1
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Wiener DM, Huynh E, Jeyakumar I, Bax S, Sama S, Cabrera JP, Todorova V, Vangipuram M, Vaid S, Otsuka F, Sakai Y, Leonetti MD, Gómez-Sjöberg R. An open-source FACS automation system for high-throughput cell biology. PLoS One 2024; 19:e0299402. [PMID: 38512845 PMCID: PMC10956866 DOI: 10.1371/journal.pone.0299402] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024] Open
Abstract
Recent advances in gene editing are enabling the engineering of cells with an unprecedented level of scale. To capitalize on this opportunity, new methods are needed to accelerate the different steps required to manufacture and handle engineered cells. Here, we describe the development of an integrated software and hardware platform to automate Fluorescence-Activated Cell Sorting (FACS), a central step for the selection of cells displaying desired molecular attributes. Sorting large numbers of samples is laborious, and, to date, no automated system exists to sequentially manage FACS samples, likely owing to the need to tailor sorting conditions ("gating") to each individual sample. Our platform is built around a commercial instrument and integrates the handling and transfer of samples to and from the instrument, autonomous control of the instrument's software, and the algorithmic generation of sorting gates, resulting in walkaway functionality. Automation eliminates operator errors, standardizes gating conditions by eliminating operator-to-operator variations, and reduces hands-on labor by 93%. Moreover, our strategy for automating the operation of a commercial instrument control software in the absence of an Application Program Interface (API) exemplifies a universal solution for other instruments that lack an API. Our software and hardware designs are fully open-source and include step-by-step build documentation to contribute to a growing open ecosystem of tools for high-throughput cell biology.
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Affiliation(s)
- Diane M. Wiener
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Emily Huynh
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Ilakkiyan Jeyakumar
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Sophie Bax
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Samia Sama
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Joana P. Cabrera
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Verina Todorova
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Madhuri Vangipuram
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Shivanshi Vaid
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Fumitaka Otsuka
- Medical Business Group, Sony Corporation, San Jose, California, United States of America
| | - Yoshitsugu Sakai
- Medical Business Group, Sony Corporation, San Jose, California, United States of America
| | - Manuel D. Leonetti
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Rafael Gómez-Sjöberg
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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2
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Theriot JA, Simonsen A, Tolić I, Leonetti MD, Mayor S, Bassereau P, Paluch EK, Han J, Covert MW, Mizushima N, Reck-Peterson S, Strasser A, Cheeseman I. Cell biology is…. Cell 2024; 187:219-224. [PMID: 38242078 DOI: 10.1016/j.cell.2023.12.020] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
50 years ago, cell biology was a nascent field. Today, it is a vast discipline whose principles and tools are also applied to other disciplines; vice versa, cell biologists are inspired by other fields. So, the question begs: what is cell biology? The answers are as diverse as the people who define it.
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3
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Ivanov IE, Hirata-Miyasaki E, Chandler T, Kovilakam RC, Liu Z, Liu C, Leonetti MD, Huang B, Mehta SB. Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells. bioRxiv 2023:2023.12.19.572435. [PMID: 38187521 PMCID: PMC10769231 DOI: 10.1101/2023.12.19.572435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
High-throughput dynamic imaging of cells and organelles is important for parsing complex cellular responses. We report a high-throughput 4D microscope, named Mantis, that combines two complementary, gentle, live-imaging technologies: remote-refocus label-free microscopy and oblique light-sheet fluorescence microscopy. We also report open-source software for automated acquisition, registration, and reconstruction, and virtual staining software for single-cell segmentation and phenotyping. Mantis enabled high-content correlative imaging of molecular components and the physical architecture of 20 cell lines every 15 minutes over 7.5 hours, and also detailed measurements of the impacts of viral infection on the architecture of host cells and host proteins. The Mantis platform can enable high-throughput profiling of intracellular dynamics, long-term imaging and analysis of cellular responses to stress, and live cell optical screens to dissect gene regulatory networks.
