1
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Everman ER, Macdonald SJ. Gene expression variation underlying tissue-specific responses to copper stress in Drosophila melanogaster. G3 (BETHESDA, MD.) 2024; 14:jkae015. [PMID: 38262701 PMCID: PMC11021028 DOI: 10.1093/g3journal/jkae015] [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: 11/17/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
Copper is one of a handful of biologically necessary heavy metals that is also a common environmental pollutant. Under normal conditions, copper ions are required for many key physiological processes. However, in excess, copper results in cell and tissue damage ranging in severity from temporary injury to permanent neurological damage. Because of its biological relevance, and because many conserved copper-responsive genes respond to nonessential heavy metal pollutants, copper resistance in Drosophila melanogaster is a useful model system with which to investigate the genetic control of the heavy metal stress response. Because heavy metal toxicity has the potential to differently impact specific tissues, we genetically characterized the control of the gene expression response to copper stress in a tissue-specific manner in this study. We assessed the copper stress response in head and gut tissue of 96 inbred strains from the Drosophila Synthetic Population Resource using a combination of differential expression analysis and expression quantitative trait locus mapping. Differential expression analysis revealed clear patterns of tissue-specific expression. Tissue and treatment specific responses to copper stress were also detected using expression quantitative trait locus mapping. Expression quantitative trait locus associated with MtnA, Mdr49, Mdr50, and Sod3 exhibited both genotype-by-tissue and genotype-by-treatment effects on gene expression under copper stress, illuminating tissue- and treatment-specific patterns of gene expression control. Together, our data build a nuanced description of the roles and interactions between allelic and expression variation in copper-responsive genes, provide valuable insight into the genomic architecture of susceptibility to metal toxicity, and highlight candidate genes for future functional characterization.
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Affiliation(s)
- Elizabeth R Everman
- School of Biological Sciences, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Stuart J Macdonald
- Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, USA
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2
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Wu C, Wang J, Luo X, Wang B, Zhang X, Song Y, Zhang K, Zhang X, Sun M. Lead exposure induced transgenerational developmental neurotoxicity by altering genome methylation in Drosophila melanogaster. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 271:115991. [PMID: 38237395 DOI: 10.1016/j.ecoenv.2024.115991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 02/05/2024]
Abstract
Heavy metal toxicity is a significant global health concern, with particular attention given to lead (Pb) exposure due to its adverse effects on cognitive development, especially in children exposed to low concentrations. While Pb neurotoxicity has been extensively studied, the analysis and molecular mechanisms underlying the transgenerational effects of Pb exposure-induced neurotoxicity remain poorly understood. In this study, we utilized Drosophila, a powerful developmental animal model, to investigate this phenomenon. Our findings demonstrated that Pb exposure during the developmental stage had a profound effect on the neurodevelopment of F0 fruit flies. Specifically, we observed a loss of correlation between the terminal motor area and muscle fiber area, along with an increased frequency of the β-lobe midline crossing phenotype in mushroom bodies. Western blot analysis indicated altered expression levels of synaptic vesicle proteins, with a decrease in Synapsin (SYN) and an increase in Bruchpilot (BRP) expression, suggesting changes in synaptic vesicle release sites. These findings were corroborated by electrophysiological data, showing an increase in the amplitude of evoked excitatory junctional potential (EJP) and an increase in the frequency of spontaneous excitatory junctional potential (mEJP) following Pb exposure. Importantly, our results further confirmed that the developmental neurotoxicity resulting from grandparental Pb exposure exhibited a transgenerational effect. The F3 offspring displayed neurodevelopmental defects, synaptic function abnormalities, and repetitive behavior despite lacking direct Pb exposure. Our MeDIP-seq analysis further revealed significant alterations in DNA methylation levels in several neurodevelopmental associated genes (eagle, happyhour, neuroglian, bazooka, and spinophilin) in the F3 offspring exposed to Pb. These findings suggest that DNA methylation modifications may underlie the inheritance of acquired phenotypic traits resulting from environmental Pb exposure.
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Affiliation(s)
- Chunyan Wu
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jie Wang
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Xiaoxiao Luo
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Binquan Wang
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Xing Zhang
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yuanyuan Song
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ke Zhang
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Xiaoyan Zhang
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mingkuan Sun
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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3
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Yang M, Zinkgraf M, Fitzgerald-Cook C, Harrison BR, Putzier A, Promislow DEL, Wang AM. Using Drosophila to identify naturally occurring genetic modifiers of amyloid beta 42- and tau-induced toxicity. G3 (BETHESDA, MD.) 2023; 13:jkad132. [PMID: 37311212 PMCID: PMC10468303 DOI: 10.1093/g3journal/jkad132] [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: 04/11/2023] [Revised: 04/15/2023] [Accepted: 05/15/2023] [Indexed: 06/15/2023]
Abstract
Alzheimer's disease is characterized by 2 pathological proteins, amyloid beta 42 and tau. The majority of Alzheimer's disease cases in the population are sporadic and late-onset Alzheimer's disease, which exhibits high levels of heritability. While several genetic risk factors for late-onset Alzheimer's disease have been identified and replicated in independent studies, including the ApoE ε4 allele, the great majority of the heritability of late-onset Alzheimer's disease remains unexplained, likely due to the aggregate effects of a very large number of genes with small effect size, as well as to biases in sample collection and statistical approaches. Here, we present an unbiased forward genetic screen in Drosophila looking for naturally occurring modifiers of amyloid beta 42- and tau-induced ommatidial degeneration. Our results identify 14 significant SNPs, which map to 12 potential genes in 8 unique genomic regions. Our hits that are significant after genome-wide correction identify genes involved in neuronal development, signal transduction, and organismal development. Looking more broadly at suggestive hits (P < 10-5), we see significant enrichment in genes associated with neurogenesis, development, and growth as well as significant enrichment in genes whose orthologs have been identified as significantly or suggestively associated with Alzheimer's disease in human GWAS studies. These latter genes include ones whose orthologs are in close proximity to regions in the human genome that are associated with Alzheimer's disease, but where a causal gene has not been identified. Together, our results illustrate the potential for complementary and convergent evidence provided through multitrait GWAS in Drosophila to supplement and inform human studies, helping to identify the remaining heritability and novel modifiers of complex diseases.
