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Holfeld A, Schuster D, Sesterhenn F, Gillingham AK, Stalder P, Haenseler W, Barrio-Hernandez I, Ghosh D, Vowles J, Cowley SA, Nagel L, Khanppnavar B, Serdiuk T, Beltrao P, Korkhov VM, Munro S, Riek R, de Souza N, Picotti P. Systematic identification of structure-specific protein-protein interactions. Mol Syst Biol 2024; 20:651-675. [PMID: 38702390 PMCID: PMC11148107 DOI: 10.1038/s44320-024-00037-6] [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: 02/01/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis-mass spectrometry (LiP-MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP-MS detects well-characterized PPIs, including antibody-target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states.
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Affiliation(s)
- Aleš Holfeld
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dina Schuster
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Fabian Sesterhenn
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Patrick Stalder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Walther Haenseler
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- University Research Priority Program AdaBD (Adaptive Brain Circuits in Development and Learning), University of Zurich, Zurich, Switzerland
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Jane Vowles
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sally A Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Luise Nagel
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Basavraj Khanppnavar
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Volodymyr M Korkhov
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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2
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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3
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Shrestha HK, Lee D, Wu Z, Wang Z, Fu Y, Wang X, Serrano GE, Beach TG, Peng J. Profiling Protein-Protein Interactions in the Human Brain by Refined Cofractionation Mass Spectrometry. J Proteome Res 2024; 23:1221-1231. [PMID: 38507900 PMCID: PMC11065482 DOI: 10.1021/acs.jproteome.3c00685] [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] [Indexed: 03/22/2024]
Abstract
Proteins usually execute their biological functions through interactions with other proteins and by forming macromolecular complexes, but global profiling of protein complexes directly from human tissue samples has been limited. In this study, we utilized cofractionation mass spectrometry (CF-MS) to map protein complexes within the postmortem human brain with experimental replicates. First, we used concatenated anion and cation Ion Exchange Chromatography (IEX) to separate native protein complexes in 192 fractions and then proceeded with Data-Independent Acquisition (DIA) mass spectrometry to analyze the proteins in each fraction, quantifying a total of 4,804 proteins with 3,260 overlapping in both replicates. We improved the DIA's quantitative accuracy by implementing a constant amount of bovine serum albumin (BSA) in each fraction as an internal standard. Next, advanced computational pipelines, which integrate both a database-based complex analysis and an unbiased protein-protein interaction (PPI) search, were applied to identify protein complexes and construct protein-protein interaction networks in the human brain. Our study led to the identification of 486 protein complexes and 10054 binary protein-protein interactions, which represents the first global profiling of human brain PPIs using CF-MS. Overall, this study offers a resource and tool for a wide range of human brain research, including the identification of disease-specific protein complexes in the future.
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Affiliation(s)
- Him K. Shrestha
- Departments of Structural Biology and Developmental Neurobiology
| | - DongGeun Lee
- Departments of Structural Biology and Developmental Neurobiology
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, USA
| | | | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology
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4
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Lapcik P, Stacey RG, Potesil D, Kulhanek P, Foster LJ, Bouchal P. Global Interactome Mapping Reveals Pro-tumorigenic Interactions of NF-κB in Breast Cancer. Mol Cell Proteomics 2024; 23:100744. [PMID: 38417630 PMCID: PMC10988130 DOI: 10.1016/j.mcpro.2024.100744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
NF-κB pathway is involved in inflammation; however, recent data shows its role also in cancer development and progression, including metastasis. To understand the role of NF-κB interactome dynamics in cancer, we study the complexity of breast cancer interactome in luminal A breast cancer model and its rearrangement associated with NF-κB modulation. Liquid chromatography-mass spectrometry measurement of 160 size-exclusion chromatography fractions identifies 5460 protein groups. Seven thousand five hundred sixty eight interactions among these proteins have been reconstructed by PrInCE algorithm, of which 2564 have been validated in independent datasets. NF-κB modulation leads to rearrangement of protein complexes involved in NF-κB signaling and immune response, cell cycle regulation, and DNA replication. Central NF-κB transcription regulator RELA co-elutes with interactors of NF-κB activator PRMT5, and these complexes are confirmed by AlphaPulldown prediction. A complementary immunoprecipitation experiment recapitulates RELA interactions with other NF-κB factors, associating NF-κB inhibition with lower binding of NF-κB activators to RELA. This study describes a network of pro-tumorigenic protein interactions and their rearrangement upon NF-κB inhibition with potential therapeutic implications in tumors with high NF-κB activity.
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Affiliation(s)
- Petr Lapcik
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - David Potesil
- Proteomics Core Facility, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Kulhanek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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5
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Skinnider MA, Akinlaja MO, Foster LJ. Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry. Nat Commun 2023; 14:8365. [PMID: 38102123 PMCID: PMC10724252 DOI: 10.1038/s41467-023-44139-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
We present CFdb, a harmonized resource of interaction proteomics data from 411 co-fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis of this resource charts protein abundance, phosphorylation, and interactions throughout the tree of life, including a reference map of the human interactome. We show how large-scale CF-MS data can enhance analyses of individual CF-MS datasets, and exemplify this strategy by mapping the honey bee interactome.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Mopelola O Akinlaja
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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6
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Zilocchi M, Rahmatbakhsh M, Moutaoufik MT, Broderick K, Gagarinova A, Jessulat M, Phanse S, Aoki H, Aly KA, Babu M. Co-fractionation-mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain. Nat Protoc 2023; 18:3918-3973. [PMID: 37985878 DOI: 10.1038/s41596-023-00901-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/09/2023] [Indexed: 11/22/2023]
Abstract
Human mitochondrial (mt) protein assemblies are vital for neuronal and brain function, and their alteration contributes to many human disorders, e.g., neurodegenerative diseases resulting from abnormal protein-protein interactions (PPIs). Knowledge of the composition of mt protein complexes is, however, still limited. Affinity purification mass spectrometry (MS) and proximity-dependent biotinylation MS have defined protein partners of some mt proteins, but are too technically challenging and laborious to be practical for analyzing large numbers of samples at the proteome level, e.g., for the study of neuronal or brain-specific mt assemblies, as well as altered mtPPIs on a proteome-wide scale for a disease of interest in brain regions, disease tissues or neurons derived from patients. To address this challenge, we adapted a co-fractionation-MS platform to survey native mt assemblies in adult mouse brain and in human NTERA-2 embryonal carcinoma stem cells or differentiated neuronal-like cells. The workflow consists of orthogonal separations of mt extracts isolated from chemically cross-linked samples to stabilize PPIs, data-dependent acquisition MS to identify co-eluted mt protein profiles from collected fractions and a computational scoring pipeline to predict mtPPIs, followed by network partitioning to define complexes linked to mt functions as well as those essential for neuronal and brain physiological homeostasis. We developed an R/CRAN software package, Macromolecular Assemblies from Co-elution Profiles for automated scoring of co-fractionation-MS data to define complexes from mtPPI networks. Presently, the co-fractionation-MS procedure takes 1.5-3.5 d of proteomic sample preparation, 31 d of MS data acquisition and 8.5 d of data analyses to produce meaningful biological insights.
