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Martin FP, Cominetti O, Berger B, Combremont S, Marquis J, Xie G, Jia W, Pinto-Sanchez MI, Bercik P, Bergonzelli G. Metabolome-associated psychological comorbidities improvement in irritable bowel syndrome patients receiving a probiotic. Gut Microbes 2024; 16:2347715. [PMID: 38717445 PMCID: PMC11085950 DOI: 10.1080/19490976.2024.2347715] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Our recent randomized, placebo-controlled study in Irritable Bowel Syndrome (IBS) patients with diarrhea or alternating bowel habits showed that the probiotic Bifidobacterium longum (BL) NCC3001 improves depression scores and decreases brain emotional reactivity. However, the involved metabolic pathways remain unclear. This analysis aimed to investigate the biochemical pathways underlying the beneficial effects of BL NCC3001 using metabolomic profiling. Patients received probiotic (1x 1010CFU, n=16) or placebo (n=19) daily for 6 weeks. Anxiety and depression were measured using the Hospital Anxiety and Depression Scale. Brain activity in response to negative emotional stimuli was assessed by functional Magnetic Resonance Imaging. Probiotic fecal abundance was quantified by qPCR. Quantitative measurement of specific panels of plasma host-microbial metabolites was performed by mass spectrometry-based metabolomics. Probiotic abundance in feces was associated with improvements in anxiety and depression scores, and a decrease in amygdala activation. The probiotic treatment increased the levels of butyric acid, tryptophan, N-acetyl tryptophan, glycine-conjugated bile acids, and free fatty acids. Butyric acid concentration correlated with lower anxiety and depression scores, and decreased amygdala activation. Furthermore, butyric acid concentration correlated with the probiotic abundance in feces. In patients with non-constipation IBS, improvements in psychological comorbidities and brain emotional reactivity were associated with an increased abundance of BL NCC3001 in feces and specific plasma metabolites, mainly butyric acid. These findings suggest the importance of a probiotic to thrive in the gut and highlight butyric acid as a potential biochemical marker linking microbial metabolism with beneficial effects on the gut-brain axis.
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Affiliation(s)
- Francois-Pierre Martin
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Ornella Cominetti
- Nestlé Institute of Food Safety and Analytical Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Bernard Berger
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Séverine Combremont
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Julien Marquis
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Guoxiang Xie
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, USA
- Human Metabolomics Institute, Inc, Shenzhen, Guangdong, China
| | - Wei Jia
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, USA
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Maria Inés Pinto-Sanchez
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Premysl Bercik
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Gabriela Bergonzelli
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
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Cominetti O, Agarwal S, Oller-Moreno S. Editorial: Advances in methods and tools for multi-omics data analysis. Front Mol Biosci 2023; 10:1186822. [PMID: 37168260 PMCID: PMC10165066 DOI: 10.3389/fmolb.2023.1186822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023] Open
Affiliation(s)
- Ornella Cominetti
- Nestlé Research Center, Lausanne, Switzerland
- *Correspondence: Ornella Cominetti,
| | | | - Sergio Oller-Moreno
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
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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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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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de Barros TT, Venancio VDP, Hernandes LC, Antunes LMG, Hillesheim E, Salomão RG, Mathias MG, Coelho-Landell CA, Toffano RBD, Almada MORDV, Camelo-Junior JS, Moco S, Cominetti O, Ued FDV, Kaput J, Monteiro JP. DNA Damage, n-3 Long-Chain PUFA Levels and Proteomic Profile in Brazilian Children and Adolescents. Nutrients 2021; 13:nu13082483. [PMID: 34444642 PMCID: PMC8401971 DOI: 10.3390/nu13082483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 12/24/2022] Open
Abstract
Fatty acids play a significant role in maintaining cellular and DNA protection and we previously found an inverse relationship between blood levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and DNA damage. The aim of this study was to explore differences in proteomic profiles, for 117 pro-inflammatory proteins, in two previously defined groups of individuals with different DNA damage and EPA and DHA levels. Healthy children and adolescents (n = 140) aged 9 to 13 years old in an urban area of Brazil were divided by k-means cluster test into two clusters of DNA damage (tail intensity) using the comet assay (cluster 1 = 5.9% ± 1.2 and cluster 2 = 13.8% ± 3.1) in our previous study. The cluster with higher DNA damage and lower levels of DHA (6.2 ± 1.6 mg/dL; 5.4 ± 1.3 mg/dL, p = 0.003) and EPA (0.6 ± 0.2 mg/dL; 0.5 ± 0.1 mg/dL, p < 0.001) presented increased expression of the proteins CDK8-CCNC, PIK3CA-PIK3R1, KYNU, and PRKCB, which are involved in pro-inflammatory pathways. Our findings support the hypothesis that low levels of n-3 long-chain PUFA may have a less protective role against DNA damage through expression of pro-inflammatory proteins, such as CDK8-CCNC, PIK3CA-PIK3R1, KYNU, and PRKCB.
