1
|
Cao X, Huang S, Wagner MM, Cho YT, Chiu DC, Wartchow KM, Lazarian A, McIntire LB, Smolka MB, Baskin JM. A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization. Nat Cell Biol 2024:10.1038/s41556-024-01495-8. [PMID: 39209962 DOI: 10.1038/s41556-024-01495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Tools for acute manipulation of protein localization enable elucidation of spatiotemporally defined functions, but their reliance on exogenous triggers can interfere with cell physiology. This limitation is particularly apparent for studying mitosis, whose highly choreographed events are sensitive to perturbations. Here we exploit the serendipitous discovery of a phosphorylation-controlled, cell cycle-dependent localization change of the adaptor protein PLEKHA5 to develop a system for mitosis-specific protein recruitment to the plasma membrane that requires no exogenous stimulus. Mitosis-enabled anchor-away/recruiter system comprises an engineered, 15 kDa module derived from PLEKHA5 capable of recruiting functional protein cargoes to the plasma membrane during mitosis, either through direct fusion or via GFP-GFP nanobody interaction. Applications of the mitosis-enabled anchor-away/recruiter system include both knock sideways to rapidly extract proteins from their native localizations during mitosis and conditional recruitment of lipid-metabolizing enzymes for mitosis-selective editing of plasma membrane lipid content, without the need for exogenous triggers or perturbative synchronization methods.
Collapse
Affiliation(s)
- Xiaofu Cao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Shiying Huang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Mateusz M Wagner
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Yuan-Ting Cho
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Din-Chi Chiu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | | | - Artur Lazarian
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | | | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
2
|
Simoni-Nieves A, Lindzen M, Giri S, Gupta N, Chatterjee R, Selvadurai BR, Van Daele M, Love D, Haga Y, Romaniello D, Salame TM, Zerbib M, Oren R, Tsutsumi Y, Lauriola M, Marrocco I, Yarden Y. A bispecific antibody targeting EGFR and AXL delays resistance to osimertinib. Cell Rep Med 2024:101703. [PMID: 39216477 DOI: 10.1016/j.xcrm.2024.101703] [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: 12/18/2023] [Revised: 06/19/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Activating EGFR (epidermal growth factor receptor) mutations can be inhibited by specific tyrosine kinase inhibitors (TKIs), which have changed the landscape of lung cancer therapy. However, due to secondary mutations and bypass receptors, such as AXL (AXL receptor tyrosine kinase), drug resistance eventually emerges in most patients treated with the first-, second-, or third-generation TKIs (e.g., osimertinib). To inhibit AXL and resistance to osimertinib, we compare two anti-AXL drugs, an antibody (mAb654) and a TKI (bemcentinib). While no pair of osimertinib and an anti-AXL drug is able to prevent relapses, triplets combining osimertinib, cetuximab (an anti-EGFR antibody), and either anti-AXL drug are initially effective. However, longer monitoring uncovers superiority of the mAb654-containing triplet, possibly due to induction of receptor endocytosis, activation of immune mechanisms, or disabling intrinsic mutators. Hence, we constructed a bispecific antibody that engages both AXL and EGFR. When combined with osimertinib, the bispecific antibody consistently inhibits tumor relapses, which warrants clinical trials.
Collapse
Affiliation(s)
- Arturo Simoni-Nieves
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshit Lindzen
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Suvendu Giri
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nitin Gupta
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rishita Chatterjee
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Boobash-Raj Selvadurai
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marieke Van Daele
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Danielle Love
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuya Haga
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Donatella Romaniello
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Tomer-Meir Salame
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mirie Zerbib
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ilaria Marrocco
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
| | - Yosef Yarden
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
3
|
Cotton MJ, Ariel P, Chen K, Walcott VA, Dixit M, Breau KA, Hinesley CM, Kedziora KM, Tang CY, Zheng A, Magness ST, Burclaff J. An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal epithelial cells. Sci Rep 2024; 14:15195. [PMID: 38956443 PMCID: PMC11219882 DOI: 10.1038/s41598-024-66042-9] [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: 03/20/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
The intestinal epithelium dynamically controls cell cycle, yet no experimental platform exists for directly analyzing cell cycle phases in non-immortalized human intestinal epithelial cells (IECs). Here, we present two reporters and a complete platform for analyzing cell cycle phases in live primary human IECs. We interrogate the transcriptional identity of IECs grown on soft collagen, develop two fluorescent cell cycle reporter IEC lines, design and 3D print a collagen press to make chamber slides for optimal imaging while supporting primary human IEC growth, live image cell cycle dynamics, then assemble a computational pipeline building upon free-to-use programs for semi-automated analysis of cell cycle phases. The PIP-FUCCI construct allows for assigning cell cycle phase from a single image of living cells, and our PIP-H2A construct allows for semi-automated direct quantification of cell cycle phase lengths using our publicly available computational pipeline. Treating PIP-FUCCI IECs with oligomycin demonstrates that inhibiting mitochondrial respiration lengthens G1 phase, and PIP-H2A cells allow us to measure that oligomycin differentially lengthens S and G2/M phases across heterogeneous IECs. These platforms provide opportunities for future studies on pharmaceutical effects on the intestinal epithelium, cell cycle regulation, and more.
Collapse
Affiliation(s)
- Michael J Cotton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Pablo Ariel
- Microscopy Services Laboratory, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kaiwen Chen
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Vanessa A Walcott
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michelle Dixit
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Caroline M Hinesley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Katarzyna M Kedziora
- Department of Cell Biology, Center for Biologic Imaging (CBI), University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Cynthia Y Tang
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna Zheng
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
4
|
Konagaya Y, Rosenthal D, Ratnayeke N, Fan Y, Meyer T. An intermediate Rb-E2F activity state safeguards proliferation commitment. Nature 2024; 631:424-431. [PMID: 38926571 PMCID: PMC11236703 DOI: 10.1038/s41586-024-07554-2] [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: 06/19/2022] [Accepted: 05/10/2024] [Indexed: 06/28/2024]
Abstract
Tissue repair, immune defence and cancer progression rely on a vital cellular decision between quiescence and proliferation1,2. Mammalian cells proliferate by triggering a positive feedback mechanism3,4. The transcription factor E2F activates cyclin-dependent kinase 2 (CDK2), which in turn phosphorylates and inactivates the E2F inhibitor protein retinoblastoma (Rb). This action further increases E2F activity to express genes needed for proliferation. Given that positive feedback can inadvertently amplify small signals, understanding how cells keep this positive feedback in check remains a puzzle. Here we measured E2F and CDK2 signal changes in single cells and found that the positive feedback mechanism engages only late in G1 phase. Cells spend variable and often extended times in a reversible state of intermediate E2F activity before committing to proliferate. This intermediate E2F activity is proportional to the amount of phosphorylation of a conserved T373 residue in Rb that is mediated by CDK2 or CDK4/CDK6. Such T373-phosphorylated Rb remains bound on chromatin but dissociates from it once Rb is hyperphosphorylated at many sites, which fully activates E2F. The preferential initial phosphorylation of T373 can be explained by its relatively slower rate of dephosphorylation. Together, our study identifies a primed state of intermediate E2F activation whereby cells sense external and internal signals and decide whether to reverse and exit to quiescence or trigger the positive feedback mechanism that initiates cell proliferation.
Collapse
Affiliation(s)
- Yumi Konagaya
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Laboratory for Quantitative Biology of Cell Fate Decision, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.
| | - David Rosenthal
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Nalin Ratnayeke
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tobias Meyer
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
5
|
Stuart A, de Lange T. Replicative senescence is ATM driven, reversible, and accelerated by hyperactivation of ATM at normoxia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600514. [PMID: 38979390 PMCID: PMC11230194 DOI: 10.1101/2024.06.24.600514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Programmed telomere shortening limits tumorigenesis through the induction of replicative senescence. Here we address three long-standing questions concerning senescence. First, we show that the ATM kinase is solely responsible for the induction of replicative senescence. Senescence was delayed by ATM inhibition (ATMi) or overexpression of TRF2, the shelterin subunit dedicated to ATM repression. In contrast, there was no evidence for ATR signaling contributing to replicative senescence even when ATMi was combined with ATR inhibition. Second, we show ATMi can induce apparently normal cell divisions in a subset of senescent cells, indicating that senescence can be reversed. Third, we show that the extended replicative life span at low (physiological) oxygen is due to diminished ATM activity. At low oxygen, cells show a decreased ATM response to dysfunctional telomeres and genome-wide DSBs compared to 20% oxygen. As this effect could be reversed by NAC, the attenuated response of ATM to critically short telomeres and the resulting extended life span at low oxygen is likely due to ROS-induced formation of cysteine disulfide-bridges that crosslink ATM dimers into a form that is not activated by DSBs. These findings show how primary human cells detect shortened telomeres and reveal the molecular mechanism underlying the telomere tumor suppressor pathway.
Collapse
Affiliation(s)
- Alexander Stuart
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, USA
| |
Collapse
|
6
|
Saito S, Adachi N. Characterization and regulation of cell cycle-independent noncanonical gene targeting. Nat Commun 2024; 15:5044. [PMID: 38890315 PMCID: PMC11189520 DOI: 10.1038/s41467-024-49385-9] [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: 11/22/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Homology-dependent targeted DNA integration, generally referred to as gene targeting, provides a powerful tool for precise genome modification; however, its fundamental mechanisms remain poorly understood in human cells. Here we reveal a noncanonical gene targeting mechanism that does not rely on the homologous recombination (HR) protein Rad51. This mechanism is suppressed by Rad52 inhibition, suggesting the involvement of single-strand annealing (SSA). The SSA-mediated gene targeting becomes prominent when DSB repair by HR or end-joining pathways is defective and does not require isogenic DNA, permitting 5% sequence divergence. Intriguingly, loss of Msh2, loss of BLM, and induction of a target-site DNA break all significantly and synergistically enhance SSA-mediated targeted integration. Most notably, SSA-mediated integration is cell cycle-independent, occurring in the G1 phase as well. Our findings provide unequivocal evidence for Rad51-independent targeted integration and unveil multiple mechanisms to regulate SSA-mediated targeted as well as random integration.