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Affiliation(s)
- Ming Yang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Matthew Zinkgraf
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Cecilia Fitzgerald-Cook
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Benjamin R Harrison
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra Putzier
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Daniel E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Adrienne M Wang
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
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4
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Rand MD, Tennessen JM, Mackay TFC, Anholt RRH. Perspectives on the Drosophila melanogaster Model for Advances in Toxicological Science. Curr Protoc 2023; 3:e870. [PMID: 37639638 PMCID: PMC10463236 DOI: 10.1002/cpz1.870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The use of Drosophila melanogaster for studies of toxicology has grown considerably in the last decade. The Drosophila model has long been appreciated as a versatile and powerful model for developmental biology and genetics because of its ease of handling, short life cycle, low cost of maintenance, molecular genetic accessibility, and availability of a wide range of publicly available strains and data resources. These features, together with recent unique developments in genomics and metabolomics, make the fly model especially relevant and timely for the development of new approach methodologies and movements toward precision toxicology. Here, we offer a perspective on how flies can be leveraged to identify risk factors relevant to environmental exposures and human health. First, we review and discuss fundamental toxicologic principles for experimental design with Drosophila. Next, we describe quantitative and systems genetics approaches to resolve the genetic architecture and candidate pathways controlling susceptibility to toxicants. Finally, we summarize the current state and future promise of the emerging field of Drosophila metabolomics for elaborating toxic mechanisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Matthew D. Rand
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | | | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
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5
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Everman ER, Macdonald SJ. Gene expression variation underlying tissue-specific responses to copper stress in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548746. [PMID: 37503205 PMCID: PMC10370140 DOI: 10.1101/2023.07.12.548746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Copper is one of a handful of biologically necessary heavy metals that is also a common environmental pollutant. Under normal conditions, copper ions are required for many key physiological processes. However, in excess, copper quickly results in cell and tissue damage that can range in severity from temporary injury to permanent neurological damage. Because of its biological relevance, and because many conserved copper-responsive genes also respond to other non-essential heavy metal pollutants, copper resistance in Drosophila melanogaster is a useful model system with which to investigate the genetic control of the response to heavy metal stress. Because heavy metal toxicity has the potential to differently impact specific tissues, we genetically characterized the control of the gene expression response to copper stress in a tissue-specific manner in this study. We assessed the copper stress response in head and gut tissue of 96 inbred strains from the Drosophila Synthetic Population Resource (DSPR) using a combination of differential expression analysis and expression quantitative trait locus (eQTL) mapping. Differential expression analysis revealed clear patterns of tissue-specific expression, primarily driven by a more pronounced gene expression response in gut tissue. eQTL mapping of gene expression under control and copper conditions as well as for the change in gene expression following copper exposure (copper response eQTL) revealed hundreds of genes with tissue-specific local cis-eQTL and many distant trans-eQTL. eQTL associated with MtnA, Mdr49, Mdr50, and Sod3 exhibited genotype by environment effects on gene expression under copper stress, illuminating several tissue- and treatment-specific patterns of gene expression control. Together, our data build a nuanced description of the roles and interactions between allelic and expression variation in copper-responsive genes, provide valuable insight into the genomic architecture of susceptibility to metal toxicity, and highlight many candidate genes for future functional characterization.
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Affiliation(s)
- Elizabeth R Everman
- 1200 Sunnyside Ave, University of Kansas, Molecular Biosciences, Lawrence, KS 66045, USA
- 730 Van Vleet Oval, University of Oklahoma, Biology, Norman, OK 73019, USA
| | - Stuart J Macdonald
- 1200 Sunnyside Ave, University of Kansas, Molecular Biosciences, Lawrence, KS 66045, USA
- 1200 Sunnyside Ave, University of Kansas, Center for Computational Biology, Lawrence, KS 66045, USA
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6
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Busquet F, Laperrouze J, Jankovic K, Krsmanovic T, Ignasiak T, Leoni B, Apic G, Asole G, Guigó R, Marangio P, Palumbo E, Perez-Lluch S, Wucher V, Vlot AH, Anholt R, Mackay T, Escher BI, Grasse N, Huchthausen J, Massei R, Reemtsma T, Scholz S, Schüürmann G, Bondesson M, Cherbas P, Freedman JH, Glaholt S, Holsopple J, Jacobson SC, Kaufman T, Popodi E, Shaw JJ, Smoot S, Tennessen JM, Churchill G, von Clausbruch CC, Dickmeis T, Hayot G, Pace G, Peravali R, Weiss C, Cistjakova N, Liu X, Slaitas A, Brown JB, Ayerbe R, Cabellos J, Cerro-Gálvez E, Diez-Ortiz M, González V, Martínez R, Vives PS, Barnett R, Lawson T, Lee RG, Sostare E, Viant M, Grafström R, Hongisto V, Kohonen P, Patyra K, Bhaskar PK, Garmendia-Cedillos M, Farooq I, Oliver B, Pohida T, Salem G, Jacobson D, Andrews E, Barnard M, Čavoški A, Chaturvedi A, Colbourne JK, Epps DJT, Holden L, Jones MR, Li X, Müller F, Ormanin-Lewandowska A, Orsini L, Roberts R, Weber RJM, Zhou J, Chung ME, Sanchez JCG, Diwan GD, Singh G, Strähle U, Russell RB, Batista D, Sansone SA, Rocca-Serra P, Du Pasquier D, Lemkine G, Robin-Duchesne B, Tindall A. The Precision Toxicology Initiative. Toxicol Lett 2023:S0378-4274(23)00180-7. [PMID: 37211341 DOI: 10.1016/j.toxlet.2023.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
The goal of PrecisionTox is to overcome conceptual barriers to replacing traditional mammalian chemical safety testing by accelerating the discovery of evolutionarily conserved toxicity pathways that are shared by descent among humans and more distantly related animals. An international consortium is systematically testing the toxicological effects of a diverse set of chemicals on a suite of five model species comprising fruit flies, nematodes, water fleas, and embryos of clawed frogs and zebrafish along with human cell lines. Multiple forms of omics and comparative toxicology data are integrated to map the evolutionary origins of biomolecular interactions, which are predictive of adverse health effects, to major branches of the animal phylogeny. These conserved elements of adverse outcome pathways (AOPs) and their biomarkers are expect to provide mechanistic insight useful for regulating groups of chemicals based on their shared modes of action. PrecisionTox also aims to quantify risk variation within populations by recognizing susceptibility as a heritable trait that varies with genetic diversity. This initiative incorporates legal experts and collaborates with risk managers to address specific needs within European chemicals legislation, including the uptake of new approach methodologies (NAMs) for setting precise regulatory limits on toxic chemicals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nico Grasse
- Helmholtz Centre for Environmental Research, DE
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7
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Everman ER, Macdonald SJ, Kelly JK. The genetic basis of adaptation to copper pollution in Drosophila melanogaster. Front Genet 2023; 14:1144221. [PMID: 37082199 PMCID: PMC10110907 DOI: 10.3389/fgene.2023.1144221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
Introduction: Heavy metal pollutants can have long lasting negative impacts on ecosystem health and can shape the evolution of species. The persistent and ubiquitous nature of heavy metal pollution provides an opportunity to characterize the genetic mechanisms that contribute to metal resistance in natural populations. Methods: We examined variation in resistance to copper, a common heavy metal contaminant, using wild collections of the model organism Drosophila melanogaster. Flies were collected from multiple sites that varied in copper contamination risk. We characterized phenotypic variation in copper resistance within and among populations using bulked segregant analysis to identify regions of the genome that contribute to copper resistance. Results and Discussion: Copper resistance varied among wild populations with a clear correspondence between resistance level and historical exposure to copper. We identified 288 SNPs distributed across the genome associated with copper resistance. Many SNPs had population-specific effects, but some had consistent effects on copper resistance in all populations. Significant SNPs map to several novel candidate genes involved in refolding disrupted proteins, energy production, and mitochondrial function. We also identified one SNP with consistent effects on copper resistance in all populations near CG11825, a gene involved in copper homeostasis and copper resistance. We compared the genetic signatures of copper resistance in the wild-derived populations to genetic control of copper resistance in the Drosophila Synthetic Population Resource (DSPR) and the Drosophila Genetic Reference Panel (DGRP), two copper-naïve laboratory populations. In addition to CG11825, which was identified as a candidate gene in the wild-derived populations and previously in the DSPR, there was modest overlap of copper-associated SNPs between the wild-derived populations and laboratory populations. Thirty-one SNPs associated with copper resistance in wild-derived populations fell within regions of the genome that were associated with copper resistance in the DSPR in a prior study. Collectively, our results demonstrate that the genetic control of copper resistance is highly polygenic, and that several loci can be clearly linked to genes involved in heavy metal toxicity response. The mixture of parallel and population-specific SNPs points to a complex interplay between genetic background and the selection regime that modifies the effects of genetic variation on copper resistance.