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Affiliation(s)
- Ivan E. Ivanov
- Chan Zuckerberg Biohub San Francisco, San Francisco, United States
| | | | - Talon Chandler
- Chan Zuckerberg Biohub San Francisco, San Francisco, United States
| | - Rasmi Cheloor Kovilakam
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, United States
| | - Ziwen Liu
- Chan Zuckerberg Biohub San Francisco, San Francisco, United States
| | - Chad Liu
- Chan Zuckerberg Biohub San Francisco, San Francisco, United States
| | | | - Bo Huang
- Chan Zuckerberg Biohub San Francisco, San Francisco, United States
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, United States
| | - Shalin B. Mehta
- Chan Zuckerberg Biohub San Francisco, San Francisco, United States
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4
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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5
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Schmidt HB, Jaafar ZA, Wulff BE, Rodencal JJ, Hong K, Aziz-Zanjani MO, Jackson PK, Leonetti MD, Dixon SJ, Rohatgi R, Brandman O. Oxaliplatin disrupts nucleolar function through biophysical disintegration. Cell Rep 2022; 41:111629. [DOI: 10.1016/j.celrep.2022.111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 08/28/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
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6
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Ivanov IE, Yeh LH, Perez-Bermejo JA, Byrum JR, Kim JYS, Leonetti MD, Mehta SB. Correlative imaging of the spatio-angular dynamics of biological systems with multimodal instant polarization microscope. Biomed Opt Express 2022; 13:3102-3119. [PMID: 35774313 PMCID: PMC9203109 DOI: 10.1364/boe.455770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 05/29/2023]
Abstract
The spatial and angular organization of biological macromolecules is a key determinant, as well as informative readout, of their function. Correlative imaging of the dynamic spatio-angular architecture of cells and organelles is valuable, but remains challenging with current methods. Correlative imaging of spatio-angular dynamics requires fast polarization-, depth-, and wavelength-diverse measurement of intrinsic optical properties and fluorescent labels. We report a multimodal instant polarization microscope (miPolScope) that combines a broadband polarization-resolved detector, automation, and reconstruction algorithms to enable label-free imaging of phase, retardance, and orientation, multiplexed with fluorescence imaging of concentration, anisotropy, and orientation of molecules at diffraction-limited resolution and high speed. miPolScope enabled multimodal imaging of myofibril architecture and contractile activity of beating cardiomyocytes, cell and organelle architecture of live HEK293T and U2OS cells, and density and anisotropy of white and grey matter of mouse brain tissue across the visible spectrum. We anticipate these developments in joint quantitative imaging of density and anisotropy to enable new studies in tissue pathology, mechanobiology, and imaging-based screens.
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Affiliation(s)
- Ivan E. Ivanov
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Li-Hao Yeh
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | | | - Janie R. Byrum
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - James Y. S. Kim
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | | | - Shalin B. Mehta
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
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7
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Cho NH, Cheveralls KC, Brunner AD, Kim K, Michaelis AC, Raghavan P, Kobayashi H, Savy L, Li JY, Canaj H, Kim JYS, Stewart EM, Gnann C, McCarthy F, Cabrera JP, Brunetti RM, Chhun BB, Dingle G, Hein MY, Huang B, Mehta SB, Weissman JS, Gómez-Sjöberg R, Itzhak DN, Royer LA, Mann M, Leonetti MD. OpenCell: Endogenous tagging for the cartography of human cellular organization. Science 2022; 375:eabi6983. [PMID: 35271311 DOI: 10.1126/science.abi6983] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery. We found that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions, and that RNA binding proteins form a specific subgroup defined by unique interaction and localization properties. Paired with a fully interactive website (opencell.czbiohub.org), our work constitutes a resource for the quantitative cartography of human cellular organization.
