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Monteiro JP, Morine MJ, Ued FV, Kaput J. Identifying and Analyzing Topic Clusters in a Nutri-, Food-, and Diet-Proteomic Corpus Using Machine Reading. Nutrients 2023; 15:nu15020270. [PMID: 36678141 PMCID: PMC9863309 DOI: 10.3390/nu15020270] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Nutrition affects the early stages of disease development, but the mechanisms remain poorly understood. High-throughput proteomic methods are being used to generate data and information on the effects of nutrients, foods, and diets on health and disease processes. In this report, a novel machine reading pipeline was used to identify all articles and abstracts on proteomics, diet, food, and nutrition in humans. The resulting proteomic corpus was further analyzed to produce seven clusters of "thematic" content defined as documents that have similar word content. Examples of publications from several of these clusters were then described in a similar way to a typical descriptive review.
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Affiliation(s)
- Jacqueline Pontes Monteiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil
- Correspondence:
| | | | - Fabio V. Ued
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil
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Misselbeck K, Parolo S, Lorenzini F, Savoca V, Leonardelli L, Bora P, Morine MJ, Mione MC, Domenici E, Priami C. A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome. Nat Commun 2019; 10:5215. [PMID: 31740673 PMCID: PMC6861239 DOI: 10.1038/s41467-019-13208-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 09/07/2018] [Accepted: 10/25/2019] [Indexed: 12/11/2022] Open
Abstract
Metabolic syndrome is a pathological condition characterized by obesity, hyperglycemia, hypertension, elevated levels of triglycerides and low levels of high-density lipoprotein cholesterol that increase cardiovascular disease risk and type 2 diabetes. Although numerous predisposing genetic risk factors have been identified, the biological mechanisms underlying this complex phenotype are not fully elucidated. Here we introduce a systems biology approach based on network analysis to investigate deregulated biological processes and subsequently identify drug repurposing candidates. A proximity score describing the interaction between drugs and pathways is defined by combining topological and functional similarities. The results of this computational framework highlight a prominent role of the immune system in metabolic syndrome and suggest a potential use of the BTK inhibitor ibrutinib as a novel pharmacological treatment. An experimental validation using a high fat diet-induced obesity model in zebrafish larvae shows the effectiveness of ibrutinib in lowering the inflammatory load due to macrophage accumulation.
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Affiliation(s)
- Karla Misselbeck
- Fondazione The Microsoft Research University of Trento, Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
- Department of Mathematics, University of Trento, Trento, Italy
| | - Silvia Parolo
- Fondazione The Microsoft Research University of Trento, Centre for Computational and Systems Biology (COSBI), Rovereto, Italy.
| | - Francesca Lorenzini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Valeria Savoca
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Lorena Leonardelli
- Fondazione The Microsoft Research University of Trento, Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Pranami Bora
- Fondazione The Microsoft Research University of Trento, Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Melissa J Morine
- Fondazione The Microsoft Research University of Trento, Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Maria Caterina Mione
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Enrico Domenici
- Fondazione The Microsoft Research University of Trento, Centre for Computational and Systems Biology (COSBI), Rovereto, Italy.
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Corrado Priami
- Fondazione The Microsoft Research University of Trento, Centre for Computational and Systems Biology (COSBI), Rovereto, Italy.
- Department of Computer Science, University of Pisa, Pisa, Italy.
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3
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McMorrow AM, Connaughton RM, Magalhães TR, McGillicuddy FC, Hughes MF, Cheishvili D, Morine MJ, Ennis S, Healy M, Roche EF, Tremblay RE, Szyf M, Lithander FE, Roche HM. Personalized Cardio-Metabolic Responses to an Anti-Inflammatory Nutrition Intervention in Obese Adolescents: A Randomized Controlled Crossover Trial. Mol Nutr Food Res 2018; 62:e1701008. [PMID: 29665620 PMCID: PMC6079645 DOI: 10.1002/mnfr.201701008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/16/2018] [Indexed: 01/04/2023]
Abstract
SCOPE Chronic inflammation and hypoadiponectinemia are characteristics of obesity-induced insulin resistance (IR). The effect of an anti-inflammatory nutrition supplement (AINS) on IR and adiponectin biology in overweight adolescents was investigated. The secondary objective was to examine the extent to which individuals' biomarker profiles, derived from baseline phenotypes, predicted response or not to the AINS. Additionally, the impact of DNA methylation on intervention efficacy was assessed. METHODS AND RESULTS Seventy overweight adolescents (13-18 years) were recruited to this randomized controlled crossover trial. Participants received an AINS (long chain n-3 PUFA, vitamin C, α-tocopherol, green tea extract, and lycopene) and placebo for 8 weeks each. Homeostatic model assessment (HOMA)-IR, adiponectin, inflammatory profiles, and DNA methylation were assessed. HOMA-IR was unchanged in the total cohort. High-molecular-weight (HMW) adiponectin was maintained following the AINS while it decreased over time following the placebo intervention. HOMA-IR decreased in 40% of subjects (responders) following the AINS. Responders' pretreatment phenotype was characterized by higher HOMA-IR, total and LDL cholesterol, but similar BMI in comparison to nonresponders. HMW adiponectin response to the AINS was associated with bidirectional modulation of adipogenic gene methylation. CONCLUSION The AINS modulated adiponectin biology, an early predictor of type 2 diabetes risk, was associated with bidirectional modulation of adipogenic gene methylation in weight-stable overweight adolescents. HOMA-IR decreased in a sub-cohort of adolescents with an adverse metabolic phenotype. Thus, suggesting that more stratified or personalized nutrition approaches may enhance efficacy of dietary interventions.
