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Lei X, Ishida E, Yoshino S, Matsumoto S, Horiguchi K, Yamada E. Calorie Restriction Using High-Fat/Low-Carbohydrate Diet Suppresses Liver Fat Accumulation and Pancreatic Beta-Cell Dedifferentiation in Obese Diabetic Mice. Nutrients 2024; 16:995. [PMID: 38613031 PMCID: PMC11013071 DOI: 10.3390/nu16070995] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
In diabetes, pancreatic β-cells gradually lose their ability to secrete insulin with disease progression. β-cell dysfunction is a contributing factor to diabetes severity. Recently, islet cell heterogeneity, exemplified by β-cell dedifferentiation and identified in diabetic animals, has attracted attention as an underlying molecular mechanism of β-cell dysfunction. Previously, we reported β-cell dedifferentiation suppression by calorie restriction, not by reducing hyperglycemia using hypoglycemic agents (including sodium-glucose cotransporter inhibitors), in an obese diabetic mice model (db/db). Here, to explore further mechanisms of the effects of food intake on β-cell function, db/db mice were fed either a high-carbohydrate/low-fat diet (db-HC) or a low-carbohydrate/high-fat diet (db-HF) using similar calorie restriction regimens. After one month of intervention, body weight reduced, and glucose intolerance improved to a similar extent in the db-HC and db-HF groups. However, β-cell dedifferentiation did not improve in the db-HC group, and β-cell mass compensatory increase occurred in this group. More prominent fat accumulation occurred in the db-HC group livers. The expression levels of genes related to lipid metabolism, mainly regulated by peroxisome proliferator-activated receptor α and γ, differed significantly between groups. In conclusion, the fat/carbohydrate ratio in food during calorie restriction in obese mice affected both liver lipid metabolism and β-cell dedifferentiation.
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Affiliation(s)
| | - Emi Ishida
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Graduate School of Medicine, Gunma University, Maebashi 371-8511, Gunma, Japan
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Wróbel S, Turek C, Stępień E, Piwowar M. Data integration through canonical correlation analysis and its application to OMICs research. J Biomed Inform 2024; 151:104575. [PMID: 38086443 DOI: 10.1016/j.jbi.2023.104575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 02/23/2024]
Abstract
The subject of the paper is a review of multidimensional data analysis methods, which is the canonical analysis with its various variants and its use in omics data research. The dynamic development of high-throughput methods, and with them the availability of large and constantly growing data resources, forces the development of new analytical approaches that allow the review of the analyzed processes, taking into account data from various levels of the organization of living organisms. The multidimensional perspective allows for the assessment of the analyzed phenomenon in a more realistic way, as it generally takes into account much more data (including OMICs data). Without omitting the complexity of an organism, the method simplifies the multidimensional view, finally giving the result so that the researcher can draw practical conclusions. This is particularly important in medical sciences, where the study of pathological processes is usually aimed at developing treatment regimens. One of the primary methods for studying biomedical processes in a multidimensional approach is the canonical correlation analysis (CCA) with various variants. The use of CCA unique methodologies for simultaneous analysis of multiset biomolecular data opens up new avenues for studying previously undiscovered processes and interdependencies such as e.g. in the tumor microenvironment (TME) connected to intercellular communication. Because of the huge and still untapped potential of canonical correlation, in this review available implementations of CCA techniques are presented. In particular, the possibility of using the technique of canonical correlation analysis for OMICs data is emphasized.
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Affiliation(s)
- Sonia Wróbel
- Department of Medical Physics, Jagiellonian University, Marian Smoluchowski Institute of Physics, Krakow, Poland
| | - Cezary Turek
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Krakow, Poland
| | - Ewa Stępień
- Department of Medical Physics, Jagiellonian University, Marian Smoluchowski Institute of Physics, Krakow, Poland; Center for Theranostics, Jagiellonian University ul. Kopernika 40, 31-034 Kraków, Poland; Total-Body Jagiellonian-PET Laboratory, Jagiellonian University, Kraków, Poland.
| | - Monika Piwowar
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Krakow, Poland.
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Pfeifer B, Bloice MD, Schimek MG. Parea: Multi-view ensemble clustering for cancer subtype discovery. J Biomed Inform 2023:104406. [PMID: 37257630 DOI: 10.1016/j.jbi.2023.104406] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/20/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
Multi-view clustering methods are essential for the stratification of patients into sub-groups of similar molecular characteristics. In recent years, a wide range of methods have been developed for this purpose. However, due to the high diversity of cancer-related data, a single method may not perform sufficiently well in all cases. We present Parea, a multi-view hierarchical ensemble clustering approach for disease subtype discovery. We demonstrate its performance on several machine learning benchmark datasets. We apply and validate our methodology on real-world multi-view cancer patient data. Parea outperforms the current state-of-the-art on six out of seven analysed cancer types. We have integrated the Parea method into our developed Python package Pyrea (https://github.com/mdbloice/Pyrea), which enables the effortless and flexible design of ensemble workflows while incorporating a wide range of fusion and clustering algorithms.
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Affiliation(s)
- Bastian Pfeifer
- Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Austria.
| | - Marcus D Bloice
- Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Austria
| | - Michael G Schimek
- Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Austria
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Mosaad YO, Hussein MA, Ateyya H, Mohamed AH, Ali AA, Ramadan Youssuf A, Wink M, El-Kholy AA. Vanin 1 Gene Role in Modulation of iNOS/MCP-1/TGF-β1 Signaling Pathway in Obese Diabetic Patients. J Inflamm Res 2022; 15:6745-6759. [PMID: 36540060 PMCID: PMC9760040 DOI: 10.2147/jir.s386506] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/23/2022] [Indexed: 01/15/2024] Open
Abstract
INTRODUCTION Cysteamine, a powerful endogenous antioxidant, is produced mostly by the vanin-1 with pantetheinase activity. With regard to glycemic, inflammatory, and redox factors, the current study sought to evaluate the association between the expression of the vanin-1 gene, oxidative stress, and inflammatory and iNOS signaling pathway in obese diabetic patients. METHODS We enrolled 67 male subjects with an average age of 53.5 ± 5.0 years, divided into 4 groups according to the WHO guideline. We determined their plasma levels of glucose, insulin, IRI, HbA1c, TC, TG, HDL-C, TNF- α, MCP-1, TGF-β1, SOD, CAT, and TBARs, as well as expression of the iNOS and Vanin1 genes. RESULTS Overweight and obese class I and II diabetics had significantly higher levels of plasma glucose, insulin, HbA1c, TNF-α, MCP-1, TGF-β1, CAT, and TBAR as well as iNOS and vanin-1 gene expression compared to healthy control individuals. In addition, as compared to healthy control individuals, overweight obese class I and II diabetics' plasma HDL-C levels and blood SOD activity were significantly lower. In addition, ultrasound and computed tomography showed that the presence of a mild obscuring fatty liver with mild hepatic echogenicity appeared in overweight, class I and II obese diabetic patients. CONCLUSION These findings provide important information for understanding the correlation between Vanin 1 and glycemic, inflammatory, and redox factors in obese patients. Furthermore, US and CT analysis were performed to visualize the observed images of fatty liver due to obesity.
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Affiliation(s)
- Yasser O Mosaad
- Department of Pharmacy, Practice & Clinical Pharmacy, Faculty of Pharmacy, Future University, Cairo, Egypt
| | - Mohammed Abdalla Hussein
- Department of Biotechnology, Faculty of Applied Health Science, October 6th University, October 6th City, Egypt
| | - Hayam Ateyya
- Department of Medical Pharmacology, Faculty of Medicine, Cairo University, Cairo, Egypt
- Department of Pharmacy Practice and Clinical Pharmacy, Faculty of Pharmacy, Future University, Cairo, Egypt
| | - Ahmed H Mohamed
- Department of Radiology and Medical Imaging, Faculty of Applied Health Science Technology, October 6th University, October 6th City, Egypt
| | - Ali A Ali
- Food Sciences Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Alaa Ramadan Youssuf
- Consultant and Head of Cardiology Department, AL-AHRAR Teaching Hospital, Zagazig University, Zagazig, Egypt
| | - Michael Wink
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Heidelberg, Germany
| | - Amal A El-Kholy
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain-Shams University, Cairo, Egypt
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Baumann A, Burger K, Brandt A, Staltner R, Jung F, Rajcic D, Lorenzo Pisarello MJ, Bergheim I. GW9662, a peroxisome proliferator-activated receptor gamma antagonist, attenuates the development of non-alcoholic fatty liver disease. Metabolism 2022; 133:155233. [PMID: 35654114 DOI: 10.1016/j.metabol.2022.155233] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 12/03/2021] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Insulin resistance is among the key risk factors for the development of non-alcoholic fatty liver disease (NAFLD). Recently, it has been reported that GW9662, shown to be a potent peroxisome proliferator-activated receptor gamma (PPARγ) antagonist, may improve insulin sensitivity in settings of type 2 diabetes. Here, we determined the effects of GW9662 on the development of NAFLD and molecular mechanisms involved. METHODS Female C57BL/6J mice were pair-fed either a liquid control diet (C) or a fat-, fructose- and cholesterol-rich diet (FFC) for 8 weeks while either being treated with GW9662 (1 mg/kg body weight; C+GW9662 and FFC+GW9662) or vehicle (C and FFC) i.p. three times weekly. Indices of liver damage and inflammation, parameters of glucose metabolism and portal endotoxin levels were determined. Lipopolysaccharide (LPS)-challenged J774A.1 cells were treated with 10 μM GW9662. RESULTS Despite similar caloric intake the development of NAFLD and insulin resistance were significantly attenuated in FFC+GW9662-treated mice when compared to FFC-fed animals. Bacterial endotoxin levels in portal plasma were almost similarly increased in both FFC-fed groups while expressions of toll-like receptor 4 (Tlr4), myeloid differentiation primary response 88 (Myd88) and interleukin 1 beta (Il1b) as well as nitrite (NO2-) concentration in liver were significantly higher in FFC-fed mice than in FFC+GW9662-treated animals. In J774A.1 cells, treatment with GW9662 significantly attenuated LPS-induced expression of Il1b, interleukin 6 (Il6) and inducible nitric oxide synthase (iNos) as well as NO2- formation. CONCLUSION In summary, our data suggest that the PPARγ antagonist GW9662 attenuates the development of a diet-induced NAFLD and that this is associated with a protection against the activation of the TLR4 signaling cascade.
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Affiliation(s)
- Anja Baumann
- Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Katharina Burger
- Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Annette Brandt
- Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Raphaela Staltner
- Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Finn Jung
- Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Dragana Rajcic
- Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | | | - Ina Bergheim
- Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria.