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Affiliation(s)
| | | | - Andreas-David Brunner
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kibeom Kim
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - André C Michaelis
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Laura Savy
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jason Y Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hera Canaj
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Christian Gnann
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | | | - Rachel M Brunetti
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | - Greg Dingle
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Bo Huang
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | | | - Jonathan S Weissman
- Whitehead Institute, Koch Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | | | | | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Brunetti RM, Kockelkoren G, Raghavan P, Bell GR, Britain D, Puri N, Collins SR, Leonetti MD, Stamou D, Weiner OD. WASP integrates substrate topology and cell polarity to guide neutrophil migration. J Cell Biol 2022; 221:e202104046. [PMID: 34964841 PMCID: PMC8719638 DOI: 10.1083/jcb.202104046] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 04/16/2021] [Revised: 10/19/2021] [Accepted: 12/10/2021] [Indexed: 12/02/2022] Open
Abstract
To control their movement, cells need to coordinate actin assembly with the geometric features of their substrate. Here, we uncover a role for the actin regulator WASP in the 3D migration of neutrophils. We show that WASP responds to substrate topology by enriching to sites of inward, substrate-induced membrane deformation. Superresolution imaging reveals that WASP preferentially enriches to the necks of these substrate-induced invaginations, a distribution that could support substrate pinching. WASP facilitates recruitment of the Arp2/3 complex to these sites, stimulating local actin assembly that couples substrate features with the cytoskeleton. Surprisingly, WASP only enriches to membrane deformations in the front half of the cell, within a permissive zone set by WASP's front-biased regulator Cdc42. While WASP KO cells exhibit relatively normal migration on flat substrates, they are defective at topology-directed migration. Our data suggest that WASP integrates substrate topology with cell polarity by selectively polymerizing actin around substrate-induced membrane deformations in the front half of the cell.
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Affiliation(s)
- Rachel M. Brunetti
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Center for Geometrically Engineered Cellular Membranes, University of California, San Francisco, San Francisco, CA
| | - Gabriele Kockelkoren
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for Geometrically Engineered Cellular Membranes, University of Copenhagen, Copenhagen, Denmark
| | - Preethi Raghavan
- University of California, Berkeley–University of California, San Francisco Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - George R.R. Bell
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA
| | - Derek Britain
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Center for Geometrically Engineered Cellular Membranes, University of California, San Francisco, San Francisco, CA
| | - Natasha Puri
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Sean R. Collins
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA
| | | | - Dimitrios Stamou
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for Geometrically Engineered Cellular Membranes, University of Copenhagen, Copenhagen, Denmark
| | - Orion D. Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Center for Geometrically Engineered Cellular Membranes, University of California, San Francisco, San Francisco, CA
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9
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Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 2021; 184:2503-2519.e17. [PMID: 33838111 PMCID: PMC8376083 DOI: 10.1016/j.cell.2021.03.025] [Citation(s) in RCA: 242] [Impact Index Per Article: 80.7] [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: 08/30/2020] [Revised: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff-a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.
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Affiliation(s)
- James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Greg C Pommier
- Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Carmen Adriaens
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Gokul N Ramadoss
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Angela N Pogson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - James Y S Kim
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amanda Chung
- Department of Urology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | | | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Volker Hovestadt
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA.
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10
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Goudeau J, Sharp CS, Paw J, Savy L, Leonetti MD, York AG, Updike DL, Kenyon C, Ingaramo M. Split-wrmScarlet and split-sfGFP: tools for faster, easier fluorescent labeling of endogenous proteins in Caenorhabditis elegans. Genetics 2021; 217:iyab014. [PMID: 33693628 PMCID: PMC8049552 DOI: 10.1093/genetics/iyab014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/21/2021] [Indexed: 11/17/2022] Open
Abstract
We create and share a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenous Caenorhabditis elegans proteins with fluorescent tags. CRISPR-mediated fluorescent labeling of C. elegans proteins is an invaluable tool, but it is much more difficult to insert fluorophore-size DNA segments than it is to make small gene edits. In principle, high-affinity asymmetrically split fluorescent proteins solve this problem in C. elegans: the small fragment can quickly and easily be fused to almost any protein of interest, and can be detected wherever the large fragment is expressed and complemented. However, there is currently only one available strain stably expressing the large fragment of a split fluorescent protein, restricting this solution to a single tissue (the germline) in the highly autofluorescent green channel. No available C. elegans lines express unbound large fragments of split red fluorescent proteins, and even state-of-the-art split red fluorescent proteins are dim compared to the canonical split-sfGFP protein. In this study, we engineer a bright, high-affinity new split red fluorophore, split-wrmScarlet. We generate transgenic C. elegans lines to allow easy single-color labeling in muscle or germline cells and dual-color labeling in somatic cells. We also describe a novel expression strategy for the germline, where traditional expression strategies struggle. We validate these strains by targeting split-wrmScarlet to several genes whose products label distinct organelles, and we provide a protocol for easy, cloning-free CRISPR/Cas9 editing. As the collection of split-FP strains for labeling in different tissues or organelles expands, we will post updates at doi.org/10.5281/zenodo.3993663.