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Affiliation(s)
- Aoibheann M. McMorrow
- Nutrigenomics Research GroupUCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublin 4D04 N2E5Ireland
| | - Ruth M. Connaughton
- Nutrigenomics Research GroupUCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublin 4D04 N2E5Ireland
| | - Tiago R. Magalhães
- School of Medicine and Medical ScienceUniversity College DublinDublin 4D04 N2E5Ireland
| | - Fiona C. McGillicuddy
- Nutrigenomics Research GroupUCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublin 4D04 N2E5Ireland
- School of Medicine and Medical ScienceUniversity College DublinDublin 4D04 N2E5Ireland
| | - Maria F. Hughes
- Nutrigenomics Research GroupUCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublin 4D04 N2E5Ireland
| | - David Cheishvili
- Department of Pharmacology and TherapeuticsMcGill University Medical SchoolMontrealQCQC H3G 2M1Canada
| | - Melissa J. Morine
- The Microsoft Research–University of Trento Centre for Computational and Systems BiologyRovereto38068Italy
| | - Sean Ennis
- School of Medicine and Medical ScienceUniversity College DublinDublin 4D04 N2E5Ireland
| | | | - Edna F. Roche
- Department of PediatricsTrinity College DublinThe University of DublinDublin 2D02 W272Ireland
- The National Children's HospitalTallaght, Dublin 24D24 AP52Ireland
| | - Richard E. Tremblay
- St‐Justine Hospital Research CentreMontrealQCQC H3T 1C5Canada
- Departments of Pediatrics and PsychologyUniversity of MontrealMontrealQCQC H4A 3J1Canada
- School of Public HealthPhysiotherapy and Sports ScienceUniversity College DublinDublin 4D04 N2E5Ireland
| | - Moshe Szyf
- Department of Pharmacology and TherapeuticsMcGill University Medical SchoolMontrealQCQC H3G 2M1Canada
| | - Fiona E. Lithander
- NIHR Bristol Biomedical Research Centre (Nutrition Theme) at University Hospitals Bristol NHS Foundation Trust and the University of BristolBS1 2LYUnited Kingdom
| | - Helen M. Roche
- Nutrigenomics Research GroupUCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublin 4D04 N2E5Ireland
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Mathias MG, Coelho‐Landell CDA, Scott‐Boyer M, Lacroix S, Morine MJ, Salomão RG, Toffano RBD, Almada MORDV, Camarneiro JM, Hillesheim E, de Barros TT, Camelo‐Junior JS, Campos Giménez E, Redeuil K, Goyon A, Bertschy E, Lévêques A, Oberson J, Giménez C, Carayol J, Kussmann M, Descombes P, Métairon S, Draper CF, Conus N, Mottaz SC, Corsini GZ, Myoshi SKB, Muniz MM, Hernandes LC, Venâncio VP, Antunes LMG, da Silva RQ, Laurito TF, Rossi IR, Ricci R, Jorge JR, Fagá ML, Quinhoneiro DCG, Reche MC, Silva PVS, Falquetti LL, da Cunha THA, Deminice TMM, Tambellini TH, de Souza GCA, de Oliveira MM, Nogueira‐Pileggi V, Matsumoto MT, Priami C, Kaput J, Monteiro JP. Clinical and Vitamin Response to a Short-Term Multi-Micronutrient Intervention in Brazilian Children and Teens: From Population Data to Interindividual Responses. Mol Nutr Food Res 2018; 62:e1700613. [PMID: 29368422 PMCID: PMC6120145 DOI: 10.1002/mnfr.201700613] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 07/18/2017] [Revised: 12/02/2017] [Indexed: 12/11/2022]
Abstract
SCOPE Micronutrients are in small amounts in foods, act in concert, and require variable amounts of time to see changes in health and risk for disease. These first principles are incorporated into an intervention study designed to develop new experimental strategies for setting target recommendations for food bioactives for populations and individuals. METHODS AND RESULTS A 6-week multivitamin/mineral intervention is conducted in 9-13 year olds. Participants (136) are (i) their own control (n-of-1); (ii) monitored for compliance; (iii) measured for 36 circulating vitamin forms, 30 clinical, anthropometric, and food intake parameters at baseline, post intervention, and following a 6-week washout; and (iv) had their ancestry accounted for as modifier of vitamin baseline or response. The same intervention is repeated the following year (135 participants). Most vitamins respond positively and many clinical parameters change in directions consistent with improved metabolic health to the intervention. Baseline levels of any metabolite predict its own response to the intervention. Elastic net penalized regression models are identified, and significantly predict response to intervention on the basis of multiple vitamin/clinical baseline measures. CONCLUSIONS The study design, computational methods, and results are a step toward developing recommendations for optimizing vitamin levels and health parameters for individuals.
