1
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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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2
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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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3
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Qiu X, Zhang Y, Martin-Rufino JD, Weng C, Hosseinzadeh S, Yang D, Pogson AN, Hein MY, Hoi Joseph Min K, Wang L, Grody EI, Shurtleff MJ, Yuan R, Xu S, Ma Y, Replogle JM, Lander ES, Darmanis S, Bahar I, Sankaran VG, Xing J, Weissman JS. Mapping transcriptomic vector fields of single cells. Cell 2022; 185:690-711.e45. [PMID: 35108499 PMCID: PMC9332140 DOI: 10.1016/j.cell.2021.12.045] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 10/08/2021] [Accepted: 12/28/2021] [Indexed: 01/03/2023]
Abstract
Single-cell (sc)-RNA-seq, together with RNA-velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo, that infers absolute RNA velocity, reconstructs continuous vector-field functions that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo’s power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically-labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1–GATA1 circuit. Leveraging the Least-Action-Path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo thus represents an important step in advancing quantitative and predictive theories of cell-state transitions.
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Affiliation(s)
- Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Yan Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jorge D Martin-Rufino
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chen Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Shayan Hosseinzadeh
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dian Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela N Pogson
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marco Y Hein
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Kyung Hoi Joseph Min
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Li Wang
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, USA
| | | | | | - Ruoshi Yuan
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | | | - Yian Ma
- Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Systems Biology Harvard Medical School, Boston, MA 02125, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA; UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA.
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4
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Kaya-Çopur A, Marchiano F, Hein MY, Alpern D, Russeil J, Luis NM, Mann M, Deplancke B, Habermann BH, Schnorrer F. The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression. eLife 2021; 10:e63726. [PMID: 33404503 PMCID: PMC7815313 DOI: 10.7554/elife.63726] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/30/2022] Open
Abstract
Skeletal muscles are composed of gigantic cells called muscle fibers, packed with force-producing myofibrils. During development, the size of individual muscle fibers must dramatically enlarge to match with skeletal growth. How muscle growth is coordinated with growth of the contractile apparatus is not understood. Here, we use the large Drosophila flight muscles to mechanistically decipher how muscle fiber growth is controlled. We find that regulated activity of core members of the Hippo pathway is required to support flight muscle growth. Interestingly, we identify Dlg5 and Slmap as regulators of the STRIPAK phosphatase, which negatively regulates Hippo to enable post-mitotic muscle growth. Mechanistically, we show that the Hippo pathway controls timing and levels of sarcomeric gene expression during development and thus regulates the key components that physically mediate muscle growth. Since Dlg5, STRIPAK and the Hippo pathway are conserved a similar mechanism may contribute to muscle or cardiomyocyte growth in humans.
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Affiliation(s)
- Aynur Kaya-Çopur
- Aix Marseille University, CNRS, IBDM, Turing Center for Living SystemsMarseilleFrance
- Max Planck Institute of BiochemistryMartinsriedGermany
| | - Fabio Marchiano
- Aix Marseille University, CNRS, IBDM, Turing Center for Living SystemsMarseilleFrance
| | - Marco Y Hein
- Max Planck Institute of BiochemistryMartinsriedGermany
| | - Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Nuno Miguel Luis
- Aix Marseille University, CNRS, IBDM, Turing Center for Living SystemsMarseilleFrance
| | - Matthias Mann
- Max Planck Institute of BiochemistryMartinsriedGermany
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bianca H Habermann
- Aix Marseille University, CNRS, IBDM, Turing Center for Living SystemsMarseilleFrance
| | - Frank Schnorrer
- Aix Marseille University, CNRS, IBDM, Turing Center for Living SystemsMarseilleFrance
- Max Planck Institute of BiochemistryMartinsriedGermany
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5
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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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6
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McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods 2019. [PMID: 31209384 DOI: 10.1101/387241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Daniel N Conrad
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Marco Y Hein
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Hu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Lyndsay M Murrow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Zena Werb
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA.
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- Chan Zuckerberg BioHub, University of California San Francisco, San Francisco, CA, USA.
- Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA.
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7
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McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods 2019; 16:619-626. [PMID: 31209384 PMCID: PMC6837808 DOI: 10.1038/s41592-019-0433-8] [Citation(s) in RCA: 275] [Impact Index Per Article: 55.0] [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: 08/12/2018] [Accepted: 04/29/2019] [Indexed: 12/12/2022]
Abstract
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Daniel N Conrad
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Marco Y Hein
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Hu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Lyndsay M Murrow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Zena Werb
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA.
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- Chan Zuckerberg BioHub, University of California San Francisco, San Francisco, CA, USA.
- Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA.