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Affiliation(s)
- Jérôme Goudeau
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Catherine S Sharp
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | - Jonathan Paw
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Laura Savy
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Dustin L Updike
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | - Cynthia Kenyon
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Maria Ingaramo
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
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11
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Mahdessian D, Cesnik AJ, Gnann C, Danielsson F, Stenström L, Arif M, Zhang C, Le T, Johansson F, Schutten R, Bäckström A, Axelsson U, Thul P, Cho NH, Carja O, Uhlén M, Mardinoglu A, Stadler C, Lindskog C, Ayoglu B, Leonetti MD, Pontén F, Sullivan DP, Lundberg E. Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. Nature 2021; 590:649-654. [PMID: 33627808 DOI: 10.1038/s41586-021-03232-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 01/12/2021] [Indexed: 01/31/2023]
Abstract
The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.
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Affiliation(s)
- Diana Mahdessian
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anthony J Cesnik
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.,Department of Genetics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | - Christian Gnann
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.,Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | - Frida Danielsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Lovisa Stenström
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Trang Le
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Rutger Schutten
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Bäckström
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Ulrika Axelsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Peter Thul
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Nathan H Cho
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | - Oana Carja
- Department of Genetics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Charlotte Stadler
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Burcu Ayoglu
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Devin P Sullivan
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden. .,Department of Genetics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
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12
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Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL. Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. PLoS Pathog 2020; 16:e1008966. [PMID: 33112933 PMCID: PMC7592773 DOI: 10.1371/journal.ppat.1008966] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Emily D. Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Irene Acosta
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Erika C. Anderson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shaun Arevalo
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel Asarnow
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shannon Axelrod
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Patrick Ayscue
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Camillia S. Azimi
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Caleigh M. Azumaya
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Stefanie Bachl
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Iris Bachmutsky
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Aparna Bhaduri
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jeremy Bancroft Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Astrid Behnert
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ryan M. Boileau
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Saumya R. Bollam
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alain R. Bonny
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - David Booth
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | | | - David Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Bryan Buie
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cassandra E. Burnett
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lauren E. Byrnes
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Katelyn A. Cabral
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
| | - Joana P. Cabrera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Gabriela Canales
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Agnes Protacio Chan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Christopher R. Chang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Arthur Charles-Orszag
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Carly Cheung
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Unseng Chio
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Eric D. Chow
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Y. Rose Citron
- University of California, Berkeley, California, United States of America
| | - Allison Cohen
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lillian B. Cohn
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Experimental Medicine, San Francisco, California, United States of America
| | - Charles Chiu
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Mitchel A. Cole
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel N. Conrad
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Angela Constantino
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Andrew Cote
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Spyros Darmanis
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Rebekah L. Dial
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Shen Dong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elias M. Duarte
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - David Dynerman
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Rebecca Egger
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Alison Fanton
- University of California, Berkeley, California, United States of America
| | - Stacey M. Frumm
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Becky Xu Hua Fu
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Valentina E. Garcia
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Julie Garcia
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Christina Gladkova
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Miriam Goldman
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - M. Grace Gordon
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - James C. R. Grove
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shweta Gupta
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alexis Haddjeri-Hopkins
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Pierce Hadley
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
| | - John Haliburton
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Samantha L. Hao
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - George Hartoularos
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Nadia Herrera
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Melissa Hilberg
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Kit Ying E. Ho
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Nicholas Hoppe
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Conor J. Howard
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jeffrey A. Hussmann
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elizabeth Hwang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Danielle Ingebrigtsen
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Julia R. Jackson
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Ziad M. Jowhar
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Danielle Kain
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - James Y. S. Kim
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Oriana Kreutzfeld
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Andrew F. Kung
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Matthew T. Laurie
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Lena Lee
