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Polachini GM, de Castro TB, Smarra LFS, Henrique T, de Paula CHD, Severino P, López RVM, Carvalho AL, de Mattos Zeri AC, Silva IDCG, Tajara EH. Plasma metabolomics of oral squamous cell carcinomas based on NMR and MS approaches provides biomarker identification and survival prediction. Sci Rep 2023; 13:8588. [PMID: 37237049 DOI: 10.1038/s41598-023-34808-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Metabolomics has proven to be an important omics approach to understand the molecular pathways underlying the tumour phenotype and to identify new clinically useful markers. The literature on cancer has illustrated the potential of this approach as a diagnostic and prognostic tool. The present study aimed to analyse the plasma metabolic profile of patients with oral squamous cell carcinoma (OSCC) and controls and to compare patients with metastatic and primary tumours at different stages and subsites using nuclear magnetic resonance and mass spectrometry. To our knowledge, this is the only report that compared patients at different stages and subsites and replicates collected in diverse institutions at different times using these methodologies. Our results showed a plasma metabolic OSCC profile suggestive of abnormal ketogenesis, lipogenesis and energy metabolism, which is already present in early phases but is more evident in advanced stages of the disease. Reduced levels of several metabolites were also associated with an unfavorable prognosis. The observed metabolomic alterations may contribute to inflammation, immune response inhibition and tumour growth, and may be explained by four nonexclusive views-differential synthesis, uptake, release, and degradation of metabolites. The interpretation that assimilates these views is the cross talk between neoplastic and normal cells in the tumour microenvironment or in more distant anatomical sites, connected by biofluids, signalling molecules and vesicles. Additional population samples to evaluate the details of these molecular processes may lead to the discovery of new biomarkers and novel strategies for OSCC prevention and treatment.
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Affiliation(s)
- Giovana Mussi Polachini
- Department of Molecular Biology, School of Medicine of São José Do Rio Preto - FAMERP, Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
| | - Tialfi Bergamin de Castro
- Department of Molecular Biology, School of Medicine of São José Do Rio Preto - FAMERP, Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
| | - Luis Fabiano Soares Smarra
- Department of Molecular Biology, School of Medicine of São José Do Rio Preto - FAMERP, Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José Do Rio Preto - FAMERP, Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
| | - Carlos Henrique Diniz de Paula
- Department of Molecular Biology, School of Medicine of São José Do Rio Preto - FAMERP, Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José Do Rio Preto - FAMERP, Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil.
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
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Liu SH, Ma XY, Hassan FU, Gao TY, Deng TX. Genome-wide analysis of runs of homozygosity in Italian Mediterranean buffalo. J Dairy Sci 2022; 105:4324-4334. [PMID: 35307184 DOI: 10.3168/jds.2021-21543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/07/2022] [Indexed: 11/19/2022]
Abstract
Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted for approximately 72.29% of all ROH. In contrast, the larger ROH (>8 Mb) class accounted for only 7.97% of all ROH segments. Estimated inbreeding coefficients from ROH (FROH) ranged from 0.0201 to 0.0371. Pearson correlations between FROH and genomic relationship matrix increased with the increase of ROH length. We identified ROH hotspots in 12 genomic regions, located on chromosomes 1, 2, 3, 5, 17, and 19, harboring a total of 122 genes. Protein-protein interaction (PPI) analysis revealed the clustering of these genes into 7 PPI networks. Many genes located in these regions were associated with different production traits. In addition, 5 ROH islands overlapped with cattle quantitative trait loci that were mainly associated with milk traits. These findings revealed the genome-wide autozygosity patterns and inbreeding levels in Mediterranean buffalo. Our study identified many candidate genes related to production traits that could be used to assist in selective breeding for genetic improvement of buffalo.
