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Soto J, Pinilla F, Olguín P, Castañeda LE. Genetic Architecture of the Thermal Tolerance Landscape in Drosophila melanogaster. Mol Ecol 2025; 34:e17697. [PMID: 40035350 DOI: 10.1111/mec.17697] [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] [Received: 07/05/2024] [Revised: 12/27/2024] [Accepted: 02/04/2025] [Indexed: 03/05/2025]
Abstract
Increased environmental temperatures associated with global warming strongly impact natural populations of ectothermic species. Therefore, it is crucial to understand the genetic basis and evolutionary potential of heat tolerance. However, heat tolerance and its genetic components depend on the methodology, making it difficult to predict the adaptive responses to global warming. Here, we measured the knockdown time for 100 lines from the Drosophila Genetic Reference Panel (DGRP) at four different static temperatures, and we estimated their thermal-death-time (TDT) curves, which incorporate the magnitude and the time of exposure to thermal stress, to determine the genetic basis of the thermal tolerance landscape. Through quantitative genetic analyses, the knockdown time showed a significant heritability at different temperatures and that its genetic correlations decreased as temperatures differences increased. Significant genotype-by-sex and genotype-by-environment interactions were noted for heat tolerance. We also discovered genetic variability for the two parameters of TDT: CTmax and thermal sensitivity. Taking advantage of the DGRP, we performed a GWAS and identified multiple variants associated with the TDT parameters, which mapped to genes related to signalling and developmental functions. We performed functional validations for some candidate genes using RNAi, which revealed that genes such as mam, KNCQ, or robo3 affect the knockdown time at a specific temperature but are not associated with the TDT parameters. In conlusion, the thermal tolerance landscape display genetic variation and plastic responses, which may facilitate the adaptation of Drosophila populations to a changing world.
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Affiliation(s)
- Juan Soto
- Program of Human Genetics, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Francisco Pinilla
- Program of Human Genetics, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Patricio Olguín
- Program of Human Genetics, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Neuroscience, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Luis E Castañeda
- Program of Human Genetics, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Research Ring in Pest Insects and Climate Change (PIC2), Santiago, Chile
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2
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Prifti MV, Nuga O, Dulay RO, Patel NC, Kula T, Libohova K, Jackson-Butler A, Tsou WL, Richardson K, Todi SV. Insights into dentatorubral-pallidoluysian atrophy from a new Drosophila model of disease. Neurobiol Dis 2025; 207:106834. [PMID: 39921111 PMCID: PMC11969221 DOI: 10.1016/j.nbd.2025.106834] [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] [Received: 12/11/2024] [Revised: 02/04/2025] [Accepted: 02/04/2025] [Indexed: 02/10/2025] Open
Abstract
Dentatorubral-pallidoluysian atrophy (DRPLA) is a neurodegenerative disorder that presents with ataxia, dementia and epilepsy. As a member of the polyglutamine family of diseases, DRPLA is caused by abnormal CAG triplet expansion beyond 48 repeats in the protein-coding region of ATROPHIN 1 (ATN1), a transcriptional co-repressor. To better understand DRPLA, we generated new Drosophila lines that can be induced to express full-length, human ATN1 with a normal (Q7) or pathogenic (Q88) repeat in a variety of cells, including neuronal, glial or any other type of tissue. Expression of ATN1 is toxic, with the polyglutamine-expanded version being consistently more problematic than wild-type ATN1. Fly motility, longevity and internal structures are negatively impacted by pathogenic ATN1. RNA-seq identified altered protein quality control and immune pathways in the presence of pathogenic ATN1. Based on these data, we conducted genetic experiments that confirmed the role of protein quality control components that ameliorate or exacerbate ATN1 toxicity. Hsc70-3, a chaperone, arose as a likely suppressor of toxicity. VCP (a proteasome-related AAA ATPase), Rpn11 (a proteasome-related deubiquitinase) and select DnaJ proteins (co-chaperones) were inconsistently protective, depending on the tissues where they were expressed. Lastly, informed by RNA-seq data that exercise-related genes may also be involved in this model of DRPLA, we conducted short-term exercise, which improved overall fly motility. This new model of DRPLA will prove important to understanding this understudied disease and will help to identify therapeutic targets for it.
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Affiliation(s)
- Matthew V Prifti
- Department of Pharmacology, Wayne State University School of Medicine, USA
| | - Oluwademilade Nuga
- Department of Pharmacology, Wayne State University School of Medicine, USA
| | - Ryan O Dulay
- Department of Pharmacology, Wayne State University School of Medicine, USA
| | - Nikhil C Patel
- Department of Pharmacology, Wayne State University School of Medicine, USA
| | - Truman Kula
- Department of Pharmacology, Wayne State University School of Medicine, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, USA
| | | | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, USA
| | - Kristin Richardson
- Department of Pharmacology, Wayne State University School of Medicine, USA.
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, USA; Department of Neurology, Wayne State University School of Medicine, USA.
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3
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Simkhada B, Nazario-Yepiz NO, Freymuth PS, Lyman RA, Shankar V, Wiggins K, Flanagan-Steet H, Basu A, Weiss RJ, Anholt RRH, Mackay TFC. A Drosophila model of mucopolysaccharidosis IIIB. Genetics 2025; 229:iyae219. [PMID: 39737777 PMCID: PMC11912869 DOI: 10.1093/genetics/iyae219] [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] [Received: 09/16/2024] [Accepted: 12/24/2024] [Indexed: 01/01/2025] Open
Abstract
Mucopolysaccharidosis type IIIB is a rare lysosomal storage disorder caused by defects in alpha-N-acetylglucosaminidase (NAGLU) and characterized by severe effects in the central nervous system. Mutations in NAGLU cause accumulation of partially degraded heparan sulfate in lysosomes. The consequences of these mutations on whole-genome gene expression and their causal relationships to neural degeneration remain unknown. Here, we used the functional Drosophila melanogaster ortholog of NAGLU, Naglu, to develop a fly model for MPS IIIB induced by gene deletion (NagluKO), missense (NagluY160C), and nonsense (NagluW422X) mutations. We used the Drosophila activity monitoring system to analyze activity and sleep and found sex- and age-dependent hyperactivity and sleep defects in mutant flies. Fluorescence microscopy on mutant fly brains using Lysotracker dye revealed a significant increase in acidic compartments. Differentially expressed genes determined from RNA sequencing of fly brains are involved in biological processes that affect nervous system development. A genetic interaction network constructed using known interacting partners of these genes consists of 2 major subnetworks, one of which is enriched in genes associated with synaptic function and the other with neurodevelopmental processes. Our data indicate that lysosomal dysfunction arising from disruption of heparan sulfate breakdown has widespread effects on the steady state of intracellular vesicle transport, including vesicles associated with synaptic transmission. Evolutionary conservation of fundamental biological processes predicts that the Drosophila model of mucopolysaccharidosis type IIIB can serve as an in vivo system for the future development of therapies for mucopolysaccharidosis type IIIB and related disorders.