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Affiliation(s)
| | - Stuart J. Macdonald
- Molecular Biosciences, University of Kansas, Lawrence, KS, United States
- Center for Computational Biology, University of Kansas, Lawrence, KS, United States
| | - John K. Kelly
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States
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8
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Saha S, Spinelli L, Castro Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Krifa S, Torres M, Brun C, Vogler G, Bodmer R, Colas AR, Ocorr K, Perrin L. Genetic architecture of natural variation of cardiac performance from flies to humans. eLife 2022; 11:82459. [DOI: 10.7554/elife.82459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome-wide associations studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict transcription factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart-specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.
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Affiliation(s)
- Saswati Saha
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Lionel Spinelli
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | | | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Kremmer
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Laurence Roder
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Sallouha Krifa
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Magali Torres
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Christine Brun
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Perrin
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
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9
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Felmlee KR, Macdonald SJ, Everman ER. Pre-adult exposure to three heavy metals leads to changes in the head transcriptome of adult flies. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000591. [PMID: 35856016 PMCID: PMC9287740 DOI: 10.17912/micropub.biology.000591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 11/15/2022]
Abstract
We examined the effect of developmental exposure to three heavy metals - cadmium, copper, and lead - on gene expression in adult head tissue in the model organism Drosophila melanogaster . All metals affected development time and/or gene expression level. While variation in the response to each metal was apparent, two differentially-expressed genes were upregulated in response to all three metal treatments, and 11 genes were downregulated in two of the three treatments. Our work reveals that developmental metal exposure has the potential to have long-lasting, metal-specific effects on gene expression in adults, even after the metal stress has been removed.
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Affiliation(s)
| | - Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas; Center for Computational Biology, University of Kansas
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10
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Beamish CR, Love TM, Rand MD. Developmental Toxicology of Metal Mixtures in Drosophila: Unique Properties of Potency and Interactions of Mercury Isoforms. Int J Mol Sci 2021; 22:12131. [PMID: 34830013 PMCID: PMC8620836 DOI: 10.3390/ijms222212131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
Mercury ranks third on the U.S. Agency of Toxic Substances and Disease Registry priority list of hazardous substances, behind only arsenic and lead. We have undertaken uncovering the mechanisms underlying the developmental toxicity of methylmercury (MeHg), inorganic mercury (HgCl2), lead acetate (Pb), and sodium arsenite (As). To probe these differences, we used the Drosophila model, taking advantage of three developmental transitions-pupariation, metamorphosis, and eclosion-to differentiate potentially unique windows of toxicity. We elaborated dose response profiles for each individual metal administered in food and accounted for internal body burden, also extending analyses to evaluate combinatorial metal mixture effects. We observed all four metals producing larval lethality and delayed pupariation, with MeHg being most potent. Compared to other metals, MeHg's potency is caused by a higher body burden with respect to dose. MeHg uniquely caused dose-dependent failure in eclosion that was unexpectedly rescued by titrating in HgCl2. Our results highlight a unique developmental window and toxicokinetic properties where MeHg acts with specificity relative to HgCl2, Pb, and As. These findings will serve to refine future studies aimed at revealing tissue morphogenesis events and cell signaling pathways, potentially conserved in higher organisms, that selectively mediate MeHg toxicity and its antagonism by HgCl2.
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Affiliation(s)
- Catherine R. Beamish
- Department of Environmental Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA;
| | - Tanzy M. Love
- Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA;
| | - Matthew D. Rand
- Department of Environmental Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA;
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11
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Merinas-Amo T, Lozano-Baena MD, Obregón-Cano S, Alonso-Moraga Á, de Haro-Bailón A. Role of Glucosinolates in the Nutraceutical Potential of Selected Cultivars of Brassica rapa. Foods 2021; 10:2720. [PMID: 34829001 PMCID: PMC8617875 DOI: 10.3390/foods10112720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022] Open
Abstract
Brassica rapa L. subsp. rapa (turnip greens), a traditionally consumed vegetable, is well-known due to its high content of glucosinolates, which are secondary metabolites with a positive biological activity for human health. Our hypothesis has been based on the relation between B. rapa glucosinolate content and its healthy properties, and our aim is to establish guidelines for safe B. rapa vegetable consumption. Three B. rapa cultivars (143N5, 143N7 and 163N7) have been characterized by HPLC analysis of purified extracts from leaf samples in order to determine their glucosinolate content and to relate this content to beneficial effects on DNA protection, lifespan extension and chemoprevention. In order to ascertain the heath properties in vitro and in vivo, toxicity activities were assayed in the Drosophila melanogaster and leukaemia cell models; genomic safety was also assessed in both models using genotoxicity, fragmentation and comet assay. The Drosophila model has also been used to study the antioxidative activity and the longevity induction. Our results showed a relationship between B. rapa glucosinolate content and its safety and benefices in its consumption. Gluconapin, the main B. rapa glucosinolate, was directly related with these wholesome effects. The relevant conclusion in the present research is focused on B. rapa cultivar 163N7 due to its high gluconapin content and low progoitrin content, which exert anti-cancer and DNA protection properties and could be recommended as being safe and healthy for human consumption.
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Affiliation(s)
- Tania Merinas-Amo
- Department of Genetics, Gregor Mendel Building, Faculty of Science, Campus Rabanales, University of Córdoba, 14014 Córdoba, Spain; (M.-D.L.-B.); (Á.A.-M.)
| | - María-Dolores Lozano-Baena
- Department of Genetics, Gregor Mendel Building, Faculty of Science, Campus Rabanales, University of Córdoba, 14014 Córdoba, Spain; (M.-D.L.-B.); (Á.A.-M.)
| | - Sara Obregón-Cano
- Department of Plant Breeding, Institute of Sustainable Agriculture, CSIC, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (S.O.-C.); (A.d.H.-B.)
| | - Ángeles Alonso-Moraga
- Department of Genetics, Gregor Mendel Building, Faculty of Science, Campus Rabanales, University of Córdoba, 14014 Córdoba, Spain; (M.-D.L.-B.); (Á.A.-M.)
| | - Antonio de Haro-Bailón
- Department of Plant Breeding, Institute of Sustainable Agriculture, CSIC, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (S.O.-C.); (A.d.H.-B.)