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Ducheix S, Piccinin E, Peres C, Garcia-Irigoyen O, Bertrand-Michel J, Fouache A, Cariello M, Lobaccaro JM, Guillou H, Sabbà C, Ntambi JM, Moschetta A. Reduction in gut-derived MUFAs via intestinal stearoyl-CoA desaturase 1 deletion drives susceptibility to NAFLD and hepatocarcinoma. Hepatol Commun 2022; 6:2937-2949. [PMID: 35903850 PMCID: PMC9512486 DOI: 10.1002/hep4.2053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/21/2022] [Accepted: 07/06/2022] [Indexed: 11/15/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is defined by a set of hepatic conditions ranging from steatosis to steatohepatitis (NASH), characterized by inflammation and fibrosis, eventually predisposing to hepatocellular carcinoma (HCC). Together with fatty acids (FAs) originated from adipose lipolysis and hepatic lipogenesis, intestinal‐derived FAs are major contributors of steatosis. However, the role of mono‐unsaturated FAs (MUFAs) in NAFLD development is still debated. We previously established the intestinal capacity to produce MUFAs, but its consequences in hepatic functions are still unknown. Here, we aimed to determine the role of the intestinal MUFA‐synthetizing enzyme stearoyl‐CoA desaturase 1 (SCD1) in NAFLD. We used intestinal‐specific Scd1‐KO (iScd1−/−) mice and studied hepatic dysfunction in different models of steatosis, NASH, and HCC. Intestinal‐specific Scd1 deletion decreased hepatic MUFA proportion. Compared with controls, iScd1−/− mice displayed increased hepatic triglyceride accumulation and derangement in cholesterol homeostasis when fed a MUFA‐deprived diet. Then, on Western diet feeding, iScd1−/− mice triggered inflammation and fibrosis compared with their wild‐type littermates. Finally, intestinal‐Scd1 deletion predisposed mice to liver cancer. Conclusions: Collectively, these results highlight the major importance of intestinal MUFA metabolism in maintaining hepatic functions and show that gut‐derived MUFAs are protective from NASH and HCC.
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Affiliation(s)
- Simon Ducheix
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Elena Piccinin
- Department of Basic Medical Science, Neurosciences, and Sense organs, University of Bari "Aldo Moro", Bari, Italy
| | - Claudia Peres
- INBB, National Institute for Biostructures and Biosystems, Rome, Italy
| | | | - Justine Bertrand-Michel
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,I2MC, Université de Toulouse, Inserm, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Allan Fouache
- INSERM U 1103, CNRS, UMR 6293, Université Clermont Auvergne, GReD, Aubière, France.,Centre de Recherche en Nutrition Humaine d'Auvergne, Clermont-Ferrand, France
| | - Marica Cariello
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Jean-Marc Lobaccaro
- INSERM U 1103, CNRS, UMR 6293, Université Clermont Auvergne, GReD, Aubière, France.,Centre de Recherche en Nutrition Humaine d'Auvergne, Clermont-Ferrand, France
| | - Hervé Guillou
- Integrative Toxicology and Metabolism Team, Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Carlo Sabbà
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - James M Ntambi
- Departments of Biochemistry and of Nutritional Sciences, University of Wisconsin Madison, Madison, Wisconsin, USA
| | - Antonio Moschetta
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy.,INBB, National Institute for Biostructures and Biosystems, Rome, Italy
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Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C. High-sensitivity pattern discovery in large, paired multiomic datasets. Bioinformatics 2022; 38:i378-i385. [PMID: 35758795 PMCID: PMC9235493 DOI: 10.1093/bioinformatics/btac232] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Modern biological screens yield enormous numbers of measurements, and identifying and interpreting statistically significant associations among features are essential. In experiments featuring multiple high-dimensional datasets collected from the same set of samples, it is useful to identify groups of associated features between the datasets in a way that provides high statistical power and false discovery rate (FDR) control. RESULTS Here, we present a novel hierarchical framework, HAllA (Hierarchical All-against-All association testing), for structured association discovery between paired high-dimensional datasets. HAllA efficiently integrates hierarchical hypothesis testing with FDR correction to reveal significant linear and non-linear block-wise relationships among continuous and/or categorical data. We optimized and evaluated HAllA using heterogeneous synthetic datasets of known association structure, where HAllA outperformed all-against-all and other block-testing approaches across a range of common similarity measures. We then applied HAllA to a series of real-world multiomics datasets, revealing new associations between gene expression and host immune activity, the microbiome and host transcriptome, metabolomic profiling and human health phenotypes. AVAILABILITY AND IMPLEMENTATION An open-source implementation of HAllA is freely available at http://huttenhower.sph.harvard.edu/halla along with documentation, demo datasets and a user group. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrew R Ghazi
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kathleen Sucipto
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ali Rahnavard
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric A Franzosa
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lauren J McIver
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jason Lloyd-Price
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Emma Schwager
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - George Weingart
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yo Sup Moon
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Levi Waldron
- Department of Epidemiology and Biostatistics, City University of New York Graduate School of Public Health and Health Policy, New York City, NY 10035, USA
| | - Curtis Huttenhower
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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Brouard C, Mariette J, Flamary R, Vialaneix N. Feature selection for kernel methods in systems biology. NAR Genom Bioinform 2022; 4:lqac014. [PMID: 35265835 PMCID: PMC8900155 DOI: 10.1093/nargab/lqac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/12/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The substantial development of high-throughput biotechnologies has rendered large-scale multi-omics datasets increasingly available. New challenges have emerged to process and integrate this large volume of information, often obtained from widely heterogeneous sources. Kernel methods have proven successful to handle the analysis of different types of datasets obtained on the same individuals. However, they usually suffer from a lack of interpretability since the original description of the individuals is lost due to the kernel embedding. We propose novel feature selection methods that are adapted to the kernel framework and go beyond the well-established work in supervised learning by addressing the more difficult tasks of unsupervised learning and kernel output learning. The method is expressed under the form of a non-convex optimization problem with a ℓ1 penalty, which is solved with a proximal gradient descent approach. It is tested on several systems biology datasets and shows good performances in selecting relevant and less redundant features compared to existing alternatives. It also proved relevant for identifying important governmental measures best explaining the time series of Covid-19 reproducing number evolution during the first months of 2020. The proposed feature selection method is embedded in the R package mixKernel version 0.8, published on CRAN. Installation instructions are available at http://mixkernel.clementine.wf/.
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Affiliation(s)
- Céline Brouard
- Université de Toulouse, INRAE, UR MIAT, F-31320, Castanet-Tolosan, France
| | - Jérôme Mariette
- Université de Toulouse, INRAE, UR MIAT, F-31320, Castanet-Tolosan, France
| | - Rémi Flamary
- École Polytechnique, CMAP, F-91120, Palaiseau, France
| | - Nathalie Vialaneix
- Université de Toulouse, INRAE, UR MIAT, F-31320, Castanet-Tolosan, France
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9
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Chen Z, Yang T, Walker DI, Thomas DC, Qiu C, Chatzi L, Alderete TL, Kim JS, Conti DV, Breton CV, Liang D, Hauser ER, Jones DP, Gilliland FD. Dysregulated lipid and fatty acid metabolism link perfluoroalkyl substances exposure and impaired glucose metabolism in young adults. Environ Int 2020; 145:106091. [PMID: 32892005 PMCID: PMC8009052 DOI: 10.1016/j.envint.2020.106091] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFASs) exposure is ubiquitous among the US population and has been linked to adverse health outcomes including cardiometabolic diseases, immune dysregulation and endocrine disruption. However, the metabolic mechanism underlying the adverse health effect of PFASs exposure is unknown. OBJECTIVE The aim of this project is to investigate the association between PFASs exposure and altered metabolic pathways linked to increased cardiometabolic risk in young adults. METHODS A total of 102 young adults with 82% overweight or obese participants were enrolled from Southern California between 2014 and 2017. Cardiometabolic outcomes were assessed including oral glucose tolerance test (OGTT) measures, body fat and lipid profiles. High-resolution metabolomics was used to quantify plasma exposure levels of three PFAS congeners and intensity profiles of the untargeted metabolome. Fasting concentrations of 45 targeted metabolites involved in fatty acid and lipid metabolism were used to verify untargeted metabolomics findings. Bayesian Kernel Machine Regression (BKMR) was used to examine the associations between PFAS exposure mixture and cardiometabolic outcomes adjusting for covariates. Mummichog pathway enrichment analysis was used to explore PFAS-associated metabolic pathways. Moreover, the effect of PFAS exposure on the metabolic network, including metabolomic profiles and cardiometabolic outcomes, was investigated. RESULTS Higher exposure to perfluorooctanoic acid (PFOA) was associated with higher 30-minute glucose levels and glucose area under the curve (AUC) during the OGTT (p < 0.001). PFAS exposure was also associated with altered lipid pathways, which contributed to the metabolic network connecting PFOA and higher glucose levels following the OGTT. Targeted metabolomics analysis indicated that higher PFOA exposure was associated with higher levels of glycerol (p = 0.006), which itself was associated with higher 30-minute glucose (p = 0.006). CONCLUSIONS Increased lipolysis and fatty acid oxidation could contribute to the biological mechanisms linking PFAS exposure and impaired glucose metabolism among young adults. Findings of this study warrants future experimental studies and epidemiological studies with larger sample size to replicate.
