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Lee S, Vander Roest AS, Blair CA, Kao K, Bremner SB, Childers MC, Pathak D, Heinrich P, Lee D, Chirikian O, Mohran SE, Roberts B, Smith JE, Jahng JW, Paik DT, Wu JC, Gunawardane RN, Ruppel KM, Mack DL, Pruitt BL, Regnier M, Wu SM, Spudich JA, Bernstein D. Incomplete-penetrant hypertrophic cardiomyopathy MYH7 G256E mutation causes hypercontractility and elevated mitochondrial respiration. Proc Natl Acad Sci U S A 2024; 121:e2318413121. [PMID: 38683993 PMCID: PMC11087781 DOI: 10.1073/pnas.2318413121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024] Open
Abstract
Determining the pathogenicity of hypertrophic cardiomyopathy-associated mutations in the β-myosin heavy chain (MYH7) can be challenging due to its variable penetrance and clinical severity. This study investigates the early pathogenic effects of the incomplete-penetrant MYH7 G256E mutation on myosin function that may trigger pathogenic adaptations and hypertrophy. We hypothesized that the G256E mutation would alter myosin biomechanical function, leading to changes in cellular functions. We developed a collaborative pipeline to characterize myosin function across protein, myofibril, cell, and tissue levels to determine the multiscale effects on structure-function of the contractile apparatus and its implications for gene regulation and metabolic state. The G256E mutation disrupts the transducer region of the S1 head and reduces the fraction of myosin in the folded-back state by 33%, resulting in more myosin heads available for contraction. Myofibrils from gene-edited MYH7WT/G256E human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) exhibited greater and faster tension development. This hypercontractile phenotype persisted in single-cell hiPSC-CMs and engineered heart tissues. We demonstrated consistent hypercontractile myosin function as a primary consequence of the MYH7 G256E mutation across scales, highlighting the pathogenicity of this gene variant. Single-cell transcriptomic and metabolic profiling demonstrated upregulated mitochondrial genes and increased mitochondrial respiration, indicating early bioenergetic alterations. This work highlights the benefit of our multiscale platform to systematically evaluate the pathogenicity of gene variants at the protein and contractile organelle level and their early consequences on cellular and tissue function. We believe this platform can help elucidate the genotype-phenotype relationships underlying other genetic cardiovascular diseases.
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Affiliation(s)
- Soah Lee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Biopharmaceutical Convergence, Sungkyunkwan University School of Pharmacy, Suwon, Gyeonggi-do16419South Korea
- School of Pharmacy, Sungkyunkwan University School of Pharmacy, Suwon, Gyeonggi-do16419, South Korea
| | - Alison S. Vander Roest
- Department of Pediatrics (Cardiology), Stanford University School of Medicine, Stanford, CA94305
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI48109
| | - Cheavar A. Blair
- Biological Engineering, University of California, Santa Barbara, CA93106
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY40536
| | - Kerry Kao
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Samantha B. Bremner
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Matthew C. Childers
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Divya Pathak
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Paul Heinrich
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Daniel Lee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Orlando Chirikian
- Biological Engineering, University of California, Santa Barbara, CA93106
| | - Saffie E. Mohran
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | | | | | - James W. Jahng
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - David T. Paik
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | | | - Kathleen M. Ruppel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - David L. Mack
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Beth L. Pruitt
- Biological Engineering, University of California, Santa Barbara, CA93106
| | - Michael Regnier
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Sean M. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - James A. Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Daniel Bernstein
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Pediatrics (Cardiology), Stanford University School of Medicine, Stanford, CA94305
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2
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Gregor BW, Coston ME, Adams EM, Arakaki J, Borensztejn A, Do TP, Fuqua MA, Haupt A, Hendershott MC, Leung W, Mueller IA, Nath A, Nelson AM, Rafelski SM, Sanchez EE, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Wiegraebe W, Whitney BP, Yan C, Gunawardane RN, Gaudreault N. Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy. Nat Protoc 2024; 19:565-594. [PMID: 38087082 DOI: 10.1038/s41596-023-00912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/08/2023] [Indexed: 02/12/2024]
Abstract
To produce abundant cell culture samples to generate large, standardized image datasets of human induced pluripotent stem (hiPS) cells, we developed an automated workflow on a Hamilton STAR liquid handler system. This was developed specifically for culturing hiPS cell lines expressing fluorescently tagged proteins, which we have used to study the principles by which cells establish and maintain robust dynamic localization of cellular structures. This protocol includes all details for the maintenance, passage and seeding of cells, as well as Matrigel coating of 6-well plastic plates and 96-well optical-grade, glass plates. We also developed an automated image-based hiPS cell colony segmentation and feature extraction pipeline to streamline the process of predicting cell count and selecting wells with consistent morphology for high-resolution three-dimensional (3D) microscopy. The imaging samples produced with this protocol have been used to study the integrated intracellular organization and cell-to-cell variability of hiPS cells to train and develop deep learning-based label-free predictions from transmitted-light microscopy images and to develop deep learning-based generative models of single-cell organization. This protocol requires some experience with robotic equipment. However, we provide details and source code to facilitate implementation by biologists less experienced with robotics. The protocol is completed in less than 10 h with minimal human interaction. Overall, automation of our cell culture procedures increased our imaging samples' standardization, reproducibility, scalability and consistency. It also reduced the need for stringent culturist training and eliminated culturist-to-culturist variability, both of which were previous pain points of our original manual pipeline workflow.
