1
|
Beyrent E, Wei DT, Beacham GM, Park S, Zheng J, Paszek MJ, Hollopeter G. Dimerization activates the Inversin complex in C. elegans. Mol Biol Cell 2024; 35:ar127. [PMID: 39110529 DOI: 10.1091/mbc.e24-05-0218] [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: 09/21/2024] Open
Abstract
Genetic, colocalization, and biochemical studies suggest that the ankyrin repeat-containing proteins Inversin (INVS) and ANKS6 function with the NEK8 kinase to control tissue patterning and maintain organ physiology. It is unknown whether these three proteins assemble into a static "Inversin complex" or one that adopts multiple bioactive forms. Through the characterization of hyperactive alleles in C. elegans, we discovered that the Inversin complex is activated by dimerization. Genome engineering of an RFP tag onto the nematode homologues of INVS (MLT-4) and NEK8 (NEKL-2) induced a gain-of-function, cyst-like phenotype that was suppressed by monomerization of the fluorescent tag. Stimulated dimerization of MLT-4 or NEKL-2 using optogenetics was sufficient to recapitulate the phenotype of a constitutively active Inversin complex. Further, dimerization of NEKL-2 bypassed a lethal MLT-4 mutant, demonstrating that the dimeric form is required for function. We propose that dynamic switching between at least two functionally distinct states - an active dimer and an inactive monomer - gates the output of the Inversin complex.
Collapse
Affiliation(s)
- Erika Beyrent
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
| | - Derek T Wei
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
| | - Gwendolyn M Beacham
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
| | - Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY 14853
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Jian Zheng
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Matthew J Paszek
- Field of Biophysics, Cornell University, Ithaca, NY 14853
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Gunther Hollopeter
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
| |
Collapse
|
2
|
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
|
3
|
Zhang J, Mosier JA, Wu Y, Waddle L, Taufalele PV, Wang W, Sun H, Reinhart‐King CA. Cellular Energy Cycle Mediates an Advection-Like Forward Cell Flow to Support Collective Invasion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400719. [PMID: 39189477 PMCID: PMC11348062 DOI: 10.1002/advs.202400719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 05/25/2024] [Indexed: 08/28/2024]
Abstract
Collective cell migration is a model for nonequilibrium biological dynamics, which is important for morphogenesis, pattern formation, and cancer metastasis. The current understanding of cellular collective dynamics is based primarily on cells moving within a 2D epithelial monolayer. However, solid tumors often invade surrounding tissues in the form of a stream-like 3D structure, and how biophysical cues are integrated at the cellular level to give rise to this collective streaming remains unclear. Here, it is shown that cell cycle-mediated bioenergetics drive a forward advective flow of cells and energy to the front to support 3D collective invasion. The cell division cycle mediates a corresponding energy cycle such that cellular adenosine triphosphate (ATP) energy peaks just before division. A reaction-advection-diffusion (RAD) type model coupled with experimental measurements further indicates that most cells enter an active division cycle at rear positions during 3D streaming. Once the cells progress to a later stage toward division, the high intracellular energy allows them to preferentially stream toward the tip and become leader cells. This energy-driven cellular flow may be a fundamental characteristic of 3D collective dynamics based on thermodynamic principles important for not only cancer invasion but also tissue morphogenesis.
Collapse
Affiliation(s)
- Jian Zhang
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
- Department of Biomedical EngineeringUniversity of Arkansas790 W. Dickson StFayettevilleAR72701USA
| | - Jenna A. Mosier
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| | - Yusheng Wu
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| | - Logan Waddle
- Department of Biomedical EngineeringUniversity of Arkansas790 W. Dickson StFayettevilleAR72701USA
| | - Paul V. Taufalele
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| | - Wenjun Wang
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| | - Heng Sun
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| | - Cynthia A. Reinhart‐King
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| |
Collapse
|
4
|
Mills J, Tessari A, Anastas V, Kumar DS, Rad NS, Lamba S, Cosentini I, Reers A, Zhu Z, Miles WO, Coppola V, Cocucci E, Magliery TJ, Shive H, Davies AE, Rizzotto L, Croce CM, Palmieri D. Nucleolin acute degradation reveals novel functions in cell cycle progression and division in TNBC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599429. [PMID: 38948867 PMCID: PMC11212942 DOI: 10.1101/2024.06.17.599429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Nucleoli are large nuclear sub-compartments where vital processes, such as ribosome assembly, take place. Technical obstacles still limit our understanding of the biological functions of nucleolar proteins in cell homeostasis and cancer pathogenesis. Since most nucleolar proteins are essential, their abrogation cannot be achieved through conventional approaches. Additionally, the biological activities of many nucleolar proteins are connected to their physiological concentration. Thus, artificial overexpression might not fully recapitulate their endogenous functions. Proteolysis-based approaches, such as the Auxin Inducible Degron (AID) system paired with CRISPR/Cas9 knock-in gene-editing, have the potential to overcome these limitations, providing unprecedented characterization of the biological activities of endogenous nucleolar proteins. We applied this system to endogenous nucleolin (NCL), one of the most abundant nucleolar proteins, and characterized the impact of its acute depletion on Triple-Negative Breast Cancer (TNBC) cell behavior. Abrogation of endogenous NCL reduced proliferation and caused defective cytokinesis, resulting in bi-nucleated tetraploid cells. Bioinformatic analysis of patient data, and quantitative proteomics using our experimental NCL-depleted model, indicated that NCL levels are correlated with the abundance of proteins involved in chromosomal segregation. In conjunction with its effects on sister chromatid dynamics, NCL abrogation enhanced the anti-proliferative effects of chemical inhibitors of mitotic modulators such as the Anaphase Promoting Complex. In summary, using the AID system in combination with CRISPR/Cas9 for endogenous gene editing, our findings indicate a novel role for NCL in supporting the completion of the cell division in TNBC models, and that its abrogation could enhance the therapeutic activity of mitotic-progression inhibitors.
Collapse
Affiliation(s)
- 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
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, 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
| | - Vollter Anastas
- 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
- Graduate School of Biomedical Sciences, Tufts University, 02155, Boston, MA, USA
| | - Damu Sunil Kumar
- 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
| | - Nastaran Samadi Rad
- 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
- Biomedical Sciences Graduate Program, The Ohio State University, 43210, Columbus, OH, USA
| | - Saranya Lamba
- 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
| | - Ilaria Cosentini
- 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
- Current address: Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy
| | - Ashley Reers
- 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
- Current address: Department of Ecology and Evolutionary Biology, Tulane University, 70118, New Orleans, LA, USA
| | - Zirui Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, 43210, Columbus, OH, USA
- Chemistry Graduate Program, The Ohio State University, 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
- Pelotonia Institute for Immuno-Oncology, The Ohio State University-James Cancer Hospital and Solove Research Institute, 43210, Columbus, OH, USA
| | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 43210, Columbus, OH, USA
| | - Thomas J. Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, 43210, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University-James Cancer Hospital and Solove Research Institute, 43210, Columbus, OH, USA
| | - Heather Shive
- 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
- Current address: Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, 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
- Current address: Division of Oncological Sciences, Department of Pediatrics, Cancer Early Detection Advanced Research Center, School of Medicine, Oregon Health and Science University, 97239, Portland, OR, USA
| | - Lara Rizzotto
- 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
| | - 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
| |
Collapse
|
5
|
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
|
6
|
Beyrent E, Wei DT, Beacham GM, Park S, Zheng J, Paszek MJ, Hollopeter G. Dimerization activates the Inversin complex in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594761. [PMID: 38798613 PMCID: PMC11118560 DOI: 10.1101/2024.05.17.594761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Genetic, colocalization, and biochemical studies suggest that the ankyrin repeat-containing proteins Inversin (INVS) and ANKS6 function with the NEK8 kinase to control tissue patterning and maintain organ physiology. It is unknown whether these three proteins assemble into a static "Inversin complex" or one that adopts multiple bioactive forms. Through characterization of hyperactive alleles in C. elegans , we discovered that the Inversin complex is activated by dimerization. Genome engineering of an RFP tag onto the nematode homologs of INVS (MLT-4) and NEK8 (NEKL-2) induced a gain-of-function, cyst-like phenotype that was suppressed by monomerization of the fluorescent tag. Stimulated dimerization of MLT-4 or NEKL-2 using optogenetics was sufficient to recapitulate the phenotype of a constitutively active Inversin complex. Further, dimerization of NEKL-2 bypassed a lethal MLT-4 mutant, demonstrating that the dimeric form is required for function. We propose that dynamic switching between at least two functionally distinct states-an active dimer and an inactive monomer-gates the output of the Inversin complex.