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Affiliation(s)
- Zhanghua Chen
- Division of Environmental Health, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Tingyu Yang
- Division of Environmental Health, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Duncan C Thomas
- Division of Biostatistics, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Chenyu Qiu
- Division of Environmental Health, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Leda Chatzi
- Division of Environmental Health, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Tanya L Alderete
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA
| | - Jeniffer S Kim
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Division of Biostatistics, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Carrie V Breton
- Division of Environmental Health, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Donghai Liang
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth R Hauser
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center Durham, NC, USA
| | - Dean P Jones
- Department of Medicine, Emory University, Atlanta, GA, USA
| | - Frank D Gilliland
- Division of Environmental Health, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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Rodosthenous T, Shahrezaei V, Evangelou M. Integrating multi-OMICS data through sparse canonical correlation analysis for the prediction of complex traits: a comparison study. Bioinformatics 2020; 36:4616-4625. [PMID: 32437529 PMCID: PMC7750936 DOI: 10.1093/bioinformatics/btaa530] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/05/2019] [Revised: 04/22/2020] [Accepted: 05/16/2020] [Indexed: 01/08/2023] Open
Abstract
Motivation Recent developments in technology have enabled researchers to collect multiple OMICS datasets for the same individuals. The conventional approach for understanding the relationships between the collected datasets and the complex trait of interest would be through the analysis of each OMIC dataset separately from the rest, or to test for associations between the OMICS datasets. In this work we show that integrating multiple OMICS datasets together, instead of analysing them separately, improves our understanding of their in-between relationships as well as the predictive accuracy for the tested trait. Several approaches have been proposed for the integration of heterogeneous and high-dimensional (p≫n) data, such as OMICS. The sparse variant of canonical correlation analysis (CCA) approach is a promising one that seeks to penalize the canonical variables for producing sparse latent variables while achieving maximal correlation between the datasets. Over the last years, a number of approaches for implementing sparse CCA (sCCA) have been proposed, where they differ on their objective functions, iterative algorithm for obtaining the sparse latent variables and make different assumptions about the original datasets. Results Through a comparative study we have explored the performance of the conventional CCA proposed by Parkhomenko et al., penalized matrix decomposition CCA proposed by Witten and Tibshirani and its extension proposed by Suo et al. The aforementioned methods were modified to allow for different penalty functions. Although sCCA is an unsupervised learning approach for understanding of the in-between relationships, we have twisted the problem as a supervised learning one and investigated how the computed latent variables can be used for predicting complex traits. The approaches were extended to allow for multiple (more than two) datasets where the trait was included as one of the input datasets. Both ways have shown improvement over conventional predictive models that include one or multiple datasets. Availability and implementation https://github.com/theorod93/sCCA. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
| | - Marina Evangelou
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
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11
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Zhang L, Qiang J, Tao YF, Bao JW, Zhu HJ, He J, Xu P. Cloning of the gene encoding acyl-CoA thioesterase 11 and its functional characterization in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) under heat stress. J Therm Biol 2020; 93:102681. [PMID: 33077108 DOI: 10.1016/j.jtherbio.2020.102681] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/09/2020] [Accepted: 08/04/2020] [Indexed: 01/20/2023]
Abstract
Members of the ACOT (acyl-CoA thioesterase) family hydrolyze fatty acyl-CoA to form free fatty acids (FFAs) and coenzyme A (CoA). These enzymes play important roles in fatty acid metabolism. Here, we report the cloning and functional analysis of acot11β in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂). The open reading frame of acot11β was found to be 594 bp in length, encoding 198 amino acids. We determined the transcript levels of acot11β in ten tissues of hybrid yellow catfish by qRT-PCR and found that it was highly expressed in the liver, so we chose the liver for further analysis. We determined the transcript levels of acot11β in hybrid yellow catfish under heat stress conditions, and analyzed the changes in serum biochemical parameters, liver biochemical parameters, and transcript levels of lipid metabolism-related genes. Healthy yellow catfish were subjected to heat stress at 35 °C for 96 h, and the experimental results were compared with those from fish in a control group (28 °C). The levels of glucose (GLU), total cholesterol (TC), and triglyceride (TG) in serum were significantly increased in the heat-stressed group compared with the control group (P < 0.05). Acute heat stress led to decreased liver glycogen contents, but significantly increased TC and TG contents in the liver (P < 0.05). The transcript levels of acot11β, acc, and fas were significantly reduced, while that of pparα was significantly increased in hybrid yellow catfish exposed to heat stress (P < 0.05). Our results indicate that acot11β plays an important role in regulating lipid metabolism in hybrid yellow catfish, and this metabolic process is greatly affected by temperature. These results may be useful for developing effective strategies to prevent or reduce metabolic disorders of yellow catfish caused by high temperature.
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Affiliation(s)
- Li Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Jun Qiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yi-Fan Tao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jing-Wen Bao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hao-Jun Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Jie He
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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12
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Abstract
A huge amount of atomized biological data collected in various databases and the need for a description of their relation by theoretical methods causes the development of data integration methods. The omics data analysis by integration of biological knowledge with mathematical procedures implemented in the OmicsON R library is presented in the paper. OmicsON is a tool for the integration of two sets of data: transcriptomics and metabolomics. In the workflow of the library, the functional grouping and statistical analysis are applied. Subgroups among the transcriptomic and metabolomics sets are created based on the biological knowledge stored in Reactome and String databases. It gives the possibility to analyze such sets of data by multivariate statistical procedures like Canonical Correlation Analysis (CCA) or Partial Least Squares (PLS). The integration of metabolomic and transcriptomic data based on the methodology contained in OmicsON helps to easily obtain information on the connection of data from two different sets. This information can significantly help in assessing the relationship between gene expression and metabolite concentrations, which in turn facilitates the biological interpretation of the analyzed process.
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Affiliation(s)
- Cezary Turek
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Medical College, Krakow, Poland
| | - Sonia Wróbel
- Department of Medical Physics, Jagiellonian University, Marian Smoluchowski Institute of Physics, Krakow, Poland
| | - Monika Piwowar
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Medical College, Krakow, Poland
- * E-mail:
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13
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Fougerat A, Montagner A, Loiseau N, Guillou H, Wahli W. Peroxisome Proliferator-Activated Receptors and Their Novel Ligands as Candidates for the Treatment of Non-Alcoholic Fatty Liver Disease. Cells 2020; 9:E1638. [PMID: 32650421 PMCID: PMC7408116 DOI: 10.3390/cells9071638] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [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: 05/29/2020] [Revised: 06/26/2020] [Accepted: 07/04/2020] [Indexed: 12/11/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a major health issue worldwide, frequently associated with obesity and type 2 diabetes. Steatosis is the initial stage of the disease, which is characterized by lipid accumulation in hepatocytes, which can progress to non-alcoholic steatohepatitis (NASH) with inflammation and various levels of fibrosis that further increase the risk of developing cirrhosis and hepatocellular carcinoma. The pathogenesis of NAFLD is influenced by interactions between genetic and environmental factors and involves several biological processes in multiple organs. No effective therapy is currently available for the treatment of NAFLD. Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors that regulate many functions that are disturbed in NAFLD, including glucose and lipid metabolism, as well as inflammation. Thus, they represent relevant clinical targets for NAFLD. In this review, we describe the determinants and mechanisms underlying the pathogenesis of NAFLD, its progression and complications, as well as the current therapeutic strategies that are employed. We also focus on the complementary and distinct roles of PPAR isotypes in many biological processes and on the effects of first-generation PPAR agonists. Finally, we review novel and safe PPAR agonists with improved efficacy and their potential use in the treatment of NAFLD.
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Affiliation(s)
- Anne Fougerat
- Institut National de la Recherche Agronomique (INRAE), ToxAlim, UMR1331 Toulouse, France; (A.M.); (N.L.); (H.G.)
| | - Alexandra Montagner
- Institut National de la Recherche Agronomique (INRAE), ToxAlim, UMR1331 Toulouse, France; (A.M.); (N.L.); (H.G.)
- Institut National de la Santé et de la Recherche Médicale (Inserm), Institute of Metabolic and Cardiovascular Diseases, UMR1048 Toulouse, France
- Institute of Metabolic and Cardiovascular Diseases, University of Toulouse, UMR1048 Toulouse, France
| | - Nicolas Loiseau
- Institut National de la Recherche Agronomique (INRAE), ToxAlim, UMR1331 Toulouse, France; (A.M.); (N.L.); (H.G.)
| | - Hervé Guillou
- Institut National de la Recherche Agronomique (INRAE), ToxAlim, UMR1331 Toulouse, France; (A.M.); (N.L.); (H.G.)
| | - Walter Wahli
- Institut National de la Recherche Agronomique (INRAE), ToxAlim, UMR1331 Toulouse, France; (A.M.); (N.L.); (H.G.)
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
- Center for Integrative Genomics, Université de Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
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14
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Liu Y, Izem L, Morton RE. Identification of a hormone response element that mediates suppression of APOF by LXR and PPARα agonists. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158583. [PMID: 31812787 DOI: 10.1016/j.bbalip.2019.158583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/21/2019] [Accepted: 12/01/2019] [Indexed: 12/18/2022]
Abstract
Apolipoprotein F (ApoF) regulates cholesteryl ester transfer protein activity. We previously observed that hepatic APOF mRNA levels are decreased by high fat, cholesterol-enriched diets. Here we show in human liver C3A cells that APOF mRNA levels are reduced by agonists of LXR and PPARα nuclear receptors. This negative regulation requires co-incubation with the RXR agonist, retinoic acid. Bioinformatic analysis of the ~2 kb sequence upstream of the APOF promoter identified one potential LXR and 4 potential PPARα binding sites clustered between nucleotides -2007 and -1961. ChIP analysis confirmed agonist-dependent binding of LXRα, PPARα, and RXRα to this hormone response element complex (HREc). A luciferase reporter containing the 2 kb 5' APOF sequence was negatively regulated by LXR and PPARα ligands as seen in cells. This regulation was maintained in constructs lacking the ~1700 nucleotides between the HREc and the APOF proximal promoter. Mutations of the HREc that disrupted LXRα and PPARα binding led to the loss of reporter construct inhibition by agonists of these nuclear receptors. siRNA knockdown studies showed that APOF gene regulation by LXRα or PPARα agonists did not require an interaction between these two nuclear receptors. Thus, APOF is subject to negative regulation by agonist-activated LXR or PPARα nuclear receptors binding to a regulatory element ~1900 bases 5' to the APOF promoter. High fat, cholesterol-enriched diets likely reduce APOF gene expression via these receptors interacting at this regulatory site.
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Affiliation(s)
- Yan Liu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States of America
| | - Lahoucine Izem
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States of America
| | - Richard E Morton
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States of America.
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15
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Jendoubi T, Strimmer K. A whitening approach to probabilistic canonical correlation analysis for omics data integration. BMC Bioinformatics 2019; 20:15. [PMID: 30626338 PMCID: PMC6327589 DOI: 10.1186/s12859-018-2572-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 07/13/2018] [Accepted: 12/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Canonical correlation analysis (CCA) is a classic statistical tool for investigating complex multivariate data. Correspondingly, it has found many diverse applications, ranging from molecular biology and medicine to social science and finance. Intriguingly, despite the importance and pervasiveness of CCA, only recently a probabilistic understanding of CCA is developing, moving from an algorithmic to a model-based perspective and enabling its application to large-scale settings. RESULTS Here, we revisit CCA from the perspective of statistical whitening of random variables and propose a simple yet flexible probabilistic model for CCA in the form of a two-layer latent variable generative model. The advantages of this variant of probabilistic CCA include non-ambiguity of the latent variables, provisions for negative canonical correlations, possibility of non-normal generative variables, as well as ease of interpretation on all levels of the model. In addition, we show that it lends itself to computationally efficient estimation in high-dimensional settings using regularized inference. We test our approach to CCA analysis in simulations and apply it to two omics data sets illustrating the integration of gene expression data, lipid concentrations and methylation levels. CONCLUSIONS Our whitening approach to CCA provides a unifying perspective on CCA, linking together sphering procedures, multivariate regression and corresponding probabilistic generative models. Furthermore, we offer an efficient computer implementation in the "whitening" R package available at https://CRAN.R-project.org/package=whitening .
