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Dombi E, Marinaki T, Spingardi P, Millar V, Hadjichristou N, Carver J, Johnston IG, Fratter C, Poulton J. Nucleoside supplements as treatments for mitochondrial DNA depletion syndrome. Front Cell Dev Biol 2024; 12:1260496. [PMID: 38665433 PMCID: PMC11043827 DOI: 10.3389/fcell.2024.1260496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction: In mitochondrial DNA (mtDNA) depletion syndrome (MDS), patients cannot maintain sufficient mtDNA for their energy needs. MDS presentations range from infantile encephalopathy with hepatopathy (Alpers syndrome) to adult chronic progressive external ophthalmoplegia. Most are caused by nucleotide imbalance or by defects in the mtDNA replisome. There is currently no curative treatment available. Nucleoside therapy is a promising experimental treatment for TK2 deficiency, where patients are supplemented with exogenous deoxypyrimidines. We aimed to explore the benefits of nucleoside supplementation in POLG and TWNK deficient fibroblasts. Methods: We used high-content fluorescence microscopy with software-based image analysis to assay mtDNA content and membrane potential quantitatively, using vital dyes PicoGreen and MitoTracker Red CMXRos respectively. We tested the effect of 15 combinations (A, T, G, C, AT, AC, AG, CT, CG, GT, ATC, ATG, AGC, TGC, ATGC) of deoxynucleoside supplements on mtDNA content of fibroblasts derived from four patients with MDS (POLG1, POLG2, DGUOK, TWNK) in both a replicating (10% dialysed FCS) and quiescent (0.1% dialysed FCS) state. We used qPCR to measure mtDNA content of supplemented and non-supplemented fibroblasts following mtDNA depletion using 20 µM ddC and after 14- and 21-day recovery in a quiescent state. Results: Nucleoside treatments at 200 µM that significantly increased mtDNA content also significantly reduced the number of cells remaining in culture after 7 days of treatment, as well as mitochondrial membrane potential. These toxic effects were abolished by reducing the concentration of nucleosides to 50 µM. In POLG1 and TWNK cells the combination of ATGC treatment increased mtDNA content the most after 7 days in non-replicating cells. ATGC nucleoside combination significantly increased the rate of mtDNA recovery in quiescent POLG1 cells following mtDNA depletion by ddC. Conclusion: High-content imaging enabled us to link mtDNA copy number with key read-outs linked to patient wellbeing. Elevated G increased mtDNA copy number but severely impaired fibroblast growth, potentially by inhibiting purine synthesis and/or causing replication stress. Combinations of nucleosides ATGC, T, or TC, benefited growth of cells harbouring POLG mutations. These combinations, one of which reflects a commercially available preparation, could be explored further for treatment of POLG patients.
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Affiliation(s)
- Eszter Dombi
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Tony Marinaki
- Purine Research Laboratory, Department of Biochemical Sciences, Guy’s and St Thomas’ Hospitals, London, United Kingdom
| | - Paolo Spingardi
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Val Millar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Janet Carver
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joanna Poulton
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
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Varadarajan SN, Mathew KA, Chandrasekharan A, Lupitha SS, Lekshmi A, Mini M, Darvin P, Santhoshkumar TR. Real-time visualization and quantitation of cell death and cell cycle progression in 2D and 3D cultures utilizing genetically encoded probes. J Cell Biochem 2022; 123:782-797. [PMID: 35106828 DOI: 10.1002/jcb.30222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022]
Abstract
Cancer cells grown as 3D-structures are better models for mimicking in vivo conditions than the 2D-culture systems employable in drug discovery applications. Cell cycle and cell death are important determinants for preclinical drug screening and tumor growth studies in laboratory conditions. Though several 3D-models and live-cell compatible approaches are available, a method for simultaneous real-time detection of cell cycle and cell death is required. Here we demonstrate a high-throughput adaptable method using genetically encoded fluorescent probes for the real-time quantitative detection of cell death and cell cycle. The cell-cycle indicator cdt1-Kusabira orange (KO) is stably integrated into cancer cells and further transfected with the Fluorescence Resonance Energy Transfer-based ECFP-DEVD-EYFP caspase activation sensor. The nuclear cdt1-KO expression serves as the readout for cell-cycle, and caspase activation is visualized by ECFP/EYFP ratiometric imaging. The image-based platform allowed imaging of growing spheres for prolonged periods in 3D-culture with excellent single-cell resolution through confocal microscopy. High-throughput screening (HTS) adaptation was achieved by targeting the caspase-sensor at the nucleus, which enabled the quantitation of cell death in 3D-models. The HTS using limited compound libraries, identified two lead compounds that induced caspase-activation both in 2D and 3D-cultures. This is the first report of an approach for noninvasive stain-free quantitative imaging of cell death and cell cycle with potential drug discovery applications.