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Affiliation(s)
- Shen-He Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xiao-Ya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Teng-Yun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ting-Xian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
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Kytikova OY, Novgorodtseva TP, Denisenko YK, Antonyuk MV, Gvozdenko TA. Associations Of Delta Fatty Acid Desaturase Gene Polymorphisms With Lipid Metabolism Disorders. RUSSIAN OPEN MEDICAL JOURNAL 2021. [DOI: 10.15275/rusomj.2021.0403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Overweight, obesity, type 2 diabetes mellitus, metabolic syndrome, cardiovascular diseases, and non-alcoholic fatty liver disease are common chronic ailments associated with lipid metabolism disorders. One of the mechanisms of these disorders is related to the deficiency and/or change in the balance of essential fatty acids (FAs). At the same time, the provision of ω3 and ω6 polyunsaturated fatty acids (PUFAs) depends, besides sufficient dietary intake, on efficiency of their endogenous biosynthesis by desaturation and elongation processes regulated by FA elongases and FA desaturases. Desaturases are encoded by PUFA desaturase genes (FADSs): FADS1 and FADS2. Alteration of FA desaturase activity and single nucleotide polymorphisms (SNPs) in the FADS1 and FADS2 gene cluster are associated with lipid metabolism dysfunction and may affect the pathogenesis of lipid-related diseases. People of different ages, from different ethnic backgrounds and countries may exhibit varying degrees of response to dietary supplements of ω3 and ω6 PUFAs. The study of the relationship between lipid metabolism disorders and genetic factors controlling FA metabolism is an important research area since the health effects of alimentary ω3 and ω6 PUFAs can depend on genetic variants of the FADS genes. This review summarizes the literature data on the association of FADS gene polymorphisms with lipid metabolism disorders and their role in the development of chronic non-communicable pathologies associated with changes in lipid metabolism.
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Affiliation(s)
- Oksana Yu. Kytikova
- Research Institute of Medical Climatology and Rehabilitative Treatment, Vladivostok, Russia
| | | | - Yulia K. Denisenko
- Research Institute of Medical Climatology and Rehabilitative Treatment, Vladivostok, Russia
| | - Marina V. Antonyuk
- Research Institute of Medical Climatology and Rehabilitative Treatment, Vladivostok, Russia
| | - Tatyana A. Gvozdenko
- Research Institute of Medical Climatology and Rehabilitative Treatment, Vladivostok, Russia
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Macciotta NPP, Colli L, Cesarani A, Ajmone-Marsan P, Low WY, Tearle R, Williams JL. The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events. Genet Sel Evol 2021; 53:20. [PMID: 33639853 PMCID: PMC7912491 DOI: 10.1186/s12711-021-00616-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/17/2021] [Indexed: 01/03/2023] Open
Abstract
Background Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. Results The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. Conclusions Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00616-3.
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Affiliation(s)
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,Centro di Ricerca sulla Biodiversità e sul DNA Antico-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italia
| | - Alberto Cesarani
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italia. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,Centro di Ricerca Nutrigenomica e Proteomica-PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italia
| | - Wai Y Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Rick Tearle
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - John L Williams
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
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5
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Hua MC, Su HM, Lai MW, Yao TC, Tsai MH, Liao SL, Lai SH, Huang JL. Palmitoleic and Dihomo-γ-Linolenic Acids Are Positively Associated With Abdominal Obesity and Increased Metabolic Risk in Children. Front Pediatr 2021; 9:628496. [PMID: 33898358 PMCID: PMC8062925 DOI: 10.3389/fped.2021.628496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: The impact of abdominal obesity (AO) on plasma fatty acid changes and cardiometabolic risk in children who are obese and overweight has rarely been investigated. This study determined whether plasma fatty acid composition differed between children with AO and those without AO and its relationship with metabolic risk, particularly in the obese and overweight groups. Methods: A total of 181 schoolchildren (aged 7-18 years) were included. Anthropometric and biochemical data and plasma fatty acid profiles were analyzed, and the indices of desaturase activity were estimated. Children were categorized based on their body weight and AO status. A continuous metabolic risk score was calculated using the sum of the z-scores of metabolic variables. A one-way analysis of variance test was used to compare the composition ratio of fatty acids between children with and without AO in the obese and overweight groups and normal-weight controls. Pearson analysis was also used to explore significant fatty acid and desaturase indicators associated with metabolic abnormalities. Results: Children who were obese and overweight (N = 126) displayed higher dihomo-γ-linolenic acid (20:3n-6) and γ-linolenic acid (18:3n-6) proportions than normal-weight controls (N = 55), but lower heptadecanoic acid (17:0) proportion, regardless of the AO status of each individual. Obese and overweight children with AO (N = 89), but not their non-AO counterparts (N = 37), exhibited a significantly higher proportion of palmitoleic acid (16:1n-7) than the remaining study groups. Pearson analysis showed that high proportions of palmitoleic acid and dihomo-γ-linolenic acid, as well as increased stearoyl-coenzyme A desaturase-1(16) and delta-6 desaturase and decreased delta-5 desaturase activities, are strongly correlated with weight-height ratio, homeostasis model of assessment values for insulin resistance, hypertriglyceridemia, and continuous metabolic risk scores. Conclusion: Higher palmitoleic acid and dihomo-γ-linolenic acid proportions, as well as increased stearoyl-coenzyme A desaturase-1(16) and delta-6 desaturase and decreased delta-5 desaturase activities are associated with AO and increased metabolic risk in children who are obese and overweight.