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Affiliation(s)
- Bibhu Simkhada
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Nestor O Nazario-Yepiz
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Patrick S Freymuth
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Rachel A Lyman
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Kali Wiggins
- Greenwood Genetic Center, JC Self Research Institute, 106 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Heather Flanagan-Steet
- Greenwood Genetic Center, JC Self Research Institute, 106 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Amrita Basu
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Ryan J Weiss
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Robert R H Anholt
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F C Mackay
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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4
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Delandre C, McMullen JPD, Marshall OJ. Dynamic changes in neuronal and glial GAL4 driver expression during Drosophila aging. Genetics 2025; 229:iyaf014. [PMID: 39950543 PMCID: PMC11912842 DOI: 10.1093/genetics/iyaf014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 12/19/2024] [Indexed: 03/19/2025] Open
Abstract
Understanding how diverse cell types come together to form a functioning brain relies on the ability to specifically target these cells. This is often done using genetic tools such as the GAL4/UAS system in Drosophila melanogaster. Surprisingly, despite its extensive usage during studies of the aging brain, detailed spatiotemporal characterization of GAL4 driver lines in adult flies has been lacking. Here, we show that 3 commonly used neuronal drivers (elav[C155]-GAL4, nSyb[R57C10]-GAL4, and ChAT-GAL4) and the commonly used glial driver repo-GAL4 all show rapid and pronounced decreases in activity over the first 1.5 weeks of adult life, with activity becoming undetectable in some regions after 30 days (at 18°C). In addition to an overall decrease in GAL4 activity over time, we found notable differences in spatial patterns, mostly occurring soon after eclosion. Although all lines showed these changes, the nSyb-GAL4 line exhibited the most consistent and stable expression patterns over aging. Our findings suggest that gene transcription of key loci decreases in the aged brain, a finding broadly similar to previous work in mammalian brains. Our results also raise questions over past work on long-term expression of disease models in the brain and stress the need to find better genetic tools for ageing studies.
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Affiliation(s)
- Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
| | - John P D McMullen
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
| | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
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5
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Bak NK, Mackay TFC, Morgante F, Nielsen KL, Nielsen JL, Kristensen TN, Rohde PD. The Role of Genetic Variation in Shaping Phenotypic Responses to Diet in Aging Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.09.632132. [PMID: 39868103 PMCID: PMC11761520 DOI: 10.1101/2025.01.09.632132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Nutrition plays a central role in healthy living, however, extensive variability in individual responses to dietary interventions complicates our understanding of its effects. Here we present a comprehensive study utilizing the Drosophila Genetic Reference Panel (DGRP), investigating how genetic variation influences responses to diet and aging. Quantitative genetic analyses of the impact of dietary restriction on lifespan, locomotor activity, dry weight, and heat knockdown time were performed. Locomotor activity, dry weight and heat knockdown time were measured on the same individual flies. We found significant genotype-by-diet interaction (GDI) and genotype-by-age interaction (GAI) for all traits. Therefore, environmental factors play a crucial role in shaping trait variation at different ages and diets, and/or distinct genetic variation influences these traits at different ages and diets. Our genome wide association study also identified a quantitative trait locus for age-dependent dietary response. The observed GDI and GAI indicates that susceptibility to environmental influences changes as organisms age, which could have significant implications for dietary recommendations and interventions aimed at promoting healthy aging in humans. The identification of associations between DNA sequence variation and age-dependent dietary responses opens new avenues for research into the genetic mechanisms underlying these interactions.
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Affiliation(s)
| | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina, United States of America
| | - Fabio Morgante
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina, United States of America
| | | | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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Beam TC, Bright M, Pearson AC, Dua I, Smith M, Dutta AK, Bhadra SC, Salman S, Strickler CN, Anderson CE, Peshkin L, Yampolsky LY. Short lifespan is one's fate, long lifespan is one's achievement: lessons from Daphnia. GeroScience 2024; 46:6361-6381. [PMID: 38900345 PMCID: PMC11493910 DOI: 10.1007/s11357-024-01244-7] [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] [Received: 04/30/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Studies of longevity rely on baseline life expectancy of reference genotypes measured in standardized conditions. Variation among labs, protocols, and genotypes makes longevity intervention studies difficult to compare. Furthermore, extending lifespan under suboptimal conditions or that of a short-lived genotype may be of a lesser theoretical and translational value than extending the maximal possible lifespan. Daphnia is becoming a model organism of choice for longevity research complementing data obtained on traditional models. In this study, we report longevity of several genotypes of a long-lived species D. magna under a variety of protocols, aiming to document the highest lifespan, factors reducing it, and parameters that change with age and correlate with longevity. Combining longevity data from 25 experiments across two labs, we report a strong intraspecific variation, moderate effects of group size and medium composition, and strong genotype-by-environment interactions with respect to food level. Specifically, short-lived genotypes show no caloric restriction (CR) effect, while long-lived ones expand their lifespan even further under CR. We find that the CR non-responsive clones show little correlation between longevity and two measures of lipid peroxidation. In contrast, the long-lived, CR-responsive clones show a positive correlation between longevity and lipid hydroperoxide abundance, and a negative correlation with MDA concentration. This indicates differences among genotypes in age-related accumulation and detoxification of LPO products and their effects on longevity. Our observations support the hypothesis that a long lifespan can be affected by CR and levels of oxidative damage, while genetically determined short lifespan remains short regardless.
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Affiliation(s)
- Thomas C Beam
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Mchale Bright
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Amelia C Pearson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Ishaan Dua
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Meridith Smith
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Ashit K Dutta
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Shymal C Bhadra
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, IN, 46805, USA
| | - Saad Salman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Caleb N Strickler
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Cora E Anderson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Lev Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA.
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7
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Collins KM, Howansky E, Macon-Foley SC, Adonay ME, Shankar V, Lyman RF, Nazario-Yepiz NO, Brooks JK, Lyman RA, Mackay TFC, Anholt RRH. Drosophila Toxicogenomics: genetic variation and sexual dimorphism in susceptibility to 4-Methylimidazole. Hum Genomics 2024; 18:119. [PMID: 39497218 PMCID: PMC11533318 DOI: 10.1186/s40246-024-00689-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 10/24/2024] [Indexed: 11/07/2024] Open
Abstract
BACKGROUND 4-methylimidazole is a ubiquitous and potentially carcinogenic environmental toxicant. Genetic factors that contribute to variation in susceptibility to its toxic effects are challenging to assess in human populations. We used the Drosophila melanogaster Genetic Reference Panel (DGRP), a living library of natural genetic variation, to identify genes with human orthologs associated with variation in susceptibility to 4-methylimidazole. RESULTS We screened 204 DGRP lines for survival following 24-hour exposure to 4-methylimidazole. We found extensive genetic variation for survival, with a broad sense heritability of 0.82; as well as genetic variation in sexual dimorphism, with a cross-sex genetic correlation of 0.59. Genome-wide association analyses identified a total of 241 candidate molecular polymorphisms in or near 273 unique genes associated with survival. These polymorphisms had either sex-specific or sex-antagonistic effects, and most had putative regulatory effects. We generated interaction networks using these candidate genes as inputs and computationally recruited genes with known physical or genetic interactions. The network genes were significantly over-represented for gene ontology terms involving all aspects of development (including nervous system development) and cellular and organismal functions as well as canonical signaling pathways, and most had human orthologs. CONCLUSIONS The genetic basis of variation in sensitivity to acute exposure to 4-methylimidazole in Drosophila is attributable to variation in genes and networks of genes known for their effects on multiple developmental and cellular processes, including possible neurotoxicity. Given evolutionary conservation of the underlying genes and pathways, these insights may be applicable to humans.
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Affiliation(s)
- Katelynne M Collins
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Elisabeth Howansky
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Sarah C Macon-Foley
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Maria E Adonay
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Vijay Shankar
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Richard F Lyman
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Nestor Octavio Nazario-Yepiz
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Jordyn K Brooks
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Rachel A Lyman
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Trudy F C Mackay
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA.