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Affiliation(s)
- Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | | | | | - Kirsten Broderick
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Alla Gagarinova
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada.
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7
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Hay BN, Akinlaja MO, Baker TC, Houfani AA, Stacey RG, Foster LJ. Integration of data-independent acquisition (DIA) with co-fractionation mass spectrometry (CF-MS) to enhance interactome mapping capabilities. Proteomics 2023; 23:e2200278. [PMID: 37144656 DOI: 10.1002/pmic.202200278] [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: 10/28/2022] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Proteomics technologies are continually advancing, providing opportunities to develop stronger and more robust protein interaction networks (PINs). In part, this is due to the ever-growing number of high-throughput proteomics methods that are available. This review discusses how data-independent acquisition (DIA) and co-fractionation mass spectrometry (CF-MS) can be integrated to enhance interactome mapping abilities. Furthermore, integrating these two techniques can improve data quality and network generation through extended protein coverage, less missing data, and reduced noise. CF-DIA-MS shows promise in expanding our knowledge of interactomes, notably for non-model organisms (NMOs). CF-MS is a valuable technique on its own, but upon the integration of DIA, the potential to develop robust PINs increases, offering a unique approach for researchers to gain an in-depth understanding into the dynamics of numerous biological processes.
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Affiliation(s)
- Brenna N Hay
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Mopelola O Akinlaja
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Teesha C Baker
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Aicha Asma Houfani
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - R Greg Stacey
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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8
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Low TY. Elucidating the dynamic remodelling of Escherichia coli interactome in different growth conditions using multiplex co-fractionation MS (mCF-MS). Proteomics 2023; 23:e2300209. [PMID: 37986683 DOI: 10.1002/pmic.202300209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 11/22/2023]
Abstract
Most proteins function by forming complexes within a dynamic interconnected network that underlies various biological mechanisms. To systematically investigate such interactomes, high-throughput techniques, including CF-MS, have been developed to capture, identify, and quantify protein-protein interactions (PPIs) on a large scale. Compared to other techniques, CF-MS allows the global identification and quantification of native protein complexes in one setting, without genetic manipulation. Furthermore, quantitative CF-MS can potentially elucidate the distribution of a protein in multiple co-elution features, informing the stoichiometries and dynamics of a target protein complex. In this issue, Youssef et al. (Proteomics 2023, 00, e2200404) combined multiplex CF-MS and a new algorithm to study the dynamics of the PPI network for Escherichia coli grown under ten different conditions. Although the results demonstrated that most proteins remained stable, the authors were able to detect disrupted interactions that were growth condition specific. Further bioinformatics analyses also revealed the biophysical properties and structural patterns that govern such a response.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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9
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Merrill NJ, Davidson WS, He Y, Díaz Ludovico I, Sarkar S, Berger MR, McDermott JE, Van Eldik LJ, Wilcock DM, Monroe ME, Kyle JE, Bruce KD, Heinecke JW, Vaisar T, Raber J, Quinn JF, Melchior JT. Human cerebrospinal fluid contains diverse lipoprotein subspecies enriched in proteins implicated in central nervous system health. SCIENCE ADVANCES 2023; 9:eadi5571. [PMID: 37647397 PMCID: PMC10468133 DOI: 10.1126/sciadv.adi5571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
Lipoproteins in cerebrospinal fluid (CSF) of the central nervous system (CNS) resemble plasma high-density lipoproteins (HDLs), which are a compositionally and structurally diverse spectrum of nanoparticles with pleiotropic functionality. Whether CSF lipoproteins (CSF-Lps) exhibit similar heterogeneity is poorly understood because they are present at 100-fold lower concentrations than plasma HDL. To investigate the diversity of CSF-Lps, we developed a sensitive fluorescent technology to characterize lipoprotein subspecies in small volumes of human CSF. We identified 10 distinctly sized populations of CSF-Lps, most of which were larger than plasma HDL. Mass spectrometric analysis identified 303 proteins across the populations, over half of which have not been reported in plasma HDL. Computational analysis revealed that CSF-Lps are enriched in proteins important for wound healing, inflammation, immune response, and both neuron generation and development. Network analysis indicated that different subpopulations of CSF-Lps contain unique combinations of these proteins. Our study demonstrates that CSF-Lp subspecies likely exist that contain compositional signatures related to CNS health.
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Affiliation(s)
- Nathaniel J. Merrill
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - W. Sean Davidson
- Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH 45237, USA
| | - Yi He
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Ivo Díaz Ludovico
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Snigdha Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Madelyn R. Berger
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jason E. McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Linda J. Van Eldik
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Donna M. Wilcock
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jennifer E. Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kimberley D. Bruce
- Division of Endocrinology, Metabolism and Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jay W. Heinecke
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Tomas Vaisar
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Jacob Raber
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA
- Division of Neuroscience, Department of Behavioral Neuroscience and Radiation Medicine, ONPRC, Oregon Health and Science University, Portland, OR 97239, USA
| | - Joseph F. Quinn
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Neurology and Parkinson’s Disease Research Education and Clinical Care Center (PADRECC), VA Portland Healthcare System, Portland OR 97239, USA
| | - John T. Melchior
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH 45237, USA
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA
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10
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van Strien J, Evers F, Lutikurti M, Berendsen SL, Garanto A, van Gemert GJ, Cabrera-Orefice A, Rodenburg RJ, Brandt U, Kooij TWA, Huynen MA. Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution. PLoS Comput Biol 2023; 19:e1011090. [PMID: 37549177 PMCID: PMC10434966 DOI: 10.1371/journal.pcbi.1011090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/17/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Complexome profiling allows large-scale, untargeted, and comprehensive characterization of protein complexes in a biological sample using a combined approach of separating intact protein complexes e.g., by native gel electrophoresis, followed by mass spectrometric analysis of the proteins in the resulting fractions. Over the last decade, its application has resulted in a large collection of complexome profiling datasets. While computational methods have been developed for the analysis of individual datasets, methods for large-scale comparative analysis of complexomes from multiple species are lacking. Here, we present Comparative Clustering (CompaCt), that performs fully automated integrative analysis of complexome profiling data from multiple species, enabling systematic characterization and comparison of complexomes. CompaCt implements a novel method for leveraging orthology in comparative analysis to allow systematic identification of conserved as well as taxon-specific elements of the analyzed complexomes. We applied this method to a collection of 53 complexome profiles spanning the major branches of the eukaryotes. We demonstrate the ability of CompaCt to robustly identify the composition of protein complexes, and show that integrated analysis of multiple datasets improves characterization of complexes from specific complexome profiles when compared to separate analyses. We identified novel candidate interactors and complexes in a number of species from previously analyzed datasets, like the emp24, the V-ATPase and mitochondrial ATP synthase complexes. Lastly, we demonstrate the utility of CompaCt for the automated large-scale characterization of the complexome of the mosquito Anopheles stephensi shedding light on the evolution of metazoan protein complexes. CompaCt is available from https://github.com/cmbi/compact-bio.
