1
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Liao SY, Rudoy D, Frank SB, Phan LT, Klezovitch O, Kwan J, Coleman I, Haffner MC, Li D, Nelson PS, Emili A, Vasioukhin V. SND1 binds to ERG and promotes tumor growth in genetic mouse models of prostate cancer. Nat Commun 2023; 14:7435. [PMID: 37973913 PMCID: PMC10654515 DOI: 10.1038/s41467-023-43245-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
SND1 and MTDH are known to promote cancer and therapy resistance, but their mechanisms and interactions with other oncogenes remain unclear. Here, we show that oncoprotein ERG interacts with SND1/MTDH complex through SND1's Tudor domain. ERG, an ETS-domain transcription factor, is overexpressed in many prostate cancers. Knocking down SND1 in human prostate epithelial cells, especially those overexpressing ERG, negatively impacts cell proliferation. Transcriptional analysis shows substantial overlap in genes regulated by ERG and SND1. Mechanistically, we show that ERG promotes nuclear localization of SND1/MTDH. Forced nuclear localization of SND1 prominently increases its growth promoting function irrespective of ERG expression. In mice, prostate-specific Snd1 deletion reduces cancer growth and tumor burden in a prostate cancer model (PB-Cre/Ptenflox/flox/ERG mice), Moreover, we find a significant overlap between prostate transcriptional signatures of ERG and SND1. These findings highlight SND1's crucial role in prostate tumorigenesis, suggesting SND1 as a potential therapeutic target in prostate cancer.
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Affiliation(s)
- Sheng-You Liao
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Dmytro Rudoy
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sander B Frank
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Luan T Phan
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Olga Klezovitch
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julian Kwan
- Center for Network Systems Biology, Departments of Biochemistry & Biology, Boston University, Boston, MA, USA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Dapei Li
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Departments of Biochemistry & Biology, Boston University, Boston, MA, USA
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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2
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Michaelis JB, Bozkurt S, Schäfer JA, Münch C. Monitoring Mitochondrial Protein Import Using Mitochondrial Targeting Sequence (MTS)-eGFP. Bio Protoc 2022; 12:e4578. [PMID: 36618095 PMCID: PMC9797355 DOI: 10.21769/bioprotoc.4578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Mitochondria are cellular organelles essential for the function and survival of eukaryotic cells. Nearly all mitochondrial proteins are nuclear-encoded and require mitochondrial import upon their synthesis in the cytosol. Various approaches have been described to study mitochondrial protein import, such as monitoring the entry of radiolabeled proteins into purified mitochondria or quantifying newly synthesized proteins within mitochondria by proteomics. Here, we provide a detailed protocol for a commonly used and straightforward assay that quantitatively examines mitochondrial protein import by monitoring the co-localization of mitochondrially targeted enhanced green fluorescent protein (eGFP) with the mitochondrial fluorescence dye MitoTracker TM Deep Red FM by live cell imaging. We describe the preparation and use of a stable mammalian cell line inducibly expressing a mitochondrial targeting sequence (MTS)-eGFP, followed by quantitative image analysis using an open-source ImageJ-based plugin. This inducible expression system avoids the need for transient transfection while enabling titration of MTS-eGFP expression and thereby avoiding protein folding stress. Overall, the assay provides a simple and robust approach to assess mitochondrial import capacity of cells in various disease-related settings. This protocol was validated in: Mol Cell (2021), DOI: 10.1016/j.molcel.2021.11.004 Graphical abstract.
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Affiliation(s)
- Jonas B. Michaelis
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
| | - Jasmin A. Schäfer
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
,
Frankfurt Cancer Institute, Frankfurt am Main, Germany
,
Cardio-Pulmonary Institute, Frankfurt am Main, Germany
,
*For correspondence:
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3
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Moonen JR, Chappell J, Shi M, Shinohara T, Li D, Mumbach MR, Zhang F, Nair RV, Nasser J, Mai DH, Taylor S, Wang L, Metzger RJ, Chang HY, Engreitz JM, Snyder MP, Rabinovitch M. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress. Nat Commun 2022; 13:4941. [PMID: 35999210 PMCID: PMC9399231 DOI: 10.1038/s41467-022-32566-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote this beneficial response. We show that under LSS, KLF4 interacts with the SWI/SNF nucleosome remodeling complex to increase accessibility at enhancer sites that promote the expression of homeostatic endothelial genes. By combining molecular and computational approaches we discover enhancers that loop to promoters of KLF4- and LSS-responsive genes that stabilize endothelial cells and suppress inflammation, such as BMPR2, SMAD5, and DUSP5. By linking enhancers to genes that they regulate under physiologic LSS, our work establishes a foundation for interpreting how non-coding DNA variants in these regions might disrupt protective gene expression to influence vascular disease.
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Affiliation(s)
- Jan-Renier Moonen
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James Chappell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tsutomu Shinohara
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dan Li
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Maxwell R Mumbach
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Fan Zhang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ramesh V Nair
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel H Mai
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shalina Taylor
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lingli Wang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ross J Metzger
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jesse M Engreitz
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael P Snyder
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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4
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Lian X, Yang X, Yang S, Zhang Z. Current status and future perspectives of computational studies on human-virus protein-protein interactions. Brief Bioinform 2021; 22:6161422. [PMID: 33693490 DOI: 10.1093/bib/bbab029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the development of highly effective drugs to break the transmission of viral infectious diseases. Recent years have witnessed the rapid accumulation of experimentally identified human-virus PPI data, which provides an unprecedented opportunity for bioinformatics studies revolving around human-virus PPIs. In this article, we provide a comprehensive overview of computational studies on human-virus PPIs, especially focusing on the method development for human-virus PPI predictions. We briefly introduce the experimental detection methods and existing database resources of human-virus PPIs, and then discuss the research progress in the development of computational prediction methods. In particular, we elaborate the machine learning-based prediction methods and highlight the need to embrace state-of-the-art deep-learning algorithms and new feature engineering techniques (e.g. the protein embedding technique derived from natural language processing). To further advance the understanding in this research topic, we also outline the practical applications of the human-virus interactome in fundamental biological discovery and new antiviral therapy development.
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Affiliation(s)
- Xianyi Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaodi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shiping Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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5
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Kougnassoukou Tchara PE, Filippakopoulos P, Lambert JP. Emerging tools to investigate bromodomain functions. Methods 2020; 184:40-52. [DOI: 10.1016/j.ymeth.2019.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022] Open
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6
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REEP5 depletion causes sarco-endoplasmic reticulum vacuolization and cardiac functional defects. Nat Commun 2020; 11:965. [PMID: 32075961 PMCID: PMC7031342 DOI: 10.1038/s41467-019-14143-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
The sarco-endoplasmic reticulum (SR/ER) plays an important role in the development and progression of many heart diseases. However, many aspects of its structural organization remain largely unknown, particularly in cells with a highly differentiated SR/ER network. Here, we report a cardiac enriched, SR/ER membrane protein, REEP5 that is centrally involved in regulating SR/ER organization and cellular stress responses in cardiac myocytes. In vitro REEP5 depletion in mouse cardiac myocytes results in SR/ER membrane destabilization and luminal vacuolization along with decreased myocyte contractility and disrupted Ca2+ cycling. Further, in vivo CRISPR/Cas9-mediated REEP5 loss-of-function zebrafish mutants show sensitized cardiac dysfunction upon short-term verapamil treatment. Additionally, in vivo adeno-associated viral (AAV9)-induced REEP5 depletion in the mouse demonstrates cardiac dysfunction. These results demonstrate the critical role of REEP5 in SR/ER organization and function as well as normal heart function and development. The sarcoplasmic (SR) and endoplasmic reticulum (ER) are involved in heart development but how this arises is unclear. Here, the authors show that loss of a SR/ER protein REEP5 causes membrane destabilization and decreased cardiac myocyte contractility, with cardiac dysfunction in mutant mouse and zebrafish models.
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7
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Joseph J, Radulovich N, Wang T, Raghavan V, Zhu CQ, Tsao MS. Rho guanine nucleotide exchange factor ARHGEF10 is a putative tumor suppressor in pancreatic ductal adenocarcinoma. Oncogene 2019; 39:308-321. [DOI: 10.1038/s41388-019-0985-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 12/18/2022]
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8
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Wu Z, Malty R, Moutaoufik MT, Zhang Q, Jessulat M, Babu M. A Tag-Based Affinity Purification Mass Spectrometry Workflow for Systematic Isolation of the Human Mitochondrial Protein Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:83-100. [PMID: 31452137 DOI: 10.1007/978-981-13-8367-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mitochondria (mt) are double-membraned, dynamic organelles that play an essential role in a large number of cellular processes, and impairments in mt function have emerged as a causative factor for a growing number of human disorders. Given that most biological functions are driven by physical associations between proteins, the first step towards understanding mt dysfunction is to map its protein-protein interaction (PPI) network in a comprehensive and systematic fashion. While mass-spectrometry (MS) based approaches possess the high sensitivity ideal for such an endeavor, it also requires stringent biochemical purification of bait proteins to avoid detecting spurious, non-specific PPIs. Here, we outline a tagging-based affinity purification coupled with mass spectrometry (AP-MS) workflow for discovering new mt protein associations and providing novel insights into their role in mt biology and human physiology/pathology. Because AP-MS relies on the creation of proteins fused with affinity tags, we employ a versatile-affinity (VA) tag, consisting of 3× FLAG, 6 × His, and Strep III epitopes. For efficient delivery of affinity-tagged open reading frames (ORF) into mammalian cells, the VA-tag is cloned onto a specific ORF using Gateway recombinant cloning, and the resulting expression vector is stably introduced in target cells using lentiviral transduction. In this chapter, we show a functional workflow for mapping the mt interactome that includes tagging, stable transduction, selection and expansion of mammalian cell lines, mt extraction, identification of interacting protein partners by AP-MS, and lastly, computational assessment of protein complexes/PPI networks.