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Gardeux V, Bevers RPJ, David FPA, Rosschaert E, Rochepeau R, Deplancke B. DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits. eLife 2024; 12:RP88981. [PMID: 39431984 PMCID: PMC11493408 DOI: 10.7554/elife.88981] [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: 10/22/2024] Open
Abstract
Genome-wide association studies have advanced our understanding of complex traits, but studying how a GWAS variant can affect a specific trait in the human population remains challenging due to environmental variability. Drosophila melanogaster is in this regard an excellent model organism for studying the relationship between genetic and phenotypic variation due to its simple handling, standardized growth conditions, low cost, and short lifespan. The Drosophila Genetic Reference Panel (DGRP) in particular has been a valuable tool for studying complex traits, but proper harmonization and indexing of DGRP phenotyping data is necessary to fully capitalize on this resource. To address this, we created a web tool called DGRPool (dgrpool.epfl.ch), which aggregates phenotyping data of 1034 phenotypes across 135 DGRP studies in a common environment. DGRPool enables users to download data and run various tools such as genome-wide (GWAS) and phenome-wide (PheWAS) association studies. As a proof-of-concept, DGRPool was used to study the longevity phenotype and uncovered both established and unexpected correlations with other phenotypes such as locomotor activity, starvation resistance, desiccation survival, and oxidative stress resistance. DGRPool has the potential to facilitate new genetic and molecular insights of complex traits in Drosophila and serve as a valuable, interactive tool for the scientific community.
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Affiliation(s)
- Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Roel PJ Bevers
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Fabrice PA David
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Bioinformatics Competence Center, EPFLLausanneSwitzerland
| | - Emily Rosschaert
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Laboratory of Behavioral and Developmental Genetics, Center for Human Genetics, KU LeuvenLeuvenBelgium
| | - Romain Rochepeau
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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9
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Coleman CR, Pallos J, Arreola-Bustos A, Wang L, Raftery D, Promislow DEL, Martin I. Natural variation in age-related dopamine neuron degeneration is glutathione dependent and linked to life span. Proc Natl Acad Sci U S A 2024; 121:e2403450121. [PMID: 39388265 PMCID: PMC11494315 DOI: 10.1073/pnas.2403450121] [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] [Received: 02/19/2024] [Accepted: 09/04/2024] [Indexed: 10/12/2024] Open
Abstract
Aging is the biggest risk factor for Parkinson's disease (PD), suggesting that age-related changes in the brain promote dopamine neuron vulnerability. It is unclear, however, whether aging alone is sufficient to cause significant dopamine neuron loss, and if so, how this intersects with PD-related neurodegeneration. Here, through examining a large collection of naturally varying Drosophila strains, we find a strong relationship between life span and age-related dopamine neuron loss. Strains with naturally short-lived animals exhibit a loss of dopamine neurons without generalized neurodegeneration, while animals from long-lived strains retain dopamine neurons across age. Metabolomic profiling reveals lower glutathione levels in short-lived strains which is associated with elevated levels of reactive oxygen species (ROS), sensitivity to oxidative stress, and vulnerability to silencing the familial PD gene parkin. Strikingly, boosting neuronal glutathione levels via glutamate-cysteine ligase (Gcl) overexpression is sufficient to normalize ROS levels, extend life span, and block dopamine neurons loss in short-lived backgrounds, demonstrating that glutathione deficiencies are central to neurodegenerative phenotypes associated with short longevity. These findings may be relevant to human PD pathogenesis, where glutathione depletion is reported to occur in the idiopathic PD patient brain through unknown mechanisms. Building on this, we find reduced expression of the Gcl catalytic subunit in both Drosophila strains vulnerable to age-related dopamine neuron loss and in the human brain from familial PD patients harboring the common LRRK2 G2019S mutation. Our study across Drosophila and human PD systems suggests that glutathione synthesis and levels play a conserved role in regulating age-related dopamine neuron health.
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Affiliation(s)
- Colin R. Coleman
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR 97239
| | - Judit Pallos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR 97239
| | - Alicia Arreola-Bustos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR 97239
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA98195
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA98109
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA98057
- Department of Biology, University of Washington School of Medicine, Seattle, WA98195
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR 97239
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10
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Hundebøl BNRG, Rohde PD, Kristensen TN, Jensen RWM, Vosegaard T, Sørensen JG. Bugs on Drugs: Paracetamol Exposure Reveals Genotype-Specific Generational Effects on Life History Traits in Drosophila melanogaster. INSECTS 2024; 15:763. [PMID: 39452339 PMCID: PMC11509061 DOI: 10.3390/insects15100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 09/26/2024] [Accepted: 09/26/2024] [Indexed: 10/26/2024]
Abstract
Few investigations have been made to determine whether pharmaceutical drugs cause any generational effects. These effects can be divided into intergenerational and transgenerational effects. In insects, the F1 offspring of exposed individuals are considered to show intergenerational effects (as they have been exposed as germ cells or early embryos), while the F2 generation is fully non-exposed and considered to show transgenerational effects. Here, the common over-the-counter (OTC) drug, paracetamol, is investigated for genotype-specific responses and effects across generations on three life-history traits: fecundity, longevity, and spontaneous locomotor activity levels in the model species Drosophila melanogaster. Seven isofemale D. melanogaster lines were exposed to a high and intermediate dose of paracetamol determined by a dose-response curve. NMR investigations verified the long-term presence of paracetamol in the food substrate. Phenotypic effects of paracetamol ingestion were investigated on flies exposed to the drug and in their offspring and grand-offspring. The dose-response curve indicated genotype-specific responses to paracetamol. In the following experiment, all traits investigated displayed significant effects of paracetamol ingestion for at least one of the seven isofemale lines, and we detected strong genotype-specific responses to paracetamol. Fecundity tended to increase in individuals directly exposed to the drug whereas fecundity in the F2 generation was reduced (transgenerational). Longevity generally decreased in directly exposed individuals but tended to increase in F1 offspring (intergenerational). Paracetamol effects on spontaneous locomotor activity were primarily detected as transgenerational effects and were rarely seen in directly exposed individuals. However, across lines, no clear overall trend could be determined for any trait. The generational effects and marked genotype-specific response to paracetamol warrants further investigation of both genotype-specific responses and generational effects in general.
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Affiliation(s)
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg Ø, Denmark;
| | | | - Rune Wittendorff Mønster Jensen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (R.W.M.J.); (T.V.)
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (R.W.M.J.); (T.V.)
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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11
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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12
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Woodling N. Sex- and strain-dependent effects of ageing on sleep and activity patterns in Drosophila. PLoS One 2024; 19:e0308652. [PMID: 39150918 PMCID: PMC11329114 DOI: 10.1371/journal.pone.0308652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/27/2024] [Indexed: 08/18/2024] Open
Abstract
The fruit fly Drosophila is a major discovery platform in the biology of ageing due to its balance of relatively short lifespan and relatively complex physiology and behaviour. Previous studies have suggested that some important phenotypes of ageing, for instance increasingly fragmented sleep, are shared from humans to Drosophila and can be useful measures of behavioural change with age: these phenotypes therefore hold potential as readouts of healthy ageing for genetic or pharmacological interventions aimed at the underpinning biology of ageing. However, some age-related phenotypes in Drosophila show differing results among studies, leading to questions regarding the source of discrepancies among experiments. In this study, I have tested females and males from three common laboratory strains of Drosophila to determine the extent to which sex and background strain influence age-related behavioural changes in sleep and activity patterns. Surprisingly, I find that some phenotypes-including age-related changes in total activity, total sleep, and sleep fragmentation-depend strongly on sex and strain, to the extent that some phenotypes show opposing age-related changes in different sexes or strains. Conversely, I identify other phenotypes, including age-related decreases in morning and evening anticipation, that are more uniform across sexes and strains. These results reinforce the importance of controlling for background strain in both behavioural and ageing experiments, and they imply that caution should be used when drawing conclusions from studies on a single sex or strain of Drosophila. At the same time, these findings also offer suggestions for behavioural measures that merit further investigation as potentially more consistent phenotypes of ageing.