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Affiliation(s)
- Joeri van Strien
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Felix Evers
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Madhurya Lutikurti
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stijn L. Berendsen
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alejandro Garanto
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Geert-Jan van Gemert
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Richard J. Rodenburg
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pediatrics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Taco W. A. Kooij
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
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11
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Chen YH, Chao KH, Wong JY, Liu CF, Leu JY, Tsai HK. A feature extraction free approach for protein interactome inference from co-elution data. Brief Bioinform 2023; 24:bbad229. [PMID: 37328692 DOI: 10.1093/bib/bbad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/01/2023] [Accepted: 05/29/2023] [Indexed: 06/18/2023] Open
Abstract
Protein complexes are key functional units in cellular processes. High-throughput techniques, such as co-fractionation coupled with mass spectrometry (CF-MS), have advanced protein complex studies by enabling global interactome inference. However, dealing with complex fractionation characteristics to define true interactions is not a simple task, since CF-MS is prone to false positives due to the co-elution of non-interacting proteins by chance. Several computational methods have been designed to analyze CF-MS data and construct probabilistic protein-protein interaction (PPI) networks. Current methods usually first infer PPIs based on handcrafted CF-MS features, and then use clustering algorithms to form potential protein complexes. While powerful, these methods suffer from the potential bias of handcrafted features and severely imbalanced data distribution. However, the handcrafted features based on domain knowledge might introduce bias, and current methods also tend to overfit due to the severely imbalanced PPI data. To address these issues, we present a balanced end-to-end learning architecture, Software for Prediction of Interactome with Feature-extraction Free Elution Data (SPIFFED), to integrate feature representation from raw CF-MS data and interactome prediction by convolutional neural network. SPIFFED outperforms the state-of-the-art methods in predicting PPIs under the conventional imbalanced training. When trained with balanced data, SPIFFED had greatly improved sensitivity for true PPIs. Moreover, the ensemble SPIFFED model provides different voting schemes to integrate predicted PPIs from multiple CF-MS data. Using the clustering software (i.e. ClusterONE), SPIFFED allows users to infer high-confidence protein complexes depending on the CF-MS experimental designs. The source code of SPIFFED is freely available at: https://github.com/bio-it-station/SPIFFED.
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Affiliation(s)
- Yu-Hsin Chen
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei 106, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academic Sinica, Taipei 11529, Taiwan
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Hao Chao
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Jin Yung Wong
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Chien-Fu Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Huai-Kuang Tsai
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei 106, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academic Sinica, Taipei 11529, Taiwan
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
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12
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Schlossarek D, Zhang Y, Sokolowska EM, Fernie AR, Luzarowski M, Skirycz A. Don't let go: co-fractionation mass spectrometry for untargeted mapping of protein-metabolite interactomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:904-914. [PMID: 36575913 DOI: 10.1111/tpj.16084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The chemical complexity of metabolomes goes hand in hand with their functional diversity. Small molecules have many essential roles, many of which are executed by binding and modulating the function of a protein partner. The complex and dynamic protein-metabolite interaction (PMI) network underlies most if not all biological processes, but remains under-characterized. Herein, we highlight how co-fractionation mass spectrometry (CF-MS), a well-established approach to map protein assemblies, can be used for proteome and metabolome identification of the PMIs. We will review recent CF-MS studies, discuss the main advantages and limitations, summarize the available CF-MS guidelines, and outline future challenges and opportunities.
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Affiliation(s)
- Dennis Schlossarek
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Youjun Zhang
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Ewelina M Sokolowska
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marcin Luzarowski
- Center for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Aleksandra Skirycz
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Boyce Thompson Institute, Ithaca, NY, 14850, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA
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13
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High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography. Methods Mol Biol 2023; 2628:53-79. [PMID: 36781779 DOI: 10.1007/978-1-0716-2978-9_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We describe a high-throughput method for co-fractionation mass spectrometry (CF-MS) profiling for native plasma protein profiling. CF-MS allows the profiling of endogenous protein complexes between samples. Proteins often interact with other proteins and form macromolecular complexes that are different in disease states as well as cell states and cell types. This protocol describes an example for the sample preparation of 954 individual size exclusion chromatography (SEC) fractions, derived from 18 plasma samples that were separated into 53 fractions. Eighteen plasma samples were chosen based on the TMTpro multiplexing, but this methodology can be adapted for fewer or larger numbers of samples as appropriate. Our automated sample preparation method allows for high-throughput native plasma profiling, and we provide detailed methods for both a label-free and an isobaric labeling approach, discuss the merits of each approach, and detail the advantages of combining these strategies for comprehensive native plasma proteome profiling.
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14
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Sharma VS, Fossati A, Ciuffa R, Buljan M, Williams EG, Chen Z, Shao W, Pedrioli PGA, Purcell AW, Martínez MR, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Brief Bioinform 2022; 23:6611913. [PMID: 35724564 PMCID: PMC9310514 DOI: 10.1093/bib/bbac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/05/2022] [Accepted: 05/21/2022] [Indexed: 11/14/2022] Open
Abstract
In molecular biology, it is a general assumption that the ensemble of expressed molecules, their activities and interactions determine biological function, cellular states and phenotypes. Stable protein complexes—or macromolecular machines—are, in turn, the key functional entities mediating and modulating most biological processes. Although identifying protein complexes and their subunit composition can now be done inexpensively and at scale, determining their function remains challenging and labor intensive. This study describes Protein Complex Function predictor (PCfun), the first computational framework for the systematic annotation of protein complex functions using Gene Ontology (GO) terms. PCfun is built upon a word embedding using natural language processing techniques based on 1 million open access PubMed Central articles. Specifically, PCfun leverages two approaches for accurately identifying protein complex function, including: (i) an unsupervised approach that obtains the nearest neighbor (NN) GO term word vectors for a protein complex query vector and (ii) a supervised approach using Random Forest (RF) models trained specifically for recovering the GO terms of protein complex queries described in the CORUM protein complex database. PCfun consolidates both approaches by performing a hypergeometric statistical test to enrich the top NN GO terms within the child terms of the GO terms predicted by the RF models. The documentation and implementation of the PCfun package are available at https://github.com/sharmavaruns/PCfun. We anticipate that PCfun will serve as a useful tool and novel paradigm for the large-scale characterization of protein complex function.