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Affiliation(s)
| | | | - Marie‐Pier Scott‐Boyer
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
| | - Sébastien Lacroix
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
| | - Melissa J. Morine
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
- Department of MathematicsUniversity of TrentoTrentoItaly
| | - Roberta Garcia Salomão
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | - Elaine Hillesheim
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nelly Conus
- Nestlé Institute of Health SciencesLausanneSwitzerland
| | | | | | | | - Mariana Mendes Muniz
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | - Vinícius Paula Venâncio
- School of Pharmaceutical Science of Ribeirao PretoUniversity of São PauloRibeirao PretoBrazil
| | | | | | - Taís Fontellas Laurito
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Isabela Ribeiro Rossi
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Raquel Ricci
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Jéssica Ré Jorge
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Mayara Leite Fagá
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | - Letícia Lima Falquetti
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | | | | | - Vicky Nogueira‐Pileggi
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | - Corrado Priami
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
- Department of MathematicsUniversity of TrentoTrentoItaly
| | - Jim Kaput
- Nestlé Institute of Health SciencesLausanneSwitzerland
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Lacroix S, Klicic Badoux J, Scott-Boyer MP, Parolo S, Matone A, Priami C, Morine MJ, Kaput J, Moco S. A computationally driven analysis of the polyphenol-protein interactome. Sci Rep 2018; 8:2232. [PMID: 29396566 PMCID: PMC5797150 DOI: 10.1038/s41598-018-20625-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/22/2018] [Indexed: 01/08/2023] Open
Abstract
Polyphenol-rich foods are part of many nutritional interventions aimed at improving health and preventing cardiometabolic diseases (CMDs). Polyphenols have oxidative, inflammatory, and/or metabolic effects. Research into the chemistry and biology of polyphenol bioactives is prolific but knowledge of their molecular interactions with proteins is limited. We mined public data to (i) identify proteins that interact with or metabolize polyphenols, (ii) mapped these proteins to pathways and networks, and (iii) annotated functions enriched within the resulting polyphenol-protein interactome. A total of 1,395 polyphenols and their metabolites were retrieved (using Phenol-Explorer and Dictionary of Natural Products) of which 369 polyphenols interacted with 5,699 unique proteins in 11,987 interactions as annotated in STITCH, Pathway Commons, and BindingDB. Pathway enrichment analysis using the KEGG repository identified a broad coverage of significant pathways of low specificity to particular polyphenol (sub)classes. When compared to drugs or micronutrients, polyphenols have pleiotropic effects across many biological processes related to metabolism and CMDs. These systems-wide effects were also found in the protein interactome of the polyphenol-rich citrus fruits, used as a case study. In sum, these findings provide a knowledgebase for identifying polyphenol classes (and polyphenol-rich foods) that individually or in combination influence metabolism.
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Affiliation(s)
- Sébastien Lacroix
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Institute of Nutrition and Functional Foods (INAF), Québec, Canada
| | | | - Marie-Pier Scott-Boyer
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Centre de Recherche du Centre Hospitalier Universitaire de Québec (CRCHUQ), Québec, Canada
| | - Silvia Parolo
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Alice Matone
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Department of Computer Science, University of Pisa, Pisa (PI), Italy
| | - Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | - Sofia Moco
- Nestle Institute of Health Sciences, Lausanne, Switzerland.
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6
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Nyima T, Müller M, Hooiveld GJEJ, Morine MJ, Scotti M. Nonlinear transcriptomic response to dietary fat intake in the small intestine of C57BL/6J mice. BMC Genomics 2016; 17:106. [PMID: 26861690 PMCID: PMC4748552 DOI: 10.1186/s12864-016-2424-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 07/30/2015] [Accepted: 02/02/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND A high caloric diet, in conjunction with low levels of physical activity, promotes obesity. Many studies are available regarding the relation between dietary saturated fats and the etiology of obesity, but most focus on liver, muscle and white adipose tissue. Furthermore, the majority of transcriptomic studies seek to identify linear effects of an external stimulus on gene expression, although such an assumption does not necessarily hold. Our work assesses the dose-dependent effects of dietary fat intake on differential gene expression in the proximal, middle and distal sections of the small intestine in C57BL/6J mice. Gene expression is analyzed in terms of either linear or nonlinear responses to fat intake. RESULTS The highest number of differentially expressed genes was observed in the middle section. In all intestine sections, most of the identified processes exhibited a linear response to increasing fat intake. The relative importance of logarithmic and exponential responses was higher in the proximal and distal sections, respectively. Functional enrichment analysis highlighted a constantly linear regulation of acute-phase response along the whole small intestine, with up-regulation of Serpina1b. The study of gene expression showed that exponential down-regulation of cholesterol transport in the middle section is coupled with logarithmic up-regulation of cholesterol homeostasis. A shift from linear to exponential response was observed in genes involved in the negative regulation of caspase activity, from middle to distal section (e.g., Birc5, up-regulated). CONCLUSIONS The transcriptomic signature associated with inflammatory processes preserved a linear response in the whole small intestine (e.g., up-regulation of Serpina1b). Processes related to cholesterol homeostasis were particularly active in the middle small intestine and only the highest fat intake down-regulated cholesterol transport and efflux (with a key role played by the down-regulation of ATP binding cassette transporters). Characterization of nonlinear patterns of gene expression triggered by different levels of dietary fat is an absolute novelty in intestinal studies. This approach helps identifying which processes are overloaded (i.e., positive, logarithmic regulation) or arrested (i.e., negative, exponential regulation) in response to excessive fat intake, and can shed light on the relationships linking lipid intake to obesity and its associated molecular disturbances.