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8
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Singh S, Hein MY, Stewart AF. msVolcano: A flexible web application for visualizing quantitative proteomics data. Proteomics 2017; 16:2491-4. [PMID: 27440201 PMCID: PMC5096246 DOI: 10.1002/pmic.201600167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/06/2016] [Accepted: 07/15/2016] [Indexed: 02/05/2023]
Abstract
We introduce msVolcano, a web application for the visualization of label‐free mass spectrometric data. It is optimized for the output of the MaxQuant data analysis pipeline of interactomics experiments and generates volcano plots with lists of interacting proteins. The user can optimize the cutoff values to find meaningful significant interactors for the tagged protein of interest. Optionally, stoichiometries of interacting proteins can be calculated. Several customization options are provided to the user for flexibility, and publication‐quality outputs can also be downloaded (tabular and graphical). Availability: msVolcano is implemented in R Statistical language using Shiny. It can be accessed freely at http://projects.biotec.tu-dresden.de/msVolcano/
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Affiliation(s)
- Sukhdeep Singh
- Genomics, Biotechnology Center, Technische Universität Dresden, Dresden, Germany.
| | - Marco Y Hein
- Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
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9
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Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell 2016; 167:1867-1882.e21. [PMID: 27984733 PMCID: PMC5315571 DOI: 10.1016/j.cell.2016.11.048] [Citation(s) in RCA: 618] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/14/2016] [Accepted: 11/19/2016] [Indexed: 12/20/2022]
Abstract
Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.
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Affiliation(s)
- Britt Adamson
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Thomas M Norman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Min Y Cho
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James K Nuñez
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuwen Chen
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacqueline E Villalta
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Luke A Gilbert
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Max A Horlbeck
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Y Hein
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ryan A Pak
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew N Gray
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atray Dixit
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02142, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Oren Parnas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Jonathan S Weissman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
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10
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Saha S, Weber CA, Nousch M, Adame-Arana O, Hoege C, Hein MY, Osborne-Nishimura E, Mahamid J, Jahnel M, Jawerth L, Pozniakovski A, Eckmann CR, Jülicher F, Hyman AA. Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism. Cell 2016; 166:1572-1584.e16. [PMID: 27594427 DOI: 10.1016/j.cell.2016.08.006] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [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: 05/18/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 12/21/2022]
Abstract
P granules are non-membrane-bound RNA-protein compartments that are involved in germline development in C. elegans. They are liquids that condense at one end of the embryo by localized phase separation, driven by gradients of polarity proteins such as the mRNA-binding protein MEX-5. To probe how polarity proteins regulate phase separation, we combined biochemistry and theoretical modeling. We reconstitute P granule-like droplets in vitro using a single protein PGL-3. By combining in vitro reconstitution with measurements of intracellular concentrations, we show that competition between PGL-3 and MEX-5 for mRNA can regulate the formation of PGL-3 droplets. Using theory, we show that, in a MEX-5 gradient, this mRNA competition mechanism can drive a gradient of P granule assembly with similar spatial and temporal characteristics to P granule assembly in vivo. We conclude that gradients of polarity proteins can position RNP granules during development by using RNA competition to regulate local phase separation.
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Affiliation(s)
- Shambaditya Saha
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Marco Nousch
- Martin Luther University, 06120 Halle (Saale), Germany
| | - Omar Adame-Arana
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Carsten Hoege
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marco Y Hein
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Julia Mahamid
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Louise Jawerth
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Andrej Pozniakovski
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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11
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Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, Mann M, Cox J. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 2016; 13:731-40. [DOI: 10.1038/nmeth.3901] [Citation(s) in RCA: 4028] [Impact Index Per Article: 503.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023]
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12
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Sarov M, Barz C, Jambor H, Hein MY, Schmied C, Suchold D, Stender B, Janosch S, K J VV, Krishnan RT, Krishnamoorthy A, Ferreira IRS, Ejsmont RK, Finkl K, Hasse S, Kämpfer P, Plewka N, Vinis E, Schloissnig S, Knust E, Hartenstein V, Mann M, Ramaswami M, VijayRaghavan K, Tomancak P, Schnorrer F. A genome-wide resource for the analysis of protein localisation in Drosophila. eLife 2016; 5:e12068. [PMID: 26896675 PMCID: PMC4805545 DOI: 10.7554/elife.12068] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
The Drosophila genome contains >13000 protein-coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here, we present a genome-wide fosmid library of 10000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins, we created transgenic lines, and for a total of 207 lines, we assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we visualised many proteins at endogenous expression levels and found a large fraction of them localising to subcellular compartments. By applying genetic complementation tests, we estimate that about two-thirds of the tagged proteins are functional. Moreover, these tagged proteins enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will boost systematic analysis of protein expression and localisation in various cellular and developmental contexts. DOI:http://dx.doi.org/10.7554/eLife.12068.001 The fruit fly Drosophila melanogaster is a popular model organism in biological research. Studies using Drosophila have led to important insights into human biology, because related proteins often fulfil similar roles in flies and humans. Thus, studying the role of a protein in Drosophila can teach us about what it might do in a human. To fulfil their biological roles, proteins often occupy particular locations inside cells, such as the cell’s nucleus or surface membrane. Many proteins are also only found in specific types of cell, such as neurons or muscle cells. A protein’s location thus provides clues about what it does, however