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Affiliation(s)
- Zhuoran Wu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Ramy Malty
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | | | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada.
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9
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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019; 18:1428-1436. [PMID: 31076518 PMCID: PMC6601208 DOI: 10.1074/mcp.ra119.001518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/13/2022] Open
Abstract
SETD1A is a SET domain-containing methyltransferase involved in epigenetic regulation of transcription. It is the main catalytic component of a multiprotein complex that methylates lysine 4 of histone H3, a histone mark associated with gene activation. In humans, six related protein complexes with partly nonredundant cellular functions share several protein subunits but are distinguished by unique catalytic SET-domain proteins. We surveyed physical interactions of the SETD1A-complex using endogenous immunoprecipitation followed by label-free quantitative proteomics on three subunits: SETD1A, RBBP5, and ASH2L. Surprisingly, SETD1A, but not RBBP5 or ASH2L, was found to interact with the DNA damage repair protein RAD18. Reciprocal RAD18 immunoprecipitation experiments confirmed the interaction with SETD1A, whereas size exclusion and protein network analysis suggested an interaction independent of the main SETD1A complex. We found evidence of SETD1A and RAD18 influence on mutual gene expression levels. Further, knockdown of the genes individually showed a DNA damage repair phenotype, whereas simultaneous knockdown resulted in an epistatic effect. This adds to a growing body of work linking epigenetic enzymes to processes involved in genome stability.
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Affiliation(s)
- Manal Alsulami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nayla Munawar
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ¶Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Eugene Dillon
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Giorgio Oliviero
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran Wynne
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ‖Maine Medical Center Research Institute, 81 Research Drive, Scarborough, Maine 04074
| | - Mona Alsolami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Catherine Moss
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peadar Ó Gaora
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fergal O'Meara
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Cotter
- **Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Gerard Cagney
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland;.
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10
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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019. [DOI: https://doi.org/10.1074/mcp.ra119.001518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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11
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Gill MK, Christova T, Zhang YY, Gregorieff A, Zhang L, Narimatsu M, Song S, Xiong S, Couzens AL, Tong J, Krieger JR, Moran MF, Zlotta AR, van der Kwast TH, Gingras AC, Sicheri F, Wrana JL, Attisano L. A feed forward loop enforces YAP/TAZ signaling during tumorigenesis. Nat Commun 2018; 9:3510. [PMID: 30158528 PMCID: PMC6115388 DOI: 10.1038/s41467-018-05939-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 07/30/2018] [Indexed: 12/13/2022] Open
Abstract
In most solid tumors, the Hippo pathway is inactivated through poorly understood mechanisms that result in the activation of the transcriptional regulators, YAP and TAZ. Here, we identify NUAK2 as a YAP/TAZ activator that directly inhibits LATS-mediated phosphorylation of YAP/TAZ and show that NUAK2 induction by YAP/TAZ and AP-1 is required for robust YAP/TAZ signaling. Pharmacological inhibition or loss of NUAK2 reduces the growth of cultured cancer cells and mammary tumors in mice. Moreover, in human patient samples, we show that NUAK2 expression is elevated in aggressive, high-grade bladder cancer and strongly correlates with a YAP/TAZ gene signature. These findings identify a positive feed forward loop in the Hippo pathway that establishes a key role for NUAK2 in enforcing the tumor-promoting activities of YAP/TAZ. Our results thus introduce a new opportunity for cancer therapeutics by delineating NUAK2 as a potential target for re-engaging the Hippo pathway. The Hippo pathway is frequently dysregulated in cancer. Here, the authors identify NUAK2 as negative regulator of the Hippo pathway from a siRNA kinome screen and show that NUAK2 promotes YAP/TAZ nuclear localisation while NUAK2 is a transcriptional target of YAP/TAZ, thus providing a feed forward loop to promote tumorigenesis.
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Affiliation(s)
- Mandeep K Gill
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Tania Christova
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ying Y Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Alex Gregorieff
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Pathology, McGill University and Research Institute of the McGill University Health Center, Montreal, H4A 3J1, QC, Canada
| | - Liang Zhang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 999077, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Masahiro Narimatsu
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Siyuan Song
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Shawn Xiong
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Amber L Couzens
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Jiefei Tong
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael F Moran
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Program in Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alexandre R Zlotta
- Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, M5G 1X5, ON, Canada
| | - Theodorus H van der Kwast
- Department of Pathology, Toronto General Hospital, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Frank Sicheri
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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12
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Cholley PE, Moehlin J, Rohmer A, Zilliox V, Nicaise S, Gronemeyer H, Mendoza-Parra MA. Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators. NPJ Syst Biol Appl 2018; 4:29. [PMID: 30083390 PMCID: PMC6070484 DOI: 10.1038/s41540-018-0066-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/13/2018] [Accepted: 06/21/2018] [Indexed: 01/10/2023] Open
Abstract
Complex organisms originate from and are maintained by the information encoded in the genome. A major challenge of systems biology is to develop algorithms that describe the dynamic regulation of genome functions from large omics datasets. Here, we describe TETRAMER, which reconstructs gene-regulatory networks from temporal transcriptome data during cell fate transitions to predict “master” regulators by simulating cascades of temporal transcription-regulatory events.
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Affiliation(s)
- Pierre-Etienne Cholley
- 1Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France.,2Present Address: Computational Systems Biology Infrastructure, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Julien Moehlin
- 1Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Alexia Rohmer
- 1Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Vincent Zilliox
- 1Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Samuel Nicaise
- 1Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Hinrich Gronemeyer
- 1Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Marco Antonio Mendoza-Parra
- 1Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France.,3Present Address: UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, 91057 Évry, France
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13
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Khalique H, López Marco J, Lim F. A haploid HSV-1 genome platform for vector development: testing of the tetracycline-responsive switch shows interference by infected cell protein 0. J Gene Med 2018; 18:302-311. [PMID: 27672733 DOI: 10.1002/jgm.2929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Although herpes simplex virus type 1 (HSV-1) has outstanding properties for gene delivery vectors and its genome is available in bacterial artificial chromosomes (BACs) for mutagenesis studies, one impediment is the presence of approximately 15.4 kb of DNA sequences that are duplicated in the HSV-1 genome, complicating vector construction and stability. METHODS As a useful platform for building HSV-1 vectors, we have constructed a fully haploid HSV-1 genome BAC by deletion of one of these repeats, confirming that viral propagation in culture is not impaired. We used this ΔIR mutant to subsequently investigate whether the insertion of tetracycline-responsive tetO elements into the ICP34.5-ICP0 gene region can be used to control HSV-1 lytic replication. RESULTS The results of the present study show that ΔIR mutants deleted for ICP34.5 are viable for replication but not when the ICP0 promoter is also disrupted, thus indicating that regulation of infected cell protein 0 (ICP0) levels in the absence of ICP34.5 could be a viable means for controlling growth of HSV-1 vectors. Surprisingly, however, the tetO elements inserted into the ICP0 promoter did not confer ligand responsiveness to growth or ICP0 expression. Further analysis by transfection experiments revealed that ICP0 itself interferes with the tetracycline switch and reduces the the inducibility of this system. CONCLUSIONS Our new haploid HSV-1 BAC is a useful platform for building multiply deleted HSV-1 vectors. Deletion of the gene for ICP34.5 in this backbone renders viral growth dependent on ICP0, although ICP0 expression could not be regulated by tet-responsive transcriptional regulators.