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Affiliation(s)
- Tenzin Nyima
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto, Italy.
| | - Michael Müller
- Nutrition, Metabolism and Genomics group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands. .,Norwich Medical School, University of East Anglia, Norwich, UK.
| | - Guido J E J Hooiveld
- Nutrition, Metabolism and Genomics group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands.
| | - Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto, Italy.
| | - Marco Scotti
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto, Italy. .,GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
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Scott-Boyer MP, Lacroix S, Scotti M, Morine MJ, Kaput J, Priami C. A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases. Sci Rep 2016; 6:19633. [PMID: 26777674 PMCID: PMC4726080 DOI: 10.1038/srep19633] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 06/03/2015] [Accepted: 12/14/2015] [Indexed: 11/09/2022] Open
Abstract
The involvement of vitamins and other micronutrients in intermediary metabolism was elucidated in the mid 1900's at the level of individual biochemical reactions. Biochemical pathways remain the foundational knowledgebase for understanding how micronutrient adequacy modulates health in all life stages. Current daily recommended intakes were usually established on the basis of the association of a single nutrient to a single, most sensitive adverse effect and thus neglect interdependent and pleiotropic effects of micronutrients on biological systems. Hence, the understanding of the impact of overt or sub-clinical nutrient deficiencies on biological processes remains incomplete. Developing a more complete view of the role of micronutrients and their metabolic products in protein-mediated reactions is of importance. We thus integrated and represented cofactor-protein interaction data from multiple and diverse sources into a multi-layer network representation that links cofactors, cofactor-interacting proteins, biological processes, and diseases. Network representation of this information is a key feature of the present analysis and enables the integration of data from individual biochemical reactions and protein-protein interactions into a systems view, which may guide strategies for targeted nutritional interventions aimed at improving health and preventing diseases.
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Affiliation(s)
- Marie Pier Scott-Boyer
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Sébastien Lacroix
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Marco Scotti
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.,GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.,Department of Mathematics, University of Trento, Italy
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Praveen P, Jordan F, Priami C, Morine MJ. The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome. Microbiome 2015; 3:41. [PMID: 26399409 PMCID: PMC4581423 DOI: 10.1186/s40168-015-0104-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/26/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota can lead to either negative or positive effects on health, depending on the colonization sequence and diet. An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship. This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies. RESULTS We re-analyzed a published metagenomics and host gene expression dataset from a systems biology perspective. Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities. The diversity of the microbiota is higher in formula-fed than breast-fed infants, potentially reflecting the weaker dependence of infants on maternal microbiome. We mapped the microbial composition and the expression patterns for host systems and studied their relationship from a systems biology perspective, focusing on the differences. CONCLUSIONS Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed. Applying network-based systems biology approach via enrichment of microbial species with host genes revealed the novel key relationships of the microbiota with immune and metabolic activity. This was supported statistically by data and literature.
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Affiliation(s)
- Paurush Praveen
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 38068, Rovereto, Italy.
| | - Ferenc Jordan
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 38068, Rovereto, Italy.
| | - Corrado Priami
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 38068, Rovereto, Italy.
- Department of Mathematics, University of Trento, 38100, Povo, Italy.
| | - Melissa J Morine
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 38068, Rovereto, Italy.
- Department of Mathematics, University of Trento, 38100, Povo, Italy.
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9
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Matone A, O'Grada CM, Dillon ET, Morris C, Ryan MF, Walsh M, Gibney ER, Brennan L, Gibney MJ, Morine MJ, Roche HM. Body mass index mediates inflammatory response to acute dietary challenges. Mol Nutr Food Res 2015; 59:2279-92. [DOI: 10.1002/mnfr.201500184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/27/2015] [Accepted: 08/06/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Alice Matone
- The Microsoft Research; University of Trento Centre for Computational Systems Biology (COSBI); Rovereto Italy
| | - Colm M. O'Grada
- Nutrigenomics Research Group; UCD Conway Institute of Biomolecular and Biomedical Research; School of Public Health and Population Science; University College Dublin; Belfield Dublin Ireland
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Eugene T. Dillon
- Nutrigenomics Research Group; UCD Conway Institute of Biomolecular and Biomedical Research; School of Public Health and Population Science; University College Dublin; Belfield Dublin Ireland
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Ciara Morris
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Miriam F. Ryan
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Marianne Walsh
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Eileen R. Gibney
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Lorraine Brennan
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research; University College Dublin; Belfield Dublin Ireland
| | - Michael J. Gibney
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Melissa J. Morine
- The Microsoft Research; University of Trento Centre for Computational Systems Biology (COSBI); Rovereto Italy
- Department of Mathematics; University of Trento; Trento Italy
| | - Helen M. Roche
- Nutrigenomics Research Group; UCD Conway Institute of Biomolecular and Biomedical Research; School of Public Health and Population Science; University College Dublin; Belfield Dublin Ireland
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research; University College Dublin; Belfield Dublin Ireland
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Finucane OM, Lyons CL, Murphy AM, Reynolds CM, Klinger R, Healy NP, Cooke AA, Coll RC, McAllan L, Nilaweera KN, O'Reilly ME, Tierney AC, Morine MJ, Alcala-Diaz JF, Lopez-Miranda J, O'Connor DP, O'Neill LA, McGillicuddy FC, Roche HM. Monounsaturated fatty acid-enriched high-fat diets impede adipose NLRP3 inflammasome-mediated IL-1β secretion and insulin resistance despite obesity. Diabetes 2015; 64:2116-28. [PMID: 25626736 DOI: 10.2337/db14-1098] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 01/14/2015] [Indexed: 12/18/2022]
Abstract
Saturated fatty acid (SFA) high-fat diets (HFDs) enhance interleukin (IL)-1β-mediated adipose inflammation and insulin resistance. However, the mechanisms by which different fatty acids regulate IL-1β and the subsequent effects on adipose tissue biology and insulin sensitivity in vivo remain elusive. We hypothesized that the replacement of SFA for monounsaturated fatty acid (MUFA) in HFDs would reduce pro-IL-1β priming in adipose tissue and attenuate insulin resistance via MUFA-driven AMPK activation. MUFA-HFD-fed mice displayed improved insulin sensitivity coincident with reduced pro-IL-1β priming, attenuated adipose IL-1β secretion, and sustained adipose AMPK activation compared with SFA-HFD-fed mice. Furthermore, MUFA-HFD-fed mice displayed hyperplastic adipose tissue, with enhanced adipogenic potential of the stromal vascular fraction and improved insulin sensitivity. In vitro, we demonstrated that the MUFA oleic acid can impede ATP-induced IL-1β secretion from lipopolysaccharide- and SFA-primed cells in an AMPK-dependent manner. Conversely, in a regression study, switching from SFA- to MUFA-HFD failed to reverse insulin resistance but improved fasting plasma insulin levels. In humans, high-SFA consumers, but not high-MUFA consumers, displayed reduced insulin sensitivity with elevated pycard-1 and caspase-1 expression in adipose tissue. These novel findings suggest that dietary MUFA can attenuate IL-1β-mediated insulin resistance and adipose dysfunction despite obesity via the preservation of AMPK activity.