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Affiliation(s)
- Nathan Woodling
- School of Molecular Biosciences, University of Glasgow, Glasgow, United Kingdom
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13
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Landis GN, Bell HS, Peng OK, Fan Y, Yan K, Baybutt B, Tower J. Conditional Inhibition of Eip75B Eliminates the Effects of Mating and Mifepristone on Lifespan in Female Drosophila. Cells 2024; 13:1123. [PMID: 38994975 PMCID: PMC11240670 DOI: 10.3390/cells13131123] [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] [Received: 05/11/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024] Open
Abstract
Mating in female Drosophila melanogaster causes midgut hypertrophy and reduced lifespan, and these effects are blocked by the drug mifepristone. Eip75B is a transcription factor previously reported to have pleiotropic effects on Drosophila lifespan. Because Eip75B null mutations are lethal, conditional systems and/or partial knock-down are needed to study Eip75B effects in adults. Previous studies showed that Eip75B is required for adult midgut cell proliferation in response to mating. To test the possible role of Eip75B in mediating the lifespan effects of mating and mifepristone, a tripartite FLP-recombinase-based conditional system was employed that provides controls for genetic background. Expression of a Hsp70-FLP transgene was induced in third instar larvae by a brief heat pulse. The FLP recombinase catalyzed the recombination and activation of an Actin5C-GAL4 transgene. The GAL4 transcription factor in turn activated expression of a UAS-Eip75B-RNAi transgene. Inhibition of Eip75B activity was confirmed by loss of midgut hypertrophy upon mating, and the lifespan effects of both mating and mifepristone were eliminated. In addition, the negative effects of mifepristone on egg production were eliminated. The data indicate that Eip75B mediates the effects of mating and mifepristone on female midgut hypertrophy, egg production, and lifespan.
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Affiliation(s)
| | | | | | | | | | | | - John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA
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14
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Yamamoto A, Huang W, Anholt RR, Mackay TF. The genetic basis of variation in Drosophila melanogaster mating behavior. iScience 2024; 27:109837. [PMID: 38766354 PMCID: PMC11099327 DOI: 10.1016/j.isci.2024.109837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Mating behavior is an essential fitness trait. We used the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP) to gain insights into the evolution of mating success and to evaluate the overlap in genetic architecture of mating behavior between the sexes. We found significant genetic variation for mating success when DGRP males and females from the same line were mated together, and when DGRP males and females were mated to an unrelated strain of the opposite sex. The mating success of DGRP males and females was not correlated when they were paired with the unrelated strain, suggesting independent genetic architecture of mating success in males and females that was confirmed by genome-wide association analyses. However, the mating success between pairs of the same or different DGRP lines was predicted accurately by the respective female and male mating success with the unrelated line.
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Affiliation(s)
- Akihiko Yamamoto
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Robert R.H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - 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 27695-7614, USA
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15
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Bylino OV, Ogienko AA, Batin MA, Georgiev PG, Omelina ES. Genetic, Environmental, and Stochastic Components of Lifespan Variability: The Drosophila Paradigm. Int J Mol Sci 2024; 25:4482. [PMID: 38674068 PMCID: PMC11050664 DOI: 10.3390/ijms25084482] [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] [Received: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Lifespan is a complex quantitative trait involving genetic and non-genetic factors as well as the peculiarities of ontogenesis. As with all quantitative traits, lifespan shows considerable variation within populations and between individuals. Drosophila, a favourite object of geneticists, has greatly advanced our understanding of how different forms of variability affect lifespan. This review considers the role of heritable genetic variability, phenotypic plasticity and stochastic variability in controlling lifespan in Drosophila melanogaster. We discuss the major historical milestones in the development of the genetic approach to study lifespan, the breeding of long-lived lines, advances in lifespan QTL mapping, the environmental factors that have the greatest influence on lifespan in laboratory maintained flies, and the mechanisms, by which individual development affects longevity. The interplay between approaches to study ageing and lifespan limitation will also be discussed. Particular attention will be paid to the interaction of different types of variability in the control of lifespan.
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Affiliation(s)
- Oleg V. Bylino
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna A. Ogienko
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Mikhail A. Batin
- Open Longevity, 15260 Ventura Blvd., Sherman Oaks, Los Angeles, CA 91403, USA
| | - Pavel G. Georgiev
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Evgeniya S. Omelina
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
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16
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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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17
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Coleman CR, Pallos J, Arreola-Bustos A, Wang L, Raftery D, Promislow DEL, Martin I. Natural Variation in Age-Related Dopamine Neuron Degeneration is Glutathione-Dependent and Linked to Life Span. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580013. [PMID: 38405950 PMCID: PMC10888861 DOI: 10.1101/2024.02.12.580013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Aging is the biggest risk factor for Parkinson's disease (PD), suggesting that age-related changes in the brain promote dopamine neuron vulnerability. It is unclear, however, whether aging alone is sufficient to cause significant dopamine neuron loss and if so, how this intersects with PD-related neurodegeneration. Here, through examining a large collection of naturally varying Drosophila strains, we find a strong relationship between life span and age-related dopamine neuron loss. Naturally short-lived strains exhibit a loss of dopamine neurons but not generalized neurodegeneration, while long-lived strains retain dopamine neurons across age. Metabolomic profiling reveals lower glutathione levels in short-lived strains which is associated with elevated levels of reactive oxygen species (ROS), sensitivity to oxidative stress and vulnerability to silencing the familial PD gene parkin . Strikingly, boosting neuronal glutathione levels via glutamate-cysteine ligase (GCL) overexpression is sufficient to normalize ROS levels, extend life span and block dopamine neurons loss in short-lived backgrounds, demonstrating that glutathione deficiencies are central to neurodegenerative phenotypes associated with short longevity. These findings may be relevant to human PD pathogenesis, where glutathione depletion is frequently reported in idiopathic PD patient brain. Building on this evidence, we detect reduced levels of GCL catalytic and modulatory subunits in brain from PD patients harboring the LRRK2 G2019S mutation, implicating possible glutathione deficits in familial LRRK2-linked PD. Our study across Drosophila and human PD systems suggests that glutathione plays an important role in the influence of aging on PD neurodegeneration.
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18
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Owings KG, Chow CY. A Drosophila screen identifies a role for histone methylation in ER stress preconditioning. G3 (BETHESDA, MD.) 2024; 14:jkad265. [PMID: 38098286 PMCID: PMC11021027 DOI: 10.1093/g3journal/jkad265] [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: 06/07/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023]
Abstract
Stress preconditioning occurs when transient, sublethal stress events impact an organism's ability to counter future stresses. Although preconditioning effects are often noted in the literature, very little is known about the underlying mechanisms. To model preconditioning, we exposed a panel of genetically diverse Drosophila melanogaster to a sublethal heat shock and measured how well the flies survived subsequent exposure to endoplasmic reticulum (ER) stress. The impact of preconditioning varied with genetic background, ranging from dying half as fast to 4 and a half times faster with preconditioning compared to no preconditioning. Subsequent association and transcriptional analyses revealed that histone methylation, and transcriptional regulation are both candidate preconditioning modifier pathways. Strikingly, almost all subunits (7/8) in the Set1/COMPASS complex were identified as candidate modifiers of preconditioning. Functional analysis of Set1 knockdown flies demonstrated that loss of Set1 led to the transcriptional dysregulation of canonical ER stress genes during preconditioning. Based on these analyses, we propose a preconditioning model in which Set1 helps to establish an interim transcriptional "memory" of previous stress events, resulting in a preconditioned response to subsequent stress.