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Affiliation(s)
- Tamiris Trevisan de Barros
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
- Correspondence:
| | - Vinicius de Paula Venancio
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (V.d.P.V.); (L.M.G.A.)
| | - Lívia Cristina Hernandes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (V.d.P.V.); (L.M.G.A.)
| | - Lusania Maria Greggi Antunes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (V.d.P.V.); (L.M.G.A.)
| | - Elaine Hillesheim
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Roberta Garcia Salomão
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Mariana Giaretta Mathias
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Carolina Almeida Coelho-Landell
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Roseli Borges Donegá Toffano
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Maria Olimpia Ribeiro do Vale Almada
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - José Simon Camelo-Junior
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Sofia Moco
- Nestlé Research, Société des Produits Nestlé SA, EPFL Innovation Park, CH1015 Lausanne, Switzerland; (S.M.); (O.C.); (J.K.)
| | - Ornella Cominetti
- Nestlé Research, Société des Produits Nestlé SA, EPFL Innovation Park, CH1015 Lausanne, Switzerland; (S.M.); (O.C.); (J.K.)
| | - Fábio da Veiga Ued
- Department of Health Sciences, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil;
| | - Jim Kaput
- Nestlé Research, Société des Produits Nestlé SA, EPFL Innovation Park, CH1015 Lausanne, Switzerland; (S.M.); (O.C.); (J.K.)
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
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Fuzo CA, da Veiga Ued F, Moco S, Cominetti O, Métairon S, Pruvost S, Charpagne A, Carayol J, Torrieri R, Silva WA, Descombes P, Kaput J, Monteiro JP. Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents. Sci Rep 2021; 11:11992. [PMID: 34099811 PMCID: PMC8184816 DOI: 10.1038/s41598-021-91530-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/30/2020] [Accepted: 05/25/2021] [Indexed: 02/08/2023] Open
Abstract
Polymorphisms in genes related to the metabolism of vitamin B12 haven’t been examined in a Brazilian population.
To (a) determine the correlation between the local genetic ancestry components and vitamin B12 levels using ninety B12-related genes; (b) determine associations between these genes and their SNPs with vitamin B12 levels; (c) determine a polygenic risk score (PRS) using significant variants. This cross-sectional study included 168 children and adolescents, aged 9–13 years old. Total cobalamin was measured in plasma. Genotyping arrays and whole exome data were combined to yield ~ 7000 SNPs in 90 genes related to vitamin B12. The Efficient Local Ancestry Inference was used to estimate local ancestry for African (AFR), Native American, and European (EUR). The association between the genotypes and vitamin B12 levels were determined with generalized estimating equation.
Vitamin B12 levels were driven by positive (EUR) and negative (AFR, AMR) correlations with genetic ancestry. A set of 36 variants were used to create a PRS that explained 42% of vitamin level variation.
Vitamin B12 levels are influenced by genetic ancestry and a PRS explained almost 50% of the variation in plasma cobalamin in Brazilian children and adolescents.