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Affiliation(s)
- Orla M Finucane
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Claire L Lyons
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Aoife M Murphy
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Clare M Reynolds
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Rut Klinger
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Niamh P Healy
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Aoife A Cooke
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Rebecca C Coll
- Inflammatory Research Group, Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Liam McAllan
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | | | - Marcella E O'Reilly
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Audrey C Tierney
- Department of Dietetics and Human Nutrition, La Trobe University, Melbourne, Victoria, Australia
| | - Melissa J Morine
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto, Italy
| | - Juan F Alcala-Diaz
- Lipids and Atherosclerosis Research Unit, Reina Sofía University Hospital, and CIBER Phyisiopathology of Obesity and Nutrition (CIBEROBN), University of Córdoba, Córdoba, Spain
| | - Jose Lopez-Miranda
- Lipids and Atherosclerosis Research Unit, Reina Sofía University Hospital, and CIBER Phyisiopathology of Obesity and Nutrition (CIBEROBN), University of Córdoba, Córdoba, Spain
| | - Darran P O'Connor
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Luke A O'Neill
- Inflammatory Research Group, Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Fiona C McGillicuddy
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
| | - Helen M Roche
- Nutrigenomics Research Group, Conway Institute of Biomedical and Biomolecular Research, and Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
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11
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Morine MJ, Monteiro JP, Wise C, Teitel C, Pence L, Williams A, Ning B, McCabe-Sellers B, Champagne C, Turner J, Shelby B, Bogle M, Beger RD, Priami C, Kaput J. Genetic associations with micronutrient levels identified in immune and gastrointestinal networks. Genes Nutr 2014; 9:408. [PMID: 24879315 PMCID: PMC4169061 DOI: 10.1007/s12263-014-0408-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/12/2014] [Indexed: 01/05/2023]
Abstract
The discovery of vitamins and clarification of their role in preventing frank essential nutrient deficiencies occurred in the early 1900s. Much vitamin research has understandably focused on public health and the effects of single nutrients to alleviate acute conditions. The physiological processes for maintaining health, however, are complex systems that depend upon interactions between multiple nutrients, environmental factors, and genetic makeup. To analyze the relationship between these factors and nutritional health, data were obtained from an observational, community-based participatory research program of children and teens (age 6–14) enrolled in a summer day camp in the Delta region of Arkansas. Assessments of erythrocyte S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), plasma homocysteine (Hcy) and 6 organic micronutrients (retinol, 25-hydroxy vitamin D3, pyridoxal, thiamin, riboflavin, and vitamin E), and 1,129 plasma proteins were performed at 3 time points in each of 2 years. Genetic makeup was analyzed with 1 M SNP genotyping arrays, and nutrient status was assessed with 24-h dietary intake questionnaires. A pattern of metabolites (met_PC1) that included the ratio of erythrocyte SAM/SAH, Hcy, and 5 vitamins were identified by principal component analysis. Met_PC1 levels were significantly associated with (1) single-nucleotide polymorphisms, (2) levels of plasma proteins, and (3) multilocus genotypes coding for gastrointestinal and immune functions, as identified in a global network of metabolic/protein–protein interactions. Subsequent mining of data from curated pathway, network, and genome-wide association studies identified genetic and functional relationships that may be explained by gene–nutrient interactions. The systems nutrition strategy described here has thus associated a multivariate metabolite pattern in blood with genes involved in immune and gastrointestinal functions.
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Affiliation(s)
- Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
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12
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Monteiro JP, Wise C, Morine MJ, Teitel C, Pence L, Williams A, McCabe-Sellers B, Champagne C, Turner J, Shelby B, Ning B, Oguntimein J, Taylor L, Toennessen T, Priami C, Beger RD, Bogle M, Kaput J. Methylation potential associated with diet, genotype, protein, and metabolite levels in the Delta Obesity Vitamin Study. Genes Nutr 2014; 9:403. [PMID: 24760553 PMCID: PMC4026438 DOI: 10.1007/s12263-014-0403-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/06/2014] [Indexed: 12/28/2022]
Abstract
Micronutrient research typically focuses on analyzing the effects of single or a few nutrients on health by analyzing a limited number of biomarkers. The observational study described here analyzed micronutrients, plasma proteins, dietary intakes, and genotype using a systems approach. Participants attended a community-based summer day program for 6-14 year old in 2 years. Genetic makeup, blood metabolite and protein levels, and dietary differences were measured in each individual. Twenty-four-hour dietary intakes, eight micronutrients (vitamins A, D, E, thiamin, folic acid, riboflavin, pyridoxal, and pyridoxine) and 3 one-carbon metabolites [homocysteine (Hcy), S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH)], and 1,129 plasma proteins were analyzed as a function of diet at metabolite level, plasma protein level, age, and sex. Cluster analysis identified two groups differing in SAM/SAH and differing in dietary intake patterns indicating that SAM/SAH was a potential marker of nutritional status. The approach used to analyze genetic association with the SAM/SAH metabolites is called middle-out: SNPs in 275 genes involved in the one-carbon pathway (folate, pyridoxal/pyridoxine, thiamin) or were correlated with SAM/SAH (vitamin A, E, Hcy) were analyzed instead of the entire 1M SNP data set. This procedure identified 46 SNPs in 25 genes associated with SAM/SAH demonstrating a genetic contribution to the methylation potential. Individual plasma metabolites correlated with 99 plasma proteins. Fourteen proteins correlated with body mass index, 49 with group age, and 30 with sex. The analytical strategy described here identified subgroups for targeted nutritional interventions.