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Affiliation(s)
- Katie G Owings
- Department of Human Genetics, University of Utah School of Medicine, EIHG 5200, 15 North 2030 East, Salt Lake City, UT 84112, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, EIHG 5200, 15 North 2030 East, Salt Lake City, UT 84112, USA
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19
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Ramya R, Venkatesh CR, Shyamala BV. olf413 an octopamine biogenesis pathway gene is required for axon growth and pathfinding during embryonic nervous system development in Drosophila melanogaster. BMC Res Notes 2024; 17:46. [PMID: 38326892 PMCID: PMC10848397 DOI: 10.1186/s13104-024-06700-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
OBJECTIVE Neurotransmitters have been extensively studied as neural communication molecules. Genetic associations discovered, and indirect intervention studies in Humans and mammals have led to a general proposition that neurotransmitters have a role in structuring of neuronal network during development. olf413 is a Drosophila gene annotated as coding for dopamine beta-monooxygenase enzyme with a predicted function in octopaminergic pathway. The biological function of this gene is very little worked out. In this study we investigate the requirement of olf413 gene function for octopamine biogenesis and developmental patterning of embryonic nervous system. RESULT In our study we have used the newly characterized neuronal specific allele olf413SG1.1, and the gene disruption strain olf413MI02014 to dissect out the function of olf413. olf413 has an enhancer activity as depicted by reporter GFP expression, in the embryonic ventral nerve cord, peripheral nervous system and the somatic muscle bundles. Homozygous loss of function mutants show reduced levels of octopamine, and this finding supports the proposed function of the gene in octopamine biogenesis. Further, loss of function of olf413 causes embryonic lethality. FasII staining of these embryos reveal a range of phenotypes in the central and peripheral motor nerves, featuring axonal growth, pathfinding, branching and misrouting defects. Our findings are important as they implicate a key functional requirement of this gene in precise axonal patterning events, a novel developmental role imparted for an octopamine biosynthesis pathway gene in structuring of embryonic nervous system.
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Affiliation(s)
- Ravindrakumar Ramya
- Developmental Genetics Laboratory, Department of Studies in Zoology, University of Mysore, Mysuru, 570006, India
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20
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Riddle NC, Biga PR, Bronikowski AM, Walters JR, Wilkinson GS. Comparative analysis of animal lifespan. GeroScience 2024; 46:171-181. [PMID: 37889438 PMCID: PMC10828364 DOI: 10.1007/s11357-023-00984-2] [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] [Received: 09/28/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Comparative studies of aging are a promising approach to identifying general properties of and processes leading to aging. While to date, many comparative studies of aging in animals have focused on relatively narrow species groups, methodological innovations now allow for studies that include evolutionary distant species. However, comparative studies of aging across a wide range of species that have distinct life histories introduce additional challenges in experimental design. Here, we discuss these challenges, highlight the most pressing problems that need to be solved, and provide suggestions based on current approaches to successfully carry out comparative aging studies across the animal kingdom.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Peggy R Biga
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anne M Bronikowski
- Department of Integrative Biology, Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - James R Walters
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
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21
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Fanara JJ, Sassi PL, Goenaga J, Hasson E. Genetic basis and repeatability for desiccation resistance in Drosophila melanogaster (Diptera: Drosophilidae). Genetica 2024; 152:1-9. [PMID: 38102503 DOI: 10.1007/s10709-023-00201-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023]
Abstract
Dehydration is a stress factor for organisms inhabiting natural habitats where water is scarce. Thus, it may be expected that species facing arid environments will develop mechanisms that maximize resistance to desiccation. Insects are excellent models for studying the effects of dehydration as well as the mechanisms and processes that prevent water loss since the effect of desiccation is greater due to the higher area/volume ratio than larger animals. Even though physiological and behavioral mechanisms to cope with desiccation are being understood, the genetic basis underlying the mechanisms related to variation in desiccation resistance and the context-dependent effect remain unsolved. Here we analyze the genetic bases of desiccation resistance in Drosophila melanogaster and identify candidate genes that underlie trait variation. Our quantitative genetic analysis of desiccation resistance revealed sexual dimorphism and extensive genetic variation. The phenotype-genotype association analyses (GWAS) identified 71 candidate genes responsible for total phenotypic variation in desiccation resistance. Half of these candidate genes were sex-specific suggesting that the genetic architecture underlying this adaptive trait differs between males and females. Moreover, the public availability of desiccation data analyzed on the same lines but in a different lab allows us to investigate the reliability and repeatability of results obtained in independent screens. Our survey indicates a pervasive micro-environment lab-dependent effect since we did not detect overlap in the sets of genes affecting desiccation resistance identified between labs.
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Affiliation(s)
- Juan Jose Fanara
- Laboratorio de Evolución, Departamento de Ecología Genética y Evolución, Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), CONICET-UBA, FCEN, Buenos Aires, Argentina.
| | - Paola Lorena Sassi
- Grupo de Ecología Integrativa de Fauna Silvestre, Instituto Argentino de Investigaciones de Zonas Áridas, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Julieta Goenaga
- Quality Control & NIR Scientist, Biomar Group, Aarhus, Denmark
| | - Esteban Hasson
- Laboratorio de Evolución, Departamento de Ecología Genética y Evolución, Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), CONICET-UBA, FCEN, Buenos Aires, Argentina
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22
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Landis GN, Bell HS, Peng O, Bognar B, Tong A, Manea TD, Bao H, Han X, Tower J. Dhr96[1] mutation and maternal tudor[1] mutation increase life span and reduce the beneficial effects of mifepristone in mated female Drosophila. PLoS One 2023; 18:e0292820. [PMID: 38127988 PMCID: PMC10735022 DOI: 10.1371/journal.pone.0292820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/28/2023] [Indexed: 12/23/2023] Open
Abstract
Mating and receipt of male Sex Peptide hormone cause increased egg laying, increased midgut size and decreased life span in female Drosophila. Feeding mated females with the synthetic steroid mifepristone decreases egg production, reduces midgut size, and increases life span. Here, several gene mutations were assayed to investigate possible mechanisms for mifepristone action. Drosophila Dhr96 is a hormone receptor, and a key positive regulator of midgut lipid uptake and metabolism. Dhr96[1] null mutation increased female life span, and reduced the effects of mifepristone on life span, suggesting that Dhr96[1] mutation and mifepristone may act in part through the same mechanism. Consistent with this idea, lipidomics analysis revealed that mating increases whole-body levels of triglycerides and fatty-acids in triglycerides, and these changes are reversed by mifepristone. Maternal tudor[1] mutation results in females that lack the germ-line and produce no eggs. Maternal tudor[1] mutation increased mated female life span, and reduced but did not eliminate the effects of mating and mifepristone on life span. This indicates that decreased egg production may be related to the life span benefits of mifepristone, but is not essential. Mifepristone increases life span in w[1118] mutant mated females, but did not increase life span in w[1118] mutant virgin females. Mifepristone decreased egg production in w[1118] mutant virgin females, indicating that decreased egg production is not sufficient for mifepristone to increase life span. Mifepristone increases life span in virgin females of some, but not all, white[+] and mini-white[+] strains. Backcrossing of mini-white[+] transgenes into the w[1118] background was not sufficient to confer a life span response to mifepristone in virgin females. Taken together, the data support the hypothesis that mechanisms for mifepristone life span increase involve reduced lipid uptake and/or metabolism, and suggest that mifepristone may increase life span in mated females and virgin females through partly different mechanisms.
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Affiliation(s)
- Gary N. Landis
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Hans S. Bell
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Oscar Peng
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Brett Bognar
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Andy Tong
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Tomás D. Manea
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Hanmei Bao
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - John Tower
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
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23
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Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Rep 2023; 42:112873. [PMID: 37527041 PMCID: PMC10546330 DOI: 10.1016/j.celrep.2023.112873] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
A vexing observation in genome-wide association studies (GWASs) is that parallel analyses in different species may not identify orthologous genes. Here, we demonstrate that cross-species translation of GWASs can be greatly improved by an analysis of co-localization within molecular networks. Using body mass index (BMI) as an example, we show that the genes associated with BMI in humans lack significant agreement with those identified in rats. However, the networks interconnecting these genes show substantial overlap, highlighting common mechanisms including synaptic signaling, epigenetic modification, and hormonal regulation. Genetic perturbations within these networks cause abnormal BMI phenotypes in mice, too, supporting their broad conservation across mammals. Other mechanisms appear species specific, including carbohydrate biosynthesis (humans) and glycerolipid metabolism (rodents). Finally, network co-localization also identifies cross-species convergence for height/body length. This study advances a general paradigm for determining whether and how phenotypes measured in model species recapitulate human biology.
