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Marco HG, Glendinning S, Ventura T, Gäde G. The gonadotropin-releasing hormone (GnRH) superfamily across Pancrustacea/Tetraconata: A role in metabolism? Mol Cell Endocrinol 2024; 590:112238. [PMID: 38616035 DOI: 10.1016/j.mce.2024.112238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Affiliation(s)
- Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa.
| | - Susan Glendinning
- Centre for BioInnovation, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Tomer Ventura
- Centre for BioInnovation, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
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2
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Foreman AL, Warth B, Hessel EVS, Price EJ, Schymanski EL, Cantelli G, Parkinson H, Hecht H, Klánová J, Vlaanderen J, Hilscherova K, Vrijheid M, Vineis P, Araujo R, Barouki R, Vermeulen R, Lanone S, Brunak S, Sebert S, Karjalainen T. Adopting Mechanistic Molecular Biology Approaches in Exposome Research for Causal Understanding. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7256-7269. [PMID: 38641325 PMCID: PMC11064223 DOI: 10.1021/acs.est.3c07961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Through investigating the combined impact of the environmental exposures experienced by an individual throughout their lifetime, exposome research provides opportunities to understand and mitigate negative health outcomes. While current exposome research is driven by epidemiological studies that identify associations between exposures and effects, new frameworks integrating more substantial population-level metadata, including electronic health and administrative records, will shed further light on characterizing environmental exposure risks. Molecular biology offers methods and concepts to study the biological and health impacts of exposomes in experimental and computational systems. Of particular importance is the growing use of omics readouts in epidemiological and clinical studies. This paper calls for the adoption of mechanistic molecular biology approaches in exposome research as an essential step in understanding the genotype and exposure interactions underlying human phenotypes. A series of recommendations are presented to make the necessary and appropriate steps to move from exposure association to causation, with a huge potential to inform precision medicine and population health. This includes establishing hypothesis-driven laboratory testing within the exposome field, supported by appropriate methods to read across from model systems research to human.
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Affiliation(s)
- Amy L. Foreman
- European
Molecular Biology Laboratory & European Bioinformatics Institute
(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K.
| | - Benedikt Warth
- Department
of Food Chemistry and Toxicology, University
of Vienna, 1090 Vienna, Austria
| | - Ellen V. S. Hessel
- National
Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Elliott J. Price
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Emma L. Schymanski
- Luxembourg
Centre for Systems Biomedicine, University
of Luxembourg, 6 avenue
du Swing, L-4367 Belvaux, Luxembourg
| | - Gaia Cantelli
- European
Molecular Biology Laboratory & European Bioinformatics Institute
(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K.
| | - Helen Parkinson
- European
Molecular Biology Laboratory & European Bioinformatics Institute
(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K.
| | - Helge Hecht
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Jana Klánová
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Jelle Vlaanderen
- Institute
for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Heidelberglaan 8 3584 CS Utrecht, The Netherlands
| | - Klara Hilscherova
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Martine Vrijheid
- Institute
for Global Health (ISGlobal), Barcelona
Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat
Pompeu Fabra, Carrer
de la Mercè, 12, Ciutat Vella, 08002 Barcelona, Spain
- Centro de Investigación Biomédica en Red
Epidemiología
y Salud Pública (CIBERESP), Av. Monforte de Lemos, 3-5. Pebellón 11, Planta 0, 28029 Madrid, Spain
| | - Paolo Vineis
- Department
of Epidemiology and Biostatistics, School of Public Health, Imperial College, London SW7 2AZ, U.K.
