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Foy R, Lew KX, Saurin AT. The search for CDK4/6 inhibitor biomarkers has been hampered by inappropriate proliferation assays. NPJ Breast Cancer 2024; 10:19. [PMID: 38438376 PMCID: PMC10912267 DOI: 10.1038/s41523-024-00624-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024] Open
Abstract
CDK4/6 inhibitors are effective at treating advanced HR+ /HER2- breast cancer, however biomarkers that can predict response are urgently needed. We demonstrate here that previous large-scale screens designed to identify which tumour types or genotypes are most sensitive to CDK4/6 inhibitors have misrepresented the responsive cell lines because of a reliance on metabolic proliferation assays. CDK4/6-inhibited cells arrest in G1 but continue to grow in size, thereby producing more mitochondria. We show that this growth obscures the arrest using ATP-based proliferation assays but not if DNA-based assays are used instead. Furthermore, lymphoma lines, previously identified as the most sensitive, simply appear to respond the best using ATP-based assays because they fail to overgrow during the G1 arrest. Similarly, the CDK4/6 inhibitor abemaciclib appears to inhibit proliferation better than palbociclib because it also restricts cellular overgrowth through off-target effects. DepMap analysis of screening data using reliable assay types, demonstrates that palbociclib-sensitive cell types are also sensitive to Cyclin D1, CDK4 and CDK6 knockout/knockdown, whereas the palbociclib-resistant lines are sensitive to Cyclin E1, CDK2 and SKP2 knockout/knockdown. Potential biomarkers of palbociclib-sensitive cells are increased expression of CCND1 and RB1, and reduced expression of CCNE1 and CDKN2A. Probing DepMap with similar data from metabolic assays fails to reveal these associations. Together, this demonstrates why CDK4/6 inhibitors, and any other anti-cancer drugs that arrest the cell cycle but permit continued cell growth, must now be re-screened against a wide-range of cell types using an appropriate proliferation assay. This would help to better inform clinical trials and to identify much needed biomarkers of response.
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Affiliation(s)
- Reece Foy
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK.
| | - Kah Xin Lew
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Adrian T Saurin
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK.
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Cortez‐Jugo C, Czuba‐Wojnilowicz E, Tan A, Caruso F. A Focus on "Bio" in Bio-Nanoscience: The Impact of Biological Factors on Nanomaterial Interactions. Adv Healthc Mater 2021; 10:e2100574. [PMID: 34170631 DOI: 10.1002/adhm.202100574] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/18/2021] [Indexed: 12/17/2022]
Abstract
Bio-nanoscience research encompasses studies on the interactions of nanomaterials with biological structures or what is commonly referred to as the biointerface. Fundamental studies on the influence of nanomaterial properties, including size, shape, composition, and charge, on the interaction with the biointerface have been central in bio-nanoscience to assess nanomaterial efficacy and safety for a range of biomedical applications. However, the state of the cells, tissues, or biological models can also influence the behavior of nanomaterials at the biointerface and their intracellular processing. Focusing on the "bio" in bio-nano, this review discusses the impact of biological properties at the cellular, tissue, and whole organism level that influences nanomaterial behavior, including cell type, cell cycle, tumor physiology, and disease states. Understanding how the biological factors can be addressed or exploited to enhance nanomaterial accumulation and uptake can guide the design of better and suitable models to improve the outcomes of materials in nanomedicine.
