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Benkirane H, Pradat Y, Michiels S, Cournède PH. CustOmics: A versatile deep-learning based strategy for multi-omics integration. PLoS Comput Biol 2023; 19:e1010921. [PMID: 36877736 PMCID: PMC10019780 DOI: 10.1371/journal.pcbi.1010921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/16/2023] [Accepted: 02/04/2023] [Indexed: 03/07/2023] Open
Abstract
The availability of patient cohorts with several types of omics data opens new perspectives for exploring the disease's underlying biological processes and developing predictive models. It also comes with new challenges in computational biology in terms of integrating high-dimensional and heterogeneous data in a fashion that captures the interrelationships between multiple genes and their functions. Deep learning methods offer promising perspectives for integrating multi-omics data. In this paper, we review the existing integration strategies based on autoencoders and propose a new customizable one whose principle relies on a two-phase approach. In the first phase, we adapt the training to each data source independently before learning cross-modality interactions in the second phase. By taking into account each source's singularity, we show that this approach succeeds at taking advantage of all the sources more efficiently than other strategies. Moreover, by adapting our architecture to the computation of Shapley additive explanations, our model can provide interpretable results in a multi-source setting. Using multiple omics sources from different TCGA cohorts, we demonstrate the performance of the proposed method for cancer on test cases for several tasks, such as the classification of tumor types and breast cancer subtypes, as well as survival outcome prediction. We show through our experiments the great performances of our architecture on seven different datasets with various sizes and provide some interpretations of the results obtained. Our code is available on (https://github.com/HakimBenkirane/CustOmics).
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Affiliation(s)
- Hakim Benkirane
- Université Paris-Saclay, CentraleSupélec, Lab of Mathematics and Informatics (MICS), Gif-sur-Yvette, France
- Oncostat U1018, Inserm, Université Paris-Saclay, Équipe Labellisée Ligue Contre le Cancer, CESP, Villejuif, France
| | - Yoann Pradat
- Université Paris-Saclay, CentraleSupélec, Lab of Mathematics and Informatics (MICS), Gif-sur-Yvette, France
| | - Stefan Michiels
- Oncostat U1018, Inserm, Université Paris-Saclay, Équipe Labellisée Ligue Contre le Cancer, CESP, Villejuif, France
- Bureau de Biostatistique et d’Épidémiologie, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Paul-Henry Cournède
- Université Paris-Saclay, CentraleSupélec, Lab of Mathematics and Informatics (MICS), Gif-sur-Yvette, France
- * E-mail:
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Lopez-Obando M, Guillory A, Boyer FD, Cornu D, Hoffmann B, Le Bris P, Pouvreau JB, Delavault P, Rameau C, de Saint Germain A, Bonhomme S. The Physcomitrium (Physcomitrella) patens PpKAI2L receptors for strigolactones and related compounds function via MAX2-dependent and -independent pathways. Plant Cell 2021; 33:3487-3512. [PMID: 34459915 PMCID: PMC8662777 DOI: 10.1093/plcell/koab217] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/24/2021] [Indexed: 05/20/2023]
Abstract
In angiosperms, the α/β hydrolase DWARF14 (D14), along with the F-box protein MORE AXILLARY GROWTH2 (MAX2), perceives strigolactones (SL) to regulate developmental processes. The key SL biosynthetic enzyme CAROTENOID CLEAVAGE DIOXYGENASE8 (CCD8) is present in the moss Physcomitrium patens, and PpCCD8-derived compounds regulate moss extension. The PpMAX2 homolog is not involved in the SL response, but 13 PpKAI2LIKE (PpKAI2L) genes homologous to the D14 ancestral paralog KARRIKIN INSENSITIVE2 (KAI2) encode candidate SL receptors. In Arabidopsis thaliana, AtKAI2 perceives karrikins and the elusive endogenous KAI2-Ligand (KL). Here, germination assays of the parasitic plant Phelipanche ramosa suggested that PpCCD8-derived compounds are likely noncanonical SLs. (+)-GR24 SL analog is a good mimic for PpCCD8-derived compounds in P. patens, while the effects of its enantiomer (-)-GR24, a KL mimic in angiosperms, are minimal. Interaction and binding assays of seven PpKAI2L proteins pointed to the stereoselectivity toward (-)-GR24 for a single clade of PpKAI2L (eu-KAI2). Enzyme assays highlighted the peculiar behavior of PpKAI2L-H. Phenotypic characterization of Ppkai2l mutants showed that eu-KAI2 genes are not involved in the perception of PpCCD8-derived compounds but act in a PpMAX2-dependent pathway. In contrast, mutations in PpKAI2L-G, and -J genes abolished the response to the (+)-GR24 enantiomer, suggesting that PpKAI2L-G, and -J proteins are receptors for moss SLs.