Collapse
|
7
|
Falcó C, Cohen DJ, Carrillo JA, Baker RE. Quantifying cell cycle regulation by tissue crowding. Biophys J 2024:S0006-3495(24)00317-5. [PMID: 38715360 DOI: 10.1016/j.bpj.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/24/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do not fully understand how cell proliferation regulation impacts cell migration phenomena. Here, we present a minimal continuum model of cell migration with cell cycle dynamics, which includes density-dependent effects and hence can account for cell proliferation regulation. By combining minimal mathematical modeling, Bayesian inference, and recent experimental data, we quantify the impact of tissue crowding across different cell cycle stages in epithelial tissue expansion experiments. Our model suggests that cells sense local density and adapt cell cycle progression in response, during G1 and the combined S/G2/M phases, providing an explicit relationship between each cell-cycle-stage duration and local tissue density, which is consistent with several experimental observations. Finally, we compare our mathematical model's predictions to different experiments studying cell cycle regulation and present a quantitative analysis on the impact of density-dependent regulation on cell migration patterns. Our work presents a systematic approach for investigating and analyzing cell cycle data, providing mechanistic insights into how individual cells regulate proliferation, based on population-based experimental measurements.
Collapse
Affiliation(s)
- Carles Falcó
- Mathematical Institute, University of Oxford, Oxford, United Kingdom.
| | - Daniel J Cohen
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey; Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - José A Carrillo
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Ruth E Baker
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
8
|
Wu W, Wu W, Zhou Y, Yang Q, Zhuang S, Zhong C, Li W, Li A, Zhao W, Yin X, Zu X, Chak-Lui Wong C, Yin D, Hu K, Cai M. The dePARylase NUDT16 promotes radiation resistance of cancer cells by blocking SETD3 for degradation via reversing its ADP-ribosylation. J Biol Chem 2024; 300:105671. [PMID: 38272222 PMCID: PMC10926213 DOI: 10.1016/j.jbc.2024.105671] [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: 06/20/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a critical posttranslational modification that plays a vital role in maintaining genomic stability via a variety of molecular mechanisms, including activation of replication stress and the DNA damage response. The nudix hydrolase NUDT16 was recently identified as a phosphodiesterase that is responsible for removing ADP-ribose units and that plays an important role in DNA repair. However, the roles of NUDT16 in coordinating replication stress and cell cycle progression remain elusive. Here, we report that SETD3, which is a member of the SET-domain containing protein (SETD) family, is a novel substrate for NUDT16, that its protein levels fluctuate during cell cycle progression, and that its stability is strictly regulated by NUDT16-mediated dePARylation. Moreover, our data indicated that the E3 ligase CHFR is responsible for the recognition and degradation of endogenous SETD3 in a PARP1-mediated PARylation-dependent manner. Mechanistically, we revealed that SETD3 associates with BRCA2 and promotes its recruitment to stalled replication fork and DNA damage sites upon replication stress or DNA double-strand breaks, respectively. Importantly, depletion of SETD3 in NUDT16-deficient cells did not further exacerbate DNA breaks or enhance the sensitivity of cancer cells to IR exposure, suggesting that the NUDT16-SETD3 pathway may play critical roles in the induction of tolerance to radiotherapy. Collectively, these data showed that NUDT16 functions as a key upstream regulator of SETD3 protein stability by reversing the ADP-ribosylation of SETD3, and NUDT16 participates in the resolution of replication stress and facilitates HR repair.
Collapse
Affiliation(s)
- Weijun Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wenjing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Breast Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yingshi Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Ultrasound, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiao Yang
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Shuting Zhuang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Caixia Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjia Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Aixin Li
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wanzhen Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaomin Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Carmen Chak-Lui Wong
- Li Ka Shing Faculty of Medicine, Department of Pathology, The University of Hong Kong, Hong Kong, Guangdong, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Manbo Cai
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
| |
Collapse
|
9
|
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
|
10
|
Liu X, Yan J, Kirschner MW. Cell size homeostasis is tightly controlled throughout the cell cycle. PLoS Biol 2024; 22:e3002453. [PMID: 38180950 PMCID: PMC10769027 DOI: 10.1371/journal.pbio.3002453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
To achieve a stable size distribution over multiple generations, proliferating cells require a means of counteracting stochastic noise in the rate of growth, the time spent in various phases of the cell cycle, and the imprecision in the placement of the plane of cell division. In the most widely accepted model, cell size is thought to be regulated at the G1/S transition, such that cells smaller than a critical size pause at the end of G1 phase until they have accumulated mass to a predetermined size threshold, at which point the cells proceed through the rest of the cell cycle. However, a model, based solely on a specific size checkpoint at G1/S, cannot readily explain why cells with deficient G1/S control mechanisms are still able to maintain a very stable cell size distribution. Furthermore, such a model would not easily account for stochastic variation in cell size during the subsequent phases of the cell cycle, which cannot be anticipated at G1/S. To address such questions, we applied computationally enhanced quantitative phase microscopy (ceQPM) to populations of cultured human cell lines, which enables highly accurate measurement of cell dry mass of individual cells throughout the cell cycle. From these measurements, we have evaluated the factors that contribute to maintaining cell mass homeostasis at any point in the cell cycle. Our findings reveal that cell mass homeostasis is accurately maintained, despite disruptions to the normal G1/S machinery or perturbations in the rate of cell growth. Control of cell mass is generally not confined to regulation of the G1 length. Instead mass homeostasis is imposed throughout the cell cycle. In the cell lines examined, we find that the coefficient of variation (CV) in dry mass of cells in the population begins to decline well before the G1/S transition and continues to decline throughout S and G2 phases. Among the different cell types tested, the detailed response of cell growth rate to cell mass differs. However, in general, when it falls below that for exponential growth, the natural increase in the CV of cell mass is effectively constrained. We find that both mass-dependent cell cycle regulation and mass-dependent growth rate modulation contribute to reducing cell mass variation within the population. Through the interplay and coordination of these 2 processes, accurate cell mass homeostasis emerges. Such findings reveal previously unappreciated and very general principles of cell size control in proliferating cells. These same regulatory processes might also be operative in terminally differentiated cells. Further quantitative dynamical studies should lead to a better understanding of the underlying molecular mechanisms of cell size control.
Collapse
Affiliation(s)
- Xili Liu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Marc W. Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
11
|
Šeflová J, Cruz-Cortés C, Guerrero-Serna G, Robia SL, Espinoza-Fonseca LM. Mechanisms for cardiac calcium pump activation by its substrate and a synthetic allosteric modulator using fluorescence lifetime imaging. PNAS NEXUS 2024; 3:pgad453. [PMID: 38222469 PMCID: PMC10785037 DOI: 10.1093/pnasnexus/pgad453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
The discovery of allosteric modulators is an emerging paradigm in drug discovery, and signal transduction is a subtle and dynamic process that is challenging to characterize. We developed a time-correlated single photon-counting imaging approach to investigate the structural mechanisms for small-molecule activation of the cardiac sarcoplasmic reticulum Ca2+-ATPase, a pharmacologically important pump that transports Ca2+ at the expense of adenosine triphosphate (ATP) hydrolysis. We first tested whether the dissociation of sarcoplasmic reticulum Ca2+-ATPase from its regulatory protein phospholamban is required for small-molecule activation. We found that CDN1163, a validated sarcoplasmic reticulum Ca2+-ATPase activator, does not have significant effects on the stability of the sarcoplasmic reticulum Ca2+-ATPase-phospholamban complex. Time-correlated single photon-counting imaging experiments using the nonhydrolyzable ATP analog β,γ-Methyleneadenosine 5'-triphosphate (AMP-PCP) showed ATP is an allosteric modulator of sarcoplasmic reticulum Ca2+-ATPase, increasing the fraction of catalytically competent structures at physiologically relevant Ca2+ concentrations. Unlike ATP, CDN1163 alone has no significant effects on the Ca2+-dependent shifts in the structural populations of sarcoplasmic reticulum Ca2+-ATPase, and it does not increase the pump's affinity for Ca2+ ions. However, we found that CDN1163 enhances the ATP-mediated modulatory effects to increase the population of catalytically competent sarcoplasmic reticulum Ca2+-ATPase structures. Importantly, this structural shift occurs within the physiological window of Ca2+ concentrations at which sarcoplasmic reticulum Ca2+-ATPase operates. We demonstrated that ATP is both a substrate and modulator of sarcoplasmic reticulum Ca2+-ATPase and showed that CDN1163 and ATP act synergistically to populate sarcoplasmic reticulum Ca2+-ATPase structures that are primed for phosphorylation. This study provides novel insights into the structural mechanisms for sarcoplasmic reticulum Ca2+-ATPase activation by its substrate and a synthetic allosteric modulator.
Collapse
Affiliation(s)
- Jaroslava Šeflová
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carlos Cruz-Cortés
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guadalupe Guerrero-Serna
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
12
|
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
|
13
|
Waters CS, Angenent SB, Altschuler SJ, Wu LF. A PINK1 input threshold arises from positive feedback in the PINK1/Parkin mitophagy decision circuit. Cell Rep 2023; 42:113260. [PMID: 37851575 PMCID: PMC10668033 DOI: 10.1016/j.celrep.2023.113260] [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: 11/11/2022] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
Mechanisms that prevent accidental activation of the PINK1/Parkin mitophagy circuit on healthy mitochondria are poorly understood. On the surface of damaged mitochondria, PINK1 accumulates and acts as the input signal to a positive feedback loop of Parkin recruitment, which in turn promotes mitochondrial degradation via mitophagy. However, PINK1 is also present on healthy mitochondria, where it could errantly recruit Parkin and thereby activate this positive feedback loop. Here, we explore emergent properties of the PINK1/Parkin circuit by quantifying the relationship between mitochondrial PINK1 concentrations and Parkin recruitment dynamics. We find that Parkin is recruited to mitochondria only if PINK1 levels exceed a threshold and then only after a delay that is inversely proportional to PINK1 levels. Furthermore, these two regulatory properties arise from the input-coupled positive feedback topology of the PINK1/Parkin circuit. These results outline an intrinsic mechanism by which the PINK1/Parkin circuit can avoid errant activation on healthy mitochondria.