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Affiliation(s)
- Varun S Sharma
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Marija Buljan
- Empa - Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Evan G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette Luxembourg
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China
| | - Wenguang Shao
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Patrick G A Pedrioli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Anthony W Purcell
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | | | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,Faculty of Science, University of Zurich, Switzerland
| | - Chen Li
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
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15
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Wang S, Wu R, Lu J, Jiang Y, Huang T, Cai YD. Protein-protein interaction networks as miners of biological discovery. Proteomics 2022; 22:e2100190. [PMID: 35567424 DOI: 10.1002/pmic.202100190] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/12/2022]
Abstract
Protein-protein interactions (PPIs) form the basis of a myriad of biological pathways and mechanism, such as the formation of protein-complexes or the components of signaling cascades. Here, we reviewed experimental methods for identifying PPI pairs, including yeast two-hybrid, mass spectrometry, co-localization, and co-immunoprecipitation. Furthermore, a range of computational methods leveraging biochemical properties, evolution history, protein structures and more have enabled identification of additional PPIs. Given the wealth of known PPIs, we reviewed important network methods to construct and analyze networks of PPIs. These methods aid biological discovery through identifying hub genes and dynamic changes in the network, and have been thoroughly applied in various fields of biological research. Lastly, we discussed the challenges and future direction of research utilizing the power of PPI networks. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Steven Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Runxin Wu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jiaqi Lu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Yijia Jiang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tao Huang
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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16
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Cabrera-Orefice A, Potter A, Evers F, Hevler JF, Guerrero-Castillo S. Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. Front Cell Dev Biol 2022; 9:796128. [PMID: 35096826 PMCID: PMC8790184 DOI: 10.3389/fcell.2021.796128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.
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Affiliation(s)
- Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alisa Potter
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Felix Evers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, University of Utrecht, Utrecht, Netherlands.,Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, Netherlands.,Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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17
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Pino L, Schilling B. Proximity labeling and other novel mass spectrometric approaches for spatiotemporal protein dynamics. Expert Rev Proteomics 2021; 18:757-765. [PMID: 34496693 PMCID: PMC8650568 DOI: 10.1080/14789450.2021.1976149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Proteins are highly dynamic and their biological function is controlled by not only temporal abundance changes but also via regulated protein-protein interaction networks, which respond to internal and external perturbations. A wealth of novel analytical reagents and workflows allow studying spatiotemporal protein environments with great granularity while maintaining high throughput and ease of analysis. AREAS COVERED We review technology advances for measuring protein-protein proximity interactions with an emphasis on proximity labeling, and briefly summarize other spatiotemporal approaches including protein localization, and their dynamic changes over time, specifically in human cells and mammalian tissues. We focus especially on novel technologies and workflows emerging within the past 5 years. This includes enrichment-based techniques (proximity labeling and crosslinking), separation-based techniques (organelle fractionation and size exclusion chromatography), and finally sorting-based techniques (laser capture microdissection and mass spectrometry imaging). EXPERT OPINION Spatiotemporal proteomics is a key step in assessing biological complexity, understanding refined regulatory mechanisms, and forming protein complexes and networks. Studying protein dynamics across space and time holds promise for gaining deep insights into how protein networks may be perturbed during disease and aging processes, and offer potential avenues for therapeutic interventions, drug discovery, and biomarker development.
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Affiliation(s)
- Lindsay Pino
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, CA 94945, USA
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18
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Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ. An atlas of protein-protein interactions across mouse tissues. Cell 2021; 184:4073-4089.e17. [PMID: 34214469 DOI: 10.1016/j.cell.2021.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the interactome has therefore been a central objective of high-throughput biology. However, the dynamics of protein interactions across physiological contexts remain poorly understood. Here, we develop a quantitative proteomic approach combining protein correlation profiling with stable isotope labeling of mammals (PCP-SILAM) to map the interactomes of seven mouse tissues. The resulting maps provide a proteome-scale survey of interactome rewiring across mammalian tissues, revealing more than 125,000 unique interactions at a quality comparable to the highest-quality human screens. We identify systematic suppression of cross-talk between the evolutionarily ancient housekeeping interactome and younger, tissue-specific modules. Rewired proteins are tightly regulated by multiple cellular mechanisms and are implicated in disease. Our study opens up new avenues to uncover regulatory mechanisms that shape in vivo interactome responses to physiological and pathophysiological stimuli in mammalian systems.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nichollas E Scott
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Peter Doherty Institute, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Anna Prudova
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Craig H Kerr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Queenie W T Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David Rattray
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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19
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Skinnider MA, Foster LJ. Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments. Nat Methods 2021; 18:806-815. [PMID: 34211188 DOI: 10.1038/s41592-021-01194-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
Co-fractionation mass spectrometry (CF-MS) has emerged as a powerful technique for interactome mapping. However, there is little consensus on optimal strategies for the design of CF-MS experiments or their computational analysis. Here, we reanalyzed a total of 206 CF-MS experiments to generate a uniformly processed resource containing over 11 million measurements of protein abundance. We used this resource to benchmark experimental designs for CF-MS studies and systematically optimize computational approaches to network inference. We then applied this optimized methodology to reconstruct a draft-quality human interactome by CF-MS and predict over 700,000 protein-protein interactions across 27 eukaryotic species or clades. Our work defines new resources to illuminate proteome organization over evolutionary timescales and establishes best practices for the design and analysis of CF-MS studies.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. .,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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20
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van Strien J, Haupt A, Schulte U, Braun HP, Cabrera-Orefice A, Choudhary JS, Evers F, Fernandez-Vizarra E, Guerrero-Castillo S, Kooij TWA, Páleníková P, Pardo M, Ugalde C, Wittig I, Wöhlbrand L, Brandt U, Arnold S, Huynen MA. CEDAR, an online resource for the reporting and exploration of complexome profiling data. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148411. [PMID: 33722514 DOI: 10.1016/j.bbabio.2021.148411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023]
Abstract
Complexome profiling is an emerging 'omics' approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the "minimum information required for a complexome profiling experiment" (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.
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Affiliation(s)
- Joeri van Strien
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alexander Haupt
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Center for Biological Signalling Studies (BIOSS) and Center for Integrative Signalling Studies (CIBSS), 79104 Freiburg, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jyoti S Choudhary
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Felix Evers
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Taco W A Kooij
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Mercedes Pardo
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Cristina Ugalde
- Hospital 12 de Octubre Research Institute, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Ilka Wittig
- Functional Proteomics, Medical School, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Arnold
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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21
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PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nat Methods 2021; 18:520-527. [PMID: 33859439 DOI: 10.1038/s41592-021-01107-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 03/03/2021] [Indexed: 02/02/2023]
Abstract
Despite the availability of methods for analyzing protein complexes, systematic analysis of complexes under multiple conditions remains challenging. Approaches based on biochemical fractionation of intact, native complexes and correlation of protein profiles have shown promise. However, most approaches for interpreting cofractionation datasets to yield complex composition and rearrangements between samples depend considerably on protein-protein interaction inference. We introduce PCprophet, a toolkit built on size exclusion chromatography-sequential window acquisition of all theoretical mass spectrometry (SEC-SWATH-MS) data to predict protein complexes and characterize their changes across experimental conditions. We demonstrate improved performance of PCprophet over state-of-the-art approaches and introduce a Bayesian approach to analyze altered protein-protein interactions across conditions. We provide both command-line and graphical interfaces to support the application of PCprophet to any cofractionation MS dataset, independent of separation or quantitative liquid chromatography-MS workflow, for the detection and quantitative tracking of protein complexes and their physiological dynamics.