Collapse
Affiliation(s)
- Shinta Saito
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan
| | - Noritaka Adachi
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan.
| |
Collapse
|
7
|
Cao X, Huang S, Wagner MM, Cho YT, Chiu DC, Wartchow KM, Lazarian A, McIntire LB, Smolka MB, Baskin JM. A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597552. [PMID: 38895347 PMCID: PMC11185714 DOI: 10.1101/2024.06.05.597552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tools for acute manipulation of protein localization enable elucidation of spatiotemporally defined functions, but their reliance on exogenous triggers can interfere with cell physiology. This limitation is particularly apparent for studying mitosis, whose highly choreographed events are sensitive to perturbations. Here we exploit the serendipitous discovery of a phosphorylation-controlled, cell cycle-dependent localization change of the adaptor protein PLEKHA5 to develop a system for mitosis-specific protein recruitment to the plasma membrane that requires no exogenous stimulus. Mitosis-enabled Anchor-away/Recruiter System (MARS) comprises an engineered, 15-kDa module derived from PLEKHA5 capable of recruiting functional protein cargoes to the plasma membrane during mitosis, either through direct fusion or via GFP-GFP nanobody interaction. Applications of MARS include both knock sideways to rapidly extract proteins from their native localizations during mitosis and conditional recruitment of lipid-metabolizing enzymes for mitosis-selective editing of plasma membrane lipid content, without the need for exogenous triggers or perturbative synchronization methods.
Collapse
Affiliation(s)
- Xiaofu Cao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Shiying Huang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Mateusz M. Wagner
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States, 14853
| | - Yuan-Ting Cho
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Din-Chi Chiu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Krista M. Wartchow
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Artur Lazarian
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Laura Beth McIntire
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Marcus B. Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States, 14853
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| |
Collapse
|
8
|
Liu Z, Tanke NT, Neal A, Yu T, Branch T, Sharma A, Cook JG, Bautch VL. Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis. Angiogenesis 2024:10.1007/s10456-024-09920-0. [PMID: 38795286 DOI: 10.1007/s10456-024-09920-0] [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: 12/21/2023] [Accepted: 04/15/2024] [Indexed: 05/27/2024]
Abstract
Cell cycle regulation is critical to blood vessel formation and function, but how the endothelial cell cycle integrates with vascular regulation is not well-understood, and available dynamic cell cycle reporters do not precisely distinguish all cell cycle stage transitions in vivo. Here we characterized a recently developed improved cell cycle reporter (PIP-FUCCI) that precisely delineates S phase and the S/G2 transition. Live image analysis of primary endothelial cells revealed predicted temporal changes and well-defined stage transitions. A new inducible mouse cell cycle reporter allele was selectively expressed in postnatal retinal endothelial cells upon Cre-mediated activation and predicted endothelial cell cycle status. We developed a semi-automated zonation program to define endothelial cell cycle status in spatially defined and developmentally distinct retinal areas and found predicted cell cycle stage differences in arteries, veins, and remodeled and angiogenic capillaries. Surprisingly, the predicted dearth of S-phase proliferative tip cells relative to stalk cells at the vascular front was accompanied by an unexpected enrichment for endothelial tip and stalk cells in G2, suggesting G2 stalling as a contribution to tip-cell arrest and dynamics at the front. Thus, this improved reporter precisely defines endothelial cell cycle status in vivo and reveals novel G2 regulation that may contribute to unique aspects of blood vessel network expansion.
Collapse
Affiliation(s)
- Ziqing Liu
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Natalie T Tanke
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC, USA
| | - Alexandra Neal
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tianji Yu
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tershona Branch
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Arya Sharma
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jean G Cook
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, USA
| | - Victoria L Bautch
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC, USA.
- McAllister Heart Institute, The University of North Carolina, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC, USA.
| |
Collapse
|
9
|
Cheraghi H, Kovács KD, Székács I, Horvath R, Szabó B. Continuous distribution of cancer cells in the cell cycle unveiled by AI-segmented imaging of 37,000 HeLa FUCCI cells. Heliyon 2024; 10:e30239. [PMID: 38707416 PMCID: PMC11066426 DOI: 10.1016/j.heliyon.2024.e30239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
Classification of live or fixed cells based on their unlabeled microscopic images would be a powerful tool for cell biology and pathology. For such software, the first step is the generation of a ground truth database that can be used for training and testing AI classification algorithms. The Application of cells expressing fluorescent reporter proteins allows the building of ground truth datasets in a straightforward way. In this study, we present an automated imaging pipeline utilizing the Cellpose algorithm for the precise cell segmentation and measurement of fluorescent cellular intensities across multiple channels. We analyzed the cell cycle of HeLa-FUCCI cells expressing fluorescent red and green reporter proteins at various levels depending on the cell cycle state. To build the dataset, 37,000 fixed cells were automatically scanned using a standard motorized microscope, capturing phase contrast and fluorescent red/green images. The fluorescent pixel intensity of each cell was integrated to calculate the total fluorescence of cells based on cell segmentation in the phase contrast channel. It resulted in a precise intensity value for each cell in both channels. Furthermore, we conducted a comparative analysis of Cellpose 1.0 and Cellpose 2.0 in cell segmentation performance. Cellpose 2.0 demonstrated notable improvements, achieving a significantly reduced false positive rate of 2.7 % and 1.4 % false negative. The cellular fluorescence was visualized in a 2D plot (map) based on the red and green intensities of the FUCCI construct revealing the continuous distribution of cells in the cell cycle. This 2D map enables the selection and potential isolation of single cells in a specific phase. In the corresponding heatmap, two clusters appeared representing cells in the red and green states. Our pipeline allows the high-throughput and accurate measurement of cellular fluorescence providing extensive statistical information on thousands of cells with potential applications in developmental and cancer biology. Furthermore, our method can be used to build ground truth datasets automatically for training and testing AI cell classification. Our automated pipeline can be used to analyze thousands of cells within 2 h after putting the sample onto the microscope.
Collapse
Affiliation(s)
- Hamid Cheraghi
- Department of Biological Physics, Eötvös University (ELTE), H-1117, Budapest, Hungary
- CellSorter Scientific Company for Innovations, Prielle Kornélia utca 4A, 1117, Budapest, Hungary
| | - Kinga Dóra Kovács
- Department of Biological Physics, Eötvös University (ELTE), H-1117, Budapest, Hungary
- Nanobiosensorics Laboratory, HUN-REN, Institute of Technical Physics and Materials Science, Centre for Energy Research, Budapest, Hungary
| | - Inna Székács
- Nanobiosensorics Laboratory, HUN-REN, Institute of Technical Physics and Materials Science, Centre for Energy Research, Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Laboratory, HUN-REN, Institute of Technical Physics and Materials Science, Centre for Energy Research, Budapest, Hungary
| | - Bálint Szabó
- Department of Biological Physics, Eötvös University (ELTE), H-1117, Budapest, Hungary
- CellSorter Scientific Company for Innovations, Prielle Kornélia utca 4A, 1117, Budapest, Hungary
| |
Collapse
|
10
|
Holtzen SE, Navid E, Kainov JD, Palmer AE. Transient Zn 2+ deficiency induces replication stress and compromises daughter cell proliferation. Proc Natl Acad Sci U S A 2024; 121:e2321216121. [PMID: 38687796 PMCID: PMC11087780 DOI: 10.1073/pnas.2321216121] [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: 12/09/2023] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S phase for timely completion of S phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is chelated during the mother cell's S phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.
Collapse
Affiliation(s)
- Samuel E. Holtzen
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO80309
| | - Elnaz Navid
- Department of Biochemistry, University of Colorado, Boulder, CO80309
| | - Joseph D. Kainov
- Department of Biochemistry, University of Colorado, Boulder, CO80309
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO80309
- BioFrontiers Institute, University of Colorado, Boulder, CO80309
| |
Collapse
|
11
|
Ganguly J, Zongming F, James M, Pan Y, Ruano J, Dahle M, Li X. Fluorescent-protein co-expression to select CHO cells expressing high quantities of vaccine antigens. Biotechnol J 2024; 19:e2300671. [PMID: 38797725 DOI: 10.1002/biot.202300671] [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: 11/27/2023] [Revised: 04/05/2024] [Accepted: 04/25/2024] [Indexed: 05/29/2024]
Abstract
Cell line development for production of vaccine antigens or therapeutic proteins typically involves transfection, selection, and enrichment for high-expressing cells. Enrichment methods include minipool enrichment, antibody-based enrichment, and enrichment based on co-expressed fluorescent biosensor proteins. However, these methods have limitations regarding labor and cost intensity, the generation of antibodies and assurance of their viral safety, and potential expression-interference or signal-saturation of the co-expressed fluorescent protein. To improve the method of fluorescent-protein co-expression, expression constructs were created that constitutively express a model vaccine antigen together with one of three fluorescent proteins having translation initiation controlled by a wildtype or mutant internal ribosome entry site (IRES), for a total of six constructs. The constructs were transfected into Chinese hamster ovary cells (CHO) cells, enriched for high fluorescence, cultured, and tested in a mini bioreactor to identify the most promising construct. The fluorescent protein, Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) with a mutant IRES performed best and was further tested with three additional vaccine antigens. Across the four vaccine antigens, the FUCCI fluorescent protein yielded productivity enhancements, without the need for generating an antibody and assuring its viral safety. Furthermore, FUCCI protein was present in negligible quantities in the cell supernatant, indicating a low risk for contaminating drug substances or vaccine antigen.