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Affiliation(s)
| | | | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Thao P Do
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Winnie Leung
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Aditya Nath
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | - W Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
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3
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Lee S, Roest ASV, Blair CA, Kao K, Bremner SB, Childers MC, Pathak D, Heinrich P, Lee D, Chirikian O, Mohran S, Roberts B, Smith JE, Jahng JW, Paik DT, Wu JC, Gunawardane RN, Spudich JA, Ruppel K, Mack D, Pruitt BL, Regnier M, Wu SM, Bernstein D. Multi-scale models reveal hypertrophic cardiomyopathy MYH7 G256E mutation drives hypercontractility and elevated mitochondrial respiration. bioRxiv 2023:2023.06.08.544276. [PMID: 37333118 PMCID: PMC10274883 DOI: 10.1101/2023.06.08.544276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Rationale Over 200 mutations in the sarcomeric protein β-myosin heavy chain (MYH7) have been linked to hypertrophic cardiomyopathy (HCM). However, different mutations in MYH7 lead to variable penetrance and clinical severity, and alter myosin function to varying degrees, making it difficult to determine genotype-phenotype relationships, especially when caused by rare gene variants such as the G256E mutation. Objective This study aims to determine the effects of low penetrant MYH7 G256E mutation on myosin function. We hypothesize that the G256E mutation would alter myosin function, precipitating compensatory responses in cellular functions. Methods We developed a collaborative pipeline to characterize myosin function at multiple scales (protein to myofibril to cell to tissue). We also used our previously published data on other mutations to compare the degree to which myosin function was altered. Results At the protein level, the G256E mutation disrupts the transducer region of the S1 head and reduces the fraction of myosin in the folded-back state by 50.9%, suggesting more myosins available for contraction. Myofibrils isolated from hiPSC-CMs CRISPR-edited with G256E (MYH7 WT/G256E ) generated greater tension, had faster tension development and slower early phase relaxation, suggesting altered myosin-actin crossbridge cycling kinetics. This hypercontractile phenotype persisted in single-cell hiPSC-CMs and engineered heart tissues. Single-cell transcriptomic and metabolic profiling demonstrated upregulation of mitochondrial genes and increased mitochondrial respiration, suggesting altered bioenergetics as an early feature of HCM. Conclusions MYH7 G256E mutation causes structural instability in the transducer region, leading to hypercontractility across scales, perhaps from increased myosin recruitment and altered crossbridge cycling. Hypercontractile function of the mutant myosin was accompanied by increased mitochondrial respiration, while cellular hypertrophy was modest in the physiological stiffness environment. We believe that this multi-scale platform will be useful to elucidate genotype-phenotype relationships underlying other genetic cardiovascular diseases.
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4
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Viana MP, Chen J, Knijnenburg TA, Vasan R, Yan C, Arakaki JE, Bailey M, Berry B, Borensztejn A, Brown EM, Carlson S, Cass JA, Chaudhuri B, Cordes Metzler KR, Coston ME, Crabtree ZJ, Davidson S, DeLizo CM, Dhaka S, Dinh SQ, Do TP, Domingus J, Donovan-Maiye RM, Ferrante AJ, Foster TJ, Frick CL, Fujioka G, Fuqua MA, Gehring JL, Gerbin KA, Grancharova T, Gregor BW, Harrylock LJ, Haupt A, Hendershott MC, Hookway C, Horwitz AR, Hughes HC, Isaac EJ, Johnson GR, Kim B, Leonard AN, Leung WW, Lucas JJ, Ludmann SA, Lyons BM, Malik H, McGregor R, Medrash GE, Meharry SL, Mitcham K, Mueller IA, Murphy-Stevens TL, Nath A, Nelson AM, Oluoch SA, Paleologu L, Popiel TA, Riel-Mehan MM, Roberts B, Schaefbauer LM, Schwarzl M, Sherman J, Slaton S, Sluzewski MF, Smith JE, Sul Y, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Toloudis DM, Tucker AP, Valencia V, Wiegraebe W, Wijeratna T, Yang R, Zaunbrecher RJ, Labitigan RLD, Sanborn AL, Johnson GT, Gunawardane RN, Gaudreault N, Theriot JA, Rafelski SM. Integrated intracellular organization and its variations in human iPS cells. Nature 2023; 613:345-354. [PMID: 36599983 PMCID: PMC9834050 DOI: 10.1038/s41586-022-05563-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/15/2022] [Indexed: 01/06/2023]
Abstract
Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduced this complexity by focusing on cellular organization-a key readout and driver of cell behaviour3,4-at the level of major cellular structures that represent distinct organelles and functional machines, and generated the WTC-11 hiPSC Single-Cell Image Dataset v1, which contains more than 200,000 live cells in 3D, spanning 25 key cellular structures. The scale and quality of this dataset permitted the creation of a generalizable analysis framework to convert raw image data of cells and their structures into dimensionally reduced, quantitative measurements that can be interpreted by humans, and to facilitate data exploration. This framework embraces the vast cell-to-cell variability that is observed within a normal population, facilitates the integration of cell-by-cell structural data and allows quantitative analyses of distinct, separable aspects of organization within and across different cell populations. We found that the integrated intracellular organization of interphase cells was robust to the wide range of variation in cell shape in the population; that the average locations of some structures became polarized in cells at the edges of colonies while maintaining the 'wiring' of their interactions with other structures; and that, by contrast, changes in the location of structures during early mitotic reorganization were accompanied by changes in their wiring.
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Affiliation(s)
| | - Jianxu Chen
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Ritvik Vasan
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Matte Bailey
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Ben Berry
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Eva M Brown
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Sara Carlson
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Julie A Cass
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | - Thao P Do
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | - Eric J Isaac
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Brian Kim
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | - Haseeb Malik
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Aditya Nath
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Youngmee Sul
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - W Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Ramon Lorenzo D Labitigan
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Adrian L Sanborn
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | | | | | | | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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5
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Grancharova T, Gerbin KA, Rosenberg AB, Roco CM, Arakaki JE, DeLizo CM, Dinh SQ, Donovan-Maiye RM, Hirano M, Nelson AM, Tang J, Theriot JA, Yan C, Menon V, Palecek SP, Seelig G, Gunawardane RN. A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes. Sci Rep 2021; 11:15845. [PMID: 34349150 PMCID: PMC8338992 DOI: 10.1038/s41598-021-94732-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
We performed a comprehensive analysis of the transcriptional changes occurring during human induced pluripotent stem cell (hiPSC) differentiation to cardiomyocytes. Using single cell RNA-seq, we sequenced > 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. Differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables.