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Affiliation(s)
- Christina Cortez‐Jugo
- ARC Centre of Excellence in Convergent Bio‐Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering The University of Melbourne Parkville Victoria 3010 Australia
| | - Ewa Czuba‐Wojnilowicz
- ARC Centre of Excellence in Convergent Bio‐Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering The University of Melbourne Parkville Victoria 3010 Australia
| | - Abigail Tan
- ARC Centre of Excellence in Convergent Bio‐Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering The University of Melbourne Parkville Victoria 3010 Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio‐Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering The University of Melbourne Parkville Victoria 3010 Australia
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Cheng X, Ge M, Zhu S, Li D, Wang R, Xu Q, Chen Z, Xie S, Liu H. mTORC1-mediated amino acid signaling is critical for cell fate determination under transplant-induced stress. FEBS Lett 2020; 595:462-475. [PMID: 33249578 DOI: 10.1002/1873-3468.14008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/17/2020] [Accepted: 11/21/2020] [Indexed: 01/05/2023]
Abstract
Transplantation of in vitro-manipulated cells is widely used in hematology. While transplantation is well recognized to impose severe stress on transplanted cells, the nature of transplant-induced stress remains elusive. Here, we propose that the lack of amino acids in serum is the major cause of transplant-induced stress. Mechanistically, amino acid deficiency decreases protein synthesis and nutrient consummation. However, in cells with overactive AKT and ERK, mTORC1 is not inhibited and protein synthesis remains relatively high. This impaired signaling causes nutrient depletion, cell cycle block, and eventually autophagy and cell death, which can be inhibited by cycloheximide or mTORC1 inhibitors. Thus, mTORC1-mediated amino acid signaling is critical in cell fate determination under transplant-induced stress, and protein synthesis inhibition can improve transplantation efficiency.
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Affiliation(s)
- Xiaoyan Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Maolin Ge
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Shouhai Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Dan Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Ruiheng Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Qiongyu Xu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Zhihong Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Shufeng Xie
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Han Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China
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4
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Cooper S. The synchronization manifesto: a critique of whole‐culture synchronization. FEBS J 2019; 286:4650-4656. [DOI: 10.1111/febs.15050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/24/2019] [Accepted: 08/22/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Stephen Cooper
- Department of Microbiology and Immunology University of Michigan Medical School Ann Arbor MI USA
- The Center for Cell Cycle Analysis (C3A) Longboat KeyFL USA
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5
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Fuge G, Zeng AP, Jandt U. Weak cell cycle dependency but strong distortive effects of transfection with Lipofectamine 2000 in near-physiologically synchronized cell culture. Eng Life Sci 2016; 17:348-356. [PMID: 32624780 DOI: 10.1002/elsc.201600113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 08/26/2016] [Accepted: 09/07/2016] [Indexed: 11/06/2022] Open
Abstract
Previously, we reported a method to generate and validate cell cycle-synchronized cultures of multiple mammalian suspension cell lines under near-physiological conditions. This method was applied to elucidate the putative interdependencies of the cell cycle and recombinant protein expression in the human producer cell line HEK293s using Lipofectamine 2000 and the reporter plasmid pcDNA3.3 enhanced green fluorescent protein, destabilized using PEST sequence. A population-resolved modeling approach was applied to quantitatively assess putative variations of cell cycle dependent expression rates based on the obtained experimental data. We could not confirm results published earlier by other groups, based on nonphysiological synchronization attempts, reporting transfection efficiency being strongly dependent on the cell cycle phase at transfection time point. On the other hand, it is demonstrated that transfection and protein expression distort the progression of the cell cycle.
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Affiliation(s)
- Grischa Fuge
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Uwe Jandt
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
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Znojek P, Willmore E, Curtin NJ. Preferential potentiation of topoisomerase I poison cytotoxicity by PARP inhibition in S phase. Br J Cancer 2014; 111:1319-26. [PMID: 25003660 PMCID: PMC4183837 DOI: 10.1038/bjc.2014.378] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/27/2014] [Accepted: 06/10/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Topoisomerase I (Topo I) poisons (e.g., camptothecin (CPT)), used to treat cancer, cause DNA breaks that are most cytotoxic during S phase. PARP-1 promotes DNA repair and PARP inhibitors (PARPi) sensitise cells to Topo I poisons. We aimed to determine whether chemosensitisation is also S phase specific using rucaparib, a potent PARPi in advanced clinical evaluation. METHODS The impact of rucaparib, on CPT-induced cytotoxicity was measured in human colon cancer (LoVo) and leukaemic (K562) cells in asynchronous and cell cycle phase-separated cultures. Topoisomerase I and PARP levels and activity and the effect of rucaparib on DNA single-strand breaks (SSBs), double-strand breaks (DSBs) and collapsed replication fork induction and repair were determined in cell cycle phase-separated cells. RESULTS The cytotoxicity of CPT was greatest during S phase, partially attributable to high Topo I activity, and rucaparib preferentially sensitised S-phase cells. Rucaparib increased CPT-induced DNA SSBs in all phases of the cell cycle, and increased DSB and γH2AX foci in S and G2, with γH2AX foci being highest in S-phase cells. Repair of SSBs and DSBs was most rapid during S then G2 phases and was substantially hindered by rucaparib. CONCLUSIONS Rucaparib preferentially sensitises S-phase cells by increasing the frequency of collapsed replication forks.