Collapse
Affiliation(s)
| | | | | | - Yan Pan
- GSK, Rockville, Maryland, USA
| | | | | | | |
Collapse
|
12
|
Omi J, Kato T, Yoshihama Y, Sawada K, Kono N, Aoki J. Phosphatidylserine synthesis controls oncogenic B cell receptor signaling in B cell lymphoma. J Cell Biol 2024; 223:e202212074. [PMID: 38048228 PMCID: PMC10694799 DOI: 10.1083/jcb.202212074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 09/13/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Cancer cells harness lipid metabolism to promote their own survival. We screened 47 cancer cell lines for survival dependency on phosphatidylserine (PS) synthesis using a PS synthase 1 (PTDSS1) inhibitor and found that B cell lymphoma is highly dependent on PS. Inhibition of PTDSS1 in B cell lymphoma cells caused a reduction of PS and phosphatidylethanolamine levels and an increase of phosphoinositide levels. The resulting imbalance of the membrane phospholipidome lowered the activation threshold for B cell receptor (BCR), a B cell-specific survival mechanism. BCR hyperactivation led to aberrant elevation of downstream Ca2+ signaling and subsequent apoptotic cell death. In a mouse xenograft model, PTDSS1 inhibition efficiently suppressed tumor growth and prolonged survival. Our findings suggest that PS synthesis may be a critical vulnerability of malignant B cell lymphomas that can be targeted pharmacologically.
Collapse
Affiliation(s)
- Jumpei Omi
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Koki Sawada
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
13
|
Liu Z, Tanke NT, Neal A, Yu T, Branch T, Cook JG, Bautch VL. Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574239. [PMID: 38249517 PMCID: PMC10798646 DOI: 10.1101/2024.01.04.574239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Cell cycle regulation is critical to blood vessel formation and function, but how the endothelial cell cycle integrates with vascular regulation is not well-understood, and available dynamic cell cycle reporters do not precisely distinguish all cell cycle stage transitions in vivo. Here we characterized a recently developed improved cell cycle reporter (PIP-FUCCI) that precisely delineates S phase and the S/G2 transition. Live image analysis of primary endothelial cells revealed predicted temporal changes and well-defined stage transitions. A new inducible mouse cell cycle reporter allele was selectively expressed in postnatal retinal endothelial cells upon Cre-mediated activation and predicted endothelial cell cycle status. We developed a semi-automated zonation program to define endothelial cell cycle status in spatially defined and developmentally distinct retinal areas and found predicted cell cycle stage differences in arteries, veins, and remodeled and angiogenic capillaries. Surprisingly, the predicted dearth of proliferative tip cells at the vascular front was accompanied by an unexpected enrichment for endothelial tip cells in G2, suggesting G2 stalling as a contribution to tip-cell arrest. Thus, this improved reporter precisely defines endothelial cell cycle status in vivo and reveals novel G2 regulation that may contribute to unique aspects of blood vessel network expansion.
Collapse
Affiliation(s)
- Ziqing Liu
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Natalie T Tanke
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC USA
| | - Alexandra Neal
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Tianji Yu
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Tershona Branch
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Jean G Cook
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC USA
| | - Victoria L Bautch
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC USA
- McAllister Heart Institute, The University of North Carolina, Chapel Hill, NC USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC USA
| |
Collapse
|
14
|
Yang HW. Investigating Heterogeneous Cell-Cycle Progression Using Single-Cell Imaging Approaches. Methods Mol Biol 2024; 2740:263-273. [PMID: 38393481 DOI: 10.1007/978-1-0716-3557-5_16] [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] [Indexed: 02/25/2024]
Abstract
Investigating cell-cycle progression has been challenging due to the complex interconnectivity of regulatory processes and inherent cell-to-cell heterogeneity, which often require synchronization procedures. However, recent advancements in cell-cycle sensors and single-cell imaging techniques have turned this heterogeneity into an advantage for investigating the molecular mechanisms underlying diverse responses. This has led to significant progress in our understanding of cell-cycle regulation. In this paper, we present a comprehensive live single-cell imaging workflow that leverages cutting-edge live-cell sensors. These advanced single-cell imaging procedures provide promising opportunities for elucidating the molecular mechanisms underpinnings of heterogeneous responses in cell-cycle progression.
Collapse
Affiliation(s)
- Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
15
|
Seino R, Uno H, Prise KM, Fukunaga H. Cell cycle dependence of cell survival following exposure to X-rays in synchronous HeLa cells expressing fluorescent ubiquitination-based cell cycle indicators. Biomed Res 2024; 45:25-31. [PMID: 38325843 DOI: 10.2220/biomedres.45.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The cell cycle dependence of radiosensitivity has yet to be fully determined, as it is technically difficult to achieve a high degree of cell cycle synchronization in cultured cell systems and accurately detect the cell cycle phase of individual cells simultaneously. We used human cervical carcinoma HeLa cells expressing fluorescent ubiquitination-based cell cycle indicators (FUCCI), and employed the mitotic harvesting method that is one of the cell cycle synchronization methods. The imaging analysis confirmed that the cell cycle is highly synchronized after mitotic cell harvesting until 18-20 h of the doubling time has elapsed. Also, flow cytometry analysis revealed that the S and G2 phases peak at approximately 12 and 14-16 h, respectively, after mitotic harvesting. In addition, the clonogenic assay showed the changes in surviving fractions following exposure to X-rays according to the progress through the cell cycle. These results indicate that HeLa-FUCCI cells become radioresistant in the G1 phase, become radiosensitive in the early S phase, rapidly become radioresistant in the late S phase, and become radiosensitive again in the G2 phase. Our findings may contribute to the further development of combinations of radiation and cell cycle-specific anticancer agents.
Collapse
Affiliation(s)
- Ryosuke Seino
- Graduate School of Health Sciences, Hokkaido University
| | - Hiroto Uno
- Department of Health Sciences, School of Medicine, Hokkaido University
| | - Kevin M Prise
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast
| | - Hisanori Fukunaga
- Department of Biomedical Engineering and Science, Faculty of Health Sciences, Hokkaido University
| |
Collapse
|
16
|
Holtzen SE, Navid E, Kainov JD, Palmer AE. Transient Zn 2+ deficiency induces replication stress and compromises daughter cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570860. [PMID: 38106081 PMCID: PMC10723434 DOI: 10.1101/2023.12.08.570860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S-phase for timely completion of S-phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is removed during the mother cell's S-phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S-phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.
Collapse
Affiliation(s)
- Samuel E. Holtzen
- Department of Molecular Cellular and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Elnaz Navid
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Joseph D. Kainov
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, 80309
| |
Collapse
|
17
|
Qian Y, Celiker OT, Wang Z, Guner-Ataman B, Boyden ES. Temporally multiplexed imaging of dynamic signaling networks in living cells. Cell 2023; 186:5656-5672.e21. [PMID: 38029746 PMCID: PMC10843875 DOI: 10.1016/j.cell.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/30/2023] [Accepted: 11/05/2023] [Indexed: 12/01/2023]
Abstract
Molecular signals interact in networks to mediate biological processes. To analyze these networks, it would be useful to image many signals at once, in the same living cell, using standard microscopes and genetically encoded fluorescent reporters. Here, we report temporally multiplexed imaging (TMI), which uses genetically encoded fluorescent proteins with different clocklike properties-such as reversibly photoswitchable fluorescent proteins with different switching kinetics-to represent different cellular signals. We linearly decompose a brief (few-second-long) trace of the fluorescence fluctuations, at each point in a cell, into a weighted sum of the traces exhibited by each fluorophore expressed in the cell. The weights then represent the signal amplitudes. We use TMI to analyze relationships between different kinase activities in individual cells, as well as between different cell-cycle signals, pointing toward broad utility throughout biology in the analysis of signal transduction cascades in living systems.
Collapse
Affiliation(s)
- Yong Qian
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA
| | - Orhan T Celiker
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 01239, USA
| | - Zeguan Wang
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA; Department of Media Arts and Sciences, MIT, Cambridge, MA 01239, USA
| | - Burcu Guner-Ataman
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA
| | - Edward S Boyden
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 01239, USA; Department of Media Arts and Sciences, MIT, Cambridge, MA 01239, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 01239, USA; Department of Biological Engineering, MIT, Cambridge, MA 01239, USA; Koch Institute, MIT, Cambridge, MA 01239, USA; Howard Hughes Medical Institute, Cambridge, MA 01239, USA; Center for Neurobiological Engineering and K. Lisa Yang Center for Bionics at MIT, Cambridge, MA 01239, USA.
| |
Collapse
|
18
|
Zhang M, Kim S, Yang HW. Non-canonical pathway for Rb inactivation and external signaling coordinate cell-cycle entry without CDK4/6 activity. Nat Commun 2023; 14:7847. [PMID: 38030655 PMCID: PMC10687137 DOI: 10.1038/s41467-023-43716-y] [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: 05/17/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
Cyclin-dependent kinases 4 and 6 (CDK4/6) are critical for initiating cell proliferation by inactivating the retinoblastoma (Rb) protein. However, mammalian cells can bypass CDK4/6 for Rb inactivation. Here we show a non-canonical pathway for Rb inactivation and its interplay with external signals. We find that the non-phosphorylated Rb protein in quiescent cells is intrinsically unstable, offering an alternative mechanism for initiating E2F activity. Nevertheless, this pathway incompletely induces Rb-protein loss, resulting in minimal E2F activity. To trigger cell proliferation, upregulation of mitogenic signaling is required for stabilizing c-Myc, thereby augmenting E2F activity. Concurrently, stress signaling promotes Cip/Kip levels, competitively regulating cell proliferation with mitogenic signaling. In cancer, driver mutations elevate c-Myc levels, facilitating adaptation to CDK4/6 inhibitors. Differentiated cells, despite Rb-protein loss, maintain quiescence through the modulation of c-Myc and Cip/Kip levels. Our findings provide mechanistic insights into an alternative model of cell-cycle entry and the maintenance of quiescence.