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Affiliation(s)
- Jacqueline Pontes Monteiro
- />Department of Pediatrics, Faculty of Medicine, Faculty of Nutrition and Metabolism, University of São Paulo, Ribeirão Prêto, SP Brazil
| | - Carolyn Wise
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Melissa J. Morine
- />Department of Mathematics, University of Trento, Trento, Italy
- />The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Candee Teitel
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Lisa Pence
- />Division of Systems Biology, NCTR/FDA, Jefferson, AR USA
| | - Anna Williams
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Beverly McCabe-Sellers
- />Delta Obesity Prevention Research Unit, United States Department of Agriculture, Agricultural Research Service, Little Rock, AR USA
| | - Catherine Champagne
- />Dietary Assessment and Nutrition Counseling, Pennington Biomedical Research Center, Baton Rouge, LA USA
| | - Jerome Turner
- />Boys, Girls, Adults Community Development Center & The Phillips County Community Partners, Marvell, AR USA
| | - Beatrice Shelby
- />Boys, Girls, Adults Community Development Center & The Phillips County Community Partners, Marvell, AR USA
| | - Baitang Ning
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Joan Oguntimein
- />Shepherd Program for the Interdisciplinary Study of Poverty and Human Capability, Washington and Lee University, Lexington, VA USA
- />Medical School, Drexel University, Philadelphia, PA USA
| | - Lauren Taylor
- />Shepherd Program for the Interdisciplinary Study of Poverty and Human Capability, Washington and Lee University, Lexington, VA USA
- />Emory School of Public Health, Atlanta, GA USA
| | - Terri Toennessen
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Corrado Priami
- />Department of Mathematics, University of Trento, Trento, Italy
- />The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | | | - Margaret Bogle
- />Delta Obesity Prevention Research Unit, United States Department of Agriculture, Agricultural Research Service, Little Rock, AR USA
| | - Jim Kaput
- />Systems Nutrition and Health Unit, Nestle Institute of Health Sciences, Innovation Square, EPFL Campus, 1015 Lausanne, Switzerland
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O'Grada CM, Morine MJ, Morris C, Ryan M, Dillon ET, Walsh M, Gibney ER, Brennan L, Gibney MJ, Roche HM. PBMCs reflect the immune component of the WAT transcriptome--implications as biomarkers of metabolic health in the postprandial state. Mol Nutr Food Res 2013; 58:808-20. [PMID: 24170299 DOI: 10.1002/mnfr.201300182] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 08/19/2013] [Accepted: 08/21/2013] [Indexed: 12/23/2022]
Abstract
SCOPE Food and nutrition studies often require accessing metabolically active tissues, including adipose tissue. This can involve invasive biopsy procedures that can be a limiting factor in study design. In contrast, peripheral blood mononuclear cells (PBMCs) are a population of circulating immune cells that are easily accessible through venipuncture. As transcriptomics is of growing importance in food and metabolism research, understanding the transcriptomic relationship between these tissue types can provide insight into the utility of PBMCs in this field. METHODS AND RESULTS We examine this relationship within eight subjects, in two postprandial states (following oral lipid tolerance test and oral glucose tolerance test). Multivariate analysis techniques were used to examine variation between tissues, samples, and subjects in order to define which genes havecommon/disparate expression profiles associated with highly defined metabolic phenotypes. We demonstrate global similarities in gene expression between PBMCs and white adipose tissue, irrespective of the metabolic challenge type. Closer examination of individual genes revealed this similarity to be strongest in pathways related to immune response/inflammation. Notably, the expression of metabolism-related nuclear receptors, including PPARs, LXR, etc. was discordant between tissues CONCLUSION The PBMC transcriptome may therefore provide a unique insight into the inflammatory component of metabolic health, as opposed to directly reflecting the metabolic component of the adipose tissue transcriptome.
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Affiliation(s)
- Colm M O'Grada
- Nutrigenomics Research Group, UCD Conway Institute of Biomolecular and Biomedical Research, School of Public Health and Population Science, University College Dublin, Belfield, Dublin, Ireland; Institute of Food and Health, University College Dublin, Belfield, Dublin, Ireland
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14
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Abstract
We review here the status of human type 2 diabetes studies from a genetic, epidemiological, and clinical (intervention) perspective. Most studies limit analyses to one or a few omic technologies providing data of components of physiological processes. Since all chronic diseases are multifactorial and arise from complex interactions between genetic makeup and environment, type 2 diabetes mellitus (T2DM) is a collection of sub-phenotypes resulting in high fasting glucose. The underlying gene–environment interactions that produce these classes of T2DM are imperfectly characterized. Based on assessments of the complexity of T2DM, we propose a systems biology approach to advance the understanding of origin, onset, development, prevention, and treatment of this complex disease. This systems-based strategy is based on new study design principles and the integrated application of omics technologies: we pursue longitudinal studies in which each subject is analyzed at both homeostasis and after (healthy and safe) challenges. Each enrolled subject functions thereby as their own case and control and this design avoids assigning the subjects a priori to case and control groups based on limited phenotyping. Analyses at different time points along this longitudinal investigation are performed with a comprehensive set of omics platforms. These data sets are generated in a biological context, rather than biochemical compound class-driven manner, which we term “systems omics.”