| | - Rita Araujo
- European Commission, DG Research and Innovation, Sq. Frère-Orban 8, 1000 Bruxelles, Belgium
| | | | - Roel Vermeulen
- Institute
for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Heidelberglaan 8 3584 CS Utrecht, The Netherlands
| | - Sophie Lanone
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France
| | - Søren Brunak
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Blegdamsvej 3B, 2200 København, Denmark
| | - Sylvain Sebert
- Research
Unit of Population Health, University of
Oulu, P.O. Box 8000, FI-90014 Oulu, Finland
| | - Tuomo Karjalainen
- European Commission, DG Research and Innovation, Sq. Frère-Orban 8, 1000 Bruxelles, Belgium
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3
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She J, Lu F, Chi Y, Cao L, Zuo Y, Yang N, Zhang X, Dai X. Ginseng Extract Attenuates the Injury from Ultraviolet Irradiation for Female Drosophila melanogaster through the Autophagy Signaling Pathway. J Med Food 2024; 27:348-358. [PMID: 38387003 DOI: 10.1089/jmf.2023.k.0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
Ginseng is an ancient medicinal and edible plant with many health benefits, and can serve as a drug and dietary supplement, but there are few relevant studies on its use to ease ultraviolet (UV) irradiation damage. After 0.8 mg/mL ginseng extract (GE) was added to the medium of female Drosophila melanogaster subjected to UV irradiation, the lifespan, climbing ability, sex ratio, developmental cycle, and antioxidant capacity of flies were examined to evaluate the GE function. In addition, the underlying mechanism by which GE enhances the irradiation tolerance of D. melanogaster was explored. With GE supplementation, female flies subjected to UV irradiation exhibited an extension in their lifespan, enhancement in their climbing ability, improvement in their offspring sex ratio, and restoration of the normal development cycle by increasing their antioxidant activity. Finally, further experiments indicated that GE could enhance the irradiation tolerance of female D. melanogaster by upregulating the gene expressions of SOD, GCL, and components of the autophagy signaling pathway. Finally, the performance of r4-Gal4;UAS-AMPKRNAi flies confirmed the regulatory role of the autophagy signaling pathway in mitigating UV irradiation injury.
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Affiliation(s)
- JiaYi She
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - FangYuan Lu
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - YiQing Chi
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - LingYao Cao
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Yaqi Zuo
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Na Yang
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xing Zhang
- Zhejiang Shengshi Bio-technology Co., Ltd, Anji, China
| | - XianJun Dai
- College of Life Sciences, China Jiliang University, Hangzhou, China
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, Hangzhou, China
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4
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Huang F, Xu P, Yue Z, Song Y, Hu K, Zhao X, Gao M, Chong Z. Body Weight Correlates with Molecular Variances in Patients with Cancer. Cancer Res 2024; 84:757-770. [PMID: 38190709 PMCID: PMC10911806 DOI: 10.1158/0008-5472.can-23-1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/27/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024]
Abstract
Overweight and obesity are identified by a high body mass index (BMI) and carry significant health risks due to associated comorbidities. Although epidemiologic data connect overweight/obesity with 13 cancer types, a better understanding of the molecular mechanisms underlying this correlation is needed to improve prevention and treatment strategies. In this study, we conducted a comprehensive analysis of molecular differences between overweight or obese patients and normal weight patients across 14 different cancer types from The Cancer Genome Atlas. Using the propensity score weighting algorithm to control for confounding factors, obesity-specific mutational features were identified, such as higher mutation burden in rectal cancer and biased mutational signatures in other cancers. Differentially expressed genes (DEG) in tumors from patients with overweight/obesity were predominantly upregulated and enriched in inflammatory and hormone-related pathways. These DEGs were significantly associated with survival rates in various cancer types, highlighting the impact of elevated body fat on gene expression profiles and clinical outcomes in patients with cancer. Interestingly, while high BMI seemed to have a negative impact on most cancer types, the normal weight-biased mutational and gene expression patterns indicated overweight/obesity may be beneficial in endometrial cancer, suggesting the presence of an "obesity paradox" in this context. Body fat also significantly impacted the tumor microenvironment by modulating immune cell infiltration, underscoring the importance of understanding the interplay between weight and immune response in cancer progression. Together, this study systematically elucidates the molecular differences corresponding to body weight in multiple cancer types, offering potentially critical insights for developing precision therapy for patients with cancer. SIGNIFICANCE Elucidation of the complex interplay between body weight and the molecular landscape of cancer could potentially guide tailored therapies and improve patient management amid the global obesity crisis.