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Affiliation(s)
- Mauricio Lopez-Obando
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, 78000 Versailles, France
- Department of Plant Biology, Swedish University of Agricultural Sciences, The
Linnean Centre for Plant Biology in Uppsala, SE-750 07 Uppsala, Sweden
- VEDAS Corporación de Investigación e Innovación (VEDASCII),
050024 Medellín, Colombia
| | - Ambre Guillory
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, 78000 Versailles, France
| | - François-Didier Boyer
- Institut de Chimie des Substances Naturelles, CNRS, Université
Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Beate Hoffmann
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, 78000 Versailles, France
| | - Philippe Le Bris
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, 78000 Versailles, France
| | - Jean-Bernard Pouvreau
- Laboratoire de Biologie et Pathologie Végétales, LBPV, Université de
Nantes, 44000 Nantes, France
| | - Philippe Delavault
- Laboratoire de Biologie et Pathologie Végétales, LBPV, Université de
Nantes, 44000 Nantes, France
| | - Catherine Rameau
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, 78000 Versailles, France
| | - Alexandre de Saint Germain
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, 78000 Versailles, France
- Author for correspondence:
(S.B.),
(A.d.S.G.)
| | - Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, 78000 Versailles, France
- Author for correspondence:
(S.B.),
(A.d.S.G.)
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Imamura F, Fretts A, Marklund M, Ardisson Korat AV, Yang WS, Lankinen M, Qureshi W, Helmer C, Chen TA, Wong K, Bassett JK, Murphy R, Tintle N, Yu CI, Brouwer IA, Chien KL, Frazier-Wood AC, del Gobbo LC, Djoussé L, Geleijnse JM, Giles GG, de Goede J, Gudnason V, Harris WS, Hodge A, Hu F, Koulman A, Laakso M, Lind L, Lin HJ, McKnight B, Rajaobelina K, Risérus U, Robinson JG, Samieri C, Siscovick DS, Soedamah-Muthu SS, Sotoodehnia N, Sun Q, Tsai MY, Uusitupa M, Wagenknecht LE, Wareham NJ, Wu JHY, Micha R, Forouhi NG, Lemaitre RN, Mozaffarian D. Fatty acid biomarkers of dairy fat consumption and incidence of type 2 diabetes: A pooled analysis of prospective cohort studies. PLoS Med 2018; 15:e1002670. [PMID: 30303968 PMCID: PMC6179183 DOI: 10.1371/journal.pmed.1002670] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/07/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND We aimed to investigate prospective associations of circulating or adipose tissue odd-chain fatty acids 15:0 and 17:0 and trans-palmitoleic acid, t16:1n-7, as potential biomarkers of dairy fat intake, with incident type 2 diabetes (T2D). METHODS AND FINDINGS Sixteen prospective cohorts from 12 countries (7 from the United States, 7 from Europe, 1 from Australia, 1 from Taiwan) performed new harmonised individual-level analysis for the prospective associations according to a standardised plan. In total, 63,682 participants with a broad range of baseline ages and BMIs and 15,180 incident cases of T2D over the average of 9 years of follow-up were evaluated. Study-specific results were pooled using inverse-variance-weighted meta-analysis. Prespecified interactions by age, sex, BMI, and race/ethnicity were explored in each cohort and were meta-analysed. Potential heterogeneity by cohort-specific characteristics (regions, lipid compartments used for fatty acid assays) was assessed with metaregression. After adjustment for potential confounders, including measures of adiposity (BMI, waist circumference) and lipogenesis (levels of palmitate, triglycerides), higher levels of 15:0, 17:0, and t16:1n-7 were associated with lower incidence of T2D. In the most adjusted model, the hazard ratio (95% CI) for incident T2D per cohort-specific 10th to 90th percentile range of 15:0 was 0.80 (0.73-0.87); of 17:0, 0.65 (0.59-0.72); of t16:1n7, 0.82 (0.70-0.96); and of their sum, 0.71 (0.63-0.79). In exploratory analyses, similar associations for 15:0, 17:0, and the sum of all three fatty acids were present in both genders but stronger in women than in men (pinteraction < 0.001). Whereas studying associations with biomarkers has several advantages, as limitations, the biomarkers do not distinguish between different food sources of dairy fat (e.g., cheese, yogurt, milk), and residual confounding by unmeasured or imprecisely measured confounders may exist. CONCLUSIONS In a large meta-analysis that pooled the findings from 16 prospective cohort studies, higher levels of 15:0, 17:0, and t16:1n-7 were associated with a lower risk of T2D.