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Affiliation(s)
- Hena Khalique
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Jorge López Marco
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Filip Lim
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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14
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Recent progress in mass spectrometry proteomics for biomedical research. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1093-1113. [DOI: 10.1007/s11427-017-9175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022]
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15
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Miskinyte G, Devaraju K, Grønning Hansen M, Monni E, Tornero D, Woods NB, Bengzon J, Ahlenius H, Lindvall O, Kokaia Z. Direct conversion of human fibroblasts to functional excitatory cortical neurons integrating into human neural networks. Stem Cell Res Ther 2017; 8:207. [PMID: 28962665 PMCID: PMC5622454 DOI: 10.1186/s13287-017-0658-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/07/2017] [Accepted: 09/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background Human fibroblasts can be directly converted to several subtypes of neurons, but cortical projection neurons have not been generated. Methods Here we screened for transcription factor combinations that could potentially convert human fibroblasts to functional excitatory cortical neurons. The induced cortical (iCtx) cells were analyzed for cortical neuronal identity using immunocytochemistry, single-cell quantitative polymerase chain reaction (qPCR), electrophysiology, and their ability to integrate into human neural networks in vitro and ex vivo using electrophysiology and rabies virus tracing. Results We show that a combination of three transcription factors, BRN2, MYT1L, and FEZF2, have the ability to directly convert human fibroblasts to functional excitatory cortical neurons. The conversion efficiency was increased to about 16% by treatment with small molecules and microRNAs. The iCtx cells exhibited electrophysiological properties of functional neurons, had pyramidal-like cell morphology, and expressed key cortical projection neuronal markers. Single-cell analysis of iCtx cells revealed a complex gene expression profile, a subpopulation of them displaying a molecular signature closely resembling that of human fetal primary cortical neurons. The iCtx cells received synaptic inputs from co-cultured human fetal primary cortical neurons, contained spines, and expressed the postsynaptic excitatory scaffold protein PSD95. When transplanted ex vivo to organotypic cultures of adult human cerebral cortex, the iCtx cells exhibited morphological and electrophysiological properties of mature neurons, integrated structurally into the cortical tissue, and received synaptic inputs from adult human neurons. Conclusions Our findings indicate that functional excitatory cortical neurons, generated here for the first time by direct conversion of human somatic cells, have the capacity for synaptic integration into adult human cortex. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0658-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giedre Miskinyte
- Laboratory of Stem Cells and Restorative Neurology, University Hospital, Lund, Sweden. .,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden.
| | - Karthikeyan Devaraju
- Laboratory of Stem Cells and Restorative Neurology, University Hospital, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Marita Grønning Hansen
- Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Emanuela Monni
- Laboratory of Stem Cells and Restorative Neurology, University Hospital, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Daniel Tornero
- Laboratory of Stem Cells and Restorative Neurology, University Hospital, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Niels Bjarne Woods
- Division of Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Johan Bengzon
- Division of Neurosurgery, Department of Clinical Sciences Lund, University Hospital, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Henrik Ahlenius
- Stem Cells, Aging and Neurodegeneration Group, University Hospital, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Olle Lindvall
- Laboratory of Stem Cells and Restorative Neurology, University Hospital, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
| | - Zaal Kokaia
- Laboratory of Stem Cells and Restorative Neurology, University Hospital, Lund, Sweden.,Lund Stem Cell Center, University Hospital BMC B10, Lund University, SE-221 84, Lund, Sweden
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16
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Kwan J, Sczaniecka A, Heidary Arash E, Nguyen L, Chen CC, Ratkovic S, Klezovitch O, Attisano L, McNeill H, Emili A, Vasioukhin V. DLG5 connects cell polarity and Hippo signaling protein networks by linking PAR-1 with MST1/2. Genes Dev 2017; 30:2696-2709. [PMID: 28087714 PMCID: PMC5238729 DOI: 10.1101/gad.284539.116] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
Abstract
Here, Kwan et al. investigated the mechanisms connecting cell polarity proteins with intracellular signaling pathways. They found that DLG5 functions as an evolutionarily conserved scaffold and negative regulator of Hippo signaling, demonstrating a direct connection between cell polarity proteins and Hippo that is needed for proper development of multicellular organisms. Disruption of apical–basal polarity is implicated in developmental disorders and cancer; however, the mechanisms connecting cell polarity proteins with intracellular signaling pathways are largely unknown. We determined previously that membrane-associated guanylate kinase (MAGUK) protein discs large homolog 5 (DLG5) functions in cell polarity and regulates cellular proliferation and differentiation via undefined mechanisms. We report here that DLG5 functions as an evolutionarily conserved scaffold and negative regulator of Hippo signaling, which controls organ size through the modulation of cell proliferation and differentiation. Affinity purification/mass spectrometry revealed a critical role of DLG5 in the formation of protein assemblies containing core Hippo kinases mammalian ste20 homologs 1/2 (MST1/2) and Par-1 polarity proteins microtubule affinity-regulating kinases 1/2/3 (MARK1/2/3). Consistent with this finding, Hippo signaling is markedly hyperactive in mammalian Dlg5−/− tissues and cells in vivo and ex vivo and in Drosophila upon dlg5 knockdown. Conditional deletion of Mst1/2 fully rescued the phenotypes of brain-specific Dlg5 knockout mice. Dlg5 also interacts genetically with Hippo effectors Yap1/Taz. Mechanistically, we show that DLG5 inhibits the association between MST1/2 and large tumor suppressor homologs 1/2 (LATS1/2), uses its scaffolding function to link MST1/2 with MARK3, and inhibits MST1/2 kinase activity. These data reveal a direct connection between cell polarity proteins and Hippo, which is essential for proper development of multicellular organisms.
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Affiliation(s)
- Julian Kwan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anna Sczaniecka
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emad Heidary Arash
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Liem Nguyen
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Chia-Chun Chen
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Srdjana Ratkovic
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Olga Klezovitch
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Liliana Attisano
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Helen McNeill
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98195, USA
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17
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Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Müller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G. An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client. Mol Cell Proteomics 2016; 15:1139-50. [PMID: 26933192 PMCID: PMC4813694 DOI: 10.1074/mcp.o115.055350] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tandem affinity purification–mass spectrometry (TAP-MS) is a popular strategy for the identification of protein–protein interactions, characterization of protein complexes, and entire networks. Its employment in cellular settings best fitting the relevant physiology is limited by convenient expression vector systems. We developed an easy-to-handle, inducible, dually selectable retroviral expression vector allowing dose- and time-dependent control of bait proteins bearing the efficient streptavidin-hemagglutinin (SH)-tag at their N- or C termini. Concomitant expression of a reporter fluorophore allows to monitor bait-expressing cells by flow cytometry or microscopy and enables high-throughput phenotypic assays. We used the system to successfully characterize the interactome of the neuroblastoma RAS viral oncogene homolog (NRAS) Gly12Asp (G12D) mutant and exploited the advantage of reporter fluorophore expression by tracking cytokine-independent cell growth using flow cytometry. Moreover, we tested the feasibility of studying cytotoxicity-mediating proteins with the vector system on the cell death-inducing mixed lineage kinase domain-like protein (MLKL) Ser358Asp (S358D) mutant. Interaction proteomics analysis of MLKL Ser358Asp (S358D) identified heat shock protein 90 (HSP90) as a high-confidence interacting protein. Further phenotypic characterization established MLKL as a novel HSP90 client. In summary, this novel inducible expression system enables SH-tag-based interaction studies in the cell line proficient for the respective phenotypic or signaling context and constitutes a valuable tool for experimental approaches requiring inducible or traceable protein expression.
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Affiliation(s)
- Johannes W Bigenzahn
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Astrid Fauster
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuele Rebsamen
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Richard K Kandasamy
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefania Scorzoni
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gregory I Vladimer
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Gstaiger
- §Department of Biology, Institute of Mol. Syst. Biol., ETH Zürich, Zürich, Switzerland
| | - Johannes Zuber
- ¶Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Keiryn L Bennett
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; ‖Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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18
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Olsen JB, Wong L, Deimling S, Miles A, Guo H, Li Y, Zhang Z, Greenblatt JF, Emili A, Tropepe V. G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. Stem Cell Reports 2016; 7:454-470. [PMID: 27546533 PMCID: PMC5031922 DOI: 10.1016/j.stemcr.2016.06.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023] Open
Abstract
Proliferating progenitor cells undergo changes in competence to give rise to post-mitotic progeny of specialized function. These cell-fate transitions typically involve dynamic regulation of gene expression by histone methyltransferase (HMT) complexes. However, the composition, roles, and regulation of these assemblies in regulating cell-fate decisions in vivo are poorly understood. Using unbiased affinity purification and mass spectrometry, we identified the uncharacterized C2H2-like zinc finger protein ZNF644 as a G9a/GLP-interacting protein and co-regulator of histone methylation. In zebrafish, functional characterization of ZNF644 orthologs, znf644a and znf644b, revealed complementary roles in regulating G9a/H3K9me2-mediated gene silencing during neurogenesis. The non-overlapping requirements for znf644a and znf644b during retinal differentiation demarcate critical aspects of retinal differentiation programs regulated by differential G9a-ZNF644 associations, such as transitioning proliferating progenitor cells toward differentiation. Collectively, our data point to ZNF644 as a critical co-regulator of G9a/H3K9me2-mediated gene silencing during neuronal differentiation.
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Affiliation(s)
- Jonathan B Olsen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada
| | - Loksum Wong
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Steven Deimling
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Amanda Miles
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Yue Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada.
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada.