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12
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Spierer AN, Mossman JA, Smith SP, Crawford L, Ramachandran S, Rand DM. Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PLoS Genet 2021; 17:e1008887. [PMID: 33735180 PMCID: PMC7971549 DOI: 10.1371/journal.pgen.1008887] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
The winged insects of the order Diptera are colloquially named for their most recognizable phenotype: flight. These insects rely on flight for a number of important life history traits, such as dispersal, foraging, and courtship. Despite the importance of flight, relatively little is known about the genetic architecture of flight performance. Accordingly, we sought to uncover the genetic modifiers of flight using a measure of flies’ reaction and response to an abrupt drop in a vertical flight column. We conducted a genome wide association study (GWAS) using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, and identified a combination of additive and marginal variants, epistatic interactions, whole genes, and enrichment across interaction networks. Egfr, a highly pleiotropic developmental gene, was among the most significant additive variants identified. We functionally validated 13 of the additive candidate genes’ (Adgf-A/Adgf-A2/CG32181, bru1, CadN, flapper (CG11073), CG15236, flippy (CG9766), CREG, Dscam4, form3, fry, Lasp/CG9692, Pde6, Snoo), and introduce a novel approach to whole gene significance screens: PEGASUS_flies. Additionally, we identified ppk23, an Acid Sensing Ion Channel (ASIC) homolog, as an important hub for epistatic interactions. We propose a model that suggests genetic modifiers of wing and muscle morphology, nervous system development and function, BMP signaling, sexually dimorphic neural wiring, and gene regulation are all important for the observed differences flight performance in a natural population. Additionally, these results represent a snapshot of the genetic modifiers affecting drop-response flight performance in Drosophila, with implications for other insects. Insect flight is a widely recognizable phenotype of many winged insects, hence the name: flies. While fruit flies, or Drosophila melanogaster, are a genetically tractable model, flight performance is a highly integrative phenotype, and therefore challenging to identify comprehensively which genetic modifiers contribute to its genetic architecture. Accordingly, we screened 197 Drosophila Genetic Reference Panel lines for their ability to react and respond to an abrupt drop. Using several computational approaches, we identified additive, marginal, and epistatic variants, as well as whole genes and altered sub-networks of gene-gene and protein-protein interaction networks that contribute to variation in flight performance. More generally, we demonstrate the benefits of employing multiple methodologies to elucidate the genetic architecture of complex traits. Many variants and genes mapped to regions of the genome that affect neurodevelopment, wing and muscle development, and regulation of gene expression. We also introduce PEGASUS_flies, a Drosophila-adapted version of the PEGASUS platform first used in human studies, to infer gene-level significance of association based on the gene’s distribution of individual variant P-values. Our results contribute to the debate over the relative importance of individual, additive factors and epistatic, or higher order, interactions, in the mapping of genotype to phenotype.
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Affiliation(s)
- Adam N Spierer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Samuel Pattillo Smith
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
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13
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Everman ER, Cloud-Richardson KM, Macdonald SJ. Characterizing the genetic basis of copper toxicity in Drosophila reveals a complex pattern of allelic, regulatory, and behavioral variation. Genetics 2021; 217:1-20. [PMID: 33683361 PMCID: PMC8045719 DOI: 10.1093/genetics/iyaa020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
A range of heavy metals are required for normal cell function and homeostasis. However, the anthropogenic release of metal compounds into soil and water sources presents a pervasive health threat. Copper is one of many heavy metals that negatively impacts diverse organisms at a global scale. Using a combination of quantitative trait locus (QTL) mapping and RNA sequencing in the Drosophila Synthetic Population Resource, we demonstrate that resistance to the toxic effects of ingested copper in D. melanogaster is genetically complex and influenced by allelic and expression variation at multiple loci. QTL mapping identified several QTL that account for a substantial fraction of heritability. Additionally, we find that copper resistance is impacted by variation in behavioral avoidance of copper and may be subject to life-stage specific regulation. Gene expression analysis further demonstrated that resistant and sensitive strains are characterized by unique expression patterns. Several of the candidate genes identified via QTL mapping and RNAseq have known copper-specific functions (e.g., Ccs, Sod3, CG11825), and others are involved in the regulation of other heavy metals (e.g., Catsup, whd). We validated several of these candidate genes with RNAi suggesting they contribute to variation in adult copper resistance. Our study illuminates the interconnected roles that allelic and expression variation, organism life stage, and behavior play in copper resistance, allowing a deeper understanding of the diverse mechanisms through which metal pollution can negatively impact organisms.
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Affiliation(s)
- Elizabeth R Everman
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | | | - Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA
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14
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Adebambo TH, Fox DT, Otitoloju AA. Toxicological Study and Genetic Basis of BTEX Susceptibility in Drosophila melanogaster. Front Genet 2020; 11:594179. [PMID: 33193742 PMCID: PMC7593870 DOI: 10.3389/fgene.2020.594179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Benzene, toluene, ethylbenzene and xylene, also known as BTEX, are released into environmental media by petroleum product exploratory and exploitative activities and are harmful to humans and animals. Testing the effects of these chemicals on a significantly large scale requires an inexpensive, rapidly developing model organism such as Drosophila melanogaster. In this study, the toxicological profile of benzene, toluene, ethylbenzene, p-xylene, m-xylene, and o-xylene in D. melanogaster was evaluated. Adult animals were monitored for acute toxicity effects. Similarly, first instar larvae reared separately on the same compounds were monitored for the ability to develop into adult flies (eclosion). Further, the impact of fixed concentrations of benzene and xylene on apoptosis and mitosis were investigated in adult progenitor tissues found in third instar larvae. Toluene is the most toxic to adult flies with an LC50 of 0.166 mM, while a significant and dose-dependent decrease in fly eclosion was observed with benzene, p-xylene, and o-xylene. An increase in apoptosis and mitosis was also observed in animals exposed to benzene and p-xylene. Through Genome Wide Association Screening (GWAS), 38 regions of the D. melanogaster genome were identified as critical for responses to p-xylene. This study reveals the strength of D. Melanogaster genetics as an accessible approach to study BTEX compounds.