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Affiliation(s)
- Takoua Jendoubi
- Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK. .,Statistics Section, Department of Mathematics, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
| | - Korbinian Strimmer
- School of Mathematics, University of Manchester, Alan Turing Building, Oxford Road, Manchester, M13 9PL, UK
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16
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Régnier M, Polizzi A, Lippi Y, Fouché E, Michel G, Lukowicz C, Smati S, Marrot A, Lasserre F, Naylies C, Batut A, Viars F, Bertrand-Michel J, Postic C, Loiseau N, Wahli W, Guillou H, Montagner A. Insights into the role of hepatocyte PPARα activity in response to fasting. Mol Cell Endocrinol 2018; 471:75-88. [PMID: 28774777 DOI: 10.1016/j.mce.2017.07.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 03/13/2017] [Revised: 07/04/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022]
Abstract
The liver plays a central role in the regulation of fatty acid metabolism. Hepatocytes are highly sensitive to nutrients and hormones that drive extensive transcriptional responses. Nuclear hormone receptors are key transcription factors involved in this process. Among these factors, PPARα is a critical regulator of hepatic lipid catabolism during fasting. This study aimed to analyse the wide array of hepatic PPARα-dependent transcriptional responses during fasting. We compared gene expression in male mice with a hepatocyte specific deletion of PPARα and their wild-type littermates in the fed (ad libitum) and 24-h fasted states. Liver samples were acquired, and transcriptome and lipidome analyses were performed. Our data extended and confirmed the critical role of hepatocyte PPARα as a central for regulator of gene expression during starvation. Interestingly, we identified novel PPARα-sensitive genes, including Cxcl-10, Rab30, and Krt23. We also found that liver phospholipid remodelling was a novel fasting-sensitive pathway regulated by PPARα. These results may contribute to investigations on transcriptional control in hepatic physiology and underscore the clinical relevance of drugs that target PPARα in liver pathologies, such as non-alcoholic fatty liver disease.
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Affiliation(s)
- Marion Régnier
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Arnaud Polizzi
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Yannick Lippi
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Edwin Fouché
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Géraldine Michel
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Céline Lukowicz
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Sarra Smati
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Alain Marrot
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Frédéric Lasserre
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Claire Naylies
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Aurélie Batut
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Fanny Viars
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Justine Bertrand-Michel
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Catherine Postic
- Institut National de La Santé et de La Recherche Médicale (INSERM), U1016, Institut Cochin, Paris, France
| | - Nicolas Loiseau
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Walter Wahli
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore; Center for Integrative Genomics, Université de Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
| | - Hervé Guillou
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France.
| | - Alexandra Montagner
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France.
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17
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Nakajima T, Yang Y, Lu Y, Kamijo Y, Yamada Y, Nakamura K, Koyama M, Yamaguchi S, Sugiyama E, Tanaka N, Aoyama T. Decreased Fatty Acid β-Oxidation Is the Main Cause of Fatty Liver Induced by Polyunsaturated Fatty Acid Deficiency in Mice. TOHOKU J EXP MED 2018; 242:229-239. [PMID: 28724855 DOI: 10.1620/tjem.242.229] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Insufficient intake of polyunsaturated fatty acids (PUFA) causes fatty liver. The mechanism responsible is primarily related to increased lipogenesis and decreased FA degradation based on rodent studies. However, these studies were limited by the fact that the typical PUFA-deficient diets contained insufficient amounts of long-chain FA, the PUFA-containing diets were primarily composed of n-3 PUFA-enriched oil, and the intake of PUFA was excessive compared with the physiological requirement. To address these issues, mice were fed a PUFA-deficient diet containing long-chain FA at a standard fed level and then were orally fed a n-3/n-6-balanced PUFA-containing oil [PUFA (+)] or a PUFA-deficient oil [PUFA (-)] at physiological relevant levels (0.1 mL/mouse/2d). We compared these groups and examined whether fatty liver in PUFA deficiency was attributable to both the effects of increased lipogenesis and decreased FA catabolism. Compared with the PUFA (+) group, the PUFA (-) group showed increases in liver triglyceride and serum FA content. Hepatic gene expression of several mitochondrial β-oxidation enzymes, the serum 3-hydroxybutyrate level, and DNA-binding ability of peroxisome proliferator-activated receptor α (PPARα) were increased in the PUFA (+) group, whereas these adaptive responses were significantly attenuated in the PUFA (-) group. The hepatic expression of typical lipogenesis genes did not differ between the groups. Therefore, fatty liver in PUFA deficiency is attributable to suppression of the FA-degrading system probably from decreased PPARα adaptive responsiveness, and PUFA may be an essential factor for PPARα functioning. This finding is helpful for managing clinical situations having a risk of PUFA deficiency.
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Affiliation(s)
- Takero Nakajima
- Department of Metabolic Regulation, Shinshu University Graduate School of Medicine.,Research Center for Agricultural Food Industry, Shinshu University
| | - Yang Yang
- Department of Metabolic Regulation, Shinshu University Graduate School of Medicine.,Department of Cardiology, The Third Hospital of Hebei Medical University
| | - Yu Lu
- Department of Metabolic Regulation, Shinshu University Graduate School of Medicine
| | - Yuji Kamijo
- Department of Metabolic Regulation, Shinshu University Graduate School of Medicine.,Department of Nephrology, Shinshu University School of Medicine
| | - Yosuke Yamada
- Department of Metabolic Regulation, Shinshu University Graduate School of Medicine.,Department of Nephrology, Shinshu University School of Medicine
| | - Kozo Nakamura
- Research Center for Agricultural Food Industry, Shinshu University.,Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University
| | - Masahiro Koyama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University
| | - Shohei Yamaguchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University
| | - Eiko Sugiyama
- Department of Nutritional Science, Nagano Prefectural College
| | - Naoki Tanaka
- Department of Metabolic Regulation, Shinshu University Graduate School of Medicine.,Research Center for Agricultural Food Industry, Shinshu University
| | - Toshifumi Aoyama
- Department of Metabolic Regulation, Shinshu University Graduate School of Medicine
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18
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Tao YF, Qiang J, Bao JW, Li HX, Yin GJ, Xu P, Chen DJ. miR-205-5p negatively regulates hepatic acetyl-CoA carboxylase β mRNA in lipid metabolism of Oreochromis niloticus. Gene 2018; 660:1-7. [DOI: 10.1016/j.gene.2018.03.064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 03/11/2018] [Accepted: 03/20/2018] [Indexed: 01/18/2023]
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19
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Hayashi Y, Shimamura A, Ishikawa T, Fujiwara Y, Ichi I. FADS2 inhibition in essential fatty acid deficiency induces hepatic lipid accumulation via impairment of very low-density lipoprotein (VLDL) secretion. Biochem Biophys Res Commun 2018; 496:549-555. [DOI: 10.1016/j.bbrc.2018.01.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 01/02/2023]
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20
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Federico A, Dallio M, Caprio GG, Gravina AG, Picascia D, Masarone M, Persico M, Loguercio C. Qualitative and Quantitative Evaluation of Dietary Intake in Patients with Non-Alcoholic Steatohepatitis. Nutrients 2017; 9:E1074. [PMID: 28956816 DOI: 10.3390/nu9101074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/23/2017] [Accepted: 09/26/2017] [Indexed: 02/07/2023] Open
Abstract
There are very few reports about the intake of nutrients for the development or progression of non-alcoholic steatohepatitis (NASH). The aim of this study was to identify the dietary habits and the nutrient intake in patients with NASH, in comparison to chronic hepatitis C (HCV)-related patients. We prospectively evaluated the intake of macronutrients and micronutrients in 124 NAFLD and 162 HCV patients, compared to 2326 subjects as a control group. We noticed major differences in macro- and micronutrients intakes in NASH and HCV patients compared to controls. Proteins, carbohydrate (glucose, fructose, sucrose, maltose and amide), saturated fatty acid (SFA), monounsaturated fatty acid (MUFA), folic acid, vitamin A and C (p < 0.0001), and thiamine (p < 0.0003) ingestion was found to be higher in patients with NASH, while total lipids, polyunsaturated fatty acid (PUFA), riboflavin and vitamin B6 daily intake were lower compared to controls (p < 0.0001). Similarly, NASH patients had significantly reduced carbohydrate intake (p < 0.0001) and an increased intake of calcium (p < 0.0001) compared to HCV positive patients. Finally, we showed in NASH males an increase in the intake of SFA, PUFA, soluble carbohydrates (p < 0.0001) and a decrease in the amount of fiber (p < 0.0001) compared to control males. In NASH female population, we showed an increase of daily total calories, SFA, MUFA, soluble carbohydrates, starch and vitamin D ingested (p < 0.0001) with a reduction of fibers and calcium (p < 0.0001) compared to control females. This study showed how NASH patients’ diets, in both male and females, is affected by a profound alteration in macro- and micronutrients intake.
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21
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Epifanio I. Intervention in prediction measure: a new approach to assessing variable importance for random forests. BMC Bioinformatics 2017; 18:230. [PMID: 28464827 PMCID: PMC5414143 DOI: 10.1186/s12859-017-1650-8] [Citation(s) in RCA: 21] [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: 01/13/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
Background Random forests are a popular method in many fields since they can be successfully applied to complex data, with a small sample size, complex interactions and correlations, mixed type predictors, etc. Furthermore, they provide variable importance measures that aid qualitative interpretation and also the selection of relevant predictors. However, most of these measures rely on the choice of a performance measure. But measures of prediction performance are not unique or there is not even a clear definition, as in the case of multivariate response random forests. Methods A new alternative importance measure, called Intervention in Prediction Measure, is investigated. It depends on the structure of the trees, without depending on performance measures. It is compared with other well-known variable importance measures in different contexts, such as a classification problem with variables of different types, another classification problem with correlated predictor variables, and problems with multivariate responses and predictors of different types. Results Several simulation studies are carried out, showing the new measure to be very competitive. In addition, it is applied in two well-known bioinformatics applications previously used in other papers. Improvements in performance are also provided for these applications by the use of this new measure. Conclusions This new measure is expressed as a percentage, which makes it attractive in terms of interpretability. It can be used with new observations. It can be defined globally, for each class (in a classification problem) and case-wise. It can easily be computed for any kind of response, including multivariate responses. Furthermore, it can be used with any algorithm employed to grow each individual tree. It can be used in place of (or in addition to) other variable importance measures. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1650-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Epifanio
- Departament de Matemàtiques and Institut de Matemàtiques i Aplicacions de Castelló, Universitat Jaume I, Campus del Riu Sec, Castelló, 12071, Spain.
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Yoshida K, Yoshimoto J, Doya K. Sparse kernel canonical correlation analysis for discovery of nonlinear interactions in high-dimensional data. BMC Bioinformatics 2017; 18:108. [PMID: 28196464 PMCID: PMC5310015 DOI: 10.1186/s12859-017-1543-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 10/14/2016] [Accepted: 02/08/2017] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Advance in high-throughput technologies in genomics, transcriptomics, and metabolomics has created demand for bioinformatics tools to integrate high-dimensional data from different sources. Canonical correlation analysis (CCA) is a statistical tool for finding linear associations between different types of information. Previous extensions of CCA used to capture nonlinear associations, such as kernel CCA, did not allow feature selection or capturing of multiple canonical components. Here we propose a novel method, two-stage kernel CCA (TSKCCA) to select appropriate kernels in the framework of multiple kernel learning. RESULTS TSKCCA first selects relevant kernels based on the HSIC criterion in the multiple kernel learning framework. Weights are then derived by non-negative matrix decomposition with L1 regularization. Using artificial datasets and nutrigenomic datasets, we show that TSKCCA can extract multiple, nonlinear associations among high-dimensional data and multiplicative interactions among variables. CONCLUSIONS TSKCCA can identify nonlinear associations among high-dimensional data more reliably than previous nonlinear CCA methods.