Collapse
Affiliation(s)
- Mimi Zhang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Sungsoo Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
| |
Collapse
|
19
|
Kim S, Armand J, Safonov A, Zhang M, Soni RK, Schwartz G, McGuinness JE, Hibshoosh H, Razavi P, Kim M, Chandarlapaty S, Yang HW. Sequential activation of E2F via Rb degradation and c-Myc drives resistance to CDK4/6 inhibitors in breast cancer. Cell Rep 2023; 42:113198. [PMID: 37865915 PMCID: PMC10757862 DOI: 10.1016/j.celrep.2023.113198] [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: 01/23/2023] [Revised: 06/27/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i) are key therapeutic agents in the management of metastatic hormone-receptor-positive breast cancer. However, the emergence of drug resistance limits their long-term efficacy. Here, we show that breast cancer cells develop CDK4/6i resistance via a sequential two-step process of E2F activation. This process entails retinoblastoma (Rb)-protein degradation, followed by c-Myc-mediated amplification of E2F transcriptional activity. CDK4/6i treatment halts cell proliferation in an Rb-dependent manner but dramatically reduces Rb-protein levels. However, this reduction in Rb levels insufficiently induces E2F activity. To develop CDK4/6i resistance, upregulation or activating mutations in mitogenic or hormone signaling are required to stabilize c-Myc levels, thereby augmenting E2F activity. Our analysis of pre-treatment tumor samples reveals a strong correlation between c-Myc levels, rather than Rb levels, and poor therapeutic outcomes after CDK4/6i treatment. Moreover, we propose that proteasome inhibitors can potentially reverse CDK4/6i resistance by restoring Rb levels.
Collapse
Affiliation(s)
- Sungsoo Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Jessica Armand
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Anton Safonov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Mimi Zhang
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Rajesh K Soni
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Gary Schwartz
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Julia E McGuinness
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
| | - Minah Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
20
|
Cossard A, Stam K, Smets A, Jossin Y. MKL/SRF and Bcl6 mutual transcriptional repression safeguards the fate and positioning of neocortical progenitor cells mediated by RhoA. SCIENCE ADVANCES 2023; 9:eadd0676. [PMID: 37967194 PMCID: PMC10651131 DOI: 10.1126/sciadv.add0676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
During embryogenesis, multiple intricate and intertwined cellular signaling pathways coordinate cell behavior. Their slightest alterations can have dramatic consequences for the cells and the organs they form. The transcriptional repressor Bcl6 was recently found as important for brain development. However, its regulation and integration with other signals is unknown. Using in vivo functional approaches combined with molecular mechanistic analysis, we identified a reciprocal regulatory loop between B cell lymphoma 6 (Bcl6) and the RhoA-regulated transcriptional complex megakaryoblastic leukemia/serum response factor (MKL/SRF). We show that Bcl6 physically interacts with MKL/SRF, resulting in a down-regulation of the transcriptional activity of both Bcl6 and MKL/SRF. This molecular cross-talk is essential for the control of proliferation, neurogenesis, and spatial positioning of neural progenitors. Overall, our data highlight a regulatory mechanism that controls neuronal production and neocortical development and reveal an MKL/SRF and Bcl6 interaction that may have broader implications in other physiological functions and in diseases.
Collapse
Affiliation(s)
- Alexia Cossard
- Laboratory of Mammalian Development and Cell Biology, Institute of Neuroscience, Université Catholique de Louvain, Brussels 1200, Belgium
| | | | | | | |
Collapse
|
21
|
Knoblochova L, Duricek T, Vaskovicova M, Zorzompokou C, Rayova D, Ferencova I, Baran V, Schultz RM, Hoffmann ER, Drutovic D. CHK1-CDC25A-CDK1 regulate cell cycle progression and protect genome integrity in early mouse embryos. EMBO Rep 2023; 24:e56530. [PMID: 37694680 PMCID: PMC10561370 DOI: 10.15252/embr.202256530] [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: 11/23/2022] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
After fertilization, remodeling of the oocyte and sperm genomes is essential to convert these highly differentiated and transcriptionally quiescent cells into early cleavage-stage blastomeres that are transcriptionally active and totipotent. This developmental transition is accompanied by cell cycle adaptation, such as lengthening or shortening of the gap phases G1 and G2. However, regulation of these cell cycle changes is poorly understood, especially in mammals. Checkpoint kinase 1 (CHK1) is a protein kinase that regulates cell cycle progression in somatic cells. Here, we show that CHK1 regulates cell cycle progression in early mouse embryos by restraining CDK1 kinase activity due to CDC25A phosphatase degradation. CHK1 kinase also ensures the long G2 phase needed for genome activation and reprogramming gene expression in two-cell stage mouse embryos. Finally, Chk1 depletion leads to DNA damage and chromosome segregation errors that result in aneuploidy and infertility.
Collapse
Affiliation(s)
- Lucie Knoblochova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomas Duricek
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Michaela Vaskovicova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Chrysoula Zorzompokou
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Diana Rayova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Ivana Ferencova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Vladimir Baran
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of SciencesKosiceSlovakia
| | - Richard M Schultz
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCAUSA
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - David Drutovic
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| |
Collapse
|
22
|
Matsuura T, Ueda Y, Harada Y, Hayashi K, Horisaka K, Yano Y, So S, Kido M, Fukumoto T, Kodama Y, Hara E, Matsumoto T. Histological diagnosis of polyploidy discriminates an aggressive subset of hepatocellular carcinomas with poor prognosis. Br J Cancer 2023; 129:1251-1260. [PMID: 37715023 PMCID: PMC10576083 DOI: 10.1038/s41416-023-02408-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Although genome duplication, or polyploidization, is believed to drive cancer evolution and affect tumor features, its significance in hepatocellular carcinoma (HCC) is unclear. We aimed to determine the characteristics of polyploid HCCs by evaluating chromosome duplication and to discover surrogate markers to discriminate polyploid HCCs. METHODS The ploidy in human HCC was assessed by fluorescence in situ hybridization for multiple chromosomes. Clinicopathological and expression features were compared between polyploid and near-diploid HCCs. Markers indicating polyploid HCC were explored by transcriptome analysis of cultured HCC cells. RESULTS Polyploidy was detected in 36% (20/56) of HCCs and discriminated an aggressive subset of HCC that typically showed high serum alpha-fetoprotein, poor differentiation, and poor prognosis compared to near-diploid HCCs. Molecular subtyping revealed that polyploid HCCs highly expressed alpha-fetoprotein but did not necessarily show progenitor features. Histological examination revealed abundant polyploid giant cancer cells (PGCCs) with a distinct appearance and frequent macrotrabecular-massive architecture in polyploid HCCs. Notably, the abundance of PGCCs and overexpression of ubiquitin-conjugating enzymes 2C indicated polyploidy in HCC and efficiently predicted poor prognosis in combination. CONCLUSIONS Histological diagnosis of polyploidy using surrogate markers discriminates an aggressive subset of HCC, apart from known HCC subgroups, and predict poor prognosis in HCC.
Collapse
Affiliation(s)
- Takanori Matsuura
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoshihide Ueda
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoshiyuki Harada
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazuki Hayashi
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kisara Horisaka
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yoshihiko Yano
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinichi So
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masahiro Kido
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takumi Fukumoto
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuzo Kodama
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Eiji Hara
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Tomonori Matsumoto
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
| |
Collapse
|
23
|
Capece M, Tessari A, Mills J, Vinciguerra GLR, Louke D, Lin C, McElwain BK, Miles WO, Coppola V, Davies AE, Palmieri D, Croce CM. A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis. Cell Death Differ 2023; 30:2078-2091. [PMID: 37537305 PMCID: PMC10482871 DOI: 10.1038/s41418-023-01191-4] [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: 11/22/2022] [Revised: 06/02/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
The discrimination of protein biological functions in different phases of the cell cycle is limited by the lack of experimental approaches that do not require pre-treatment with compounds affecting the cell cycle progression. Therefore, potential cycle-specific biological functions of a protein of interest could be biased by the effects of cell treatments. The OsTIR1/auxin-inducible degron (AID) system allows "on demand" selective and reversible protein degradation upon exposure to the phytohormone auxin. In the current format, this technology does not allow to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespectively of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population, as with previously available approaches. Here, we introduce a new AID system to Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS system), which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. We validated the ROLECCS technology by down regulating the protein levels of TP53, one of the most studied tumor suppressor genes, with a widely known role in cell cycle progression. By using our novel tool, we observed that TP53 degradation is associated with increased number of micronuclei, and this phenotype is specifically achieved when TP53 is lost in S/G2/M phases of the cell cycle, but not in G1. Therefore, we propose the use of the ROLECCS system as a new improved way of studying the differential roles that target proteins may have in specific phases of the cell cycle.
Collapse
Affiliation(s)
- Marina Capece
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Anna Tessari
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Joseph Mills
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Darian Louke
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Bryan K McElwain
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Alexander E Davies
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
- Gene Editing Shared Resource, The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
| |
Collapse
|
24
|
Salim A, Werther P, Hatzopoulos GN, Reymond L, Wombacher R, Gönczy P, Johnsson K. Chemical Probe for Imaging of Polo-like Kinase 4 and Centrioles. JACS AU 2023; 3:2247-2256. [PMID: 37654580 PMCID: PMC10466336 DOI: 10.1021/jacsau.3c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Polo-like kinase (Plk4) is a serine/threonine-protein kinase that is essential for biogenesis of the centriole organelle and is enriched at centrioles. Herein, we introduce Cen-TCO, a chemical probe based on the Plk4 inhibitor centrinone, to image Plk4 and centrioles in live or fixed cultured human cells. Specifically, we established a bio-orthogonal two-step labeling system that enables the Cen-TCO-mediated imaging of Plk4 by STED super-resolution microscopy. Such direct labeling of Plk4 results in an increased resolution in STED imaging compared with using anti-Plk4 antibodies, underlining the importance of direct labeling strategies for super-resolution microscopy. We anticipate that Cen-TCO will become an important tool for investigating the biology of Plk4 and of centrioles.