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Affiliation(s)
- Sarah N Wright
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Brittany S Leger
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA; Program in Biomedical Sciences, University of California San Diego, La Jolla, CA 93093, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sophie N Liu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Tongqiu Jia
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Katie Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Anthony George
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA
| | - Alexander F Gileta
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Wenyan Han
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Alesa H Netzley
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher P King
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA; Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | | | - Connor Martin
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA; Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | | | - Tengfei Wang
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Hannah Bimschleger
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Jerry Richards
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA; Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY 14203, USA
| | - Hao Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Shelly B Flagel
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul Meyer
- Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | - Terry E Robinson
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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24
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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: 17] [Impact Index Per Article: 8.5] [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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25
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Lin YC, Zhang M, Chang YJ, Kuo TH. Comparisons of lifespan and stress resistance between sexes in Drosophila melanogaster. Heliyon 2023; 9:e18178. [PMID: 37576293 PMCID: PMC10415617 DOI: 10.1016/j.heliyon.2023.e18178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Animals exhibit different extents of sexual dimorphism in a variety of phenotypes. Sex differences in longevity, one of the most complex life history traits, have also been reported. Although lifespan regulation has been studied extensively in the fruit fly, Drosophila melanogaster, the sex differences in lifespan have not been consistent in previous studies. To explore this issue, we revisited this question by examining the lifespan and stress resistance of both sexes among 15 inbred strains. We first found positive correlations between males and females from the same strain in terms of lifespan and resistance to starvation and desiccation stress. Although the lifespan difference between male and female flies varied greatly depending on the strain, males across all strains collectively had a longer lifespan. In contrast, females showed better resistance to starvation and desiccation stress. We also observed greater variation in lifespan and resistance to starvation and desiccation stress in females. Unexpectedly, there was no notable correlation observed between lifespan and the three types of stress resistance in either males or females. Overall, our study provides new data regarding sexual dimorphism in fly lifespan and stress resistance; this information may promote the investigation of mechanisms underlying longevity in future research.
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Affiliation(s)
- Yu-Chiao Lin
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | - MingYang Zhang
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Tsung-Han Kuo
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan
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26
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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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27
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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: 2.0] [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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28
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Owings KG, Chow CY. A Drosophila screen identifies a role for histone methylation in ER stress preconditioning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.532109. [PMID: 36945590 PMCID: PMC10028959 DOI: 10.1101/2023.03.10.532109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Stress preconditioning occurs when transient, sublethal stress events impact an organism's ability to counter future stresses. Although preconditioning effects are often noted in the literature, very little is known about the underlying mechanisms. To model preconditioning, we exposed a panel of genetically diverse Drosophila melanogaster to a sublethal heat shock and measured how well the flies survived subsequent exposure to endoplasmic reticulum (ER) stress. The impact of preconditioning varied with genetic background, ranging from dying half as fast to four and a half times faster with preconditioning compared to no preconditioning. Subsequent association and transcriptional analyses revealed that histone methylation, transcriptional regulation, and immune status are all candidate preconditioning modifier pathways. Strikingly, almost all subunits (7/8) in the Set1/COMPASS complex were identified as candidate modifiers of preconditioning. Functional analysis of Set1 knockdown flies demonstrated that loss of Set1 led to the transcriptional dysregulation of canonical ER stress genes during preconditioning. Based on these analyses, we propose a model of preconditioning in which Set1 helps to establish an interim transcriptional 'memory' of previous stress events, resulting in a preconditioned response to subsequent stress.
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Affiliation(s)
- Katie G. Owings
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Clement Y. Chow
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
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29
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Katzenberger RJ, Ganetzky B, Wassarman DA. Lissencephaly-1 mutations enhance traumatic brain injury outcomes in Drosophila. Genetics 2023; 223:iyad008. [PMID: 36683334 PMCID: PMC9991514 DOI: 10.1093/genetics/iyad008] [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] [Received: 11/14/2022] [Revised: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Traumatic brain injury (TBI) outcomes vary greatly among individuals, but most of the variation remains unexplained. Using a Drosophila melanogaster TBI model and 178 genetically diverse lines from the Drosophila Genetic Reference Panel (DGRP), we investigated the role that genetic variation plays in determining TBI outcomes. Following injury at 20-27 days old, DGRP lines varied considerably in mortality within 24 h ("early mortality"). Additionally, the disparity in early mortality resulting from injury at 20-27 vs 0-7 days old differed among DGRP lines. These data support a polygenic basis for differences in TBI outcomes, where some gene variants elicit their effects by acting on aging-related processes. Our genome-wide association study of DGRP lines identified associations between single nucleotide polymorphisms in Lissencephaly-1 (Lis-1) and Patronin and early mortality following injury at 20-27 days old. Lis-1 regulates dynein, a microtubule motor required for retrograde transport of many cargoes, and Patronin protects microtubule minus ends against depolymerization. While Patronin mutants did not affect early mortality, Lis-1 compound heterozygotes (Lis-1x/Lis-1y) had increased early mortality following injury at 20-27 or 0-7 days old compared with Lis-1 heterozygotes (Lis-1x/+), and flies that survived 24 h after injury had increased neurodegeneration but an unaltered lifespan, indicating that Lis-1 affects TBI outcomes independently of effects on aging. These data suggest that Lis-1 activity is required in the brain to ameliorate TBI outcomes through effects on axonal transport, microtubule stability, and other microtubule proteins, such as tau, implicated in chronic traumatic encephalopathy, a TBI-associated neurodegenerative disease in humans.
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Affiliation(s)
- Rebeccah J Katzenberger
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Barry Ganetzky
- Department of Genetics, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David A Wassarman
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
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30
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Hoedjes KM, Kostic H, Flatt T, Keller L. A Single Nucleotide Variant in the PPARγ-homolog Eip75B Affects Fecundity in Drosophila. Mol Biol Evol 2023; 40:7005670. [PMID: 36703226 PMCID: PMC9922802 DOI: 10.1093/molbev/msad018] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/04/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Single nucleotide polymorphisms are the most common type of genetic variation, but how these variants contribute to the adaptation of complex phenotypes is largely unknown. Experimental evolution and genome-wide association studies have demonstrated that variation in the PPARγ-homolog Eip75B has associated with longevity and life-history differences in the fruit fly Drosophila melanogaster. Using RNAi knockdown, we first demonstrate that reduced expression of Eip75B in adult flies affects lifespan, egg-laying rate, and egg volume. We then tested the effects of a naturally occurring SNP within a cis-regulatory domain of Eip75B by applying two complementary approaches: a Mendelian randomization approach using lines of the Drosophila Genetic Reference Panel, and allelic replacement using precise CRISPR/Cas9-induced genome editing. Our experiments reveal that this natural polymorphism has a significant pleiotropic effect on fecundity and egg-to-adult viability, but not on longevity or other life-history traits. Our results provide a rare functional validation at the nucleotide level and identify a natural allelic variant affecting fitness and life-history adaptation.
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Affiliation(s)
| | - Hristina Kostic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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31
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Pallares LF, Lea AJ, Han C, Filippova EV, Andolfatto P, Ayroles JF. Dietary stress remodels the genetic architecture of lifespan variation in outbred Drosophila. Nat Genet 2023; 55:123-129. [PMID: 36550361 DOI: 10.1038/s41588-022-01246-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Evolutionary theory suggests that lifespan-reducing alleles should be purged from the gene pool, and yet decades of genome-wide association and model organism studies have shown that they persist. One potential explanation is that alleles that regulate lifespan do so only in certain environmental contexts. We exposed outbred Drosophila to control and high-sugar diets and genotyped more than 10,000 adult flies to track allele frequency changes over the course of a single adult lifespan. We identified thousands of lifespan-associated alleles associated with early versus late-life trade-offs, late-onset effects and genotype-by-environment interactions. Remarkably, a third of lifespan-associated genetic variation had environmentally dependent effects on lifespan. We find that lifespan-reducing alleles are often recently derived, have stronger effects on a high-sugar diet and show signatures of selection in wild Drosophila populations, consistent with the evolutionary mismatch hypothesis. Our results provide insight into the highly polygenic and context-dependent genetic architecture of lifespan variation and the evolutionary processes that shape this key trait.