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Kun Leng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Kristoffer E. Leon
- Gladstone Institute, San Francisco, California, United States of America
| | - Manuel D. Leonetti
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sophia R. Levan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Sam Li
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Aileen W. Li
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jamin Liu
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Heidi S. Lubin
- eSix Development, Oakland, California, United States of America
| | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jennifer Mann
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sabrina Mann
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Gorica Margulis
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Diana M. Marquez
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Bryan P. Marsh
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Calla Martyn
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elizabeth E. McCarthy
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Aaron McGeever
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Lauren K. Meyer
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Steve Miller
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Megan K. Moore
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cody T. Mowery
- Gladstone Institute, San Francisco, California, United States of America
| | - Tanzila Mukhtar
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Noelle Narez
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Norma F. Neff
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Lindsay A. Osso
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Diter Oviedo
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Suping Peng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Kiet Phong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Peter Picard
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Lindsey M. Pieper
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Neha Pincha
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Angela Pogson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Sergei Pourmal
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | | | | | - Elze Rackaityte
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Preethi Raghavan
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Madhura Raghavan
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - James Reese
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joseph M. Replogle
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Hanna Retallack
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Helen Reyes
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Donald Rose
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Marci F. Rosenberg
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Sydney M. Sattler
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Laura Savy
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Stephanie K. See
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Kristin K. Sellers
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Paula Hayakawa Serpa
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Maureen Sheehy
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jonathan Sheu
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sukrit Silas
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jessica A. Streithorst
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jack Strickland
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Doug Stryke
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Sara Sunshine
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Peter Suslow
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Renaldo Sutanto
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Serena Tamura
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jiongyi Tan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alice Tang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jack C. Taylor
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Iliana Tenvooren
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Erin M. Thompson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Edward C. Thornborrow
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Eric Tse
- Joint Bioengineering Graduate Program, University of California, Berkeley, California, United States of America
| | - Tony Tung
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Marc L. Turner
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Victoria S. Turner
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Rigney E. Turnham
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Mary J. Turocy
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Trisha V. Vaidyanathan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ilia D. Vainchtein
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Manu Vanaerschot
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sara E. Vazquez
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Anica M. Wandler
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Anne Wapniarski
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - James T. Webber
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Zara Y. Weinberg
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alexandra Westbrook
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Allison W. Wong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Emily Wong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Gajus Worthington
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Fang Xie
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Albert Xu
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Terrina Yamamoto
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ying Yang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Fauna Yarza
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Yefim Zaltsman
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Tina Zheng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
- * E-mail:
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13
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Jiménez-Rojo N, Leonetti MD, Zoni V, Colom A, Feng S, Iyengar NR, Matile S, Roux A, Vanni S, Weissman JS, Riezman H. Conserved Functions of Ether Lipids and Sphingolipids in the Early Secretory Pathway. Curr Biol 2020; 30:3775-3787.e7. [DOI: 10.1016/j.cub.2020.07.059] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/05/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]
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14
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Stenström L, Mahdessian D, Gnann C, Cesnik AJ, Ouyang W, Leonetti MD, Uhlén M, Cuylen‐Haering S, Thul PJ, Lundberg E. Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. Mol Syst Biol 2020; 16:e9469. [PMID: 32744794 PMCID: PMC7397901 DOI: 10.15252/msb.20209469] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023] Open
Abstract
The nucleolus is essential for ribosome biogenesis and is involved in many other cellular functions. We performed a systematic spatiotemporal dissection of the human nucleolar proteome using confocal microscopy. In total, 1,318 nucleolar proteins were identified; 287 were localized to fibrillar components, and 157 were enriched along the nucleoplasmic border, indicating a potential fourth nucleolar subcompartment: the nucleoli rim. We found 65 nucleolar proteins (36 uncharacterized) to relocate to the chromosomal periphery during mitosis. Interestingly, we observed temporal partitioning into two recruitment phenotypes: early (prometaphase) and late (after metaphase), suggesting phase-specific functions. We further show that the expression of MKI67 is critical for this temporal partitioning. We provide the first proteome-wide analysis of intrinsic protein disorder for the human nucleolus and show that nucleolar proteins in general, and mitotic chromosome proteins in particular, have significantly higher intrinsic disorder level compared to cytosolic proteins. In summary, this study provides a comprehensive and essential resource of spatiotemporal expression data for the nucleolar proteome as part of the Human Protein Atlas.