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Affiliation(s)
| | | | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,, Parse Biosciences, Seattle, WA, USA
| | - Charles M Roco
- , Parse Biosciences, Seattle, WA, USA.,Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Matthew Hirano
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA
| | | | - Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Julie A Theriot
- Allen Institute for Cell Science, Seattle, WA, USA.,Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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6
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Gerbin KA, Grancharova T, Donovan-Maiye RM, Hendershott MC, Anderson HG, Brown JM, Chen J, Dinh SQ, Gehring JL, Johnson GR, Lee H, Nath A, Nelson AM, Sluzewski MF, Viana MP, Yan C, Zaunbrecher RJ, Cordes Metzler KR, Gaudreault N, Knijnenburg TA, Rafelski SM, Theriot JA, Gunawardane RN. Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes. Cell Syst 2021; 12:670-687.e10. [PMID: 34043964 DOI: 10.1016/j.cels.2021.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/07/2020] [Accepted: 04/30/2021] [Indexed: 12/11/2022]
Abstract
Although some cell types may be defined anatomically or by physiological function, a rigorous definition of cell state remains elusive. Here, we develop a quantitative, imaging-based platform for the systematic and automated classification of subcellular organization in single cells. We use this platform to quantify subcellular organization and gene expression in >30,000 individual human induced pluripotent stem cell-derived cardiomyocytes, producing a publicly available dataset that describes the population distributions of local and global sarcomere organization, mRNA abundance, and correlations between these traits. While the mRNA abundance of some phenotypically important genes correlates with subcellular organization (e.g., the beta-myosin heavy chain, MYH7), these two cellular metrics are heterogeneous and often uncorrelated, which suggests that gene expression alone is not sufficient to classify cell states. Instead, we posit that cell state should be defined by observing full distributions of quantitative, multidimensional traits in single cells that also account for space, time, and function.
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Affiliation(s)
- Kaytlyn A Gerbin
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Tanya Grancharova
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | | | - Helen G Anderson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jackson M Brown
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jianxu Chen
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Stephanie Q Dinh
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jamie L Gehring
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Gregory R Johnson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - HyeonWoo Lee
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Aditya Nath
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | - M Filip Sluzewski
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Matheus P Viana
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | | | | | | | | | - Julie A Theriot
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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7
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Roberts B, Hendershott MC, Arakaki J, Gerbin KA, Malik H, Nelson A, Gehring J, Hookway C, Ludmann SA, Yang R, Haupt A, Grancharova T, Valencia V, Fuqua MA, Tucker A, Rafelski SM, Gunawardane RN. Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs. Stem Cell Reports 2019; 12:1145-1158. [PMID: 30956114 PMCID: PMC6522946 DOI: 10.1016/j.stemcr.2019.03.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/27/2022] Open
Abstract
We describe a multistep method for endogenous tagging of transcriptionally silent genes in human induced pluripotent stem cells (hiPSCs). A monomeric EGFP (mEGFP) fusion tag and a constitutively expressed mCherry fluorescence selection cassette were delivered in tandem via homology-directed repair to five genes not expressed in hiPSCs but important for cardiomyocyte sarcomere function: TTN, MYL7, MYL2, TNNI1, and ACTN2. CRISPR/Cas9 was used to deliver the selection cassette and subsequently mediate its excision via microhomology-mediated end-joining and non-homologous end-joining. Most excised clones were effectively tagged, and all properly tagged clones expressed the mEGFP fusion protein upon differentiation into cardiomyocytes, allowing live visualization of these cardiac proteins at the sarcomere. This methodology provides a broadly applicable strategy for endogenously tagging transcriptionally silent genes in hiPSCs, potentially enabling their systematic and dynamic study during differentiation and morphogenesis.
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Affiliation(s)
- Brock Roberts
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Haseeb Malik
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Jamie Gehring
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | | | | | - Andrew Tucker
- Allen Institute for Cell Science, Seattle, WA 98109, USA
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8
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Abstract
A protocol is presented for generating human induced pluripotent stem cells (hiPSCs) that express endogenous proteins fused to in-frame N- or C-terminal fluorescent tags. The prokaryotic CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeats/CRISPR-associated 9) may be used to introduce large exogenous sequences into genomic loci via homology directed repair (HDR). To achieve the desired knock-in, this protocol employs the ribonucleoprotein (RNP)-based approach where wild type Streptococcus pyogenes Cas9 protein, synthetic 2-part guide RNA (gRNA), and a donor template plasmid are delivered to the cells via electroporation. Putatively edited cells expressing the fluorescently tagged proteins are enriched by fluorescence activated cell sorting (FACS). Clonal lines are then generated and can be analyzed for precise editing outcomes. By introducing the fluorescent tag at the genomic locus of the gene of interest, the resulting subcellular localization and dynamics of the fusion protein can be studied under endogenous regulatory control, a key improvement over conventional overexpression systems. The use of hiPSCs as a model system for gene tagging provides the opportunity to study the tagged proteins in diploid, nontransformed cells. Since hiPSCs can be differentiated into multiple cell types, this approach provides the opportunity to create and study tagged proteins in a variety of isogenic cellular contexts.