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Affiliation(s)
- Carlos Alessandro Fuzo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutics Sciences, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio da Veiga Ued
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil
| | - Sofia Moco
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteite Amsterdam, Amsterdam, The Netherlands
| | - Ornella Cominetti
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Sylviane Métairon
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Aline Charpagne
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,Sophia Genetics, Campus Biotech, 1202, Geneva, Switzerland
| | - Jerome Carayol
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Raul Torrieri
- Center for Medical Genomics, Ribeirão Preto Medical School Hospital, University of São Paulo, Ribeirão Preto, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Patrick Descombes
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Jim Kaput
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,, Vydiant, Folsom, CA, USA
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil.
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Cominetti O, Hosking J, Jeffery A, Pinkney J, Martin FP. Contributions of Fat and Carbohydrate Metabolism to Glucose Homeostasis in Childhood Change With Age and Puberty: A 12-Years Cohort Study (EARLYBIRD 77). Front Nutr 2020; 7:139. [PMID: 32984398 PMCID: PMC7483556 DOI: 10.3389/fnut.2020.00139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/30/2020] [Accepted: 07/17/2020] [Indexed: 12/22/2022] Open
Abstract
Puberty-a period when susceptibility to the onset of Type 2 diabetes (T2D) increases-is marked with profound physiological and metabolic changes. In the EarlyBird cohort, children who developed impaired fasting glycemia in adolescence already exhibited higher fasting blood glucose at 5 years of age, independent of their body mass index (BMI), suggesting that pubertal factors may modify existing predisposition. Understanding how the physiological changes during childhood influence glucose homeostasis and how the central energy metabolism may help deciphering the mechanisms that underlie the risk of developing T2D in children and adults. We investigated these associations by analyzing glycemic variations with molecular markers of central energy metabolism, substrate oxidation status and pubertal stages in the EarlyBird cohort. The EarlyBird study is a non-interventional, prospective cohort study, that recruited 307 healthy UK children at age 5, and followed them annually throughout childhood for 12 years. Longitudinal data on blood biochemistry, respiratory exchange ratio, and anthropometry, available from 150 children were integrated with fasting glycemia. The gradual rise in blood glucose during childhood associates with age-dependent changes in molecular processes and substrate oxidation status, namely (i) greater pre-pubertal fat utilization, ketogenesis, and fatty acid oxidation, and (ii) greater pubertal carbohydrate oxidation and glycolytic metabolism (Cori and Cahill Cycles) associated with different amino acid exchanges between muscle and other tissues (proline, glutamine, alanine). Since children's metabolic and nutritional requirements evolve during childhood, this study has potential clinical implications for the development of nutritional strategies for disease prevention in children.
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Affiliation(s)
- Ornella Cominetti
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland
| | - Joanne Hosking
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, United Kingdom
| | - Alison Jeffery
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, United Kingdom
| | - Jonathan Pinkney
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, United Kingdom
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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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10
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Hosking J, Pinkney J, Jeffery A, Cominetti O, Da Silva L, Collino S, Kussmann M, Hager J, Martin FP. Insulin Resistance during normal child growth and development is associated with a distinct blood metabolic phenotype (Earlybird 72). Pediatr Diabetes 2019; 20:832-841. [PMID: 31254470 DOI: 10.1111/pedi.12884] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/22/2019] [Accepted: 06/19/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND While insulin resistance (IR) is associated with specific metabolite signatures in adults, there have been few truly longitudinal studies in healthy children, either to confirm which abnormalities are present, or to determine whether they precede or result from IR. Therefore, we investigated the association of serum metabolites with IR in childhood in the Earlybird cohort. METHODS The Earlybird cohort is a well-characterized cohort of healthy children with annual measurements from age 5 to 16 years. For the first time, longitudinal association analyses between individual serum metabolites and homeostatic model assessment (HOMA) of insulin resistance (HOMA-IR) have been performed taking into account the effects of age, growth, puberty, adiposity, and physical activity. RESULTS IR was higher in girls than in boys and was associated with increasing body mass index (BMI). In longitudinal analysis IR was associated with reduced concentrations of branched-chain amino acids (BCAA), 2-ketobutyrate, citrate and 3-hydroxybutyrate, and higher concentrations of lactate and alanine. These findings demonstrate the widespread biochemical consequences of IR for intermediary metabolism, ketogenesis, and pyruvate oxidation during normal child growth and development. CONCLUSIONS Longitudinal analysis can differentiate metabolite signatures that precede or follow the development of greater levels of IR. In healthy normal weight children, higher levels of IR are associated with reduced levels of BCAA, ketogenesis, and fuel oxidation. In contrast, elevated lactate concentrations preceded the rise in IR. These changes reveal the metabolite signature of insulin action during normal growth, and they contrast with previous findings in obese children and adults that represent the consequences of IR and obesity.
