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Bludau I, Nicod C, Martelli C, Xue P, Heusel M, Fossati A, Uliana F, Frommelt F, Aebersold R, Collins BC. Rapid Profiling of Protein Complex Reorganization in Perturbed Systems. J Proteome Res 2023; 22:1520-1536. [PMID: 37058003 PMCID: PMC10167687 DOI: 10.1021/acs.jproteome.3c00125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, complexes undergo changes in their abundance, subunit composition, or state of modification. Understanding the function of biological systems requires global strategies to capture this contextual state information. Methods based on cofractionation paired with mass spectrometry have demonstrated the capability for deep biological insight, but the scope of studies using this approach has been limited by the large measurement time per biological sample and challenges with data analysis. There has been little uptake of this strategy into the broader life science community despite its rich biological information content. We present a rapid integrated experimental and computational workflow to assess the reorganization of protein complexes across multiple cellular states. The workflow combines short gradient chromatography and DIA/SWATH mass spectrometry with a data analysis toolset to quantify changes in a complex organization. We applied the workflow to study the global protein complex rearrangements of THP-1 cells undergoing monocyte to macrophage differentiation and subsequent stimulation of macrophage cells with lipopolysaccharide. We observed substantial proteome reorganization on differentiation and less pronounced changes in macrophage stimulation. We establish our integrated differential pipeline for rapid and state-specific profiling of protein complex organization.
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Affiliation(s)
- Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany 82152
| | - Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Division of Infection Medicine (BMC), Department of Clinical Sciences, Lund University, Lund, Sweden 22184
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- J. David Gladstone Institutes, San Francisco, California 94158, United States
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland 8052
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Ben C Collins
- School of Biological Sciences, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, U.K
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Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC. Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis. Curr Opin Microbiol 2017; 39:64-72. [PMID: 29032348 DOI: 10.1016/j.mib.2017.09.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
Abstract
Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host. Here we review omic studies in Mycobacterium tuberculosis, the causative agent of tuberculosis, with a particular focus on proteomic methods and their application to the bacilli. Likewise, the discussed methods are directly portable to other bacterial pathogens.
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Affiliation(s)
- Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Nicod C, Banaei-Esfahani A, Collins BC. Elucidation of host-pathogen protein-protein interactions to uncover mechanisms of host cell rewiring. Curr Opin Microbiol 2017; 39:7-15. [PMID: 28806587 DOI: 10.1016/j.mib.2017.07.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/27/2017] [Indexed: 01/08/2023]
Abstract
Infectious diseases are the result of molecular cross-talks between hosts and their pathogens. These cross-talks are in part mediated by host-pathogen protein-protein interactions (HP-PPI). HP-PPI play crucial roles in infections, as they may tilt the balance either in favor of the pathogens' spread or their clearance. The identification of host proteins targeted by viral or bacterial pathogenic proteins necessary for the infection can provide insights into their underlying molecular mechanisms of pathogenicity, and potentially even single out pharmacological intervention targets. Here, we review the available methods to study HP-PPI, with a focus on recent mass spectrometry based methods to decipher bacterial-human infectious diseases and examine their relevance in uncovering host cell rewiring by pathogens.
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Affiliation(s)
- Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, CH-8093 Zurich, Switzerland
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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Brauner R, Rappaport R, Nicod C, Malandry F, Thibaud E, Pierre-Kahn A, Renier D, Sainte-Rose C, Hirsch JF. [True precocious puberty in non-tumor hydrocephalus. An analysis of 16 cases]. Arch Fr Pediatr 1987; 44:433-6. [PMID: 3304186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
True precocious puberty occurred in 16 children (15 girls and 1 boy) with non tumoral shunted hydrocephalus at a mean age of 6.8 years. They had mild clinical manifestations of precocious puberty, and the other pituitary functions were found to be normal. Except for one child, precocious puberty did not correlate with raised intracranial pressure or lack of cerebral drainage by the shunt. Growth was the main concern in this group as the predicted height fell at a mean value of 1.7 SD below the parental target height, and even more in children with myelomeningocele. This growth retardation is due to an early progression of bone age observed even prior to the appearance of breast or pubic hair. Therefore we suggest that these children might benefit from early treatment by an LHRH analogue as soon as precocious puberty occurs.
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