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9
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Roberts B, Haupt A, Tucker A, Grancharova T, Arakaki J, Fuqua MA, Nelson A, Hookway C, Ludmann SA, Mueller IA, Yang R, Horwitz R, Rafelski SM, Gunawardane RN. Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization. Mol Biol Cell 2017; 28:2854-2874. [PMID: 28814507 PMCID: PMC5638588 DOI: 10.1091/mbc.e17-03-0209] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
The generation of a collection of human induced pluripotent stem cell (hiPSC) lines expressing endogenously GFP-tagged proteins using CRISPR/Cas9 methods is described. The methods used and the genomic and cell biological data validating the GFP-tagged hiPSC lines are also presented. We present a CRISPR/Cas9 genome-editing strategy to systematically tag endogenous proteins with fluorescent tags in human induced pluripotent stem cells (hiPSC). To date, we have generated multiple hiPSC lines with monoallelic green fluorescent protein tags labeling 10 proteins representing major cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, nuclear lamin B1, nonmuscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20. Our genome-editing methodology using Cas9/crRNA ribonuclear protein and donor plasmid coelectroporation, followed by fluorescence-based enrichment of edited cells, typically resulted in <0.1–4% homology-directed repair (HDR). Twenty-five percent of clones generated from each edited population were precisely edited. Furthermore, 92% (36/39) of expanded clonal lines displayed robust morphology, genomic stability, expression and localization of the tagged protein to the appropriate subcellular structure, pluripotency-marker expression, and multilineage differentiation. It is our conclusion that, if cell lines are confirmed to harbor an appropriate gene edit, pluripotency, differentiation potential, and genomic stability are typically maintained during the clonal line–generation process. The data described here reveal general trends that emerged from this systematic gene-tagging approach. Final clonal lines corresponding to each of the 10 cellular structures are now available to the research community.
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Affiliation(s)
| | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA 98109
| | | | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA 98109
| | | | | | | | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA 98109
| | - Rick Horwitz
- Allen Institute for Cell Science, Seattle, WA 98109
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10
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Gunawardane RN, Fordstrom P, Piper DE, Masterman S, Siu S, Liu D, Brown M, Lu M, Tang J, Zhang R, Cheng J, Gates A, Meininger D, Chan J, Carlson T, Walker N, Schwarz M, Delaney J, Zhou M. Agonistic Human Antibodies Binding to Lecithin-Cholesterol Acyltransferase Modulate High Density Lipoprotein Metabolism. J Biol Chem 2015; 291:2799-811. [PMID: 26644477 PMCID: PMC4742745 DOI: 10.1074/jbc.m115.672790] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Indexed: 11/28/2022] Open
Abstract
Drug discovery opportunities where loss-of-function alleles of a target gene link to a disease-relevant phenotype often require an agonism approach to up-regulate or re-establish the activity of the target gene. Antibody therapy is increasingly recognized as a favored drug modality due to multiple desirable pharmacological properties. However, agonistic antibodies that enhance the activities of the target enzymes are rarely developed because the discovery of agonistic antibodies remains elusive. Here we report an innovative scheme of discovery and characterization of human antibodies capable of binding to and agonizing a circulating enzyme lecithin cholesterol acyltransferase (LCAT). Utilizing a modified human LCAT protein with enhanced enzymatic activity as an immunogen, we generated fully human monoclonal antibodies using the XenoMouseTM platform. One of the resultant agonistic antibodies, 27C3, binds to and substantially enhances the activity of LCAT from humans and cynomolgus macaques. X-ray crystallographic analysis of the 2.45 Å LCAT-27C3 complex shows that 27C3 binding does not induce notable structural changes in LCAT. A single administration of 27C3 to cynomolgus monkeys led to a rapid increase of plasma LCAT enzymatic activity and a 35% increase of the high density lipoprotein cholesterol that was observed up to 32 days after 27C3 administration. Thus, this novel scheme of immunization in conjunction with high throughput screening may represent an effective strategy for discovering agonistic antibodies against other enzyme targets. 27C3 and other agonistic human anti-human LCAT monoclonal antibodies described herein hold potential for therapeutic development for the treatment of dyslipidemia and cardiovascular disease.
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Affiliation(s)
| | | | | | - Stephanie Masterman
- Therapeutic Discovery, Amgen Inc., Burnaby, British Columbia V5A 1V7, Canada
| | - Sophia Siu
- From Therapeutic Discovery, Amgen Inc., Seattle, Washington 98119
| | | | - Mike Brown
- From Therapeutic Discovery, Amgen Inc., Seattle, Washington 98119
| | - Mei Lu
- Therapeutic Discovery, and
| | | | | | - Janet Cheng
- From Therapeutic Discovery, Amgen Inc., Seattle, Washington 98119
| | - Andrew Gates
- From Therapeutic Discovery, Amgen Inc., Seattle, Washington 98119
| | - David Meininger
- From Therapeutic Discovery, Amgen Inc., Seattle, Washington 98119
| | | | - Tim Carlson
- PKDM Department, Amgen Inc., South San Francisco, California 94080, and
| | | | | | - John Delaney
- Therapeutic Discovery, Amgen Inc., Burnaby, British Columbia V5A 1V7, Canada
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11
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Piper DE, Romanow WG, Gunawardane RN, Fordstrom P, Masterman S, Pan O, Thibault ST, Zhang R, Meininger D, Schwarz M, Wang Z, King C, Zhou M, Walker NPC. The high-resolution crystal structure of human LCAT. J Lipid Res 2015. [PMID: 26195816 DOI: 10.1194/jlr.m059873] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
LCAT is intimately involved in HDL maturation and is a key component of the reverse cholesterol transport (RCT) pathway which removes excess cholesterol molecules from the peripheral tissues to the liver for excretion. Patients with loss-of-function LCAT mutations exhibit low levels of HDL cholesterol and corneal opacity. Here we report the 2.65 Å crystal structure of the human LCAT protein. Crystallization required enzymatic removal of N-linked glycans and complex formation with a Fab fragment from a tool antibody. The crystal structure reveals that LCAT has an α/β hydrolase core with two additional subdomains that play important roles in LCAT function. Subdomain 1 contains the region of LCAT shown to be required for interfacial activation, while subdomain 2 contains the lid and amino acids that shape the substrate binding pocket. Mapping the naturally occurring mutations onto the structure provides insight into how they may affect LCAT enzymatic activity.
