis
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Michael Schubert
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Silvia Taglietti
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Chiara Soriani
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Simon Gemble
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Renata Basto
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Nick Rhind
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Ylli Doksani
- IFOM ETS - The AIRC Institute of Molecular Oncology, via Adamello 16, 20139, Milan, Italy
| | - Stefano Santaguida
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9/1, 20122, Milan, Italy.
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10
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Mañas A, Aaltonen K, Andersson N, Hansson K, Adamska A, Seger A, Yasui H, van den Bos H, Radke K, Esfandyari J, Bhave MS, Karlsson J, Spierings D, Foijer F, Gisselsson D, Bexell D. Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance. SCIENCE ADVANCES 2022; 8:eabq4617. [PMID: 36306349 PMCID: PMC9616506 DOI: 10.1126/sciadv.abq4617] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Chemotherapy resistance and relapses are common in high-risk neuroblastoma (NB). Here, we developed a clinically relevant in vivo treatment protocol mimicking the first-line five-chemotherapy treatment regimen of high-risk NB and applied this protocol to mice with MYCN-amplified NB patient-derived xenografts (PDXs). Genomic and transcriptomic analyses were used to reveal NB chemoresistance mechanisms. Intrinsic resistance was associated with high genetic diversity and an embryonic phenotype. Relapsed NB with acquired resistance showed a decreased adrenergic phenotype and an enhanced immature mesenchymal-like phenotype, resembling multipotent Schwann cell precursors. NBs with a favorable treatment response presented a lineage-committed adrenergic phenotype similar to normal neuroblasts. Novel integrated phenotypic gene signatures reflected treatment response and patient prognosis. NB organoids established from relapsed PDX tumors retained drug resistance, tumorigenicity, and transcriptional cell states. This work sheds light on the mechanisms of NB chemotherapy response and emphasizes the importance of transcriptional cell states in chemoresistance.
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Affiliation(s)
- Adriana Mañas
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Kristina Aaltonen
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
| | - Karin Hansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
- Cancer Stem Cell Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Aleksandra Adamska
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Alexandra Seger
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Hiroaki Yasui
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
- Department of Gynecologic Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - Katarzyna Radke
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Javanshir Esfandyari
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Madhura Satish Bhave
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
| | - Diana Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
- Department of Pathology, Laboratory Medicine, Skane University Hospital, Lund 22184, Sweden
| | - Daniel Bexell
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
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11
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cGAS-STING drives the IL-6-dependent survival of chromosomally instable cancers. Nature 2022; 607:366-373. [PMID: 35705809 DOI: 10.1038/s41586-022-04847-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/10/2022] [Indexed: 12/14/2022]
Abstract
Chromosomal instability (CIN) drives cancer cell evolution, metastasis and therapy resistance, and is associated with poor prognosis1. CIN leads to micronuclei that release DNA into the cytoplasm after rupture, which triggers activation of inflammatory signalling mediated by cGAS and STING2,3. These two proteins are considered to be tumour suppressors as they promote apoptosis and immunosurveillance. However, cGAS and STING are rarely inactivated in cancer4, and, although they have been implicated in metastasis5, it is not known why loss-of-function mutations do not arise in primary tumours4. Here we show that inactivation of cGAS-STING signalling selectively impairs the survival of triple-negative breast cancer cells that display CIN. CIN triggers IL-6-STAT3-mediated signalling, which depends on the cGAS-STING pathway and the non-canonical NF-κB pathway. Blockade of IL-6 signalling by tocilizumab, a clinically used drug that targets the IL-6 receptor (IL-6R), selectively impairs the growth of cultured triple-negative breast cancer cells that exhibit CIN. Moreover, outgrowth of chromosomally instable tumours is significantly delayed compared with tumours that do not display CIN. Notably, this targetable vulnerability is conserved across cancer types that express high levels of IL-6 and/or IL-6R in vitro and in vivo. Together, our work demonstrates pro-tumorigenic traits of cGAS-STING signalling and explains why the cGAS-STING pathway is rarely inactivated in primary tumours. Repurposing tocilizumab could be a strategy to treat cancers with CIN that overexpress IL-6R.
