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Santo-Domingo J, Lassueur S, Galindo AN, Alvarez-Illera P, Romero-Sanz S, Caldero-Escudero E, de la Fuente S, Dayon L, Wiederkehr A. SLC25A46 promotes mitochondrial fission and mediates resistance to lipotoxic stress in INS-1E insulin-secreting cells. J Cell Sci 2023; 136:jcs260049. [PMID: 36942724 DOI: 10.1242/jcs.260049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Glucose sensing in pancreatic β-cells depends on oxidative phosphorylation and mitochondria-derived signals that promote insulin secretion. Using mass spectrometry-based phosphoproteomics to search for downstream effectors of glucose-dependent signal transduction in INS-1E insulinoma cells, we identified the outer mitochondrial membrane protein SLC25A46. Under resting glucose concentrations, SLC25A46 was phosphorylated on a pair of threonine residues (T44/T45) and was dephosphorylated in response to glucose-induced Ca2+ signals. Overexpression of SLC25A46 in INS-1E cells caused complete mitochondrial fragmentation, resulting in a mild mitochondrial defect associated with lowered glucose-induced insulin secretion. In contrast, inactivation of the Slc25a46 gene resulted in dramatic mitochondrial hyperfusion, without affecting respiratory activity or insulin secretion. Consequently, SLC25A46 is not essential for metabolism-secretion coupling under normal nutrient conditions. Importantly, insulin-secreting cells lacking SLC25A46 had an exacerbated sensitivity to lipotoxic conditions, undergoing massive apoptosis when exposed to palmitate. Therefore, in addition to its role in mitochondrial dynamics, SLC25A46 plays a role in preventing mitochondria-induced apoptosis in INS-E cells exposed to nutrient stress. By protecting mitochondria, SLC25A46 might help to maintain β-cell mass essential for blood glucose control.
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Affiliation(s)
- Jaime Santo-Domingo
- Department of Cell Biology, Nestlé Institute of Health Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Steve Lassueur
- Department of Cell Biology, Nestlé Institute of Health Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Pilar Alvarez-Illera
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Silvia Romero-Sanz
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Elena Caldero-Escudero
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Sergio de la Fuente
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Andreas Wiederkehr
- Department of Cell Biology, Nestlé Institute of Health Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Kozhinov AN, Johnson A, Nagornov KO, Stadlmeier M, Martin WL, Dayon L, Corthésy J, Wühr M, Tsybin YO. Super-Resolution Mass Spectrometry Enables Rapid, Accurate, and Highly Multiplexed Proteomics at the MS2 Level. Anal Chem 2023; 95:3712-3719. [PMID: 36749928 PMCID: PMC9974827 DOI: 10.1021/acs.analchem.2c04742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
In tandem mass spectrometry (MS2)-based multiplexed quantitative proteomics, the complement reporter ion approaches (TMTc and TMTproC) were developed to eliminate the ratio-compression problem of conventional MS2-level approaches. Resolving all high m/z complement reporter ions (∼6.32 mDa-spaced) requires mass resolution and scan speeds above the performance levels of OrbitrapTM instruments. Therefore, complement reporter ion quantification with TMT/TMTpro reagents is currently limited to 5 out of 11 (TMT) or 9 out of 18 (TMTpro) channels (∼1 Da spaced). We first demonstrate that a FusionTM LumosTM Orbitrap can resolve 6.32 mDa-spaced complement reporter ions with standard acquisition modes extended with 3 s transients. We then implemented a super-resolution mass spectrometry approach using the least-squares fitting (LSF) method for processing Orbitrap transients to achieve shotgun proteomics-compatible scan rates. The LSF performance resolves the 6.32 mDa doublets for all TMTproC channels in the standard mass range with transients as short as ∼108 ms (Orbitrap resolution setting of 50,000 at m/z 200). However, we observe a slight decrease in measurement precision compared to 1 Da spacing with the 108 ms transients. With 256 ms transients (resolution of 120,000 at m/z 200), coefficients of variation are essentially indistinguishable from 1 Da samples. We thus demonstrate the feasibility of highly multiplexed, accurate, and precise shotgun proteomics at the MS2 level.
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Affiliation(s)
| | - Alex Johnson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | | | - Michael Stadlmeier
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Warham Lance Martin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Loïc Dayon
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, 1015 Lausanne, Switzerland
| | - John Corthésy
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, 1015 Lausanne, Switzerland
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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Rabl M, Clark C, Dayon L, Bowman GL, Popp J. Blood plasma protein profiles of neuropsychiatric symptoms and related cognitive decline in older people. J Neurochem 2023; 164:242-254. [PMID: 36281546 DOI: 10.1111/jnc.15715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 01/31/2023]
Abstract
Neuropsychiatric symptoms (NPS) severely affect patients and their caregivers, and are associated with worse long-term outcomes. This study tested the hypothesis that altered protein levels in blood plasma could serve as biomarkers of NPS; and that altered protein levels are associated with persisting NPS and cognitive decline over time. We performed a cross-sectional and longitudinal study in older subjects with cognitive impairment and cognitively unimpaired in a memory clinic setting. NPS were recorded through the Neuropsychiatric Inventory Questionnaire (NPI-Q) while cognitive and functional impairment was assessed using the clinical dementia rating sum of boxes (CDR-SoB) score at baseline and follow-up visits. Shotgun proteomic analysis based on liquid chromatography-mass spectrometry was conducted in blood plasma samples, identifying 420 proteins. The presence of Alzheimer's Disease (AD) pathology was determined by cerebrospinal fluid biomarkers. Eighty-five subjects with a mean age of 70 (±7.4) years, 62% female and 54% with mild cognitive impairment or mild dementia were included. We found 15 plasma proteins with altered baseline levels in participants with NPS (NPI-Q score > 0). Adding those 15 proteins to a reference model based on clinical data (age, CDR-SoB) significantly improved the prediction of NPS (from receiver operating characteristic area under the curve [AUC] 0.75 to AUC 0.91, p = 0.004) with a specificity of 89% and a sensitivity of 74%. The identified proteins additionally predicted both persisting NPS and cognitive decline at follow-up visits. The observed associations were independent of the presence of AD pathology. Using proteomics, we identified a panel of specific blood proteins associated with current and future NPS, and related cognitive decline in older people. These findings show the potential of untargeted proteomics to identify blood-based biomarkers of pathological alterations relevant for NPS and related clinical disease progression.
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Affiliation(s)
- Miriam Rabl
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland.,University of Lausanne, Lausanne, Switzerland
| | - Christopher Clark
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zurich, Zurich, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland.,Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gene L Bowman
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Julius Popp
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zurich, Zurich, Switzerland.,Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
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Clark C, Rabl M, Dayon L, Popp J. The promise of multi-omics approaches to discover biological alterations with clinical relevance in Alzheimer's disease. Front Aging Neurosci 2022; 14:1065904. [PMID: 36570537 PMCID: PMC9768448 DOI: 10.3389/fnagi.2022.1065904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Beyond the core features of Alzheimer's disease (AD) pathology, i.e. amyloid pathology, tau-related neurodegeneration and microglia response, multiple other molecular alterations and pathway dysregulations have been observed in AD. Their inter-individual variations, complex interactions and relevance for clinical manifestation and disease progression remain poorly understood, however. Heterogeneity at both pathophysiological and clinical levels complicates diagnosis, prognosis, treatment and drug design and testing. High-throughput "omics" comprise unbiased and untargeted data-driven methods which allow the exploration of a wide spectrum of disease-related changes at different endophenotype levels without focussing a priori on specific molecular pathways or molecules. Crucially, new methodological and statistical advances now allow for the integrative analysis of data resulting from multiple and different omics methods. These multi-omics approaches offer the unique advantage of providing a more comprehensive characterisation of the AD endophenotype and to capture molecular signatures and interactions spanning various biological levels. These new insights can then help decipher disease mechanisms more deeply. In this review, we describe the different multi-omics tools and approaches currently available and how they have been applied in AD research so far. We discuss how multi-omics can be used to explore molecular alterations related to core features of the AD pathologies and how they interact with comorbid pathological alterations. We further discuss whether the identified pathophysiological changes are relevant for the clinical manifestation of AD, in terms of both cognitive impairment and neuropsychiatric symptoms, and for clinical disease progression over time. Finally, we address the opportunities for multi-omics approaches to help discover novel biomarkers for diagnosis and monitoring of relevant pathophysiological processes, along with personalised intervention strategies in AD.
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Affiliation(s)
- Christopher Clark
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zürich, Zürich, Switzerland,Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland,*Correspondence: Christopher Clark,
| | - Miriam Rabl
- Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland,University of Lausanne, Lausanne, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julius Popp
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zürich, Zürich, Switzerland,Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland,Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
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Cominetti O, Núñez Galindo A, Corthésy J, Carayol J, Germain N, Galusca B, Estour B, Hager J, Gheldof N, Dayon L. Proteomics reveals unique plasma signatures in constitutional thinness. Proteomics Clin Appl 2022; 16:e2100114. [PMID: 35579096 PMCID: PMC9787820 DOI: 10.1002/prca.202100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE Studying the plasma proteome of control versus constitutionally thin (CT) individuals, exposed to overfeeding, may give insights into weight-gain management, providing relevant information to the clinical entity of weight-gain resistant CT, and discovering new markers for the condition. EXPERIMENTAL DESIGN Untargeted protein relative quantification of 63 CT and normal-weight individuals was obtained in blood plasma at baseline, during and after an overfeeding challenge using mass spectrometry-based proteomics. RESULTS The plasma proteome of CT subjects presented limited specificity with respect to controls at baseline. Yet, CT showed lower levels of inflammatory C-reactive protein and larger levels of protective insulin-like growth factor-binding protein 2. Differences were more marked during and after overfeeding. CT plasma proteome showed larger magnitude and significance in response, suggesting enhanced "resilience" and more rapid adaptation to changes. Four proteins behaved similarly between CT and controls, while five were regulated in opposite fashion. Ten proteins were differential during overfeeding in CT only (including increased fatty acid-binding protein and glyceraldehyde-3-phosphate dehydrogenase, and decreased apolipoprotein C-II and transferrin receptor protein 1). CONCLUSIONS AND CLINICAL RELEVANCE This first proteomic profiling of a CT cohort reveals different plasma proteomes between CT subjects and controls in a longitudinal clinical trial. Our molecular observations further support that the resistance to weight gain in CT subjects appears predominantly biological. CLINICALTRIALS gov Identifier: NCT02004821.