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19
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Wang Y, Chen J, Yang W, Mo F, Senz J, Yap D, Anglesio MS, Gilks B, Morin GB, Huntsman DG. The oncogenic roles of DICER1 RNase IIIb domain mutations in ovarian Sertoli-Leydig cell tumors. Neoplasia 2016; 17:650-60. [PMID: 26408257 PMCID: PMC4674484 DOI: 10.1016/j.neo.2015.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/11/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022] Open
Abstract
DICER1, an endoribonuclease required for microRNA (miRNA) biogenesis, is essential for embryogenesis and the development of many organs including ovaries. We have recently identified somatic hotspot mutations in RNase IIIb domain of DICER1 in half of ovarian Sertoli-Leydig cell tumors, a rare class of sex-cord stromal cell tumors in young women. These hotspot mutations lost IIIb cleavage activity of DICER1 in vitro and failed to produce 5p-derived miRNAs in mouse Dicer1-null ES cells. However, the oncogenic potential of these hotspot DICER1 mutations has not been studied. Here, we further revealed that the global expression of 5p-derived miRNAs was dramatically reduced in ovarian Sertoli-Leydig cell tumors carrying DICER1 hotspot mutations compared with those without DICER1 hotspot mutation. The miRNA production defect was associated with the deregulation of genes controlling cell proliferation and the cell fate. Using an immortalized human granulosa cell line, SVOG3e, we determined that the D1709N-DICER1 hotspot mutation failed to produce 5p-derived miRNAs, deregulated the expression of several genes that control gonadal differentiation and cell proliferation, and promoted cell growth. Re-expression of let-7 significantly inhibited the growth of D1709N-DICER1 SVOG3e cells, accompanied by the suppression of key regulators of cell cycle control and ovarian gonad differentiation. Taken together, our data revealed that DICER1 hotspot mutations cause systemic loss of 5p-miRNAs that can both drive pseudodifferentiation of testicular elements and cause oncogenic transformation in the ovary.
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Affiliation(s)
- Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, British Columbia Cancer Agency Cancer Research Centre, Vancouver, BC, Canada
| | - Jiamin Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Winnie Yang
- Department of Molecular Oncology, British Columbia Cancer Agency Cancer Research Centre, Vancouver, BC, Canada
| | - Fan Mo
- Vancouver Prostate Cancer Centre, Vancouver, BC, Canada
| | - Janine Senz
- Department of Molecular Oncology, British Columbia Cancer Agency Cancer Research Centre, Vancouver, BC, Canada
| | - Damian Yap
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, British Columbia Cancer Agency Cancer Research Centre, Vancouver, BC, Canada
| | - Michael S Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, British Columbia Cancer Agency Cancer Research Centre, Vancouver, BC, Canada
| | - Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, British Columbia Cancer Agency Cancer Research Centre, Vancouver, BC, Canada.
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20
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Yanling Zhao D, Gish G, Braunschweig U, Li Y, Ni Z, Schmitges FW, Zhong G, Liu K, Li W, Moffat J, Vedadi M, Min J, Pawson TJ, Blencowe BJ, Greenblatt JF. SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination. Nature 2015; 529:48-53. [DOI: 10.1038/nature16469] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 11/20/2015] [Indexed: 12/13/2022]
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21
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Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One 2015; 10:e0139695. [PMID: 26437229 PMCID: PMC4593582 DOI: 10.1371/journal.pone.0139695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 01/18/2023] Open
Abstract
We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols.
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Affiliation(s)
- Nan Zhong
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Maria Fenner
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Anandi Bhattacharya
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Michal Olszewski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Haiming Huang
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Vincent Nadeem
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S. Sidhu
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jack F. Greenblatt
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, MSB-4180, Toronto, ON M5S 1A8, Canada
| | - Edyta Marcon
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
- * E-mail:
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22
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Sharma P, Abbasi C, Lazic S, Teng ACT, Wang D, Dubois N, Ignatchenko V, Wong V, Liu J, Araki T, Tiburcy M, Ackerley C, Zimmermann WH, Hamilton R, Sun Y, Liu PP, Keller G, Stagljar I, Scott IC, Kislinger T, Gramolini AO. Evolutionarily conserved intercalated disc protein Tmem65 regulates cardiac conduction and connexin 43 function. Nat Commun 2015; 6:8391. [PMID: 26403541 DOI: 10.1038/ncomms9391] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 08/18/2015] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins are crucial to heart function and development. Here we combine cationic silica-bead coating with shotgun proteomics to enrich for and identify plasma membrane-associated proteins from primary mouse neonatal and human fetal ventricular cardiomyocytes. We identify Tmem65 as a cardiac-enriched, intercalated disc protein that increases during development in both mouse and human hearts. Functional analysis of Tmem65 both in vitro using lentiviral shRNA-mediated knockdown in mouse cardiomyocytes and in vivo using morpholino-based knockdown in zebrafish show marked alterations in gap junction function and cardiac morphology. Molecular analyses suggest that Tmem65 interaction with connexin 43 (Cx43) is required for correct localization of Cx43 to the intercalated disc, since Tmem65 deletion results in marked internalization of Cx43, a shorter half-life through increased degradation, and loss of Cx43 function. Our data demonstrate that the membrane protein Tmem65 is an intercalated disc protein that interacts with and functionally regulates ventricular Cx43.
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Affiliation(s)
- Parveen Sharma
- Department of Physiology, University of Toronto, Toronto General Hospital Research Institute, Toronto, Ontario, Canada M5G 1L7
| | - Cynthia Abbasi
- Department of Physiology, University of Toronto, Toronto General Hospital Research Institute, Toronto, Ontario, Canada M5G 1L7
| | - Savo Lazic
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Allen C T Teng
- Department of Physiology, University of Toronto, Toronto General Hospital Research Institute, Toronto, Ontario, Canada M5G 1L7
| | - Dingyan Wang
- Department of Physiology, University of Toronto, Toronto General Hospital Research Institute, Toronto, Ontario, Canada M5G 1L7
| | - Nicole Dubois
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Victoria Wong
- Departments of Molecular Genetics and Biochemistry, Donnelly Centre,, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Jun Liu
- Department of Mechanical and Industrial Engineering, Advanced Micro and Nanosystems Laboratory, University of Toronto, Toronto, Ontario, Canada M5S 3G8
| | - Toshiyuki Araki
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Malte Tiburcy
- Institute of Pharmacology, University Medical Center Göttingen and DZHK (German Center for Cardiovascular Research) partner site Göttingen, Göttingen 37075, Germany
| | - Cameron Ackerley
- The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Wolfram H Zimmermann
- Institute of Pharmacology, University Medical Center Göttingen and DZHK (German Center for Cardiovascular Research) partner site Göttingen, Göttingen 37075, Germany
| | - Robert Hamilton
- The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8.,Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada M5G 1L7
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, Advanced Micro and Nanosystems Laboratory, University of Toronto, Toronto, Ontario, Canada M5S 3G8
| | - Peter P Liu
- Toronto General Hospital, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Igor Stagljar
- Departments of Molecular Genetics and Biochemistry, Donnelly Centre,, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Ian C Scott
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8.,Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada M5G 1L7
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Anthony O Gramolini
- Department of Physiology, University of Toronto, Toronto General Hospital Research Institute, Toronto, Ontario, Canada M5G 1L7.,Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada M5G 1L7
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23
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Radulovich N, Leung L, Ibrahimov E, Navab R, Sakashita S, Zhu CQ, Kaufman E, Lockwood WW, Thu KL, Fedyshyn Y, Moffat J, Lam WL, Tsao MS. Coiled-coil domain containing 68 (CCDC68) demonstrates a tumor-suppressive role in pancreatic ductal adenocarcinoma. Oncogene 2015; 34:4238-47. [PMID: 25381825 PMCID: PMC5153324 DOI: 10.1038/onc.2014.357] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 09/09/2014] [Accepted: 09/16/2014] [Indexed: 12/26/2022]
Abstract
Using integrative genomics and functional screening, we identified coiled-coil domain containing 68 (CCDC68) as a novel putative tumor suppressor gene (TSG) in pancreatic ductal adenocarcinoma (PDAC). CCDC68 allelic losses were documented in 48% of primary PDAC patient tumors, 50% of PDAC cell lines and 30% of primary patient derived xenografts. We also discovered a single nucleotide polymorphism (SNP) variant (SNP rs1344011) that leads to exon skipping and generation of an unstable protein isoform CCDC68Δ(69-114) in 31% of PDAC patients. Overexpression of full length CCDC68 (CCDC68(wt)) in PANC-1 and Hs.766T PDAC cell lines lacking CDCC68 expression decreased proliferation and tumorigenicity in scid mice. In contrast, the downregulation of endogenous CCDC68 in MIAPaca-2 cells increased tumor growth rate. These effects were not observed with the deletion-containing isoform, CCDC68Δ(69-114).