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12
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Leukapheresis increases circulating tumour cell yield in non-small cell lung cancer, counts related to tumour response and survival. Br J Cancer 2021; 126:409-418. [PMID: 34848855 DOI: 10.1038/s41416-021-01634-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/04/2021] [Accepted: 11/09/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Circulating tumour cells (CTCs) can be used to monitor cancer longitudinally, but their use in non-small cell lung cancer (NSCLC) is limited due to low numbers in the peripheral blood. Through diagnostic leukapheresis (DLA) CTCs can be obtained from larger blood volumes. METHODS Patients with all stages of NSCLC were selected. One total body blood volume was screened by DLA before and after treatment. Peripheral blood was drawn pre- and post DLA for CTC enumeration by CellSearch. CTCs were detected in the DLA product (volume equalling 2 × 108 leucocytes) and after leucocyte depletion (RosetteSep, 9 mL DLA product). Single-cell, whole-genome sequencing was performed on isolated CTCs. RESULTS Fifty-six patients were included. Before treatment, CTCs were more often detected in DLA (32/55, 58%) than in the peripheral blood (pre-DLA: 18/55, 33%; post DLA: 13/55, 23%, both at p < 0.01). CTCs per 7.5 mL DLA product were median 9.2 times (interquartile range = 5.6-24.0) higher than CTCs in 7.5 mL blood. RosetteSEP did not significantly improve CTC detection (pretreatment: 34/55, 62%, post treatment: 16/34, 47%) and CTCs per mL even decreased compared to DLA (p = 0.04).. Patients with advanced-stage disease with DLA-CTC after treatment showed fewer tumour responses and shorter progression-free survival (PFS) than those without DLA-CTC (median PFS, 2.0 vs 12.0 months, p < 0.01). DLA-CTC persistence after treatment was independent of clinical factors associated with shorter PFS (hazard ratio (HR) = 5.8, 95% confidence interval (CI), 1.4-35.5, p = 0.02). All evaluable CTCs showed aneuploidy. CONCLUSIONS DLA detected nine times more CTCs than in the peripheral blood. The sustained presence of CTCs in DLA after treatment was associated with therapy failure and shortened PFS. TRIAL REGISTRATION The study was approved by the Medical Ethical Committee (NL55754.042.15) and was registered in the Dutch trial register (NL5423).
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13
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Bočkaj I, Martini TEI, de Camargo Magalhães ES, Bakker PL, Meeuwsen-de Boer TGJ, Armandari I, Meuleman SL, Mondria MT, Stok C, Kok YP, Bakker B, Wardenaar R, Seiler J, Broekhuis MJC, van den Bos H, Spierings DCJ, Ringnalda FCA, Clevers H, Schüller U, van Vugt MATM, Foijer F, Bruggeman SWM. The H3.3K27M oncohistone affects replication stress outcome and provokes genomic instability in pediatric glioma. PLoS Genet 2021; 17:e1009868. [PMID: 34752469 PMCID: PMC8604337 DOI: 10.1371/journal.pgen.1009868] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 11/19/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
While comprehensive molecular profiling of histone H3.3 mutant pediatric high-grade glioma has revealed extensive dysregulation of the chromatin landscape, the exact mechanisms driving tumor formation remain poorly understood. Since H3.3 mutant gliomas also exhibit high levels of copy number alterations, we set out to address if the H3.3K27M oncohistone leads to destabilization of the genome. Hereto, we established a cell culture model allowing inducible H3.3K27M expression and observed an increase in mitotic abnormalities. We also found enhanced interaction of DNA replication factors with H3.3K27M during mitosis, indicating replication defects. Further functional analyses revealed increased genomic instability upon replication stress, as represented by mitotic bulky and ultrafine DNA bridges. This co-occurred with suboptimal 53BP1 nuclear body formation after mitosis in vitro, and in human glioma. Finally, we observed a decrease in ultrafine DNA bridges following deletion of the K27M mutant H3F3A allele in primary high-grade glioma cells. Together, our data uncover a role for H3.3 in DNA replication under stress conditions that is altered by the K27M mutation, promoting genomic instability and potentially glioma development.