cells contain many thousands of proteins and identifying the location of each one is a herculean task. Sarov et al. took on this challenge and developed a new resource to study the localisation of all Drosophila proteins during this animal’s development. First, genetic engineering was used to tag thousands of Drosophila proteins with a green fluorescent protein, so that they could be tracked under a microscope. Sarov et al. tagged about 10000 Drosophila proteins in bacteria, and then introduced almost 900 of them into flies to create genetically modified flies. Each fly line contains an extra copy of the tagged gene that codes for one tagged protein. About two-thirds of these tagged proteins appeared to work normally after they were introduced into flies. Sarov et al. then looked at over 200 of these fly lines in more detail and observed that many of the proteins were found in particular cell types and localized to specific parts of the cells. Video imaging of the tagged proteins in living fruit fly embryos and pupae revealed the proteins’ movements, while other techniques showed which proteins bind to the tagged proteins, and may therefore work together in protein complexes. This resource is openly available to the community, and so researchers can use it to study their favourite protein and gain new insights into how proteins work and are regulated during Drosophila development. Following on from this work, the next challenge will be to create more flies carrying tagged proteins, and to swap the green fluorescent tag with other experimentally useful tags. DOI:http://dx.doi.org/10.7554/eLife.12068.002
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Affiliation(s)
- Mihail Sarov
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Christiane Barz
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Helena Jambor
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Dana Suchold
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Bettina Stender
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stephan Janosch
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Vinay Vikas K J
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - R T Krishnan
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Aishwarya Krishnamoorthy
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Irene R S Ferreira
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Katja Finkl
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Susanne Hasse
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Philipp Kämpfer
- Heidelberg Institute of Theoretical Studies, Heidelberg, Germany
| | - Nicole Plewka
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elisabeth Vinis
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | | | - Elisabeth Knust
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mani Ramaswami
- Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - K VijayRaghavan
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Pavel Tomancak
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Frank Schnorrer
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
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13
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Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 2015; 163:712-23. [PMID: 26496610 DOI: 10.1016/j.cell.2015.09.053] [Citation(s) in RCA: 856] [Impact Index Per Article: 95.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023]
Abstract
The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, we have generated a library of HeLa cell lines expressing 1,125 GFP-tagged proteins under near-endogenous control, which we used as input for a next-generation interaction survey. Using quantitative proteomics, we detect specific interactions, estimate interaction stoichiometries, and measure cellular abundances of interacting proteins. These three quantitative dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topology. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quantitative network analysis.
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Affiliation(s)
- Marco Y Hein
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nina C Hubner
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Yusuke Toyoda
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Igor A Gak
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Ina Weisswange
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Eupheria Biotech GmbH, 01307 Dresden, Germany
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Matthias Mann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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14
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Gebhardt A, Habjan M, Benda C, Meiler A, Haas DA, Hein MY, Mann A, Mann M, Habermann B, Pichlmair A. mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3. Nat Commun 2015; 6:8192. [PMID: 26382858 PMCID: PMC4595607 DOI: 10.1038/ncomms9192] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023] Open
Abstract
The flow of genetic information from DNA to protein requires polymerase-II-transcribed RNA characterized by the presence of a 5'-cap. The cap-binding complex (CBC), consisting of the nuclear cap-binding protein (NCBP) 2 and its adaptor NCBP1, is believed to bind all capped RNA and to be necessary for its processing and intracellular localization. Here we show that NCBP1, but not NCBP2, is required for cell viability and poly(A) RNA export. We identify C17orf85 (here named NCBP3) as a cap-binding protein that together with NCBP1 forms an alternative CBC in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to poly(A) RNA export. Loss of NCBP3 can be compensated by NCBP2 under steady-state conditions. However, NCBP3 becomes pivotal under stress conditions, such as virus infection. We propose the existence of an alternative CBC involving NCBP1 and NCBP3 that plays a key role in mRNA biogenesis.
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Affiliation(s)
- Anna Gebhardt
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Christian Benda
- Department of Structural Cell Biology, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Arno Meiler
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Darya A Haas
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Angelika Mann
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Bianca Habermann
- Bioinformatics Core Facility, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Andreas Pichlmair
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
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15
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Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M. DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. Science 2015; 348:1253671. [PMID: 25931565 DOI: 10.1126/science.1253671] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/19/2015] [Indexed: 12/15/2022]
Abstract
DNA interstrand cross-links (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. We devised a technique called chromatin mass spectrometry (CHROMASS) to study protein recruitment dynamics during perturbed DNA replication in Xenopus egg extracts. Using CHROMASS, we systematically monitored protein assembly and disassembly on ICL-containing chromatin. Among numerous prospective DNA repair factors, we identified SLF1 and SLF2, which form a complex with RAD18 and together define a pathway that suppresses genome instability by recruiting the SMC5/6 cohesion complex to DNA lesions. Our study provides a global analysis of an entire DNA repair pathway and reveals the mechanism of SMC5/6 relocalization to damaged DNA in vertebrate cells.