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22
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Nolte H, Langer T. ComplexFinder: A software package for the analysis of native protein complex fractionation experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148444. [PMID: 33940038 DOI: 10.1016/j.bbabio.2021.148444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/28/2022]
Abstract
Identification of protein complexes and quantitative distribution of a single protein across different complexes are fundamental to unravel cellular mechanisms and of biological and clinical relevance. A recently introduced method, complexome profiling, combines fractionation techniques to separate native protein complexes with high-resolution mass spectrometry and allows to identify protein complexes in an unbiased manner. Due to recent advances in mass spectrometry instrumentation, the analysis time can be reduced dramatically while the coverage of thousands of proteins remains constant, which leads to an increased data acquisition rate and reduces the burden to initiate such complex experiments. Therefore, the development of novel computational pipelines for the analysis of such comprehensive complexome profiles is required. Usually, potential complex formations are assembled by correlation analysis. However, a major challenge in such an analysis is, that a protein can occur in multiple complexes of varying composition. Hence, signal profiles of proteins of the same complex might show high local similarities but do correlate poorly over all acquired fractions. Here, we describe ComplexFinder; a python-based computational pipeline that enables machine-learning based prediction of novel protein-protein interactions incorporating numerous measures of distance between signal profiles. Importantly, each signal profile is represented by an ensemble of peak-like models. These models allow the calculation of local similarities, enabling peak-centric comparison between biological conditions and the estimation of the composition of specific complexes. From the predicted protein-protein interactions, a protein connectivity network is constructed, which is used to assemble proteins into macromolecular complexes incorporating peak-centric information. ComplexFinder enables the peak-centric analysis of complexome profiling data utilizing various LC-MS/MS quantification strategies including label-free, SILAC, TMT as well as pulseSILAC. The source code is freely available at https://github.com/hnolcol/ComplexFinder.
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Affiliation(s)
- Hendrik Nolte
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann Str. 9b, 50931 Cologne, Germany.
| | - Thomas Langer
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann Str. 9b, 50931 Cologne, Germany; Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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23
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Bludau I. Discovery-Versus Hypothesis-Driven Detection of Protein-Protein Interactions and Complexes. Int J Mol Sci 2021; 22:4450. [PMID: 33923221 PMCID: PMC8123138 DOI: 10.3390/ijms22094450] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Protein complexes are the main functional modules in the cell that coordinate and perform the vast majority of molecular functions. The main approaches to identify and quantify the interactome to date are based on mass spectrometry (MS). Here I summarize the benefits and limitations of different MS-based interactome screens, with a focus on untargeted interactome acquisition, such as co-fractionation MS. Specific emphasis is given to the discussion of discovery- versus hypothesis-driven data analysis concepts and their applicability to large, proteome-wide interactome screens. Hypothesis-driven analysis approaches, i.e., complex- or network-centric, are highlighted as promising strategies for comparative studies. While these approaches require prior information from public databases, also reviewed herein, the available wealth of interactomic data continuously increases, thereby providing more exhaustive information for future studies. Finally, guidance on the selection of interactome acquisition and analysis methods is provided to aid the reader in the design of protein-protein interaction studies.
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Affiliation(s)
- Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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24
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Kyrilis FL, Belapure J, Kastritis PL. Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. Front Mol Biosci 2021; 8:660542. [PMID: 33937337 PMCID: PMC8082361 DOI: 10.3389/fmolb.2021.660542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Native cell extracts hold great promise for understanding the molecular structure of ordered biological systems at high resolution. This is because higher-order biomolecular interactions, dubbed as protein communities, may be retained in their (near-)native state, in contrast to extensively purifying or artificially overexpressing the proteins of interest. The distinct machine-learning approaches are applied to discover protein-protein interactions within cell extracts, reconstruct dedicated biological networks, and report on protein community members from various organisms. Their validation is also important, e.g., by the cross-linking mass spectrometry or cell biology methods. In addition, the cell extracts are amenable to structural analysis by cryo-electron microscopy (cryo-EM), but due to their inherent complexity, sorting structural signatures of protein communities derived by cryo-EM comprises a formidable task. The application of image-processing workflows inspired by machine-learning techniques would provide improvements in distinguishing structural signatures, correlating proteomic and network data to structural signatures and subsequently reconstructed cryo-EM maps, and, ultimately, characterizing unidentified protein communities at high resolution. In this review article, we summarize recent literature in detecting protein communities from native cell extracts and identify the remaining challenges and opportunities. We argue that the progress in, and the integration of, machine learning, cryo-EM, and complementary structural proteomics approaches would provide the basis for a multi-scale molecular description of protein communities within native cell extracts.
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Affiliation(s)
- Fotis L. Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jaydeep Belapure
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Panagiotis L. Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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25
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Skinnider MA, Cai C, Stacey RG, Foster LJ. PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. Bioinformatics 2021; 37:2775-2777. [PMID: 33471077 DOI: 10.1093/bioinformatics/btab022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/03/2021] [Accepted: 01/08/2021] [Indexed: 11/12/2022] Open
Abstract
SUMMARY We present PrInCE, an R/Bioconductor package that employs a machine-learning approach to infer protein-protein interaction networks from co-fractionation mass spectrometry (CF-MS) data. Previously distributed as a collection of Matlab scripts, our ground-up rewrite of this software package in an open-source language dramatically improves runtime and memory requirements. We describe several new features in the R implementation, including a test for the detection of co-eluting protein complexes and a method for differential network analysis. PrInCE is extensively documented and fully compatible with Bioconductor classes, ensuring it can fit seamlessly into existing proteomics workflows. AVAILABILITY AND IMPLEMENTATION PrInCE is available from Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/PrInCE.html). Source code is freely available from GitHub under the MIT license (https://github.com/fosterlab/PrInCE). Support is provided via the GitHub issues tracker (https://github.com/fosterlab/PrInCE/issues). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British
| | - Charley Cai
- Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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26
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Chen Z, Chen J. Mass spectrometry-based protein‒protein interaction techniques and their applications in studies of DNA damage repair. J Zhejiang Univ Sci B 2021; 22:1-20. [PMID: 33448183 PMCID: PMC7818012 DOI: 10.1631/jzus.b2000356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
Abstract
Proteins are major functional units that are tightly connected to form complex and dynamic networks. These networks enable cells and organisms to operate properly and respond efficiently to environmental cues. Over the past decades, many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected. At the same time, rapid development in proteomics and mass spectrometry (MS) techniques makes it possible to identify interacting proteins and build comprehensive protein‒protein interaction networks. The resulting interactomes and networks have proven informative in the investigation of biological functions, such as in the field of DNA damage repair. In recent years, a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein‒protein interaction studies. As the technologies for enriching associated proteins and MS become more sophisticated, the studies of protein‒protein interactions are entering a new era. In this review, we summarize the strategies and recent developments for exploring protein‒protein interaction. In addition, we discuss the application of these tools in the investigation of protein‒protein interaction networks involved in DNA damage response and DNA repair.