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Affiliation(s)
- Ornella Cominetti
- Nestlé Institute of Food Safety & Analytical SciencesNestlé ResearchLausanneSwitzerland
| | - Antonio Núñez Galindo
- Nestlé Institute of Food Safety & Analytical SciencesNestlé ResearchLausanneSwitzerland
| | - John Corthésy
- Nestlé Institute of Food Safety & Analytical SciencesNestlé ResearchLausanneSwitzerland
| | - Jérôme Carayol
- Nestlé Institute of Health SciencesNestlé ResearchLausanneSwitzerland,Present address:
Playtika Switzerland SARue du Port‐Franc 2ALausanne1003Switzerland
| | - Natacha Germain
- Division of EndocrinologyDiabetes, Metabolism and Eating Disorders, CHU St‐EtienneFrance
| | - Bogdan Galusca
- Division of EndocrinologyDiabetes, Metabolism and Eating Disorders, CHU St‐EtienneFrance
| | - Bruno Estour
- Division of EndocrinologyDiabetes, Metabolism and Eating Disorders, CHU St‐EtienneFrance
| | - Jörg Hager
- Nestlé Institute of Health SciencesNestlé ResearchLausanneSwitzerland
| | - Nele Gheldof
- Nestlé Institute of Health SciencesNestlé ResearchLausanneSwitzerland,Present address:
VPA ‐ AVP‐R‐Administration, EPFLBI A2 483, Station 7Lausanne1015Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety & Analytical SciencesNestlé ResearchLausanneSwitzerland,Institut des Sciences et Ingénierie ChimiquesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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Clark C, Richiardi J, Maréchal B, Bowman GL, Dayon L, Popp J. Systemic and central nervous system neuroinflammatory signatures of neuropsychiatric symptoms and related cognitive decline in older people. J Neuroinflammation 2022; 19:127. [PMID: 35643540 PMCID: PMC9148517 DOI: 10.1186/s12974-022-02473-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/15/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Neuroinflammation may contribute to psychiatric symptoms in older people, in particular in the context of Alzheimer's disease (AD). We sought to identify systemic and central nervous system (CNS) inflammatory alterations associated with neuropsychiatric symptoms (NPS); and to investigate their relationships with AD pathology and clinical disease progression. METHODS We quantified a panel of 38 neuroinflammation and vascular injury markers in paired serum and cerebrospinal fluid (CSF) samples in a cohort of cognitively normal and impaired older subjects. We performed neuropsychiatric and cognitive evaluations and measured CSF biomarkers of AD pathology. Multivariate analysis determined serum and CSF neuroinflammatory alterations associated with NPS, considering cognitive status, AD pathology, and cognitive decline at follow-up visits. RESULTS NPS were associated with distinct inflammatory profiles in serum, involving eotaxin-3, interleukin (IL)-6 and C-reactive protein (CRP); and in CSF, including soluble intracellular cell adhesion molecule-1 (sICAM-1), IL-8, 10-kDa interferon-γ-induced protein, and CRP. AD pathology interacted with CSF sICAM-1 in association with NPS. Presenting NPS was associated with subsequent cognitive decline which was mediated by CSF sICAM-1. CONCLUSIONS Distinct systemic and CNS inflammatory processes are involved in the pathophysiology of NPS in older people. Neuroinflammation may explain the link between NPS and more rapid clinical disease progression.
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Affiliation(s)
- Christopher Clark
- Institute for Regenerative Medicine, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric Hospital of the University of Zurich, Lengstrasse 31, Zürich, Switzerland
| | - Jonas Richiardi
- Department of Radiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - Bénédicte Maréchal
- Advanced Clinical Imaging Technologies Group, Siemens Healthcare Switzerland, 1015 Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Bâtiment H, 1015 Lausanne, Switzerland
- Department of Neurology, NIA-Layton Aging and Alzheimer’s Disease Research Center, Oregon Health & Science University, Portland, Oregon USA
- Helfgott Research Institute, National University of Natural Medicine, Portland, Oregon USA
| | - Loïc Dayon
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Bâtiment H, 1015 Lausanne, Switzerland
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, Bâtiment H, CH-1015 Lausanne, Switzerland
- Institut Des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Julius Popp
- Institute for Regenerative Medicine, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland
- Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 46, 1011 Lausanne, Switzerland
- Department of Geriatric Psychiatry, Centre for Gerontopsychiatric Medicine, University Hospital of Psychiatry Zürich, Minervastrasse 145, P.O. Box 341, 8032 Zurich, Switzerland
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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Dubois E, Galindo AN, Dayon L, Cominetti O. Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples. Biosystems 2022; 215-216:104661. [PMID: 35247480 DOI: 10.1016/j.biosystems.2022.104661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinical research study, from human biological sample collection and storage, sample preparation, spectral data acquisition, to peptide and protein quantification. In order to remove such diverse and unwanted variability, normalization of the protein data is performed. There have been already several published reviews comparing normalization methods in the -omics field, but reports focusing on proteomic data generated with mass spectrometry (MS) are much fewer. Additionally, most of these reports have only dealt with small datasets. RESULTS As a case study, here we focused on the normalization of a large MS-based proteomic dataset obtained from an overweight and obese pan-European cohort, where different normalization methods were evaluated, namely: center standardize, quantile protein, quantile sample, global standardization, ComBat, median centering, mean centering, single standard and removal of unwanted variation (RUV); some of these are generic normalization methods while others have been specifically created to deal with genomic or metabolomic data. We checked how relationships between proteins and clinical variables (e.g., gender, levels of triglycerides or cholesterol) were improved after normalizing the data with the different methods. CONCLUSIONS Some normalization methods were better adapted for this particular large-scale shotgun proteomic dataset of human plasma samples labeled with isobaric tags and analyzed with liquid chromatography-tandem MS. In particular, quantile sample normalization, RUV, mean and median centering showed very good performance, while quantile protein normalization provided worse results than those obtained with unnormalized data.
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Affiliation(s)
- Etienne Dubois
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland; Chemistry and Chemical Engineering Section, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Ornella Cominetti
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland.
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Valera-Alberni M, Joffraud M, Miro-Blanch J, Capellades J, Junza A, Dayon L, Núñez Galindo A, Sanchez-Garcia JL, Valsesia A, Cercillieux A, Söllner F, Ladurner AG, Yanes O, Cantó C. Crosstalk between Drp1 phosphorylation sites during mitochondrial remodeling and their impact on metabolic adaptation. Cell Rep 2021; 36:109565. [PMID: 34433037 PMCID: PMC8411118 DOI: 10.1016/j.celrep.2021.109565] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 06/07/2021] [Accepted: 07/29/2021] [Indexed: 01/03/2023] Open
Abstract
Mitochondria constantly undergo fusion and fission events, referred as mitochondrial dynamics, which determine mitochondrial architecture and bioenergetics. Cultured cell studies demonstrate that mitochondrial dynamics are acutely regulated by phosphorylation of the mitochondrial fission orchestrator dynamin-related protein 1 (Drp1) at S579 or S600. However, the physiological impact and crosstalk of these phosphorylation sites is poorly understood. Here, we describe the functional interrelation between S579 and S600 phosphorylation sites in vivo and their role on mitochondrial remodeling. Mice carrying a homozygous Drp1 S600A knockin (Drp1 KI) mutation display larger mitochondria and enhanced lipid oxidation and respiratory capacities, granting improved glucose tolerance and thermogenic response upon high-fat feeding. Housing mice at thermoneutrality blunts these differences, suggesting a role for the brown adipose tissue in the protection of Drp1 KI mice against metabolic damage. Overall, we demonstrate crosstalk between Drp1 phosphorylation sites and provide evidence that their modulation could be used in the treatment and prevention of metabolic diseases. Drp1 phosphorylation at S600 promotes the phosphorylation at the S579 site Both Drp1 P-S600 and P-S579 are required for maximal mitochondrial fragmentation Drp1 S600A knockin mice are protected against diet-induced metabolic damage Drp1 phosphorylation controls brown adipose tissue thermogenic capacity in mice
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Affiliation(s)
- Miriam Valera-Alberni
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Magali Joffraud
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland
| | - Joan Miro-Blanch
- Universitat Rovira i Virgili, Department of Electronic Engineering & IISPV, 43003 Tarragona, Spain; CIBER de Diabetes y Enfermedates Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
| | - Jordi Capellades
- Universitat Rovira i Virgili, Department of Electronic Engineering & IISPV, 43003 Tarragona, Spain; CIBER de Diabetes y Enfermedates Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
| | - Alexandra Junza
- Universitat Rovira i Virgili, Department of Electronic Engineering & IISPV, 43003 Tarragona, Spain; CIBER de Diabetes y Enfermedates Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
| | - Loïc Dayon
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland; Institut des Sciences et Ingénierie Chimiques, EPFL, Lausanne 1015, Switzerland
| | - Antonio Núñez Galindo
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland
| | - Jose L Sanchez-Garcia
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland
| | - Armand Valsesia
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland
| | - Angelique Cercillieux
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Flavia Söllner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Oscar Yanes
- Universitat Rovira i Virgili, Department of Electronic Engineering & IISPV, 43003 Tarragona, Spain; CIBER de Diabetes y Enfermedates Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
| | - Carles Cantó
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., Lausanne 1015, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.
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10
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Clark C, Dayon L, Masoodi M, Bowman GL, Popp J. An integrative multi-omics approach reveals new central nervous system pathway alterations in Alzheimer's disease. Alzheimers Res Ther 2021; 13:71. [PMID: 33794997 PMCID: PMC8015070 DOI: 10.1186/s13195-021-00814-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/23/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Multiple pathophysiological processes have been described in Alzheimer's disease (AD). Their inter-individual variations, complex interrelations, and relevance for clinical manifestation and disease progression remain poorly understood. We hypothesize that specific molecular patterns indicating both known and yet unidentified pathway alterations are associated with distinct aspects of AD pathology. METHODS We performed multi-level cerebrospinal fluid (CSF) omics in a well-characterized cohort of older adults with normal cognition, mild cognitive impairment, and mild dementia. Proteomics, metabolomics, lipidomics, one-carbon metabolism, and neuroinflammation related molecules were analyzed at single-omic level with correlation and regression approaches. Multi-omics factor analysis was used to integrate all biological levels. Identified analytes were used to construct best predictive models of the presence of AD pathology and of cognitive decline with multifactorial regression analysis. Pathway enrichment analysis identified pathway alterations in AD. RESULTS Multi-omics integration identified five major dimensions of heterogeneity explaining the variance within the cohort and differentially associated with AD. Further analysis exposed multiple interactions between single 'omics modalities and distinct multi-omics molecular signatures differentially related to amyloid pathology, neuronal injury, and tau hyperphosphorylation. Enrichment pathway analysis revealed overrepresentation of the hemostasis, immune response, and extracellular matrix signaling pathways in association with AD. Finally, combinations of four molecules improved prediction of both AD (protein 14-3-3 zeta/delta, clusterin, interleukin-15, and transgelin-2) and cognitive decline (protein 14-3-3 zeta/delta, clusterin, cholesteryl ester 27:1 16:0 and monocyte chemoattractant protein-1). CONCLUSIONS Applying an integrative multi-omics approach we report novel molecular and pathways alterations associated with AD pathology. These findings are relevant for the development of personalized diagnosis and treatment approaches in AD.
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Affiliation(s)
- Christopher Clark
- Institute for Regenerative Medicine, University of Zürich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland.,Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Mojgan Masoodi
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland.,Institute of Clinical Chemistry, University Hospital Bern, Bern, Switzerland
| | - Gene L Bowman
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland.,Department of Neurology, NIA-Layton Aging and Alzheimer's Disease Center, Oregon Health & Science University, Portland, USA
| | - Julius Popp
- Old Age Psychiatry, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 46, 1011, Lausanne, Switzerland. .,Department of Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Centre for Gerontopsychiatric Medicine, Minervastrasse 145, P.O. Box 341, 8032, Zürich, Switzerland.