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Affiliation(s)
- Nikolina Radulovich
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology Department, University of Toronto, Ontario, Canada
| | - Lisa Leung
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Emin Ibrahimov
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Roya Navab
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Ethan Kaufman
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - William W. Lockwood
- British Columbia Cancer Research Centre and Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Kelsie L. Thu
- British Columbia Cancer Research Centre and Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Yaroslav Fedyshyn
- Department of Molecular Genetics, Banting & Best Department of Medical Research, University of Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, Banting & Best Department of Medical Research, University of Toronto, ON, Canada
| | - Wan L. Lam
- British Columbia Cancer Research Centre and Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology Department, University of Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
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24
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Chen J, Wang Y, McMonechy MK, Anglesio MS, Yang W, Senz J, Maines-Bandiera S, Rosner J, Trigo-Gonzalez G, Grace Cheng SW, Kim J, Matzuk MM, Morin GB, Huntsman DG. Recurrent DICER1 hotspot mutations in endometrial tumours and their impact on microRNA biogenesis. J Pathol 2015; 237:215-25. [PMID: 26033159 DOI: 10.1002/path.4569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/15/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022]
Abstract
DICER1 plays a critical role in microRNA (miRNA) biogenesis. Recurrent somatic 'hotspot' mutations at the four metal-binding sites within the RNase IIIb domain of DICER1 were identified in ovarian sex cord-stromal tumours and have since been described in other paediatric tumours. In this study, we screened the RNase IIIb domain of DICER1 in 290 endometrial tumours and identified six cases with hotspot mutations, including two cases affected by an atypical G1809R mutation directly adjacent to a metal-binding site. Using Illumina and Sanger targeted resequencing, we observed and validated biallelic DICER1 mutations in several cases with hotspot mutations. Through in vitro DICER1 cleavage assays, small RNA deep sequencing and real-time PCR, we demonstrated that mutations adding a positively charged side chain to residue 1809 have similar detrimental effects on 5p miRNA production to mutations at the metal-binding sites. As expected, 5p miRNAs were globally reduced in tumours and cell lines with hotspot mutations. Pathway analysis of gene expression profiles indicated that genes de-repressed due to loss of 5p miRNAs are strongly associated with pathways regulating the cell cycle. Using a Dicer1-null mouse cell line model, we found that expression of DICER1 hotspot mutants promoted cell proliferation, whereas wild-type (WT) DICER1 inhibited cell proliferation. Furthermore, targets of let-7 family miRNAs are enriched among the up-regulated genes, suggesting that loss of let-7 may be impacting downstream pathways. Our results reveal that DICER1 hotspot mutations are implicated in common malignancies and may constitute a unique oncogenic pathway.
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Affiliation(s)
- Jiamin Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Melissa K McMonechy
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Michael S Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Winnie Yang
- Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Janine Senz
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sarah Maines-Bandiera
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jamie Rosner
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | | | - S W Grace Cheng
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Jaeyeon Kim
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Martin M Matzuk
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Gregg B Morin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
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25
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Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods 2015; 12:725-31. [PMID: 26121405 DOI: 10.1038/nmeth.3472] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/06/2015] [Indexed: 01/12/2023]
Abstract
Antibodies are used in multiple cell biology applications, but there are no standardized methods to assess antibody quality-an absence that risks data integrity and reproducibility. We describe a mass spectrometry-based standard operating procedure for scoring immunoprecipitation antibody quality. We quantified the abundance of all the proteins in immunoprecipitates of 1,124 new recombinant antibodies for 152 chromatin-related human proteins by comparing normalized spectral abundance factors from the target antigen with those of all other proteins. We validated the performance of the standard operating procedure in blinded studies in five independent laboratories. Antibodies for which the target antigen or a member of its known protein complex was the most abundant protein were classified as 'IP gold standard'. This method generates quantitative outputs that can be stored and archived in public databases, and it represents a step toward a platform for community benchmarking of antibody quality.
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26
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Jin K, Musso G, Vlasblom J, Jessulat M, Deineko V, Negroni J, Mosca R, Malty R, Nguyen-Tran DH, Aoki H, Minic Z, Freywald T, Phanse S, Xiang Q, Freywald A, Aloy P, Zhang Z, Babu M. Yeast Mitochondrial Protein–Protein Interactions Reveal Diverse Complexes and Disease-Relevant Functional Relationships. J Proteome Res 2015; 14:1220-37. [DOI: 10.1021/pr501148q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ke Jin
- Terrence
Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Gabriel Musso
- Cardiovascular
Division, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - James Vlasblom
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Matthew Jessulat
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Viktor Deineko
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Jacopo Negroni
- Joint
IRB−BSC Program in Computational Biology, IRB, Barcelona 08028, Spain
| | - Roberto Mosca
- Joint
IRB−BSC Program in Computational Biology, IRB, Barcelona 08028, Spain
| | - Ramy Malty
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Diem-Hang Nguyen-Tran
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Zoran Minic
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Tanya Freywald
- Cancer Research
Unit, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Sadhna Phanse
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Qian Xiang
- Terrence
Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Andrew Freywald
- Cancer Research
Unit, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Patrick Aloy
- Joint
IRB−BSC Program in Computational Biology, IRB, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Zhaolei Zhang
- Terrence
Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Mohan Babu
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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27
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Malty RH, Jessulat M, Jin K, Musso G, Vlasblom J, Phanse S, Zhang Z, Babu M. Mitochondrial targets for pharmacological intervention in human disease. J Proteome Res 2014; 14:5-21. [PMID: 25367773 PMCID: PMC4286170 DOI: 10.1021/pr500813f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Over the past several years, mitochondrial
dysfunction has been
linked to an increasing number of human illnesses, making mitochondrial
proteins (MPs) an ever more appealing target for therapeutic intervention.
With 20% of the mitochondrial proteome (312 of an estimated 1500 MPs)
having known interactions with small molecules, MPs appear to be highly
targetable. Yet, despite these targeted proteins functioning in a
range of biological processes (including induction of apoptosis, calcium
homeostasis, and metabolism), very few of the compounds targeting
MPs find clinical use. Recent work has greatly expanded the number
of proteins known to localize to the mitochondria and has generated
a considerable increase in MP 3D structures available in public databases,
allowing experimental screening and in silico prediction of mitochondrial
drug targets on an unprecedented scale. Here, we summarize the current
literature on clinically active drugs that target MPs, with a focus
on how existing drug targets are distributed across biochemical pathways
and organelle substructures. Also, we examine current strategies for
mitochondrial drug discovery, focusing on genetic, proteomic, and
chemogenomic assays, and relevant model systems. As cell models and
screening techniques improve, MPs appear poised to emerge as relevant
targets for a wide range of complex human diseases, an eventuality
that can be expedited through systematic analysis of MP function.
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Affiliation(s)
- Ramy H Malty
- Department of Biochemistry, Research and Innovation Centre, University of Regina , Regina, Saskatchewan S4S 0A2, Canada
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28
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Schoenrock A, Samanfar B, Pitre S, Hooshyar M, Jin K, Phillips CA, Wang H, Phanse S, Omidi K, Gui Y, Alamgir M, Wong A, Barrenäs F, Babu M, Benson M, Langston MA, Green JR, Dehne F, Golshani A. Efficient prediction of human protein-protein interactions at a global scale. BMC Bioinformatics 2014; 15:383. [PMID: 25492630 PMCID: PMC4272565 DOI: 10.1186/s12859-014-0383-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 11/12/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments. CONCLUSIONS The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.
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Affiliation(s)
| | | | - Sylvain Pitre
- School of Computer Science, Carleton University, Ottawa, Canada.
| | | | - Ke Jin
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
| | - Charles A Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, USA.
| | - Hui Wang
- Department of Pediatrics, Gothenburg University, Gothenburg, Sweden. .,The Centre for Individualized Medication, Linköping University, Linköping, Sweden.
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
| | - Katayoun Omidi
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Yuan Gui
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Md Alamgir
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Fredrik Barrenäs
- Department of Pediatrics, Gothenburg University, Gothenburg, Sweden. .,The Centre for Individualized Medication, Linköping University, Linköping, Sweden.
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada.
| | - Mikael Benson
- Department of Pediatrics, Gothenburg University, Gothenburg, Sweden. .,The Centre for Individualized Medication, Linköping University, Linköping, Sweden.
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, USA.
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada.
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, Canada.