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Affiliation(s)
- Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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27
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Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Syst 2020; 11:589-607.e8. [PMID: 33333029 PMCID: PMC8034988 DOI: 10.1016/j.cels.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions (PPIs) play critical functional and regulatory roles in cellular processes. They are essential for macromolecular complex formation, which in turn constitutes the basis for protein interaction networks that determine the functional state of a cell. We and others have previously shown that chromatographic fractionation of native protein complexes in combination with bottom-up mass spectrometric analysis of consecutive fractions supports the multiplexed characterization and detection of state-specific changes of protein complexes. In this study, we extend co-fractionation and mass spectrometric data analysis to perform quantitative, network-based studies of proteome organization, via the size-exclusion chromatography algorithmic toolkit (SECAT). This framework explicitly accounts for the dynamic nature and rewiring of protein complexes across multiple cell states and samples, thus, elucidating molecular mechanisms that are differentially implemented across different experimental settings. Systematic analysis of multiple datasets shows that SECAT represents a highly scalable and effective methodology to assess condition/state-specific protein-network state. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven CT, USA; Department of Pharmacology, Yale University School of Medicine, New Haven CT, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland.
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York NY, USA; Department of Biomedical Informatics, Columbia University, New York NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York NY, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York NY, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA.
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28
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Stacey RG, Skinnider MA, Foster LJ. On the Robustness of Graph-Based Clustering to Random Network Alterations. Mol Cell Proteomics 2020; 20:100002. [PMID: 33592499 PMCID: PMC7896145 DOI: 10.1074/mcp.ra120.002275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 11/23/2022] Open
Abstract
Biological functions emerge from complex and dynamic networks of protein-protein interactions. Because these protein-protein interaction networks, or interactomes, represent pairwise connections within a hierarchically organized system, it is often useful to identify higher-order associations embedded within them, such as multimember protein complexes. Graph-based clustering techniques are widely used to accomplish this goal, and dozens of field-specific and general clustering algorithms exist. However, interactomes can be prone to errors, especially when inferred from high-throughput biochemical assays. Therefore, robustness to network-level noise is an important criterion. Here, we tested the robustness of a range of graph-based clustering algorithms in the presence of noise, including algorithms common across domains and those specific to protein networks. Strikingly, we found that all of the clustering algorithms tested here markedly amplified network-level noise. Randomly rewiring only 1% of network edges yielded more than a 50% change in clustering results. Moreover, we found the impact of network noise on individual clusters was not uniform: some clusters were consistently robust to injected noise, whereas others were not. Therefore we developed the clust.perturb R package and Shiny web application to measure the reproducibility of clusters by randomly perturbing the network. We show that clust.perturb results are predictive of real-world cluster stability: poorly reproducible clusters as identified by clust.perturb are significantly less likely to be reclustered across experiments. We conclude that graph-based clustering amplifies noise in protein interaction networks, but quantifying the robustness of a cluster to network noise can separate stable protein complexes from spurious associations.
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Affiliation(s)
- R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
| | - Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada
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29
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Pang CNI, Ballouz S, Weissberger D, Thibaut LM, Hamey JJ, Gillis J, Wilkins MR, Hart-Smith G. Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. Mol Cell Proteomics 2020; 19:1876-1895. [PMID: 32817346 PMCID: PMC7664123 DOI: 10.1074/mcp.ra120.002154] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/14/2020] [Indexed: 11/06/2022] Open
Abstract
Co-fractionation MS (CF-MS) is a technique with potential to characterize endogenous and unmanipulated protein complexes on an unprecedented scale. However this potential has been offset by a lack of guidelines for best-practice CF-MS data collection and analysis. To obtain such guidelines, this study thoroughly evaluates novel and published Saccharomyces cerevisiae CF-MS data sets using very high proteome coverage libraries of yeast gold standard complexes. A new method for identifying gold standard complexes in CF-MS data, Reference Complex Profiling, and the Extending 'Guilt-by-Association' by Degree (EGAD) R package are used for these evaluations, which are verified with concurrent analyses of published human data. By evaluating data collection designs, which involve fractionation of cell lysates, it is found that near-maximum recall of complexes can be achieved with fewer samples than published studies. Distributing sample collection across orthogonal fractionation methods, rather than a single high resolution data set, leads to particularly efficient recall. By evaluating 17 different similarity scoring metrics, which are central to CF-MS data analysis, it is found that two metrics rarely used in past CF-MS studies - Spearman and Kendall correlations - and the recently introduced Co-apex metric frequently maximize recall, whereas a popular metric-Euclidean distance-delivers poor recall. The common practice of integrating external genomic data into CF-MS data analysis is also evaluated, revealing that this practice may improve the precision and recall of known complexes but is generally unsuitable for predicting novel complexes in model organisms. If studying nonmodel organisms using orthologous genomic data, it is found that particular subsets of fractionation profiles (e.g. the lowest abundance quartile) should be excluded to minimize false discovery. These assessments are summarized in a series of universally applicable guidelines for precise, sensitive and efficient CF-MS studies of known complexes, and effective predictions of novel complexes for orthogonal experimental validation.
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Affiliation(s)
- Chi Nam Ignatius Pang
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sara Ballouz
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
| | - Daniel Weissberger
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Loïc M Thibaut
- School of Mathematics and Statistics, University of New South Wales, Sydney, New South Wales, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, USA
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Gene Hart-Smith
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia; Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia.
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30
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Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
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31
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Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nat Protoc 2020; 15:2341-2386. [PMID: 32690956 DOI: 10.1038/s41596-020-0332-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 04/17/2020] [Indexed: 01/03/2023]
Abstract
Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect and quantify protein complexes with high selectivity and statistical error control via the computational framework CCprofiler (https://github.com/CCprofiler/CCprofiler). Complex-centric proteome profiling captures most proteins in complex-assembled state and reveals their organization into hundreds of complexes and complex variants observable in a given cellular state. The protocol is applicable to cultured cells and can potentially also be adapted to primary tissue and does not require any genetic engineering of the respective sample sources. At present, it requires ~8 d of wet-laboratory work, 15 d of mass spectrometry measurement time and 7 d of computational analysis.
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32
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Kerr CH, Skinnider MA, Andrews DDT, Madero AM, Chan QWT, Stacey RG, Stoynov N, Jan E, Foster LJ. Dynamic rewiring of the human interactome by interferon signaling. Genome Biol 2020; 21:140. [PMID: 32539747 PMCID: PMC7294662 DOI: 10.1186/s13059-020-02050-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulated genes have been established across species and cell types by transcriptomic and biochemical approaches, but their antiviral mechanisms remain incompletely characterized. Here, we apply a combination of quantitative proteomic approaches to describe the effects of IFN signaling on the human proteome, and apply protein correlation profiling to map IFN-induced rearrangements in the human protein-protein interaction network. RESULTS We identify > 26,000 protein interactions in IFN-stimulated and unstimulated cells, many of which involve proteins associated with human disease and are observed exclusively within the IFN-stimulated network. Differential network analysis reveals interaction rewiring across a surprisingly broad spectrum of cellular pathways in the antiviral response. We identify IFN-dependent protein-protein interactions mediating novel regulatory mechanisms at the transcriptional and translational levels, with one such interaction modulating the transcriptional activity of STAT1. Moreover, we reveal IFN-dependent changes in ribosomal composition that act to buffer IFN-stimulated gene protein synthesis. CONCLUSIONS Our map of the IFN interactome provides a global view of the complex cellular networks activated during the antiviral response, placing IFN-stimulated genes in a functional context, and serves as a framework to understand how these networks are dysregulated in autoimmune or inflammatory disease.