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11
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Dayon L, Macron C, Lahrichi S, Núñez Galindo A, Affolter M. Proteomics of Human Milk: Definition of a Discovery Workflow for Clinical Research Studies. J Proteome Res 2021; 20:2283-2290. [PMID: 33769819 DOI: 10.1021/acs.jproteome.0c00816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Milk is a complex biological fluid composed mainly of water, carbohydrates, lipids, proteins, and diverse bioactive factors. Human milk represents a unique tailored source of nutrients that adapts during lactation to the specific needs of the developing infant. Proteins in milk have been studied for decades, and proteomics, peptidomics, and glycoproteomics are the main approaches previously deployed to decipher the proteome of human milk. In the present work, we aimed at implementing a highly automated pipeline for the proteomic analysis of human milk with liquid chromatography mass spectrometry (MS). Commercial human milk samples were used to evaluate and optimize workflows. Centrifugation for defatting milk samples was assessed before and after reduction, alkylation, and enzymatic digestion of proteins, without and with presence of surfactants. Skimmed milk samples were analyzed using isobaric labeling-based quantitative MS on an Orbitrap Tribrid mass spectrometer. Sample fractionation using isoelectric focusing was also evaluated to more deeply profile the human milk proteome. Finally, the most appropriate workflow was transferred to a liquid handling workstation for automated sample preparation. In conclusion, we have defined and describe herein an efficient highly automated proteomic workflow for human milk sample analysis. It is compatible with clinical research, possibly allowing the analysis of sufficiently large cohorts of samples.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne 1015, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Charlotte Macron
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne 1015, Switzerland
| | - Sabine Lahrichi
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne 1015, Switzerland
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne 1015, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne 1015, Switzerland
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12
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Chareyron I, Christen S, Moco S, Valsesia A, Lassueur S, Dayon L, Wollheim CB, Santo Domingo J, Wiederkehr A. Augmented mitochondrial energy metabolism is an early response to chronic glucose stress in human pancreatic beta cells. Diabetologia 2020; 63:2628-2640. [PMID: 32960311 PMCID: PMC7641954 DOI: 10.1007/s00125-020-05275-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/04/2020] [Indexed: 01/15/2023]
Abstract
AIMS/HYPOTHESIS In islets from individuals with type 2 diabetes and in islets exposed to chronic elevated glucose, mitochondrial energy metabolism is impaired. Here, we studied early metabolic changes and mitochondrial adaptations in human beta cells during chronic glucose stress. METHODS Respiration and cytosolic ATP changes were measured in human islet cell clusters after culture for 4 days in 11.1 mmol/l glucose. Metabolomics was applied to analyse intracellular metabolite changes as a result of glucose stress conditions. Alterations in beta cell function were followed using insulin secretion assays or cytosolic calcium signalling after expression of the calcium probe YC3.6 specifically in beta cells of islet clusters. RESULTS At early stages of glucose stress, mitochondrial energy metabolism was augmented in contrast to the previously described mitochondrial dysfunction in beta cells from islets of diabetic donors. Following chronic glucose stress, mitochondrial respiration increased (by 52.4%, p < 0.001) and, as a consequence, the cytosolic ATP/ADP ratio in resting human pancreatic islet cells was elevated (by 27.8%, p < 0.05). Because of mitochondrial overactivation in the resting state, nutrient-induced beta cell activation was reduced. In addition, chronic glucose stress caused metabolic adaptations that resulted in the accumulation of intermediates of the glycolytic pathway, the pentose phosphate pathway and the TCA cycle; the most strongly augmented metabolite was glycerol 3-phosphate. The changes in metabolites observed are likely to be due to the inability of mitochondria to cope with continuous nutrient oversupply. To protect beta cells from chronic glucose stress, we inhibited mitochondrial pyruvate transport. Metabolite concentrations were partially normalised and the mitochondrial respiratory response to nutrients was markedly improved. Furthermore, stimulus-secretion coupling as assessed by cytosolic calcium signalling, was restored. CONCLUSION/INTERPRETATION We propose that metabolic changes and associated mitochondrial overactivation are early adaptations to glucose stress, and may reflect what happens as a result of poor blood glucose control. Inhibition of mitochondrial pyruvate transport reduces mitochondrial nutrient overload and allows beta cells to recover from chronic glucose stress. Graphical abstract.
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Affiliation(s)
- Isabelle Chareyron
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefan Christen
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Sofia Moco
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Armand Valsesia
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Steve Lassueur
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Claes B Wollheim
- Department of Cell Physiology and Metabolism, University Medical Center, Geneva, Switzerland
| | - Jaime Santo Domingo
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Andreas Wiederkehr
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland.
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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13
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Macron C, Núñez Galindo A, Cominetti O, Dayon L. A Versatile Workflow for Cerebrospinal Fluid Proteomic Analysis with Mass Spectrometry: A Matter of Choice between Deep Coverage and Sample Throughput. Methods Mol Biol 2020; 2044:129-154. [PMID: 31432411 DOI: 10.1007/978-1-4939-9706-0_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human cerebrospinal fluid (CSF) is a sample of choice in the study of brain disorders. This biological fluid circulates in the brain and the spinal cord and contains tissue-specific proteins, indicative of health and disease conditions. Despite its potential as a valid source of biological markers, CSF remains largely understudied as compared to blood, in particular due to its more invasive way of sampling.Challenges remain when performing proteomic analysis in clinical research studies. State-of-the-art mass spectrometry (MS) enables deep characterization of the human proteome. But some technical limitations are cardinal to be addressed, such as the capacity to routinely analyze large cohorts of samples. Importantly, a trade-off still needs to be made between the proteome coverage depth and the number of measured samples. In this context, we developed a scalable automated proteomic pipeline for the analysis of CSF. Because of its versatility, this workflow can be adapted to accommodate proteome coverage and/or sample throughput. It allows us to prepare and quantitatively analyze hundreds to thousands of CSF samples; it can also allow identification of more than 3000 proteins in a CSF sample when coupled with isoelectric focusing fractionation.In this chapter, we describe an end-to-end pipeline for the proteomic analysis of CSF. The main steps of the sample preparation comprise spiking of a standard, protein digestion, isobaric labeling, and purification; these are performed in a 96-well plate format enabling automation. Depending on the targeted depth of the CSF proteome, optional analytical steps can be included, such as the removal of abundant proteins and sample pre-fractionation. Liquid chromatography tandem MS as well as data processing and analysis complete the pipeline.
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Affiliation(s)
- Charlotte Macron
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
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14
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Macron C, Lavigne R, Núñez Galindo A, Affolter M, Pineau C, Dayon L. Exploration of human cerebrospinal fluid: A large proteome dataset revealed by trapped ion mobility time-of-flight mass spectrometry. Data Brief 2020; 31:105704. [PMID: 32478154 PMCID: PMC7251648 DOI: 10.1016/j.dib.2020.105704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/06/2020] [Indexed: 01/16/2023] Open
Abstract
Cerebrospinal fluid (CSF) is a biofluid in direct contact with the brain and as such constitutes a sample of choice in neurological disorder research, including neurodegenerative diseases such as Alzheimer or Parkinson. Human CSF has still been less studied using proteomic technologies compared to other biological fluids such as blood plasma or serum. In this work, a pool of "normal" human CSF samples was analysed using a shotgun proteomic workflow that combined removal of highly abundant proteins by immunoaffinity depletion and isoelectric focussing fractionation of tryptic peptides to alleviate the complexity of the biofluid. The resulting 24 fractions were analysed using liquid chromatography coupled to a high-resolution and high-accuracy timsTOF Pro mass spectrometer. This state-of-the-art mass spectrometry-based proteomic workflow allowed the identification of 3'174 proteins in CSF. The dataset reported herein completes the pool of the most comprehensive human CSF proteomes obtained so far. An overview of the identified proteins is provided based on gene ontology annotation. Mass and tandem mass spectra are made available as a possible starting point for further studies exploring the human CSF proteome.
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Affiliation(s)
- Charlotte Macron
- Proteomics, Nestlé Institute for Food Safety & Analytical Sciences, Nestlé Research, 1015 Lausanne, Switzerland
| | - Regis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35042 Rennes cedex, France.,Protim, Univ Rennes, F-35042 Rennes, France
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute for Food Safety & Analytical Sciences, Nestlé Research, 1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute for Food Safety & Analytical Sciences, Nestlé Research, 1015 Lausanne, Switzerland
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35042 Rennes cedex, France.,Protim, Univ Rennes, F-35042 Rennes, France
| | - Loïc Dayon
- Proteomics, Nestlé Institute for Food Safety & Analytical Sciences, Nestlé Research, 1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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15
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Abstract
Introduction: Quantitative proteomics using mass spectrometry is performed via label-free or label-based approaches. Labeling strategies rely on the incorporation of stable heavy isotopes by metabolic, enzymatic, or chemical routes. Isobaric labeling uses chemical labels of identical masses but of different fragmentation behaviors to allow the relative quantitative comparison of peptide/protein abundances between biological samples.Areas covered: We have carried out a systematic review on the use of isobaric mass tags in proteomic research since their inception in 2003. We focused on their quantitative performances, their multiplexing evolution, as well as their broad use for relative quantification of proteins in pre-clinical models and clinical studies. Current limitations, primarily linked to the quantitative ratio distortion, as well as state-of-the-art and emerging solutions to improve their quantitative readouts are discussed.Expert opinion: The isobaric mass tag technology offers a unique opportunity to compare multiple protein samples simultaneously, allowing higher sample throughput and internal relative quantification for improved trueness and precision. Large studies can be performed when shared reference samples are introduced in multiple experiments. The technology is well suited for proteome profiling in the context of proteomic discovery studies.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland
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16
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Santo-Domingo J, Dayon L, Wiederkehr A. Protein Lysine Acetylation: Grease or Sand in the Gears of β-Cell Mitochondria? J Mol Biol 2019; 432:1446-1460. [PMID: 31628953 DOI: 10.1016/j.jmb.2019.09.011] [Citation(s) in RCA: 5] [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] [Received: 06/04/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 02/06/2023]
Abstract
Mitochondria carry out many essential functions in metabolism. A central task is the oxidation of nutrients and the generation of ATP by oxidative phosphorylation. Mitochondrial metabolism needs to be tightly regulated for the cell to respond to changes in ATP demand and nutrient supply. Here, we review how protein lysine acetylation contributes to the regulation of mitochondrial metabolism in insulin target tissues and the insulin-secreting pancreatic β-cell. We summarize recent evidence showing that in pancreatic β-cells, lysine acetylation occurs on a large number of proteins involved in metabolism. Furthermore, we give a brief overview of the molecular mechanism that controls lysine acetylation dynamics. We propose that protein lysine acetylation is an important mechanism for the fine-tuning of mitochondrial activity in β-cells during normal physiology. In contrast, nutrient oversupply, oxidative stress, or inhibition of the mitochondrial deacetylase SIRT3 leads to protein lysine hyperacetylation, which impairs mitochondrial function. By perturbing mitochondrial activity in β-cells and insulin target tissues, protein lysine hyperacetylation may contribute to the development of type 2 diabetes.
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Affiliation(s)
- Jaime Santo-Domingo
- Mitochondrial Function, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Andreas Wiederkehr
- Mitochondrial Function, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland.