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Affiliation(s)
- Fumiaki Imamura
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Amanda Fretts
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Matti Marklund
- Department of Public Health and Caring Sciences, Clinical Nutrition and Metabolism, Uppsala University, Sweden
| | - Andres V. Ardisson Korat
- Department of Nutrition and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Wei-Sin Yang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Maria Lankinen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Waqas Qureshi
- Section of Cardiovascular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Bowman Gray Center, Winston-Salem, North Carolina, United States of America
| | - Catherine Helmer
- INSERM, UMR 1219, Bordeaux Population Health Research Center, University of Bordeaux, Bordeaux, France
| | - Tzu-An Chen
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kerry Wong
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
| | - Julie K. Bassett
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
| | - Rachel Murphy
- Centre of Excellence in Cancer Prevention, School of Population & Public Health, Faculty of Medicine, The University of British Columbia, Vancouver, Canada
| | - Nathan Tintle
- Department of Mathematics and Statistics, Dordt College, Sioux Center, Iowa, United States of America
| | - Chaoyu Ian Yu
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Ingeborg A. Brouwer
- Department of Health Sciences, Faculty of Earth & Life Sciences, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Kuo-Liong Chien
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Alexis C. Frazier-Wood
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Liana C. del Gobbo
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Luc Djoussé
- Divisions of Aging, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Graham G. Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Australia
| | - Janette de Goede
- Division of Human Nutrition, Wageningen University, Wageningen, the Netherlands
| | - Vilmundur Gudnason
- Icelandic Heart Association Research Institute, Holtasmári 1, Kópavogur, Iceland, Iceland
| | - William S. Harris
- Department of Internal Medicine, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, United States of America
- OmegaQuant Analytics LLC, Sioux Falls, South Dakota, United States of America
| | - Allison Hodge
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Australia
| | - Frank Hu
- Department of Nutrition and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - InterAct Consortium
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Albert Koulman
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- National Institute for Health Research Biomedical Research Centres Core Nutritional Biomarker Laboratory, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
- National Institute for Health Research Biomedical Research Centres Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
- Medical Research Council Elsie Widdowson Laboratory, Cambridge, United Kingdom
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Hung-Ju Lin
- Department of Internal Medicine, National Taiwan University Hospital, Zhongzheng District, Taipei City, Taiwan
| | - Barbara McKnight
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Kalina Rajaobelina
- INSERM, UMR 1219, Bordeaux Population Health Research Center, University of Bordeaux, Bordeaux, France
| | - Ulf Risérus
- Department of Public Health and Caring Sciences, Clinical Nutrition and Metabolism, Uppsala University, Sweden
| | - Jennifer G. Robinson
- Departments of Epidemiology and Medicine at the University of Iowa College of Public Health, Iowa City, Iowa, United States of America
| | - Cécilia Samieri
- INSERM, UMR 1219, Bordeaux Population Health Research Center, University of Bordeaux, Bordeaux, France
| | - David S. Siscovick
- The New York Academy of Medicine, New York, New York, United States of America
| | - Sabita S. Soedamah-Muthu
- Division of Human Nutrition, Wageningen University, Wageningen, the Netherlands
- Center of Research on Psychology in Somatic Diseases, Department of Medical and Clinical Psychology, Tilburg University, Tilburg, the Netherlands
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Qi Sun