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Affiliation(s)
- Craig H Kerr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Current Address: Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Daniel D T Andrews
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Angel M Madero
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Queenie W T Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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33
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A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Syst 2020; 10:133-155.e6. [PMID: 32027860 PMCID: PMC7042714 DOI: 10.1016/j.cels.2020.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/08/2019] [Accepted: 01/10/2020] [Indexed: 12/19/2022]
Abstract
Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes that affects their activity and/or function and is thus of great interest for biological research. Here, we describe the implementation of an integrated technique to quantify cell-state-specific changes in the physical arrangement of protein complexes concurrently for thousands of proteins and hundreds of complexes. Applying this technique to a comparison of human cells in interphase and mitosis, we provide a systematic overview of mitotic proteome reorganization. The results recall key hallmarks of mitotic complex remodeling and suggest a model of nuclear pore complex disassembly, which we validate by orthogonal methods. To support the interpretation of quantitative SEC-SWATH-MS datasets, we extend the software CCprofiler and provide an interactive exploration tool, SECexplorer-cc. Global quantification of assembly state changes in the mitotic proteome Improved performance over thermostability measurement of proteome states Discovery of a mitotic disassembly intermediate of the nuclear pore complex Introduction of SECexplorer-cc, a publicly available online platform
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34
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de Souza N, Picotti P. Mass spectrometry analysis of the structural proteome. Curr Opin Struct Biol 2020; 60:57-65. [DOI: 10.1016/j.sbi.2019.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/16/2019] [Indexed: 01/01/2023]
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35
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Salas D, Stacey RG, Akinlaja M, Foster LJ. Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks. Mol Cell Proteomics 2020; 19:1-10. [PMID: 31792070 PMCID: PMC6944233 DOI: 10.1074/mcp.r119.001803] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/26/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding how proteins interact is crucial to understanding cellular processes. Among the available interactome mapping methods, co-elution stands out as a method that is simultaneous in nature and capable of identifying interactions between all the proteins detected in a sample. The general workflow in co-elution methods involves the mild extraction of protein complexes and their separation into several fractions, across which proteins bound together in the same complex will show similar co-elution profiles when analyzed appropriately. In this review we discuss the different separation, quantification and bioinformatic strategies used in co-elution studies, and the important considerations in designing these studies. The benefits of co-elution versus other methods makes it a valuable starting point when asking questions that involve the perturbation of the interactome.
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Affiliation(s)
- Daniela Salas
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | - R Greg Stacey
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Mopelola Akinlaja
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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36
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Liebeskind BJ, Aldrich RW, Marcotte EM. Ancestral reconstruction of protein interaction networks. PLoS Comput Biol 2019; 15:e1007396. [PMID: 31658251 PMCID: PMC6837550 DOI: 10.1371/journal.pcbi.1007396] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/07/2019] [Accepted: 09/11/2019] [Indexed: 11/19/2022] Open
Abstract
The molecular and cellular basis of novelty is an active area of research in evolutionary biology. Until very recently, the vast majority of cellular phenomena were so difficult to sample that cross-species studies of biochemistry were rare and comparative analysis at the level of biochemical systems was almost impossible. Recent advances in systems biology are changing what is possible, however, and comparative phylogenetic methods that can handle this new data are wanted. Here, we introduce the term “phylogenetic latent variable models” (PLVMs, pronounced “plums”) for a class of models that has recently been used to infer the evolution of cellular states from systems-level molecular data, and develop a new parameterization and fitting strategy that is useful for comparative inference of biochemical networks. We deploy this new framework to infer the ancestral states and evolutionary dynamics of protein-interaction networks by analyzing >16,000 predominantly metazoan co-fractionation and affinity-purification mass spectrometry experiments. Based on these data, we estimate ancestral interactions across unikonts, broadly recovering protein complexes involved in translation, transcription, proteostasis, transport, and membrane trafficking. Using these results, we predict an ancient core of the Commander complex made up of CCDC22, CCDC93, C16orf62, and DSCR3, with more recent additions of COMMD-containing proteins in tetrapods. We also use simulations to develop model fitting strategies and discuss future model developments. Our ability to probe the inner workings of cells is constantly growing. This is true not only for workhorse model organisms like fruit flies and brewer’s yeast, but increasingly for organisms whose biology is less well trodden—corals, butterflies, exotic plants and fungi, and even precious clinical samples are all fair game. However, the mathematical models that we use to compare biology across species and infer evolutionary dynamics have not kept pace. Sophisticated models exist for DNA and protein sequences, but models that can handle functional cellular data are in their infancy. In this study we introduce a new model that we use to infer the evolutionary history of protein interaction networks from cutting-edge high-throughput proteomics data. We use this model to reconstruct the cell biology of the ancestors we share with fungi and slime molds, and propose a path by which a recently described protein complex involved in human development might have evolved.
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Affiliation(s)
- Benjamin J. Liebeskind
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
- Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America
| | - Richard W. Aldrich
- Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Valerius O, Asif AR, Beißbarth T, Bohrer R, Dihazi H, Feussner K, Jahn O, Majcherczyk A, Schmidt B, Schmitt K, Urlaub H, Lenz C. Mapping Cellular Microenvironments: Proximity Labeling and Complexome Profiling (Seventh Symposium of the Göttingen Proteomics Forum). Cells 2019; 8:cells8101192. [PMID: 31581721 PMCID: PMC6830108 DOI: 10.3390/cells8101192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022] Open
Abstract
Mass spectrometry-based proteomics methods are finding increasing use in structural biology research. Beyond simple interaction networks, information about stable protein-protein complexes or spatially proximal proteins helps to elucidate the biological functions of proteins in a wider cellular context. To shed light on new developments in this field, the Göttingen Proteomics Forum organized a one-day symposium focused on complexome profiling and proximity labeling, two emerging technologies that are gaining significant attention in biomolecular research. The symposium was held in Göttingen, Germany on 23 May, 2019, as part of a series of regular symposia organized by the Göttingen Proteomics Forum.
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Affiliation(s)
- Oliver Valerius
- Institute for Microbiology and Genetics, Georg August University, 37077 Göttingen, Germany.
| | - Abdul R Asif
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Rainer Bohrer
- Gesellschaft für Wissenschaftliche Datenverarbeitung mbH Göttingen, 37077 Göttingen, Germany.
| | - Hassan Dihazi
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, 37075 Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences, Georg August University, 37073 Göttingen, Germany.