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17
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Ling Y, Carayol J, Galusca B, Canto C, Montaurier C, Matone A, Vassallo I, Minehira K, Alexandre V, Cominetti O, Núñez Galindo A, Corthésy J, Dayon L, Charpagne A, Métairon S, Raymond F, Descombes P, Casteillo F, Peoc'h M, Palaghiu R, Féasson L, Boirie Y, Estour B, Hager J, Germain N, Gheldof N. Persistent low body weight in humans is associated with higher mitochondrial activity in white adipose tissue. Am J Clin Nutr 2019; 110:605-616. [PMID: 31374571 PMCID: PMC6736451 DOI: 10.1093/ajcn/nqz144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/19/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Constitutional thinness (CT) is a state of low but stable body weight (BMI ≤18 kg/m2). CT subjects have normal-range hormonal profiles and food intake but exhibit resistance to weight gain despite living in the modern world's obesogenic environment. OBJECTIVE The goal of this study is to identify molecular mechanisms underlying this protective phenotype against weight gain. METHODS We conducted a clinical overfeeding study on 30 CT subjects and 30 controls (BMI 20-25 kg/m2) matched for age and sex. We performed clinical and integrative molecular and transcriptomic analyses on white adipose and muscle tissues. RESULTS Our results demonstrate that adipocytes were markedly smaller in CT individuals (mean ± SEM: 2174 ± 142 μm 2) compared with controls (3586 ± 216 μm2) (P < 0.01). The mitochondrial respiratory capacity was higher in CT adipose tissue, particularly at the level of complex II of the electron transport chain (2.2-fold increase; P < 0.01). This higher activity was paralleled by an increase in mitochondrial number (CT compared with control: 784 ± 27 compared with 675 ± 30 mitochondrial DNA molecules per cell; P < 0.05). No evidence for uncoupled respiration or "browning" of the white adipose tissue was found. In accordance with the mitochondrial differences, CT subjects had a distinct adipose transcriptomic profile [62 differentially expressed genes (false discovery rate of 0.1 and log fold change >0.75)], with many differentially expressed genes associating with positive metabolic outcomes. Pathway analyses revealed an increase in fatty acid oxidation ( P = 3 × 10-04) but also triglyceride biosynthesis (P = 3.6 × 10-04). No differential response to the overfeeding was observed in the 2 groups. CONCLUSIONS The distinct molecular signature of the adipose tissue in CT individuals suggests the presence of augm ented futile lipid cycling, rather than mitochondrial uncoupling, as a way to increase energy expenditure in CT individuals. We propose that increased mitochondrial function in adipose tissue is an important mediator in sustaining the low body weight in CT individuals. This knowledge could ultimately allow more targeted approaches for weight management treatment strategies. This trial was registered at clinicaltrials.gov as NCT02004821.
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Affiliation(s)
- Yiin Ling
- Division of Endocrinology, Diabetes, Metabolism, and Eating Disorders, CHU St-Etienne, France,Eating Disorders, Addictions, and Extreme Bodyweight Research Group (TAPE) EA 7423, Jean Monnet University, St-Etienne, France
| | - Jérôme Carayol
- Metabolic Health, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Bogdan Galusca
- Division of Endocrinology, Diabetes, Metabolism, and Eating Disorders, CHU St-Etienne, France,Eating Disorders, Addictions, and Extreme Bodyweight Research Group (TAPE) EA 7423, Jean Monnet University, St-Etienne, France
| | - Carles Canto
- Metabolic Health, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Christophe Montaurier
- Clermont Auvergne University, INRA, Human Nutrition Unit, CHU Clermont-Ferrand, Service de Nutrition Clinique, CRNH Auvergne, Clermont-Ferrand, France
| | - Alice Matone
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Rovereto, Italy
| | - Irene Vassallo
- Precision Medicine Group, Quartz Bio SA, Geneva, Switzerland
| | - Kaori Minehira
- Metabolic Health, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Virginie Alexandre
- Metabolic Health, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | | | - John Corthésy
- Proteomics, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Aline Charpagne
- Genomics, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Sylviane Métairon
- Genomics, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Frédéric Raymond
- Genomics, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Patrick Descombes
- Genomics, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | | | | | | | - Léonard Féasson
- Interuniversity Laboratory of Motricity and Biology (LIBM) EA 7424, Jean Monnet University, St-Etienne, France
| | - Yves Boirie
- Clermont Auvergne University, INRA, Human Nutrition Unit, CHU Clermont-Ferrand, Service de Nutrition Clinique, CRNH Auvergne, Clermont-Ferrand, France
| | - Bruno Estour
- Division of Endocrinology, Diabetes, Metabolism, and Eating Disorders, CHU St-Etienne, France,Eating Disorders, Addictions, and Extreme Bodyweight Research Group (TAPE) EA 7423, Jean Monnet University, St-Etienne, France
| | - Jörg Hager
- Metabolic Health, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Natacha Germain
- Division of Endocrinology, Diabetes, Metabolism, and Eating Disorders, CHU St-Etienne, France,Eating Disorders, Addictions, and Extreme Bodyweight Research Group (TAPE) EA 7423, Jean Monnet University, St-Etienne, France,N Germain (E-mail: )
| | - Nele Gheldof
- Metabolic Health, Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland,Address correspondence to N Gheldof (E-mail: )
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18
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Bruderer R, Muntel J, Müller S, Bernhardt OM, Gandhi T, Cominetti O, Macron C, Carayol J, Rinner O, Astrup A, Saris WHM, Hager J, Valsesia A, Dayon L, Reiter L. Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance. Mol Cell Proteomics 2019; 18:1242-1254. [PMID: 30948622 PMCID: PMC6553938 DOI: 10.1074/mcp.ra118.001288] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/26/2019] [Indexed: 12/14/2022] Open
Abstract
Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform can measure 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1508 samples. Proving the robustness, the complete acquisition was achieved on a single analytical column. Totally, 565 proteins (459 identified with two or more peptide sequences) were profiled with 74% data set completeness. On average 408 proteins (5246 peptides) were identified per acquisition (319 proteins in 90% of all acquisitions). The workflow reproducibility was assessed using 34 quality control pools acquired at regular intervals, resulting in 92% data set completeness with CVs for protein measurements of 10.9%.The profiles of 20 apolipoproteins could be profiled revealing distinct changes. The weight loss and weight maintenance resulted in sustained effects on low-grade inflammation, as well as steroid hormone and lipid metabolism, indicating beneficial effects. Comparison to other large-scale plasma weight loss studies demonstrated high robustness and quality of biomarker candidates identified. Tracking of nonenzymatic glycation indicated a delayed, slight reduction of glycation in the weight maintenance phase. Using stable-isotope-references, we could directly and absolutely quantify 60 proteins in the DIA.In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma.
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Affiliation(s)
| | - Jan Muntel
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | | | | | - Tejas Gandhi
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | | | - Charlotte Macron
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Jérôme Carayol
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Oliver Rinner
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | - Arne Astrup
- ¶Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Wim H M Saris
- ‖NUTRIM, School for Nutrition, Toxicology and Metabolism, Department of Human Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Jörg Hager
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Armand Valsesia
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Lukas Reiter
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland;
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Santo-Domingo J, Galindo AN, Cominetti O, De Marchi U, Cutillas P, Dayon L, Wiederkehr A. Glucose-dependent phosphorylation signaling pathways and crosstalk to mitochondrial respiration in insulin secreting cells. Cell Commun Signal 2019; 17:14. [PMID: 30786936 PMCID: PMC6381748 DOI: 10.1186/s12964-019-0326-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/08/2019] [Indexed: 01/13/2023] Open
Abstract
Background Glucose is the main secretagogue of pancreatic beta-cells. Uptake and metabolism of the nutrient stimulates the beta-cell to release the blood glucose lowering hormone insulin. This metabolic activation is associated with a pronounced increase in mitochondrial respiration. Glucose stimulation also initiates a number of signal transduction pathways for the coordinated regulation of multiple biological processes required for insulin secretion. Methods Shotgun proteomics including TiO2 enrichment of phosphorylated peptides followed by liquid chromatography tandem mass spectrometry on lysates from glucose-stimulated INS-1E cells was used to identify glucose regulated phosphorylated proteins and signal transduction pathways. Kinase substrate enrichment analysis (KSEA) was applied to identify key regulated kinases and phosphatases. Glucose-induced oxygen consumption was measured using a XF96 Seahorse instrument to reveal cross talk between glucose-regulated kinases and mitochondrial activation. Results Our kinetic analysis of substrate phosphorylation reveal the molecular mechanism leading to rapid activation of insulin biogenesis, vesicle trafficking, insulin granule exocytosis and cytoskeleton remodeling. Kinase-substrate enrichment identified upstream kinases and phosphatases and time-dependent activity changes during glucose stimulation. Activity trajectories of well-known glucose-regulated kinases and phosphatases are described. In addition, we predict activity changes in a number of kinases including NUAK1, not or only poorly studied in the context of the pancreatic beta-cell. Furthermore, we pharmacologically tested whether signaling pathways predicted by kinase-substrate enrichment analysis affected glucose-dependent acceleration of mitochondrial respiration. We find that phosphoinositide 3-kinase, Ca2+/calmodulin dependent protein kinase and protein kinase C contribute to short-term regulation of energy metabolism. Conclusions Our results provide a global view into the regulation of kinases and phosphatases in insulin secreting cells and suggest cross talk between glucose-induced signal transduction and mitochondrial activation. Electronic supplementary material The online version of this article (10.1186/s12964-019-0326-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaime Santo-Domingo
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park Bâtiment G, 1015, Lausanne, Switzerland.
| | - Antonio Núñez Galindo
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park Bâtiment G, 1015, Lausanne, Switzerland
| | - Ornella Cominetti
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park Bâtiment G, 1015, Lausanne, Switzerland
| | - Umberto De Marchi
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park Bâtiment G, 1015, Lausanne, Switzerland
| | - Pedro Cutillas
- Analytical Signalling Group, Centre for Cell Signalling, Queen Mary University of London, London, UK
| | - Loïc Dayon
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park Bâtiment G, 1015, Lausanne, Switzerland
| | - Andreas Wiederkehr
- Nestlé Institute of Health Sciences, Nestlé Research, EPFL Innovation Park Bâtiment G, 1015, Lausanne, Switzerland
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Dayon L, Cominetti O, Wojcik J, Galindo AN, Oikonomidi A, Henry H, Migliavacca E, Kussmann M, Bowman GL, Popp J. Proteomes of Paired Human Cerebrospinal Fluid and Plasma: Relation to Blood–Brain Barrier Permeability in Older Adults. J Proteome Res 2019; 18:1162-1174. [DOI: 10.1021/acs.jproteome.8b00809] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | | | | | | | | | - Hugues Henry
- Department of Laboratories, CHUV, 1011 Lausanne, Switzerland
| | | | - Martin Kussmann
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV, 1011 Lausanne, Switzerland
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, HUG, 1226 Geneva, Switzerland
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21
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De Marchi U, Galindo AN, Thevenet J, Hermant A, Bermont F, Lassueur S, Domingo JS, Kussmann M, Dayon L, Wiederkehr A. Mitochondrial lysine deacetylation promotes energy metabolism and calcium signaling in insulin-secreting cells. FASEB J 2018; 33:4660-4674. [PMID: 30589571 DOI: 10.1096/fj.201801424r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In pancreatic β-cells, mitochondria generate signals that promote insulin granule exocytosis. Here we study how lysine acetylation of mitochondrial proteins mechanistically affects metabolism-secretion coupling in insulin-secreting cells. Using mass spectrometry-based proteomics, we identified lysine acetylation sites in rat insulinoma cell line clone 1E cells. In cells lacking the mitochondrial lysine deacetylase sirtuin-3 (SIRT3), several matrix proteins are hyperacetylated. Disruption of the SIRT3 gene has a deleterious effect on mitochondrial energy metabolism and Ca2+ signaling. Under resting conditions, SIRT3 deficient cells are overactivated, which elevates the respiratory rate and enhances calcium signaling and basal insulin secretion. In response to glucose, the SIRT3 knockout cells are unable to mount a sustained cytosolic ATP response. Calcium signaling is strongly reduced and the respiratory response as well as insulin secretion are blunted. We propose mitochondrial protein lysine acetylation as a control mechanism in β-cell energy metabolism and Ca2+ signaling.-De Marchi, U., Galindo, A. N., Thevenet, J., Hermant, A., Bermont, F., Lassueur, S., Domingo, J. S., Kussmann, M., Dayon, L., Wiederkehr, A. Mitochondrial lysine deacetylation promotes energy metabolism and calcium signaling in insulin-secreting cells.
