1
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Sharifi S, Chaudhari P, Martirosyan A, Eberhardt AO, Witt F, Gollowitzer A, Lange L, Woitzat Y, Okoli EM, Li H, Rahnis N, Kirkpatrick J, Werz O, Ori A, Koeberle A, Bierhoff H, Ermolaeva M. Reducing the metabolic burden of rRNA synthesis promotes healthy longevity in Caenorhabditis elegans. Nat Commun 2024; 15:1702. [PMID: 38402241 PMCID: PMC10894287 DOI: 10.1038/s41467-024-46037-w] [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: 03/25/2022] [Accepted: 02/12/2024] [Indexed: 02/26/2024] Open
Abstract
Ribosome biogenesis is initiated by RNA polymerase I (Pol I)-mediated synthesis of pre-ribosomal RNA (pre-rRNA). Pol I activity was previously linked to longevity, but the underlying mechanisms were not studied beyond effects on nucleolar structure and protein translation. Here we use multi-omics and functional tests to show that curtailment of Pol I activity remodels the lipidome and preserves mitochondrial function to promote longevity in Caenorhabditis elegans. Reduced pre-rRNA synthesis improves energy homeostasis and metabolic plasticity also in human primary cells. Conversely, the enhancement of pre-rRNA synthesis boosts growth and neuromuscular performance of young nematodes at the cost of accelerated metabolic decline, mitochondrial stress and premature aging. Moreover, restriction of Pol I activity extends lifespan more potently than direct repression of protein synthesis, and confers geroprotection even when initiated late in life, showcasing this intervention as an effective longevity and metabolic health treatment not limited by aging.
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Affiliation(s)
- Samim Sharifi
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, Jena, 07745, Germany
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
- Matter Bio, Inc., Brooklyn, NY, 11237, USA
| | - Prerana Chaudhari
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Asya Martirosyan
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Joseph-Stelzmann-Straße 26, 50931, Cologne, Germany
| | - Alexander Otto Eberhardt
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, Jena, 07745, Germany
| | - Finja Witt
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - André Gollowitzer
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Lisa Lange
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, Jena, 07745, Germany
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Yvonne Woitzat
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | | | - Huahui Li
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, PR China
| | - Norman Rahnis
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Joanna Kirkpatrick
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
- Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Andreas Koeberle
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, Jena, 07745, Germany.
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany.
| | - Maria Ermolaeva
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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2
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Helbing DL, Kirkpatrick JM, Reuter M, Bischoff J, Stockdale A, Carlstedt A, Cirri E, Bauer R, Morrison H. Proteomic analysis of peripheral nerve myelin during murine aging. Front Cell Neurosci 2023; 17:1214003. [PMID: 37964793 PMCID: PMC10642449 DOI: 10.3389/fncel.2023.1214003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023] Open
Abstract
Aging of the peripheral nervous system (PNS) is associated with structural and functional changes that lead to a reduction in regenerative capacity and the development of age-related peripheral neuropathy. Myelin is central to maintaining physiological peripheral nerve function and differences in myelin maintenance, degradation, formation and clearance have been suggested to contribute to age-related PNS changes. Recent proteomic studies have elucidated the complex composition of the total myelin proteome in health and its changes in neuropathy models. However, changes in the myelin proteome of peripheral nerves during aging have not been investigated. Here we show that the proteomes of myelin fractions isolated from young and old nerves show only subtle changes. In particular, we found that the three most abundant peripheral myelin proteins (MPZ, MBP, and PRX) do not change in old myelin fractions. We also show a tendency for high-abundance myelin proteins other than these three to be downregulated, with only a small number of ribosome-related proteins significantly downregulated and extracellular matrix proteins such as collagens upregulated. In addition, we illustrate that the peripheral nerve myelin proteome reported in this study is suitable for assessing myelin degradation and renewal during peripheral nerve degeneration and regeneration. Our results suggest that the peripheral nerve myelin proteome is relatively stable and undergoes only subtle changes in composition during mouse aging. We proffer the resultant dataset as a resource and starting point for future studies aimed at investigating peripheral nerve myelin during aging. Said datasets are available in the PRIDE archive under the identifier PXD040719 (aging myelin proteome) and PXD041026 (sciatic nerve injury proteome).