Collapse
Affiliation(s)
- Christopher S Waters
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sigurd B Angenent
- Mathematics Department, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
14
|
Lyons AC, Mehta S, Zhang J. Fluorescent biosensors illuminate the spatial regulation of cell signaling across scales. Biochem J 2023; 480:1693-1717. [PMID: 37903110 PMCID: PMC10657186 DOI: 10.1042/bcj20220223] [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: 03/24/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023]
Abstract
As cell signaling research has advanced, it has become clearer that signal transduction has complex spatiotemporal regulation that goes beyond foundational linear transduction models. Several technologies have enabled these discoveries, including fluorescent biosensors designed to report live biochemical signaling events. As genetically encoded and live-cell compatible tools, fluorescent biosensors are well suited to address diverse cell signaling questions across different spatial scales of regulation. In this review, methods of examining spatial signaling regulation and the design of fluorescent biosensors are introduced. Then, recent biosensor developments that illuminate the importance of spatial regulation in cell signaling are highlighted at several scales, including membranes and organelles, molecular assemblies, and cell/tissue heterogeneity. In closing, perspectives on how fluorescent biosensors will continue enhancing cell signaling research are discussed.
Collapse
Affiliation(s)
- Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, U.S.A
| |
Collapse
|
15
|
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
|
16
|
Fischer AD, Veronese Paniagua DA, Swaminathan S, Kashima H, Rubin DC, Madison BB. The oncogenic function of PLAGL2 is mediated via ASCL2 and IGF2 and a Wnt-independent mechanism in colorectal cancer. Am J Physiol Gastrointest Liver Physiol 2023; 325:G196-G211. [PMID: 37310750 PMCID: PMC10396286 DOI: 10.1152/ajpgi.00058.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
Colorectal cancer (CRC) tumorigenesis and progression are linked to common oncogenic mutations, especially in the tumor suppressor APC, whose loss triggers the deregulation of TCF4/β-Catenin activity. CRC tumorigenesis is also driven by multiple epimutational modifiers such as transcriptional regulators. We describe the common (and near-universal) activation of the zinc finger transcription factor and Let-7 target PLAGL2 in CRC and find that it is a key driver of intestinal epithelial transformation. PLAGL2 drives proliferation, cell cycle progression, and anchorage-independent growth in CRC cell lines and nontransformed intestinal cells. Investigating effects of PLAGL2 on downstream pathways revealed very modest effects on canonical Wnt signaling. Alternatively, we find pronounced effects on the direct PLAGL2 target genes IGF2, a fetal growth factor, and ASCL2, an intestinal stem cell-specific bHLH transcription factor. Inactivation of PLAGL2 in CRC cell lines has pronounced effects on ASCL2 reporter activity. Furthermore, ASCL2 expression can partially rescue deficits of proliferation and cell cycle progression caused by depletion of PLAGL2 in CRC cell lines. Thus, the oncogenic effects of PLAGL2 appear to be mediated via core stem cell and onco-fetal pathways, with minimal effects on downstream Wnt signaling.NEW & NOTEWORTHY A Let-7 target called PLAGL2 drives oncogenic transformation via Wnt-independent pathways. This work illustrates the robust effects of this zinc finger transcription factor in colorectal cancer (CRC) cell lines and nontransformed intestinal epithelium, with effects mediated, in part, via the direct target genes ASCL2 and IGF2. This has implications for the role of PLAGL2 in activation of onco-fetal and onco-stem cell pathways, contributing to immature and highly proliferative phenotypes in CRC.
Collapse
Affiliation(s)
- Anthony D Fischer
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Daniel A Veronese Paniagua
- Washington University School of Medicine, Saint Louis, Missouri, United States
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, United States
| | - Shriya Swaminathan
- Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Hajime Kashima
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Blair B Madison
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| |
Collapse
|
17
|
Zheng D, Mao Y, Gao Y, He F, Ma J. Daughter cell fate choice instructed preemptively by mother cells facing nutrient limitation. iScience 2023; 26:107198. [PMID: 37485365 PMCID: PMC10359942 DOI: 10.1016/j.isci.2023.107198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Nutrients are vital to cellular activities, yet it is largely unknown how individual cells respond to nutrient deprivation. Live imaging results show that unlike the removal of amino acids or glutamine that immediately halts cell cycle progression, glucose withdrawal does not prevent cells from completing their current cycle. Although cells that begin to experience glucose withdrawal in S phase give rise to daughter cells with an equal choice of proliferation or quiescence, those enduring such experience in G1 phase give rise to daughter cells that predominantly enter quiescence. This fate choice difference stems from p21 protein accumulated during G2/M of the latter cells. Induced degradation of p21 permits daughter cells to enter S phase but with a consequent accumulation of DNA damage. These results suggest that mother cells that begin to experience glucose limitation in G1 phase take preemptive steps toward preventing daughter cells from making a harmful choice.
Collapse
Affiliation(s)
- Dianpeng Zheng
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Yaowen Mao
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Yinglong Gao
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
| | - Feng He
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
| | - Jun Ma
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
- Women’s Reproductive Health Research Laboratory of Zhejiang Province, Hangzhou, Zhejiang 310006, China
| |
Collapse
|
18
|
Moretton A, Kourtis S, Gañez Zapater A, Calabrò C, Espinar Calvo ML, Fontaine F, Darai E, Abad Cortel E, Block S, Pascual‐Reguant L, Pardo‐Lorente N, Ghose R, Vander Heiden MG, Janic A, Müller AC, Loizou JI, Sdelci S. A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability. Mol Syst Biol 2023; 19:e11267. [PMID: 37259925 PMCID: PMC10333845 DOI: 10.15252/msb.202211267] [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: 08/01/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential for the resolution of DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Further analysis identified that Peroxiredoxin 1, PRDX1, contributes to the DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it reduces DNA damage-induced nuclear reactive oxygen species. Moreover, PRDX1 loss lowers aspartate availability, which is required for the DNA damage-induced upregulation of de novo nucleotide synthesis. In the absence of PRDX1, cells accumulate replication stress and DNA damage, leading to proliferation defects that are exacerbated in the presence of etoposide, thus revealing a role for PRDX1 as a DNA damage surveillance factor.
Collapse
Affiliation(s)
- Amandine Moretton
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Antoni Gañez Zapater
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Chiara Calabrò
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | | | - Frédéric Fontaine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Evangelia Darai
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Etna Abad Cortel
- Department of Medicine and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Samuel Block
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Laura Pascual‐Reguant
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Natalia Pardo‐Lorente
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Ritobrata Ghose
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Dana‐Farber Cancer InstituteBostonMAUSA
| | - Ana Janic
- Department of Medicine and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| |
Collapse
|
19
|
Schvartzman JM, Forsyth G, Walch H, Chatila W, Taglialatela A, Lee BJ, Zhu X, Gershik S, Cimino FV, Santella A, Menghrajani K, Ciccia A, Koche R, Sánchez-Vega F, Zha S, Thompson CB. Oncogenic IDH mutations increase heterochromatin-related replication stress without impacting homologous recombination. Mol Cell 2023; 83:2347-2356.e8. [PMID: 37311462 PMCID: PMC10845120 DOI: 10.1016/j.molcel.2023.05.026] [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: 08/19/2022] [Revised: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/15/2023]
Abstract
Oncogenic mutations in isocitrate dehydrogenases 1 and 2 (IDH1/2) produce 2-hydroxyglutarate (2HG), which inhibits dioxygenases that modulate chromatin dynamics. The effects of 2HG have been reported to sensitize IDH tumors to poly-(ADP-ribose) polymerase (PARP) inhibitors. However, unlike PARP-inhibitor-sensitive BRCA1/2 tumors, which exhibit impaired homologous recombination, IDH-mutant tumors have a silent mutational profile and lack signatures associated with impaired homologous recombination. Instead, 2HG-producing IDH mutations lead to a heterochromatin-dependent slowing of DNA replication accompanied by increased replication stress and DNA double-strand breaks. This replicative stress manifests as replication fork slowing, but the breaks are repaired without a significant increase in mutation burden. Faithful resolution of replicative stress in IDH-mutant cells is dependent on poly-(ADP-ribosylation). Treatment with PARP inhibitors increases DNA replication but results in incomplete DNA repair. These findings demonstrate a role for PARP in the replication of heterochromatin and further validate PARP as a therapeutic target in IDH-mutant tumors.