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Affiliation(s)
- Martin Kussmann
- Nestlé Institute of Health Sciences SA Lausanne, Switzerland ; Faculty of Life Sciences, Ecole Polytechnique Fédérale Lausanne, Switzerland ; Faculty of Science, Aarhus University Aarhus, Denmark
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15
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Morine MJ, Toomey S, McGillicuddy FC, Reynolds CM, Power KA, Browne JA, Loscher C, Mills KHG, Roche HM. Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high-fat-diet-fed IL-1RI knockout mice. J Nutr Biochem 2012; 24:788-95. [PMID: 22841542 DOI: 10.1016/j.jnutbio.2012.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 04/22/2012] [Accepted: 04/26/2012] [Indexed: 11/27/2022]
Abstract
A subacute inflammatory phenotype is implicated in the pathology of insulin resistance (IR) and type 2 diabetes mellitus. Interleukin (IL)-1α and IL-1β are produced by innate immune cells, including macrophages, and mediate their inflammatory response through the IL-1 type I receptor (IL-IRI). This study sought to understand the transcriptomic signature of adipose tissue in obese IL-1RI(-/-) mice. Following dietary intervention, markers of insulin sensitivity and inflammation in adipose tissue were determined, and gene expression was assessed with microarrays. IL-1RI(-/-) mice fed a high-fat diet (HFD) had significantly lower plasma inflammatory cytokine concentrations than wild-type mice. Metabolic network analysis of transcriptomic effects identified up-regulation and co-expression of genes involved in lipolysis, lipogenesis and tricarboxylic acid (TCA) cycle. Further assessment of gene expression in a network of protein interactions related to innate immunity highlighted Stat3 as a potential transcriptional regulator of IL-1 signalling. The complex, downstream effects of IL-1 signalling through the IL-1RI receptor remain poorly defined. Using network-based analyses of transcriptomic signatures in IL-1RI(-/-) mice, we have identified expression changes in genes involved in lipid cycling and TCA cycle, which may be more broadly indicative of a restoration of mitochondrial function in the context of HFD. Our results also highlight a potential role for Stat3 in linking IL-1 signalling to adipogenesis and IR.
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Affiliation(s)
- Melissa J Morine
- Nutrigenomics Research Group, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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16
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Brennan EP, Morine MJ, Walsh DW, Roxburgh SA, Lindenmeyer MT, Brazil DP, Gaora PÓ, Roche HM, Sadlier DM, Cohen CD, Godson C, Martin F. Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy. Biochim Biophys Acta Mol Basis Dis 2012; 1822:589-99. [PMID: 22266139 DOI: 10.1016/j.bbadis.2012.01.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/06/2012] [Accepted: 01/08/2012] [Indexed: 01/09/2023]
Abstract
Transforming growth factor-beta (TGF-β1) is implicated in the onset and progression of renal fibrosis and diabetic nephropathy (DN), leading to a loss of epithelial characteristics of tubular cells. The transcriptional profile of renal tubular epithelial cells stimulated with TGF-β1 was assessed using RNA-Seq, with 2027 differentially expressed genes identified. Promoter analysis of transcription factor binding sites in the TGF-β1 responsive gene set predicted activation of multiple transcriptional networks, including NFκB. Comparison of RNA-Seq with microarray data from identical experimental conditions identified low abundance transcripts exclusive to RNA-Seq data. We compared these findings to human disease by analyzing transcriptomic data from renal biopsies of patients with DN versus control groups, identifying a shared subset of 179 regulated genes. ARK5, encoding an AMP-related kinase, and TGFBI - encoding transforming growth factor, beta-induced protein were induced by TGF-β1 and also upregulated in human DN. Suppression of ARK5 attenuated fibrotic responses of renal epithelia to TGF-β1 exposure; and silencing of TGFBI induced expression of the epithelial cell marker - E-cadherin. We identified low abundance transcripts in sequence data and validated expression levels of several transcripts (ANKRD56, ENTPD8) in tubular enriched kidney biopsies of DN patients versus living donors. In conclusion, we have defined a TGF-β1-driven pro-fibrotic signal in renal epithelial cells that is also evident in the DN renal transcriptome.