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Affiliation(s)
- Umberto De Marchi
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Jonathan Thevenet
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Aurélie Hermant
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Flavien Bermont
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Steve Lassueur
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Jaime Santo Domingo
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Martin Kussmann
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland; and
| | - Andreas Wiederkehr
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
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22
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Cominetti O, Núñez Galindo A, Corthésy J, Valsesia A, Irincheeva I, Kussmann M, Saris WHM, Astrup A, McPherson R, Harper ME, Dent R, Hager J, Dayon L. Obesity shows preserved plasma proteome in large independent clinical cohorts. Sci Rep 2018; 8:16981. [PMID: 30451909 PMCID: PMC6242904 DOI: 10.1038/s41598-018-35321-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/02/2018] [Indexed: 12/21/2022] Open
Abstract
Holistic human proteome maps are expected to complement comprehensive profile assessment of health and disease phenotypes. However, methodologies to analyze proteomes in human tissue or body fluid samples at relevant scale and performance are still limited in clinical research. Their deployment and demonstration in large enough human populations are even sparser. In the present study, we have characterized and compared the plasma proteomes of two large independent cohorts of obese and overweight individuals using shotgun mass spectrometry (MS)-based proteomics. Herein, we showed, in both populations from different continents of about 500 individuals each, the concordance of plasma protein MS measurements in terms of variability, gender-specificity, and age-relationship. Additionally, we replicated several known and new associations between proteins, clinical and molecular variables, such as insulin and glucose concentrations. In conclusion, our MS-based analyses of plasma samples from independent human cohorts proved the practical feasibility and efficiency of a large and unified discovery/replication approach in proteomics, which was also recently coined “rectangular” design.
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Affiliation(s)
- Ornella Cominetti
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - John Corthésy
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,Nutrition Analytics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Armand Valsesia
- Nutrition and Metabolic Health, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Irina Irincheeva
- Nutrition and Metabolic Health, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,Clinical Trial Unit, University of Bern, Bern, Switzerland
| | - Martin Kussmann
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,The Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Wim H M Saris
- NUTRIM, School for Nutrition, Toxicology and Metabolism, Department of Human Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Arne Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Robert Dent
- Ottawa Hospital Weight Management Clinic, The Ottawa Hospital, Ottawa, Canada
| | - Jörg Hager
- Nutrition and Metabolic Health, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland.
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Macron C, Lane L, Núñez Galindo A, Dayon L. Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification. J Proteome Res 2018; 17:4113-4126. [PMID: 30124047 DOI: 10.1021/acs.jproteome.8b00300] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cerebrospinal fluid (CSF) is a body fluid of choice for biomarker studies of brain disorders but remains relatively under-studied compared with other biological fluids such as plasma, partly due to the more invasive means of its sample collection. The present study establishes an in-depth CSF proteome through the analysis of a unique CSF sample from a pool of donors. After immunoaffinity depletion, the CSF sample was fractionated using off-gel electrophoresis and analyzed with liquid chromatography tandem mass spectrometry (MS) using the latest generation of hybrid Orbitrap mass spectrometers. The shotgun proteomic analysis allowed the identification of 20 689 peptides mapping on 3379 proteins. To the best of our knowledge, the obtained data set constitutes the largest CSF proteome published so far. Among the CSF proteins identified, 34% correspond to genes whose transcripts are highly expressed in brain according to the Human Protein Atlas. The principal Alzheimer's disease biomarkers (e.g., tau protein, amyloid-β, apolipoprotein E, and neurogranin) were detected. Importantly, our data set significantly contributes to the Chromosome-centric Human Proteome Project (C-HPP), and 12 proteins considered as missing are proposed for validation in accordance with the HPP guidelines. Of these 12 proteins, 8 proteins are based on 2 to 6 uniquely mapping peptides from this CSF analysis, and 4 match a new peptide with a "stranded" single peptide in PeptideAtlas from previous CSF studies. The MS proteomic data are available to the ProteomeXchange Consortium ( http://www.proteomexchange.org/ ) with the data set identifier PXD009646.
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Affiliation(s)
- Charlotte Macron
- Proteomics , Nestlé Institute of Health Sciences , 1015 Lausanne , Switzerland
| | - Lydie Lane
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics , CMU, rue Michel-Servet 1 , 1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , rue Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| | | | - Loïc Dayon
- Proteomics , Nestlé Institute of Health Sciences , 1015 Lausanne , Switzerland
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24
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Affiliation(s)
- Charlotte Macron
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Lydie Lane
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU, rue Michel-Servet 1, 1211 Geneva 4, Switzerland
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | | | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
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25
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Bowman GL, Dayon L, Kirkland R, Wojcik J, Peyratout G, Severin IC, Henry H, Oikonomidi A, Migliavacca E, Bacher M, Popp J. Blood‐brain barrier breakdown, neuroinflammation, and cognitive decline in older adults. Alzheimers Dement 2018; 14:1640-1650. [DOI: 10.1016/j.jalz.2018.06.2857] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/22/2018] [Accepted: 06/15/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Gene L. Bowman
- Nestlé Institute of Health SciencesEPFL CampusLausanneSwitzerland
| | - Loïc Dayon
- Nestlé Institute of Health SciencesEPFL CampusLausanneSwitzerland
| | | | | | - Gwendoline Peyratout
- Old Age PsychiatryDepartment of PsychiatryUniversity Hospital of LausanneLausanneSwitzerland
| | - India C. Severin
- Nestlé Institute of Health SciencesEPFL CampusLausanneSwitzerland
| | - Hugues Henry
- CHUVDepartment of LaboratoriesLausanneSwitzerland
| | - Aikaterini Oikonomidi
- Old Age PsychiatryDepartment of PsychiatryUniversity Hospital of LausanneLausanneSwitzerland
| | | | - Michael Bacher
- Philipps University of MarburgInstitute of ImmunologyMarburgGermany
| | - Julius Popp
- Old Age PsychiatryDepartment of PsychiatryUniversity Hospital of LausanneLausanneSwitzerland
- Geriatric PsychiatryDepartment of Mental Health and PsychiatryUniversity Hospitals of GenevaGenevaSwitzerland
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26
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Méhul B, Perrin A, Grisendi K, Galindo AN, Dayon L, Ménigot C, Rival Y, Voegel JJ. Mass spectrometry and DigiWest technology emphasize protein acetylation profile from Quisinostat-treated HuT78 CTCL cell line. J Proteomics 2018; 187:126-143. [PMID: 30012418 DOI: 10.1016/j.jprot.2018.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/20/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023]
Abstract
Histone deacetylases (HDACs) are key enzymes involved in epigenetic modulation and were targeted by HDAC inhibitors (HDACis) for cancer treatment. The action of HDACis is not restricted to histones and also prevents deacetylation of other proteins, supporting their wide biological actions. The HuT78 cell line is recognized as a key tool to support and understand cutaneous T-cell lymphoma (CTCL) biology and was used as a predictive model since HDACi such as Vorinostat and Panobinostat have both demonstrated apoptotic activities in HuT78 cells and in primary blood CTCL cells. In this study, Quisinostat (JNJ-26481585) a novel second-generation HDACi with highest potency for HDAC1, was tested on HuT78 cell line. Quantitative mass spectrometry (MS)-based proteomics after acetylated-lysine peptide enrichment and a targeted antibody-based immunoassay (DigiWest) were used as complementary technologies to assess the modifications of the acetylated proteome. As expected, several acetylated lysines of histones were increased by the HDACi. Additional acetylated non-histone proteins were modulated after treatment with Quisinostat including the nucleolin (a major nucleolar protein), the replication protein A 70 kDa DNA-binding subunit, the phosphoglycerate kinase 1, the stress-70 protein, the proto-oncogene Myc and the serine hydroxymethyltransferase. A better knowledge of histone and non-histone acetylated protein profile after Quisinostat treatment can strongly support the understanding of non-clinical and clinical results of this HDACi. These technological tools can also help in designing new HDACis in a pharmaceutical drug discovery program. SIGNIFICANCE A better knowledge of histone and non-histone acetylated protein profile after HDAC inhibitors (HDACis) treatment can strongly support the understanding of non-clinical and clinical investigations in a pharmaceutical drug discovery program. Relative quantification using mass spectrometry -based proteomics after acetylated-lysine peptide enrichment and a targeted antibody-based immunoassay (DigiWest) are proposed as complementary technologies to assess the modifications of the acetylated proteome. Quisinostat (JNJ-26481585) a novel second-generation HDACi with highest potency for HDAC1 was better characterized in vitro in HuT78 cells to support and understand cutaneous T-cell lymphoma (CTCL) therapeutic research program.
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Affiliation(s)
- Bruno Méhul
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France.
| | - Agnes Perrin
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | - Karine Grisendi
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | | | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Corinne Ménigot
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | - Yves Rival
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | - Johannes J Voegel
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
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27
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Dayon L, Núñez Galindo A, Wojcik J, Cominetti O, Corthésy J, Oikonomidi A, Henry H, Kussmann M, Migliavacca E, Severin I, Bowman GL, Popp J. Alzheimer disease pathology and the cerebrospinal fluid proteome. Alzheimers Res Ther 2018; 10:66. [PMID: 30021611 PMCID: PMC6052524 DOI: 10.1186/s13195-018-0397-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/11/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Altered proteome profiles have been reported in both postmortem brain tissues and body fluids of subjects with Alzheimer disease (AD), but their broad relationships with AD pathology, amyloid pathology, and tau-related neurodegeneration have not yet been fully explored. Using a robust automated MS-based proteomic biomarker discovery workflow, we measured cerebrospinal fluid (CSF) proteomes to explore their association with well-established markers of core AD pathology. METHODS Cross-sectional analysis was performed on CSF collected from 120 older community-dwelling adults with normal (n = 48) or impaired cognition (n = 72). LC-MS quantified hundreds of proteins in the CSF. CSF concentrations of β-amyloid 1-42 (Aβ1-42), tau, and tau phosphorylated at threonine 181 (P-tau181) were determined with immunoassays. First, we explored proteins relevant to biomarker-defined AD. Then, correlation analysis of CSF proteins with CSF markers of amyloid pathology, neuronal injury, and tau hyperphosphorylation (i.e., Aβ1-42, tau, P-tau181) was performed using Pearson's correlation coefficient and Bonferroni correction for multiple comparisons. RESULTS We quantified 790 proteins in CSF samples with MS. Four CSF proteins showed an association with CSF Aβ1-42 levels (p value ≤ 0.05 with correlation coefficient (R) ≥ 0.38). We identified 50 additional CSF proteins associated with CSF tau and 46 proteins associated with CSF P-tau181 (p value ≤ 0.05 with R ≥ 0.37). The majority of those proteins that showed such associations were brain-enriched proteins. Gene Ontology annotation revealed an enrichment for synaptic proteins and proteins originating from reelin-producing cells and the myelin sheath. CONCLUSIONS We used an MS-based proteomic workflow to profile the CSF proteome in relation to cerebral AD pathology. We report strong evidence of previously reported CSF proteins and several novel CSF proteins specifically associated with amyloid pathology or neuronal injury and tau hyperphosphorylation.
