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Yalaz C, Bridges E, Alham NK, Zois CE, Chen J, Bensaad K, Miar A, Pires E, Muschel RJ, McCullagh JSO, Harris AL. Cone photoreceptor phosphodiesterase PDE6H inhibition regulates cancer cell growth and metabolism, replicating the dark retina response. Cancer Metab 2024; 12:5. [PMID: 38350962 PMCID: PMC10863171 DOI: 10.1186/s40170-023-00326-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/24/2023] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND PDE6H encodes PDE6γ', the inhibitory subunit of the cGMP-specific phosphodiesterase 6 in cone photoreceptors. Inhibition of PDE6, which has been widely studied for its role in light transduction, increases cGMP levels. The purpose of this study is to characterise the role of PDE6H in cancer cell growth. METHODS From an siRNA screen for 487 genes involved in metabolism, PDE6H was identified as a controller of cell cycle progression in HCT116 cells. Role of PDE6H in cancer cell growth and metabolism was studied through the effects of its depletion on levels of cell cycle controllers, mTOR effectors, metabolite levels, and metabolic energy assays. Effect of PDE6H deletion on tumour growth was also studied in a xenograft model. RESULTS PDE6H knockout resulted in an increase of intracellular cGMP levels, as well as changes to the levels of nucleotides and key energy metabolism intermediates. PDE6H knockdown induced G1 cell cycle arrest and cell death and reduced mTORC1 signalling in cancer cell lines. Both knockdown and knockout of PDE6H resulted in the suppression of mitochondrial function. HCT116 xenografts revealed that PDE6H deletion, as well as treatment with the PDE5/6 inhibitor sildenafil, slowed down tumour growth and improved survival, while sildenafil treatment did not have an additive effect on slowing the growth of PDE6γ'-deficient tumours. CONCLUSIONS Our results indicate that the changes in cGMP and purine pools, as well as mitochondrial function which is observed upon PDE6γ' depletion, are independent of the PKG pathway. We show that in HCT116, PDE6H deletion replicates many effects of the dark retina response and identify PDE6H as a new target in preventing cancer cell proliferation and tumour growth.
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Affiliation(s)
- Ceren Yalaz
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Esther Bridges
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nasullah K Alham
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Christos E Zois
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jianzhou Chen
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Karim Bensaad
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Miar
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ruth J Muschel
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - James S O McCullagh
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
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2
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Eames A, Chandrasekaran S. Leveraging metabolic modeling and machine learning to uncover modulators of quiescence depth. PNAS NEXUS 2024; 3:pgae013. [PMID: 38292544 PMCID: PMC10825626 DOI: 10.1093/pnasnexus/pgae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 12/28/2023] [Indexed: 02/01/2024]
Abstract
Quiescence, a temporary withdrawal from the cell cycle, plays a key role in tissue homeostasis and regeneration. Quiescence is increasingly viewed as a continuum between shallow and deep quiescence, reflecting different potentials to proliferate. The depth of quiescence is altered in a range of diseases and during aging. Here, we leveraged genome-scale metabolic modeling (GEM) to define the metabolic and epigenetic changes that take place with quiescence deepening. We discovered contrasting changes in lipid catabolism and anabolism and diverging trends in histone methylation and acetylation. We then built a multi-cell type machine learning model that accurately predicts quiescence depth in diverse biological contexts. Using both machine learning and genome-scale flux simulations, we performed high-throughput screening of chemical and genetic modulators of quiescence and identified novel small molecule and genetic modulators with relevance to cancer and aging.
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Affiliation(s)
- Alec Eames
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Center for Bioinformatics and Computational Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Megarioti AH, Esch BM, Athanasopoulos A, Koulouris D, Makridakis M, Lygirou V, Samiotaki M, Zoidakis J, Sophianopoulou V, André B, Fröhlich F, Gournas C. Ferroptosis-protective membrane domains in quiescence. Cell Rep 2023; 42:113561. [PMID: 38096056 DOI: 10.1016/j.celrep.2023.113561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 11/02/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Quiescence is a common cellular state, required for stem cell maintenance and microorganismal survival under stress conditions or starvation. However, the mechanisms promoting quiescence maintenance remain poorly known. Plasma membrane components segregate into distinct microdomains, yet the role of this compartmentalization in quiescence remains unexplored. Here, we show that flavodoxin-like proteins (FLPs), ubiquinone reductases of the yeast eisosome membrane compartment, protect quiescent cells from lipid peroxidation and ferroptosis. Eisosomes and FLPs expand specifically in respiratory-active quiescent cells, and mutants lacking either show accelerated aging and defective quiescence maintenance and accumulate peroxidized phospholipids with monounsaturated or polyunsaturated fatty acids (PUFAs). FLPs are essential for the extramitochondrial regeneration of the lipophilic antioxidant ubiquinol. FLPs, alongside the Gpx1/2/3 glutathione peroxidases, prevent iron-driven, PUFA-dependent ferroptotic cell death. Our work describes ferroptosis-protective mechanisms in yeast and introduces plasma membrane compartmentalization as an important factor in the long-term survival of quiescent cells.
