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Rinschen MM, Limbutara K, Knepper MA, Payne DM, Pisitkun T. From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. Physiol Rev 2019; 98:2571-2606. [PMID: 30182799 DOI: 10.1152/physrev.00057.2017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Classical physiological studies using electrophysiological, biophysical, biochemical, and molecular techniques have created a detailed picture of molecular transport, bioenergetics, contractility and movement, and growth, as well as the regulation of these processes by external stimuli in cells and organisms. Newer systems biology approaches are beginning to provide deeper and broader understanding of these complex biological processes and their dynamic responses to a variety of environmental cues. In the past decade, advances in mass spectrometry-based proteomic technologies have provided invaluable tools to further elucidate these complex cellular processes, thereby confirming, complementing, and advancing common views of physiology. As one notable example, the application of proteomics to study the regulation of kidney function has yielded novel insights into the chemical and physical processes that tightly control body fluids, electrolytes, and metabolites to provide optimal microenvironments for various cellular and organ functions. Here, we systematically review, summarize, and discuss the most significant key findings from functional proteomic studies in renal epithelial physiology. We also identify further improvements in technological and bioinformatics methods that will be essential to advance precision medicine in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Kavee Limbutara
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Mark A Knepper
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - D Michael Payne
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Trairak Pisitkun
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
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Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 2015; 15:930-49. [PMID: 25158685 PMCID: PMC4409848 DOI: 10.1002/pmic.201400302] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/06/2014] [Accepted: 08/22/2014] [Indexed: 01/10/2023]
Abstract
Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data.
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Affiliation(s)
- Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Titz B, Elamin A, Martin F, Schneider T, Dijon S, Ivanov NV, Hoeng J, Peitsch MC. Proteomics for systems toxicology. Comput Struct Biotechnol J 2014; 11:73-90. [PMID: 25379146 PMCID: PMC4212285 DOI: 10.1016/j.csbj.2014.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of proteomics for systems toxicology studies. With a focus on mass spectrometry-based proteomics, we summarize the experimental methods for quantitative proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, proteomics will be an integral part of integrative systems toxicology approaches in the future.
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