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Affiliation(s)
- P Znojek
- Newcastle University, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - E Willmore
- Newcastle University, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - N J Curtin
- Newcastle University, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle upon Tyne NE2 4HH, UK
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Barradas OP, Jandt U, Becker M, Bahnemann J, Pörtner R, Zeng AP. Synchronized mammalian cell culture: Part I-A physical strategy for synchronized cultivation under physiological conditions. Biotechnol Prog 2014; 31:165-74. [DOI: 10.1002/btpr.1944] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/10/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Oscar Platas Barradas
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Uwe Jandt
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Max Becker
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Janina Bahnemann
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Ralf Pörtner
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - An-Ping Zeng
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
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8
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Jandt U, Platas Barradas O, Pörtner R, Zeng AP. Mammalian cell culture synchronization under physiological conditions and population dynamic simulation. Appl Microbiol Biotechnol 2014; 98:4311-9. [DOI: 10.1007/s00253-014-5553-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/14/2014] [Accepted: 01/18/2014] [Indexed: 02/05/2023]
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9
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Cooper S. On a heuristic point of view concerning the expression of numerous genes during the cell cycle. IUBMB Life 2011; 64:10-7. [DOI: 10.1002/iub.571] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/08/2011] [Indexed: 12/12/2022]
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Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius. Proc Natl Acad Sci U S A 2008; 105:16737-42. [PMID: 18922777 DOI: 10.1073/pnas.0806414105] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The "baby machine" provides a means of generating synchronized cultures of minimally perturbed cells. We describe the use of this technique to establish the key cell-cycle parameters of hyperthermophilic archaea of the genus Sulfolobus. The 3 DNA replication origins of Sulfolobus acidocaldarius were mapped by 2D gel analysis to near 0 (oriC2), 579 (oriC1), and 1,197 kb (oriC3) on the 2,226-kb circular genome, and we present a direct demonstration of their activity within the first few minutes of a synchronous cell cycle. We also detected X-shaped DNA molecules at the origins in log-phase cells, but these were not directly associated with replication initiation or ongoing chromosome replication in synchronized cells. Whole-genome marker frequency analyses of both synchronous and log-phase cultures showed that origin utilization was close to 100% for all 3 origins per round of replication. However, oriC2 was activated slightly later on average compared with oriC1 and oriC3. The DNA replication forks moved bidirectionally away from each origin at approximately 88 bp per second in synchronous culture. Analysis of the 3 Orc1/Cdc6 initiator proteins showed a uniformity of cellular abundance and origin binding throughout the cell cycle. In contrast, although levels of the MCM helicase were constant across the cell cycle, its origin localization was regulated, because it was strongly enriched at all 3 origins in early S phase.
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11
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Cooper S. On the fiftieth anniversary of the Schaechter, Maaløe, Kjeldgaard experiments: implications for cell-cycle and cell-growth control. Bioessays 2008; 30:1019-24. [PMID: 18800382 DOI: 10.1002/bies.20814] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Schaechter-Maaløe-Kjeldgaard papers, which have their 50(th) anniversary this year, have major implications for understanding the cell cycle, control of cell growth, control of cell size, metabolic control, the basic bacterial growth curve, and myriad other bacterial and eukaryotic growth phenomena. These ideas have broad applications that should be considered in current studies of the cell cycle. In particular, the emphasis on steady-state growth conditions, and clear and sharp changes in growth conditions were fundamental to their experiments and have been codified in the principles of the Copenhagen School of Microbiology.
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Affiliation(s)
- Stephen Cooper
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA.
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