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Affiliation(s)
- Irena Bočkaj
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tosca E. I. Martini
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eduardo S. de Camargo Magalhães
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Glial Cell Biology Laboratory, Biomedical Sciences Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Petra L. Bakker
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tiny G. J. Meeuwsen-de Boer
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Inna Armandari
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Histology and Cell Biology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Saskia L. Meuleman
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marin T. Mondria
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Colin Stok
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Yannick P. Kok
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bjorn Bakker
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - René Wardenaar
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jonas Seiler
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- iPSC/CRISPR facility, Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mathilde J. C. Broekhuis
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- iPSC/CRISPR facility, Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hilda van den Bos
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Diana C. J. Spierings
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Femke C. A. Ringnalda
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ulrich Schüller
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcel A. T. M. van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Floris Foijer
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- iPSC/CRISPR facility, Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sophia W. M. Bruggeman
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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14
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Ippolito MR, Martis V, Martin S, Tijhuis AE, Hong C, Wardenaar R, Dumont M, Zerbib J, Spierings DCJ, Fachinetti D, Ben-David U, Foijer F, Santaguida S. Gene copy-number changes and chromosomal instability induced by aneuploidy confer resistance to chemotherapy. Dev Cell 2021; 56:2440-2454.e6. [PMID: 34352223 DOI: 10.1016/j.devcel.2021.07.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 05/09/2021] [Accepted: 07/09/2021] [Indexed: 12/30/2022]
Abstract
Mitotic errors lead to aneuploidy, a condition of karyotype imbalance, frequently found in cancer cells. Alterations in chromosome copy number induce a wide variety of cellular stresses, including genome instability. Here, we show that cancer cells might exploit aneuploidy-induced genome instability and the resulting gene copy-number changes to survive under conditions of selective pressure, such as chemotherapy. Resistance to chemotherapeutic drugs was dictated by the acquisition of recurrent karyotypes, indicating that gene dosage might play a role in driving chemoresistance. Thus, our study establishes a causal link between aneuploidy-driven changes in gene copy number and chemoresistance and might explain why some chemotherapies fail to succeed.
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Affiliation(s)
- Marica Rosaria Ippolito
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Valentino Martis
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sara Martin
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Andréa E Tijhuis
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Christy Hong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Johanna Zerbib
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | | | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Stefano Santaguida
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9/1, 20122 Milan, Italy.
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15
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Sieben CJ, Jeganathan KB, Nelson GG, Sturmlechner I, Zhang C, van Deursen WH, Bakker B, Foijer F, Li H, Baker DJ, van Deursen JM. BubR1 allelic effects drive phenotypic heterogeneity in mosaic-variegated aneuploidy progeria syndrome. J Clin Invest 2020; 130:171-188. [PMID: 31738183 DOI: 10.1172/jci126863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 09/18/2019] [Indexed: 12/21/2022] Open
Abstract
Mosaic-variegated aneuploidy (MVA) syndrome is a rare childhood disorder characterized by biallelic BUBR1, CEP57, or TRIP13 aberrations; increased chromosome missegregation; and a broad spectrum of clinical features, including various cancers, congenital defects, and progeroid pathologies. To investigate the mechanisms underlying this disorder and its phenotypic heterogeneity, we mimicked the BUBR1L1012P mutation in mice (BubR1L1002P) and combined it with 2 other MVA variants, BUBR1X753 and BUBR1H, generating a truncated protein and low amounts of wild-type protein, respectively. Whereas BubR1X753/L1002P and BubR1H/X753 mice died prematurely, BubR1H/L1002P mice were viable and exhibited many MVA features, including cancer predisposition and various progeroid phenotypes, such as short lifespan, dwarfism, lipodystrophy, sarcopenia, and low cardiac stress tolerance. Strikingly, although these mice had a reduction in total BUBR1 and spectrum of MVA phenotypes similar to that of BubR1H/H mice, several progeroid pathologies were attenuated in severity, which in skeletal muscle coincided with reduced senescence-associated secretory phenotype complexity. Additionally, mice carrying monoallelic BubR1 mutations were prone to select MVA-related pathologies later in life, with predisposition to sarcopenia correlating with mTORC1 hyperactivity. Together, these data demonstrate that BUBR1 allelic effects beyond protein level and aneuploidy contribute to disease heterogeneity in both MVA patients and heterozygous carriers of MVA mutations.