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Affiliation(s)
- Derek E Piper
- Therapeutic Discovery Amgen Inc., South San Francisco, CA 94080
| | | | | | | | | | - Oscar Pan
- Therapeutic Discovery, Amgen Inc., Burnaby, BC V5A1V7, Canada
| | | | - Richard Zhang
- Therapeutic Discovery Amgen Inc., South San Francisco, CA 94080
| | | | - Margrit Schwarz
- Metabolic Disorders, Amgen Inc., South San Francisco, CA 94080
| | - Zhulun Wang
- Therapeutic Discovery Amgen Inc., South San Francisco, CA 94080
| | - Chadwick King
- Therapeutic Discovery, Amgen Inc., Burnaby, BC V5A1V7, Canada
| | - Mingyue Zhou
- Metabolic Disorders, Amgen Inc., South San Francisco, CA 94080
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12
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Buchwalter G, Hickey MM, Cromer A, Selfors LM, Gunawardane RN, Frishman J, Jeselsohn R, Lim E, Chi D, Fu X, Schiff R, Brown M, Brugge JS. PDEF promotes luminal differentiation and acts as a survival factor for ER-positive breast cancer cells. Cancer Cell 2013; 23:753-67. [PMID: 23764000 PMCID: PMC3711136 DOI: 10.1016/j.ccr.2013.04.026] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 02/19/2013] [Accepted: 04/23/2013] [Indexed: 01/25/2023]
Abstract
Breast cancer is a heterogeneous disease and can be classified based on gene expression profiles that reflect distinct epithelial subtypes. We identify prostate-derived ETS factor (PDEF) as a mediator of mammary luminal epithelial lineage-specific gene expression and as a factor required for tumorigenesis in a subset of breast cancers. PDEF levels strongly correlate with estrogen receptor (ER)-positive luminal breast cancer, and PDEF transcription is inversely regulated by ER and GATA3. Furthermore, PDEF is essential for luminal breast cancer cell survival and is required in models of endocrine resistance. These results offer insights into the function of this ETS factor that are clinically relevant and may be of therapeutic value for patients with breast cancer treated with endocrine therapy.
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Affiliation(s)
- Gilles Buchwalter
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School
| | - Michele M. Hickey
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Anne Cromer
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Laura M. Selfors
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | | | - Jason Frishman
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School
| | - Rinath Jeselsohn
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School
| | - Elgene Lim
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School
| | - David Chi
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School
| | - Xiaosong Fu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77054, USA
| | - Rachel Schiff
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77054, USA
| | - Myles Brown
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School
- Correspondence: (J.S.B.), (M.B.)
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Correspondence: (J.S.B.), (M.B.)
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13
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Gunawardane RN, Nepomuceno RR, Rooks AM, Hunt JP, Ricono JM, Belli B, Armstrong RC. Transient exposure to quizartinib mediates sustained inhibition of FLT3 signaling while specifically inducing apoptosis in FLT3-activated leukemia cells. Mol Cancer Ther 2013; 12:438-47. [PMID: 23412931 DOI: 10.1158/1535-7163.mct-12-0305] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fms-like tyrosine kinase 3 (FLT3) is implicated in the pathogenesis of acute myeloid leukemia (AML). FLT3-activating internal tandem duplication (ITD) mutations are found in approximately 30% of patients with AML and are associated with poor outcome in this patient population. Quizartinib (AC220) has previously been shown to be a potent and selective FLT3 inhibitor. In the current study, we expand on previous observations by showing that quizartinib potently inhibits the phosphorylation of FLT3 and downstream signaling molecules independent of FLT3 genotype, yet induces loss of viability only in cells expressing constitutively activated FLT3. We further show that transient exposure to quizartinib, whether in vitro or in vivo, leads to prolonged inhibition of FLT3 signaling, induction of apoptosis, and drastic reductions in tumor volume and pharmacodynamic endpoints. In vitro experiments suggest that these prolonged effects are mediated by slow binding kinetics that provide for durable inhibition of the kinase following drug removal/clearance. Together these data suggest quizartinib, with its unique combination of selectivity and potent/sustained inhibition of FLT3, may provide a safe and effective treatment against FLT3-driven leukemia.