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Affiliation(s)
- Kosuke Yoshida
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
- Neural Computation Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Junichiro Yoshimoto
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara, Japan
| | - Kenji Doya
- Neural Computation Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
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Franko A, Neschen S, Rozman J, Rathkolb B, Aichler M, Feuchtinger A, Brachthäuser L, Neff F, Kovarova M, Wolf E, Fuchs H, Häring HU, Peter A, Hrabě de Angelis M. Bezafibrate ameliorates diabetes via reduced steatosis and improved hepatic insulin sensitivity in diabetic TallyHo mice. Mol Metab 2017; 6:256-266. [PMID: 28271032 PMCID: PMC5323884 DOI: 10.1016/j.molmet.2016.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE Recently, we have shown that Bezafibrate (BEZ), the pan-PPAR (peroxisome proliferator-activated receptor) activator, ameliorated diabetes in insulin deficient streptozotocin treated diabetic mice. In order to study whether BEZ can also improve glucose metabolism in a mouse model for fatty liver and type 2 diabetes, the drug was applied to TallyHo mice. METHODS TallyHo mice were divided into an early (ED) and late (LD) diabetes progression group and both groups were treated with 0.5% BEZ (BEZ group) or standard diet (SD group) for 8 weeks. We analyzed plasma parameters, pancreatic beta-cell morphology, and mass as well as glucose metabolism of the BEZ-treated and control mice. Furthermore, liver fat content and composition as well as hepatic gluconeogenesis and mitochondrial mass were determined. RESULTS Plasma lipid and glucose levels were markedly reduced upon BEZ treatment, which was accompanied by elevated insulin sensitivity index as well as glucose tolerance, respectively. BEZ increased islet area in the pancreas. Furthermore, BEZ treatment improved energy expenditure and metabolic flexibility. In the liver, BEZ ameliorated steatosis, modified lipid composition and increased mitochondrial mass, which was accompanied by reduced hepatic gluconeogenesis. CONCLUSIONS Our data showed that BEZ ameliorates diabetes probably via reduced steatosis, enhanced hepatic mitochondrial mass, improved metabolic flexibility and elevated hepatic insulin sensitivity in TallyHo mice, suggesting that BEZ treatment could be beneficial for patients with NAFLD and impaired glucose metabolism.
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Key Words
- BEZ, Bezafibrate
- BG, blood glucose
- Bezafibrate
- ED, early onset of diabetes
- EM, electron microscopy
- FA, fatty acid
- Glucose metabolism
- HOMA-IR, homeostatic model assessment of insulin resistance
- Insulin resistance
- LD, late onset of diabetes
- Lipid metabolism
- NAFLD
- NAFLD, non-alcoholic fatty liver disease
- NEFA, non-esterified fatty acid
- PPAR, peroxisome proliferator-activated receptor
- RER, respiratory exchange ratios
- SD, standard diet
- T2D, type 2 diabetes
- TG, triglyceride
- qNMR, quantitative nuclear magnetic resonance
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Affiliation(s)
- Andras Franko
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Department of Internal Medicine IV, Division of Endocrinology, Diabetology, Angiology, Nephrology and Clinical Chemistry, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Susanne Neschen
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jan Rozman
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität-München, Hackerstr. 27, 85764 Oberschleißheim, Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Laura Brachthäuser
- Institute of Pathology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Frauke Neff
- Institute of Pathology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Marketa Kovarova
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology, Angiology, Nephrology and Clinical Chemistry, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität-München, Hackerstr. 27, 85764 Oberschleißheim, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Hans-Ulrich Häring
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology, Angiology, Nephrology and Clinical Chemistry, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Andreas Peter
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology, Angiology, Nephrology and Clinical Chemistry, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Center of Life and Food Sciences Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany.
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Mello T, Materozzi M, Galli A. PPARs and Mitochondrial Metabolism: From NAFLD to HCC. PPAR Res 2016; 2016:7403230. [PMID: 28115925 DOI: 10.1155/2016/7403230] [Citation(s) in RCA: 297] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/08/2016] [Accepted: 11/10/2016] [Indexed: 11/17/2022] Open
Abstract
Metabolic related diseases, such as type 2 diabetes, metabolic syndrome, and nonalcoholic fatty liver disease (NAFLD), are widespread threats which bring about a significant burden of deaths worldwide, mainly due to cardiovascular events and cancer. The pathogenesis of these diseases is extremely complex, multifactorial, and only partially understood. As the main metabolic organ, the liver is central to maintain whole body energetic homeostasis. At the cellular level, mitochondria are the metabolic hub connecting and integrating all the main biochemical, hormonal, and inflammatory signaling pathways to fulfill the energetic and biosynthetic demand of the cell. In the liver, mitochondria metabolism needs to cope with the energetic regulation of the whole body. The nuclear receptors PPARs orchestrate lipid and glucose metabolism and are involved in a variety of diseases, from metabolic disorders to cancer. In this review, focus is placed on the roles of PPARs in the regulation of liver mitochondrial metabolism in physiology and pathology, from NAFLD to HCC.
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Polizzi A, Fouché E, Ducheix S, Lasserre F, Marmugi AP, Mselli-Lakhal L, Loiseau N, Wahli W, Guillou H, Montagner A. Hepatic Fasting-Induced PPARα Activity Does Not Depend on Essential Fatty Acids. Int J Mol Sci 2016; 17:ijms17101624. [PMID: 27669233 PMCID: PMC5085657 DOI: 10.3390/ijms17101624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 07/26/2016] [Revised: 09/05/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022] Open
Abstract
The liver plays a central role in the regulation of fatty acid metabolism, which is highly sensitive to transcriptional responses to nutrients and hormones. Transcription factors involved in this process include nuclear hormone receptors. One such receptor, PPARα, which is highly expressed in the liver and activated by a variety of fatty acids, is a critical regulator of hepatic fatty acid catabolism during fasting. The present study compared the influence of dietary fatty acids and fasting on hepatic PPARα-dependent responses. Pparα−/− male mice and their wild-type controls were fed diets containing different fatty acids for 10 weeks prior to being subjected to fasting or normal feeding. In line with the role of PPARα in sensing dietary fatty acids, changes in chronic dietary fat consumption influenced liver damage during fasting. The changes were particularly marked in mice fed diets lacking essential fatty acids. However, fasting, rather than specific dietary fatty acids, induced acute PPARα activity in the liver. Taken together, the data imply that the potent signalling involved in triggering PPARα activity during fasting does not rely on essential fatty acid-derived ligand.
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Affiliation(s)
- Arnaud Polizzi
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
| | - Edwin Fouché
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
| | - Simon Ducheix
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
| | - Frédéric Lasserre
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
| | - Alice P Marmugi
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
| | | | - Nicolas Loiseau
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
| | - Walter Wahli
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
- Lee Kong Chian School of Medicine, Nanyang Technological University, 637553 Singapore, Singapore.
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Hervé Guillou
- INRA ToxAlim, 180, Chemin de Tournefeuille, 31027 Toulouse Cedex 3, France.
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Galmiche G, Huneau J, Mathé V, Mourot J, Simon N, Le Guillou C, Hermier D. n -3 Fatty acids preserve muscle mass and insulin sensitivity in a rat model of energy restriction. Br J Nutr 2016; 116:1141-52. [DOI: 10.1017/s0007114516003111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AbstractIn obese subjects, the loss of fat mass during energy restriction is often accompanied by a loss of muscle mass. The hypothesis thatn-3 PUFA, which modulate protein homoeostasis via effects on insulin sensitivity, could contribute to maintain muscle mass during energy restriction was tested in rats fed a high-fat diet (4 weeks) rich in 18 : 1n-9 (oleic acid, OLE-R), 18 : 3n-3 (α-linolenic acid, ALA-R) orn-3 long-chain (LC-R) fatty acid and then energy restricted (8 weeks). A control group (OLE-ad libitum(AL)) was maintained with AL diet throughout the study. Rats were killed 10 min after an i.v. insulin injection. All energy-restricted rats lost weight and fat mass, but only the OLE-R group showed a significant muscle loss. TheGastrocnemiusmuscle was enriched with ALA in the ALA-R group and with LC-PUFA in the ALA-R and LC-R groups. The proteolytic ubiquitin–proteasome system was differentially affected by energy restriction, with MAFbx and muscle ring finger-1 mRNA levels being decreased in the LC-R group (−30 and −20 %, respectively). RAC-αserine/threonine-protein kinase and insulin receptor substrate 1 phosphorylation levels increased in the LC-R group (+70 %), together with insulin receptor mRNA (+50 %). The ALA-R group showed the same overall activation pattern as the LC-R group, although to a lesser extent. In conclusion, dietaryn-3 PUFA prevent the loss of muscle mass associated with energy restriction, probably by an improvement in the insulin-signalling pathway activation, in relation to enrichment of plasma membranes inn-3 LC-PUFA.
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Abstract
Background Canonical correlation analysis (CCA) is a multivariate statistical method which describes the associations between two sets of variables. The objective is to find linear combinations of the variables in each data set having maximal correlation. In genomics, CCA has become increasingly important to estimate the associations between gene expression data and DNA copy number change data. The identification of such associations might help to increase our understanding of the development of diseases such as cancer. However, these data sets are typically high-dimensional, containing a lot of variables relative to the number of objects. Moreover, the data sets might contain atypical observations since it is likely that objects react differently to treatments. We discuss a method for Robust Sparse CCA, thereby providing a solution to both issues. Sparse estimation produces canonical vectors with some of their elements estimated as exactly zero. As such, their interpretability is improved. Robust methods can cope with atypical observations in the data. Results We illustrate the good performance of the Robust Sparse CCA method by several simulation studies and three biometric examples. Robust Sparse CCA considerably outperforms its main alternatives in (1) correctly detecting the main associations between the data sets, in (2) accurately estimating these associations, and in (3) detecting outliers. Conclusions Robust Sparse CCA delivers interpretable canonical vectors, while at the same time coping with outlying observations. The proposed method is able to describe the associations between high-dimensional data sets, which are nowadays commonplace in genomics. Furthermore, the Robust Sparse CCA method allows to characterize outliers. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0317-9) contains supplementary material, which is available to authorized users.