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Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | | | | | - John Corthésy
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Hugues Henry
- Department of Laboratories, CHUV, Lausanne, Switzerland
| | - Martin Kussmann
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Present address: Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - India Severin
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV, Lausanne, Switzerland
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, HUG, Geneva, Switzerland
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Haller C, Chaskar P, Piccand J, Cominetti O, Macron C, Dayon L, Kraus MRC. Insights into Islet Differentiation and Maturation through Proteomic Characterization of a Human iPSC-Derived Pancreatic Endocrine Model. Proteomics Clin Appl 2018; 12:e1600173. [PMID: 29578310 DOI: 10.1002/prca.201600173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 02/09/2018] [Indexed: 12/16/2022]
Abstract
PURPOSE Great progresses have been made for generating in vitro pluripotent stem cell pancreatic β-like cells. However, the maturation stage of the cells still requires in vivo maturation to recreate the environmental niche. A deeper understanding of the factors promoting maturation of the cells is of great interest for clinical applications. EXPERIMENTAL DESIGN Label-free mass spectrometry based proteomic analysis is performed on samples from a longitudinal study of differentiation of human induced pluripotent stem cells toward glucose responsive insulin producing cells. RESULTS Proteome patterns correlate with specific transcription factor gene expression levels during in vitro differentiation, showing the relevance of the technology for identification of pancreatic-specific markers. The analysis of proteomes of the implanted cells in a longitudinal study shows that the neovascularization process linked to the extracellular matrix environment is time-dependent and conditions the proper maturation of the cells in β-like cells secreting insulin in response to glucose. CONCLUSIONS AND CLINICAL RELEVANCE Proteomic profiling is valuable to qualify and better understand in vivo maturation of progenitor cells toward β-cells. This is critical for future clinical trials where in vivo maturation still needs to be improved for robustness and effectiveness of cell therapy. Novel biomarkers for predicting the efficiency of maturation represents noninvasive monitoring tools for following efficiency of the implant.
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Affiliation(s)
- Corinne Haller
- Stem Cells, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Prasad Chaskar
- Stem Cells, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Julie Piccand
- Stem Cells, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Charlotte Macron
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Marine R-C Kraus
- Stem Cells, Nestlé Institute of Health Sciences, Lausanne, Switzerland
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29
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Corthésy J, Theofilatos K, Mavroudi S, Macron C, Cominetti O, Remlawi M, Ferraro F, Núñez Galindo A, Kussmann M, Likothanassis S, Dayon L. An Adaptive Pipeline To Maximize Isobaric Tagging Data in Large-Scale MS-Based Proteomics. J Proteome Res 2018; 17:2165-2173. [DOI: 10.1021/acs.jproteome.8b00110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John Corthésy
- Nestlé Institute of Health Sciences, Lausanne 1015, Switzerland
| | | | - Seferina Mavroudi
- InSybio, Ltd., Innovations House, 19 Staple Gardens, Winchester SO238SR, United Kingdom
- Department of Social Work, School of Sciences of Health and Care, Technological Educational Institute of Western Greece, Patras 26334, Greece
| | | | | | - Mona Remlawi
- Nestlé Institute of Health Sciences, Lausanne 1015, Switzerland
| | | | | | - Martin Kussmann
- Nestlé Institute of Health Sciences, Lausanne 1015, Switzerland
| | - Spiridon Likothanassis
- InSybio, Ltd., Innovations House, 19 Staple Gardens, Winchester SO238SR, United Kingdom
- Department of Computer Engineering and Informatics, University of Patras, Patras 26500, Greece
| | - Loïc Dayon
- Nestlé Institute of Health Sciences, Lausanne 1015, Switzerland
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30
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Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L. Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics. J Proteome Res 2018; 17:1426-1435. [DOI: 10.1021/acs.jproteome.7b00788] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiayi Lan
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | | | - James Doecke
- CSIRO Health and Biosecurity/Australian E-Health Research Centre, Brisbane, Queensland 4029, Australia
| | - Christopher Fowler
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ralph N. Martins
- Centre of Excellence for Alzheimer’s Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
- Department of Biomedical Sciences, Macquarie University, North Ryde, New South Wales 2109, Australia
| | - Stephanie R. Rainey-Smith
- Centre of Excellence for Alzheimer’s Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
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31
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Oller Moreno S, Cominetti O, Núñez Galindo A, Irincheeva I, Corthésy J, Astrup A, Saris WH, Hager J, Kussmann M, Dayon L. Front Cover: The differential plasma proteome of obese and overweight individuals undergoing a nutritional weight loss and maintenance intervention. Proteomics Clin Appl 2018. [DOI: 10.1002/prca.201870001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Turku Finland
| | - Domitille Schvartz
- Human Protein Sciences Department; Centre Medical Universitaire; University of Geneva; Geneva, Switzerland
| | - David R. Goodlett
- Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Turku Finland
- Department of Pharmaceutical Sciences; University of Maryland; Baltimore MD USA
| | - Loïc Dayon
- Nestlé Institute of Health Sciences; EPFL Innovation Park; Lausanne Switzerland
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Dayon L, Wojcik J, Núñez Galindo A, Corthésy J, Cominetti O, Oikonomidi A, Henry H, Migliavacca E, Bowman GL, Popp J. Plasma Proteomic Profiles of Cerebrospinal Fluid-Defined Alzheimer’s Disease Pathology in Older Adults. J Alzheimers Dis 2017; 60:1641-1652. [DOI: 10.3233/jad-170426] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | | | - John Corthésy
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | | | - Hugues Henry
- CHUV, Department of Laboratories, Lausanne, Switzerland
| | | | - Gene L. Bowman
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Julius Popp
- CHUV, Old Age Psychiatry, Department of Psychiatry, Lausanne, Switzerland
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Mauvoisin D, Atger F, Dayon L, Núñez Galindo A, Wang J, Martin E, Da Silva L, Montoliu I, Collino S, Martin FP, Ratajczak J, Cantó C, Kussmann M, Naef F, Gachon F. Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome. Cell Rep 2017; 20:1729-1743. [PMID: 28813682 PMCID: PMC5568034 DOI: 10.1016/j.celrep.2017.07.065] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/12/2017] [Accepted: 07/24/2017] [Indexed: 12/24/2022] Open
Abstract
Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is therefore highly relevant in the context of circadian biology, but its characterization on the proteome-wide scale and its circadian clock dependence are still poorly described. Here, we provide a comprehensive and rhythmic acetylome map of the mouse liver. Rhythmic acetylated proteins showed subcellular localization-specific phases that correlated with the related metabolites in the regulated pathways. Mitochondrial proteins were over-represented among the rhythmically acetylated proteins and were highly correlated with SIRT3-dependent deacetylation. SIRT3 activity being nicotinamide adenine dinucleotide (NAD)+ level-dependent, we show that NAD+ is orchestrated by both feeding rhythms and the circadian clock through the NAD+ salvage pathway but also via the nicotinamide riboside pathway. Hence, the diurnal acetylome relies on a functional circadian clock and affects important diurnal metabolic pathways in the mouse liver.
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Affiliation(s)
- Daniel Mauvoisin
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Florian Atger
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; Department of Pharmacology and Toxicology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Jingkui Wang
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Eva Martin
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Laetitia Da Silva
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Ivan Montoliu
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Sebastiano Collino
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Francois-Pierre Martin
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Joanna Ratajczak
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Carles Cantó
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Martin Kussmann
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Frédéric Gachon
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland.
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Dayon L, Guiraud SP, Corthésy J, Da Silva L, Migliavacca E, Tautvydaitė D, Oikonomidi A, Moullet B, Henry H, Métairon S, Marquis J, Descombes P, Collino S, Martin FPJ, Montoliu I, Kussmann M, Wojcik J, Bowman GL, Popp J. One-carbon metabolism, cognitive impairment and CSF measures of Alzheimer pathology: homocysteine and beyond. Alzheimers Res Ther 2017. [PMID: 28623948 PMCID: PMC5473969 DOI: 10.1186/s13195-017-0270-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Hyperhomocysteinemia is a risk factor for cognitive decline and dementia, including Alzheimer disease (AD). Homocysteine (Hcy) is a sulfur-containing amino acid and metabolite of the methionine pathway. The interrelated methionine, purine, and thymidylate cycles constitute the one-carbon metabolism that plays a critical role in the synthesis of DNA, neurotransmitters, phospholipids, and myelin. In this study, we tested the hypothesis that one-carbon metabolites beyond Hcy are relevant to cognitive function and cerebrospinal fluid (CSF) measures of AD pathology in older adults. Methods Cross-sectional analysis was performed on matched CSF and plasma collected from 120 older community-dwelling adults with (n = 72) or without (n = 48) cognitive impairment. Liquid chromatography-mass spectrometry was performed to quantify one-carbon metabolites and their cofactors. Least absolute shrinkage and selection operator (LASSO) regression was initially applied to clinical and biomarker measures that generate the highest diagnostic accuracy of a priori-defined cognitive impairment (Clinical Dementia Rating-based) and AD pathology (i.e., CSF tau phosphorylated at threonine 181 [p-tau181]/β-Amyloid 1–42 peptide chain [Aβ1–42] >0.0779) to establish a reference benchmark. Two other LASSO-determined models were generated that included the one-carbon metabolites in CSF and then plasma. Correlations of CSF and plasma one-carbon metabolites with CSF amyloid and tau were explored. LASSO-determined models were stratified by apolipoprotein E (APOE) ε4 carrier status. Results The diagnostic accuracy of cognitive impairment for the reference model was 80.8% and included age, years of education, Aβ1–42, tau, and p-tau181. A model including CSF cystathionine, methionine, S-adenosyl-L-homocysteine (SAH), S-adenosylmethionine (SAM), serine, cysteine, and 5-methyltetrahydrofolate (5-MTHF) improved the diagnostic accuracy to 87.4%. A second model derived from plasma included cystathionine, glycine, methionine, SAH, SAM, serine, cysteine, and Hcy and reached a diagnostic accuracy of 87.5%. CSF SAH and 5-MTHF were associated with CSF tau and p-tau181. Plasma one-carbon metabolites were able to diagnose subjects with a positive CSF profile of AD pathology in APOE ε4 carriers. Conclusions We observed significant improvements in the prediction of cognitive impairment by adding one-carbon metabolites. This is partially explained by associations with CSF tau and p-tau181, suggesting a role for one-carbon metabolism in the aggregation of tau and neuronal injury. These metabolites may be particularly critical in APOE ε4 carriers. Electronic supplementary material The online version of this article (doi:10.1186/s13195-017-0270-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland.