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29
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Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. J Proteomics 2014; 118:81-94. [PMID: 25281560 DOI: 10.1016/j.jprot.2014.09.011] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 09/04/2014] [Accepted: 09/07/2014] [Indexed: 12/19/2022]
Abstract
UNLABELLED Mapping protein-protein interactions for chromatin-associated proteins remains challenging. Here we explore the use of BioID, a proximity biotinylation approach in which a mutated biotin ligase (BirA*) is fused to a bait of interest, allowing for the local activation of biotin and subsequent biotinylation of proteins in the bait vicinity. BioID allowed for successful interactome mapping of core histones and members of the mediator complex. We explored the background signal produced by the BioID approach and found that using distinct types of controls increased the stringency of our statistical analysis with SAINTexpress. A direct comparison of BioID with our AP-MS protocol optimized for chromatin-associated protein complexes revealed that the approaches identified few shared interaction partners and enriched for distinct biological processes; yet, both approaches permitted the recovery of biologically meaningful interactions. While no clear bias could be observed for either technique toward protein complexes of particular functions, BioID allowed for the purification of proteins of lower cellular abundance. Finally, we were able to identify a strong association of MED4 with the centrosome by BioID and validated this finding by immunofluorescence. In summary, BioID complements AP-MS for the study of chromatin-associated protein complexes. BIOLOGICAL SIGNIFICANCE This manuscript describes the application of BioID, a proximity biotinylation approach, to chromatin-associated proteins, namely core histones and members of the mediator complex. We observed that BioID was successful at identifying known interaction partners for the baits tested, but also allowed novel putative interaction partners to be identified. By performing a detailed comparison of BioID versus a standard method for interactome mapping (affinity purification coupled to mass spectrometry, AP-MS), we show that the approaches were complementary, allowing for purification of different interaction partners. These interaction partners were different in the biological processes they are associated with, but also in their abundance. BioID represents a significant technical development in the field of chromatin research by expanding the search space for interactome mapping beyond what is possible with AP-MS. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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30
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RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Nat Struct Mol Biol 2014; 21:686-695. [PMID: 24997600 PMCID: PMC4124035 DOI: 10.1038/nsmb.2853] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 06/02/2014] [Indexed: 01/16/2023]
Abstract
The RNA polymerase II (RNAPII) C-terminal domain (CTD) heptapeptide repeats (1-YSPTSPS-7) undergo dynamic phosphorylation and dephosphorylation during the transcription cycle to recruit factors that regulate transcription, RNA processing and chromatin modification. We show here that RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains and interact preferentially via CTD-interaction domains (CIDs) with RNAPII CTD repeats phosphorylated at S2 and S7. Crystal structures of the RPRD1A, RPRD1B and RPRD2 CIDs, alone and in complex with RNAPII CTD phosphoisoforms, elucidate the molecular basis of CTD recognition. In an example of cross-talk between different CTD modifications, our data also indicate that RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and, by interacting with CTD repeats where phospho-S2 and/or phospho-S7 bracket a phospho-S5 residue, serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2.
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31
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Human-Chromatin-Related Protein Interactions Identify a Demethylase Complex Required for Chromosome Segregation. Cell Rep 2014; 8:297-310. [DOI: 10.1016/j.celrep.2014.05.050] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/24/2014] [Accepted: 05/27/2014] [Indexed: 01/14/2023] Open
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Whole-genome sequencing identifies genetic variances in culture-expanded human mesenchymal stem cells. Stem Cell Reports 2014; 3:227-33. [PMID: 25254336 PMCID: PMC4176531 DOI: 10.1016/j.stemcr.2014.05.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 12/30/2022] Open
Abstract
Culture-expanded human mesenchymal stem cells (MSCs) are increasingly used in clinics, yet full characterization of the genomic compositions of these cells is lacking. We present a whole-genome investigation on the genetic dynamics of cultured MSCs under ex vivo establishment (passage 1 [p1]) and serial expansion (p8 and p13). We detected no significant changes in copy-number alterations (CNAs) and low levels of single-nucleotide changes (SNCs) until p8. Strikingly, a significant number (677) of SNCs were found in p13 MSCs. Using a sensitive Droplet Digital PCR assay, we tested the nonsynonymous SNCs detected by whole-genome sequencing and found that they were preexisting low-frequency mutations in uncultured mononuclear cells (∼0.01%) and early-passage MSCs (0.1%-1% at p1 and p8) but reached 17%-36% in p13. Our data demonstrate that human MSCs maintain a stable genomic composition in the early stages of ex vivo culture but are subject to clonal growth upon extended expansion.
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Post-translational regulation of CD133 by ATase1/ATase2-mediated lysine acetylation. J Mol Biol 2014; 426:2175-82. [PMID: 24556617 DOI: 10.1016/j.jmb.2014.02.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/23/2014] [Accepted: 02/07/2014] [Indexed: 11/20/2022]
Abstract
The CD133 cell-surface protein expresses the AC133 epitope that is associated with cancer progenitor cells and cancer resistance to traditional anticancer therapies. We report that the endoplasmic reticulum Golgi intermediate compartment residing acetyltransferases, ATase1 (NAT8B) and ATase2 (NAT8), can physically interact with CD133 to acetylate the protein on three lysine residues predicted to reside on the first extracellular loop of CD133. Site-directed mutagenesis of these residues mimicking a loss of acetylation and downregulation or inhibition of ATase1/ATase2 resulted in near-complete abolishment of CD133 protein expression. We also demonstrate that targeting ATase1/ATase2 results in apoptosis of CD133 expressing acute lymphoblastic leukemia cells. Taken together, we suggest that lysine acetylation on predicted extracellular residues plays a key role in expression and trafficking of CD133 protein to the cell surface and can be targeted to disrupt CD133 regulation and function.
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Lambert JP, Tucholska M, Pawson T, Gingras AC. Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners. J Proteomics 2014; 100:55-9. [PMID: 24412199 DOI: 10.1016/j.jprot.2013.12.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 12/14/2013] [Accepted: 12/27/2013] [Indexed: 10/25/2022]
Abstract
UNLABELLED Affinity purification coupled to mass spectrometry (AP-MS) is an effective means of identifying protein-protein interactions to better understand biological functions. However, issues associated with sample preparation still limit the success of AP-MS for specific classes of proteins, including those associated with chromatin that exhibit overall poor solubility in the protocols normally used for AP-MS analysis. Here, we wanted to provide a generally applicable method to simultaneously identify interactors for the chromatin-bound and the soluble fractions of a given bait protein. Using four FLAG-tagged canonical histone proteins (H2A, H2B, H3.1 and H4) we demonstrate that the chromatin solubility issue can be robustly alleviated by fragmenting DNA prior to AP-MS using a combination of sonication and nuclease treatment. We show that - in comparison to a commonly used AP-MS method - our optimized protocol greatly improves the recovery of chromatin-associated interactors for core histones. Critically, this is achieved while preserving the interaction partners associated with the soluble portion of the histones. Detailed protocols amenable to the study of both histone and non-histone baits are presented here. BIOLOGICAL SIGNIFICANCE This manuscript describes workflow improvements to enable the recovery of chromatin-bound interactors by affinity purification coupled to mass spectrometry (AP-MS). This is significant, as most of the high-throughput studies to date can only monitor protein-protein interactions for soluble (not bound to chromatin) components. By consequence, we still poorly understand how protein complexes form on chromatin, which greatly hampers our understanding of gene expression. Using core histones as test cases, we show here a simple and universally applicable workflow that permits the identification of chromatin-bound protein-protein interactions. As exemplified in our manuscript, this revised protocol should result in a much deeper understanding of chromatin biology. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto M5G 1X5, Canada
| | - Monika Tucholska
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto M5G 1X5, Canada
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.
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Vlasblom J, Jin K, Kassir S, Babu M. Exploring mitochondrial system properties of neurodegenerative diseases through interactome mapping. J Proteomics 2013; 100:8-24. [PMID: 24262152 DOI: 10.1016/j.jprot.2013.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/08/2013] [Accepted: 11/06/2013] [Indexed: 12/20/2022]
Abstract
UNLABELLED Mitochondria are double membraned, dynamic organelles that are required for a large number of cellular processes, and defects in their function have emerged as causative factors for a growing number of human disorders and are highly associated with cancer, metabolic, and neurodegenerative (ND) diseases. Biochemical and genetic investigations have uncovered small numbers of candidate mitochondrial proteins (MPs) involved in ND disease, but given the diversity of processes affected by MP function and the difficulty of detecting interactions involving these proteins, many more likely remain unknown. However, high-throughput proteomic and genomic approaches developed in genetically tractable model prokaryotes and lower eukaryotes have proven to be effective tools for querying the physical (protein-protein) and functional (gene-gene) relationships between diverse types of proteins, including cytosolic and membrane proteins. In this review, we highlight how experimental and computational approaches developed recently by our group and others can be effectively used towards elucidating the mitochondrial interactome in an unbiased and systematic manner to uncover network-based connections. We discuss how the knowledge from the resulting interaction networks can effectively contribute towards the identification of new mitochondrial disease gene candidates, and thus further clarify the role of mitochondrial biology and the complex etiologies of ND disease. BIOLOGICAL SIGNIFICANCE Biochemical and genetic investigations have uncovered small numbers of candidate mitochondrial proteins (MPs) involved in neurodegenerative (ND) diseases, but given the diversity of processes affected by MP function and the difficulty of detecting interactions involving these proteins, many more likely remain unknown. Large-scale proteomic and genomic approaches developed in model prokaryotes and lower eukaryotes have proven to be effective tools for querying the physical (protein-protein) and functional (gene-gene) relationships between diverse types of proteins. Extension of this new framework to the mitochondrial sub-system in human will likewise provide a universally informative systems-level view of the physical and functional landscape for exploring the evolutionary principles underlying mitochondrial function. In this review, we highlight how experimental and computational approaches developed recently by our group and others can be effectively used towards elucidating the mitochondrial interactome in an unbiased and systematic manner to uncover network-based connections. We anticipate that the knowledge from these resulting interaction networks can effectively contribute towards the identification of new mitochondrial disease gene candidates, and thus foster a deeper molecular understanding of mitochondrial biology as well as the etiology of mitochondrial diseases. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- James Vlasblom
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Ke Jin
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Sandy Kassir
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada.
