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Wu X, Seraia E, Hatch SB, Wan X, Ebner DV, Aroldi F, Jiang Y, Ryan AJ, Bogenrieder T, Weyer-Czernilofsky U, Rieunier G, Macaulay VM. CHK1 inhibition exacerbates replication stress induced by IGF blockade. Oncogene 2022; 41:476-488. [PMID: 34773074 PMCID: PMC8782724 DOI: 10.1038/s41388-021-02080-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/08/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022]
Abstract
We recently reported that genetic or pharmacological inhibition of insulin-like growth factor receptor (IGF-1R) slows DNA replication and induces replication stress by downregulating the regulatory subunit RRM2 of ribonucleotide reductase, perturbing deoxynucleotide triphosphate (dNTP) supply. Aiming to exploit this effect in therapy we performed a compound screen in five breast cancer cell lines with IGF neutralising antibody xentuzumab. Inhibitor of checkpoint kinase CHK1 was identified as a top screen hit. Co-inhibition of IGF and CHK1 caused synergistic suppression of cell viability, cell survival and tumour growth in 2D cell culture, 3D spheroid cultures and in vivo. Investigating the mechanism of synthetic lethality, we reveal that CHK1 inhibition in IGF-1R depleted or inhibited cells further downregulated RRM2, reduced dNTP supply and profoundly delayed replication fork progression. These effects resulted in significant accumulation of unreplicated single-stranded DNA and increased cell death, indicative of replication catastrophe. Similar phenotypes were induced by IGF:WEE1 co-inhibition, also via exacerbation of RRM2 downregulation. Exogenous RRM2 expression rescued hallmarks of replication stress induced by co-inhibiting IGF with CHK1 or WEE1, identifying RRM2 as a critical target of the functional IGF:CHK1 and IGF:WEE1 interactions. These data identify novel therapeutic vulnerabilities and may inform future trials of IGF inhibitory drugs.
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Affiliation(s)
- Xiaoning Wu
- Department of Oncology, University of Oxford, Oxford, UK
| | - Elena Seraia
- Target Discovery Institute, University of Oxford, Oxford, UK
| | | | - Xiao Wan
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Daniel V Ebner
- Target Discovery Institute, University of Oxford, Oxford, UK
| | | | - Yanyan Jiang
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Anderson J Ryan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Thomas Bogenrieder
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
- AMAL Therapeutics, c/o Fondation pour Recherches Médicales, 1205 Geneva, Switzerland
- Department of Urology, University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany
| | | | - Guillaume Rieunier
- Department of Oncology, University of Oxford, Oxford, UK.
- Immunocore Ltd, Abingdon, UK.
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Landoni JC, Wang L, Suomalainen A. Whole-Cell and Mitochondrial dNTP Pool Quantification from Cells and Tissues. Methods Mol Biol 2021; 2276:143-151. [PMID: 34060038 DOI: 10.1007/978-1-0716-1266-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Deoxynucleoside 5'-triphosphates (dNTPs) are the molecular building blocks for DNA synthesis, and their balanced concentration in the cell is fundamental for health. dNTP imbalance can lead to genomic instability and other metabolic disturbances, resulting in devastating mitochondrial diseases.The accurate and efficient measurement of dNTPs from different biological samples and cellular compartments is vital to understand the mechanisms behind these diseases and develop and scrutinize their possible treatments. This chapter describes an update on the most recent development of the traditional radiolabeled polymerase extension method and its adaptation for the measurement of whole-cell and mitochondrial dNTP pools from cultured cells and tissue samples. The solid-phase reaction setting enables an increase in efficiency, accuracy, and measurement scale.
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Affiliation(s)
- Juan C Landoni
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anu Suomalainen
- University Hospital, Department of Neurology, Helsinki, Finland.
- Neuroscience Center, University of Helsinki, Helsinki, Finland.