| | - Seu Ping Guiraud
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - John Corthésy
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Laeticia Da Silva
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Eugenia Migliavacca
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Domilė Tautvydaitė
- Old Age Psychiatry, Department of Psychiatry, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Aikaterini Oikonomidi
- Old Age Psychiatry, Department of Psychiatry, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Barbara Moullet
- Old Age Psychiatry, Department of Psychiatry, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Hugues Henry
- Department of Laboratories, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Sylviane Métairon
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Julien Marquis
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Patrick Descombes
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Sebastiano Collino
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - François-Pierre J Martin
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Ivan Montoliu
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Martin Kussmann
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland.,Present address: Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Gene L Bowman
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne (EPFL) Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
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Oller Moreno S, Cominetti O, Núñez Galindo A, Irincheeva I, Corthésy J, Astrup A, Saris WHM, Hager J, Kussmann M, Dayon L. The differential plasma proteome of obese and overweight individuals undergoing a nutritional weight loss and maintenance intervention. Proteomics Clin Appl 2017; 12. [PMID: 28371297 DOI: 10.1002/prca.201600150] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/01/2017] [Accepted: 03/27/2017] [Indexed: 01/24/2023]
Abstract
PURPOSE The nutritional intervention program "DiOGenes" focuses on how obesity can be prevented and treated from a dietary perspective. We generated differential plasma proteome profiles in the DiOGenes cohort to identify proteins associated with weight loss and maintenance and explore their relation to body mass index, fat mass, insulin resistance, and sensitivity. EXPERIMENTAL DESIGN Relative protein quantification was obtained at baseline and after combined weight loss/maintenance phases using isobaric tagging and MS/MS. A Welch t-test determined proteins differentially present after intervention. Protein relationships with clinical variables were explored using univariate linear models, considering collection center, gender and age as confounding factors. RESULTS Four hundred and seventy three subjects were measured at baseline and end of the intervention; 39 proteins were longitudinally differential. Proteins with largest changes were sex hormone-binding globulin, adiponectin, C-reactive protein, calprotectin, serum amyloid A, and proteoglycan 4 (PRG4), whose association with obesity and weight loss is known. We identified new putative biomarkers for weight loss/maintenance. Correlation between PRG4 and proline-rich acidic protein 1 variation and Matsuda insulin sensitivity increment was showed. CONCLUSION AND CLINICAL RELEVANCE MS-based proteomic analysis of a large cohort of non-diabetic overweight and obese individuals concomitantly identified known and novel proteins associated with weight loss and maintenance.
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Affiliation(s)
- Sergio Oller Moreno
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia, Barcelona, Spain
| | - Ornella Cominetti
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Irina Irincheeva
- Nutrition and Metabolic Health, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - John Corthésy
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Arne Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Wim H M Saris
- Department of Human Biology, NUTRIM, School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jörg Hager
- Nutrition and Metabolic Health, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Martin Kussmann
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Loïc Dayon
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
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37
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Konz T, Migliavacca E, Dayon L, Bowman G, Oikonomidi A, Popp J, Rezzi S. ICP-MS/MS-Based Ionomics: A Validated Methodology to Investigate the Biological Variability of the Human Ionome. J Proteome Res 2017; 16:2080-2090. [PMID: 28383921 DOI: 10.1021/acs.jproteome.7b00055] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We here describe the development, validation and application of a quantitative methodology for the simultaneous determination of 29 elements in human serum using state-of-the-art inductively coupled plasma triple quadrupole mass spectrometry (ICP-MS/MS). This new methodology offers high-throughput elemental profiling using simple dilution of minimal quantity of serum samples. We report the outcomes of the validation procedure including limits of detection/quantification, linearity of calibration curves, precision, recovery and measurement uncertainty. ICP-MS/MS-based ionomics was used to analyze human serum of 120 older adults. Following a metabolomic data mining approach, the generated ionome profiles were subjected to principal component analysis revealing gender and age-specific differences. The ionome of female individuals was marked by higher levels of calcium, phosphorus, copper and copper to zinc ratio, while iron concentration was lower with respect to male subjects. Age was associated with lower concentrations of zinc. These findings were complemented with additional readouts to interpret micronutrient status including ceruloplasmin, ferritin and inorganic phosphate. Our data supports a gender-specific compartmentalization of the ionome that may reflect different bone remodelling in female individuals. Our ICP-MS/MS methodology enriches the panel of validated "Omics" approaches to study molecular relationships between the exposome and the ionome in relation with nutrition and health.
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Affiliation(s)
- Tobias Konz
- Nestlé Institute of Health Sciences , 1015 Lausanne, Switzerland
| | | | - Loïc Dayon
- Nestlé Institute of Health Sciences , 1015 Lausanne, Switzerland
| | - Gene Bowman
- Nestlé Institute of Health Sciences , 1015 Lausanne, Switzerland
| | | | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV , 1011 Lausanne, Switzerland.,Leenaards Memory Center, Department of Clinical Neurosciences, CHUV , 1011 Lausanne, Switzerland
| | - Serge Rezzi
- Nestlé Institute of Health Sciences , 1015 Lausanne, Switzerland
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38
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Wang J, Mauvoisin D, Martin E, Atger F, Galindo AN, Dayon L, Sizzano F, Palini A, Kussmann M, Waridel P, Quadroni M, Dulić V, Naef F, Gachon F. Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver. Cell Metab 2017; 25:102-117. [PMID: 27818260 PMCID: PMC5241201 DOI: 10.1016/j.cmet.2016.10.003] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/25/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022]
Abstract
Diurnal oscillations of gene expression controlled by the circadian clock and its connected feeding rhythm enable organisms to coordinate their physiologies with daily environmental cycles. While available techniques yielded crucial insights into regulation at the transcriptional level, much less is known about temporally controlled functions within the nucleus and their regulation at the protein level. Here, we quantified the temporal nuclear accumulation of proteins and phosphoproteins from mouse liver by SILAC proteomics. We identified around 5,000 nuclear proteins, over 500 of which showed a diurnal accumulation. Parallel analysis of the nuclear phosphoproteome enabled the inference of the temporal activity of kinases accounting for rhythmic phosphorylation. Many identified rhythmic proteins were parts of nuclear complexes involved in transcriptional regulation, ribosome biogenesis, DNA repair, and the cell cycle and its potentially associated diurnal rhythm of hepatocyte polyploidy. Taken together, these findings provide unprecedented insights into the diurnal regulatory landscape of the mouse liver nucleus.
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Affiliation(s)
- Jingkui Wang
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Daniel Mauvoisin
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Eva Martin
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Florian Atger
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland; Department of Pharmacology and Toxicology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Systems Nutrition, Metabonomics, and Proteomics, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Loïc Dayon
- Systems Nutrition, Metabonomics, and Proteomics, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Federico Sizzano
- Department of Cell Biology, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Alessio Palini
- Department of Cell Biology, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Martin Kussmann
- Systems Nutrition, Metabonomics, and Proteomics, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Vjekoslav Dulić
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, 34090 Montpellier, France
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Frédéric Gachon
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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Dayon L, Núñez Galindo A, Cominetti O, Corthésy J, Kussmann M. A Highly Automated Shotgun Proteomic Workflow: Clinical Scale and Robustness for Biomarker Discovery in Blood. Methods Mol Biol 2017; 1619:433-449. [PMID: 28674902 DOI: 10.1007/978-1-4939-7057-5_30] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
With recent technological developments, protein biomarker discoveries directly from blood have regained interest due to elevated feasibility. Mass spectrometry (MS)-based proteomics can now characterize human plasma proteomes to a greater extent than has ever been possible before. Such deep proteome coverage comes, however, with important limitations in terms of analysis time which is a critical factor in the case of clinical studies. As a consequence, compromises still need to be made to balance the proteome coverage with realistic analysis time frame in clinical research. The analysis of a sufficient number of samples is compulsory to empower statistically robust candidate biomarker findings. We have, therefore, recently developed a scalable automated proteomic pipeline (ASAP2) to enable the proteomic analysis of large numbers of plasma and cerebrospinal fluid (CSF) samples, from dozens to a thousand of samples, with the latter number being currently processed in 15 weeks. A distinct characteristic of ASAP2 relies on the possibility to prepare samples in a highly automated way, mostly using 96-well plates. We describe herein a sample preparation procedure for human plasma that includes internal standard spiking, abundant protein removal, buffer exchange, reduction, alkylation, tryptic digestion, isobaric labeling, pooling, and sample purification. Other key elements of the pipeline (i.e., study design, sample tracking, liquid chromatography (LC) tandem MS (MS/MS), data processing, and data analysis) are also highlighted.
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Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences SA, EPFL Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland.
| | - Antonio Núñez Galindo
- Nestlé Institute of Health Sciences SA, EPFL Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Ornella Cominetti
- Nestlé Institute of Health Sciences SA, EPFL Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - John Corthésy
- Nestlé Institute of Health Sciences SA, EPFL Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
| | - Martin Kussmann
- Nestlé Institute of Health Sciences SA, EPFL Innovation Park, Bâtiment H, 1015, Lausanne, Switzerland
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Santo-Domingo J, Chareyron I, Dayon L, Núñez Galindo A, Cominetti O, Pilar Giner Giménez M, De Marchi U, Canto C, Kussmann M, Wiederkehr A. Coordinated activation of mitochondrial respiration and exocytosis mediated by PKC signaling in pancreatic β cells. FASEB J 2016; 31:1028-1045. [PMID: 27927723 DOI: 10.1096/fj.201600837r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/22/2016] [Indexed: 12/17/2022]
Abstract
Mitochondria play a central role in pancreatic β-cell nutrient sensing by coupling their metabolism to plasma membrane excitability and insulin granule exocytosis. Whether non-nutrient secretagogues stimulate mitochondria as part of the molecular mechanism to promote insulin secretion is not known. Here, we show that PKC signaling, which is employed by many non-nutrient secretagogues, augments mitochondrial respiration in INS-1E (rat insulinoma cell line clone 1E) and human pancreatic β cells. The phorbol ester, phorbol 12-myristate 13-acetate, accelerates mitochondrial respiration at both resting and stimulatory glucose concentrations. A range of inhibitors of novel PKC isoforms prevent phorbol ester-induced respiration. Respiratory response was blocked by oligomycin that demonstrated PKC-dependent acceleration of mitochondrial ATP synthesis. Enhanced respiration was observed even when glycolysis was bypassed or fatty acid transport was blocked, which suggested that PKC regulates mitochondrial processes rather than upstream catabolic fluxes. A phosphoproteome study of phorbol ester-stimulated INS-1E cells maintained under resting (2.5 mM) glucose revealed a large number of phosphorylation sites that were altered during short-term activation of PKC signaling. The data set was enriched for proteins that are involved in gene expression, cytoskeleton remodeling, secretory vesicle transport, and exocytosis. Interactome analysis identified PKC, C-Raf, and ERK1/2 as the central phosphointeraction cluster. Prevention of ERK1/2 signaling by using a MEK1 inhibitor caused a marked decreased in phorbol 12-myristate 13-acetate-induced mitochondrial respiration. ERK1/2 signaling module therefore links PKC activation to downstream mitochondrial activation. We conclude that non-nutrient secretagogues act, in part, via PKC and downstream ERK1/2 signaling to stimulate mitochondrial energy production to compensate for energy expenditure that is linked to β-cell activation.-Santo-Domingo, J., Chareyron, I., Dayon, L., Galindo, A. N., Cominetti, O., Giménez, M. P. G., De Marchi, U., Canto, C., Kussmann, M., Wiederkehr, A. Coordinated activation of mitochondrial respiration and exocytosis mediated by PKC signaling in pancreatic β cells.