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Affiliation(s)
- Man-Chin Hua
- Department of Pediatrics, Chang Gung Memorial Hospital, Keelung, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hui-Min Su
- Department of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ming-Wei Lai
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Division of Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tsung-Chieh Yao
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Division of Allergy, Asthma and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ming-Han Tsai
- Department of Pediatrics, Chang Gung Memorial Hospital, Keelung, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Sui-Ling Liao
- Department of Pediatrics, Chang Gung Memorial Hospital, Keelung, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Shen-Hao Lai
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Division of Chest, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jing-Long Huang
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Department of Pediatrics, Municipal TuCheng Hospital, Chang Gung Memorial Hospital, New Taipei City, Taiwan
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6
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Schulze MB, Minihane AM, Saleh RNM, Risérus U. Intake and metabolism of omega-3 and omega-6 polyunsaturated fatty acids: nutritional implications for cardiometabolic diseases. Lancet Diabetes Endocrinol 2020; 8:915-930. [PMID: 32949497 DOI: 10.1016/s2213-8587(20)30148-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/12/2022]
Abstract
Prospective observational studies support the use of long-chain omega-3 polyunsaturated fatty acids (PUFAs) in the primary prevention of atherosclerotic cardiovascular disease; however, randomised controlled trials, have often reported neutral findings. There is a long history of debate about the potential harmful effects of a high intake of omega-6 PUFAs, although this idea is not supported by prospective observational studies or randomised controlled trials. Health effects of PUFAs might be influenced by Δ-5 and Δ-6 desaturases, the key enzymes in the metabolism of PUFAs. The activity of these enzymes and modulation by variants in encoding genes (FADS1-2-3 gene cluster) are linked to several cardiometabolic traits. This Review will further consider non-genetic determinants of desaturase activity, which have the potential to modify the availability of PUFAs to tissues. Finally, we discuss the consequences of altered desaturase activity in the context of PUFA intake, that is, gene-diet interactions and their clinical and public health implications.
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Affiliation(s)
- Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany; German Center for Diabetes Research, Neuherberg, Germany.
| | - Anne Marie Minihane
- Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rasha Noureldin M Saleh
- Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, UK; Clinical Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Ulf Risérus
- Department of Public Health and Caring Sciences, Clinical Nutrition and Metabolism, Uppsala University, Uppsala, Sweden
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7
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Jäger S, Cuadrat R, Hoffmann P, Wittenbecher C, Schulze MB. Desaturase Activity and the Risk of Type 2 Diabetes and Coronary Artery Disease: A Mendelian Randomization Study. Nutrients 2020; 12:E2261. [PMID: 32731631 PMCID: PMC7469057 DOI: 10.3390/nu12082261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/22/2022] Open
Abstract
Estimated Δ5-desaturase (D5D) and Δ6-desaturase (D6D) are key enzymes in metabolism of polyunsaturated fatty acids (PUFA) and have been associated with cardiometabolic risk; however, causality needs to be clarified. We applied two-sample Mendelian randomization (MR) approach using a representative sub-cohort of the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam Study and public data from DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) and Coronary ARtery DIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) genome-wide association studies (GWAS). Furthermore, we addressed confounding by linkage disequilibrium (LD) as all instruments from FADS1 (encoding D5D) are in LD with FADS2 (encoding D6D) variants. Our univariable MRs revealed risk-increasing total effects of both, D6D and D5D on type 2 diabetes (T2DM) risk; and risk-increasing total effect of D6D on risk of coronary artery disease (CAD). The multivariable MR approach could not unambiguously allocate a direct causal effect to either of the individual desaturases. Our results suggest that D6D is causally linked to cardiometabolic risk, which is likely due to downstream production of fatty acids and products resulting from high D6D activity. For D5D, we found indication for causal effects on T2DM and CAD, which could, however, still be confounded by LD.