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Affiliation(s)
- Temitope H Adebambo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States.,Department of Zoology, University of Lagos, Lagos, Nigeria
| | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States
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15
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Insulin Potentiates JAK/STAT Signaling to Broadly Inhibit Flavivirus Replication in Insect Vectors. Cell Rep 2020; 29:1946-1960.e5. [PMID: 31722209 PMCID: PMC6871768 DOI: 10.1016/j.celrep.2019.10.029] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/03/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
The World Health Organization estimates that more than half of the world’s population is at risk for vector-borne diseases, including arboviruses. Because many arboviruses are mosquito borne, investigation of the insect immune response will help identify targets to reduce the spread of arboviruses. Here, we use a genetic screening approach to identify an insulin-like receptor as a component of the immune response to arboviral infection. We determine that vertebrate insulin reduces West Nile virus (WNV) replication in Drosophila melanogaster as well as WNV, Zika, and dengue virus titers in mosquito cells. Mechanistically, we show that insulin signaling activates the JAK/STAT, but not RNAi, pathway via ERK to control infection in Drosophila cells and Culex mosquitoes through an integrated immune response. Finally, we validate that insulin priming of adult female Culex mosquitoes through a blood meal reduces WNV infection, demonstrating an essential role for insulin signaling in insect antiviral responses to human pathogens. The world’s population is at risk for infection with several flaviviruses. Ahlers et al. use a living library of insects to determine that an insulin-like receptor controls West Nile virus infection. Insulin signaling is antiviral via the JAK/STAT pathway in both fly and mosquito models and against a range of flaviviruses.
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16
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Peterson EK, Stark A, Varian-Ramos CW, Hollocher KT, Possidente B. Exposure to Lead (Pb 2+) Eliminates Avoidance of Pb-Treated Oviposition Substrates in a Dose-Dependent Manner in Female Vinegar Flies. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 104:588-594. [PMID: 32193571 DOI: 10.1007/s00128-020-02825-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
Female vinegar flies (Drosophila melanogaster) preferentially oviposit eggs on oviposition substrates that decrease larval foraging costs. We tested whether female D. melanogaster would avoid oviposition substrates containing lead (Pb2+), which could potentially decrease offspring fitness. Wild type D. melanogaster were reared on control or Pb-treated medium from egg stage to adulthood and tested for differences in oviposition substrate preference, fecundity (number of eggs laid) and Pb accumulation. Control females laid a significantly lower proportion of eggs on Pb-treated substrates than Pb-treated females. Pb-treated females laid significantly more eggs than control females. Pb-treated adults accumulated significantly more Pb than control-treated adults. These results indicate that Pb exposure disrupts normal oviposition avoidance behaviors, which could increase larval foraging costs for larval offspring. These factors could induce population declines and have cascading implications for the ecosystem.
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Affiliation(s)
- Elizabeth K Peterson
- Department of Biological Sciences, State University of New York-Albany, Albany, NY, USA.
| | - Austin Stark
- Department of Biological Sciences, State University of New York-Albany, Albany, NY, USA
| | - Claire W Varian-Ramos
- Department of Biology, Colorado State University-Pueblo, 2200 Bonforte Boulevard, Pueblo, CO, 81001-4901, USA
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17
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Zhang W, Reeves GR, Tautz D. Identification of a genetic network for an ecologically relevant behavioural phenotype in Drosophila melanogaster. Mol Ecol 2019; 29:502-518. [PMID: 31867742 DOI: 10.1111/mec.15341] [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: 08/09/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
Pupation site choice of Drosophila third-instar larvae is critical for the survival of individuals, as pupae are exposed to various biotic and abiotic dangers while immobilized during the 3-4 days of metamorphosis. This singular behavioural choice is sensitive to both environmental and genetic factors. Here, we developed a high-throughput phenotyping approach to assay the variation in pupation height in Drosophila melanogaster, while controlling for possibly confounding factors. We find substantial variation of mean pupation height among sampled natural stocks and we show that the Drosophila Genetic Reference Panel (DGRP) reflects this variation. Using the DGRP stocks for genome-wide association (GWA) mapping, 16 loci involved in determining pupation height could be resolved. The candidate genes in these loci are enriched for high expression in the larval central nervous system. A genetic network could be constructed from the candidate loci, which places scribble (scrib) at the centre, plus other genes known to be involved in nervous system development, such as Epidermal growth factor receptor (Egfr) and p53. Using gene disruption lines, we could functionally validate several of the initially identified loci, as well as additional loci predicted from network analysis. Our study shows that the combination of high-throughput phenotyping with a genetic analysis of variation captured from the wild can be used to approach the genetic dissection of an environmentally relevant behavioural phenotype.
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Affiliation(s)
- Wenyu Zhang
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Guy Richard Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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18
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Nanda KP, Kumari C, Dubey M, Firdaus H. Chronic lead (Pb) exposure results in diminished hemocyte count and increased susceptibility to bacterial infection in Drosophila melanogaster. CHEMOSPHERE 2019; 236:124349. [PMID: 31326753 DOI: 10.1016/j.chemosphere.2019.124349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Heavy metal Pb is a common toxic pollutant present in our environment adversely affecting health of the living organisms. Recent studies suggest positive correlation between heavy metal exposure and immune dysfunction and present work utilizes Drosophila to address this issue in relation to Pb exposure. In-vivo Pb toxicity was established by dietary intake where essential parameters like development and life span were found to be hampered and augmented upon metallothionein B (mtnB) downregulation hinting towards potential role of mtnB in Pb detoxification. Further response of Drosophila to B. subtilis bacterial infection was monitored by carrying out oral infections. Pb fed flies showed increased susceptibility to infection as compared to their controls. Since Drosophila hemocytes play dual role as immune cells, we checked for the total hemocyte count and found significant decrease in hemocyte numbers in Pb fed larvae. Both crystal cells and plasmatocytes, the two major hemocytes in third instar larval hemolymph were reduced. However we did not find any visible morphological changes in Giemsa stained hemocytes. Crystal cells are crucial for synthesis and release of phenoloxidase (PO), an enzyme required for melanin clot synthesis and deposition. PO activity assessed from total hemolymph protein isolates was found to be substantially decreased in Pb raised animals. Results were also confirmed by spot test and native gel activity assay of PO. Overall our results suggest immunotoxic effect of Pb through decrease in hemocyte count including crystal cell which in turn leads to decreased PO activity and increased susceptibility to B. subtilis.
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Affiliation(s)
- Kumari Pragati Nanda
- Department of Life Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, 835205, Jharkhand, India
| | - Chandani Kumari
- Department of Life Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, 835205, Jharkhand, India
| | - Madhavi Dubey
- Department of Life Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, 835205, Jharkhand, India
| | - Hena Firdaus
- Department of Life Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, 835205, Jharkhand, India.