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany.
| | - Andrzej Majcherczyk
- Büsgen Institute, Section Molecular Wood Biotechnology and Technical Mycology, Georg August University, 37077 Göttingen, Germany.
| | - Bernhard Schmidt
- Institute for Biochemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Kerstin Schmitt
- Institute for Microbiology and Genetics, Georg August University, 37077 Göttingen, Germany.
| | - Henning Urlaub
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- DFG Collaborative Research Centre SFB1190 "Compartmental Gates and Contact Sites in Cells", 37075 Göttingen, Germany.
| | - Christof Lenz
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- DFG Collaborative Research Centre SFB1190 "Compartmental Gates and Contact Sites in Cells", 37075 Göttingen, Germany.
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38
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Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A. EPIC: software toolkit for elution profile-based inference of protein complexes. Nat Methods 2019; 16:737-742. [PMID: 31308550 PMCID: PMC7995176 DOI: 10.1038/s41592-019-0461-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/15/2019] [Indexed: 11/08/2022]
Abstract
Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectrometry analysis (chromatographic fractionation-mass spectrometry, CF-MS), but the resulting data are challenging to process and interpret. Here, we describe EPIC (elution profile-based inference of complexes), a software toolkit for automated scoring of large-scale CF-MS data to define high-confidence multi-component macromolecules from diverse biological specimens. As a case study, we used EPIC to map the global interactome of Caenorhabditis elegans, defining 612 putative worm protein complexes linked to diverse biological processes. These included novel subunits and assemblies unique to nematodes that we validated using orthogonal methods. The open source EPIC software is freely available as a Jupyter notebook packaged in a Docker container (https://hub.docker.com/r/baderlab/bio-epic/).
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Affiliation(s)
- Lucas ZhongMing Hu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Florian Goebels
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - June H Tan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Eric Wolf
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Uros Kuzmanov
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Cuihong Wan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- School of Life Science, Central China Normal University, Wuhan, China
| | - Sadhna Phanse
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Changjiang Xu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Mike Schertzberg
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew G Fraser
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Departments of Biochemistry and Biology, Boston University, Boston, MA, USA.
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Carlson ML, Stacey RG, Young JW, Wason IS, Zhao Z, Rattray DG, Scott N, Kerr CH, Babu M, Foster LJ, Duong Van Hoa F. Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries. eLife 2019; 8:46615. [PMID: 31364989 PMCID: PMC6697469 DOI: 10.7554/elife.46615] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane interactome has lagged, partly due to the necessary use of detergents to maintain protein solubility. Here, we apply the peptidisc, a ‘one-size fits all’ membrane mimetic, for the capture of the Escherichia coli cell envelope proteome and its high-resolution fractionation in the absence of detergent. Analysis of the SILAC-labeled peptidisc library via PCP allows generation of over 4900 possible binary interactions out of >700,000 random associations. Using well-characterized membrane protein systems such as the SecY translocon, the Bam complex and the MetNI transporter, we demonstrate that our dataset is a useful resource for identifying transient and surprisingly novel protein interactions. For example, we discover a trans-periplasmic supercomplex comprising subunits of the Bam and Sec machineries, including membrane-bound chaperones YfgM and PpiD. We identify RcsF and OmpA as bone fide interactors of BamA, and we show that MetQ association with the ABC transporter MetNI depends on its N-terminal lipid anchor. We also discover NlpA as a novel interactor of MetNI complex. Most of these interactions are largely undetected by standard detergent-based purification. Together, the peptidisc workflow applied to the proteomic field is emerging as a promising novel approach to characterize membrane protein interactions under native expression conditions and without genetic manipulation.
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Affiliation(s)
- Michael Luke Carlson
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - R Greg Stacey
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - John William Young
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Irvinder Singh Wason
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Zhiyu Zhao
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - David G Rattray
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Nichollas Scott
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Craig H Kerr
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mohan Babu
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Canada
| | - Leonard J Foster
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Franck Duong Van Hoa
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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40
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Rattray DG, Foster LJ. Dynamics of protein complex components. Curr Opin Chem Biol 2019; 48:81-85. [DOI: 10.1016/j.cbpa.2018.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 11/28/2022]
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41
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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42
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Stacey RG, Skinnider MA, Chik JHL, Foster LJ. Context-specific interactions in literature-curated protein interaction databases. BMC Genomics 2018; 19:758. [PMID: 30340458 PMCID: PMC6194712 DOI: 10.1186/s12864-018-5139-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/03/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Databases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates. These databases combine interactions across thousands of published studies and experimental techniques. Because the tendency for two proteins to interact depends on the local conditions, this heterogeneity of conditions means that only a subset of database PPIs are interacting during any given experiment. A typical use of these databases as gold standards in interactome mapping projects, however, assumes that PPIs included in the database are indeed interacting under the experimental conditions of the study. RESULTS Using raw data from 20 co-fractionation experiments and six published interactomes, we demonstrate that this assumption is often false, with up to 55% of purported gold standard interactions showing no evidence of interaction, on average. We identify a subset of CORUM database complexes that do show consistent evidence of interaction in co-fractionation studies, and we use this subset as gold standards to dramatically improve interactome mapping as judged by the number of predicted interactions at a given error rate. CONCLUSIONS We recommend using this CORUM subset as the gold standard set in future co-fractionation studies. More generally, we recommend using the subset of literature-curated PPIs that are specific to the experimental context whenever possible.
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Affiliation(s)
- R. Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Michael A. Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Jenny H. L. Chik
- Current Address: International Collaboration On Repair Discoveries (ICORD), Vancouver Coastal Health Research Institute and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Leonard J. Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 Canada
- Department of Biochemistry, University of British Columbia, Vancouver, V6T 1Z3 Canada
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Skinnider MA, Stacey RG, Foster LJ. Genomic data integration systematically biases interactome mapping. PLoS Comput Biol 2018; 14:e1006474. [PMID: 30332399 PMCID: PMC6192561 DOI: 10.1371/journal.pcbi.1006474] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
Elucidating the complete network of protein-protein interactions, or interactome, is a fundamental goal of the post-genomic era, yet existing interactome maps are far from complete. To increase the throughput and resolution of interactome mapping, methods for protein-protein interaction discovery by co-migration have been introduced. However, accurate identification of interacting protein pairs within the resulting large-scale proteomic datasets is challenging. Consequently, most computational pipelines for co-migration data analysis incorporate external genomic datasets to distinguish interacting from non-interacting protein pairs. The effect of this procedure on interactome mapping is poorly understood. Here, we conduct a rigorous analysis of genomic data integration for interactome recovery across a large number of co-migration datasets, spanning diverse experimental and computational methods. We find that genomic data integration leads to an increase in the functional coherence of the resulting interactome maps, but this comes at the expense of a decrease in power to discover novel interactions. Importantly, putative novel interactions predicted by genomic data integration are no more likely to later be experimentally discovered than those predicted from co-migration data alone. Our results reveal a widespread and unappreciated limitation in a methodology that has been widely used to map the interactome of humans and model organisms.
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Affiliation(s)
| | - R. Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Leonard J. Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Biochemistry, University of British Columbia, Vancouver, Canada
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