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Abstract
Background Pathway expression is multivariate in nature. Thus, from a statistical perspective, to detect differentially expressed pathways between two conditions, methods for inferring differences between mean vectors need to be applied. Maximum mean discrepancy (MMD) is a statistical test to determine whether two samples are from the same distribution, its implementation being greatly simplified using the kernel method. Results An MMD-based test successfully detected the differential expression between two conditions, specifically the expression of a set of genes involved in certain fatty acid metabolic pathways. Furthermore, we exploited the ability of the kernel method to integrate data and successfully added hepatic fatty acid levels to the test procedure. Conclusion MMD is a non-parametric test that acquires several advantages when combined with the kernelization of data: 1) the number of variables can be greater than the sample size; 2) omics data can be integrated; 3) it can be applied not only to vectors, but to strings, sequences and other common structured data types arising in molecular biology.
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Affiliation(s)
- Esteban Vegas
- Department of Statistics, University of Barcelona, Diagonal, 643, Barcelona, 08028, Spain.
| | - Josep M Oller
- Department of Statistics, University of Barcelona, Diagonal, 643, Barcelona, 08028, Spain
| | - Ferran Reverter
- Department of Statistics, University of Barcelona, Diagonal, 643, Barcelona, 08028, Spain.,Center of Genomic Regulation, Parc de Recerca Biomedica de Barcelona, Dr. Aiguader, 88, Barcelona, 08003, Spain
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Hermier D, Guelzim N, Martin PG, Huneau JF, Mathé V, Quignard-Boulangé A, Lasserre F, Mariotti F. NO synthesis from arginine is favored by α-linolenic acid in mice fed a high-fat diet. Amino Acids 2016; 48:2157-68. [PMID: 27178023 DOI: 10.1007/s00726-016-2243-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/23/2016] [Indexed: 10/21/2022]
Abstract
Alterations in NO availability and signaling play a pivotal role at early stages of the metabolic syndrome (MetSynd). We hypothesized that dietary α-linolenic acid (ALA, 18:3 n-3) favors NO availability by modulating amino acid metabolism, with a specific impact on the arginine-NO pathway. Mice were fed a hyperlipidic diet (285 g lipid/kg, 51.1 % energy), rich in either saturated fatty acids (SFA, provided by palm oil, PALM group) or ALA (provided by linseed oil, LIN group). We measured whole-body NO synthesis and systemic arginine hydrolysis with a tracer-based method, plasma concentration of related metabolites, and hepatic mRNA level of related enzymes, and the study was completed by a transcriptomic analysis in the liver. As expected with this model, hyperlipidic diets resulted in increased adiposity and glycemia after 5 weeks. As compared to PALM mice, LIN mice had a higher plasma nitrite and nitrate concentration, a higher whole-body conversion of arginine into NO vs urea, and a similar plasma concentration of asymmetric dimethylarginine (ADMA), despite a higher expression of the liver dimethylargininase-1. In LIN mice, there was a higher expression of genes involved in PPARα signaling, but a little impact on gene expression related to amino acids and arginine metabolism. This effect cannot be directly ascribed to changes in arginase activity in the liver or ADMA metabolism, nor to direct regulation of the related target genes. In conclusion, dietary ALA favors NO synthesis, which could contribute to rescue NO availability when jeopardized by the nutritional conditions in relation with the initiation of the MetSynd.
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Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are a novel group of universally present, non-coding RNAs (>200 nt) that are increasingly recognized as key regulators of many physiological and pathological processes. SCOPE OF REVIEW Recent publications have shown that lncRNAs influence lipid homeostasis by controlling lipid metabolism in the liver and by regulating adipogenesis. lncRNAs control lipid metabolism-related gene expression by either base-pairing with RNA and DNA or by binding to proteins. MAJOR CONCLUSIONS The recent advances and future prospects in understanding the roles of lncRNAs in lipid homeostasis are discussed.
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Affiliation(s)
- Zheng Chen
- School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China.
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Abstract
BACKGROUND The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of "multi-omics" data. Our tool supports a range of complex analyses, including - among others - low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions. RESULTS We demonstrate the characteristics and benefits of the DNA Microarray Integromics Analysis Platform using two different test cases. The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids. The second test case involves the analysis of miRNA-mRNA interactions in polysaccharide-stimulated human dermal fibroblasts infected with porcine endogenous retroviruses. CONCLUSIONS The DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for "multi-omics" data management and analysis. Its intuitive nature and wide range of available workflows make it an effective tool for molecular biology research. The platform is hosted at https://lifescience.plgrid.pl/.
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Affiliation(s)
- Tomasz Waller
- Institute of Computer Science, Division of Biomedical Computer Systems, University of Silesia, Katowice, Poland ; Academic Computer Centre CYFRONET, AGH University of Science and Technology, Kraków, Poland
| | - Tomasz Gubała
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Kraków, Poland
| | - Krzysztof Sarapata
- Molecular Biology and Clinical Genetics Laboratory, Department of Medicine, Jagiellonian University, Kraków, Poland
| | - Monika Piwowar
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Kraków, Poland
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Pawlak M, Baugé E, Lalloyer F, Lefebvre P, Staels B. Ketone Body Therapy Protects From Lipotoxicity and Acute Liver Failure Upon Pparα Deficiency. Mol Endocrinol 2015; 29:1134-43. [PMID: 26087172 DOI: 10.1210/me.2014-1383] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Acute liver failure (ALF) is a severe and rapid liver injury, often occurring without any preexisting liver disease, which may precipitate multiorgan failure and death. ALF is often associated with impaired β-oxidation and increased oxidative stress (OS), characterized by elevated levels of hepatic reactive oxygen species (ROS) and lipid peroxidation (LPO) products. Peroxisome proliferator-activated receptor (PPAR)α has been shown to confer hepatoprotection in acute and chronic liver injury, at least in part, related to its ability to control peroxisomal and mitochondrial β-oxidation. To study the pathophysiological role of PPARα in hepatic response to high OS, we induced a pronounced LPO by treating wild-type and Pparα-deficient mice with high doses of fish oil (FO), containing n-3 polyunsaturated fatty acids. FO feeding of Pparα-deficient mice, in contrast to control sunflower oil, surprisingly induced coma and death due to ALF as indicated by elevated serum alanine aminotransferase, aspartate aminotransferase, ammonia, and a liver-specific increase of ROS and LPO-derived malondialdehyde. Reconstitution of PPARα specifically in the liver using adeno-associated serotype 8 virus-PPARα in Pparα-deficient mice restored β-oxidation and ketogenesis and protected mice from FO-induced lipotoxicity and death. Interestingly, administration of the ketone body β-hydroxybutyrate prevented FO-induced ALF in Pparα-deficient mice, and normalized liver ROS and malondialdehyde levels. Therefore, PPARα protects the liver from FO-induced OS through its regulatory actions on ketone body levels. β-Hydroxybutyrate treatment could thus be an option to prevent LPO-induced liver damage.
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Affiliation(s)
- Michal Pawlak
- European Genomic Institute for Diabetes, Inserm UMR1011, and University Lille, F-59000 Lille Cédex, France; and Institut Pasteur de Lille, F-59019 Lille Cédex, France
| | - Eric Baugé
- European Genomic Institute for Diabetes, Inserm UMR1011, and University Lille, F-59000 Lille Cédex, France; and Institut Pasteur de Lille, F-59019 Lille Cédex, France
| | - Fanny Lalloyer
- European Genomic Institute for Diabetes, Inserm UMR1011, and University Lille, F-59000 Lille Cédex, France; and Institut Pasteur de Lille, F-59019 Lille Cédex, France
| | - Philippe Lefebvre
- European Genomic Institute for Diabetes, Inserm UMR1011, and University Lille, F-59000 Lille Cédex, France; and Institut Pasteur de Lille, F-59019 Lille Cédex, France
| | - Bart Staels
- European Genomic Institute for Diabetes, Inserm UMR1011, and University Lille, F-59000 Lille Cédex, France; and Institut Pasteur de Lille, F-59019 Lille Cédex, France
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Abstract
To date, the massive quantity of data generated by high-throughput techniques has not yet met bioinformatics treatment required to make full use of it. This is partially due to a mismatch in experimental and analytical study design but primarily due to a lack of adequate analytical approaches. When integrating multiple data types e.g. transcriptomics and metabolomics, multidimensional statistical methods are currently the techniques of choice. Typical statistical approaches, such as canonical correlation analysis (CCA), that are applied to find associations between metabolites and genes are failing due to small numbers of observations (e.g. conditions, diet etc.) in comparison to data size (number of genes, metabolites). Modifications designed to cope with this issue are not ideal due to the need to add simulated data resulting in a lack of p-value computation or by pruning of variables hence losing potentially valid information. Instead, our approach makes use of verified or putative molecular interactions or functional association to guide analysis. The workflow includes dividing of data sets to reach the expected data structure, statistical analysis within groups and interpretation of results. By applying pathway and network analysis, data obtained by various platforms are grouped with moderate stringency to avoid functional bias. As a consequence CCA and other multivariate models can be applied to calculate robust statistics and provide easy to interpret associations between metabolites and genes to leverage understanding of metabolic response. Effective integration of lipidomics and transcriptomics is demonstrated on publically available murine nutrigenomics data sets. We are able to demonstrate that our approach improves detection of genes related to lipid metabolism, in comparison to applying statistics alone. This is measured by increased percentage of explained variance (95% vs. 75–80%) and by identifying new metabolite-gene associations related to lipid metabolism.
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Affiliation(s)
- Monika Piwowar
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Kopernika 7E, 31–062 Kraków, Poland
| | - Wiktor Jurkowski
- The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- * E-mail:
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Ebrahimi M, Rajion MA, Meng GY, Farjam AS, Oskoueian E, Jafari S. Diet high in α-linolenic acid up-regulate PPAR-α gene expression in the liver of goats. ELECTRON J BIOTECHN 2015; 18:210-4. [DOI: 10.1016/j.ejbt.2015.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Hachero-Cruzado I, Rodríguez-Rua A, Román-Padilla J, Ponce M, Fernández-Díaz C, Manchado M. Characterization of the genomic responses in early Senegalese sole larvae fed diets with different dietary triacylglycerol and total lipids levels. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 2014; 12:61-73. [DOI: 10.1016/j.cbd.2014.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 12/16/2022]
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Guelzim N, Huneau JF, Mathé V, Tesseraud S, Mourot J, Simon N, Hermier D. N-3 fatty acids improve body composition and insulin sensitivity during energy restriction in the rat. Prostaglandins Leukot Essent Fatty Acids 2014; 91:203-11. [PMID: 25172359 DOI: 10.1016/j.plefa.2014.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 03/19/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 01/19/2023]
Abstract
The hypothesis that n-3 polyunsaturated fatty acids (PUFA) could contribute to maintain muscle mass during energy restriction aiming to weight loss was tested in the rat, with special attention paid to insulin signalling. After 10 weeks on a diet rich in lipids and sucrose, male rats were energy restricted and fed diets rich in 18:1 n-9 (OLE), 18:3 n-3 (ALA) or n-3 long-chain (LC, >18 carbons) PUFA. After 4 weeks, they were killed after an insulin injection. Red blood cells, liver, and Gastrocnemius muscle were enriched in ALA in the ALA group, and in LC-PUFA in the ALA and LC groups. The LC diet resulted in a higher weight loss, without negative impact on the muscle weight. In parallel, hepatic phosphorylation of insulin receptor and IRS1 was the highest in this group. This suggests that the trend we observed in the preservation of protein homeostasis in the LC group is mediated, at least partly, by an enhancement of the early steps of insulin signalling resulting from cell membrane enrichment in n-3 PUFA.