Collapse
Affiliation(s)
- Aleksandar Salim
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Philipp Werther
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Georgios N. Hatzopoulos
- Swiss
Institute for Experimental Cancer Research (ISREC), School of Life
Sciences, Swiss Federal Institute of Technology
Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Luc Reymond
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Richard Wombacher
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Pierre Gönczy
- Swiss
Institute for Experimental Cancer Research (ISREC), School of Life
Sciences, Swiss Federal Institute of Technology
Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| |
Collapse
|
25
|
Marrocco I, Giri S, Simoni-Nieves A, Gupta N, Rudnitsky A, Haga Y, Romaniello D, Sekar A, Zerbib M, Oren R, Lindzen M, Fard D, Tsutsumi Y, Lauriola M, Tamagnone L, Yarden Y. L858R emerges as a potential biomarker predicting response of lung cancer models to anti-EGFR antibodies: Comparison of osimertinib vs. cetuximab. Cell Rep Med 2023; 4:101142. [PMID: 37557179 PMCID: PMC10439256 DOI: 10.1016/j.xcrm.2023.101142] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/21/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
EGFR-specific tyrosine kinase inhibitors (TKIs), especially osimertinib, have changed lung cancer therapy, but secondary mutations confer drug resistance. Because other EGFR mutations promote dimerization-independent active conformations but L858R strictly depends on receptor dimerization, we herein evaluate the therapeutic potential of dimerization-inhibitory monoclonal antibodies (mAbs), including cetuximab. This mAb reduces viability of cells expressing L858R-EGFR and blocks the FOXM1-aurora survival pathway, but other mutants show no responses. Unlike TKI-treated patient-derived xenografts, which relapse post osimertinib treatment, cetuximab completely prevents relapses of L858R+ tumors. We report that osimertinib's inferiority associates with induction of mutagenic reactive oxygen species, whereas cetuximab's superiority is due to downregulation of adaptive survival pathways (e.g., HER2) and avoidance of mutation-prone mechanisms that engage AXL, RAD18, and the proliferating cell nuclear antigen. These results identify L858R as a predictive biomarker, which may pave the way for relapse-free mAb monotherapy relevant to a large fraction of patients with lung cancer.
Collapse
Affiliation(s)
- Ilaria Marrocco
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Suvendu Giri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Arturo Simoni-Nieves
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nitin Gupta
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anna Rudnitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuya Haga
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Donatella Romaniello
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Arunachalam Sekar
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mirie Zerbib
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshit Lindzen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Damon Fard
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Luca Tamagnone
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Gemelli - IRCCS, 00168 Rome, Italy
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
26
|
Ando R, Sakaue-Sawano A, Shoda K, Miyawaki A. Two coral fluorescent proteins of distinct colors for sharp visualization of cell-cycle progression. Cell Struct Funct 2023; 48:135-144. [PMID: 37394513 PMCID: PMC10958192 DOI: 10.1247/csf.23028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023] Open
Abstract
We cloned and characterized two new coral fluorescent proteins: h2-3 and 1-41. h2-3 formed an obligate dimeric complex and exhibited bright green fluorescence. On the other hand, 1-41 formed a highly multimeric complex and exhibited dim red fluorescence. We engineered 1-41 into AzaleaB5, a practically useful red-emitting fluorescent protein for cellular labeling applications. We fused h2-3 and AzaleaB5 to the ubiquitination domains of human Geminin and Cdt1, respectively, to generate a new color variant of Fucci (Fluorescent Ubiquitination-based Cell-Cycle Indicator): Fucci5. We found Fucci5 provided more reliable nuclear labeling for monitoring cell-cycle progression than the 1st and 2nd generations that used mAG/mKO2 and mVenus/mCherry, respectively.Key words: fluorescent protein, cell cycle, time-lapse imaging, flow cytometry.
Collapse
Affiliation(s)
- Ryoko Ando
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Asako Sakaue-Sawano
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
- Department of Optical Biomedical Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Keiko Shoda
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
- Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
- Laboratory of Bioresponse Analysis, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| |
Collapse
|
27
|
Harada Y, Mizote Y, Suzuki T, Hirayama A, Ikeda S, Nishida M, Hiratsuka T, Ueda A, Imagawa Y, Maeda K, Ohkawa Y, Murai J, Freeze HH, Miyoshi E, Higashiyama S, Udono H, Dohmae N, Tahara H, Taniguchi N. Metabolic clogging of mannose triggers dNTP loss and genomic instability in human cancer cells. eLife 2023; 12:e83870. [PMID: 37461317 DOI: 10.7554/elife.83870] [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: 09/30/2022] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Mannose has anticancer activity that inhibits cell proliferation and enhances the efficacy of chemotherapy. How mannose exerts its anticancer activity, however, remains poorly understood. Here, using genetically engineered human cancer cells that permit the precise control of mannose metabolic flux, we demonstrate that the large influx of mannose exceeding its metabolic capacity induced metabolic remodeling, leading to the generation of slow-cycling cells with limited deoxyribonucleoside triphosphates (dNTPs). This metabolic remodeling impaired dormant origin firing required to rescue stalled forks by cisplatin, thus exacerbating replication stress. Importantly, pharmacological inhibition of de novo dNTP biosynthesis was sufficient to retard cell cycle progression, sensitize cells to cisplatin, and inhibit dormant origin firing, suggesting dNTP loss-induced genomic instability as a central mechanism for the anticancer activity of mannose.
Collapse
Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yu Mizote
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Mikako Nishida
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toru Hiratsuka
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Ayaka Ueda
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yusuke Imagawa
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Kento Maeda
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeki Higashiyama
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Hideaki Tahara
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Project Division of Cancer Biomolecular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| |
Collapse
|
28
|
Hammond T, Sage J. Monitoring the Cell Cycle of Tumor Cells in Mouse Models of Human Cancer. Cold Spring Harb Perspect Med 2023; 13:a041383. [PMID: 37460156 PMCID: PMC10691483 DOI: 10.1101/cshperspect.a041383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Cell division is obligatory to tumor growth. However, both cancer cells and noncancer cells in tumors can be found in distinct stages of the cell cycle, which may inform the growth potential of these tumors, their propensity to metastasize, and their response to therapy. Hence, it is of utmost importance to monitor the cell cycle of tumor cells. Here we discuss well-established methods and new genetic advances to track the cell cycle of tumor cells in mouse models of human cancer. We also review recent genetic studies investigating the role of the cell-cycle machinery in the growth of tumors in vivo, with a focus on the machinery regulating the G1/S transition of the cell cycle.
Collapse
Affiliation(s)
- Taylar Hammond
- Department of Pediatrics, Stanford University, Stanford, California 94305, USA
- Department of Biology, and Stanford University, Stanford, California 94305, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
29
|
Kamikawa Y, Wu Z, Nakazawa N, Ito T, Saito A, Imaizumi K. Impact of cell cycle on repair of ruptured nuclear envelope and sensitivity to nuclear envelope stress in glioblastoma. Cell Death Discov 2023; 9:233. [PMID: 37422516 DOI: 10.1038/s41420-023-01534-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
The nuclear envelope (NE) is often challenged by various stresses (known as "NE stress"), leading to its dysfunction. Accumulating evidence has proven the pathological relevance of NE stress in numerous diseases ranging from cancer to neurodegenerative diseases. Although several proteins involved in the reassembly of the NE after mitosis have been identified as the NE repair factors, the regulatory mechanisms modulating the efficiency of NE repair remain unclear. Here, we showed that response to NE stress varied among different types of cancer cell lines. U251MG derived from glioblastoma exhibited severe nuclear deformation and massive DNA damage at the deformed nuclear region upon mechanical NE stress. In contrast, another cell line derived from glioblastoma, U87MG, only presented mild nuclear deformation without DNA damage. Time-lapse imaging demonstrated that repairing of ruptured NE often failed in U251MG, but not in U87MG. These differences were unlikely to have been due to weakened NE in U251MG because the expression levels of lamin A/C, determinants of the physical property of the NE, were comparable and loss of compartmentalization across the NE was observed just after laser ablation of the NE in both cell lines. U251MG proliferated more rapidly than U87MG concomitant with reduced expression of p21, a major inhibitor of cyclin-dependent kinases, suggesting a correlation between NE stress response and cell cycle progression. Indeed, visualization of cell cycle stages using fluorescent ubiquitination-based cell cycle indicator reporters revealed greater resistance of U251MG to NE stress at G1 phase than at S and G2 phases. Furthermore, attenuation of cell cycle progression by inducing p21 in U251MG counteracted the nuclear deformation and DNA damage upon NE stress. These findings imply that dysregulation of cell cycle progression in cancer cells causes loss of the NE integrity and its consequences such as DNA damage and cell death upon mechanical NE stress.
Collapse
Affiliation(s)
- Yasunao Kamikawa
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
| | - Zuqian Wu
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Nayuta Nakazawa
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Taichi Ito
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Atsushi Saito
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
| |
Collapse
|
30
|
She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA. Comparative landscape of genetic dependencies in human and chimpanzee stem cells. Cell 2023; 186:2977-2994.e23. [PMID: 37343560 PMCID: PMC10461406 DOI: 10.1016/j.cell.2023.05.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/14/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether human cells exhibit distinct genetic dependencies. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell-cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells and cerebral organoids, supporting the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells reshaped the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.
Collapse
Affiliation(s)
- Richard She
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan K Schaefer
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute Technology, Cambridge, MA 02142, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
31
|
Divan A, Alzahrani A, Shaik F, Mitchell J, Harrison MA, Odell A, Ponnambalam S. A research-led flexible cell biology practical for biological sciences undergraduate and postgraduate degree courses. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:394-401. [PMID: 37022101 DOI: 10.1002/bmb.21735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 03/06/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
A challenge in the pandemic era is to implement effective but flexible practical teaching for biological sciences courses. Such teaching needs to deliver conceptual, analytical and practical skills training while having the option to rapidly respond to health and safety issues, local regulations, staff and student concerns. In this paper, we describe a set of cell biology practicals (mini-project) that meets many of these requirements and provides flexibility in providing skills training both through online and in practical laboratory environments. We have used a human adenocarcinoma cell line A431 stably transfected with a fluorescent cell cycle reporter as a biological model to deliver training through discrete work packages encompassing cell culture, fluorescence microscopy, biochemistry and statistics. How such work packages can be modified to, an online format either partially or completely is also described. Furthermore, the activities can be adapted for teaching both undergraduate and postgraduate level courses to ensure effective skills training which is applicable to a wide range of biological degree programs and levels of study.