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Affiliation(s)
- Susanne Jäger
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (S.J.); (R.C.); (C.W.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Rafael Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (S.J.); (R.C.); (C.W.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Per Hoffmann
- Human Genomics Research Group, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland;
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Clemens Wittenbecher
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (S.J.); (R.C.); (C.W.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (S.J.); (R.C.); (C.W.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, 14558 Nuthetal, Germany
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8
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Yang C, Wan X, Lin X, Chen M, Zhou X, Liu J. CoMM: a collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information. Bioinformatics 2020; 35:1644-1652. [PMID: 30295737 DOI: 10.1093/bioinformatics/bty865] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/15/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Genome-wide association studies (GWASs) have been successful in identifying many genetic variants associated with complex traits. However, the mechanistic links between these variants and complex traits remain elusive. A scientific hypothesis is that genetic variants influence complex traits at the organismal level via affecting cellular traits, such as regulating gene expression and altering protein abundance. Although earlier works have already presented some scientific insights about this hypothesis and their findings are very promising, statistical methods that effectively harness multilayered data (e.g. genetic variants, cellular traits and organismal traits) on a large scale for functional and mechanistic exploration are highly demanding. RESULTS In this study, we propose a collaborative mixed model (CoMM) to investigate the mechanistic role of associated variants in complex traits. The key idea is built upon the emerging scientific evidence that genetic effects at the cellular level are much stronger than those at the organismal level. Briefly, CoMM combines two models: the first model relating gene expression with genotype and the second model relating phenotype with predicted gene expression using the first model. The two models are fitted jointly in CoMM, such that the uncertainty in predicting gene expression has been fully accounted. To demonstrate the advantages of CoMM over existing methods, we conducted extensive simulation studies, and also applied CoMM to analyze 25 traits in NFBC1966 and Genetic Epidemiology Research on Aging (GERA) studies by integrating transcriptome information from the Genetic European in Health and Disease (GEUVADIS) Project. The results indicate that by leveraging regulatory information, CoMM can effectively improve the power of prioritizing risk variants. Regarding the computational efficiency, CoMM can complete the analysis of NFBC1966 dataset and GERA datasets in 2 and 18 min, respectively. AVAILABILITY AND IMPLEMENTATION The developed R package is available at https://github.com/gordonliu810822/CoMM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Can Yang
- Department of Mathematics, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiang Wan
- Shenzhen Research Institute of Big Data, Shenzhen, China
| | - Xinyi Lin
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore
| | - Mengjie Chen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Jin Liu
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore
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9
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Czumaj A, Śledziński T. Biological Role of Unsaturated Fatty Acid Desaturases in Health and Disease. Nutrients 2020; 12:E356. [PMID: 32013225 PMCID: PMC7071289 DOI: 10.3390/nu12020356] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Polyunsaturated fatty acids (PUFAs) are considered one of the most important components of cells that influence normal development and function of many organisms, both eukaryotes and prokaryotes. Unsaturated fatty acid desaturases play a crucial role in the synthesis of PUFAs, inserting additional unsaturated bonds into the acyl chain. The level of expression and activity of different types of desaturases determines profiles of PUFAs. It is well recognized that qualitative and quantitative changes in the PUFA profile, resulting from alterations in the expression and activity of fatty acid desaturases, are associated with many pathological conditions. Understanding of underlying mechanisms of fatty acid desaturase activity and their functional modification will facilitate the development of novel therapeutic strategies in diseases associated with qualitative and quantitative disorders of PUFA.