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Affiliation(s)
- Lovisa Stenström
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Diana Mahdessian
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Christian Gnann
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Anthony J Cesnik
- Chan Zuckerberg BiohubSan FranciscoCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Wei Ouyang
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | | | - Mathias Uhlén
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Sara Cuylen‐Haering
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Peter J Thul
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Emma Lundberg
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
- Chan Zuckerberg BiohubSan FranciscoCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
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15
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Guo SM, Yeh LH, Folkesson J, Ivanov IE, Krishnan AP, Keefe MG, Hashemi E, Shin D, Chhun BB, Cho NH, Leonetti MD, Han MH, Nowakowski TJ, Mehta SB. Revealing architectural order with quantitative label-free imaging and deep learning. eLife 2020; 9:e55502. [PMID: 32716843 PMCID: PMC7431134 DOI: 10.7554/elife.55502] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/24/2020] [Indexed: 01/21/2023] Open
Abstract
We report quantitative label-free imaging with phase and polarization (QLIPP) for simultaneous measurement of density, anisotropy, and orientation of structures in unlabeled live cells and tissue slices. We combine QLIPP with deep neural networks to predict fluorescence images of diverse cell and tissue structures. QLIPP images reveal anatomical regions and axon tract orientation in prenatal human brain tissue sections that are not visible using brightfield imaging. We report a variant of U-Net architecture, multi-channel 2.5D U-Net, for computationally efficient prediction of fluorescence images in three dimensions and over large fields of view. Further, we develop data normalization methods for accurate prediction of myelin distribution over large brain regions. We show that experimental defects in labeling the human tissue can be rescued with quantitative label-free imaging and neural network model. We anticipate that the proposed method will enable new studies of architectural order at spatial scales ranging from organelles to tissue.
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Affiliation(s)
| | - Li-Hao Yeh
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | | | | | | | - Matthew G Keefe
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
| | - Ezzat Hashemi
- Department of Neurology, Stanford UniversityStanfordUnited States
| | - David Shin
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
| | | | - Nathan H Cho
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | | | - May H Han
- Department of Neurology, Stanford UniversityStanfordUnited States
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
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16
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Chen J, Brunner AD, Cogan JZ, Nuñez JK, Fields AP, Adamson B, Itzhak DN, Li JY, Mann M, Leonetti MD, Weissman JS. Pervasive functional translation of noncanonical human open reading frames. Science 2020; 367:1140-1146. [PMID: 32139545 DOI: 10.1126/science.aay0262] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/22/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022]
Abstract
Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based screening strategy to identify hundreds of noncanonical CDSs that are essential for cellular growth and whose disruption elicits specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds of microproteins that are presented by the human leukocyte antigen system. We find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same messenger RNA, thereby revealing the use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.
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Affiliation(s)
- Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Andreas-David Brunner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Alexander P Fields
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel N Itzhak
- Cell Atlas Initiative, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jason Y Li
- Cell Atlas Initiative, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.,Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Manuel D Leonetti
- Cell Atlas Initiative, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
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17
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Chen JJ, Nathaniel DL, Raghavan P, Nelson M, Tian R, Tse E, Hong JY, See SK, Mok SA, Hein MY, Southworth DR, Grinberg LT, Gestwicki JE, Leonetti MD, Kampmann M. Compromised function of the ESCRT pathway promotes endolysosomal escape of tau seeds and propagation of tau aggregation. J Biol Chem 2019; 294:18952-18966. [PMID: 31578281 PMCID: PMC6916486 DOI: 10.1074/jbc.ra119.009432] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [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: 05/19/2019] [Revised: 09/26/2019] [Indexed: 12/22/2022] Open
Abstract
Intercellular propagation of protein aggregation is emerging as a key mechanism in the progression of several neurodegenerative diseases, including Alzheimer's disease and frontotemporal dementia (FTD). However, we lack a systematic understanding of the cellular pathways controlling prion-like propagation of aggregation. To uncover such pathways, here we performed CRISPR interference (CRISPRi) screens in a human cell-based model of propagation of tau aggregation monitored by FRET. Our screens uncovered that knockdown of several components of the endosomal sorting complexes required for transport (ESCRT) machinery, including charged multivesicular body protein 6 (CHMP6), or CHMP2A in combination with CHMP2B (whose gene is linked to familial FTD), promote propagation of tau aggregation. We found that knocking down the genes encoding these proteins also causes damage to endolysosomal membranes, consistent with a role for the ESCRT pathway in endolysosomal membrane repair. Leakiness of the endolysosomal compartment significantly enhanced prion-like propagation of tau aggregation, likely by making tau seeds more available to pools of cytoplasmic tau. Together, these findings suggest that endolysosomal escape is a critical step in tau propagation in neurodegenerative diseases.