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Affiliation(s)
| | | | | | | | - Cheng Zhang
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Bjorn Bakker
- European Research Institute for the Biology of Aging, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Aging, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Hu Li
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Darren J Baker
- Departments of Biochemistry and Molecular Biology.,Pediatric and Adolescent Medicine, and
| | - Jan M van Deursen
- Departments of Biochemistry and Molecular Biology.,Pediatric and Adolescent Medicine, and
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16
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Saba KH, Cornmark L, Hofvander J, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Foijer F, Staaf J, Brosjö O, Sumathi VP, Lam SW, Szuhai K, Bovée JV, Kovac M, Baumhoer D, Styring E, Nord KH. Loss of NF2 defines a genetic subgroup of non-FOS-rearranged osteoblastoma. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2020; 6:231-237. [PMID: 32542935 PMCID: PMC7578308 DOI: 10.1002/cjp2.172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022]
Abstract
Osteoblastoma is a locally aggressive tumour of bone. Until recently, its underlying genetic features were largely unknown. During the past two years, reports have demonstrated that acquired structural variations affect the transcription factor FOS in a high proportion of cases. These rearrangements modify the terminal exon of the gene and are believed to stabilise both the FOS transcript and the encoded protein, resulting in high expression levels. Here, we applied in‐depth genetic analyses to a series of 29 osteoblastomas, including five classified as epithelioid osteoblastoma. We found recurrent homozygous deletions of the NF2 gene in three of the five epithelioid cases and in one conventional osteoblastoma. These events were mutually exclusive from FOS mutations. Structural variations were determined by deep whole genome sequencing and the number of FOS‐rearranged cases was less than previously reported (10/23, 43%). One conventional osteoblastoma displayed a novel mechanism of FOS upregulation; bringing the entire FOS gene under the control of the WNT5A enhancer that is itself activated by FOS. Taken together, we show that NF2 loss characterises a subgroup of osteoblastomas, distinct from FOS‐rearranged cases. Both NF2 and FOS are involved in regulating bone homeostasis, thereby providing a mechanistic link to the excessive bone growth of osteoblastoma.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Louise Cornmark
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jakob Hofvander
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Suk Wai Lam
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith Vmg Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michal Kovac
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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17
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Middelkamp S, van Tol HTA, Spierings DCJ, Boymans S, Guryev V, Roelen BAJ, Lansdorp PM, Cuppen E, Kuijk EW. Sperm DNA damage causes genomic instability in early embryonic development. SCIENCE ADVANCES 2020; 6:eaaz7602. [PMID: 32494621 PMCID: PMC7159919 DOI: 10.1126/sciadv.aaz7602] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 05/03/2023]
Abstract
Genomic instability is common in human embryos, but the underlying causes are largely unknown. Here, we examined the consequences of sperm DNA damage on the embryonic genome by single-cell whole-genome sequencing of individual blastomeres from bovine embryos produced with sperm damaged by γ-radiation. Sperm DNA damage primarily leads to fragmentation of the paternal chromosomes followed by random distribution of the chromosomal fragments over the two sister cells in the first cell division. An unexpected secondary effect of sperm DNA damage is the induction of direct unequal cleavages, which include the poorly understood heterogoneic cell divisions. As a result, chaotic mosaicism is common in embryos derived from fertilizations with damaged sperm. The mosaic aneuploidies, uniparental disomies, and de novo structural variation induced by sperm DNA damage may compromise fertility and lead to rare congenital disorders when embryos escape developmental arrest.
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Affiliation(s)
- Sjors Middelkamp
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
| | - Helena T. A. van Tol
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, Netherlands
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Bernard A. J. Roelen
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, Netherlands
| | - Peter M. Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
- Hartwig Medical Foundation, Amsterdam, Netherlands
- Corresponding author.
| | - Ewart W. Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
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18
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Kim HR, Santhakumar K, Markham E, Baldera D, Greenald D, Bryant HE, El-Khamisy SF, van Eeden FJ. Investigation of the role of VHL-HIF signaling in DNA repair and apoptosis in zebrafish. Oncotarget 2020; 11:1109-1130. [PMID: 32284789 PMCID: PMC7138166 DOI: 10.18632/oncotarget.27521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
pVHL is a tumor suppressor. The lack of its function leads to various tumors, among which ccRCC (clear cell renal cell carcinoma) has the most serious outcome due to its resistance to chemotherapies and radiotherapies. Although HIF promotes the progression of ccRCC, the precise mechanism by which the loss of VHL leads to tumor initiation remains unclear. We exploited two zebrafish vhl mutants, vhl and vll, and Tg (phd3:: EGFP)i144 fish to identify crucial functions of Vhl in tumor initiation. Through the mutant analysis, we found that the role of pVHL in DNA repair is conserved in zebrafish Vll. Interestingly, we also discovered that Hif activation strongly suppressed genotoxic stress induced DNA repair defects and apoptosis in vll and brca2 mutants and in embryos lacking ATM activity. These results suggest the potential of HIF as a clinical modulator that can protect cells from accumulating DNA damage and apoptosis which can lead to cancers and neurodegenerative disorders.