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Affiliation(s)
- Markus Räschle
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Godelieve Smeenk
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Rebecca K Hansen
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Tikira Temu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Yasuyoshi Oka
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nagarjuna Nagaraj
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - David T Long
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes C Walter
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kay Hofmann
- Institute of Genetics, University of Cologne, 50674 Cologne, Germany
| | - Zuzana Storchova
- Maintenance of Genome Stability Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Niels Mailand
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. Novo Nordisk Foundation Center for Protein Research, Proteomics Program, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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Wiśniewski JR, Hein MY, Cox J, Mann M. A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards. Mol Cell Proteomics 2014; 13:3497-506. [PMID: 25225357 PMCID: PMC4256500 DOI: 10.1074/mcp.m113.037309] [Citation(s) in RCA: 545] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 09/08/2014] [Indexed: 12/12/2022] Open
Abstract
Absolute protein quantification using mass spectrometry (MS)-based proteomics delivers protein concentrations or copy numbers per cell. Existing methodologies typically require a combination of isotope-labeled spike-in references, cell counting, and protein concentration measurements. Here we present a novel method that delivers similar quantitative results directly from deep eukaryotic proteome datasets without any additional experimental steps. We show that the MS signal of histones can be used as a "proteomic ruler" because it is proportional to the amount of DNA in the sample, which in turn depends on the number of cells. As a result, our proteomic ruler approach adds an absolute scale to the MS readout and allows estimation of the copy numbers of individual proteins per cell. We compare our protein quantifications with values derived via the use of stable isotope labeling by amino acids in cell culture and protein epitope signature tags in a method that combines spike-in protein fragment standards with precise isotope label quantification. The proteomic ruler approach yields quantitative readouts that are in remarkably good agreement with results from the precision method. We attribute this surprising result to the fact that the proteomic ruler approach omits error-prone steps such as cell counting or protein concentration measurements. The proteomic ruler approach is readily applicable to any deep eukaryotic proteome dataset-even in retrospective analysis-and we demonstrate its usefulness with a series of mouse organ proteomes.
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Affiliation(s)
- Jacek R Wiśniewski
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marco Y Hein
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen Cox
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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17
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Vahl JC, Drees C, Heger K, Heink S, Fischer JC, Nedjic J, Ohkura N, Morikawa H, Poeck H, Schallenberg S, Rieß D, Hein MY, Buch T, Polic B, Schönle A, Zeiser R, Schmitt-Gräff A, Kretschmer K, Klein L, Korn T, Sakaguchi S, Schmidt-Supprian M. Continuous T cell receptor signals maintain a functional regulatory T cell pool. Immunity 2014; 41:722-36. [PMID: 25464853 DOI: 10.1016/j.immuni.2014.10.012] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/22/2014] [Indexed: 12/13/2022]
Abstract
Regulatory T (Treg) cells maintain immune homeostasis and prevent inflammatory and autoimmune responses. During development, thymocytes bearing a moderately self-reactive T cell receptor (TCR) can be selected to become Treg cells. Several observations suggest that also in the periphery mature Treg cells continuously receive self-reactive TCR signals. However, the importance of this inherent autoreactivity for Treg cell biology remains poorly defined. To address this open question, we genetically ablated the TCR of mature Treg cells in vivo. These experiments revealed that TCR-induced Treg lineage-defining Foxp3 expression and gene hypomethylation were uncoupled from TCR input in mature Treg cells. However, Treg cell homeostasis, cell-type-specific gene expression and suppressive function critically depend on continuous triggering of their TCR.
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Affiliation(s)
- J Christoph Vahl
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christoph Drees
- Department of Hematology, Oncology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany
| | - Klaus Heger
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Hematology, Oncology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany
| | - Sylvia Heink
- Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany
| | - Julius C Fischer
- Department of Hematology, Oncology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany
| | - Jelena Nedjic
- Institute for Immunology, Ludwig-Maximilians University, Goethestraße 31, 80336 Munich, Germany
| | - Naganari Ohkura
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Hiromasa Morikawa
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Hendrik Poeck
- Department of Hematology, Oncology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany
| | - Sonja Schallenberg
- Molecular and Cellular Immunology/Immune Regulation, DFG-Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - David Rieß
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Hematology, Oncology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany
| | - Marco Y Hein
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Thorsten Buch
- Institute for Medical Microbiology, Immunology & Hygiene, Trogerstraße 30, Technische Universität München, 81675 Munich, Germany and Institute of Laboratory Animal Sciences, University of Zurich, Winterthurer Straße 190, 8057 Zurich, Switzerland
| | - Bojan Polic
- University of Rijeka School of Medicine, B. Branchetta 20, HR-51000 Rijeka, Croatia
| | - Anne Schönle
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Robert Zeiser
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Annette Schmitt-Gräff
- Department of Pathology, University Hospital Freiburg, Breisacher Straße 115a, 79106 Freiburg Germany
| | - Karsten Kretschmer
- Molecular and Cellular Immunology/Immune Regulation, DFG-Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Ludger Klein
- Institute for Immunology, Ludwig-Maximilians University, Goethestraße 31, 80336 Munich, Germany
| | - Thomas Korn
- Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany
| | - Shimon Sakaguchi
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Marc Schmidt-Supprian
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Hematology, Oncology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 15, 81675 Munich, Germany.
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18
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Keilhauer EC, Hein MY, Mann M. Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics 2014; 14:120-35. [PMID: 25363814 PMCID: PMC4288248 DOI: 10.1074/mcp.m114.041012] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein–protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, todays mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry method for investigating protein–protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. First the background serves for accurate normalization. Second, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Third, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable, and can be performed in any laboratory with access to high-resolution mass spectrometers.