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14
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Liu G, Abraham S, Tran L, Vickers TD, Xu S, Hadd MJ, Quiambao S, Holladay MW, Hua H, Ford Pulido JM, Gunawardane RN, Davis MI, Eichelberger SR, Apuy JL, Gitnick D, Gardner MF, James J, Breider MA, Belli B, Armstrong RC, Treiber DK. Discovery of Highly Potent and Selective Pan-Aurora Kinase Inhibitors with Enhanced in Vivo Antitumor Therapeutic Index. J Med Chem 2012; 55:3250-60. [DOI: 10.1021/jm201702g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Gang Liu
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Sunny Abraham
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Lan Tran
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Troy D. Vickers
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Shimin Xu
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Michael J. Hadd
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Sheena Quiambao
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Mark W. Holladay
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Helen Hua
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Julia M. Ford Pulido
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Ruwanthi N. Gunawardane
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Mindy I. Davis
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Shawn R. Eichelberger
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Julius L. Apuy
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Dana Gitnick
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Michael F. Gardner
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Joyce James
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Mike A. Breider
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Barbara Belli
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Robert C. Armstrong
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - Daniel K. Treiber
- Departments of †Medicinal Chemistry, ‡Cell Biology and
Pharmacology, §Technology Development, ∥DMPK and Toxicology, and ⊥CMC, Ambit Biosciences Corporation, 4215
Sorrento Valley Boulevard, San Diego, California 92121, United States
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15
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James J, Ruggeri B, Armstrong RC, Rowbottom MW, Jones-Bolin S, Gunawardane RN, Dobrzanski P, Gardner MF, Zhao H, Cramer MD, Hunter K, Nepomuceno RR, Cheng M, Gitnick D, Yazdanian M, Insko DE, Ator MA, Apuy JL, Faraoni R, Dorsey BD, Williams M, Bhagwat SS, Holladay MW. CEP-32496: a novel orally active BRAF(V600E) inhibitor with selective cellular and in vivo antitumor activity. Mol Cancer Ther 2012; 11:930-41. [PMID: 22319199 DOI: 10.1158/1535-7163.mct-11-0645] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutations in the BRAF gene have been identified in approximately 7% of cancers, including 60% to 70% of melanomas, 29% to 83% of papillary thyroid carcinomas, 4% to 16% colorectal cancers, and a lesser extent in serous ovarian and non-small cell lung cancers. The V600E mutation is found in the vast majority of cases and is an activating mutation, conferring transforming and immortalization potential to cells. CEP-32496 is a potent BRAF inhibitor in an in vitro binding assay for mutated BRAF(V600E) (K(d) BRAF(V600E) = 14 nmol/L) and in a mitogen-activated protein (MAP)/extracellular signal-regulated (ER) kinase (MEK) phosphorylation (pMEK) inhibition assay in human melanoma (A375) and colorectal cancer (Colo-205) cell lines (IC(50) = 78 and 60 nmol/L). In vitro, CEP-32496 has multikinase binding activity at other cancer targets of interest; however, it exhibits selective cellular cytotoxicity for BRAF(V600E) versus wild-type cells. CEP-32496 is orally bioavailable in multiple preclinical species (>95% in rats, dogs, and monkeys) and has single oral dose pharmacodynamic inhibition (10-55 mg/kg) of both pMEK and pERK in BRAF(V600E) colon carcinoma xenografts in nude mice. Sustained tumor stasis and regressions are observed with oral administration (30-100 mg/kg twice daily) against BRAF(V600E) melanoma and colon carcinoma xenografts, with no adverse effects. Little or no epithelial hyperplasia was observed in rodents and primates with prolonged oral administration and sustained exposure. CEP-32496 benchmarks favorably with respect to other kinase inhibitors, including RAF-265 (phase I), sorafenib, (approved), and vemurafenib (PLX4032/RG7204, approved). CEP-32496 represents a novel and pharmacologically active BRAF inhibitor with a favorable side effect profile currently in clinical development.
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Affiliation(s)
- Joyce James
- Ambit Biosciences Corporation, San Diego, CA 92121, USA.
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16
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Rowbottom MW, Faraoni R, Chao Q, Campbell BT, Lai AG, Setti E, Ezawa M, Sprankle KG, Abraham S, Tran L, Struss B, Gibney M, Armstrong RC, Gunawardane RN, Nepomuceno RR, Valenta I, Hua H, Gardner MF, Cramer MD, Gitnick D, Insko DE, Apuy JL, Jones-Bolin S, Ghose AK, Herbertz T, Ator MA, Dorsey BD, Ruggeri B, Williams M, Bhagwat S, James J, Holladay MW. Identification of 1-(3-(6,7-Dimethoxyquinazolin-4-yloxy)phenyl)-3-(5-(1,1,1-trifluoro-2-methylpropan-2-yl)isoxazol-3-yl)urea Hydrochloride (CEP-32496), a Highly Potent and Orally Efficacious Inhibitor of V-RAF Murine Sarcoma Viral Oncogene Homologue B1 (BRAF) V600E. J Med Chem 2012; 55:1082-105. [DOI: 10.1021/jm2009925] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin W. Rowbottom
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Raffaella Faraoni
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Qi Chao
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Brian T. Campbell
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Andiliy G. Lai
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Eduardo Setti
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Maiko Ezawa
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Kelly G. Sprankle
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Sunny Abraham
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Lan Tran
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Brian Struss
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Michael Gibney
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Robert C. Armstrong
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Ruwanthi N. Gunawardane
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Ronald R. Nepomuceno
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Ianina Valenta
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Helen Hua
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Michael F. Gardner
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Merryl D. Cramer
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Dana Gitnick
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Darren E. Insko
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Julius L. Apuy
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Susan Jones-Bolin
- Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania
19380, United
States
| | - Arup K. Ghose
- Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania
19380, United
States
| | - Torsten Herbertz
- Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania
19380, United
States
| | - Mark A. Ator
- Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania
19380, United
States
| | - Bruce D. Dorsey
- Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania
19380, United
States
| | - Bruce Ruggeri
- Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania
19380, United
States
| | - Michael Williams
- Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania
19380, United
States
| | - Shripad Bhagwat
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Joyce James
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
| | - Mark W. Holladay
- Ambit Biosciences, 4215 Sorrento Valley
Boulevard, San Diego, California 92121, United
States
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17
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Holladay MW, Campbell BT, Rowbottom MW, Chao Q, Sprankle KG, Lai AG, Abraham S, Setti E, Faraoni R, Tran L, Armstrong RC, Gunawardane RN, Gardner MF, Cramer MD, Gitnick D, Ator MA, Dorsey BD, Ruggeri BR, Williams M, Bhagwat SS, James J. 4-Quinazolinyloxy-diaryl ureas as novel BRAFV600E inhibitors. Bioorg Med Chem Lett 2011; 21:5342-6. [PMID: 21807507 DOI: 10.1016/j.bmcl.2011.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
Abstract
Aryl phenyl ureas with a 4-quinazolinoxy substituent at the meta-position of the phenyl ring are potent inhibitors of mutant and wild type BRAF kinase. Compound 7 (1-(5-tert-butylisoxazol-3-yl)-3-(3-(6,7-dimethoxyquinazolin-4-yloxy)phenyl)urea hydrochloride) exhibits good pharmacokinetic properties in rat and mouse and is efficacious in a mouse tumor xenograft model following oral dosing.