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Affiliation(s)
- Luisa F Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Amanda J Lea
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Clair Han
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Elena V Filippova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | - Julien F Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA.
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32
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Hoedjes KM, Kostic H, Keller L, Flatt T. Natural alleles at the Doa locus underpin evolutionary changes in Drosophila lifespan and fecundity. Proc Biol Sci 2022; 289:20221989. [PMID: 36350205 PMCID: PMC9653240 DOI: 10.1098/rspb.2022.1989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
'Evolve and resequence' (E&R) studies in Drosophila melanogaster have identified many candidate loci underlying the evolution of ageing and life history, but experiments that validate the effects of such candidates remain rare. In a recent E&R study we have identified several alleles of the LAMMER kinase Darkener of apricot (Doa) as candidates for evolutionary changes in lifespan and fecundity. Here, we use two complementary approaches to confirm a functional role of Doa in life-history evolution. First, we used transgenic RNAi to study the effects of Doa at the whole-gene level. Ubiquitous silencing of expression in adult flies reduced both lifespan and fecundity, indicating pleiotropic effects. Second, to characterize segregating variation at Doa, we examined four candidate single nucleotide polymorphisms (SNPs; Doa-1, -2, -3, -4) using a genetic association approach. Three candidate SNPs had effects that were qualitatively consistent with expectations based on our E&R study: Doa-2 pleiotropically affected both lifespan and late-life fecundity; Doa-1 affected lifespan (but not fecundity); and Doa-4 affected late-life fecundity (but not lifespan). Finally, the last candidate allele (Doa-3) also affected lifespan, but in the opposite direction from predicted.
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Affiliation(s)
- Katja M. Hoedjes
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hristina Kostic
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland,Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
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33
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Corbally MK, Regan JC. Fly immunity comes of age: The utility of Drosophila as a model for studying variation in immunosenescence. FRONTIERS IN AGING 2022; 3:1016962. [PMID: 36268532 PMCID: PMC9576847 DOI: 10.3389/fragi.2022.1016962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022]
Affiliation(s)
| | - Jennifer C. Regan
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
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34
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Shenoi VN, Brengdahl MI, Grace JL, Eriksson B, Rydén P, Friberg U. A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster. Proc Biol Sci 2022; 289:20212707. [PMID: 35538781 PMCID: PMC9091837 DOI: 10.1098/rspb.2021.2707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exposing sires to various environmental manipulations has demonstrated that paternal effects can be non-trivial also in species where male investment in offspring is almost exclusively limited to sperm. Whether paternal effects also have a genetic component (i.e. paternal indirect genetic effects (PIGEs)) in such species is however largely unknown, primarily because of methodological difficulties separating indirect from direct effects of genes. PIGEs may nevertheless be important since they have the capacity to contribute to evolutionary change. Here we use Drosophila genetics to construct a breeding design that allows testing nearly complete haploid genomes (more than 99%) for PIGEs. Using this technique, we estimate the variance in male lifespan due to PIGEs among four populations and compare this to the total paternal genetic variance (the sum of paternal indirect and direct genetic effects). Our results indicate that a substantial part of the total paternal genetic variance results from PIGEs. A screen of 38 haploid genomes, randomly sampled from a single population, suggests that PIGEs also influence variation in lifespan within populations. Collectively, our results demonstrate that PIGEs may constitute an underappreciated source of phenotypic variation.
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Affiliation(s)
| | | | - Jaime L. Grace
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Björn Eriksson
- Unit of Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 14, Box 102, 230 53 Alnarp, Sweden
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, 901 87 Umeå, Sweden,Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden
| | - Urban Friberg
- IFM Biology, Linköping University, 581 83 Linköping, Sweden
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35
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McHugh KM, Burke MK. From microbes to mammals: The experimental evolution of aging and longevity across species. Evolution 2022; 76:692-707. [PMID: 35112358 DOI: 10.1111/evo.14442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/09/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023]
Abstract
Senescence, the functional deterioration of cells or organisms associated with increased age, is pervasive across the tree of life. Yet our understanding of the genetic and physiological basis underlying age-related declines in health and reproduction remains limited. Experimental evolution allows empirical examination of the question of why aging occurs; imposing selection for age-specific fitness traits shifts patterns of aging in experimental populations, enabling investigations of the variation underlying senescence and the mechanisms governing it. Whole-genome sequencing of experimentally evolved populations may reveal candidate genomic variants underlying particular aging patterns; unfortunately, most study systems suffer from limitations that weaken associations between genotypes and phenotypes. In this review, we provide a survey of experimental evolution studies that have altered population-level patterns of reproductive timing and senescence in a variety of species. We discuss the specific selection conditions that have increased longevity, the phenotypic responses and trade-offs that accompany these increases, and examine genomic data collected from these experiments. Additionally, we consider how selected field studies complement laboratory experiments on life-history evolution. Finally, we address the strengths and weaknesses of existing study systems, and evaluate which model organisms appear most promising for future genomic investigations of the evolutionary biology of aging.
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Affiliation(s)
- Kaitlin M McHugh
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
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36
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Gabrawy MM, Khosravian N, Morcos GS, Morozova TV, Jezek M, Walston JD, Huang W, Abadir PM, Leips J. Genome-Wide Analysis in Drosophila Reveals the Genetic Basis of Variation in Age-Specific Physical Performance and Response to ACE Inhibition. Genes (Basel) 2022; 13:143. [PMID: 35052483 PMCID: PMC8775566 DOI: 10.3390/genes13010143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 01/20/2023] Open
Abstract
Despite impressive results in restoring physical performance in rodent models, treatment with renin-angiotensin system (RAS) inhibitors, such as Lisinopril, have highly mixed results in humans, likely, in part, due to genetic variation in human populations. To date, the genetic determinants of responses to drugs, such as RAS inhibitors, remain unknown. Given the complexity of the relationship between physical traits and genetic background, genomic studies which predict genotype- and age-specific responses to drug treatments in humans or vertebrate animals are difficult. Here, using 126 genetically distinct lines of Drosophila melanogaster, we tested the effects of Lisinopril on age-specific climbing speed and endurance. Our data show that functional response and sensitivity to Lisinopril treatment ranges from significant protection against physical decline to increased weakness depending on genotype and age. Furthermore, genome-wide analyses led to identification of evolutionarily conserved genes in the WNT signaling pathway as being significantly associated with variations in physical performance traits and sensitivity to Lisinopril treatment. Genetic knockdown of genes in the WNT signaling pathway, Axin, frizzled, nemo, and wingless, diminished or abolished the effects of Lisinopril treatment on climbing speed traits. Our results implicate these genes as contributors to the genotype- and age-specific effects of Lisinopril treatment and because they have orthologs in humans, they are potential therapeutic targets for improvement of resiliency. Our approach should be widely applicable for identifying genomic variants that predict age- and sex-dependent responses to any type of pharmaceutical treatment.
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Affiliation(s)
- Mariann M. Gabrawy
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA; (M.M.G.); (N.K.); (G.S.M.); (M.J.)