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Affiliation(s)
- Fengyuan Huang
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Peng Xu
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zongliang Yue
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yuwei Song
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kaili Hu
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xinyang Zhao
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, Kansas
| | - Min Gao
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zechen Chong
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
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Singh P, Kuder H, Ritz A. Identification of disease modules using higher-order network structure. BIOINFORMATICS ADVANCES 2023; 3:vbad140. [PMID: 37860106 PMCID: PMC10582521 DOI: 10.1093/bioadv/vbad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/18/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023]
Abstract
Motivation Higher-order interaction patterns among proteins have the potential to reveal mechanisms behind molecular processes and diseases. While clustering methods are used to identify functional groups within molecular interaction networks, these methods largely focus on edge density and do not explicitly take into consideration higher-order interactions. Disease genes in these networks have been shown to exhibit rich higher-order structure in their vicinity, and considering these higher-order interaction patterns in network clustering have the potential to reveal new disease-associated modules. Results We propose a higher-order community detection method which identifies community structure in networks with respect to specific higher-order connectivity patterns beyond edges. Higher-order community detection on four different protein-protein interaction networks identifies biologically significant modules and disease modules that conventional edge-based clustering methods fail to discover. Higher-order clusters also identify disease modules from genome-wide association study data, including new modules that were not discovered by top-performing approaches in a Disease Module DREAM Challenge. Our approach provides a more comprehensive view of community structure that enables us to predict new disease-gene associations. Availability and implementation https://github.com/Reed-CompBio/graphlet-clustering.
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Affiliation(s)
- Pramesh Singh
- Biology Department, Reed College, Portland, OR 97202, United States
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, United States
| | - Hannah Kuder
- Physics Department, Reed College, Portland, OR 97202, United States
| | - Anna Ritz
- Biology Department, Reed College, Portland, OR 97202, United States
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Šimon M, Mikec Š, Morton NM, Atanur SS, Konc J, Horvat S, Kunej T. Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness. Mamm Genome 2023; 34:12-31. [PMID: 36414820 PMCID: PMC9684942 DOI: 10.1007/s00335-022-09967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.
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Affiliation(s)
- Martin Šimon
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Špela Mikec
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M. Morton
- grid.511172.10000 0004 0613 128XUniversity of Edinburgh, The Queen’s Medical Research Institute, Centre for Cardiovascular Science, Edinburgh, UK
| | - Santosh S. Atanur
- grid.7445.20000 0001 2113 8111Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- grid.4305.20000 0004 1936 7988Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Janez Konc
- grid.454324.00000 0001 0661 0844Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Simon Horvat
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Tanja Kunej
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
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7
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Metabolic Syndrome: Lessons from Rodent and Drosophila Models. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5850507. [PMID: 35782067 PMCID: PMC9242782 DOI: 10.1155/2022/5850507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 05/20/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022]
Abstract
Overweight and obesity are health conditions tightly related to a number of metabolic complications collectively called “metabolic syndrome” (MetS). Clinical diagnosis of MetS includes the presence of the increased waist circumference or so-called abdominal obesity, reduced high density lipoprotein level, elevated blood pressure, and increased blood glucose and triacylglyceride levels. Different approaches, including diet-induced and genetically induced animal models, have been developed to study MetS pathogenesis and underlying mechanisms. Studies of metabolic disturbances in the fruit fly Drosophila and mammalian models along with humans have demonstrated that fruit flies and small mammalian models like rats and mice have many similarities with humans in basic metabolic functions and share many molecular mechanisms which regulate these metabolic processes. In this paper, we describe diet-induced, chemically and genetically induced animal models of the MetS. The advantages and limitations of rodent and Drosophila models of MetS and obesity are also analyzed.
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Eickelberg V, Lüersen K, Staats S, Rimbach G. Phenotyping of Drosophila Melanogaster-A Nutritional Perspective. Biomolecules 2022; 12:221. [PMID: 35204721 PMCID: PMC8961528 DOI: 10.3390/biom12020221] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
The model organism Drosophila melanogaster was increasingly applied in nutrition research in recent years. A range of methods are available for the phenotyping of D. melanogaster, which are outlined in the first part of this review. The methods include determinations of body weight, body composition, food intake, lifespan, locomotor activity, reproductive capacity and stress tolerance. In the second part, the practical application of the phenotyping of flies is demonstrated via a discussion of obese phenotypes in response to high-sugar diet (HSD) and high-fat diet (HFD) feeding. HSD feeding and HFD feeding are dietary interventions that lead to an increase in fat storage and affect carbohydrate-insulin homeostasis, lifespan, locomotor activity, reproductive capacity and stress tolerance. Furthermore, studies regarding the impacts of HSD and HFD on the transcriptome and metabolome of D. melanogaster are important for relating phenotypic changes to underlying molecular mechanisms. Overall, D. melanogaster was demonstrated to be a valuable model organism with which to examine the pathogeneses and underlying molecular mechanisms of common chronic metabolic diseases in a nutritional context.
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Affiliation(s)
- Virginia Eickelberg
- Department of Food Science, Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6-8, D-24118 Kiel, Germany; (K.L.); (S.S.); (G.R.)
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