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Affiliation(s)
- Jaime Santo-Domingo
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Isabelle Chareyron
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Loïc Dayon
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Ornella Cominetti
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - María Pilar Giner Giménez
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Umberto De Marchi
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Carles Canto
- Diabetes and Metabolic Health, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Martin Kussmann
- Systems Nutrition, Metabonomics and Proteomics, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Andreas Wiederkehr
- Mitochondrial Function, Nestlé Institute of Health Sciences, Lausanne, Switzerland;
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41
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Guiraud SP, Montoliu I, Da Silva L, Dayon L, Galindo AN, Corthésy J, Kussmann M, Martin FP. High-throughput and simultaneous quantitative analysis of homocysteine-methionine cycle metabolites and co-factors in blood plasma and cerebrospinal fluid by isotope dilution LC-MS/MS. Anal Bioanal Chem 2016; 409:295-305. [PMID: 27757515 PMCID: PMC5203846 DOI: 10.1007/s00216-016-0003-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/30/2016] [Accepted: 10/04/2016] [Indexed: 01/04/2023]
Abstract
The methionine cycle is a key pathway contributing to the regulation of human health, with well-established involvement in cardiovascular diseases and cognitive function. Changes in one-carbon cycle metabolites have also been associated with mild cognitive decline, vascular dementia, and Alzheimer's disease. Today, there is no single analytical method to monitor both metabolites and co-factors of the methionine cycle. To address this limitation, we here report for the first time a new method for the simultaneous quantitation of 17 metabolites in the methionine cycle, which are homocysteic acid, taurine, serine, cysteine, glycine, homocysteine, riboflavin, methionine, pyridoxine, cystathionine, pyridoxamine, S-adenosylhomocysteine, S-adenosylmethionine, betaine, choline, dimethylglycine, and 5-methyltetrahydrofolic acid. This multianalyte method, developed using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), provides a highly accurate and precise quantitation of these 17 metabolites for both plasma and cerebrospinal fluid metabolite monitoring. The method requires a simple sample preparation, which, combined with a short chromatographic run time, ensures a high sample throughput. This analytical strategy will thus provide a novel metabolomics approach to be employed in large-scale observational and intervention studies. We expect such a robust method to be particularly relevant for broad and deep molecular phenotyping of individuals in relation to their nutritional requirements, health monitoring, and disease risk management.
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Affiliation(s)
- Seu Ping Guiraud
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland.
| | - Ivan Montoliu
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland
| | - Laeticia Da Silva
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland
| | - John Corthésy
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland
| | - Martin Kussmann
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland
| | - Francois-Pierre Martin
- Nestlé Institute of Health Sciences SA, Campus EPFL, Innovation Park, CH-1015, Lausanne, Switzerland
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Cominetti O, Núñez Galindo A, Corthésy J, Oller Moreno S, Irincheeva I, Valsesia A, Astrup A, Saris WHM, Hager J, Kussmann M, Dayon L. Proteomic Biomarker Discovery in 1000 Human Plasma Samples with Mass Spectrometry. J Proteome Res 2015; 15:389-99. [DOI: 10.1021/acs.jproteome.5b00901] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ornella Cominetti
- Molecular
Biomarkers Core, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Molecular
Biomarkers Core, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - John Corthésy
- Molecular
Biomarkers Core, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Sergio Oller Moreno
- Molecular
Biomarkers Core, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Irina Irincheeva
- Nutrition
and Metabolic Health Group, Nestlé Institute of Health Sciences, CH-1015
Lausanne, Switzerland
| | - Armand Valsesia
- Nutrition
and Metabolic Health Group, Nestlé Institute of Health Sciences, CH-1015
Lausanne, Switzerland
| | - Arne Astrup
- Department
of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Wim H. M. Saris
- NUTRIM,
School for Nutrition and Translational Research In Metabolism, Maastricht University Medical Centre, 6200 MD Maastricht, Netherlands
| | - Jörg Hager
- Nutrition
and Metabolic Health Group, Nestlé Institute of Health Sciences, CH-1015
Lausanne, Switzerland
| | - Martin Kussmann
- Molecular
Biomarkers Core, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Loïc Dayon
- Molecular
Biomarkers Core, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
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43
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Núñez Galindo A, Kussmann M, Dayon L. Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery. Anal Chem 2015; 87:10755-61. [PMID: 26452177 DOI: 10.1021/acs.analchem.5b02748] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cerebrospinal fluid (CSF) is a body fluid of high clinical relevance and an important source of potential biomarkers for brain-associated damages, such as traumatic brain injury and stroke, and for brain diseases, such as Alzheimer's and Parkinson's. Herein, we have implemented, evaluated, and validated a scalable automated proteomic pipeline (ASAP(2)) for the sample preparation and proteomic analysis of CSF, enabling increased throughput and robustness for biomarker discovery. Human CSF samples were depleted from abundant proteins and subjected to automated reduction, alkylation, protein digestion, tandem mass tag (TMT) 6-plex labeling, pooling, and sample cleanup in a 96-well-plate format before reversed-phase liquid chromatography tandem mass spectrometry (RP-LC MS/MS). We showed the impact on the CSF proteome coverage of applying the depletion of abundant proteins, which is usually performed on blood plasma or serum samples. Using ASAP(2) to analyze 96 identical CSF samples, we determined the analytical figures of merit of our shotgun proteomic approach regarding proteome coverage consistency (i.e., 387 proteins), quantitative accuracy, and individual protein variability. We demonstrated that, as for human plasma samples, ASAP(2) is efficient in analyzing large numbers of human CSF samples and is a valuable tool for biomarker discovery. The data has been deposited to the ProteomeXchange with identifier PXD003024.
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Affiliation(s)
- Antonio Núñez Galindo
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Bâtiment H, Lausanne, Switzerland
| | - Martin Kussmann
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Bâtiment H, Lausanne, Switzerland
| | - Loïc Dayon
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Bâtiment H, Lausanne, Switzerland
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44
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Ducommun S, Deak M, Sumpton D, Ford RJ, Núñez Galindo A, Kussmann M, Viollet B, Steinberg GR, Foretz M, Dayon L, Morrice NA, Sakamoto K. Motif affinity and mass spectrometry proteomic approach for the discovery of cellular AMPK targets: Identification of mitochondrial fission factor as a new AMPK substrate. Cell Signal 2015; 27:978-88. [DOI: 10.1016/j.cellsig.2015.02.008] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 11/15/2022]
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45
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Mauvoisin D, Dayon L, Gachon F, Kussmann M. Proteomics and circadian rhythms: it's all about signaling! Proteomics 2014; 15:310-7. [PMID: 25103677 DOI: 10.1002/pmic.201400187] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 05/02/2014] [Accepted: 08/04/2014] [Indexed: 01/11/2023]
Abstract
Proteomic technologies using MS offer new perspectives in circadian biology, in particular the possibility to study PTMs. To date, only very few studies have been carried out to decipher the rhythmicity of protein expression in mammals with large-scale proteomics. Although signaling has been shown to be of high relevance, comprehensive characterization studies of PTMs are even more rare. This review aims at describing the actual landscape of circadian proteomics and the opportunities and challenges appearing on the horizon. Emphasis was given to signaling processes for their role in metabolic health as regulated by circadian clocks and environmental factors. Those signaling processes are expected to be better and more deeply characterized in the coming years with proteomics.
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Affiliation(s)
- Daniel Mauvoisin
- Circadian Rhythm Group, Nestlé Institute of Health Sciences (NIHS), Lausanne, Switzerland
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46
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Dayon L, Núñez Galindo A, Corthésy J, Cominetti O, Kussmann M. Comprehensive and Scalable Highly Automated MS-Based Proteomic Workflow for Clinical Biomarker Discovery in Human Plasma. J Proteome Res 2014; 13:3837-3845. [DOI: 10.1021/pr500635f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Loïc Dayon
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences, Campus EPFL, Quartier de l’innovation, Lausanne CH-1015, Switzerland
| | - Antonio Núñez Galindo
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences, Campus EPFL, Quartier de l’innovation, Lausanne CH-1015, Switzerland
| | - John Corthésy
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences, Campus EPFL, Quartier de l’innovation, Lausanne CH-1015, Switzerland
| | - Ornella Cominetti
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences, Campus EPFL, Quartier de l’innovation, Lausanne CH-1015, Switzerland
| | - Martin Kussmann
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences, Campus EPFL, Quartier de l’innovation, Lausanne CH-1015, Switzerland
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47
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García-Berrocoso T, Penalba A, Boada C, Giralt D, Cuadrado E, Colomé N, Dayon L, Canals F, Sanchez JC, Rosell A, Montaner J. From brain to blood: New biomarkers for ischemic stroke prognosis. J Proteomics 2013; 94:138-48. [DOI: 10.1016/j.jprot.2013.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/02/2013] [Accepted: 09/14/2013] [Indexed: 11/26/2022]
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48
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Gluck F, Hoogland C, Antinori P, Robin X, Nikitin F, Zufferey A, Pasquarello C, Fétaud V, Dayon L, Müller M, Lisacek F, Geiser L, Hochstrasser D, Sanchez JC, Scherl A. EasyProt — An easy-to-use graphical platform for proteomics data analysis. J Proteomics 2013; 79:146-60. [DOI: 10.1016/j.jprot.2012.12.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/08/2012] [Accepted: 12/18/2012] [Indexed: 11/17/2022]
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49
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Dayon L, Sonderegger B, Kussmann M. Combination of Gas-Phase Fractionation and MS3 Acquisition Modes for Relative Protein Quantification with Isobaric Tagging. J Proteome Res 2012; 11:5081-9. [DOI: 10.1021/pr300519c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Loïc Dayon
- Proteomics and Metabonomics
Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Bernhard Sonderegger
- Proteomics and Metabonomics
Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Martin Kussmann
- Proteomics and Metabonomics
Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Faculty of Life Sciences, Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne, Switzerland
- Faculty of Science, Aarhus University (AU), Aarhus, Denmark
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50
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Breitwieser FP, Müller A, Dayon L, Köcher T, Hainard A, Pichler P, Schmidt-Erfurth U, Superti-Furga G, Sanchez JC, Mechtler K, Bennett KL, Colinge J. General statistical modeling of data from protein relative expression isobaric tags. J Proteome Res 2011; 10:2758-66. [PMID: 21526793 DOI: 10.1021/pr1012784] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitative comparison of the protein content of biological samples is a fundamental tool of research. The TMT and iTRAQ isobaric labeling technologies allow the comparison of 2, 4, 6, or 8 samples in one mass spectrometric analysis. Sound statistical models that scale with the most advanced mass spectrometry (MS) instruments are essential for their efficient use. Through the application of robust statistical methods, we developed models that capture variability from individual spectra to biological samples. Classical experimental designs with a distinct sample in each channel as well as the use of replicates in multiple channels are integrated into a single statistical framework. We have prepared complex test samples including controlled ratios ranging from 100:1 to 1:100 to characterize the performance of our method. We demonstrate its application to actual biological data sets originating from three different laboratories and MS platforms. Finally, test data and an R package, named isobar, which can read Mascot, Phenyx, and mzIdentML files, are made available. The isobar package can also be used as an independent software that requires very little or no R programming skills.
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Affiliation(s)
- Florian P Breitwieser
- CeMM , Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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