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Affiliation(s)
- John J Chen
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Diane L Nathaniel
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | | | - Maxine Nelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94158
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Biophysics Graduate Program, University of California, San Francisco, California 94158
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Jason Y Hong
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Stephanie K See
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94158
| | - Sue-Ann Mok
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Marco Y Hein
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Lea T Grinberg
- Department of Neurology, University of California, San Francisco, California 94158
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | | | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Chan Zuckerberg Biohub, San Francisco, California 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
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18
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Leenay RT, Aghazadeh A, Hiatt J, Tse D, Roth TL, Apathy R, Shifrut E, Hultquist JF, Krogan N, Wu Z, Cirolia G, Canaj H, Leonetti MD, Marson A, May AP, Zou J. Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. Nat Biotechnol 2019; 37:1034-1037. [PMID: 31359007 PMCID: PMC7388783 DOI: 10.1038/s41587-019-0203-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [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] [Received: 10/19/2018] [Accepted: 06/27/2019] [Indexed: 01/21/2023]
Abstract
Understanding of repair outcomes after Cas9-induced DNA cleavage is still limited, especially in primary human cells. We sequence repair outcomes at 1,656 on-target genomic sites in primary human T cells and use these data to train a machine learning model, which we have called CRISPR Repair Outcome (SPROUT). SPROUT accurately predicts the length, probability and sequence of nucleotide insertions and deletions, and will facilitate design of SpCas9 guide RNAs in therapeutically important primary human cells.
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Affiliation(s)
| | - Amirali Aghazadeh
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Joseph Hiatt
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
| | - David Tse
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Theodore L Roth
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan Apathy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Judd F Hultquist
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nevan Krogan
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA
| | - Zhenqin Wu
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Hera Canaj
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Alexander Marson
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Andrew P May
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Sana Biotechnology, South San Francisco, CA, USA.
| | - James Zou
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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19
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Yang B, Chen X, Wang Y, Feng S, Pessino V, Stuurman N, Cho NH, Cheng KW, Lord SJ, Xu L, Xie D, Mullins RD, Leonetti MD, Huang B. Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution. Nat Methods 2019; 16:501-504. [PMID: 31061492 PMCID: PMC6557432 DOI: 10.1038/s41592-019-0401-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [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: 02/28/2018] [Accepted: 03/29/2019] [Indexed: 11/16/2022]
Abstract
We designed an epi-illumination SPIM system that uses a single objective and has a sample interface identical to that of an inverted fluorescence microscope with no additional reflection elements. It achieves subcellular resolution and single-molecule sensitivity, and is compatible with common biological sample holders, including multi-well plates. We demonstrated multicolor fast volumetric imaging, single-molecule localization microscopy, parallel imaging of 16 cell lines and parallel recording of cellular responses to perturbations.