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19
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Genome-Wide Association Analysis of Anoxia Tolerance in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:2989-2999. [PMID: 31311780 PMCID: PMC6723132 DOI: 10.1534/g3.119.400421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
As the genetic bases to variation in anoxia tolerance are poorly understood, we used the Drosophila Genetics Reference Panel (DGRP) to conduct a genome-wide association study (GWAS) of anoxia tolerance in adult and larval Drosophila melanogaster Survival ranged from 0-100% in adults exposed to 6 h of anoxia and from 20-98% for larvae exposed to 1 h of anoxia. Anoxia tolerance had a broad-sense heritability of 0.552 in adults and 0.433 in larvae. Larval and adult phenotypes were weakly correlated but the anoxia tolerance of adult males and females were strongly correlated. The GWA identified 180 SNPs in adults and 32 SNPs in larvae associated with anoxia tolerance. Gene ontology enrichment analysis indicated that many of the 119 polymorphic genes associated with adult anoxia-tolerance were associated with ionic transport or immune function. In contrast, the 22 polymorphic genes associated with larval anoxia-tolerance were mostly associated with regulation of transcription and DNA replication. RNAi of mapped genes generally supported the hypothesis that disruption of these genes reduces anoxia tolerance. For two ion transport genes, we tested predicted directional and sex-specific effects of SNP alleles on adult anoxia tolerance and found strong support in one case but not the other. Correlating our phenotype to prior DGRP studies suggests that genes affecting anoxia tolerance also influence stress-resistance, immune function and ionic balance. Overall, our results provide evidence for multiple new potential genetic influences on anoxia tolerance and provide additional support for important roles of ion balance and immune processes in determining variation in anoxia tolerance.
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20
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Peterson EK, Possidente B, Stark A, Hollocher KT, Carrico P. Intraspecific Genetic Variation for Lead-Induced Changes in Reproductive Strategies. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 103:233-239. [PMID: 31230133 DOI: 10.1007/s00128-019-02650-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
We aimed to identify genetic variation in the response of reproductive behaviors to lead (Pb2+) exposure. We reared a subset of the Drosophila Genetic Reference Panel (DGRP) inbred lines on control or Pb-treated (500 μM PbAc) medium and tested for differences in copulation latency, copulation duration, and fecundity. Pb exposure decreased fecundity (p < 0.05) and increased copulation duration (p < 0.05) across DGRP lines. We found intraspecific genetic variation in latency, duration, and fecundity in both control and Pb-treated flies, with heritability ranging from 0.45 to 0.80. We found a significant genotype-by-environment interaction for copulation duration (p < 0.05). Genetic correlation matrices revealed significant genetic variation in common between control and Pb-treated flies for each trait (p < 0.05). Our results indicate that intraspecific genetic variation plays a role in Pb susceptibility and emphasize the importance of considering the impacts of variation in susceptibility to Pb pollution.
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Affiliation(s)
- Elizabeth K Peterson
- Department of Biological Sciences, State University of New York-Albany, Albany, NY, USA.
- Communities to Build Active STEM Engagement, Colorado State University-Pueblo, 2200 Bonforte Boulevard, Pueblo, CO, 81001-4901, USA.
| | | | - Austin Stark
- Department of Biological Sciences, State University of New York-Albany, Albany, NY, USA
| | | | - Pauline Carrico
- Department of Biological Sciences, State University of New York-Albany, Albany, NY, USA
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21
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Highfill CA, Baker BM, Stevens SD, Anholt RRH, Mackay TFC. Genetics of cocaine and methamphetamine consumption and preference in Drosophila melanogaster. PLoS Genet 2019; 15:e1007834. [PMID: 31107875 PMCID: PMC6527214 DOI: 10.1371/journal.pgen.1007834] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/27/2019] [Indexed: 12/11/2022] Open
Abstract
Illicit use of psychostimulants, such as cocaine and methamphetamine, constitutes a significant public health problem. Whereas neural mechanisms that mediate the effects of these drugs are well-characterized, genetic factors that account for individual variation in susceptibility to substance abuse and addiction remain largely unknown. Drosophila melanogaster can serve as a translational model for studies on substance abuse, since flies have a dopamine transporter that can bind cocaine and methamphetamine, and exposure to these compounds elicits effects similar to those observed in people, suggesting conserved evolutionary mechanisms underlying drug responses. Here, we used the D. melanogaster Genetic Reference Panel to investigate the genetic basis for variation in psychostimulant drug consumption, to determine whether similar or distinct genetic networks underlie variation in consumption of cocaine and methamphetamine, and to assess the extent of sexual dimorphism and effect of genetic context on variation in voluntary drug consumption. Quantification of natural genetic variation in voluntary consumption, preference, and change in consumption and preference over time for cocaine and methamphetamine uncovered significant genetic variation for all traits, including sex-, exposure- and drug-specific genetic variation. Genome wide association analyses identified both shared and drug-specific candidate genes, which could be integrated in genetic interaction networks. We assessed the effects of ubiquitous RNA interference (RNAi) on consumption behaviors for 34 candidate genes: all affected at least one behavior. Finally, we utilized RNAi knockdown in the nervous system to implicate dopaminergic neurons and the mushroom bodies as part of the neural circuitry underlying experience-dependent development of drug preference. Illicit use of cocaine and methamphetamine is a major public health problem. Whereas the neurological effects of these drugs are well characterized, it remains challenging to determine genetic risk factors for substance abuse in human populations. The fruit fly, Drosophila melanogaster, presents an excellent model for identifying evolutionarily conserved genes that affect drug consumption, since genetic background and exposure can be controlled precisely. We took advantage of natural variation in a panel of inbred wild derived fly lines with complete genome sequences to assess the extent of genetic variation among these lines for voluntary consumption of cocaine and methamphetamine and to explore whether some genetic backgrounds might show experience-dependent development of drug preference. The drug consumption traits were highly variable among the lines with strong sex-, drug- and exposure time-specific components. We identified candidate genes and gene networks associated with variation in consumption of cocaine and methamphetamine and development of drug preference. Using tissue-specific suppression of gene expression, we were able to functionally implicate candidate genes that affected at least one consumption trait in at least one drug and sex. In humans, the mesolimbic dopaminergic projection plays a role in drug addiction. We asked whether in Drosophila the mushroom bodies could play an analogous role, as they are integrative brain centers associated with experience-dependent learning. Indeed, our results suggest that variation in consumption and development of preference for both cocaine and methamphetamine is mediated, at least in part, through a neural network that comprises dopaminergic projections to the mushroom bodies.
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Affiliation(s)
- Chad A. Highfill
- Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, and Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
| | - Brandon M. Baker
- Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, and Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
| | - Stephenie D. Stevens
- Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, and Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
| | - Robert R. H. Anholt
- Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, and Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
| | - Trudy F. C. Mackay
- Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, and Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
- * E-mail:
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22
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Jaffee SR. Lead exposure and child maltreatment as models for how to conceptualize early-in-life risk factors for violence. Infant Ment Health J 2019; 40:23-38. [DOI: 10.1002/imhj.21756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Qu W, Gurdziel K, Pique-Regi R, Ruden DM. Lead Modulates trans- and cis-Expression Quantitative Trait Loci (eQTLs) in Drosophila melanogaster Heads. Front Genet 2018; 9:395. [PMID: 30294342 PMCID: PMC6158337 DOI: 10.3389/fgene.2018.00395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/30/2018] [Indexed: 11/13/2022] Open
Abstract
Lead exposure has long been one of the most important topics in global public health because it is a potent developmental neurotoxin. Here, an eQTL analysis, which is the genome-wide association analysis of genetic variants with gene expression, was performed. In this analysis, the male heads of 79 Drosophila melanogaster inbred lines from Drosophila Synthetic Population Resource (DSPR) were treated with or without developmental exposure, from hatching to adults, to 250 μM lead acetate [Pb(C2H3O2)2]. The goal was to identify genomic intervals that influence the gene-expression response to lead. After detecting 1798 cis-eQTLs and performing an initial trans-eQTL analysis, we focused our analysis on lead-sensitive "trans-eQTL hotspots," defined as genomic regions that are associated with a cluster of genes in a lead-dependent manner. We noticed that the genes associated with one of the 14 detected trans-eQTL hotspots, Chr 2L: 6,250,000 could be roughly divided into two groups based on their differential expression profile patterns and different categories of function. This trans-eQTL hotspot validates one identified in a previous study using different recombinant inbred lines. The expression of all the associated genes in the trans-eQTL hotspot was visualized with hierarchical clustering analysis. Besides the overall expression profile patterns, the heatmap displayed the segregation of differential parental genetic contributions. This suggested that trans-regulatory regions with different genetic contributions from the parental lines have significantly different expression changes after lead exposure. We believe this study confirms our earlier study, and provides important insights to unravel the genetic variation in lead susceptibility in Drosophila model.