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Affiliation(s)
- Eva C Keilhauer
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marco Y Hein
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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19
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Phillips-Krawczak CA, Singla A, Starokadomskyy P, Deng Z, Osborne DG, Li H, Dick CJ, Gomez TS, Koenecke M, Zhang JS, Dai H, Sifuentes-Dominguez LF, Geng LN, Kaufmann SH, Hein MY, Wallis M, McGaughran J, Gecz J, Sluis BVD, Billadeau DD, Burstein E. COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Mol Biol Cell 2014; 26:91-103. [PMID: 25355947 PMCID: PMC4279232 DOI: 10.1091/mbc.e14-06-1073] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
COMMD1 deficiency results in defective copper homeostasis, but the mechanism for this has remained elusive. Here we report that COMMD1 is directly linked to early endosomes through its interaction with a protein complex containing CCDC22, CCDC93, and C16orf62. This COMMD/CCDC22/CCDC93 (CCC) complex interacts with the multisubunit WASH complex, an evolutionarily conserved system, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. Interactions between the WASH complex subunit FAM21, and the carboxyl-terminal ends of CCDC22 and CCDC93 are responsible for CCC complex recruitment to endosomes. We show that depletion of CCC complex components leads to lack of copper-dependent movement of the copper transporter ATP7A from endosomes, resulting in intracellular copper accumulation and modest alterations in copper homeostasis in humans with CCDC22 mutations. This work provides a mechanistic explanation for the role of COMMD1 in copper homeostasis and uncovers additional genes involved in the regulation of copper transporter recycling.
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Affiliation(s)
| | | | | | - Zhihui Deng
- Department of Immunology, Department of Pathophysiology, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, China
| | | | | | | | | | | | - Jin-San Zhang
- Department of Immunology, School of Pharmaceutical Sciences and Key Laboratory of Biotechnology and Pharmaceutical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Haiming Dai
- Department of Molecular Pharmacology and Experimental Therapeutics, and
| | | | | | - Scott H Kaufmann
- Department of Molecular Pharmacology and Experimental Therapeutics, and
| | - Marco Y Hein
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mathew Wallis
- Genetic Health Queensland at the Royal Brisbane and Women's Hospital, Herston, Queensland 4029, Australia
| | - Julie McGaughran
- Genetic Health Queensland at the Royal Brisbane and Women's Hospital, Herston, Queensland 4029, Australia School of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jozef Gecz
- Robinson Institute and Department of Paediatrics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bart van de Sluis
- Section of Molecular Genetics at the Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 Groningen, Netherlands
| | - Daniel D Billadeau
- Department of Immunology, Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN 55905
| | - Ezra Burstein
- Department of Internal Medicine and Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9151
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20
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Borner GHH, Hein MY, Hirst J, Edgar JR, Mann M, Robinson MS. Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol Biol Cell 2014; 25:3178-94. [PMID: 25165137 PMCID: PMC4196868 DOI: 10.1091/mbc.e14-07-1198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Fractionation profiling is a universal method for the rapid proteomic characterization of membrane vesicles and protein particles. Although initially developed for the analysis of clathrin-coated vesicles, it also provides a versatile tool for generating high-resolution protein-interaction maps, allowing detailed analysis of protein complexes. We developed “fractionation profiling,” a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps.
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Affiliation(s)
- Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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21
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Nández R, Balkin DM, Messa M, Liang L, Paradise S, Czapla H, Hein MY, Duncan JS, Mann M, De Camilli P. A role of OCRL in clathrin-coated pit dynamics and uncoating revealed by studies of Lowe syndrome cells. eLife 2014; 3:e02975. [PMID: 25107275 PMCID: PMC4358339 DOI: 10.7554/elife.02975] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/07/2014] [Indexed: 12/15/2022] Open
Abstract
Mutations in the inositol 5-phosphatase OCRL cause Lowe syndrome and Dent's disease. Although OCRL, a direct clathrin interactor, is recruited to late-stage clathrin-coated pits, clinical manifestations have been primarily attributed to intracellular sorting defects. Here we show that OCRL loss in Lowe syndrome patient fibroblasts impacts clathrin-mediated endocytosis and results in an endocytic defect. These cells exhibit an accumulation of clathrin-coated vesicles and an increase in U-shaped clathrin-coated pits, which may result from sequestration of coat components on uncoated vesicles. Endocytic vesicles that fail to lose their coat nucleate the majority of the numerous actin comets present in patient cells. SNX9, an adaptor that couples late-stage endocytic coated pits to actin polymerization and which we found to bind OCRL directly, remains associated with such vesicles. These results indicate that OCRL acts as an uncoating factor and that defects in clathrin-mediated endocytosis likely contribute to pathology in patients with OCRL mutations. DOI:http://dx.doi.org/10.7554/eLife.02975.001 Oculo-Cerebro-Renal syndrome of Lowe (Lowe syndrome) is a rare genetic disorder that can cause cataracts, mental disabilities and kidney dysfunction. It is caused by mutations in the gene encoding OCRL, a protein that modifies a membrane lipid and that is found on membranes transporting molecules (cargo) into cells by a process known as endocytosis. During endocytosis, the cell outer membrane is deformed into a pit that engulfs the cargo to be taken up by the cell. The pit then pinches off from the outer membrane to form a vesicle—a bubble-like compartment—inside the cell that transports the cargo to its destination. In one type of endocytosis, this process is mediated by a basket-like coat primarily made up from the protein clathrin that assembles at the membrane patch to be internalized. After the vesicle is released from the cell membrane, the clathrin coat is broken apart and its components are shed and recycled for use by new budding endocytic vesicles. The OCRL protein had previously been observed associated to newly forming clathrin-coated vesicles, but the significance of this was not known. Now, Nández et al. have used a range of imaging and analytical techniques to further investigate the properties of OCRL, taking advantage of cells from patients with Lowe syndrome. These cells lack OCRL, and so allow the effect of OCRL's absence on cell function to be deduced. OCRL destroys the membrane lipid that helps to connect the clathrin coat to the membrane, and Nández et al. show that without OCRL the newly formed vesicle moves into the cell but fails to efficiently shed its clathrin coat. Thus, a large fraction of clathrin coat components remain trapped on the vesicles, reducing the amount of such components available to help new pits develop into vesicles. As a consequence, the cell has difficulty internalizing molecules. Collectively, the findings of Nández et al. outline that OCRL plays a role in the regulation of endocytosis in addition to its previously reported actions in the control of intracellular membrane traffic. The results also help to explain some of the symptoms seen in Lowe syndrome patients. DOI:http://dx.doi.org/10.7554/eLife.02975.002