- Department of Nutrition and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Michael Y. Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Lynne E. Wagenknecht
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nick J. Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Jason HY Wu
- The George Institute for Global Health and the Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Renata Micha
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, United States of America
| | - Nita G. Forouhi
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Rozenn N. Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Dariush Mozaffarian
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, United States of America
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Deschodt-Arsac V, Arsac L, Magat J, Naulin J, Quesson B, Dos Santos P. Energy Deregulation Precedes Alteration in Heart Energy Balance in Young Spontaneously Hypertensive Rats: A Non Invasive In Vivo31P-MR Spectroscopy Follow-Up Study. PLoS One 2016; 11:e0162677. [PMID: 27622548 PMCID: PMC5021382 DOI: 10.1371/journal.pone.0162677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 08/27/2016] [Indexed: 12/03/2022] Open
Abstract
Introduction Gradual alterations in cardiac energy balance, as assessed by the myocardial PCr/ATP-ratio, are frequently associated with the development of cardiac disease. Despite great interest for the follow-up of myocardial PCr and ATP content, cardiac MR-spectroscopy in rat models in vivo is challenged by sensitivity issues and cross-contamination from other organs. Methods Here we combined MR-Imaging and MR-Spectroscopy (Bruker BioSpec 9.4T) to follow-up for the first time in vivo the cardiac energy balance in the SHR, a genetic rat model of cardiac hypertrophy known to develop early disturbances in cytosolic calcium dynamics. Results We obtained consistent 31P-spectra with high signal/noise ratio from the left ventricle in vivo by using a double-tuned (31P/1H) surface coil. Reasonable acquisition time (<3.2min) allowed assessing the PCr/ATP-ratio comparatively in SHR and age-matched control rats (WKY): i) weekly from 12 to 21 weeks of age; ii) in response to a bolus injection of the ß-adrenoreceptor agonist isoproterenol at age 21 weeks. Discussion Along weeks, the cardiac PCr/ATP-ratio was highly reproducible, steady and similar (2.35±0.06) in SHR and WKY, in spite of detectable ventricular hypertrophy in SHR. At the age 21 weeks, PCr/ATP dropped more markedly (-17.1%±0.8% vs. -3,5%±1.4%, P<0.001) after isoproterenol injection in SHR and recovered slowly thereafter (time constant 21.2min vs. 6.6min, P<0.05) despite similar profiles of tachycardia among rats. Conclusion The exacerbated PCr/ATP drop under ß-adrenergic stimulation indicates a defect in cardiac energy regulation possibly due to calcium-mediated abnormalities in the SHR heart. Of note, defects in energy regulation were present before detectable abnormalities in cardiac energy balance at rest.
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Affiliation(s)
- Veronique Deschodt-Arsac
- L'Institut de Rythmologie et Modélisation Cardiaque LIRYC, Université de Bordeaux, Pessac, France; Inserm U1045 CRCTB, Université de Bordeaux, Bordeaux, France
- * E-mail:
| | - Laurent Arsac
- L'Institut de Rythmologie et Modélisation Cardiaque LIRYC, Université de Bordeaux, Pessac, France; Inserm U1045 CRCTB, Université de Bordeaux, Bordeaux, France
| | - Julie Magat
- L'Institut de Rythmologie et Modélisation Cardiaque LIRYC, Université de Bordeaux, Pessac, France; Inserm U1045 CRCTB, Université de Bordeaux, Bordeaux, France
| | - Jerome Naulin
- L'Institut de Rythmologie et Modélisation Cardiaque LIRYC, Université de Bordeaux, Pessac, France; Inserm U1045 CRCTB, Université de Bordeaux, Bordeaux, France
| | - Bruno Quesson
- L'Institut de Rythmologie et Modélisation Cardiaque LIRYC, Université de Bordeaux, Pessac, France; Inserm U1045 CRCTB, Université de Bordeaux, Bordeaux, France
| | - Pierre Dos Santos
- L'Institut de Rythmologie et Modélisation Cardiaque LIRYC, Université de Bordeaux, Pessac, France; Inserm U1045 CRCTB, Université de Bordeaux, Bordeaux, France; Hôpital cardiologique Haut-Lévêque, CHU de Bordeaux, Pessac, France
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