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Affiliation(s)
- Dario Lucas Helbing
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Center for Intervention and Research on Adaptive and Maladaptive Brain Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, Germany
- German Center for Mental Health (DZPG), Jena, Germany
- Institute of Molecular Cell Biology, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | | | - Michael Reuter
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Julia Bischoff
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Amy Stockdale
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | | | - Emilio Cirri
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Reinhard Bauer
- Institute of Molecular Cell Biology, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Helen Morrison
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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3
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Valerio HP, Ravagnani FG, Yaya Candela AP, Dias Carvalho da Costa B, Ronsein GE, Di Mascio P. Spatial proteomics reveals subcellular reorganization in human keratinocytes exposed to UVA light. iScience 2022; 25:104093. [PMID: 35372811 PMCID: PMC8971936 DOI: 10.1016/j.isci.2022.104093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/16/2021] [Accepted: 03/14/2022] [Indexed: 12/16/2022] Open
Abstract
The effects of UV light on the skin have been extensively investigated. However, systematic information about how the exposure to ultraviolet-A (UVA) light, the least energetic but the most abundant UV radiation reaching the Earth, shapes the subcellular organization of proteins is lacking. Using subcellular fractionation, mass-spectrometry-based proteomics, machine learning algorithms, immunofluorescence, and functional assays, we mapped the subcellular reorganization of the proteome of human keratinocytes in response to UVA light. Our workflow quantified and assigned subcellular localization for over 1,600 proteins, of which about 200 were found to redistribute upon UVA exposure. Reorganization of the proteome affected modulators of signaling pathways, cellular metabolism, and DNA damage response. Strikingly, mitochondria were identified as one of the main targets of UVA-induced stress. Further investigation demonstrated that UVA induces mitochondrial fragmentation, up-regulates redox-responsive proteins, and attenuates respiratory rates. These observations emphasize the role of this radiation as a potent metabolic stressor in the skin.
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Affiliation(s)
- Hellen Paula Valerio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Felipe Gustavo Ravagnani
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Angela Paola Yaya Candela
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | | | - Graziella Eliza Ronsein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
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4
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Optimization of metabolomic data processing using NOREVA. Nat Protoc 2022; 17:129-151. [PMID: 34952956 DOI: 10.1038/s41596-021-00636-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022]
Abstract
A typical output of a metabolomic experiment is a peak table corresponding to the intensity of measured signals. Peak table processing, an essential procedure in metabolomics, is characterized by its study dependency and combinatorial diversity. While various methods and tools have been developed to facilitate metabolomic data processing, it is challenging to determine which processing workflow will give good performance for a specific metabolomic study. NOREVA, an out-of-the-box protocol, was therefore developed to meet this challenge. First, the peak table is subjected to many processing workflows that consist of three to five defined calculations in combinatorially determined sequences. Second, the results of each workflow are judged against objective performance criteria. Third, various benchmarks are analyzed to highlight the uniqueness of this newly developed protocol in (1) evaluating the processing performance based on multiple criteria, (2) optimizing data processing by scanning thousands of workflows, and (3) allowing data processing for time-course and multiclass metabolomics. This protocol is implemented in an R package for convenient accessibility and to protect users' data privacy. Preliminary experience in R language would facilitate the usage of this protocol, and the execution time may vary from several minutes to a couple of hours depending on the size of the analyzed data.
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Valerio HP, Ravagnani FG, Ronsein GE, Di Mascio P. A single dose of Ultraviolet-A induces proteome remodeling and senescence in primary human keratinocytes. Sci Rep 2021; 11:23355. [PMID: 34857819 PMCID: PMC8639817 DOI: 10.1038/s41598-021-02658-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/19/2021] [Indexed: 01/10/2023] Open
Abstract
Epidermal photoaging contributes to skin fragility over time and it is a risk factor for skin cancer. Photoaging has been associated for a long time with exposure to Ultraviolet-A (UVA) light, the predominant component of the solar ultraviolet radiation. While the cellular mechanisms underlying UVA-induced photoaging in the dermis have been well characterized, UVA's action on the epidermis remains elusive. Here, proteomic analysis was conducted to derive the cellular responses induced by an environmentally relevant dose of UVA in primary human keratinocytes. We also investigated the effects of UVA on non-transformed immortalized keratinocytes (HaCaT cells), bearing potentially oncogenic mutations. We showed that UVA induces proteome remodeling and senescence in primary keratinocytes, eliciting potent antioxidant and pro-inflammatory responses. Additionally, we showed that UVA modulates the secretory phenotype of these cells to the extent of inducing paracrine oxidative stress and immune system activation in pre-malignant keratinocytes. These observations offer insights into the cellular mechanisms by which UVA drives photoaging in the skin.