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Affiliation(s)
- Ramiro Nández
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Daniel M Balkin
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Mirko Messa
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Liang Liang
- Department of Diagnostic Radiology, Yale University School of Medicine, New Haven, United States
| | - Summer Paradise
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Heather Czapla
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - James S Duncan
- Department of Diagnostic Radiology, Yale University School of Medicine, New Haven, United States
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Pietro De Camilli
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
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22
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Wueseke O, Bunkenborg J, Hein MY, Zinke A, Viscardi V, Woodruff JB, Oegema K, Mann M, Andersen JS, Hyman AA. The Caenorhabditis elegans pericentriolar material components SPD-2 and SPD-5 are monomeric in the cytoplasm before incorporation into the PCM matrix. Mol Biol Cell 2014; 25:2984-92. [PMID: 25103243 PMCID: PMC4230587 DOI: 10.1091/mbc.e13-09-0514] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Centrosomes are the main microtubule-organizing centers in animal cells. Centrosomes consist of a pair of centrioles surrounded by a matrix of pericentriolar material (PCM) that assembles from cytoplasmic components. In Caenorhabditis elegans embryos, interactions between the coiled-coil proteins SPD-5 and SPD-2 and the kinase PLK-1 are critical for PCM assembly. However, it is not known whether these interactions promote the formation of cytoplasmic complexes that are added to the PCM or whether the components interact only during incorporation into the PCM matrix. Here we address this problem by using a combination of live-cell fluorescence correlation spectroscopy, mass spectrometry, and hydrodynamic techniques to investigate the native state of PCM components in the cytoplasm. We show that SPD-2 is monomeric, and neither SPD-2 nor SPD-5 exists in complex with PLK-1. SPD-5 exists mostly as a monomer but also forms complexes with the PP2A-regulatory proteins RSA-1 and RSA-2, which are required for microtubule organization at centrosomes. These results suggest that the interactions between SPD-2, SPD-5, and PLK-1 do not result in formation of cytoplasmic complexes, but instead occur in the context of PCM assembly.
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Affiliation(s)
- Oliver Wueseke
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jakob Bunkenborg
- Department of Clinical Biochemistry, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Andrea Zinke
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Valeria Viscardi
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093
| | - Jeffrey B Woodruff
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Karen Oegema
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Anthony A Hyman
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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23
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Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 2014; 13:2513-26. [PMID: 24942700 PMCID: PMC4159666 DOI: 10.1074/mcp.m113.031591] [Citation(s) in RCA: 3035] [Impact Index Per Article: 303.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide quantification with label-free approaches remains a challenge. We developed a new intensity determination and normalization procedure called MaxLFQ that is fully compatible with any peptide or protein separation prior to LC-MS analysis. Protein abundance profiles are assembled using the maximum possible information from MS signals, given that the presence of quantifiable peptides varies from sample to sample. For a benchmark dataset with two proteomes mixed at known ratios, we accurately detected the mixing ratio over the entire protein expression range, with greater precision for abundant proteins. The significance of individual label-free quantifications was obtained via a t test approach. For a second benchmark dataset, we accurately quantify fold changes over several orders of magnitude, a task that is challenging with label-based methods. MaxLFQ is a generic label-free quantification technology that is readily applicable to many biological questions; it is compatible with standard statistical analysis workflows, and it has been validated in many and diverse biological projects. Our algorithms can handle very large experiments of 500+ samples in a manageable computing time. It is implemented in the freely available MaxQuant computational proteomics platform and works completely seamlessly at the click of a button.
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Affiliation(s)
- Jürgen Cox
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Marco Y Hein
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Christian A Luber
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Igor Paron
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nagarjuna Nagaraj
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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24
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Zanivan S, Maione F, Hein MY, Hernández-Fernaud JR, Ostasiewicz P, Giraudo E, Mann M. SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers. Mol Cell Proteomics 2013; 12:3599-611. [PMID: 23979707 PMCID: PMC3861710 DOI: 10.1074/mcp.m113.031344] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [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: 05/27/2013] [Revised: 07/21/2013] [Indexed: 02/04/2023] Open
Abstract
Proteomics has been successfully used for cell culture on dishes, but more complex cellular systems have proven to be challenging and so far poorly approached with proteomics. Because of the complexity of the angiogenic program, we still do not have a complete understanding of the molecular mechanisms involved in this process, and there have been no in depth quantitative proteomic studies. Plating endothelial cells on matrigel recapitulates aspects of vessel growth, and here we investigate this mechanism by using a spike-in SILAC quantitative proteomic approach. By comparing proteomic changes in primary human endothelial cells morphogenesis on matrigel to general adhesion mechanisms in cells spreading on culture dish, we pinpoint pathways and proteins modulated by endothelial cells. The cell-extracellular matrix adhesion proteome depends on the adhesion substrate, and a detailed proteomic profile of the extracellular matrix secreted by endothelial cells identified CLEC14A as a matrix component, which binds to MMRN2. We verify deregulated levels of these proteins during tumor angiogenesis in models of multistage carcinogenesis. This is the most in depth quantitative proteomic study of endothelial cell morphogenesis, which shows the potential of applying high accuracy quantitative proteomics to in vitro models of vessel growth to shed new light on mechanisms that accompany pathological angiogenesis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000359.