Collapse
Affiliation(s)
- Aysha Divan
- School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Areej Alzahrani
- School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Faheem Shaik
- School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Joanna Mitchell
- School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Adam Odell
- School of Biomedical Sciences, York St. John University, York, UK
| | | |
Collapse
|
32
|
Maeda Y, Isomura A, Masaki T, Kageyama R. Differential cell-cycle control by oscillatory versus sustained Hes1 expression via p21. Cell Rep 2023; 42:112520. [PMID: 37200191 DOI: 10.1016/j.celrep.2023.112520] [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: 06/23/2022] [Revised: 01/06/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023] Open
Abstract
Oscillatory Hes1 expression activates cell proliferation, while high and sustained Hes1 expression induces quiescence, but the mechanism by which Hes1 differentially controls cell proliferation depending on its expression dynamics is unclear. Here, we show that oscillatory Hes1 expression down-regulates the expression of the cyclin-dependent kinase inhibitor p21 (Cdkn1a), which delays cell-cycle progression, and thereby activates the proliferation of mouse neural stem cells (NSCs). By contrast, sustained Hes1 overexpression up-regulates p21 expression and inhibits NSC proliferation, although it initially down-regulates p21 expression. Compared with Hes1 oscillation, sustained Hes1 overexpression represses Dusp7, a phosphatase for phosphorylated Erk (p-Erk), and increases the levels of p-Erk, which can up-regulate p21 expression. These results indicate that p21 expression is directly repressed by oscillatory Hes1 expression, but indirectly up-regulated by sustained Hes1 overexpression, suggesting that depending on its expression dynamics, Hes1 differentially controls NSC proliferation via p21.
Collapse
Affiliation(s)
- Yuki Maeda
- RIKEN Center for Brain Science, Wako 351-0198, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Akihiro Isomura
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan; Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
| | - Taimu Masaki
- RIKEN Center for Brain Science, Wako 351-0198, Japan
| | - Ryoichiro Kageyama
- RIKEN Center for Brain Science, Wako 351-0198, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
| |
Collapse
|
33
|
Lebrec V, Gavet O. Monitoring Chk1 kinase activity dynamics in live single cell imaging assays. Methods Cell Biol 2023; 182:221-236. [PMID: 38359979 DOI: 10.1016/bs.mcb.2022.12.018] [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] [Indexed: 02/16/2023]
Abstract
The ATR/Chk1 pathway is an important regulator of cell cycle progression, notably upon genotoxic stress where it can detect a large variety of DNA alterations and induce a transient cell cycle arrest that promotes DNA repair. In addition to its role in DNA damage response (DDR), Chk1 is also active during a non-perturbed S phase and contributes to prevent a premature entry into mitosis with an incompletely replicated genome, meaning the ATR/Chk1 pathway is an integral part of the cell cycle machinery that preserves genome integrity during cell growth. We recently developed a FRET-based Chk1 kinase activity reporter to directly monitor and quantify the kinetics of Chk1 activation in live single cell imaging assays with unprecedented sensitivity and time resolution. This tool allowed us to monitor Chk1 activity dynamics over time during a normal S phase and following genotoxic stress, and to elucidate the underlying mechanisms leading to its activation. Here, we review available fluorescent tools to study the interplay of cell cycle progression, DNA damage and DDR in individual live cells, and present the full protocol and image analysis pipeline to monitor Chk1 activity in two imaging assays.
Collapse
Affiliation(s)
- Vivianne Lebrec
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Olivier Gavet
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR927, Paris, France; UMR9019 CNRS, Université Paris-Saclay, Villejuif, Cedex, France.
| |
Collapse
|
34
|
Cyclin E-induced replicative stress drives p53-dependent whole-genome duplication. Cell 2023; 186:528-542.e14. [PMID: 36681079 DOI: 10.1016/j.cell.2022.12.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 11/08/2022] [Accepted: 12/20/2022] [Indexed: 01/22/2023]
Abstract
Whole-genome duplication (WGD) is a frequent event in cancer evolution and an important driver of aneuploidy. The role of the p53 tumor suppressor in WGD has been enigmatic: p53 can block the proliferation of tetraploid cells, acting as a barrier to WGD, but can also promote mitotic bypass, a key step in WGD via endoreduplication. In wild-type (WT) p53 tumors, WGD is frequently associated with activation of the E2F pathway, especially amplification of CCNE1, encoding cyclin E1. Here, we show that elevated cyclin E1 expression causes replicative stress, which activates ATR- and Chk1-dependent G2 phase arrest. p53, via its downstream target p21, together with Wee1, then inhibits mitotic cyclin-dependent kinase activity sufficiently to activate APC/CCdh1 and promote mitotic bypass. Cyclin E expression suppresses p53-dependent senescence after mitotic bypass, allowing cells to complete endoreduplication. Our results indicate that p53 can contribute to cancer evolution through the promotion of WGD.
Collapse
|
35
|
Downregulation of CDC25C in NPCs Disturbed Cortical Neurogenesis. Int J Mol Sci 2023; 24:ijms24021505. [PMID: 36675024 PMCID: PMC9863197 DOI: 10.3390/ijms24021505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Cell division regulators play a vital role in neural progenitor cell (NPC) proliferation and differentiation. Cell division cycle 25C (CDC25C) is a member of the CDC25 family of phosphatases which positively regulate cell division by activating cyclin-dependent protein kinases (CDKs). However, mice with the Cdc25c gene knocked out were shown to be viable and lacked the apparent phenotype due to genetic compensation by Cdc25a and/or Cdc25b. Here, we investigate the function of Cdc25c in developing rat brains by knocking down Cdc25c in NPCs using in utero electroporation. Our results indicate that Cdc25c plays an essential role in maintaining the proliferative state of NPCs during cortical development. The knockdown of Cdc25c causes early cell cycle exit and the premature differentiation of NPCs. Our study uncovers a novel role of CDC25C in NPC division and cell fate determination. In addition, our study presents a functional approach to studying the role of genes, which elicit genetic compensation with knockout, in cortical neurogenesis by knocking down in vivo.
Collapse
|
36
|
Ratnayeke N, Baris Y, Chung M, Yeeles JTP, Meyer T. CDT1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis. Mol Cell 2023; 83:26-42.e13. [PMID: 36608667 DOI: 10.1016/j.molcel.2022.12.004] [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: 07/12/2022] [Revised: 09/16/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023]
Abstract
Human cells license tens of thousands of origins of replication in G1 and then must stop all licensing before DNA synthesis in S phase to prevent re-replication and genome instability that ensue when an origin is licensed on replicated DNA. However, the E3 ubiquitin ligase CRL4Cdt2 only starts to degrade the licensing factor CDT1 after origin firing, raising the question of how cells prevent re-replication before CDT1 is fully degraded. Here, using quantitative microscopy and in-vitro-reconstituted human DNA replication, we show that CDT1 inhibits DNA synthesis during an overlap period when CDT1 is still present after origin firing. CDT1 inhibits DNA synthesis by suppressing CMG helicase at replication forks, and DNA synthesis commences once CDT1 is degraded. Thus, in contrast to the prevailing model that human cells prevent re-replication by strictly separating licensing from firing, licensing and firing overlap, and cells instead separate licensing from DNA synthesis.
Collapse
Affiliation(s)
- Nalin Ratnayeke
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Yasemin Baris
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph T P Yeeles
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA.
| |
Collapse
|
37
|
Humbert S, Barnat M. Huntington's disease and brain development. C R Biol 2022; 345:77-90. [PMID: 36847466 DOI: 10.5802/crbiol.93] [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: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Huntington's disease is a rare inherited neurological disorder that generally manifests in mild-adulthood. The disease is characterized by the dysfunction and the degeneration of specific brain structures leading progressively to psychiatric, cognitive and motor disorders. The disease is caused by a mutation in the gene coding for huntingtin and, although it appears in adulthood, embryos carry the mutated gene from their development in utero. Studies based on mouse models and human stem cells have reported altered developmental mechanisms in disease conditions. However, does the mutation affect development in humans? Focusing on the early stages of brain development in human fetuses carrying the HD mutation, we have identified abnormalities in the development of the neocortex, the structure that ensure higher cerebral functions. Altogether, these studies suggests that developmental defects could contribute to the onset symptoms in adults, changing the perspective on disease and thus the health care of patients.
Collapse
|
38
|
Airik M, Phua YL, Huynh AB, McCourt BT, Rush BM, Tan RJ, Vockley J, Murray SL, Dorman A, Conlon PJ, Airik R. Persistent DNA damage underlies tubular cell polyploidization and progression to chronic kidney disease in kidneys deficient in the DNA repair protein FAN1. Kidney Int 2022; 102:1042-1056. [PMID: 35931300 PMCID: PMC9588672 DOI: 10.1016/j.kint.2022.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 12/14/2022]
Abstract
Defective DNA repair pathways contribute to the development of chronic kidney disease (CKD) in humans. However, the molecular mechanisms underlying DNA damage-induced CKD pathogenesis are not well understood. Here, we investigated the role of tubular cell DNA damage in the pathogenesis of CKD using mice in which the DNA repair protein Fan1 was knocked out. The phenotype of these mice is orthologous to the human DNA damage syndrome, karyomegalic interstitial nephritis (KIN). Inactivation of Fan1 in kidney proximal tubule cells sensitized the kidneys to genotoxic and obstructive injury characterized by replication stress and persistent DNA damage response activity. Accumulation of DNA damage in Fan1 tubular cells induced epithelial dedifferentiation and tubular injury. Characteristic to KIN, cells with chronic DNA damage failed to complete mitosis and underwent polyploidization. In vitro and in vivo studies showed that polyploidization was caused by the overexpression of DNA replication factors CDT1 and CDC6 in FAN1 deficient cells. Mechanistically, inhibiting DNA replication with Roscovitine reduced tubular injury, blocked the development of KIN and mitigated kidney function in these Fan1 knockout mice. Thus, our data delineate a mechanistic pathway by which persistent DNA damage in the kidney tubular cells leads to kidney injury and development of CKD. Furthermore, therapeutic modulation of cell cycle activity may provide an opportunity to mitigate the DNA damage response induced CKD progression.