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Affiliation(s)
- Joanne Hosking
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, UK
| | - Jonathan Pinkney
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, UK
| | - Alison Jeffery
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, UK
| | - Ornella Cominetti
- Department of Analytical Sciences, Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Laeticia Da Silva
- Department of Analytical Sciences, Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Sebastiano Collino
- Department of Analytical Sciences, Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Martin Kussmann
- Department of Analytical Sciences, Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Jorg Hager
- Department of Nutrition and Dietary recommendations, Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Francois-Pierre Martin
- Department of Metabolic Health, Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
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11
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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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12
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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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13
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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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14
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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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15
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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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16
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Cominetti O, Smith D, Hoffman F, Jallow M, Thézénas ML, Huang H, Kwiatkowski D, Maini PK, Casals-Pascual C. Identification of a Novel Clinical Phenotype of Severe Malaria using a Network-Based Clustering Approach. Sci Rep 2018; 8:12849. [PMID: 30150696 PMCID: PMC6110866 DOI: 10.1038/s41598-018-31320-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/14/2018] [Indexed: 11/29/2022] Open
Abstract
The parasite Plasmodium falciparum is the main cause of severe malaria (SM). Despite treatment with antimalarial drugs, more than 400,000 deaths are reported every year, mainly in African children. The diversity of clinical presentations associated with SM highlights important differences in disease pathogenesis that often require specific therapeutic options. The clinical heterogeneity of SM is largely unresolved. Here we report a network-based analysis of clinical phenotypes associated with SM in 2,915 Gambian children admitted to hospital with Plasmodium falciparum malaria. We used a network-based clustering method which revealed a strong correlation between disease heterogeneity and mortality. The analysis identified four distinct clusters of SM and respiratory distress that departed from the WHO definition. Patients in these clusters characteristically presented with liver enlargement and high concentrations of brain natriuretic peptide (BNP), giving support to the potential role of circulatory overload and/or right-sided heart failure as a mechanism of disease. The role of heart failure is controversial in SM and our work suggests that standard clinical management may not be appropriate. We find that our clustering can be a powerful data exploration tool to identify novel disease phenotypes and therapeutic options to reduce malaria-associated mortality.
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Affiliation(s)
- Ornella Cominetti
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - David Smith
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Fred Hoffman
- Department of Computer Science, University of Oxford, Oxford, UK
- XL Catlin, London, UK
| | | | - Marie L Thézénas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Honglei Huang
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Climent Casals-Pascual
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- ISGlobal, Hospital Clínic i Provincial de Barcelona, Centre Diagnòstic Biomèdic- Universitat de Barcelona, Barcelona, Spain.