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Affiliation(s)
- Mark W Holladay
- Ambit Biosciences Corporation, 4215 Sorrento Valley Boulevard, San Diego, CA 92121, USA.
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18
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Chao Q, Sprankle KG, Grotzfeld RM, Lai AG, Carter TA, Velasco AM, Gunawardane RN, Cramer MD, Gardner MF, James J, Zarrinkar PP, Patel HK, Bhagwat SS. Identification of N-(5-tert-butyl-isoxazol-3-yl)-N'-{4-[7-(2-morpholin-4-yl-ethoxy)imidazo[2,1-b][1,3]benzothiazol-2-yl]phenyl}urea dihydrochloride (AC220), a uniquely potent, selective, and efficacious FMS-like tyrosine kinase-3 (FLT3) inhibitor. J Med Chem 2009; 52:7808-16. [PMID: 19754199 DOI: 10.1021/jm9007533] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Treatment of AML patients with small molecule inhibitors of FLT3 kinase has been explored as a viable therapy. However, these agents are found to be less than optimal for the treatment of AML because of lack of sufficient potency or suboptimal oral pharmacokinetics (PK) or lack of adequate tolerability at efficacious doses. We have developed a series of extremely potent and highly selective FLT3 inhibitors with good oral PK properties. The first series of compounds represented by 1 (AB530) was found to be a potent and selective FLT3 kinase inhibitor with good PK properties. The aqueous solubility and oral PK properties at higher doses in rodents were found to be less than optimal for clinical development. A novel series of compounds were designed lacking the carboxamide group of 1 with an added water solubilizing group. Compound 7 (AC220) was identified from this series to be the most potent and selective FLT3 inhibitor with good pharmaceutical properties, excellent PK profile, and superior efficacy and tolerability in tumor xenograft models. Compound 7 has demonstrated a desirable safety and PK profile in humans and is currently in phase II clinical trials.
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Affiliation(s)
- Qi Chao
- Ambit Biosciences, 4215 Sorrento Valley Boulevard, San Diego, California 92121, USA
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Witt A, Hines LM, Collins NL, Hu Y, Gunawardane RN, Moriera D, Raphael J, Jepson D, Koundinya M, Rolfs A, Taron B, Isakoff SJ, Brugge JS, LaBaer J. Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer. J Proteome Res 2007; 5:599-610. [PMID: 16512675 PMCID: PMC2522320 DOI: 10.1021/pr050395r] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Functional proteomics approaches that comprehensively evaluate the biological activities of human cDNAs may provide novel insights into disease pathogenesis. To systematically investigate the functional activity of cDNAs that have been implicated in breast carcinogenesis, we generated a collection of cDNAs relevant to breast cancer, the Breast Cancer 1000 (BC1000), and conducted screens to identify proteins that induce phenotypic changes that resemble events which occur during tumor initiation and progression. Genes were selected for this set using bioinformatics and data mining tools that identify genes associated with breast cancer. Greater than 1000 cDNAs were assembled and sequence verified with high-throughput recombination-based cloning. To our knowledge, the BC1000 represents the first publicly available sequence-validated human disease gene collection. The functional activity of a subset of the BC1000 collection was evaluated in cell-based assays that monitor changes in cell proliferation, migration, and morphogenesis in MCF-10A mammary epithelial cells expressing a variant of ErbB2 that can be inducibly activated through dimerization. Using this approach, we identified many cDNAs, encoding diverse classes of cellular proteins, that displayed activity in one or more of the assays, thus providing insights into a large set of cellular proteins capable of inducing functional alterations associated with breast cancer development.
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Affiliation(s)
- Abigail Witt
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
| | - Lisa M. Hines
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | | | - Yanhui Hu
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | | | - Donna Moriera
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | - Jacob Raphael
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | - Daniel Jepson
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | - Malvika Koundinya
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | - Andreas Rolfs
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | - Barbara Taron
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
| | - Steven J. Isakoff
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
- Corresponding authors Joshua LaBaer, Ph. 617 324-0827, Fax 617 324-0824, , Joan S. Brugge, Ph. 617 432 3974, Fax 617 432 3969,
| | - Joshua LaBaer
- Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141
- Corresponding authors Joshua LaBaer, Ph. 617 324-0827, Fax 617 324-0824, , Joan S. Brugge, Ph. 617 432 3974, Fax 617 432 3969,
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Abstract
Cell migration and invasion are two critical cellular processes that are often deregulated during tumorigenesis. To identify factors that contribute to oncogenic progression by stimulating cell migration, we conducted a powerful retroviral based migration screen using an MCF7 cDNA library and the immortalized human breast epithelial cell line MCF-10A. We identified prostate derived Ets factor (PDEF), an Ets transcription factor that is overexpressed in both prostate and breast carcinoma, as a candidate promigratory gene from this screen. Whereas PDEF induced limited motility of MCF-10A cells, coexpression of PDEF with the receptor tyrosine kinases (RTK) ErbB2 and colony-stimulating factor receptor (CSF-1R)/CSF-1 significantly enhanced MCF-10A motility. Furthermore, cells coexpressing PDEF with either ErbB2 or CSF-1R/CSF-1 induced a dramatic invasive phenotype in three-dimensional cultures. Constitutive activation of the extracellular signal-regulated kinase (ERK) pathway also enhanced PDEF-induced motility and invasion, suggesting that activation of the ERK/mitogen-activated protein kinase by ErbB2 and CSF-1R/CSF-1 can cooperate with PDEF to promote motility and invasion. Furthermore, PDEF promoted anchorage-independent growth of ErbB2 and CSF-1R/CSF-1-expressing cells. Using laser capture microdissection, we also found that PDEF mRNA is overexpressed in breast tumor epithelia throughout tumor progression. Taken together, these findings suggest that the transcription factor PDEF may play an important role in breast tumorigenesis and that PDEF overexpression may be particularly significant in tumors that exhibit activation of oncogenic RTKs such as ErbB2 and CSF-1R.