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Affiliation(s)
- Hellen Paula Valerio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
| | - Felipe Gustavo Ravagnani
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Graziella Eliza Ronsein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
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6
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Schüler SC, Kirkpatrick JM, Schmidt M, Santinha D, Koch P, Di Sanzo S, Cirri E, Hemberg M, Ori A, von Maltzahn J. Extensive remodeling of the extracellular matrix during aging contributes to age-dependent impairments of muscle stem cell functionality. Cell Rep 2021; 35:109223. [PMID: 34107247 DOI: 10.1016/j.celrep.2021.109223] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/25/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022] Open
Abstract
During aging, the regenerative capacity of skeletal muscle decreases due to intrinsic changes in muscle stem cells (MuSCs) and alterations in their niche. Here, we use quantitative mass spectrometry to characterize intrinsic changes in the MuSC proteome and remodeling of the MuSC niche during aging. We generate a network connecting age-affected ligands located in the niche and cell surface receptors on MuSCs. Thereby, we reveal signaling by integrins, Lrp1, Egfr, and Cd44 as the major cell communication axes perturbed through aging. We investigate the effect of Smoc2, a secreted protein that accumulates with aging, primarily originating from fibro-adipogenic progenitors. Increased levels of Smoc2 contribute to the aberrant Integrin beta-1 (Itgb1)/mitogen-activated protein kinase (MAPK) signaling observed during aging, thereby causing impaired MuSC functionality and muscle regeneration. By connecting changes in the proteome of MuSCs to alterations of their niche, our work will enable a better understanding of how MuSCs are affected during aging.
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Affiliation(s)
- Svenja C Schüler
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Joanna M Kirkpatrick
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Manuel Schmidt
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Deolinda Santinha
- Faculty of Medicine and Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal
| | - Philipp Koch
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Simone Di Sanzo
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Emilio Cirri
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany.
| | - Julia von Maltzahn
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany.
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7
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Gebert N, Cheng CW, Kirkpatrick JM, Di Fraia D, Yun J, Schädel P, Pace S, Garside GB, Werz O, Rudolph KL, Jasper H, Yilmaz ÖH, Ori A. Region-Specific Proteome Changes of the Intestinal Epithelium during Aging and Dietary Restriction. Cell Rep 2020; 31:107565. [PMID: 32348758 PMCID: PMC7446723 DOI: 10.1016/j.celrep.2020.107565] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 02/05/2020] [Accepted: 04/02/2020] [Indexed: 01/18/2023] Open
Abstract
The small intestine is responsible for nutrient absorption and one of the most important interfaces between the environment and the body. During aging, changes of the epithelium lead to food malabsorption and reduced barrier function, thus increasing disease risk. The drivers of these alterations remain poorly understood. Here, we compare the proteomes of intestinal crypts from mice across different anatomical regions and ages. We find that aging alters epithelial immunity, metabolism, and cell proliferation and is accompanied by region-dependent skewing in the cellular composition of the epithelium. Of note, short-term dietary restriction followed by refeeding partially restores the epithelium by promoting stem cell differentiation toward the secretory lineage. We identify Hmgcs2 (3-hydroxy-3-methylglutaryl-coenzyme A [CoA] synthetase 2), the rate-limiting enzyme for ketogenesis, as a modulator of stem cell differentiation that responds to dietary changes, and we provide an atlas of region- and age-dependent proteome changes of the small intestine.