Collapse
Affiliation(s)
- Juan-Manuel Schvartzman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Grace Forsyth
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Human Oncology and Pathogenesis Program, and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Human Oncology and Pathogenesis Program, and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xiaolu Zhu
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Steven Gershik
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Francesco V Cimino
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anthony Santella
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, 417 E 68th St, New York, NY 10065, USA
| | - Kamal Menghrajani
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sánchez-Vega
- Department of Epidemiology and Biostatistics and Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
20
|
Gross SM, Mohammadi F, Sanchez-Aguila C, Zhan PJ, Liby TA, Dane MA, Meyer AS, Heiser LM. Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects. Nat Commun 2023; 14:3450. [PMID: 37301933 PMCID: PMC10257663 DOI: 10.1038/s41467-023-39122-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Identifying effective therapeutic treatment strategies is a major challenge to improving outcomes for patients with breast cancer. To gain a comprehensive understanding of how clinically relevant anti-cancer agents modulate cell cycle progression, here we use genetically engineered breast cancer cell lines to track drug-induced changes in cell number and cell cycle phase to reveal drug-specific cell cycle effects that vary across time. We use a linear chain trick (LCT) computational model, which faithfully captures drug-induced dynamic responses, correctly infers drug effects, and reproduces influences on specific cell cycle phases. We use the LCT model to predict the effects of unseen drug combinations and confirm these in independent validation experiments. Our integrated experimental and modeling approach opens avenues to assess drug responses, predict effective drug combinations, and identify optimal drug sequencing strategies.
Collapse
Affiliation(s)
- Sean M Gross
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Farnaz Mohammadi
- Department of Bioengineering, University of California, Los Angeles; Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
| | - Crystal Sanchez-Aguila
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Paulina J Zhan
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tiera A Liby
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark A Dane
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Aaron S Meyer
- Department of Bioengineering, University of California, Los Angeles; Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| |
Collapse
|
21
|
Venkatachalapathy H, Brzakala C, Batchelor E, Azarin SM, Sarkar CA. Inertial effect of cell state velocity on the quiescence-proliferation fate decision in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541793. [PMID: 37292599 PMCID: PMC10245870 DOI: 10.1101/2023.05.22.541793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Energy landscapes can provide intuitive depictions of population heterogeneity and dynamics. However, it is unclear whether individual cell behavior, hypothesized to be determined by initial position and noise, is faithfully recapitulated. Using the p21-/Cdk2-dependent quiescence-proliferation decision in breast cancer dormancy as a testbed, we examined single-cell dynamics on the landscape when perturbed by hypoxia, a dormancy-inducing stress. Combining trajectory-based energy landscape generation with single-cell time-lapse microscopy, we found that initial position on a p21/Cdk2 landscape did not fully explain the observed cell-fate heterogeneity under hypoxia. Instead, cells with higher cell state velocities prior to hypoxia, influenced by epigenetic parameters, tended to remain proliferative under hypoxia. Thus, the fate decision on this landscape is significantly influenced by "inertia", a velocity-dependent ability to resist directional changes despite reshaping of the underlying landscape, superseding positional effects. Such inertial effects may markedly influence cell-fate trajectories in tumors and other dynamically changing microenvironments.
Collapse
Affiliation(s)
- Harish Venkatachalapathy
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cole Brzakala
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric Batchelor
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samira M. Azarin
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
22
|
van der Noord VE, van der Stel W, Louwerens G, Verhoeven D, Kuiken HJ, Lieftink C, Grandits M, Ecker GF, Beijersbergen RL, Bouwman P, Le Dévédec SE, van de Water B. Systematic screening identifies ABCG2 as critical factor underlying synergy of kinase inhibitors with transcriptional CDK inhibitors. Breast Cancer Res 2023; 25:51. [PMID: 37147730 PMCID: PMC10161439 DOI: 10.1186/s13058-023-01648-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/07/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a subtype of breast cancer with limited treatment options and poor clinical prognosis. Inhibitors of transcriptional CDKs are currently under thorough investigation for application in the treatment of multiple cancer types, including breast cancer. These studies have raised interest in combining these inhibitors, including CDK12/13 inhibitor THZ531, with a variety of other anti-cancer agents. However, the full scope of these potential synergistic interactions of transcriptional CDK inhibitors with kinase inhibitors has not been systematically investigated. Moreover, the mechanisms behind these previously described synergistic interactions remain largely elusive. METHODS Kinase inhibitor combination screenings were performed to identify kinase inhibitors that synergize with CDK7 inhibitor THZ1 and CDK12/13 inhibitor THZ531 in TNBC cell lines. CRISPR-Cas9 knockout screening and transcriptomic evaluation of resistant versus sensitive cell lines were performed to identify genes critical for THZ531 resistance. RNA sequencing analysis after treatment with individual and combined synergistic treatments was performed to gain further insights into the mechanism of this synergy. Kinase inhibitor screening in combination with visualization of ABCG2-substrate pheophorbide A was used to identify kinase inhibitors that inhibit ABCG2. Multiple transcriptional CDK inhibitors were evaluated to extend the significance of the found mechanism to other transcriptional CDK inhibitors. RESULTS We show that a very high number of tyrosine kinase inhibitors synergize with the CDK12/13 inhibitor THZ531. Yet, we identified the multidrug transporter ABCG2 as key determinant of THZ531 resistance in TNBC cells. Mechanistically, we demonstrate that most synergistic kinase inhibitors block ABCG2 function, thereby sensitizing cells to transcriptional CDK inhibitors, including THZ531. Accordingly, these kinase inhibitors potentiate the effects of THZ531, disrupting gene expression and increasing intronic polyadenylation. CONCLUSION Overall, this study demonstrates the critical role of ABCG2 in limiting the efficacy of transcriptional CDK inhibitors and identifies multiple kinase inhibitors that disrupt ABCG2 transporter function and thereby synergize with these CDK inhibitors. These findings therefore further facilitate the development of new (combination) therapies targeting transcriptional CDKs and highlight the importance of evaluating the role of ABC transporters in synergistic drug-drug interactions in general.
Collapse
Affiliation(s)
- Vera E van der Noord
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs Louwerens
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Danielle Verhoeven
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Melanie Grandits
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| |
Collapse
|
23
|
Mertens S, Huismans MA, Verissimo CS, Ponsioen B, Overmeer R, Proost N, van Tellingen O, van de Ven M, Begthel H, Boj SF, Clevers H, Roodhart JML, Bos JL, Snippert HJG. Drug-repurposing screen on patient-derived organoids identifies therapy-induced vulnerability in KRAS-mutant colon cancer. Cell Rep 2023; 42:112324. [PMID: 37000626 DOI: 10.1016/j.celrep.2023.112324] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 01/06/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
Patient-derived organoids (PDOs) are widely heralded as a drug-screening platform to develop new anti-cancer therapies. Here, we use a drug-repurposing library to screen PDOs of colorectal cancer (CRC) to identify hidden vulnerabilities within therapy-induced phenotypes. Using a microscopy-based screen that accurately scores drug-induced cell killing, we have tested 414 putative anti-cancer drugs for their ability to switch the EGFRi/MEKi-induced cytostatic phenotype toward cytotoxicity. A majority of validated hits (9/37) are microtubule-targeting agents that are commonly used in clinical oncology, such as taxanes and vinca-alkaloids. One of these drugs, vinorelbine, is consistently effective across a panel of >25 different CRC PDOs, independent of RAS mutational status. Unlike vinorelbine alone, its combination with EGFR/MEK inhibition induces apoptosis at all stages of the cell cycle and shows tolerability and effective anti-tumor activity in vivo, setting the basis for a clinical trial to treat patients with metastatic RAS-mutant CRC.
Collapse
Affiliation(s)
- Sander Mertens
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Maarten A Huismans
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Carla S Verissimo
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bas Ponsioen
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rene Overmeer
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Aging Research (MCCA), Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Olaf van Tellingen
- Mouse Clinic for Cancer and Aging Research (MCCA), Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Clinical Pharmacology, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging Research (MCCA), Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sylvia F Boj
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeanine M L Roodhart
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Johannes L Bos
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hugo J G Snippert
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.
| |
Collapse
|
24
|
Cheung AHK, Hui CHL, Wong KY, Liu X, Chen B, Kang W, To KF. Out of the cycle: Impact of cell cycle aberrations on cancer metabolism and metastasis. Int J Cancer 2023; 152:1510-1525. [PMID: 36093588 DOI: 10.1002/ijc.34288] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/17/2022] [Accepted: 09/02/2022] [Indexed: 11/11/2022]
Abstract
The use of cell cycle inhibitors has necessitated a better understanding of the cell cycle in tumor biology to optimize the therapeutic approach. Cell cycle aberrations are common in cancers, and it is increasingly acknowledged that these aberrations exert oncogenic effects beyond the cell cycle. Multiple facets such as cancer metabolism, immunity and metastasis are also affected, all of which are beyond the effect of cell proliferation alone. This review comprehensively summarized the important recent findings and advances in these interrelated processes. In cancer metabolism, cell cycle regulators can modulate various pathways in aerobic glycolysis, glucose uptake and gluconeogenesis, mainly through transcriptional regulation and kinase activities. Amino acid metabolism is also regulated through cell cycle progression. On cancer metastasis, metabolic plasticity, immune evasion, tumor microenvironment adaptation and metastatic site colonization are intricately related to the cell cycle, with distinct regulatory mechanisms at each step of invasion and dissemination. Throughout the synthesis of current understanding, knowledge gaps and limitations in the literature are also highlighted, as are new therapeutic approaches such as combinational therapy and challenges in tackling emerging targeted therapy resistance. A greater understanding of how the cell cycle modulates diverse aspects of cancer biology can hopefully shed light on identifying new molecular targets by harnessing the vast potential of the cell cycle.