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Affiliation(s)
| | - Krupa Ann Mathew
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Aneesh Chandrasekharan
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | - Asha Lekshmi
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Minsa Mini
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Pramod Darvin
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - T R Santhoshkumar
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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Genome-wide CRISPR screen identifies RACK1 as a critical host factor for flavivirus replication. J Virol 2021; 95:e0059621. [PMID: 34586867 PMCID: PMC8610583 DOI: 10.1128/jvi.00596-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cellular factors have important roles in all facets of the flavivirus replication cycle. Deciphering viral-host protein interactions is essential for understanding the flavivirus lifecycle as well as development of effective antiviral strategies. To uncover novel host factors that are co-opted by multiple flaviviruses, a CRISPR/Cas9 genome wide knockout (KO) screen was employed to identify genes required for replication of Zika virus (ZIKV). Receptor for Activated Protein C Kinase 1 (RACK1) was identified as a novel host factor required for ZIKV replication, which was confirmed via complementary experiments. Depletion of RACK1 via siRNA demonstrated that RACK1 is important for replication of a wide range of mosquito- and tick-borne flaviviruses, including West Nile Virus (WNV), Dengue Virus (DENV), Powassan Virus (POWV) and Langat Virus (LGTV) as well as the coronavirus SARS-CoV-2, but not for YFV, EBOV, VSV or HSV. Notably, flavivirus replication was only abrogated when RACK1 expression was dampened prior to infection. Utilising a non-replicative flavivirus model, we show altered morphology of viral replication factories and reduced formation of vesicle packets (VPs) in cells lacking RACK1 expression. In addition, RACK1 interacted with NS1 protein from multiple flaviviruses; a key protein for replication complex formation. Overall, these findings reveal RACK1's crucial role to the biogenesis of pan-flavivirus replication organelles. Importance Cellular factors are critical in all facets of viral lifecycles, where overlapping interactions between the virus and host can be exploited as possible avenues for the development of antiviral therapeutics. Using a genome-wide CRISPR knock-out screening approach to identify novel cellular factors important for flavivirus replication we identified RACK1 as a pro-viral host factor for both mosquito- and tick-borne flaviviruses in addition to SARS-CoV-2. Using an innovative flavivirus protein expression system, we demonstrate for the first time the impact of the loss of RACK1 on the formation of viral replication factories known as 'vesicle packets' (VPs). In addition, we show that RACK1 can interact with numerous flavivirus NS1 proteins as a potential mechanism by which VP formation can be induced by the former.
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Sack U, Tarnok A, Preijers F, Köhl U, Na IK. Editorial: Modulation of Human Immune Parameters by Anticancer Therapies. Front Immunol 2020; 11:621556. [PMID: 33343586 PMCID: PMC7738630 DOI: 10.3389/fimmu.2020.621556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ulrich Sack
- Medical Faculty, Institute of Clinical Immunology, Leipzig University, Leipzig, Germany
| | - Attila Tarnok
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany.,Department Precision Instruments, Tsinghua University, Beijing, China
| | - Frank Preijers
- Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Ulrike Köhl
- Medical Faculty, Institute of Clinical Immunology, Leipzig University, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany.,Institute for Cellular Therapeutics, Hannover Medical School, Hannover, Germany
| | - Il-Kang Na
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Experimental and Clinical Research Center (ECRC), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Heidelberg, Germany
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Affiliation(s)
- Marc Thilo Figge
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Jena, Germany.,Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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