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Purhonen J, Banerjee R, McDonald AE, Fellman V, Kallijärvi J. A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase. Nucleic Acids Res 2020; 48:e87. [PMID: 32573728 PMCID: PMC7470940 DOI: 10.1093/nar/gkaa516] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/15/2022] Open
Abstract
Deoxyribonucleoside triphosphates (dNTPs) are vital for the biosynthesis and repair of DNA. Their cellular concentration peaks during the S phase of the cell cycle. In non-proliferating cells, dNTP concentrations are low, making their reliable quantification from tissue samples of heterogeneous cellular composition challenging. Partly because of this, the current knowledge related to the regulation of and disturbances in cellular dNTP concentrations derive mostly from cell culture experiments with little corroboration at the tissue or organismal level. Here, we fill the methodological gap by presenting a simple non-radioactive microplate assay for the quantification of dNTPs with a minimum requirement of 4-12 mg of biopsy material. In contrast to published assays, this assay is based on long synthetic single-stranded DNA templates (50-200 nucleotides), an inhibitor-resistant high-fidelity DNA polymerase, and the double-stranded-DNA-binding EvaGreen dye. The assay quantified reliably less than 50 fmol of each of the four dNTPs and discriminated well against ribonucleotides. Additionally, thermostable RNAse HII-mediated nicking of the reaction products and a subsequent shift in their melting temperature allowed near-complete elimination of the interfering ribonucleotide signal, if present. Importantly, the assay allowed measurement of minute dNTP concentrations in mouse liver, heart and skeletal muscle.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Rishi Banerjee
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | | | - Vineta Fellman
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland.,Department of Clinical Sciences, Lund, Pediatrics, Lund University, Sweden.,Children's Hospital, Helsinki University Hospital, Finland
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
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Hämäläinen RH, Landoni JC, Ahlqvist KJ, Goffart S, Ryytty S, Rahman MO, Brilhante V, Icay K, Hautaniemi S, Wang L, Laiho M, Suomalainen A. Reply to: Proofreading deficiency in mitochondrial DNA polymerase does not affect total dNTP pools in mouse embryos. Nat Metab 2020; 2:676-677. [PMID: 32778835 DOI: 10.1038/s42255-020-0265-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/14/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Riikka H Hämäläinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland.
| | - Juan C Landoni
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Kati J Ahlqvist
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sanna Ryytty
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - M Obaidur Rahman
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Virginia Brilhante
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Katherine Icay
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anu Suomalainen
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland.
- University Hospital, Department of Neurology, Helsinki, Finland.
- Neuroscience Center, University of Helsinki, Helsinki, Finland.
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Sharma S, Koolmeister C, Tran P, Nilsson AK, Larsson NG, Chabes A. Proofreading deficiency in mitochondrial DNA polymerase does not affect total dNTP pools in mouse embryos. Nat Metab 2020; 2:673-675. [PMID: 32778836 DOI: 10.1038/s42255-020-0264-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Phong Tran
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Anna Karin Nilsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
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Hämäläinen RH, Landoni JC, Ahlqvist KJ, Goffart S, Ryytty S, Rahman MO, Brilhante V, Icay K, Hautaniemi S, Wang L, Laiho M, Suomalainen A. Defects in mtDNA replication challenge nuclear genome stability through nucleotide depletion and provide a unifying mechanism for mouse progerias. Nat Metab 2019; 1:958-965. [PMID: 32694840 DOI: 10.1038/s42255-019-0120-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/04/2019] [Indexed: 01/07/2023]
Abstract
Mitochondrial DNA (mtDNA) mutagenesis and nuclear DNA repair defects are considered cellular mechanisms of ageing. mtDNA mutator mice with increased mtDNA mutagenesis show signs of premature ageing. However, why patients with mitochondrial diseases, or mice with other forms of mitochondrial dysfunction, do not age prematurely remains unknown. Here, we show that cells from mutator mice display challenged nuclear genome maintenance similar to that observed in progeric cells with defects in nuclear DNA repair. Cells from mutator mice show slow nuclear DNA replication fork progression, cell cycle stalling and chronic DNA replication stress, leading to double-strand DNA breaks in proliferating progenitor or stem cells. The underlying mechanism involves increased mtDNA replication frequency, sequestering of nucleotides to mitochondria, depletion of total cellular nucleotide pools, decreased deoxynucleoside 5'-triphosphate (dNTP) availability for nuclear genome replication and compromised nuclear genome maintenance. Our data indicate that defects in mtDNA replication can challenge nuclear genome stability. We suggest that defects in nuclear genome maintenance, particularly in the stem cell compartment, represent a unified mechanism for mouse progerias. Therefore, through their destabilizing effects on the nuclear genome, mtDNA mutations are indirect contributors to organismal ageing, suggesting that the direct role of mtDNA mutations in driving ageing-like symptoms might need to be revisited.
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Affiliation(s)
- Riikka H Hämäläinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
- Research Program in Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland.
| | - Juan C Landoni
- Research Program in Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Kati J Ahlqvist
- Research Program in Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sanna Ryytty
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - M Obaidur Rahman
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Virginia Brilhante
- Research Program in Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Katherine Icay
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anu Suomalainen
- Research Program in Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland.
- Helsinki University Hospital, Department of Neurosciences, Helsinki, Finland.
- Neuroscience Center, University of Helsinki, Helsinki, Finland.
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