Collapse
Affiliation(s)
- Alvin Ho-Kwan Cheung
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Chris Ho-Lam Hui
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Kit Yee Wong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoli Liu
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
25
|
Gangemi CG, Sabapathy RT, Janovjak H. CDK6 activity in a recurring convergent kinase network motif. FASEB J 2023; 37:e22845. [PMID: 36884374 DOI: 10.1096/fj.202201344r] [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: 08/16/2022] [Revised: 01/30/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
In humans, more than 500 kinases phosphorylate ~15% of all proteins in an emerging phosphorylation network. Convergent local interaction motifs, in which ≥two kinases phosphorylate the same substrate, underlie feedback loops and signal amplification events but have not been systematically analyzed. Here, we first report a network-wide computational analysis of convergent kinase-substrate relationships (cKSRs). In experimentally validated phosphorylation sites, we find that cKSRs are common and involve >80% of all human kinases and >24% of all substrates. We show that cKSRs occur over a wide range of stoichiometries, in many instances harnessing co-expressed kinases from family subgroups. We then experimentally demonstrate for the prototypical convergent CDK4/6 kinase pair how multiple inputs phosphorylate the tumor suppressor retinoblastoma protein (RB) and thereby hamper in situ analysis of the individual kinases. We hypothesize that overexpression of one kinase combined with a CDK4/6 inhibitor can dissect convergence. In breast cancer cells expressing high levels of CDK4, we confirm this hypothesis and develop a high-throughput compatible assay that quantifies genetically modified CDK6 variants and inhibitors. Collectively, our work reveals the occurrence, topology, and experimental dissection of convergent interactions toward a deeper understanding of kinase networks and functions.
Collapse
Affiliation(s)
- Christina G Gangemi
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Clayton/Melbourne, Australia.,European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Victoria, Clayton/Melbourne, Australia.,Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Bedford Park/Adelaide, Australia
| | - Rahkesh T Sabapathy
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Bedford Park/Adelaide, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Clayton/Melbourne, Australia.,European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Victoria, Clayton/Melbourne, Australia.,Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Bedford Park/Adelaide, Australia
| |
Collapse
|
26
|
Wu T, Kumar M, Zhang J, Zhao S, Drobizhev M, McCollum M, Anderson CT, Wang Y, Pokorny A, Tian X, Zhang Y, Tzounopoulos T, Ai HW. A genetically encoded far-red fluorescent indicator for imaging synaptically released Zn 2. SCIENCE ADVANCES 2023; 9:eadd2058. [PMID: 36857451 PMCID: PMC9977179 DOI: 10.1126/sciadv.add2058] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Synaptic zinc ion (Zn2+) has emerged as a key neuromodulator in the brain. However, the lack of research tools for directly tracking synaptic Zn2+ in the brain of awake animals hinders our rigorous understanding of the physiological and pathological roles of synaptic Zn2+. In this study, we developed a genetically encoded far-red fluorescent indicator for monitoring synaptic Zn2+ dynamics in the nervous system. Our engineered far-red fluorescent indicator for synaptic Zn2+ (FRISZ) displayed a substantial Zn2+-specific turn-on response and low-micromolar affinity. We genetically anchored FRISZ to the mammalian extracellular membrane via a transmembrane (TM) ⍺ helix and characterized the resultant FRISZ-TM construct at the mammalian cell surface. We used FRISZ-TM to image synaptic Zn2+ in the auditory cortex in acute brain slices and awake mice in response to electric and sound stimuli, respectively. Thus, this study establishes a technology for studying the roles of synaptic Zn2+ in the nervous system.
Collapse
Affiliation(s)
- Tianchen Wu
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Manoj Kumar
- Department of Otolaryngology, Pittsburgh Hearing Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jing Zhang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Shengyu Zhao
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717-384, USA
| | - Mason McCollum
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA
| | - Charles T. Anderson
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA
| | - Ying Wang
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Antje Pokorny
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Xiaodong Tian
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yiyu Zhang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Thanos Tzounopoulos
- Department of Otolaryngology, Pittsburgh Hearing Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
- The UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
27
|
Schimmel J, Muñoz-Subirana N, Kool H, van Schendel R, van der Vlies S, Kamp JA, de Vrij FMS, Kushner SA, Smith GCM, Boulton SJ, Tijsterman M. Modulating mutational outcomes and improving precise gene editing at CRISPR-Cas9-induced breaks by chemical inhibition of end-joining pathways. Cell Rep 2023; 42:112019. [PMID: 36701230 DOI: 10.1016/j.celrep.2023.112019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/18/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Gene editing through repair of CRISPR-Cas9-induced chromosomal breaks offers a means to correct a wide range of genetic defects. Directing repair to produce desirable outcomes by modulating DNA repair pathways holds considerable promise to increase the efficiency of genome engineering. Here, we show that inhibition of non-homologous end joining (NHEJ) or polymerase theta-mediated end joining (TMEJ) can be exploited to alter the mutational outcomes of CRISPR-Cas9. We show robust inhibition of TMEJ activity at CRISPR-Cas9-induced double-strand breaks (DSBs) using ART558, a potent polymerase theta (Polϴ) inhibitor. Using targeted sequencing, we show that ART558 suppresses the formation of microhomology-driven deletions in favor of NHEJ-specific outcomes. Conversely, NHEJ deficiency triggers the formation of large kb-sized deletions, which we show are the products of mutagenic TMEJ. Finally, we show that combined chemical inhibition of TMEJ and NHEJ increases the efficiency of homology-driven repair (HDR)-mediated precise gene editing. Our work reports a robust strategy to improve the fidelity and safety of genome engineering.
Collapse
Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Núria Muñoz-Subirana
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sven van der Vlies
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Juliette A Kamp
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Femke M S de Vrij
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Simon J Boulton
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK; The Francis Crick Institute, London, UK
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
| |
Collapse
|
28
|
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
|
29
|
Subach OM, Vlaskina AV, Agapova YK, Nikolaeva AY, Anokhin KV, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers. Int J Mol Sci 2023; 24:ijms24043279. [PMID: 36834686 PMCID: PMC9963904 DOI: 10.3390/ijms24043279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
True genetically encoded monomeric fluorescent timers (tFTs) change their fluorescent color as a result of the complete transition of the blue form into the red form over time. Tandem FTs (tdFTs) change their color as a consequence of the fast and slow independent maturation of two forms with different colors. However, tFTs are limited to derivatives of the mCherry and mRuby red fluorescent proteins and have low brightness and photostability. The number of tdFTs is also limited, and there are no blue-to-red or green-to-far-red tdFTs. tFTs and tdFTs have not previously been directly compared. Here, we engineered novel blue-to-red tFTs, called TagFT and mTagFT, which were derived from the TagRFP protein. The main spectral and timing characteristics of the TagFT and mTagFT timers were determined in vitro. The brightnesses and photoconversions of the TagFT and mTagFT tFTs were characterized in live mammalian cells. The engineered split version of the TagFT timer matured in mammalian cells at 37 °C and allowed the detection of interactions between two proteins. The TagFT timer under the control of the minimal arc promoter, successfully visualized immediate-early gene induction in neuronal cultures. We also developed and optimized green-to-far-red and blue-to-red tdFTs, named mNeptusFT and mTsFT, which were based on mNeptune-sfGFP and mTagBFP2-mScarlet fusion proteins, respectively. We developed the FucciFT2 system based on the TagFT-hCdt1-100/mNeptusFT2-hGeminin combination, which could visualize the transitions between the G1 and S/G2/M phases of the cell cycle with better resolution than the conventional Fucci system because of the fluorescent color changes of the timers over time in different phases of the cell cycle. Finally, we determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis.
Collapse
Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Yulia K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kiryl D. Piatkevich
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maxim V. Patrushev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Correspondence: ; Tel.: +7-499-196-7100-3389
| |
Collapse
|
30
|
Xu ST, Yang C, Yan XP. Organic Mass Cytometry Discriminating Cycle Stages of Single Cells with Small Molecular Indicators. Anal Chem 2023; 95:2312-2320. [PMID: 36651064 DOI: 10.1021/acs.analchem.2c04165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell cycle is a significant factor toward cellular heterogeneity, so cell cycle discrimination is a precise measurement on the top of single-cell analysis. Single-cell analysis based on organic mass spectrometry has received great attention for its unique ability to profile single-cell metabolome, but the influence of cell cycle on cellular metabolome heterogeneity has been overlooked until now due to the lack of a compatible cell cycle discrimination method. Here, we report a robust protocol based on the combination of three small molecular indicators, consisting of two small molecular labels (Hoechst and docetaxel) and one cellular endogenous compound [phosphocholine (34:1)], to discriminate single cells at different cycle stages in real time by organic mass cytometry. More than 6000 HeLa cells were acquired by an improved organic mass cytometry system to build a cell cycle differentiation model. The model successfully discriminated single HeLa cells, SCC7, and Hep G2 cells, at G0/G1, S, and G2/M stages with larger than 85% sensitivity and larger than 89% specificity. Along with cell cycle discrimination, obvious heterogeneity of amino acids, nucleotides, energy metabolic intermediates, and phospholipids was observed among single cells at different cycle stages by this protocol, further demonstrating the necessity of cell cycle discrimination for cellular metabolome heterogeneity research and the potential of more endogenous small molecular compounds for cell cycle discrimination.