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Abstract
Previous work in insulinoma cell lines has established that calcineurin plays a critical role in the activation of cAMP-responsive element binding protein (Creb), a key transcription factor required for β-cell function and survival, by dephosphorylating the Creb coactivator Creb-regulated transcription coactivator (Crtc)2 at 2 regulatory sites, Ser171 and Ser275. Here, we report that Crtc2 is essential both for glucose-stimulated insulin secretion and cell survival in the β-cell. Endogenous Crtc2 activation is achieved via increasing glucose levels to the physiological feeding range, indicating that Crtc2 is a sensor that couples ambient glucose concentrations to Creb activity in the β-cell. Immunosuppressant drugs such as cyclosporin A and tacrolimus that target the protein phosphatase calcineurin are commonly administered after organ transplantation. Chronic use is associated with reduced insulin secretion and new onset diabetes, suggestive of pancreatic β-cell dysfunction. Importantly, we show that overexpression of a Crtc2 mutant rendered constitutively active by introduction of nonphosphorylatable alanine residues at Ser171 and Ser275 permits Creb target gene activation under conditions when calcineurin is inhibited. Taken together, these data suggest that promoting Crtc2-Creb activity is required for β-cell function and proliferation and promoting this pathway could ameliorate symptoms of new onset diabetes after transplantation.
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Affiliation(s)
- Chandra E Eberhard
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
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37
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Mak AB, Moffat J. RNA interference screens to uncover membrane protein biology. Brief Funct Genomics 2013; 12:422-9. [PMID: 23793263 DOI: 10.1093/bfgp/elt022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this review, we discuss the use of RNA interference screens to identify genes involved in the regulation and function of membrane proteins. Briefly, cells expressing the membrane protein of interest can be transduced with a pooled lentiviral short-hairpin RNA (shRNA) library containing tens of thousands of unique shRNAs. Transduced cells are then selected or fractionated based on specific critera, such as membrane protein expression or function. shRNAs from selected cell populations are then deconvoluted and quantified using microarray analyses or high-throughput sequencing technologies. This allows individual shRNAs to be scored and cutoffs can be made to generate a list of shRNA hits. Bioinformatic analyses of gene targets of shRNA hits can be used to identify pathways and processes associated with membrane protein biology. To illustrate this functional genomics approach, we discuss pooled lentiviral shRNA screens that were performed to identify genes that regulate the transcription and cell-surface expression of the cancer stem cell marker CD133. This approach can be adapted to study other membrane proteins, as well as specific aspects of membrane proteins, such as their function or downstream signaling effects.
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Affiliation(s)
- Anthony B Mak
- Donnelly Centre and Banting and Best Department of Medical Research/Department of Molecular Genetics, University of Toronto, 830-160 College Street, Toronto, ON M5S 3E1, Canada.
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38
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Kuzmanov U, Emili A. Protein-protein interaction networks: probing disease mechanisms using model systems. Genome Med 2013; 5:37. [PMID: 23635424 PMCID: PMC3706760 DOI: 10.1186/gm441] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) and multi-protein complexes perform central roles in the cellular systems of all living organisms. In humans, disruptions of the normal patterns of PPIs and protein complexes can be causative or indicative of a disease state. Recent developments in the biological applications of mass spectrometry (MS)-based proteomics have expanded the horizon for the application of systematic large-scale mapping of physical interactions to probe disease mechanisms. In this review, we examine the application of MS-based approaches for the experimental analysis of PPI networks and protein complexes, focusing on the different model systems (including human cells) used to study the molecular basis of common diseases such as cancer, cardiomyopathies, diabetes, microbial infections, and genetic and neurodegenerative disorders.
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Affiliation(s)
- Uros Kuzmanov
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
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39
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Li Y, Zhao DY, Greenblatt JF, Zhang Z. RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Res 2013; 41:e94. [PMID: 23455476 PMCID: PMC3632129 DOI: 10.1093/nar/gkt142] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
RIP-seq has recently been developed to discover genome-wide RNA transcripts that interact with a protein or protein complex. RIP-seq is similar to both RNA-seq and ChIP-seq, but presents unique properties and challenges. Currently, no statistical tool is dedicated to RIP-seq analysis. We developed RIPSeeker (http://www.bioconductor.org/packages/2.12/bioc/html/RIPSeeker.html), a free open-source Bioconductor/R package for de novo RIP peak predictions based on HMM. To demonstrate the utility of the software package, we applied RIPSeeker and six other published programs to three independent RIP-seq datasets and two PAR-CLIP datasets corresponding to six distinct RNA-binding proteins. Based on receiver operating curves, RIPSeeker demonstrates superior sensitivity and specificity in discriminating high-confidence peaks that are consistently agreed on among a majority of the comparison methods, and dominated 9 of the 12 evaluations, averaging 80% area under the curve. The peaks from RIPSeeker are further confirmed based on their significant enrichment for biologically meaningful genomic elements, published sequence motifs and association with canonical transcripts known to interact with the proteins examined. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within a self-contained software package comprehensively addressing issues ranging from post-alignments' processing to visualization and annotation.
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Affiliation(s)
- Yue Li
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
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40
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Anglesio MS, Wang Y, Yang W, Senz J, Wan A, Heravi-Moussavi A, Salamanca C, Maines-Bandiera S, Huntsman DG, Morin GB. Cancer-associated somatic DICER1 hotspot mutations cause defective miRNA processing and reverse-strand expression bias to predominantly mature 3p strands through loss of 5p strand cleavage. J Pathol 2013; 229:400-9. [PMID: 23132766 DOI: 10.1002/path.4135] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 09/26/2012] [Accepted: 10/10/2012] [Indexed: 12/19/2022]
Abstract
Our group recently described recurrent somatic mutations of the miRNA processing gene DICER1 in non-epithelial ovarian cancer. Mutations appeared to be clustered around each of four critical metal-binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3' end of the 5p miRNA strand of a pre-mRNA hairpin. To investigate the effects of these cancer-associated 'hotspot' mutations, we engineered mouse DICER1-deficient ES cells to express wild-type and an allelic series of the mutant DICER1 variants. Global miRNA and mRNA profiles from cells carrying the metal-binding site mutations were compared to each other and to wild-type DICER1. The miRNA and mRNA profiles generated through the expression of the hotspot mutations were virtually identical, and the DICER1 hotspot mutation-carrying cells were distinct from both wild-type and DICER1-deficient cells. Further, miRNA profiles showed that mutant DICER1 results in a dramatic loss in processing of mature 5p miRNA strands but were still able to create 3p strand miRNAs. Messenger RNA (mRNA) profile changes were consistent with the loss of 5p strand miRNAs and showed enriched expression for predicted targets of the lost 5p-derived miRNAs. We therefore conclude that cancer-associated somatic hotspot mutations of DICER1, affecting any one of four metal-binding residues in the RNase IIIB domain, are functionally equivalent with respect to miRNA processing and are hypomorphic alleles, yielding a global loss in processing of mature 5p strand miRNA. We further propose that this resulting 3p strand bias in mature miRNA expression likely underpins the oncogenic potential of these hotspot mutations.
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Affiliation(s)
- M S Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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41
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Biran A, Meshorer E. Concise review: chromatin and genome organization in reprogramming. Stem Cells 2013; 30:1793-9. [PMID: 22782851 DOI: 10.1002/stem.1169] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ability to reprogram somatic cells to pluripotency is continuingly attracting increasing amounts of attention, providing both potential opportunities for regenerative medicine, as well as an intriguing model to study basic mechanisms of developmental reversal and epigenetic erasure. Currently, nuclear reprogramming is an inefficient process and a better understanding of its components and the underlying mechanisms will no doubt enable us to increase its robustness and to gain a deeper understanding of its regulation. Here we focus on the reprogramming process from the chromatin and genome organization perspective, describing the chromatin changes that occur both globally and locally. At the global level, chromatin decondenses toward the characteristic 'open' state, while locally, chromatin reorganization supports the silencing of lineage-specific genes and the activation of pluripotency-related genes. Importantly, the proteins that regulate this process are being identified, revealing different layers of chromatin regulation, including histone modifications, histone variants, chromatin remodeling and genomic DNA methylation. The emerging theme is that chromatin and genome organization are not only altered during the transition from a somatic to a pluripotent state, but also play active, regulatory roles during the reprogramming process.