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Affiliation(s)
- Wen Qu
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Katherine Gurdziel
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
| | - Roger Pique-Regi
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Douglas M Ruden
- Department of Pharmacology, Wayne State University, Detroit, MI, United States.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States.,Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States
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24
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Peterson EK, Long HE. Experimental Protocol for Using Drosophila As an Invertebrate Model System for Toxicity Testing in the Laboratory. J Vis Exp 2018:57450. [PMID: 30059035 PMCID: PMC6124635 DOI: 10.3791/57450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Emergent properties and external factors (population-level and ecosystem-level interactions, in particular) play important roles in mediating ecologically-important endpoints, though they are rarely considered in toxicological studies. D. melanogaster is emerging as a toxicology model for the behavioral, neurological, and genetic impacts of toxicants, to name a few. More importantly, species in the genus Drosophila can be utilized as a model system for an integrative framework approach to incorporate emergent properties and answer ecologically-relevant questions in toxicology research. The aim of this paper is to provide a protocol for exposing species in the genus Drosophila to pollutants to be used as a model system for a range of phenotypic outputs and ecologically-relevant questions. More specifically, this protocol can be used to 1) link multiple biological levels of organization and understand the impact of toxicants on both individual- and population-level fitness; 2) test the impact of toxicants at different stages of developmental exposure; 3) test multigenerational and evolutionary implications of pollutants; and 4) test multiple contaminants and stressors simultaneously.
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Affiliation(s)
- Elizabeth K Peterson
- Communities for Building Active STEM Engagement, Colorado State University-Pueblo; Department of Biology, Colorado State University-Pueblo;
| | - Hugh E Long
- Communities for Building Active STEM Engagement, Colorado State University-Pueblo; Department of Biology, Colorado State University-Pueblo
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25
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Lamichhane DK, Leem JH, Park CS, Ha M, Ha EH, Kim HC, Lee JY, Ko JK, Kim Y, Hong YC. Associations between prenatal lead exposure and birth outcomes: Modification by sex and GSTM1/GSTT1 polymorphism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:176-184. [PMID: 29145054 DOI: 10.1016/j.scitotenv.2017.09.159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 06/07/2023]
Abstract
Maternal lead exposure is associated with poor birth outcomes. However, modifying effects of polymorphism in glutathione S-transferases (GST) gene and infant sex remain unexplored. Our aim was to evaluate whether associations between prenatal lead and birth outcomes differed by maternal GST genes and infant sex. Prospective data of 782 mother-child pairs from Mothers and Children's Environmental Health (MOCEH) study were used. The genotyping of GST-mu 1 (GSTM1) and theta-1 (GSTT1) polymorphisms was carried out using polymerase chain reaction. Multivariable linear regression was used to examine whether the association between blood lead (BPb) level and birth outcomes (birthweight, length, and head circumference) varied by maternal GST genes and sex. We did not find a statistically significant association between prenatal BPb levels and birth outcomes; in stratified analyses, the association between higher BPb level during early pregnancy and lower birthweight (β=-224 per square root increase in BPb; 95% confidence interval (CI): -426, -21; false discovery rate p=0.036) was significant in males of mothers with GSTM1 null. Results were similar for head circumference model (β=-0.78 per square root increase in BPb; 95% CI: -1.69, 0.14, p=0.095), but the level of significance was borderline. Head circumference model showed a significant three-way interaction among BPb during early pregnancy, GSTM1, and sex (p=0.046). For combined analysis with GSTM1 and GSTT1, GSTM1 null and GSTT1 present group showed a significant inverse association of BPb with birthweight and head circumference in males. Our findings of the most evident effects of BPb on the reduced birthweight and head circumference in male born to the mother with GSTM1 null may suggest a biological interaction among lead, GST genes and sex in detoxification process during fetal development.
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Affiliation(s)
- Dirga Kumar Lamichhane
- Department of Social and Preventive Medicine, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Jong-Han Leem
- Department of Social and Preventive Medicine, College of Medicine, Inha University, Incheon, Republic of Korea; Department of Occupational and Environmental Medicine, Inha University Hospital, Incheon, Republic of Korea.
| | - Chang-Shin Park
- Department of Pharmacology, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Mina Ha
- Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, Republic of Korea
| | - Eun-Hee Ha
- Department of Preventive Medicine, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Hwan-Cheol Kim
- Department of Social and Preventive Medicine, College of Medicine, Inha University, Incheon, Republic of Korea; Department of Occupational and Environmental Medicine, Inha University Hospital, Incheon, Republic of Korea
| | - Ji-Young Lee
- Department of Preventive Medicine, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Jung Keun Ko
- Department of Social and Preventive Medicine, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Yangho Kim
- Department of Occupational and Environmental Medicine, University of Ulsan, College of Medicine, Ulsan University Hospital, Ulsan, Republic of Korea
| | - Yun-Chul Hong
- Department of Preventive Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
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26
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289+10.1002/wdev.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2024]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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27
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289 10.1002/wdev.289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2023]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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28
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Ruden DM, Gurdziel K, Aschner M. Frontiers in Toxicogenomics in the Twenty-First Century-the Grand Challenge: To Understand How the Genome and Epigenome Interact with the Toxic Environment at the Single-Cell, Whole-Organism, and Multi-Generational Level. Front Genet 2017; 8:173. [PMID: 29170679 PMCID: PMC5684185 DOI: 10.3389/fgene.2017.00173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/23/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Douglas M Ruden
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States.,C. S. Mott Center for Human Health and Development, Wayne State University, Detroit, MI, United States.,Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States
| | - Katherine Gurdziel
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States.,C. S. Mott Center for Human Health and Development, Wayne State University, Detroit, MI, United States.,Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
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29
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The road less traveled: from genotype to phenotype in flies and humans. Mamm Genome 2017; 29:5-23. [DOI: 10.1007/s00335-017-9722-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
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30
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Ritz BR, Chatterjee N, Garcia-Closas M, Gauderman WJ, Pierce BL, Kraft P, Tanner CM, Mechanic LE, McAllister K. Lessons Learned From Past Gene-Environment Interaction Successes. Am J Epidemiol 2017; 186:778-786. [PMID: 28978190 PMCID: PMC5860326 DOI: 10.1093/aje/kwx230] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/01/2017] [Accepted: 04/04/2017] [Indexed: 12/20/2022] Open
Abstract
Genetic and environmental factors are both known to contribute to susceptibility to complex diseases. Therefore, the study of gene-environment interaction (G×E) has been a focus of research for several years. In this article, select examples of G×E from the literature are described to highlight different approaches and underlying principles related to the success of these studies. These examples can be broadly categorized as studies of single metabolism genes, genes in complex metabolism pathways, ranges of exposure levels, functional approaches and model systems, and pharmacogenomics. Some studies illustrated the success of studying exposure metabolism for which candidate genes can be identified. Moreover, some G×E successes depended on the availability of high-quality exposure assessment and longitudinal measures, study populations with a wide range of exposure levels, and the inclusion of ethnically and geographically diverse populations. In several examples, large population sizes were required to detect G×Es. Other examples illustrated the impact of accurately defining scale of the interactions (i.e., additive or multiplicative). Last, model systems and functional approaches provided insights into G×E in several examples. Future studies may benefit from these lessons learned.