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MESH Headings
- Animals
- Antigens, Surface/genetics
- Antigens, Surface/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carbon Isotopes
- Cell Adhesion
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/metabolism
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Collagen/chemistry
- Drug Combinations
- Extracellular Matrix/chemistry
- Extracellular Matrix/genetics
- Extracellular Matrix/metabolism
- Gene Expression Regulation, Neoplastic
- Human Umbilical Vein Endothelial Cells/metabolism
- Human Umbilical Vein Endothelial Cells/pathology
- Humans
- Isotope Labeling
- Laminin/chemistry
- Lectins, C-Type/genetics
- Lectins, C-Type/metabolism
- Mass Spectrometry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Morphogenesis/genetics
- Neovascularization, Pathologic
- Primary Cell Culture
- Protein Binding
- Proteoglycans/chemistry
- Proteomics
- Signal Transduction
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Affiliation(s)
- Sara Zanivan
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- §The Beatson Institute for Cancer Research, Glasgow G61 1BD, United Kingdom
| | - Federica Maione
- ¶Laboratory of Transgenic Mouse Models, Institute for Cancer Research at Candiolo (IRCC), 10060 Candiolo, Italy
- ‖Department of Science and Drug Technology, University of Torino, 10125, Torino, Italy
| | - Marco Y. Hein
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | - Pawel Ostasiewicz
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- **Department of Pathology, Wroclaw Medical University, 50-368, Wroclaw, Poland
| | - Enrico Giraudo
- ¶Laboratory of Transgenic Mouse Models, Institute for Cancer Research at Candiolo (IRCC), 10060 Candiolo, Italy
- ‖Department of Science and Drug Technology, University of Torino, 10125, Torino, Italy
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- ‡‡The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Hirst J, Borner GHH, Edgar J, Hein MY, Mann M, Buchholz F, Antrobus R, Robinson MS. Interaction between AP-5 and the hereditary spastic paraplegia proteins SPG11 and SPG15. Mol Biol Cell 2013; 24:2558-69. [PMID: 23825025 PMCID: PMC3744948 DOI: 10.1091/mbc.e13-03-0170] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The AP-5 complex is a recently identified but evolutionarily ancient member of the family of heterotetrameric adaptor proteins (AP complexes). It is associated with two proteins that are mutated in patients with hereditary spastic paraplegia, SPG11 and SPG15. Here we show that the four AP-5 subunits can be coimmunoprecipitated with SPG11 and SPG15, both from cytosol and from detergent-extracted membranes, with a stoichiometry of ∼1:1:1:1:1:1. Knockdowns of SPG11 or SPG15 phenocopy knockdowns of AP-5 subunits: all six knockdowns cause the cation-independent mannose 6-phosphate receptor to become trapped in clusters of early endosomes. In addition, AP-5, SPG11, and SPG15 colocalize on a late endosomal/lysosomal compartment. Both SPG11 and SPG15 have predicted secondary structures containing α-solenoids related to those of clathrin heavy chain and COPI subunits. SPG11 also has an N-terminal, β-propeller-like domain, which interacts in vitro with AP-5. We propose that AP-5, SPG15, and SPG11 form a coat-like complex, with AP-5 involved in protein sorting, SPG15 facilitating the docking of the coat onto membranes by interacting with PI3P via its FYVE domain, and SPG11 (possibly together with SPG15) forming a scaffold.
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Affiliation(s)
- Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom.
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Vahl JC, Heger K, Knies N, Hein MY, Boon L, Yagita H, Polic B, Schmidt-Supprian M. NKT cell-TCR expression activates conventional T cells in vivo, but is largely dispensable for mature NKT cell biology. PLoS Biol 2013; 11:e1001589. [PMID: 23853545 PMCID: PMC3708704 DOI: 10.1371/journal.pbio.1001589] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 05/07/2013] [Indexed: 12/24/2022] Open
Abstract
Natural killer T (NKT) cell development depends on recognition of self-glycolipids via their semi-invariant Vα14i-TCR. However, to what extent TCR-mediated signals determine identity and function of mature NKT cells remains incompletely understood. To address this issue, we developed a mouse strain allowing conditional Vα14i-TCR expression from within the endogenous Tcrα locus. We demonstrate that naïve T cells are activated upon replacement of their endogenous TCR repertoire with Vα14i-restricted TCRs, but they do not differentiate into NKT cells. On the other hand, induced TCR ablation on mature NKT cells did not affect their lineage identity, homeostasis, or innate rapid cytokine secretion abilities. We therefore propose that peripheral NKT cells become unresponsive to and thus are independent of their autoreactive TCR. Immune system natural killer T (NKT) cells help to protect against certain strains of bacteria and viruses, and suppress the development of autoimmune diseases and cancer. However, NKT cells are also central mediators of allergic responses. The recognition of one's own glycolipid antigens (self-glycolipids) in the thymus via the unique Vα14i T cell receptor, Vα14i-TCR, triggers the NKT cell developmental program, which differs considerably from that of conventional T cells. We generated a mouse model to investigate whether the Vα14i-TCR on mature NKT cells constantly recognizes self-glycolipids and to assess whether this TCR is required for survival and continued NKT cell identity. Switching the peptide-recognizing TCR of a mature conventional T cell to a glycolipid-recognizing Vα14i-TCR led to activation of the T cells, indicating that this TCR is also autoreactive on peripheral T cells or can signal autonomously. But TCR ablation did not affect the half-life, characteristic gene expression or innate functions of mature NKT cells. Therefore, the inherently autoreactive Vα14i-TCR is dispensable for the functions of mature peripheral NKT cells after instructing thymic NKT cell development. Thus the Vα14i-TCR serves a similar function to pattern-recognition receptors, in mediating immune recognition of foreign invasion or diseased cells.