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Affiliation(s)
- Bin Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Xingye Chen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Yina Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Siyu Feng
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Veronica Pessino
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Nico Stuurman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | | | - Karen W Cheng
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Samuel J Lord
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Linfeng Xu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dan Xie
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | | | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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20
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Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B. Versatile protein tagging in cells with split fluorescent protein. Nat Commun 2016; 7:11046. [PMID: 26988139 PMCID: PMC4802074 DOI: 10.1038/ncomms11046] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/15/2016] [Indexed: 12/26/2022] Open
Abstract
In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respectively. The small size of FP11-tags enables a cost-effective and scalable way to insert them into endogenous genomic loci via CRISPR-mediated homology-directed repair. Tandem arrangement FP11-tags allows proportional enhancement of fluorescence signal in tracking intraflagellar transport particles, or reduction of photobleaching for live microtubule imaging. Finally, we show the utility of tandem GFP11-tag in scaffolding protein oligomerization. These experiments illustrate the versatility of FP11-tag as a labelling tool as well as a multimerization-control tool for both imaging and non-imaging applications. Tagging proteins with fluorescent proteins is a powerful method for both imaging and non-imaging applications. Here the authors use the eleventh β-strand of sfGFP and sfCherry as epitope tags for multicolour imaging and amplified signals by tandem arrangement; shortness of the tag enabled introduction into genomic loci using CRISPR/Cas9.
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Affiliation(s)
- Daichi Kamiyama
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Sayaka Sekine
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Benjamin Barsi-Rhyne
- Tetrad Graduate Program, University of California, San Francisco, California 94143, USA
| | - Jeffrey Hu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Baohui Chen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
| | - Hiroaki Ishikawa
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
| | - Manuel D Leonetti
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA.,Howard Hughes Medical Institute, San Francisco, California 94143, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
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21
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Yuan P, Leonetti MD, Hsiung Y, MacKinnon R. Open structure of the Ca2+ gating ring in the high-conductance Ca2+-activated K+ channel. Nature 2011; 481:94-7. [PMID: 22139424 PMCID: PMC3319005 DOI: 10.1038/nature10670] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/24/2011] [Indexed: 12/30/2022]
Abstract
High-conductance voltage- and Ca(2+)-activated K(+) channels function in many physiological processes that link cell membrane voltage and intracellular Ca(2+) concentration, including neuronal electrical activity, skeletal and smooth muscle contraction, and hair cell tuning. Like other voltage-dependent K(+) channels, Ca(2+)-activated K(+) channels open when the cell membrane depolarizes, but in contrast to other voltage-dependent K(+) channels, they also open when intracellular Ca(2+) concentrations rise. Channel opening by Ca(2+) is made possible by a structure called the gating ring, which is located in the cytoplasm. Recent structural studies have defined the Ca(2+)-free, closed, conformation of the gating ring, but the Ca(2+)-bound, open, conformation is not yet known. Here we present the Ca(2+)-bound conformation of the gating ring. This structure shows how one layer of the gating ring, in response to the binding of Ca(2+), opens like the petals of a flower. The degree to which it opens explains how Ca(2+) binding can open the transmembrane pore. These findings present a molecular basis for Ca(2+) activation of K(+) channels and suggest new possibilities for targeting the gating ring to treat conditions such as asthma and hypertension.
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Affiliation(s)
- Peng Yuan
- Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10065, USA
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22
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Abstract
High-conductance voltage- and Ca2+-activated K+ (BK) channels encode negative feedback regulation of membrane voltage and Ca2+ signaling, playing a central role in numerous physiological processes. We determined the x-ray structure of the human BK Ca2+ gating apparatus at a resolution of 3.0 angstroms and deduced its tetrameric assembly by solving a 6 angstrom resolution structure of a Na+-activated homolog. Two tandem C-terminal regulator of K+ conductance (RCK) domains from each of four channel subunits form a 350-kilodalton gating ring at the intracellular membrane surface. A sequence of aspartic amino acids that is known as the Ca2+ bowl, and is located within the second of the tandem RCK domains, creates four Ca2+ binding sites on the outer perimeter of the gating ring at the "assembly interface" between RCK domains. Functionally important mutations cluster near the Ca2+ bowl, near the "flexible interface" between RCK domains, and on the surface of the gating ring that faces the voltage sensors. The structure suggests that the Ca2+ gating ring, in addition to regulating the pore directly, may also modulate the voltage sensor.
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Affiliation(s)
- Peng Yuan
- Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA
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