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Affiliation(s)
- Beate R. Ritz
- Correspondence to Dr. Beate R. Ritz, Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, 650 Charles Young Drive South, Los Angeles, CA 90095 (e-mail: )
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31
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28834395 DOI: 10.1002/wdev.289] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/08/2022]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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32
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Fochler S, Morozova TV, Davis MR, Gearhart AW, Huang W, Mackay TFC, Anholt RRH. Genetics of alcohol consumption in Drosophila melanogaster. GENES BRAIN AND BEHAVIOR 2017. [PMID: 28627812 DOI: 10.1111/gbb.12399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Individual variation in alcohol consumption in human populations is determined by genetic, environmental, social and cultural factors. In contrast to humans, genetic contributions to complex behavioral phenotypes can be readily dissected in Drosophila, where both the genetic background and environment can be controlled and behaviors quantified through simple high-throughput assays. Here, we measured voluntary consumption of ethanol in ∼3000 individuals of each sex from an advanced intercross population derived from 37 lines of the Drosophila melanogaster Genetic Reference Panel. Extreme quantitative trait loci mapping identified 385 differentially segregating allelic variants located in or near 291 genes at P < 10-8 . The effects of single nucleotide polymorphisms associated with voluntary ethanol consumption are sex-specific, as found for other alcohol-related phenotypes. To assess causality, we used RNA interference knockdown or P{MiET1} mutants and their corresponding controls and functionally validated 86% of candidate genes in at least one sex. We constructed a genetic network comprised of 23 genes along with a separate trio and a pair of connected genes. Gene ontology analyses showed enrichment of developmental genes, including development of the nervous system. Furthermore, a network of human orthologs showed enrichment for signal transduction processes, protein metabolism and developmental processes, including nervous system development. Our results show that the genetic architecture that underlies variation in voluntary ethanol consumption is sexually dimorphic and partially overlaps with genetic factors that control variation in feeding behavior and alcohol sensitivity. This integrative genetic architecture is rooted in evolutionarily conserved features that can be extrapolated to human genetic interaction networks.
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Affiliation(s)
- S Fochler
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - T V Morozova
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - M R Davis
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - A W Gearhart
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - W Huang
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - T F C Mackay
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - R R H Anholt
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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33
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Zhou S, Luoma SE, St. Armour GE, Thakkar E, Mackay TFC, Anholt RRH. A Drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure. PLoS Genet 2017; 13:e1006907. [PMID: 28732062 PMCID: PMC5544243 DOI: 10.1371/journal.pgen.1006907] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/04/2017] [Accepted: 07/06/2017] [Indexed: 12/20/2022] Open
Abstract
The genetic factors that give rise to variation in susceptibility to environmental toxins remain largely unexplored. Studies on genetic variation in susceptibility to environmental toxins are challenging in human populations, due to the variety of clinical symptoms and difficulty in determining which symptoms causally result from toxic exposure; uncontrolled environments, often with exposure to multiple toxicants; and difficulty in relating phenotypic effect size to toxic dose, especially when symptoms become manifest with a substantial time lag. Drosophila melanogaster is a powerful model that enables genome-wide studies for the identification of allelic variants that contribute to variation in susceptibility to environmental toxins, since the genetic background, environmental rearing conditions and toxic exposure can be precisely controlled. Here, we used extreme QTL mapping in an outbred population derived from the D. melanogaster Genetic Reference Panel to identify alleles associated with resistance to lead and/or cadmium, two ubiquitous environmental toxins that present serious health risks. We identified single nucleotide polymorphisms (SNPs) associated with variation in resistance to both heavy metals as well as SNPs associated with resistance specific to each of them. The effects of these SNPs were largely sex-specific. We applied mutational and RNAi analyses to 33 candidate genes and functionally validated 28 of them. We constructed networks of candidate genes as blueprints for orthologous networks of human genes. The latter not only provided functional contexts for known human targets of heavy metal toxicity, but also implicated novel candidate susceptibility genes. These studies validate Drosophila as a translational toxicogenomics gene discovery system. Although physiological effects of environmental toxins are well documented, we know little about the genetic factors that determine individual variation in susceptibility to toxins. Such information is difficult to obtain in human populations due to heterogeneity in genetic background and environmental exposure, and the diversity of symptoms and time lag with which they appear after toxic exposure. Here, we show that the fruit fly, Drosophila, can serve as a powerful genetic model system to elucidate the genetic underpinnings that contribute to individual variation in resistance to toxicity, using lead and cadmium exposure as an experimental paradigm. We identified genes that harbor genetic variants that contribute to individual variation in resistance to heavy metal exposure. Furthermore, we constructed genetic networks on which we could superimpose human counterparts of Drosophila genes. We were able to place human genes previously implicated in heavy metal toxicity in biological context and identify novel targets for heavy metal toxicity. Thus, we demonstrate that based on evolutionary conservation of fundamental biological processes, we can use Drosophila as a powerful translational model for toxicogenomics studies.
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Affiliation(s)
- Shanshan Zhou
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Sarah E. Luoma
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Genevieve E. St. Armour
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Esha Thakkar
- Enloe Magnet High School, Raleigh, North Carolina, United States of America
| | - Trudy F. C. Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert R. H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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34
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Chow CY, Reiter LT. Etiology of Human Genetic Disease on the Fly. Trends Genet 2017; 33:391-398. [DOI: 10.1016/j.tig.2017.03.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 01/08/2023]
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35
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Barrett JR. Different People, Different Outcomes: Assessing Genetic Susceptibility to Lead Exposures. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:A131. [PMID: 27479021 PMCID: PMC4937845 DOI: 10.1289/ehp.124-a131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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