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Affiliation(s)
- N Guelzim
- INRA, UMR914 Nutrition Physiology and Ingestive Behavior, AgroParisTech, 16 rue Claude Bernard, F-75005 Paris, France; AgroParisTech, UMR914 Nutrition Physiology and Ingestive Behavior, F-75005 Paris, France
| | - J-F Huneau
- INRA, UMR914 Nutrition Physiology and Ingestive Behavior, AgroParisTech, 16 rue Claude Bernard, F-75005 Paris, France; AgroParisTech, UMR914 Nutrition Physiology and Ingestive Behavior, F-75005 Paris, France
| | - V Mathé
- INRA, UMR914 Nutrition Physiology and Ingestive Behavior, AgroParisTech, 16 rue Claude Bernard, F-75005 Paris, France; AgroParisTech, UMR914 Nutrition Physiology and Ingestive Behavior, F-75005 Paris, France
| | - S Tesseraud
- INRA, UR83 Recherches Avicoles, F-37380 Nouzilly, France
| | - J Mourot
- INRA, UMR1348 PEGASE, F- 35590 Saint Gilles, France
| | - N Simon
- ONIDOL, 11 rue de Monceau, CS 60003, F-75008 Paris, France
| | - D Hermier
- INRA, UMR914 Nutrition Physiology and Ingestive Behavior, AgroParisTech, 16 rue Claude Bernard, F-75005 Paris, France; AgroParisTech, UMR914 Nutrition Physiology and Ingestive Behavior, F-75005 Paris, France.
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Justus J, Weigand E. The effect of a moderate zinc deficiency and dietary fat source on the activity and expression of the Δ(3)Δ (2)-enoyl-CoA isomerase in the liver of growing rats. Biol Trace Elem Res 2014; 158:365-75. [PMID: 24682920 DOI: 10.1007/s12011-014-9940-8] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/09/2014] [Indexed: 10/25/2022]
Abstract
Auxiliary enzymes participate in β-oxidation of unsaturated fatty acids. The objective of the study was to investigate the impact of a moderate zinc deficiency and a high intake of polyunsaturated fat on Δ(3)Δ(2)-enoyl-CoA isomerase (ECI) in the liver and other tissues. Five groups of eight weanling rats each were fed moderately zinc-deficient (ZD) or zinc-adequate (ZA) semisynthetic diets (7 or 50 mg Zn/kg) enriched with 22 % cocoa butter (CB) or 22 % safflower oil (SO) for 4 weeks: (1) ZD-CB, fed free choice; (2) ZA-CBR, ZA-CB diet fed in equivalent amounts consumed by the ZD-CB group; (3) ZD-SO, fed free choice; (4) ZA-SOR, ZA-SO diet fed in equivalent amounts consumed by the ZD-SO group; and (5) ZA-SO, fed free choice. Growth and Zn status markers were markedly reduced in the ZD groups. ECI activity in the liver of the animals fed the ZD- and ZA-SO diets were significantly higher (approximately 2- and 3-fold, respectively) as compared with the CB-fed animals, whereas activities in extrahepatic tissues (kidneys, heart, skeletal muscle, testes, adipose tissue) were not altered by dietary treatments. Transcript levels of the mitochondrial Eci gene in the liver did not significantly differ between ZD and ZA rats, but were 1.6-fold higher in the ZA-SO- than in the ZD-CB-fed animals (P < 0.05). It is concluded that diets enriched with safflower oil as a source high in linoleic acid induce markedly increased hepatic ECI activities and that a moderate Zn deficiency does not affect transcription of the mitochondrial Eci gene in the liver.
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Affiliation(s)
- Jennifer Justus
- Dussmann Service Deutschland GmbH, Frankfurt am Main, Germany
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Justus J, Weigand E. A Moderate Zinc Deficiency Does Not Impair Gene Expression of PPARα, PPARγ, and Mitochondrial Enoyl-CoA Delta Isomerase in the Liver of Growing Rats. Nutr Metab Insights 2014; 7:29-37. [PMID: 24855375 PMCID: PMC4024054 DOI: 10.4137/nmi.s14003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 12/23/2013] [Revised: 03/24/2014] [Accepted: 03/24/2014] [Indexed: 11/12/2022] Open
Abstract
The aim of the study was to investigate the impact of a moderate zinc deficiency and a high intake of polyunsaturated fat on the mRNA expression of peroxisome-proliferator-activated receptor alpha (PPARα), peroxisome-proliferator-activated receptor gamma (PPARγ), and mitochondrial Δ3Δ2-enoyl-CoA isomerase (ECI) in the liver. Weanling rats were assigned to five groups (eight animals each) and fed semi-synthetic, low-carbohydrate diets containing 7 or 50 mg Zn/kg (low-Zn (LZ) or high-Zn (HZ)) and 22% cocoa butter (CB) or 22% safflower (SF) oil for four weeks. One group each was fed the LZ-CB, LZ-SF, or HZ-SF diet free choice, and one group each was fed the HZ-CB and HZ-SF diets in restricted amounts according to intake of the respective LZ diets. The LZ diets markedly lowered growth and zinc concentrations in plasma and femur. Hepatic mRNA levels of PPARα, PPARγ, and ECI were not reduced by the moderate zinc deficiency. Overall, ECI-mRNA abundance was marginally higher in the SF-fed than in the CB-fed animals.
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Affiliation(s)
- Jennifer Justus
- Dussmann Service Deutschland GmbH, Frankfurt am Main, Germany
| | - Edgar Weigand
- Institute of Animal Nutrition and Nutritional Physiology, Justus Liebig University, Giessen, Germany
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Abstract
Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge.
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Abstract
The Peroxisome Proliferator Activated Receptor alpha (PPARα) is a transcription factor that plays a major role in metabolic regulation. This review addresses the functional role of PPARα in intermediary metabolism and provides a detailed overview of metabolic genes targeted by PPARα, with a focus on liver. A distinction is made between the impact of PPARα on metabolism upon physiological, pharmacological, and nutritional activation. Low and high throughput gene expression analyses have allowed the creation of a comprehensive map illustrating the role of PPARα as master regulator of lipid metabolism via regulation of numerous genes. The map puts PPARα at the center of a regulatory hub impacting fatty acid uptake, fatty acid activation, intracellular fatty acid binding, mitochondrial and peroxisomal fatty acid oxidation, ketogenesis, triglyceride turnover, lipid droplet biology, gluconeogenesis, and bile synthesis/secretion. In addition, PPARα governs the expression of several secreted proteins that exert local and endocrine functions.
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Corton JC, Cunningham ML, Hummer BT, Lau C, Meek B, Peters JM, Popp JA, Rhomberg L, Seed J, Klaunig JE. Mode of action framework analysis for receptor-mediated toxicity: The peroxisome proliferator-activated receptor alpha (PPARα) as a case study. Crit Rev Toxicol 2013; 44:1-49. [PMID: 24180432 DOI: 10.3109/10408444.2013.835784] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Several therapeutic agents and industrial chemicals induce liver tumors in rodents through the activation of the peroxisome proliferator-activated receptor alpha (PPARα). The cellular and molecular events by which PPARα activators induce rodent hepatocarcinogenesis has been extensively studied and elucidated. This review summarizes the weight of evidence relevant to the hypothesized mode of action (MOA) for PPARα activator-induced rodent hepatocarcinogenesis and identifies gaps in our knowledge of this MOA. Chemical-specific and mechanistic data support concordance of temporal and dose-response relationships for the key events associated with many PPARα activators including a phthalate ester plasticizer di(2-ethylhexyl) phthalate (DEHP) and the drug gemfibrozil. While biologically plausible in humans, the hypothesized key events in the rodent MOA, for PPARα activators, are unlikely to induce liver tumors in humans because of toxicodynamic and biological differences in responses. This conclusion is based on minimal or no effects observed on growth pathways, hepatocellular proliferation and liver tumors in humans and/or species (including hamsters, guinea pigs and cynomolgous monkeys) that are more appropriate human surrogates than mice and rats at overlapping dose levels. Overall, the panel concluded that significant quantitative differences in PPARα activator-induced effects related to liver cancer formation exist between rodents and humans. On the basis of these quantitative differences, most of the workgroup felt that the rodent MOA is "not relevant to humans" with the remaining members concluding that the MOA is "unlikely to be relevant to humans". The two groups differed in their level of confidence based on perceived limitations of the quantitative and mechanistic knowledge of the species differences, which for some panel members strongly supports but cannot preclude the absence of effects under unlikely exposure scenarios.
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Abstract
Large datasets from -omics studies need to be deeply investigated. The aim of this paper is to provide a new method (LEM method) for the search of transcriptome and metabolome connections. The heuristic algorithm here described extends the classical canonical correlation analysis (CCA) to a high number of variables (without regularization) and combines well-conditioning and fast-computing in "R." Reduced CCA models are summarized in PageRank matrices, the product of which gives a stochastic matrix that resumes the self-avoiding walk covered by the algorithm. Then, a homogeneous Markov process applied to this stochastic matrix converges the probabilities of interconnection between genes, providing a selection of disjointed subsets of genes. This is an alternative to regularized generalized CCA for the determination of blocks within the structure matrix. Each gene subset is thus linked to the whole metabolic or clinical dataset that represents the biological phenotype of interest. Moreover, this selection process reaches the aim of biologists who often need small sets of genes for further validation or extended phenotyping. The algorithm is shown to work efficiently on three published datasets, resulting in meaningfully broadened gene networks.
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Affiliation(s)
- D Valour
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
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Abstract
Peroxisome proliferator-activated receptors (PPARs) are transcription factors that belong to the superfamily of nuclear hormone receptors and regulate the expression of several genes involved in metabolic processes that are potentially linked to the development of some diseases such as hyperlipidemia, diabetes, and obesity. One type of PPAR, PPAR-α, is a transcription factor that regulates the metabolism of lipids, carbohydrates, and amino acids and is activated by ligands such as polyunsaturated fatty acids and drugs used to treat dyslipidemias. There is evidence that genetic variants within the PPARα gene have been associated with a risk of the development of dyslipidemia and cardiovascular disease by influencing fasting and postprandial lipid concentrations; the gene variants have also been associated with an acceleration of the progression of type 2 diabetes. The interactions between genetic PPARα variants and the response to dietary factors will help to identify individuals or populations who can benefit from specific dietary recommendations. Interestingly, certain nutritional conditions, such as the prolonged consumption of a protein-restricted diet, can produce long-lasting effects on PPARα gene expression through modifications in the methylation of a specific locus surrounding the PPARα gene. Thus, this review underlines our current knowledge about the important role of PPAR-α as a mediator of the metabolic response to nutritional and environmental factors.