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Affiliation(s)
- Alva Biran
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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42
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SOX15 is a candidate tumor suppressor in pancreatic cancer with a potential role in Wnt/β-catenin signaling. Oncogene 2013; 33:279-88. [PMID: 23318427 DOI: 10.1038/onc.2012.595] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/23/2012] [Accepted: 11/02/2012] [Indexed: 12/19/2022]
Abstract
Pancreatic cancer is among the top five deadliest cancers in developed countries. Better knowledge of the molecular mechanisms contributing to its tumorigenesis is imperative to improve patient prognosis. Identification of novel tumor suppressor genes (TSGs) in pancreatic cancer will reveal new mechanisms of pathway deregulation and will ultimately help improve our understanding of this aggressive disease. According to Knudson's two-hit model, TSGs are classically disrupted by two concerted genetic events. In this study, we combined DNA methylation profiling with copy number and mRNA expression profiling to identify novel TSGs in a set of 20 pancreatic cancer cell lines. These data sets were integrated for each of ∼12 000 genes in each cell line enabling the elucidation of those genes that undergo DNA hypermethylation, copy-number loss and mRNA downregulation simultaneously in multiple cell lines. Using this integrative genomics strategy, we identified SOX15 (sex determining region Y-box 15) as a candidate TSG in pancreatic cancer. Expression of SOX15 in pancreatic cancer cell lines with undetectable expression resulted in reduced viability of cancer cells both in vitro and in vivo demonstrating its tumor suppressive capability. We also found reduced expression, homozygous deletion and aberrant DNA methylation of SOX15 in clinical pancreatic tumor data sets. Furthermore, we deduced a novel role for SOX15 in suppressing the Wnt/β-catenin signaling pathway, which we hypothesize is a pathway through which SOX15 may exert its tumor suppressive effects in pancreatic cancer.
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43
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Kranenburg O, Emmink BL, Knol J, van Houdt WJ, Rinkes IHMB, Jimenez CR. Proteomics in studying cancer stem cell biology. Expert Rev Proteomics 2013; 9:325-36. [PMID: 22809210 DOI: 10.1586/epr.12.24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Normal multipotent tissue stem cells (SCs) are the driving force behind tissue turnover and repair. The cancer stem cell theory holds that tumors also contain stem-like cells that drive tumor growth and metastasis formation. However, very little is known about the regulation of SC maintenance pathways in cancer and how these are affected by cancer-specific genetic alterations and by treatment. Proteomics is emerging as a powerful tool to identify the signaling complexes and pathways that control multi- and pluri-potency and SC differentiation. Here, the authors review the novel insights that these studies have provided and present a comprehensive strategy for the use of proteomics in studying cancer SC biology.
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Affiliation(s)
- Onno Kranenburg
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584CX, The Netherlands.
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44
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Babu M, Kagan O, Guo H, Greenblatt J, Emili A. Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry. J Vis Exp 2012:4057. [PMID: 23168686 DOI: 10.3791/4057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems(1, 2). Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria(1-6). In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes(1, 2, 7). Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast(8, 9), and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system(10). Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits). Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking.
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Affiliation(s)
- Mohan Babu
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Canada
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45
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Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VUN, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ERM, Paccanaro A, Marcotte EM, Emili A. A census of human soluble protein complexes. Cell 2012; 150:1068-81. [PMID: 22939629 DOI: 10.1016/j.cell.2012.08.011] [Citation(s) in RCA: 629] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 07/30/2012] [Accepted: 08/10/2012] [Indexed: 12/19/2022]
Abstract
Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition of human protein complexes remains limited. To close this gap, we applied an integrative global proteomic profiling approach, based on chromatographic separation of cultured human cell extracts into more than one thousand biochemical fractions that were subsequently analyzed by quantitative tandem mass spectrometry, to systematically identify a network of 13,993 high-confidence physical interactions among 3,006 stably associated soluble human proteins. Most of the 622 putative protein complexes we report are linked to core biological processes and encompass both candidate disease genes and unannotated proteins to inform on mechanism. Strikingly, whereas larger multiprotein assemblies tend to be more extensively annotated and evolutionarily conserved, human protein complexes with five or fewer subunits are far more likely to be functionally unannotated or restricted to vertebrates, suggesting more recent functional innovations.
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Affiliation(s)
- Pierre C Havugimana
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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46
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Mak AB, Nixon AML, Kittanakom S, Stewart JM, Chen GI, Curak J, Gingras AC, Mazitschek R, Neel BG, Stagljar I, Moffat J. Regulation of CD133 by HDAC6 promotes β-catenin signaling to suppress cancer cell differentiation. Cell Rep 2012; 2:951-63. [PMID: 23084749 DOI: 10.1016/j.celrep.2012.09.016] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 07/21/2012] [Accepted: 09/14/2012] [Indexed: 12/21/2022] Open
Abstract
The pentaspan membrane glycoprotein CD133 marks lineage-specific cancer progenitor cells and is associated with poor prognosis in a number of tumor types. Despite its utility as a cancer progenitor cell marker, CD133 protein regulation and molecular function remain poorly understood. We find that the deacetylase HDAC6 physically associates with CD133 to negatively regulate CD133 trafficking down the endosomal-lysosomal pathway for degradation. We further demonstrate that CD133, HDAC6, and the central molecule of the canonical Wnt signaling pathway, β-catenin, can physically associate as a ternary complex. This association stabilizes β-catenin via HDAC6 deacetylase activity, which leads to activation of β-catenin signaling targets. Downregulation of either CD133 or HDAC6 results in increased β-catenin acetylation and degradation, which correlates with decreased proliferation in vitro and tumor xenograft growth in vivo. Given that CD133 marks progenitor cells in a wide range of cancers, targeting CD133 may be a means to treat multiple cancer types.
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Affiliation(s)
- Anthony B Mak
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
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47
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Dunham WH, Mullin M, Gingras AC. Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics 2012; 12:1576-90. [PMID: 22611051 DOI: 10.1002/pmic.201100523] [Citation(s) in RCA: 226] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known function. While many techniques have been developed to characterize protein-protein interactions, one strategy that has gained considerable momentum over the past decade for identification and quantification of protein-protein interactions, is affinity-purification followed by mass spectrometry (AP-MS). Here, we briefly review the basic principles used in affinity-purification coupled to mass spectrometry, with an emphasis on tools (both biochemical and computational), which enable the discovery and reporting of high quality protein-protein interactions.
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Affiliation(s)
- Wade H Dunham
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
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48
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A versatile lentiviral expression system to identify mammalian protein–protein interactions. Methods 2012; 57:409-16. [DOI: 10.1016/j.ymeth.2012.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/31/2012] [Accepted: 06/08/2012] [Indexed: 11/21/2022] Open
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49
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Dykhuizen EC, Carmody LC, Tolliday N, Crabtree GR, Palmer MAJ. Screening for inhibitors of an essential chromatin remodeler in mouse embryonic stem cells by monitoring transcriptional regulation. ACTA ACUST UNITED AC 2012; 17:1221-30. [PMID: 22853929 DOI: 10.1177/1087057112455060] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The SWI/SNF-like adenosine triphosphate (ATP)-dependent chromatin remodeling complex, esBAF, is both necessary and, in some contexts, sufficient to induce the pluripotent state. Furthermore, mutations in various BAF subunits are associated with cancer. Little is known regarding the precise mechanism(s) by which this complex exerts its activities. Thus, it is unclear which protein interactions would be important to disrupt to isolate a relevant readout of mechanism. To address this, we developed a gene expression-based assay to identify inhibitors of the native esBAF complex. Specifically, a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assay was developed in mouse embryonic stem (ES) cells to monitor expression of Bmi1, a developmentally important gene repressed by the esBAF complex. The assay was miniaturized to a 384-well format and used to screen a diverse collection of compounds, including novel products of diversity-oriented synthesis (DOS). Confirmed hits were validated using a knock-in ES cell reporter line in which luciferase is inserted into the Bmi1 locus. Several of the validated hits regulate a panel of target genes in a manner similar to the BAF chromatin-remodeling complex. Together these data indicate that expression-based screening using qRT-PCR is a successful approach to identify compounds targeting the regulation of key developmental genes in ES cells.
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Affiliation(s)
- Emily C Dykhuizen
- Department of Pathology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Ni Z, Olsen JB, Guo X, Zhong G, Ruan ED, Marcon E, Young P, Guo H, Li J, Moffat J, Emili A, Greenblatt JF. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. Transcription 2012; 2:237-42. [PMID: 22231121 DOI: 10.4161/trns.2.5.17803] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RNA polymerase II (RNAP II) C-terminal domain (CTD) phosphorylation is important for various transcription-related processes. Here, we identify by affinity purification and mass spectrometry three previously uncharacterized human CTD-interaction domain (CID)-containing proteins, RPRD1A, RPRD1B and RPRD2, which co-purify with RNAP II and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. RPRD1A and RPRD1B can accompany RNAP II from promoter regions to 3'-untranslated regions during transcription in vivo, predominantly interact with phosphorylated RNAP II, and can reduce CTD S5- and S7-phosphorylated RNAP II at target gene promoters. Thus, the RPRD proteins are likely to have multiple important roles in transcription.
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Affiliation(s)
- Zuyao Ni
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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