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Affiliation(s)
- J. Christoph Vahl
- Molecular Immunology and Signaltransduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Klaus Heger
- Molecular Immunology and Signaltransduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nathalie Knies
- Molecular Immunology and Signaltransduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marco Y. Hein
- Molecular Immunology and Signaltransduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Louis Boon
- Bioceros, Yalelaan 46, Utrecht, The Netherlands
| | - Hideo Yagita
- Juntendo University School of Medicine, Tokyo, Japan
| | - Bojan Polic
- University of Rijeka School of Medicine, Rijeka, Croatia
| | - Marc Schmidt-Supprian
- Molecular Immunology and Signaltransduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- * E-mail:
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Starokadomskyy P, Gluck N, Li H, Chen B, Wallis M, Maine GN, Mao X, Zaidi IW, Hein MY, McDonald FJ, Lenzner S, Zecha A, Ropers HH, Kuss AW, McGaughran J, Gecz J, Burstein E. CCDC22 deficiency in humans blunts activation of proinflammatory NF-κB signaling. J Clin Invest 2013; 123:2244-56. [PMID: 23563313 DOI: 10.1172/jci66466] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 02/14/2013] [Indexed: 01/11/2023] Open
Abstract
NF-κB is a master regulator of inflammation and has been implicated in the pathogenesis of immune disorders and cancer. Its regulation involves a variety of steps, including the controlled degradation of inhibitory IκB proteins. In addition, the inactivation of DNA-bound NF-κB is essential for its regulation. This step requires a factor known as copper metabolism Murr1 domain-containing 1 (COMMD1), the prototype member of a conserved gene family. While COMMD proteins have been linked to the ubiquitination pathway, little else is known about other family members. Here we demonstrate that all COMMD proteins bind to CCDC22, a factor recently implicated in X-linked intellectual disability (XLID). We showed that an XLID-associated CCDC22 mutation decreased CCDC22 protein expression and impaired its binding to COMMD proteins. Moreover, some affected individuals displayed ectodermal dysplasia, a congenital condition that can result from developmental NF-κB blockade. Indeed, patient-derived cells demonstrated impaired NF-κB activation due to decreased IκB ubiquitination and degradation. In addition, we found that COMMD8 acted in conjunction with CCDC22 to direct the degradation of IκB proteins. Taken together, our results indicate that CCDC22 participates in NF-κB activation and that its deficiency leads to decreased IκB turnover in humans, highlighting an important regulatory component of this pathway.
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Affiliation(s)
- Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Bassik MC, Kampmann M, Lebbink RJ, Wang S, Hein MY, Poser I, Weibezahn J, Horlbeck MA, Chen S, Mann M, Hyman AA, Leproust EM, McManus MT, Weissman JS. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell 2013; 152:909-22. [PMID: 23394947 DOI: 10.1016/j.cell.2013.01.030] [Citation(s) in RCA: 278] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/29/2012] [Accepted: 01/18/2013] [Indexed: 11/27/2022]
Abstract
Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultracomplex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a noncanonical role for COPI, a previously uncharacterized protein complex affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs.
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Affiliation(s)
- Michael C Bassik
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94122, USA.
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Stern-Ginossar N, Weisburd B, Michalski A, Le VTK, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS. Decoding human cytomegalovirus. Science 2012; 338:1088-93. [PMID: 23180859 PMCID: PMC3817102 DOI: 10.1126/science.1227919] [Citation(s) in RCA: 456] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The human cytomegalovirus (HCMV) genome was sequenced 20 years ago. However, like those of other complex viruses, our understanding of its protein coding potential is far from complete. We used ribosome profiling and transcript analysis to experimentally define the HCMV translation products and follow their temporal expression. We identified hundreds of previously unidentified open reading frames and confirmed a fraction by means of mass spectrometry. We found that regulated use of alternative transcript start sites plays a broad role in enabling tight temporal control of HCMV protein expression and allowing multiple distinct polypeptides to be generated from a single genomic locus. Our results reveal an unanticipated complexity to the HCMV coding capacity and illustrate the role of regulated changes in transcript start sites in generating this complexity.
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Affiliation(s)
- Noam Stern-Ginossar
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisico, CA 94158, USA
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