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Affiliation(s)
| | - Kirankumar Santhakumar
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur 603203, India
| | - Eleanor Markham
- Bateson Centre/BMS, Firth Court, University of Sheffield, Sheffield S10 2TN, UK
| | - Davide Baldera
- Bateson Centre/BMS, Firth Court, University of Sheffield, Sheffield S10 2TN, UK
| | - David Greenald
- Centre for Discovery Brain Sciences, University of Edinburgh, Chancellor's Building, Edinburgh EH16 4SB, UK
| | - Helen E Bryant
- Department of Oncology & Metabolism, The Medical School, Sheffield S10 2RX, UK
| | - Sherif F El-Khamisy
- Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, Sheffield S10 2TN, UK
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19
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Andersson N, Bakker B, Karlsson J, Valind A, Holmquist Mengelbier L, Spierings DCJ, Foijer F, Gisselsson D. Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers. Cancer Res 2020; 80:1512-1523. [PMID: 32041836 DOI: 10.1158/0008-5472.can-19-3468] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/18/2019] [Accepted: 02/04/2020] [Indexed: 11/16/2022]
Abstract
Darwinian evolution of tumor cells remains underexplored in childhood cancer. We here reconstruct the evolutionary histories of 56 pediatric primary tumors, including 24 neuroblastomas, 24 Wilms tumors, and 8 rhabdomyosarcomas. Whole-genome copy-number and whole-exome mutational profiling of multiple regions per tumor were performed, followed by clonal deconvolution to reconstruct a phylogenetic tree for each tumor. Overall, 88% of the tumors exhibited genetic variation among primary tumor regions. This variability typically emerged through collateral phylogenetic branching, leading to spatial variability in the distribution of more than 50% (96/173) of detected diagnostically informative genetic aberrations. Single-cell sequencing of 547 individual cancer cells from eight solid pediatric tumors confirmed branching evolution to be a fundamental underlying principle of genetic variation in all cases. Strikingly, cell-to-cell genetic diversity was almost twice as high in aggressive compared with clinically favorable tumors (median Simpson index of diversity 0.45 vs. 0.88; P = 0.029). Similarly, a comparison of multiregional sampling data from a total of 274 tumor regions showed that new phylogenetic branches emerge at a higher frequency per sample and carry a higher mutational load in high-risk than in low-risk tumors. Timelines based on spatial genetic variation showed that the mutations most influencing relapse risk occur at initiation of clonal expansion in neuroblastoma and rhabdomyosarcoma, whereas in Wilms tumor, they are late events. Thus, from an evolutionary standpoint, some high-risk childhood cancers are born bad, whereas others grow worse over time. SIGNIFICANCE: Different pediatric cancers with a high risk of relapse share a common generic pattern of extensively branching evolution of somatic mutations. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/7/1512/F1.large.jpg.
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Affiliation(s)
- Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | | | - Diana C J Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden. .,Division of Oncology-Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Clinical Genetics and Pathology, Laboratory Medicine, Lund University Hospital, Skåne Healthcare Region, Lund, Sweden
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20
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E2F-Family Members Engage the PIDDosome to Limit Hepatocyte Ploidy in Liver Development and Regeneration. Dev Cell 2020; 52:335-349.e7. [PMID: 31983631 DOI: 10.1016/j.devcel.2019.12.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/27/2019] [Accepted: 12/24/2019] [Indexed: 01/12/2023]
Abstract
E2F transcription factors control the cytokinesis machinery and thereby ploidy in hepatocytes. If or how these proteins limit proliferation of polyploid cells with extra centrosomes remains unknown. Here, we show that the PIDDosome, a signaling platform essential for caspase-2-activation, limits hepatocyte ploidy and is instructed by the E2F network to control p53 in the developing as well as regenerating liver. Casp2 and Pidd1 act as direct transcriptional targets of E2F1 and its antagonists, E2F7 and E2F8, that together co-regulate PIDDosome expression during juvenile liver growth and regeneration. Of note, whereas hepatocyte aneuploidy correlates with the basal ploidy state, the degree of aneuploidy itself is not limited by PIDDosome-dependent p53 activation. Finally, we provide evidence that the same signaling network is engaged to control ploidy in the human liver after resection. Our study defines the PIDDosome as a primary target to manipulate hepatocyte ploidy and proliferation rates in the regenerating liver.