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Affiliation(s)
- Amalia H Megarioti
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece; Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece
| | - Bianca M Esch
- Bioanalytical Chemistry Section, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Alexandros Athanasopoulos
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece
| | - Dimitrios Koulouris
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece
| | - Manousos Makridakis
- Biotechnology Division, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Division, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," 16672 Vari, Greece
| | - Jerome Zoidakis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece; Biotechnology Division, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vicky Sophianopoulou
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece
| | - Bruno André
- Molecular Physiology of the Cell Laboratory, Université Libre de Bruxelles (ULB), IBMM, 6041 Gosselies, Belgium
| | - Florian Fröhlich
- Bioanalytical Chemistry Section, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany; Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany.
| | - Christos Gournas
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece.
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Lu X, Zhong L, Lindell E, Veanes M, Guo J, Zhao M, Salehi M, Swartling FJ, Chen X, Sjöblom T, Zhang X. Identification of ATF3 as a novel protective signature of quiescent colorectal tumor cells. Cell Death Dis 2023; 14:676. [PMID: 37833290 PMCID: PMC10576032 DOI: 10.1038/s41419-023-06204-1] [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: 07/06/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death in the world. In most cases, drug resistance and tumor recurrence are ultimately inevitable. One obstacle is the presence of chemotherapy-insensitive quiescent cancer cells (QCCs). Identification of unique features of QCCs may facilitate the development of new targeted therapeutic strategies to eliminate tumor cells and thereby delay tumor recurrence. Here, using single-cell RNA sequencing, we classified proliferating and quiescent cancer cell populations in the human colorectal cancer spheroid model and identified ATF3 as a novel signature of QCCs that could support cells living in a metabolically restricted microenvironment. RNA velocity further showed a shift from the QCC group to the PCC group indicating the regenerative capacity of the QCCs. Our further results of epigenetic analysis, STING analysis, and evaluation of TCGA COAD datasets build a conclusion that ATF3 can interact with DDIT4 and TRIB3 at the transcriptional level. In addition, decreasing the expression level of ATF3 could enhance the efficacy of 5-FU on CRC MCTS models. In conclusion, ATF3 was identified as a novel marker of QCCs, and combining conventional drugs targeting PCCs with an option to target QCCs by reducing ATF3 expression levels may be a promising strategy for more efficient removal of tumor cells.
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Affiliation(s)
- Xi Lu
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lei Zhong
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, Sichuan, China
| | - Emma Lindell
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Margus Veanes
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jing Guo
- Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Miao Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maede Salehi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xiaonan Zhang
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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Du Y, Gupta P, Qin S, Sieber M. The role of metabolism in cellular quiescence. J Cell Sci 2023; 136:jcs260787. [PMID: 37589342 PMCID: PMC10445740 DOI: 10.1242/jcs.260787] [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] [Indexed: 08/18/2023] Open
Abstract
Cellular quiescence is a dormant, non-dividing cell state characterized by significant shifts in physiology and metabolism. Quiescence plays essential roles in a wide variety of biological processes, ranging from microbial sporulation to human reproduction and wound repair. Moreover, when the regulation of quiescence is disrupted, it can drive cancer growth and compromise tissue regeneration after injury. In this Review, we examine the dynamic changes in metabolism that drive and support dormant and transiently quiescent cells, including spores, oocytes and adult stem cells. We begin by defining quiescent cells and discussing their roles in key biological processes. We then examine metabolic factors that influence cellular quiescence in both healthy and disease contexts, and how these could be leveraged in the treatment of cancer.
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Affiliation(s)
- Yipeng Du
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
| | - Parul Gupta
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
| | - Shenlu Qin
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
| | - Matthew Sieber
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC9040 ND13.214, Dallas, TX 75390, USA
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6
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Lindell E, Zhong L, Zhang X. Quiescent Cancer Cells-A Potential Therapeutic Target to Overcome Tumor Resistance and Relapse. Int J Mol Sci 2023; 24:ijms24043762. [PMID: 36835173 PMCID: PMC9959385 DOI: 10.3390/ijms24043762] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Quiescent cancer cells (QCCs) are nonproliferating cells arrested in the G0 phase, characterized by ki67low and p27high. QCCs avoid most chemotherapies, and some treatments could further lead to a higher proportion of QCCs in tumors. QCCs are also associated with cancer recurrence since they can re-enter a proliferative state when conditions are favorable. As QCCs lead to drug resistance and tumor recurrence, there is a great need to understand the characteristics of QCCs, decipher the mechanisms that regulate the proliferative-quiescent transition in cancer cells, and develop new strategies to eliminate QCCs residing in solid tumors. In this review, we discussed the mechanisms of QCC-induced drug resistance and tumor recurrence. We also discussed therapeutic strategies to overcome resistance and relapse by targeting QCCs, including (i) identifying reactive quiescent cancer cells and removing them via cell-cycle-dependent anticancer reagents; (ii) modulating the quiescence-to-proliferation switch; and (iii) eliminating QCCs by targeting their unique features. It is believed that the simultaneous co-targeting of proliferating and quiescent cancer cells may ultimately lead to the development of more effective therapeutic strategies for the treatment of solid tumors.
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