Collapse
Affiliation(s)
- Shu-Ting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Ping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
31
|
Wang Z, Bartholomai BM, Loros JJ, Dunlap JC. Optimized fluorescent proteins for 4-color and photoconvertible live-cell imaging in Neurospora crassa. Fungal Genet Biol 2023; 164:103763. [PMID: 36481248 PMCID: PMC10501358 DOI: 10.1016/j.fgb.2022.103763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/27/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Fungal cells are quite unique among life in their organization and structure, and yet implementation of many tools recently developed for fluorescence imaging in animal systems and yeast has been slow in filamentous fungi. Here we present analysis of properties of fluorescent proteins in Neurospora crassa as well as describing genetic tools for the expression of these proteins that may be useful beyond cell biology applications. The brightness and photostability of ten different fluorescent protein tags were compared in a well-controlled system; six different promoters are described for the assessment of the fluorescent proteins and varying levels of expression, as well as a customizable bidirectional promoter system. We present an array of fluorescent proteins suitable for use across the visible light spectrum to allow for 4-color imaging, in addition to a photoconvertible fluorescent protein that enables a change in the color of a small subset of proteins in the cell. These tools build on the rich history of cell biology research in filamentous fungi and provide new tools to help expand research capabilities.
Collapse
Affiliation(s)
- Ziyan Wang
- Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology, Hanover, NH, USA
| | - Bradley M Bartholomai
- Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology, Hanover, NH, USA
| | - Jennifer J Loros
- Geisel School of Medicine at Dartmouth, Department of Biochemistry and Cell Biology, Hanover, NH, USA
| | - Jay C Dunlap
- Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology, Hanover, NH, USA.
| |
Collapse
|
32
|
Balasubramanian H, Sankaran J, Pandey S, Goh CJH, Wohland T. The dependence of EGFR oligomerization on environment and structure: A camera-based N&B study. Biophys J 2022; 121:4452-4466. [PMID: 36335429 PMCID: PMC9748371 DOI: 10.1016/j.bpj.2022.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Number and brightness (N&B) analysis is a fluorescence spectroscopy technique to quantify oligomerization of the mobile fraction of proteins. Accurate results, however, rely on a good knowledge of nonfluorescent states of the fluorescent labels, especially of fluorescent proteins, which are widely used in biology. Fluorescent proteins have been characterized for confocal, but not camera-based, N&B, which allows, in principle, faster measurements over larger areas. Here, we calibrate camera-based N&B implemented on a total internal reflection fluorescence microscope for various fluorescent proteins by determining their propensity to be fluorescent. We then apply camera-based N&B in live CHO-K1 cells to determine the oligomerization state of the epidermal growth factor receptor (EGFR), a transmembrane receptor tyrosine kinase that is a crucial regulator of cell proliferation and survival with implications in many cancers. EGFR oligomerization in resting cells and its regulation by the plasma membrane microenvironment are still under debate. Therefore, we investigate the effects of extrinsic factors, including membrane organization, cytoskeletal structure, and ligand stimulation, and intrinsic factors, including mutations in various EGFR domains, on the receptor's oligomerization. Our results demonstrate that EGFR oligomerization increases with removal of cholesterol or sphingolipids or the disruption of GM3-EGFR interactions, indicating raft association. However, oligomerization is not significantly influenced by the cytoskeleton. Mutations in either I706/V948 residues or E685/E687/E690 residues in the kinase and juxtamembrane domains, respectively, lead to a decrease in oligomerization, indicating their necessity for EGFR dimerization. Finally, EGFR phosphorylation is oligomerization dependent, involving the extracellular domain (550-580 residues). Coupled with biochemical investigations, camera-based N&B indicates that EGFR oligomerization and phosphorylation are the outcomes of several molecular interactions involving the lipid content and structure of the cell membrane and multiple residues in the kinase, juxtamembrane, and extracellular domains.
Collapse
Affiliation(s)
- Harikrushnan Balasubramanian
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Jagadish Sankaran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shambhavi Pandey
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Corinna Jie Hui Goh
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
33
|
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
|
34
|
Donker L, Houtekamer R, Vliem M, Sipieter F, Canever H, Gómez-González M, Bosch-Padrós M, Pannekoek WJ, Trepat X, Borghi N, Gloerich M. A mechanical G2 checkpoint controls epithelial cell division through E-cadherin-mediated regulation of Wee1-Cdk1. Cell Rep 2022; 41:111475. [DOI: 10.1016/j.celrep.2022.111475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
|
35
|
The TRESLIN-MTBP complex couples completion of DNA replication with S/G2 transition. Mol Cell 2022; 82:3350-3365.e7. [PMID: 36049481 PMCID: PMC9506001 DOI: 10.1016/j.molcel.2022.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/16/2022] [Accepted: 08/04/2022] [Indexed: 12/14/2022]
Abstract
It has been proposed that ATR kinase senses the completion of DNA replication to initiate the S/G2 transition. In contrast to this model, we show here that the TRESLIN-MTBP complex prevents a premature entry into G2 from early S-phase independently of ATR/CHK1 kinases. TRESLIN-MTBP acts transiently at pre-replication complexes (preRCs) to initiate origin firing and is released after the subsequent recruitment of CDC45. This dynamic behavior of TRESLIN-MTBP implements a monitoring system that checks the activation of replication forks and senses the rate of origin firing to prevent the entry into G2. This system detects the decline in the number of origins of replication that naturally occurs in very late S, which is the signature that cells use to determine the completion of DNA replication and permit the S/G2 transition. Our work introduces TRESLIN-MTBP as a key player in cell-cycle control independent of canonical checkpoints.
Collapse
|
36
|
Aouad P, Zhang Y, De Martino F, Stibolt C, Ali S, Ambrosini G, Mani SA, Maggs K, Quinn HM, Sflomos G, Brisken C. Epithelial-mesenchymal plasticity determines estrogen receptor positive breast cancer dormancy and epithelial reconversion drives recurrence. Nat Commun 2022; 13:4975. [PMID: 36008376 PMCID: PMC9411634 DOI: 10.1038/s41467-022-32523-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/02/2022] [Indexed: 01/06/2023] Open
Abstract
More than 70% of human breast cancers (BCs) are estrogen receptor α-positive (ER+). A clinical challenge of ER+ BC is that they can recur decades after initial treatments. Mechanisms governing latent disease remain elusive due to lack of adequate in vivo models. We compare intraductal xenografts of ER+ and triple-negative (TN) BC cells and demonstrate that disseminated TNBC cells proliferate similarly as TNBC cells at the primary site whereas disseminated ER+ BC cells proliferate slower, they decrease CDH1 and increase ZEB1,2 expressions, and exhibit characteristics of epithelial-mesenchymal plasticity (EMP) and dormancy. Forced E-cadherin expression overcomes ER+ BC dormancy. Cytokine signalings are enriched in more active versus inactive disseminated tumour cells, suggesting microenvironmental triggers for awakening. We conclude that intraductal xenografts model ER + BC dormancy and reveal that EMP is essential for the generation of a dormant cell state and that targeting exit from EMP has therapeutic potential.
Collapse
Affiliation(s)
- Patrick Aouad
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Yueyun Zhang
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Fabio De Martino
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Céline Stibolt
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Simak Ali
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Giovanna Ambrosini
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kelly Maggs
- Laboratory for Topology and Neuroscience, Brain Mind Institute, EPFL, CH-1015, Lausanne, Switzerland
| | - Hazel M Quinn
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - George Sflomos
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Cathrin Brisken
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland. .,The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK.
| |
Collapse
|
37
|
Aulicino F, Pelosse M, Toelzer C, Capin J, Ilegems E, Meysami P, Rollarson R, Berggren PO, Dillingham M, Schaffitzel C, Saleem M, Welsh G, Berger I. Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus. Nucleic Acids Res 2022; 50:7783-7799. [PMID: 35801912 PMCID: PMC9303279 DOI: 10.1093/nar/gkac587] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
CRISPR-based precise gene-editing requires simultaneous delivery of multiple components into living cells, rapidly exceeding the cargo capacity of traditional viral vector systems. This challenge represents a major roadblock to genome engineering applications. Here we exploit the unmatched heterologous DNA cargo capacity of baculovirus to resolve this bottleneck in human cells. By encoding Cas9, sgRNA and Donor DNAs on a single, rapidly assembled baculoviral vector, we achieve with up to 30% efficacy whole-exon replacement in the intronic β-actin (ACTB) locus, including site-specific docking of very large DNA payloads. We use our approach to rescue wild-type podocin expression in steroid-resistant nephrotic syndrome (SRNS) patient derived podocytes. We demonstrate single baculovirus vectored delivery of single and multiplexed prime-editing toolkits, achieving up to 100% cleavage-free DNA search-and-replace interventions without detectable indels. Taken together, we provide a versatile delivery platform for single base to multi-gene level genome interventions, addressing the currently unmet need for a powerful delivery system accommodating current and future CRISPR technologies without the burden of limited cargo capacity.