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21
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Aziz K, Limzerwala JF, Sturmlechner I, Hurley E, Zhang C, Jeganathan KB, Nelson G, Bronk S, Velasco RF, van Deursen EJ, O’Brien DR, Kocher JPA, Youssef SA, van Ree JH, de Bruin A, van den Bos H, Spierings DC, Foijer F, van de Sluis B, Roberts LR, Gores G, Li H, van Deursen JM. Ccne1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice. Gastroenterology 2019; 157:210-226.e12. [PMID: 30878468 PMCID: PMC6800187 DOI: 10.1053/j.gastro.2019.03.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 02/15/2019] [Accepted: 03/07/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS The CCNE1 locus, which encodes cyclin E1, is amplified in many types of cancer cells and is activated in hepatocellular carcinomas (HCCs) from patients infected with hepatitis B virus or adeno-associated virus type 2, due to integration of the virus nearby. We investigated cell-cycle and oncogenic effects of cyclin E1 overexpression in tissues of mice. METHODS We generated mice with doxycycline-inducible expression of Ccne1 (Ccne1T mice) and activated overexpression of cyclin E1 from age 3 weeks onward. At 14 months of age, livers were collected from mice that overexpress cyclin E1 and nontransgenic mice (controls) and analyzed for tumor burden and by histology. Mouse embryonic fibroblasts (MEFs) and hepatocytes from Ccne1T and control mice were analyzed to determine the extent to which cyclin E1 overexpression perturbs S-phase entry, DNA replication, and numbers and structures of chromosomes. Tissues from 4-month-old Ccne1T and control mice (at that age were free of tumors) were analyzed for chromosome alterations, to investigate the mechanisms by which cyclin E1 predisposes hepatocytes to transformation. RESULTS Ccne1T mice developed more hepatocellular adenomas and HCCs than control mice. Tumors developed only in livers of Ccne1T mice, despite high levels of cyclin E1 in other tissues. Ccne1T MEFs had defects that promoted chromosome missegregation and aneuploidy, including incomplete replication of DNA, centrosome amplification, and formation of nonperpendicular mitotic spindles. Whereas Ccne1T mice accumulated near-diploid aneuploid cells in multiple tissues and organs, polyploidization was observed only in hepatocytes, with losses and gains of whole chromosomes, DNA damage, and oxidative stress. CONCLUSIONS Livers, but not other tissues of mice with inducible overexpression of cyclin E1, develop tumors. More hepatocytes from the cyclin E1-overexpressing mice were polyploid than from control mice, and had losses or gains of whole chromosomes, DNA damage, and oxidative stress; all of these have been observed in human HCC cells. The increased risk of HCC in patients with hepatitis B virus or adeno-associated virus type 2 infection might involve activation of cyclin E1 and its effects on chromosomes and genomes of liver cells.
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Affiliation(s)
- Khaled Aziz
- Departments of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jazeel F. Limzerwala
- Departments of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ines Sturmlechner
- Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA,Department of Pediatrics, and, University Medical Center Groningen, Groningen, The Netherlands
| | - Erin Hurley
- Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Cheng Zhang
- Departments of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Karthik B. Jeganathan
- Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Grace Nelson
- Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steve Bronk
- Departments of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Raul Fierro Velasco
- Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Erik-Jan van Deursen
- Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel R. O’Brien
- Departments of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA,Departments of Health Sciences Research, and, Mayo Clinic, Rochester, MN 55905, USA
| | - Jean-Pierre A. Kocher
- Departments of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA,Departments of Health Sciences Research, and, Mayo Clinic, Rochester, MN 55905, USA
| | - Sameh A. Youssef
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Janine H. van Ree
- Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Alain de Bruin
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands,Department of Pediatrics, and, University Medical Center Groningen, Groningen, The Netherlands
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bart van de Sluis
- Department of Pediatrics, and, University Medical Center Groningen, Groningen, The Netherlands
| | - Lewis R. Roberts
- Departments of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory Gores
- Departments of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hu Li
- Departments of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jan M. van Deursen
- Departments of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA,Departments of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA,Department of Pediatrics, and, University Medical Center Groningen, Groningen, The Netherlands,Correspondence: Please address all correspondence to Dr. Jan M. van Deursen, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA. Phone: 507.284.2524;
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