Collapse
Affiliation(s)
- Merlin Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yu Leng Phua
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amy B Huynh
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Blake T McCourt
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brittney M Rush
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Roderick J Tan
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Susan L Murray
- Department of Nephrology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Anthony Dorman
- Department of Nephrology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter J Conlon
- Department of Nephrology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rannar Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| |
Collapse
|
39
|
Paul D, Kales SC, Cornwell JA, Afifi MM, Rai G, Zakharov A, Simeonov A, Cappell SD. Revealing β-TrCP activity dynamics in live cells with a genetically encoded biosensor. Nat Commun 2022; 13:6364. [PMID: 36289220 PMCID: PMC9606124 DOI: 10.1038/s41467-022-33762-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/30/2022] [Indexed: 12/25/2022] Open
Abstract
The F-box protein beta-transducin repeat containing protein (β-TrCP) acts as a substrate adapter for the SCF E3 ubiquitin ligase complex, plays a crucial role in cell physiology, and is often deregulated in many types of cancers. Here, we develop a fluorescent biosensor to quantitatively measure β-TrCP activity in live, single cells in real-time. We find β-TrCP remains constitutively active throughout the cell cycle and functions to maintain discreet steady-state levels of its substrates. We find no correlation between expression levels of β-TrCP and β-TrCP activity, indicating post-transcriptional regulation. A high throughput screen of small-molecules using our reporter identifies receptor-tyrosine kinase signaling as a key axis for regulating β-TrCP activity by inhibiting binding between β-TrCP and the core SCF complex. Our study introduces a method to monitor β-TrCP activity in live cells and identifies a key signaling network that regulates β-TrCP activity throughout the cell cycle.
Collapse
Affiliation(s)
- Debasish Paul
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Stephen C. Kales
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - James A. Cornwell
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Marwa M. Afifi
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Ganesha Rai
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - Alexey Zakharov
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - Anton Simeonov
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - Steven D. Cappell
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| |
Collapse
|
40
|
Wong MK, Ho VWS, Huang X, Chan LY, Xie D, Li R, Ren X, Guan G, Ma Y, Hu B, Yan H, Zhao Z. Initial characterization of gap phase introduction in every cell cycle of C. elegans embryogenesis. Front Cell Dev Biol 2022; 10:978962. [PMID: 36393848 PMCID: PMC9641140 DOI: 10.3389/fcell.2022.978962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Early embryonic cell cycles usually alternate between S and M phases without any gap phase. When the gap phases are developmentally introduced in various cell types remains poorly defined especially during embryogenesis. To establish the cell-specific introduction of gap phases in embryo, we generate multiple fluorescence ubiquitin cell cycle indicators (FUCCI) in C. elegans. Time-lapse 3D imaging followed by lineal expression profiling reveals sharp and differential accumulation of the FUCCI reporters, allowing the systematic demarcation of cell cycle phases throughout embryogenesis. Accumulation of the reporters reliably identifies both G1 and G2 phases only in two embryonic cells with an extended cell cycle length, suggesting that the remaining cells divide either without a G1 phase, or with a brief G1 phase that is too short to be picked up by our reporters. In summary, we provide an initial picture of gap phase introduction in a metazoan embryo. The newly developed FUCCI reporters pave the way for further characterization of developmental control of cell cycle progression.
Collapse
Affiliation(s)
- Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, Xi’an, China
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Boyi Hu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Hong Yan
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- *Correspondence: Zhongying Zhao,
| |
Collapse
|
41
|
Wen L, Tang F. Organoid research on human early development and beyond. MEDICAL REVIEW (BERLIN, GERMANY) 2022; 2:512-523. [PMID: 37724162 PMCID: PMC10471100 DOI: 10.1515/mr-2022-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/03/2022] [Indexed: 09/20/2023]
Abstract
The organoid field has been developing rapidly during the last decade. Organoids for human pre-, peri- and post-implantation development have opened an avenue to study these biological processes in vitro, which have been hampered by lack of accessible research models for long term. The technologies of four fields, single cell omics sequencing, genome editing and lineage tracing, microfluidics and tissue engineering, have fueled the rapid development of the organoid field. In this review, we will discuss the organoid research on human early development as well as future directions of the organoid field combining with other powerful technologies.
Collapse
Affiliation(s)
- Lu Wen
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, P. R. China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, P. R. China
| |
Collapse
|
42
|
Ender P, Gagliardi PA, Dobrzyński M, Frismantiene A, Dessauges C, Höhener T, Jacques MA, Cohen AR, Pertz O. Spatiotemporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis. Dev Cell 2022; 57:2153-2167.e6. [PMID: 36113484 DOI: 10.1016/j.devcel.2022.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/06/2022] [Accepted: 08/20/2022] [Indexed: 12/30/2022]
Abstract
The signaling events controlling proliferation, survival, and apoptosis during mammary epithelial acinar morphogenesis remain poorly characterized. By imaging single-cell ERK activity dynamics in MCF10A acini, we find that these fates depend on the average frequency of non-periodic ERK pulses. High pulse frequency is observed during initial acinus growth, correlating with rapid cell motility and proliferation. Subsequent decrease in motility correlates with lower ERK pulse frequency and quiescence. Later, during lumen formation, coordinated multicellular ERK waves emerge, correlating with high and low ERK pulse frequencies in outer surviving and inner dying cells, respectively. Optogenetic entrainment of ERK pulses causally connects high ERK pulse frequency with inner cell survival. Acini harboring the PIK3CA H1047R mutation display increased ERK pulse frequency and inner cell survival. Thus, fate decisions during acinar morphogenesis are coordinated by different spatiotemporal modalities of ERK pulse frequency.
Collapse
Affiliation(s)
- Pascal Ender
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | | | - Maciej Dobrzyński
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Agne Frismantiene
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Coralie Dessauges
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Thomas Höhener
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Marc-Antoine Jacques
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Andrew R Cohen
- Department of Electrical and Computer Engineering, Drexel University, 3120-40 Market Street, Suite 313, Philadelphia, PA 19104, USA
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
| |
Collapse
|
43
|
Siddaway R, Milos S, Coyaud É, Yun HY, Morcos SM, Pajovic S, Campos EI, Raught B, Hawkins C. The in vivo Interaction Landscape of Histones H3.1 and H3.3. Mol Cell Proteomics 2022; 21:100411. [PMID: 36089195 PMCID: PMC9540345 DOI: 10.1016/j.mcpro.2022.100411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/10/2022] [Accepted: 09/06/2022] [Indexed: 01/18/2023] Open
Abstract
Chromatin structure, transcription, DNA replication, and repair are regulated via locus-specific incorporation of histone variants and posttranslational modifications that guide effector chromatin-binding proteins. Here we report unbiased, quantitative interactomes for the replication-coupled (H3.1) and replication-independent (H3.3) histone H3 variants based on BioID proximity labeling, which allows interactions in intact, living cells to be detected. Along with a significant proportion of previously reported interactions detected by affinity purification followed by mass spectrometry, three quarters of the 608 histone-associated proteins that we identified are new, uncharacterized histone associations. The data reveal important biological nuances not captured by traditional biochemical means. For example, we found that the chromatin assembly factor-1 histone chaperone not only deposits the replication-coupled H3.1 histone variant during S-phase but also associates with H3.3 throughout the cell cycle in vivo. We also identified other variant-specific associations, such as with transcription factors, chromatin regulators, and with the mitotic machinery. Our proximity-based analysis is thus a rich resource that extends the H3 interactome and reveals new sets of variant-specific associations.
Collapse
Affiliation(s)
- Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada,Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Milos
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada,Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Université de Lille, Lille, France
| | - Hwa Young Yun
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shahir M. Morcos
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sanja Pajovic
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eric I. Campos
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada,Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada,For correspondence: Cynthia Hawkins
| |
Collapse
|
44
|
Stepanov AI, Besedovskaia ZV, Moshareva MA, Lukyanov KA, Putlyaeva LV. Studying Chromatin Epigenetics with Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms23168988. [PMID: 36012253 PMCID: PMC9409072 DOI: 10.3390/ijms23168988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Epigenetic modifications of histones (methylation, acetylation, phosphorylation, etc.) are of great importance in determining the functional state of chromatin. Changes in epigenome underlay all basic biological processes, such as cell division, differentiation, aging, and cancerous transformation. Post-translational histone modifications are mainly studied by immunoprecipitation with high-throughput sequencing (ChIP-Seq). It enables an accurate profiling of target modifications along the genome, but suffers from the high cost of analysis and the inability to work with living cells. Fluorescence microscopy represents an attractive complementary approach to characterize epigenetics. It can be applied to both live and fixed cells, easily compatible with high-throughput screening, and provide access to rich spatial information down to the single cell level. In this review, we discuss various fluorescent probes for histone modification detection. Various types of live-cell imaging epigenetic sensors suitable for conventional as well as super-resolution fluorescence microscopy are described. We also focus on problems and future perspectives in the development of fluorescent probes for epigenetics.