Collapse
Affiliation(s)
- Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Martin Pelosse
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Christine Toelzer
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Julien Capin
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Erwin Ilegems
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Parisa Meysami
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Ruth Rollarson
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Mark Simon Dillingham
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Christiane Schaffitzel
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Moin A Saleem
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Gavin I Welsh
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Imre Berger
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| |
Collapse
|
38
|
Taïeb HM, Bertinetti L, Robinson T, Cipitria A. FUCCItrack: An all-in-one software for single cell tracking and cell cycle analysis. PLoS One 2022; 17:e0268297. [PMID: 35793313 PMCID: PMC9258891 DOI: 10.1371/journal.pone.0268297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
Abstract
Beyond the more conventional single-cell segmentation and tracking, single-cell cycle dynamics is gaining a growing interest in the field of cell biology. Thanks to sophisticated systems, such as the fluorescent ubiquitination-based cell cycle indicator (FUCCI), it is now possible to study cell proliferation, migration, changes in nuclear morphology and single cell cycle dynamics, quantitatively and in real time. In this work, we introduce FUCCItrack, an all-in-one, semi-automated software to segment, track and visualize FUCCI modified cell lines. A user-friendly complete graphical user interface is presented to record and quantitatively analyze both collective cell proliferation as well as single cell information, including migration and changes in nuclear or cell morphology as a function of cell cycle. To enable full control over the analysis, FUCCItrack also contains features for identification of errors and manual corrections.
Collapse
Affiliation(s)
- Hubert M. Taïeb
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail: (AC); (HMT)
| | - Luca Bertinetti
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- B CUBE Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Tom Robinson
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Amaia Cipitria
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Biodonostia Health Research Institute, Group of Bioengineering in Regeneration and Cancer, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail: (AC); (HMT)
| |
Collapse
|
39
|
Kim JA, Berlow NE, Lathara M, Bharathy N, Martin LR, Purohit R, Cleary MM, Liu Q, Michalek JE, Srinivasa G, Cole BL, Chen SD, Keller C. Sensitization of osteosarcoma to irradiation by targeting nuclear FGFR1. Biochem Biophys Res Commun 2022; 621:101-108. [DOI: 10.1016/j.bbrc.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
|
40
|
Martinez MAQ, Matus DQ. CDK activity sensors: genetically encoded ratiometric biosensors for live analysis of the cell cycle. Biochem Soc Trans 2022; 50:1081-1090. [PMID: 35674434 PMCID: PMC9661961 DOI: 10.1042/bst20211131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/09/2022] [Accepted: 05/18/2022] [Indexed: 01/04/2023]
Abstract
Cyclin-dependent kinase (CDK) sensors have facilitated investigations of the cell cycle in living cells. These genetically encoded fluorescent biosensors change their subcellular location upon activation of CDKs. Activation is primarily regulated by their association with cyclins, which in turn trigger cell-cycle progression. In the absence of CDK activity, cells exit the cell cycle and become quiescent, a key step in stem cell maintenance and cancer cell dormancy. The evolutionary conservation of CDKs has allowed for the rapid development of CDK activity sensors for cell lines and several research organisms, including nematodes, fish, and flies. CDK activity sensors are utilized for their ability to visualize the exact moment of cell-cycle commitment. This has provided a breakthrough in understanding the proliferation-quiescence decision. Further adoption of these biosensors will usher in new discoveries focused on the cell-cycle regulation of development, ageing, and cancer.
Collapse
Affiliation(s)
- Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, U.S.A
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, U.S.A
| |
Collapse
|
41
|
Greenberg A, Simon I. S Phase Duration Is Determined by Local Rate and Global Organization of Replication. BIOLOGY 2022; 11:718. [PMID: 35625446 PMCID: PMC9139170 DOI: 10.3390/biology11050718] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
Abstract
The duration of the cell cycle has been extensively studied and a wide degree of variability exists between cells, tissues and organisms. However, the duration of S phase has often been neglected, due to the false assumption that S phase duration is relatively constant. In this paper, we describe the methodologies to measure S phase duration, summarize the existing knowledge about its variability and discuss the key factors that control it. The local rate of replication (LRR), which is a combination of fork rate (FR) and inter-origin distance (IOD), has a limited influence on S phase duration, partially due to the compensation between FR and IOD. On the other hand, the organization of the replication program, specifically the amount of replication domains that fire simultaneously and the degree of overlap between the firing of distinct replication timing domains, is the main determinant of S phase duration. We use these principles to explain the variation in S phase length in different tissues and conditions.
Collapse
Affiliation(s)
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel;
| |
Collapse
|
42
|
Yu HG, Bijian K, da Silva SD, Su J, Morand G, Spatz A, Alaoui-Jamali MA. NEDD9 links anaplastic thyroid cancer stemness to chromosomal instability through integrated centrosome asymmetry and DNA sensing regulation. Oncogene 2022; 41:2984-2999. [PMID: 35449243 DOI: 10.1038/s41388-022-02317-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/09/2022]
Abstract
Stemness and chromosomal instability (CIN) are two common contributors to intratumor heterogeneity and therapy relapse in advanced cancer, but their interplays are poorly defined. Here, in anaplastic thyroid cancer (ATC), we show that ALDH+ stem-like cancer cells possess increased CIN-tolerance owing to transcriptional upregulation of the scaffolding protein NEDD9. Thyroid patient tissues and transcriptomic data reveals NEDD9/ALDH1A3 to be co-expressed and co-upregulated in ATC. Compared to bulk ALDH- cells, ALDH+ cells were highly efficient at propagating CIN due to their intrinsic tolerance of both centrosome amplification and micronuclei. ALDH+ cells mitigated the fitness-impairing effects of centrosome amplification by partially inactivating supernumerary centrosomes. Meanwhile, ALDH+ cells also mitigated cell death caused by micronuclei-mediated type 1 interferon secretion by suppressing the expression of the DNA-sensor protein STING. Both mechanisms of CIN-tolerance were lost upon RNAi-mediated NEDD9 silencing. Both in vitro and in vivo, NEDD9-depletion attenuated stemness, CIN, cell/tumor growth, while enhancing paclitaxel effectiveness. Collectively, these findings reveal that ATC progression can involve an ALDH1A3/NEDD9-regulated program linking their stemness to CIN-tolerance that could be leveraged for ATC treatment.
Collapse
Affiliation(s)
- Henry G Yu
- Departments of Medicine, Oncology, Lady Davis Institute for Medical Research and Segal Cancer Centre, the Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Krikor Bijian
- Departments of Medicine, Oncology, Lady Davis Institute for Medical Research and Segal Cancer Centre, the Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Sabrina D da Silva
- Departments of Medicine, Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, the Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Jie Su
- Departments of Medicine, Oncology, Lady Davis Institute for Medical Research and Segal Cancer Centre, the Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Gregoire Morand
- Departments of Medicine, Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, the Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Alan Spatz
- Departments of Medicine, Pathology, Lady Davis Institute for Medical Research and Segal Cancer Centre, the Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Moulay A Alaoui-Jamali
- Departments of Medicine, Oncology, Lady Davis Institute for Medical Research and Segal Cancer Centre, the Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada.
| |
Collapse
|
43
|
Oncogenic RAS sensitizes cells to drug-induced replication stress via transcriptional silencing of P53. Oncogene 2022; 41:2719-2733. [PMID: 35393546 PMCID: PMC9076537 DOI: 10.1038/s41388-022-02291-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022]
Abstract
Cancer cells often experience high basal levels of DNA replication stress (RS), for example due to hyperactivation of oncoproteins like MYC or RAS. Therefore, cancer cells are considered to be sensitive to drugs that exacerbate the level of RS or block the intra S-phase checkpoint. Consequently, RS-inducing drugs including ATR and CHK1 inhibitors are used or evaluated as anti-cancer therapies. However, drug resistance and lack of biomarkers predicting therapeutic efficacy limit efficient use. This raises the question what determines sensitivity of individual cancer cells to RS. Here, we report that oncogenic RAS does not only enhance the sensitivity to ATR/CHK1 inhibitors by directly causing RS. Instead, we observed that HRASG12V dampens the activation of the P53-dependent transcriptional response to drug-induced RS, which in turn confers sensitivity to RS. We demonstrate that inducible expression of HRASG12V sensitized cells to ATR and CHK1 inhibitors. Using RNA-sequencing of FACS-sorted cells we discovered that P53 signaling is the sole transcriptional response to RS. However, oncogenic RAS attenuates the transcription of P53 and TGF-β pathway components which consequently dampens P53 target gene expression. Accordingly, live cell imaging showed that HRASG12V exacerbates RS in S/G2-phase, which could be rescued by stabilization of P53. Thus, our results demonstrate that transcriptional control of P53 target genes is the prime determinant in the response to ATR/CHK1 inhibitors and show that hyperactivation of the MAPK pathway impedes this response. Our findings suggest that the level of oncogenic MAPK signaling could predict sensitivity to intra-S-phase checkpoint inhibition in cancers with intact P53.