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Affiliation(s)
- Nadja Gebert
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Chia-Wei Cheng
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | | | - Domenico Di Fraia
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jina Yun
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patrick Schädel
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Simona Pace
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - George B Garside
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Oliver Werz
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - K Lenhard Rudolph
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Henri Jasper
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ömer H Yilmaz
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
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8
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Tang J, Fu J, Wang Y, Luo Y, Yang Q, Li B, Tu G, Hong J, Cui X, Chen Y, Yao L, Xue W, Zhu F. Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains. Mol Cell Proteomics 2019; 18:1683-1699. [PMID: 31097671 PMCID: PMC6682996 DOI: 10.1074/mcp.ra118.001169] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
The label-free proteome quantification (LFQ) is multistep workflow collectively defined by quantification tools and subsequent data manipulation methods that has been extensively applied in current biomedical, agricultural, and environmental studies. Despite recent advances, in-depth and high-quality quantification remains extremely challenging and requires the optimization of LFQs by comparatively evaluating their performance. However, the evaluation results using different criteria (precision, accuracy, and robustness) vary greatly, and the huge number of potential LFQs becomes one of the bottlenecks in comprehensively optimizing proteome quantification. In this study, a novel strategy, enabling the discovery of the LFQs of simultaneously enhanced performance from thousands of workflows (integrating 18 quantification tools with 3,128 manipulation chains), was therefore proposed. First, the feasibility of achieving simultaneous improvement in the precision, accuracy, and robustness of LFQ was systematically assessed by collectively optimizing its multistep manipulation chains. Second, based on a variety of benchmark datasets acquired by various quantification measurements of different modes of acquisition, this novel strategy successfully identified a number of manipulation chains that simultaneously improved the performance across multiple criteria. Finally, to further enhance proteome quantification and discover the LFQs of optimal performance, an online tool (https://idrblab.org/anpela/) enabling collective performance assessment (from multiple perspectives) of the entire LFQ workflow was developed. This study confirmed the feasibility of achieving simultaneous improvement in precision, accuracy, and robustness. The novel strategy proposed and validated in this study together with the online tool might provide useful guidance for the research field requiring the mass-spectrometry-based LFQ technique.
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Affiliation(s)
- Jing Tang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China; ¶Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Fu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingxia Yang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Bo Li
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Gao Tu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jiajun Hong
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xuejiao Cui
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yuzong Chen
- ‖Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Lixia Yao
- **Department of Health Sciences Research, Mayo Clinic, Rochester MN 55905, United States
| | - Weiwei Xue
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
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9
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Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P. Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals. Cell 2019; 177:1308-1318.e10. [PMID: 31031010 PMCID: PMC6988111 DOI: 10.1016/j.cell.2019.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/18/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
Proteotypes, like genotypes, have been found to vary between individuals in several studies, but consistent molecular functional traits across studies remain to be quantified. In a meta-analysis of 11 proteomics datasets from humans and mice, we use co-variation of proteins in known functional modules across datasets and individuals to obtain a consensus landscape of proteotype variation. We find that individuals differ considerably in both protein complex abundances and stoichiometry. We disentangle genetic and environmental factors impacting these metrics, with genetic sex and specific diets together explaining 13.5% and 11.6% of the observed variation of complex abundance and stoichiometry, respectively. Sex-specific differences, for example, include various proteins and complexes, where the respective genes are not located on sex-specific chromosomes. Diet-specific differences, added to the individual genetic backgrounds, might become a starting point for personalized proteotype modulation toward desired features. Benchmarking of datasets on human and mouse proteotypes Consistent co-variation landscape of functional modules across individuals Protein complexes vary in their stoichiometry across individuals Quantifying effects of genetic sex and specific diets on complexes
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Affiliation(s)
- Natalie Romanov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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10
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Parca L, Beck M, Bork P, Ori A. Quantifying compartment-associated variations of protein abundance in proteomics data. Mol Syst Biol 2018; 14:e8131. [PMID: 29967062 PMCID: PMC6056770 DOI: 10.15252/msb.20178131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022] Open
Abstract
Quantitative mass spectrometry enables to monitor the abundance of thousands of proteins across biological conditions. Currently, most data analysis approaches rely on the assumption that the majority of the observed proteins remain unchanged across compared samples. Thus, gross morphological differences between cell states, deriving from, e.g., differences in size or number of organelles, are often not taken into account. Here, we analyzed multiple published datasets and frequently observed that proteins associated with a particular cellular compartment collectively increase or decrease in their abundance between conditions tested. We show that such effects, arising from underlying morphological differences, can skew the outcome of differential expression analysis. We propose a method to detect and normalize morphological effects underlying proteomics data. We demonstrate the applicability of our method to different datasets and biological questions including the analysis of sub-cellular proteomes in the context of Caenorhabditis elegans aging. Our method provides a complementary perspective to classical differential expression analysis and enables to uncouple overall abundance changes from stoichiometric variations within defined group of proteins.
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Affiliation(s)
- Luca Parca
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
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