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Affiliation(s)
- Alejandra V. Contreras
- Faculty of Medicine, National University Autonomous of Mexico, PhD Program in Biomedical Sciences,National Institute of Genomic Medicine
| | - Nimbe Torres
- Nutrition Physiology Department, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Mexico D.F. Mexico
| | - Armando R. Tovar
- Nutrition Physiology Department, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Mexico D.F. Mexico,To whom correspondence should be addressed. E-mail:
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Ducheix S, Montagner A, Polizzi A, Lasserre F, Marmugi A, Bertrand-Michel J, Podechard N, Al Saati T, Chétiveaux M, Baron S, Boué J, Dietrich G, Mselli-Lakhal L, Costet P, Lobaccaro JMA, Pineau T, Theodorou V, Postic C, Martin PGP, Guillou H. Essential fatty acids deficiency promotes lipogenic gene expression and hepatic steatosis through the liver X receptor. J Hepatol 2013; 58:984-92. [PMID: 23333450 DOI: 10.1016/j.jhep.2013.01.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 01/22/2023]
Abstract
BACKGROUND & AIMS Nutrients influence non-alcoholic fatty liver disease. Essential fatty acids deficiency promotes various syndromes, including hepatic steatosis, through increased de novo lipogenesis. The mechanisms underlying such increased lipogenic response remain unidentified. METHODS We used wild type mice and mice lacking Liver X Receptors to perform a nutrigenomic study that aimed at examining the role of these transcription factors. RESULTS We showed that, in the absence of Liver X Receptors, essential fatty acids deficiency does not promote steatosis. Consistent with this, Liver X Receptors are required for the elevated expression of genes involved in lipogenesis in response to essential fatty acids deficiency. CONCLUSIONS This work identifies, for the first time, the central role of Liver X Receptors in steatosis induced by essential fatty acids deficiency.
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Affiliation(s)
- Simon Ducheix
- INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse, France
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Maqdasy S, Baptissart M, Vega A, Baron S, Lobaccaro JMA, Volle DH. Cholesterol and male fertility: what about orphans and adopted? Mol Cell Endocrinol 2013; 368:30-46. [PMID: 22766106 DOI: 10.1016/j.mce.2012.06.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [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: 01/16/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 12/24/2022]
Abstract
The link between cholesterol homeostasis and male fertility has been clearly suggested in patients who suffer from hyperlipidemia and metabolic syndrome. This has been confirmed by the generation of several transgenic mouse models or in animals fed with high cholesterol diet. Next to the alteration of the endocrine signaling pathways through steroid receptors (androgen and estrogen receptors); "orphan" and "adopted" nuclear receptors, such as the Liver X Receptors (LXRs), the Proliferating Peroxisomal Activated Receptors (PPARs) or the Liver Receptor Homolog-1 (LRH-1), have been involved in this cross-talk. These transcription factors show distinct expression patterns in the male genital tract, explaining the large panel of phenotypes observed in transgenic male mice and highlighting the importance of lipid homesostasis and the complexity of the molecular pathways involved. Increasing our knowledge of the roles of these nuclear receptors in male germ cell differentiation could help in proposing new approaches to either treat infertile men or define new strategies for contraception.
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Li S, Chen W, Kang X, Han R, Sun G, Huang Y. Distinct tissue expression profiles of chicken Lpin1-α/β isoforms and the effect of the variation on muscle fiber traits. Gene 2013; 515:281-90. [PMID: 23266642 DOI: 10.1016/j.gene.2012.11.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/14/2012] [Accepted: 11/27/2012] [Indexed: 11/17/2022]
Affiliation(s)
- Suya Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, Henan, China
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Watanabe M, Uesugi M. Small-molecule inhibitors of SREBP activation – potential for new treatment of metabolic disorders. Med Chem Commun 2013. [DOI: 10.1039/c3md00177f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Ortuño Sahagún D, Márquez-Aguirre AL, Quintero-Fabián S, López-Roa RI, Rojas-Mayorquín AE. Modulation of PPAR-γ by Nutraceutics as Complementary Treatment for Obesity-Related Disorders and Inflammatory Diseases. PPAR Res 2012; 2012:318613. [PMID: 23251142 PMCID: PMC3515933 DOI: 10.1155/2012/318613] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/03/2012] [Accepted: 10/23/2012] [Indexed: 12/16/2022] Open
Abstract
A direct correlation between adequate nutrition and health is a universally accepted truth. The Western lifestyle, with a high intake of simple sugars, saturated fat, and physical inactivity, promotes pathologic conditions. The main adverse consequences range from cardiovascular disease, type 2 diabetes, and metabolic syndrome to several cancers. Dietary components influence tissue homeostasis in multiple ways and many different functional foods have been associated with various health benefits when consumed. Natural products are an important and promising source for drug discovery. Many anti-inflammatory natural products activate peroxisome proliferator-activated receptors (PPAR); therefore, compounds that activate or modulate PPAR-gamma (PPAR-γ) may help to fight all of these pathological conditions. Consequently, the discovery and optimization of novel PPAR-γ agonists and modulators that would display reduced side effects is of great interest. In this paper, we present some of the main naturally derived products studied that exert an influence on metabolism through the activation or modulation of PPAR-γ, and we also present PPAR-γ-related diseases that can be complementarily treated with nutraceutics from functional foods.
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Affiliation(s)
- D. Ortuño Sahagún
- Laboratorio de Desarrollo y Regeneración Neural, Instituto de Neurobiología, Departamento de Biología Celular y Molecular, CUCBA, Universidad de Guadalajara, camino Ing. R. Padilla Sánchez 2100, Las Agujas, 44600 Zapopan JAL, Mexico
| | - A. L. Márquez-Aguirre
- Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., 44270 Guadalajara, JAL, Mexico
| | - S. Quintero-Fabián
- Laboratorio de Desarrollo y Regeneración Neural, Instituto de Neurobiología, Departamento de Biología Celular y Molecular, CUCBA, Universidad de Guadalajara, camino Ing. R. Padilla Sánchez 2100, Las Agujas, 44600 Zapopan JAL, Mexico
- Departamento de Farmacobiología, CUCEI, Universidad de Guadalajara, Boulevard Marcelino García Barragán, 44430 Tlaquepaque, JAL, Mexico
| | - R. I. López-Roa
- Departamento de Farmacobiología, CUCEI, Universidad de Guadalajara, Boulevard Marcelino García Barragán, 44430 Tlaquepaque, JAL, Mexico
| | - A. E. Rojas-Mayorquín
- Departamento de Ciencias Ambientales, Instituto de Neurociencias, CUCBA, Universidad de Guadalajara, 45100, JAL, Mexico
- Departamento de Investigación Básica, Instituto Nacional de Geriatría (INGER), Periférico Sur No. 2767, Col, San Jerónimo Lídice, Delegación Magdalena Contreras 10200, México DF, Mexico
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Abstract
BACKGROUND Each omics platform is now able to generate a large amount of data. Genomics, proteomics, metabolomics, interactomics are compiled at an ever increasing pace and now form a core part of the fundamental systems biology framework. Recently, several integrative approaches have been proposed to extract meaningful information. However, these approaches lack of visualisation outputs to fully unravel the complex associations between different biological entities. RESULTS The multivariate statistical approaches 'regularized Canonical Correlation Analysis' and 'sparse Partial Least Squares regression' were recently developed to integrate two types of highly dimensional 'omics' data and to select relevant information. Using the results of these methods, we propose to revisit few graphical outputs to better understand the relationships between two 'omics' data and to better visualise the correlation structure between the different biological entities. These graphical outputs include Correlation Circle plots, Relevance Networks and Clustered Image Maps. We demonstrate the usefulness of such graphical outputs on several biological data sets and further assess their biological relevance using gene ontology analysis. CONCLUSIONS Such graphical outputs are undoubtedly useful to aid the interpretation of these promising integrative analysis tools and will certainly help in addressing fundamental biological questions and understanding systems as a whole. AVAILABILITY The graphical tools described in this paper are implemented in the freely available R package mixOmics and in its associated web application.
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Affiliation(s)
- Ignacio González
- , Institut de Mathématiques - Université de Toulouse III et CNRS, UMR 5219, F-31062 Toulouse, France
| | - Kim-Anh Lê Cao
- Queensland Facility for Advanced Bioinformatics and the Institute for Molecular Bioscience, The University of Queensland, 4072 St Lucia, QLD, Australia
| | - Melissa J Davis
- Queensland Facility for Advanced Bioinformatics and the Institute for Molecular Bioscience, The University of Queensland, 4072 St Lucia, QLD, Australia
| | - Sébastien Déjean
- , Institut de Mathématiques - Université de Toulouse III et CNRS, UMR 5219, F-31062 Toulouse, France
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50
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Shi X, Yao D, Gosnell BA, Chen C. Lipidomic profiling reveals protective function of fatty acid oxidation in cocaine-induced hepatotoxicity. J Lipid Res 2012; 53:2318-30. [PMID: 22904346 PMCID: PMC3466001 DOI: 10.1194/jlr.m027656] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 08/02/2012] [Indexed: 12/14/2022] Open
Abstract
During cocaine-induced hepatotoxicity, lipid accumulation occurs prior to necrotic cell death in the liver. However, the exact influences of cocaine on the homeostasis of lipid metabolism remain largely unknown. In this study, the progression of subacute hepatotoxicity, including centrilobular necrosis in the liver and elevation of transaminase activity in serum, was observed in a three-day cocaine treatment, accompanying the disruption of triacylglycerol (TAG) turnover. Serum TAG level increased on day 1 of cocaine treatment but remained unchanged afterwards. In contrast, hepatic TAG level was elevated continuously during three days of cocaine treatment and was better correlated with the development of hepatotoxicity. Lipidomic analyses of serum and liver samples revealed time-dependent separation of the control and cocaine-treated mice in multivariate models, which was due to the accumulation of long-chain acylcarnitines together with the disturbances of many bioactive phospholipid species in the cocaine-treated mice. An in vitro function assay confirmed the progressive inhibition of mitochondrial fatty acid oxidation after the cocaine treatment. Cotreatment of fenofibrate significantly increased the expression of peroxisome proliferator-activated receptor α (PPARα)-targeted genes and the mitochondrial fatty acid oxidation activity in the cocaine-treated mice, resulting in the inhibition of cocaine-induced acylcarnitine accumulation and other hepatotoxic effects. Overall, the results from this lipidomics-guided study revealed that the inhibition of fatty acid oxidation plays an important role in cocaine-induced liver injury.
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Affiliation(s)
- Xiaolei Shi
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
| | - Dan Yao
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
| | - Blake A. Gosnell
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
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