Collapse
Affiliation(s)
- Afanasii I. Stepanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Zlata V. Besedovskaia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Maria A. Moshareva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklay St. 16/10, 117997 Moscow, Russia
| | - Konstantin A. Lukyanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
| | - Lidia V. Putlyaeva
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
| |
Collapse
|
45
|
Ohta Y, Fujii M, Takahashi S, Takano A, Nanki K, Matano M, Hanyu H, Saito M, Shimokawa M, Nishikori S, Hatano Y, Ishii R, Sawada K, Machinaga A, Ikeda W, Imamura T, Sato T. Cell-matrix interface regulates dormancy in human colon cancer stem cells. Nature 2022; 608:784-794. [PMID: 35798028 DOI: 10.1038/s41586-022-05043-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Cancer relapse after chemotherapy remains a main cause of cancer-related death. Although the relapse is thought to result from the propagation of resident cancer stem cells1, a lack of experimental platforms that enable the prospective analysis of cancer stem cell dynamics with sufficient spatiotemporal resolution has hindered the testing of this hypothesis. Here we develop a live genetic lineage-tracing system that allows the longitudinal tracking of individual cells in xenotransplanted human colorectal cancer organoids, and identify LGR5+ cancer stem cells that exhibit a dormant behaviour in a chemo-naive state. Dormant LGR5+ cells are marked by the expression of p27, and intravital imaging provides direct evidence of the persistence of LGR5+p27+ cells during chemotherapy, followed by clonal expansion. Transcriptome analysis reveals that COL17A1-a cell-adhesion molecule that strengthens hemidesmosomes-is upregulated in dormant LGR5+p27+ cells. Organoids in which COL17A1 is knocked out lose the dormant LGR5+p27+ subpopulation and become sensitive to chemotherapy, which suggests that the cell-matrix interface has a role in the maintenance of dormancy. Chemotherapy disrupts COL17A1 and breaks the dormancy in LGR5+p27+ cells through FAK-YAP activation. Abrogation of YAP signalling prevents chemoresistant cells from exiting dormancy and delays the regrowth of tumours, highlighting the therapeutic potential of YAP inhibition in preventing cancer relapse. These results offer a viable therapeutic approach to overcome the refractoriness of human colorectal cancer to conventional chemotherapy.
Collapse
Affiliation(s)
- Yuki Ohta
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Masayuki Fujii
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Sirirat Takahashi
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Ai Takano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kosaku Nanki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Mami Matano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Hikaru Hanyu
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Megumu Saito
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Fujii Memorial Research Institute, Otsuka Pharmaceutical Company, Otsu, Japan
| | - Mariko Shimokawa
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Shingo Nishikori
- Fujii Memorial Research Institute, Otsuka Pharmaceutical Company, Otsu, Japan
| | - Yoshiko Hatano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Ryota Ishii
- Department of Biostatistics, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuaki Sawada
- Center for Integrated Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | | | | | - Takeshi Imamura
- Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Matsuyama, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan.
| |
Collapse
|
46
|
Suski JM, Ratnayeke N, Braun M, Zhang T, Strmiska V, Michowski W, Can G, Simoneau A, Snioch K, Cup M, Sullivan CM, Wu X, Nowacka J, Branigan TB, Pack LR, DeCaprio JA, Geng Y, Zou L, Gygi SP, Walter JC, Meyer T, Sicinski P. CDC7-independent G1/S transition revealed by targeted protein degradation. Nature 2022; 605:357-365. [PMID: 35508654 PMCID: PMC9106935 DOI: 10.1038/s41586-022-04698-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 03/29/2022] [Indexed: 12/30/2022]
Abstract
The entry of mammalian cells into the DNA synthesis phase (S phase) represents a key event in cell division1. According to current models of the cell cycle, the kinase CDC7 constitutes an essential and rate-limiting trigger of DNA replication, acting together with the cyclin-dependent kinase CDK2. Here we show that CDC7 is dispensable for cell division of many different cell types, as determined using chemical genetic systems that enable acute shutdown of CDC7 in cultured cells and in live mice. We demonstrate that another cell cycle kinase, CDK1, is also active during G1/S transition both in cycling cells and in cells exiting quiescence. We show that CDC7 and CDK1 perform functionally redundant roles during G1/S transition, and at least one of these kinases must be present to allow S-phase entry. These observations revise our understanding of cell cycle progression by demonstrating that CDK1 physiologically regulates two distinct transitions during cell division cycle, whereas CDC7 has a redundant function in DNA replication.
Collapse
Affiliation(s)
- Jan M Suski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Nalin Ratnayeke
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Marcin Braun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Vladislav Strmiska
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Wojciech Michowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Geylani Can
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Konrad Snioch
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Mikolaj Cup
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Caitlin M Sullivan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xiaoji Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joanna Nowacka
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lindsey R Pack
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tobias Meyer
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
47
|
He Y, He S, Kandel ME, Lee YJ, Hu C, Sobh N, Anastasio MA, Popescu G. Cell Cycle Stage Classification Using Phase Imaging with Computational Specificity. ACS PHOTONICS 2022; 9:1264-1273. [PMID: 35480491 PMCID: PMC9026251 DOI: 10.1021/acsphotonics.1c01779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Indexed: 06/01/2023]
Abstract
Traditional methods for cell cycle stage classification rely heavily on fluorescence microscopy to monitor nuclear dynamics. These methods inevitably face the typical phototoxicity and photobleaching limitations of fluorescence imaging. Here, we present a cell cycle detection workflow using the principle of phase imaging with computational specificity (PICS). The proposed method uses neural networks to extract cell cycle-dependent features from quantitative phase imaging (QPI) measurements directly. Our results indicate that this approach attains very good accuracy in classifying live cells into G1, S, and G2/M stages, respectively. We also demonstrate that the proposed method can be applied to study single-cell dynamics within the cell cycle as well as cell population distribution across different stages of the cell cycle. We envision that the proposed method can become a nondestructive tool to analyze cell cycle progression in fields ranging from cell biology to biopharma applications.
Collapse
Affiliation(s)
- Yuchen
R. He
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Shenghua He
- Department
of Computer Science & Engineering, Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mikhail E. Kandel
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Young Jae Lee
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Chenfei Hu
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Nahil Sobh
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- NCSA
Center for Artificial Intelligence Innovation, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Mark A. Anastasio
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Gabriel Popescu
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
48
|
San Martín A, Arce-Molina R, Aburto C, Baeza-Lehnert F, Barros LF, Contreras-Baeza Y, Pinilla A, Ruminot I, Rauseo D, Sandoval PY. Visualizing physiological parameters in cells and tissues using genetically encoded indicators for metabolites. Free Radic Biol Med 2022; 182:34-58. [PMID: 35183660 DOI: 10.1016/j.freeradbiomed.2022.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
The study of metabolism is undergoing a renaissance. Since the year 2002, over 50 genetically-encoded fluorescent indicators (GEFIs) have been introduced, capable of monitoring metabolites with high spatial/temporal resolution using fluorescence microscopy. Indicators are fusion proteins that change their fluorescence upon binding a specific metabolite. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides. They permit monitoring relative levels, concentrations, and fluxes in living systems. At a minimum they report relative levels and, in some cases, absolute concentrations may be obtained by performing ad hoc calibration protocols. Proper data collection, processing, and interpretation are critical to take full advantage of these new tools. This review offers a survey of the metabolic indicators that have been validated in mammalian systems. Minimally invasive, these indicators have been instrumental for the purposes of confirmation, rebuttal and discovery. We envision that this powerful technology will foster metabolic physiology.
Collapse
Affiliation(s)
- A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile.
| | - R Arce-Molina
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - C Aburto
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | | | - L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Y Contreras-Baeza
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - A Pinilla
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - D Rauseo
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| |
Collapse
|
49
|
Zheng SC, Stein-O'Brien G, Augustin JJ, Slosberg J, Carosso GA, Winer B, Shin G, Bjornsson HT, Goff LA, Hansen KD. Universal prediction of cell-cycle position using transfer learning. Genome Biol 2022; 23:41. [PMID: 35101061 PMCID: PMC8802487 DOI: 10.1186/s13059-021-02581-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle both as a biological process of interest and as a possible confounding factor. Despite its importance and conservation, there is no universally applicable approach to infer position in the cell cycle with high-resolution from single-cell RNA-seq data. RESULTS Here, we present tricycle, an R/Bioconductor package, to address this challenge by leveraging key features of the biology of the cell cycle, the mathematical properties of principal component analysis of periodic functions, and the use of transfer learning. We estimate a cell-cycle embedding using a fixed reference dataset and project new data into this reference embedding, an approach that overcomes key limitations of learning a dataset-dependent embedding. Tricycle then predicts a cell-specific position in the cell cycle based on the data projection. The accuracy of tricycle compares favorably to gold-standard experimental assays, which generally require specialized measurements in specifically constructed in vitro systems. Using internal controls which are available for any dataset, we show that tricycle predictions generalize to datasets with multiple cell types, across tissues, species, and even sequencing assays. CONCLUSIONS Tricycle generalizes across datasets and is highly scalable and applicable to atlas-level single-cell RNA-seq data.
Collapse
Affiliation(s)
- Shijie C Zheng
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Genevieve Stein-O'Brien
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, USA
- Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, USA
| | - Jonathan J Augustin
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Jared Slosberg
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Giovanni A Carosso
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Briana Winer
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Gloria Shin
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, USA
- Faculty of Medicine, Univeristy of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Loyal A Goff
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA.
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, USA.
- Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, USA.
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA.
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA.
| |
Collapse
|
50
|
Frei MS, Tarnawski M, Roberti MJ, Koch B, Hiblot J, Johnsson K. Engineered HaloTag variants for fluorescence lifetime multiplexing. Nat Methods 2022; 19:65-70. [PMID: 34916672 PMCID: PMC8748199 DOI: 10.1038/s41592-021-01341-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Self-labeling protein tags such as HaloTag are powerful tools that can label fusion proteins with synthetic fluorophores for use in fluorescence microscopy. Here we introduce HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines. Combining these HaloTag variants enabled live-cell fluorescence lifetime multiplexing of three cellular targets in one spectral channel using a single fluorophore and the generation of a fluorescence lifetime-based biosensor. Additionally, the brightest HaloTag variant showed up to 40% higher brightness in live-cell imaging applications.
Collapse
Affiliation(s)
- Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|