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Affiliation(s)
- Eoin P Brennan
- UCD Diabetes Research Centre, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
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17
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Nguyen TP, Scotti M, Morine MJ, Priami C. Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins. BMC Syst Biol 2011; 5:195. [PMID: 22136443 PMCID: PMC3264545 DOI: 10.1186/1752-0509-5-195] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 12/02/2011] [Indexed: 01/20/2023]
Abstract
Background Nutritional systems biology offers the potential for comprehensive predictions that account for all metabolic changes with the intricate biological organization and the multitudinous interactions between the cellular proteins. Protein-protein interaction (PPI) networks can be used for an integrative description of molecular processes. Although widely adopted in nutritional systems biology, these networks typically encompass a single category of functional interaction (i.e., metabolic, regulatory or signaling) or nutrient. Incorporating multiple nutrients and functional interaction categories under an integrated framework represents an informative approach for gaining system level insight on nutrient metabolism. Results We constructed a multi-level PPI network starting from the interactions of 200 vitamin-related proteins. Its final size was 1,657 proteins, with 2,700 interactions. To characterize the role of the proteins we computed 6 centrality indices and applied model-based clustering. We detected a subgroup of 22 proteins that were highly central and significantly related to vitamin D. Immune system and cancer-related processes were strongly represented among these proteins. Clustering of the centralities revealed a degree of redundancy among the indices; a repeated analysis using subsets of the centralities performed well in identifying the original set of 22 most central proteins. Conclusions Hierarchical and model-based clustering revealed multi-centrality hubs in a vitamin PPI network and redundancies among the centrality indices. Vitamin D-related proteins were strongly represented among network hubs, highlighting the pervasive effects of this nutrient. Our integrated approach to network construction identified promiscuous transcription factors, cytokines and enzymes - primarily related to immune system and cancer processes - representing potential gatekeepers linking vitamin intake to disease.
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Affiliation(s)
- Thanh-Phuong Nguyen
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (Trento), Italy
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18
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Morine MJ, Tierney AC, van Ommen B, Daniel H, Toomey S, Gjelstad IMF, Gormley IC, Pérez-Martinez P, Drevon CA, López-Miranda J, Roche HM. Transcriptomic coordination in the human metabolic network reveals links between n-3 fat intake, adipose tissue gene expression and metabolic health. PLoS Comput Biol 2011; 7:e1002223. [PMID: 22072950 PMCID: PMC3207936 DOI: 10.1371/journal.pcbi.1002223] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 08/25/2011] [Indexed: 12/22/2022] Open
Abstract
Understanding the molecular link between diet and health is a key goal in nutritional systems biology. As an alternative to pathway analysis, we have developed a joint multivariate and network-based approach to analysis of a dataset of habitual dietary records, adipose tissue transcriptomics and comprehensive plasma marker profiles from human volunteers with the Metabolic Syndrome. With this approach we identified prominent co-expressed sub-networks in the global metabolic network, which showed correlated expression with habitual n-3 PUFA intake and urinary levels of the oxidative stress marker 8-iso-PGF(2α). These sub-networks illustrated inherent cross-talk between distinct metabolic pathways, such as between triglyceride metabolism and production of lipid signalling molecules. In a parallel promoter analysis, we identified several adipogenic transcription factors as potential transcriptional regulators associated with habitual n-3 PUFA intake. Our results illustrate advantages of network-based analysis, and generate novel hypotheses on the transcriptomic link between habitual n-3 PUFA intake, adipose tissue function and oxidative stress.
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Affiliation(s)
- Melissa J. Morine
- Nutrigenomics Research Group, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Audrey C. Tierney
- Nutrigenomics Research Group, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | | | - Hannelore Daniel
- Molecular Nutrition Unit, Center of Life and Food Science, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Sinead Toomey
- Nutrigenomics Research Group, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Ingrid M. F. Gjelstad
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Endocrinology, Oslo University Hospital, Oslo, Norway
| | - Isobel C. Gormley
- School of Mathematical Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Pablo Pérez-Martinez
- Lipids and Atherosclerosis Research Unit, Reina Sofía University Hospital, Maimonides Institute for Biomedical Research at Cordoba (IMIBIC), University of Cordoba, Ciber Phyisiopatology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Christian A. Drevon
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jose López-Miranda
- Lipids and Atherosclerosis Research Unit, Reina Sofía University Hospital, Maimonides Institute for Biomedical Research at Cordoba (IMIBIC), University of Cordoba, Ciber Phyisiopatology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Helen M. Roche
- Nutrigenomics Research Group, UCD Conway Institute, University College Dublin, Dublin, Ireland
- * E-mail:
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19
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Morine MJ, McMonagle J, Toomey S, Reynolds CM, Moloney AP, Gormley IC, Gaora PO, Roche HM. Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome. BMC Bioinformatics 2010; 11:499. [PMID: 20929581 PMCID: PMC3098081 DOI: 10.1186/1471-2105-11-499] [Citation(s) in RCA: 18] [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: 11/24/2009] [Accepted: 10/07/2010] [Indexed: 11/25/2022] Open
Abstract
Background Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer options exist to contextualise those lists. The development and validation of such methods is crucial to the wider application of microarray technology in the clinical setting. Two key challenges in clinical bioinformatics involve appropriate statistical modelling of dynamic transcriptomic changes, and extraction of clinically relevant meaning from very large datasets. Results Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary intervention with high-CLA beef, a range of plasma markers indicated a marked improvement in the metabolic health of genetically obese mice. Tissue transcriptomic profiles indicated that the effects were most dramatic in liver (1270 genes significantly changed; p < 0.05), followed by muscle (601 genes) and adipose (16 genes). Results from modified GSEA showed that the high-CLA beef diet affected diverse biological processes across the three tissues, and that the majority of pathway changes reached significance only with the bi-directional test. Combining the liver tissue microarray results with plasma marker data revealed 110 CLA-sensitive genes showing strong canonical correlation with one or more plasma markers of metabolic health, and 9 significantly overrepresented pathways among this set; each of these pathways was also significantly changed by the high-CLA diet. Closer inspection of two of these pathways - selenoamino acid metabolism and steroid biosynthesis - illustrated clear diet-sensitive changes in constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect. Conclusion Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease.
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Affiliation(s)
- Melissa J Morine
- Nutrigenomics Research Group, School of Public Health, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
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