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MESH Headings
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Cell Movement
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lasers
- Macrophage Colony-Stimulating Factor/metabolism
- Mitogen-Activated Protein Kinases/metabolism
- Neoplasm Invasiveness
- Proto-Oncogene Proteins c-ets/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, ErbB-2/metabolism
- Receptor, Macrophage Colony-Stimulating Factor/metabolism
- Retroviridae/genetics
- Tumor Cells, Cultured
- Wound Healing
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Affiliation(s)
| | - Dennis C. Sgroi
- Department of Pathology, Harvard Medical School, Molecular Pathology Research Unit, Massachusetts General Hospital
| | | | - Eugene Koh
- Brown University, Providence, Rhode Island
| | - George Q. Daley
- Children’s Hospital, Harvard Medical School, Boston, Massachusetts
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Abstract
The gamma-tubulin ring complex (gammaTuRC), consisting of multiple protein subunits, can nucleate microtubule assembly. Although many subunits of the gammaTuRC have been identified, a complete set remains to be defined in any organism. In addition, how the subunits interact with each other to assemble into gammaTuRC remains largely unknown. Here, we report the characterization of a novel gammaTuRC subunit, Drosophila gamma ring protein with WD repeats (Dgp71WD). With the exception of gamma-tubulin, Dgp71WD is the only gammaTuRC component identified to date that does not contain the grip motifs, which are signature sequences conserved in gammaTuRC components. By performing immunoprecipitations after pair-wise coexpression in Sf9 cells, we show that Dgp71WD directly interacts with the grip motif-containing gammaTuRC subunits, Dgrips84, 91, 128, and 163, suggesting that Dgp71WD may play a scaffolding role in gammaTuRC organization. We also show that Dgrips128 and 163, like Dgrips84 and 91, can interact directly with gamma-tubulin. Coexpression of any of these grip motif-containing proteins with gamma-tubulin promotes gamma-tubulin binding to guanine nucleotide. In contrast, in the same assay Dgp71WD interacts with gamma-tubulin but does not facilitate nucleotide binding.
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Affiliation(s)
- Ruwanthi N Gunawardane
- Carnegie Institution of Washington/Howard Hughes Medical Institute, Baltimore, Maryland 21210, USA
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Affiliation(s)
- R N Gunawardane
- Howard Hughes Medical Institute, Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
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Affiliation(s)
- R N Gunawardane
- Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
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24
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Abstract
The gamma-tubulin ring complex (gammaTuRC) is important for microtubule nucleation from the centrosome. In addition to gamma-tubulin, the Drosophila gammaTuRC contains at least six subunits, three of which [Drosophila gamma ring proteins (Dgrips) 75/d75p, 84, and 91] have been characterized previously. Dgrips84 and 91 are present in both the small gamma-tubulin complex (gammaTuSC) and the gammaTuRC, while the remaining subunits are found only in the gammaTuRC. To study gammaTuRC assembly and function, we first reconstituted gammaTuSC using the baculovirus expression system. Using the reconstituted gammaTuSC, we showed for the first time that this subcomplex of the gammaTuRC has microtubule binding and capping activities. Next, we characterized two new gammaTuRC subunits, Dgrips128 and 163, and showed that they are centrosomal proteins. Sequence comparisons among all known gammaTuRC subunits revealed two novel sequence motifs, which we named grip motifs 1 and 2. We found that Dgrips128 and 163 can each interact with gammaTuSC. However, this interaction is insufficient for gammaTuRC assembly.
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Affiliation(s)
- R N Gunawardane
- Howard Hughes Medical Institute, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
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Martin OC, Gunawardane RN, Iwamatsu A, Zheng Y. Xgrip109: a gamma tubulin-associated protein with an essential role in gamma tubulin ring complex (gammaTuRC) assembly and centrosome function. J Cell Biol 1998; 141:675-87. [PMID: 9566968 PMCID: PMC2132744 DOI: 10.1083/jcb.141.3.675] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/1998] [Revised: 03/11/1998] [Indexed: 02/07/2023] Open
Abstract
Previous studies indicate that gamma tubulin ring complex (gammaTuRC) can nucleate microtubule assembly and may be important in centrosome formation. gammaTuRC contains approximately eight subunits, which we refer to as Xenopus gamma ring proteins (Xgrips), in addition to gamma tubulin. We found that one gammaTuRC subunit, Xgrip109, is a highly conserved protein, with homologues present in yeast, rice, flies, zebrafish, mice, and humans. The yeast Xgrip109 homologue, Spc98, is a spindle-pole body component that interacts with gamma tubulin. In vertebrates, Xgrip109 identifies two families of related proteins. Xgrip109 and Spc98 have more homology to one family than the other. We show that Xgrip109 is a centrosomal protein that directly interacts with gamma tubulin. We have developed a complementation assay for centrosome formation using demembranated Xenopus sperm and Xenopus egg extract. Using this assay, we show that Xgrip109 is necessary for the reassembly of salt-disrupted gammaTuRC and for the recruitment of gamma tubulin to the centrosome. Xgrip109, therefore, is essential for the formation of a functional centrosome.
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Affiliation(s)
- O C Martin
- Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
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