Collapse
|
44
|
Kim BB, Wu H, Hao YA, Pan M, Chavarha M, Zhao Y, Westberg M, St-Pierre F, Wu JC, Lin MZ. A red fluorescent protein with improved monomericity enables ratiometric voltage imaging with ASAP3. Sci Rep 2022; 12:3678. [PMID: 35256624 PMCID: PMC8901740 DOI: 10.1038/s41598-022-07313-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 01/18/2022] [Indexed: 02/07/2023] Open
Abstract
A ratiometric genetically encoded voltage indicator (GEVI) would be desirable for tracking transmembrane voltage changes in the presence of sample motion. We performed combinatorial multi-site mutagenesis on a cyan-excitable red fluorescent protein to create the bright and monomeric mCyRFP3, which proved to be uniquely non-perturbing when fused to the GEVI ASAP3. The green/red ratio from ASAP3-mCyRFP3 (ASAP3-R3) reported voltage while correcting for motion artifacts, allowing the visualization of membrane voltage changes in contracting cardiomyocytes and throughout the cell cycle of motile cells.
Collapse
Affiliation(s)
- Benjamin B Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Haodi Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, USA
- Department of Medicine, Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yukun A Hao
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael Pan
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Mariya Chavarha
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yufeng Zhao
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Michael Westberg
- Department of Neurobiology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Neurobiology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
45
|
Babakhanova S, Jung EE, Namikawa K, Zhang H, Wang Y, Subach OM, Korzhenevskiy DA, Rakitina TV, Xiao X, Wang W, Shi J, Drobizhev M, Park D, Eisenhard L, Tang H, Köster RW, Subach FV, Boyden ES, Piatkevich KD. Rapid directed molecular evolution of fluorescent proteins in mammalian cells. Protein Sci 2022; 31:728-751. [PMID: 34913537 PMCID: PMC8862398 DOI: 10.1002/pro.4261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 12/31/2022]
Abstract
In vivo imaging of model organisms is heavily reliant on fluorescent proteins with high intracellular brightness. Here we describe a practical method for rapid optimization of fluorescent proteins via directed molecular evolution in cultured mammalian cells. Using this method, we were able to perform screening of large gene libraries containing up to 2 × 107 independent random genes of fluorescent proteins expressed in HEK cells, completing one iteration of directed evolution in a course of 8 days. We employed this approach to develop a set of green and near-infrared fluorescent proteins with enhanced intracellular brightness. The developed near-infrared fluorescent proteins demonstrated high performance for fluorescent labeling of neurons in culture and in vivo in model organisms such as Caenorhabditis elegans, Drosophila, zebrafish, and mice. Spectral properties of the optimized near-infrared fluorescent proteins enabled crosstalk-free multicolor imaging in combination with common green and red fluorescent proteins, as well as dual-color near-infrared fluorescence imaging. The described method has a great potential to be adopted by protein engineers due to its simplicity and practicality. We also believe that the new enhanced fluorescent proteins will find wide application for in vivo multicolor imaging of small model organisms.
Collapse
|
46
|
Legault S, Fraser-Halberg DP, McAnelly RL, Eason MG, Thompson MC, Chica RA. Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing. Chem Sci 2022; 13:1408-1418. [PMID: 35222925 PMCID: PMC8809391 DOI: 10.1039/d1sc05088e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022] Open
Abstract
Red fluorescent proteins (RFPs) have found widespread application in chemical and biological research due to their longer emission wavelengths. Here, we use computational protein design to increase the quantum yield and thereby brightness of a dim monomeric RFP (mRojoA, quantum yield = 0.02) by optimizing chromophore packing with aliphatic residues, which we hypothesized would reduce torsional motions causing non-radiative decay. Experimental characterization of the top 10 designed sequences yielded mSandy1 (λ em = 609 nm, quantum yield = 0.26), a variant with equivalent brightness to mCherry, a widely used RFP. We next used directed evolution to further increase brightness, resulting in mSandy2 (λ em = 606 nm, quantum yield = 0.35), the brightest Discosoma sp. derived monomeric RFP with an emission maximum above 600 nm reported to date. Crystallographic analysis of mSandy2 showed that the chromophore p-hydroxybenzylidene moiety is sandwiched between the side chains of Leu63 and Ile197, a structural motif that has not previously been observed in RFPs, and confirms that aliphatic packing leads to chromophore rigidification. Our results demonstrate that computational protein design can be used to generate bright monomeric RFPs, which can serve as templates for the evolution of novel far-red fluorescent proteins.
Collapse
Affiliation(s)
- Sandrine Legault
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Derek P Fraser-Halberg
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Ralph L McAnelly
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Matthew G Eason
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| |
Collapse
|
47
|
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
|
48
|
Seleit A, Aulehla A, Paix A. Endogenous protein tagging in medaka using a simplified CRISPR/Cas9 knock-in approach. eLife 2021; 10:75050. [PMID: 34870593 PMCID: PMC8691840 DOI: 10.7554/elife.75050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/05/2021] [Indexed: 12/19/2022] Open
Abstract
The CRISPR/Cas9 system has been used to generate fluorescently labelled fusion proteins by homology-directed repair in a variety of species. Despite its revolutionary success, there remains an urgent need for increased simplicity and efficiency of genome editing in research organisms. Here, we establish a simplified, highly efficient, and precise strategy for CRISPR/Cas9-mediated endogenous protein tagging in medaka (Oryzias latipes). We use a cloning-free approach that relies on PCR-amplified donor fragments containing the fluorescent reporter sequences flanked by short homology arms (30–40 bp), a synthetic single-guide RNA and Cas9 mRNA. We generate eight novel knock-in lines with high efficiency of F0 targeting and germline transmission. Whole genome sequencing results reveal single-copy integration events only at the targeted loci. We provide an initial characterization of these fusion protein lines, significantly expanding the repertoire of genetic tools available in medaka. In particular, we show that the mScarlet-pcna line has the potential to serve as an organismal-wide label for proliferative zones and an endogenous cell cycle reporter.
Collapse
Affiliation(s)
- Ali Seleit
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alexandre Paix
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| |
Collapse
|
49
|
Echevarría C, Gutierrez C, Desvoyes B. Tools for Assessing Cell-Cycle Progression in Plants. PLANT & CELL PHYSIOLOGY 2021; 62:1231-1238. [PMID: 34021583 PMCID: PMC8579159 DOI: 10.1093/pcp/pcab066] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/27/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Estimation of cell-cycle parameters is crucial for understanding the developmental programs established during the formation of an organism. A number of complementary approaches have been developed and adapted to plants to assess the cell-cycle status in different proliferative tissues. The most classical methods relying on metabolic labeling are still very much employed and give valuable information on cell-cycle progression in fixed tissues. However, the growing knowledge of plant cell-cycle regulators with defined expression pattern together with the development of fluorescent proteins technology enabled the generation of fusion proteins that function individually or in conjunction as cell-cycle reporters. Together with the improvement of imaging techniques, in vivo live imaging to monitor plant cell-cycle progression in normal growth conditions or in response to different stimuli has been possible. Here, we review these tools and their specific outputs for plant cell-cycle analysis.
Collapse
Affiliation(s)
- Clara Echevarría
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Crisanto Gutierrez
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Madrid 28049, Spain
| | | |
Collapse
|
50
|
Wu T, Pang Y, Ai HW. Circularly Permuted Far-Red Fluorescent Proteins. BIOSENSORS 2021; 11:438. [PMID: 34821654 PMCID: PMC8615523 DOI: 10.3390/bios11110438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
The color palette of genetically encoded fluorescent protein indicators (GEFPIs) has expanded rapidly in recent years. GEFPIs with excitation and emission within the "optical window" above 600 nm are expected to be superior in many aspects, such as enhanced tissue penetration, reduced autofluorescence and scattering, and lower phototoxicity. Circular permutation of fluorescent proteins (FPs) is often the first step in the process of developing single-FP-based GEFPIs. This study explored the tolerance of two far-red FPs, mMaroon1 and mCarmine, towards circular permutation. Several initial constructs were built according to previously reported circularly permuted topologies for other FP analogs. Mutagenesis was then performed on these constructs and screened for fluorescent variants. As a result, five circularly permuted far-red FPs (cpFrFPs) with excitation and emission maxima longer than 600 nm were identified. Some displayed appreciable brightness and efficient chromophore maturation. These cpFrFPs variants could be intriguing starting points to further engineer far-red GEFPIs for in vivo tissue imaging.
Collapse
Affiliation(s)
- Tianchen Wu
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
| | - Yu Pang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
- The UVA Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|