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Affiliation(s)
- Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, Dębinki, 80-211 Gdansk, Poland;
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10
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Franck M, de Toro-Martín J, Guénard F, Rudkowska I, Lemieux S, Lamarche B, Couture P, Vohl MC. Prevention of Potential Adverse Metabolic Effects of a Supplementation with Omega-3 Fatty Acids Using a Genetic Score Approach. Lifestyle Genom 2019; 13:32-42. [PMID: 31779001 DOI: 10.1159/000504022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/07/2019] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION The consumption of long-chain omega-3 polyunsaturated fatty acids (n-3 PUFA) has been reported to have beneficial health effects, notably, by reducing plasma triglyceride levels. Nonetheless, a concomitant decrease in insulin sensitivity has also been observed, but is highly variable among subjects. Herein, we aimed to determine the importance of the genetic background in the interindividual variability of the insulin sensitivity response following an n-3 PUFA supplementation. METHODS A total of 210 participants completed a 6-week n-3 PUFA supplementation with 5 g/day of fish oil (providing 1.9-2.2 g of eicosapentaenoic acid + 1.1 g of docosahexaenoic acid). Insulin resistance was estimated by the homeostatic model assessment (HOMA-IR), and participants were further classified as high-risk or low-risk depending on their HOMA-IR change following the n-3 PUFA supplementation, as compared to pre-supplementation values. Genome-wide genotyping data were obtained for 138 participants using HumanOmni-5-Quad BeadChips containing 4,301,331 single nucleotide polymorphisms. A genome-wide association analysis (GWAS) was carried out between high-risk and low-risk participants. The population study was split into training (60%) and testing (40%) datasets to assess the predictive accuracy of a genetic risk score (GRS) constructed by summing the number of risk alleles. RESULTS Following the n-3 PUFA supplementation, 32 participants had increased HOMA-IR as compared to initial values and were classified as high risk (23.2%), whereas remaining subjects were classified as low risk (n = 106, 76.8%). A total of 8 loci had frequency differences between high-risk and low-risk participants at a suggestive GWAS association threshold (p value <1 × 10-5). After applying 10-fold cross validation, the GRS showed a significant association with the risk of increased HOMA-IR in the testing dataset (OR = 3.16 [95% CI, 1.85-7.14]), with a predictive accuracy of 0.85, and explained 40% of variation in HOMA-IR change. CONCLUSIONS These results suggest that the genetic background has a relevant role in the interindividual variability observed in the insulin sensitivity response following an n-3 PUFA supplementation. Subjects being at risk of insulin sensitivity lowering following an n-3 PUFA supplementation may be identified using genetic-based precision nutrition approaches.
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Affiliation(s)
- Maximilien Franck
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Juan de Toro-Martín
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Iwona Rudkowska
- Department of Kinesiology, Laval University, Quebec City, Québec, Canada.,Endocrinology and Nephrology Unit, CHU de Quebec Research Center, Quebec City, Québec, Canada
| | - Simone Lemieux
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Benoît Lamarche
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Patrick Couture
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,Endocrinology and Nephrology Unit, CHU de Quebec Research Center, Quebec City, Québec, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada, .,School of Nutrition, Laval University, Quebec City, Québec, Canada,
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Tremblay BL, Guénard F, Lamarche B, Pérusse L, Vohl MC. Integrative Network Analysis of Multi-Omics Data in the Link between Plasma Carotenoid Concentrations and Lipid Profile. Lifestyle Genom 2019; 13:11-19. [PMID: 31770753 DOI: 10.1159/000503828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/24/2019] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Carotenoids, which are a reliable biomarker of fruit and vegetable consumption, are positively associated with the lipid profile. Circulating carotenoid concentrations may interact with several omics profiles including genome, transcriptome, and epigenome. Few studies have used multi-omics approaches, and they rarely include environmental factors, such as diet. OBJECTIVE The objective of this observational study was to examine the potential role of multi-omics data in the interconnection between diet, represented by total carotenoids, and lipid profile using weighted gene correlation network analysis (WGCNA). METHODS Blood leukocyte DNA methylation levels of 472,245 CpG sites and whole blood gene expression levels of 18,160 transcripts were tested for associations with total carotenoid concentrations using regressions in 48 healthy subjects. WGCNA was used to identify co-omics modules and hub genes related to the lipid profile. RESULTS Among genes associated with total carotenoid concentrations, a total of 236 genes were identified at both DNA methylation and gene expression levels. Using WGCNA, six modules, consisting of groups of highly correlated genes represented by colors, were identified and linked to the lipid profile. Probes clustered in the turquoise and green modules correlated with plasma lipid concentrations. A total of 28 hub genes were identified. CONCLUSIONS Genome-wide DNA methylation and gene expression levels were both associated with plasma total carotenoid concentrations. Several hub genes, mostly involved in lipid metabolism and inflammatory response with several genetic variants associated with plasma lipid concentrations, came out of the integrative analysis. This provides a comprehensive understanding of the interactive molecular system between carotenoids, omics, and plasma lipid profile.
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Affiliation(s)
- Bénédicte L Tremblay
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Benoît Lamarche
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Louis Pérusse
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,Department of Kinesiology, Laval University, Quebec City, Québec, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada, .,School of Nutrition, Laval University, Quebec City, Québec, Canada,
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