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17
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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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18
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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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19
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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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20
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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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21
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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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22
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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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23
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Pinto-Sanchez MI, Hall GB, Ghajar K, Nardelli A, Bolino C, Lau JT, Martin FP, Cominetti O, Welsh C, Rieder A, Traynor J, Gregory C, De Palma G, Pigrau M, Ford AC, Macri J, Berger B, Bergonzelli G, Surette MG, Collins SM, Moayyedi P, Bercik P. Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: A Pilot Study in Patients With Irritable Bowel Syndrome. Gastroenterology 2017; 153:448-459.e8. [PMID: 28483500 DOI: 10.1053/j.gastro.2017.05.003] [Citation(s) in RCA: 451] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 04/07/2017] [Accepted: 05/02/2017] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Probiotics can reduce symptoms of irritable bowel syndrome (IBS), but little is known about their effects on psychiatric comorbidities. We performed a prospective study to evaluate the effects of Bifidobacterium longum NCC3001 (BL) on anxiety and depression in patients with IBS. METHODS We performed a randomized, double-blind, placebo-controlled study of 44 adults with IBS and diarrhea or a mixed-stool pattern (based on Rome III criteria) and mild to moderate anxiety and/or depression (based on the Hospital Anxiety and Depression scale) at McMaster University in Canada, from March 2011 to May 2014. At the screening visit, clinical history and symptoms were assessed and blood samples were collected. Patients were then randomly assigned to groups and given daily BL (n = 22) or placebo (n = 22) for 6 weeks. At weeks 0, 6, and 10, we determined patients' levels of anxiety and depression, IBS symptoms, quality of life, and somatization using validated questionnaires. At weeks 0 and 6, stool, urine and blood samples were collected, and functional magnetic resonance imaging (fMRI) test was performed. We assessed brain activation patterns, fecal microbiota, urine metabolome profiles, serum markers of inflammation, neurotransmitters, and neurotrophin levels. RESULTS At week 6, 14 of 22 patients in the BL group had reduction in depression scores of 2 points or more on the Hospital Anxiety and Depression scale, vs 7 of 22 patients in the placebo group (P = .04). BL had no significant effect on anxiety or IBS symptoms. Patients in the BL group had a mean increase in quality of life score compared with the placebo group. The fMRI analysis showed that BL reduced responses to negative emotional stimuli in multiple brain areas, including amygdala and fronto-limbic regions, compared with placebo. The groups had similar fecal microbiota profiles, serum markers of inflammation, and levels of neurotrophins and neurotransmitters, but the BL group had reduced urine levels of methylamines and aromatic amino acids metabolites. At week 10, depression scores were reduced in patients given BL vs placebo. CONCLUSION In a placebo-controlled trial, we found that the probiotic BL reduces depression but not anxiety scores and increases quality of life in patients with IBS. These improvements were associated with changes in brain activation patterns that indicate that this probiotic reduces limbic reactivity. ClinicalTrials.gov no. NCT01276626.
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Affiliation(s)
- Maria Ines Pinto-Sanchez
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Geoffrey B Hall
- Department of Psychology, Neuroscience, and Behavior, McMaster University, Hamilton, ON, Canada
| | - Kathy Ghajar
- Department of Psychology, Neuroscience, and Behavior, McMaster University, Hamilton, ON, Canada
| | - Andrea Nardelli
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Carolina Bolino
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Jennifer T Lau
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | | | | | - Christopher Welsh
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Amber Rieder
- Department of Psychology, Neuroscience, and Behavior, McMaster University, Hamilton, ON, Canada
| | - Jenna Traynor
- Department of Psychology, Neuroscience, and Behavior, McMaster University, Hamilton, ON, Canada
| | - Caitlin Gregory
- Department of Psychology, Neuroscience, and Behavior, McMaster University, Hamilton, ON, Canada
| | - Giada De Palma
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Marc Pigrau
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Alexander C Ford
- Leeds Gastroenterology Institute, St. James's University Hospital, and Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Joseph Macri
- Department of Pathology, McMaster University, Hamilton, ON, Canada
| | - Bernard Berger
- Nestlé Research Center, Nutrition Institute, Lausanne, Switzerland
| | | | - Michael G Surette
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Stephen M Collins
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Paul Moayyedi
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Premysl Bercik
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada.
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24
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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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25
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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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26
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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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27
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Montoliu I, Cominetti O, Boulangé CL, Berger B, Siddharth J, Nicholson J, Martin FPJ. Modeling Longitudinal Metabonomics and Microbiota Interactions in C57BL/6 Mice Fed a High Fat Diet. Anal Chem 2016; 88:7617-26. [PMID: 27396289 DOI: 10.1021/acs.analchem.6b01343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Longitudinal studies aim typically at following populations of subjects over time and are important to understand the global evolution of biological processes. When it comes to longitudinal omics data, it will often depend on the overall objective of the study, and constraints imposed by the data, to define the appropriate modeling tools. Here, we report the use of multilevel simultaneous component analysis (MSCA), orthogonal projection on latent structures (OPLS), and regularized canonical correlation analysis (rCCA) to study associations between specific longitudinal urine metabonomics data and microbiome data in a diet-induced obesity model using C57BL/6 mice. (1)H NMR urine metabolic profiling was performed on samples collected weekly over a period of 13 weeks, and stool microbial composition was assessed using 16S rRNA gene sequencing at three specific time periods (baseline, first week response, end of study). MSCA and OPLS allowed us to explore longitudinal urine metabonomics data in relation to the dietary groups, as well as dietary effects on body weight. In addition, we report a data integration strategy based on regularized CCA and correlation analyses of urine metabonomics data and 16S rRNA gene sequencing data to investigate the functional relationships between metabolites and gut microbial composition. Thanks to this workflow enabling the breakdown of this data set complexity, the most relevant patterns could be extracted to further explore physiological processes at an anthropometric, cellular, and molecular level.
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Affiliation(s)
- Ivan Montoliu
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland.,Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ornella Cominetti
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland
| | - Claire L Boulangé
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Bernard Berger
- Nestlé Research Center , Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland
| | - Jay Siddharth
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland
| | - Jeremy Nicholson
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - François-Pierre J Martin
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland
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28
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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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29
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Sperisen P, Cominetti O, Martin FPJ. Longitudinal omics modeling and integration in clinical metabonomics research: challenges in childhood metabolic health research. Front Mol Biosci 2015; 2:44. [PMID: 26301225 PMCID: PMC4525019 DOI: 10.3389/fmolb.2015.00044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 05/11/2015] [Accepted: 07/20/2015] [Indexed: 12/14/2022] Open
Abstract
Systems biology is an important approach for deciphering the complex processes in health maintenance and the etiology of metabolic diseases. Such integrative methodologies will help better understand the molecular mechanisms involved in growth and development throughout childhood, and consequently will result in new insights about metabolic and nutritional requirements of infants, children and adults. To achieve this, a better understanding of the physiological processes at anthropometric, cellular and molecular level for any given individual is needed. In this respect, novel omics technologies in combination with sophisticated data modeling techniques are key. Due to the highly complex network of influential factors determining individual trajectories, it becomes imperative to develop proper tools and solutions that will comprehensively model biological information related to growth and maturation of our body functions. The aim of this review and perspective is to evaluate, succinctly, promising data analysis approaches to enable data integration for clinical research, with an emphasis on the longitudinal component. Approaches based on empirical and mechanistic modeling of omics data are essential to leverage findings from high dimensional omics datasets and enable biological interpretation and clinical translation. On the one hand, empirical methods, which provide quantitative descriptions of patterns in the data, are mostly used for exploring and mining datasets. On the other hand, mechanistic models are based on an understanding of the behavior of a system's components and condense information about the known functions, allowing robust and reliable analyses to be performed by bioinformatics pipelines and similar tools. Herein, we will illustrate current examples, challenges and perspectives in the applications of empirical and mechanistic modeling in the context of childhood metabolic health research.
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Affiliation(s)
- Peter Sperisen
- GI Health and Microbiome Department, Nestle Institute of Health Sciences Lausanne, Switzerland
| | - Ornella Cominetti
- Molecular Biomarkers Department, Nestle Institute of Health Sciences Lausanne, Switzerland
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30
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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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