- Biology of Healthy Aging Program, Division of Geriatric Medicine and Gerontology, School of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA; (J.D.W.); (P.M.A.)
| | - Nick Khosravian
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA; (M.M.G.); (N.K.); (G.S.M.); (M.J.)
| | - George S. Morcos
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA; (M.M.G.); (N.K.); (G.S.M.); (M.J.)
| | - Tatiana V. Morozova
- Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA;
| | - Meagan Jezek
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA; (M.M.G.); (N.K.); (G.S.M.); (M.J.)
| | - Jeremy D. Walston
- Biology of Healthy Aging Program, Division of Geriatric Medicine and Gerontology, School of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA; (J.D.W.); (P.M.A.)
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA;
| | - Peter M. Abadir
- Biology of Healthy Aging Program, Division of Geriatric Medicine and Gerontology, School of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA; (J.D.W.); (P.M.A.)
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA; (M.M.G.); (N.K.); (G.S.M.); (M.J.)
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Willi Y, Kristensen TN, Sgrò CM, Weeks AR, Ørsted M, Hoffmann AA. Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species. Proc Natl Acad Sci U S A 2022; 119:e2105076119. [PMID: 34930821 PMCID: PMC8740573 DOI: 10.1073/pnas.2105076119] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Torsten N Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew R Weeks
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Cesar Australia, Brunswick, VIC 3056, Australia
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
- Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia;
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Jayaraj P, Sarkar P, Routh S, Sarathe C, Rajagopal D, Thirumurugan K. A promising discovery of anti-aging chemical conjugate derived from lipoic acid and sesamol established in Drosophila melanogaster. NEW J CHEM 2022. [DOI: 10.1039/d2nj00720g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phytonutrients, lipoic acid and sesamol, were chemically combined to yield medically important lipoic acid-sesamol conjugate (LSC). NMR and LC-MS/MS techniques were used to determine the chemical structure of LSC. The...
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Strachan EL, Mac White-Begg D, Crean J, Reynolds AL, Kennedy BN, O’Sullivan NC. The Role of Mitochondria in Optic Atrophy With Autosomal Inheritance. Front Neurosci 2021; 15:784987. [PMID: 34867178 PMCID: PMC8634724 DOI: 10.3389/fnins.2021.784987] [Citation(s) in RCA: 4] [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: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Optic atrophy (OA) with autosomal inheritance is a form of optic neuropathy characterized by the progressive and irreversible loss of vision. In some cases, this is accompanied by additional, typically neurological, extra-ocular symptoms. Underlying the loss of vision is the specific degeneration of the retinal ganglion cells (RGCs) which form the optic nerve. Whilst autosomal OA is genetically heterogenous, all currently identified causative genes appear to be associated with mitochondrial organization and function. However, it is unclear why RGCs are particularly vulnerable to mitochondrial aberration. Despite the relatively high prevalence of this disorder, there are currently no approved treatments. Combined with the lack of knowledge concerning the mechanisms through which aberrant mitochondrial function leads to RGC death, there remains a clear need for further research to identify the underlying mechanisms and develop treatments for this condition. This review summarizes the genes known to be causative of autosomal OA and the mitochondrial dysfunction caused by pathogenic mutations. Furthermore, we discuss the suitability of available in vivo models for autosomal OA with regards to both treatment development and furthering the understanding of autosomal OA pathology.
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Affiliation(s)
- Elin L. Strachan
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Delphi Mac White-Begg
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - John Crean
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Alison L. Reynolds
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Breandán N. Kennedy
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Niamh C. O’Sullivan
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
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Baker BM, Mokashi SS, Shankar V, Hatfield JS, Hannah RC, Mackay TFC, Anholt RRH. The Drosophila brain on cocaine at single-cell resolution. Genome Res 2021; 31:1927-1937. [PMID: 34035044 PMCID: PMC8494231 DOI: 10.1101/gr.268037.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/02/2021] [Indexed: 11/24/2022]
Abstract
Whereas the neurological effects of cocaine have been well documented, effects of acute cocaine consumption on genome-wide gene expression across the brain remain largely unexplored. This question cannot be readily addressed in humans but can be approached using the Drosophila melanogaster model, where gene expression in the entire brain can be surveyed at once. Flies exposed to cocaine show impaired locomotor activity, including climbing behavior and startle response (a measure of sensorimotor integration), and increased incidence of seizures and compulsive grooming. To identify specific cell populations that respond to acute cocaine exposure, we analyzed single-cell transcriptional responses in duplicate samples of flies that consumed fixed amounts of sucrose or sucrose supplemented with cocaine, in both sexes. Unsupervised clustering of the transcriptional profiles of a total of 86,224 cells yielded 36 distinct clusters. Annotation of clusters based on gene markers revealed that all major cell types (neuronal and glial) as well as neurotransmitter types from most brain regions were represented. The brain transcriptional responses to cocaine showed profound sexual dimorphism and were considerably more pronounced in males than females. Differential expression analysis within individual clusters indicated cluster-specific responses to cocaine. Clusters corresponding to Kenyon cells of the mushroom bodies and glia showed especially large transcriptional responses following cocaine exposure. Cluster specific coexpression networks and global interaction networks revealed a diverse array of cellular processes affected by acute cocaine exposure. These results provide an atlas of sexually dimorphic cocaine-modulated gene expression in a model brain.
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Affiliation(s)
- Brandon M Baker
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646, USA
| | - Sneha S Mokashi
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646, USA
| | - Vijay Shankar
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646, USA
| | - Jeffrey S Hatfield
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646, USA
| | - Rachel C Hannah
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646, USA
| | - Trudy F C Mackay
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646, USA
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Marderstein AR, Kulm S, Peng C, Tamimi R, Clark AG, Elemento O. A polygenic-score-based approach for identification of gene-drug interactions stratifying breast cancer risk. Am J Hum Genet 2021; 108:1752-1764. [PMID: 34363748 PMCID: PMC8456164 DOI: 10.1016/j.ajhg.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022] Open
Abstract
An individual's genetics can dramatically influence breast cancer (BC) risk. Although clinical measures for prevention do exist, non-invasive personalized measures for reducing BC risk are limited. Commonly used medications are a promising set of modifiable factors, but no previous study has explored whether a range of widely taken approved drugs modulate BC genetics. In this study, we describe a quantitative framework for exploring the interaction between the genetic susceptibility of BC and medication usage among UK Biobank women. We computed BC polygenic scores (PGSs) that summarize BC genetic risk and find that the PGS explains nearly three-times greater variation in disease risk within corticosteroid users compared to non-users. We map 35 genes significantly interacting with corticosteroid use (FDR < 0.1), highlighting the transcription factor NRF2 as a common regulator of gene-corticosteroid interactions in BC. Finally, we discover a regulatory variant strongly stratifying BC risk according to corticosteroid use. Within risk allele carriers, 18.2% of women taking corticosteroids developed BC, compared to 5.1% of the non-users (with an HR = 3.41 per-allele within corticosteroid users). In comparison, there are no differences in BC risk within the reference allele homozygotes. Overall, this work highlights the clinical relevance of gene-drug interactions in disease risk and provides a roadmap for repurposing biobanks in drug repositioning and precision medicine.
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Affiliation(s)
- Andrew R Marderstein
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Scott Kulm
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Cheng Peng
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Rulla Tamimi
- Population Health Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew G Clark
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA.
| | - Olivier Elemento
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
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Hoffman JM, Dudeck SK, Patterson HK, Austad SN. Sex, mating and repeatability of Drosophila melanogaster longevity. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210273. [PMID: 34457337 PMCID: PMC8371361 DOI: 10.1098/rsos.210273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/26/2021] [Indexed: 05/25/2023]
Abstract
Costs of reproduction are seemingly ubiquitous across the animal kingdom, and these reproductive costs are generally defined by increased reproduction leading to decreases in other fitness components, often longevity. However, some recent reports question whether reproductive costs exist in every species or population. To provide insight on this issue, we sought to determine the extent to which genetic variation might play a role in one type of reproductive cost-survival-using Drosophila melanogaster. We found, surprisingly, no costs of reproduction nor sex differences in longevity across all 15 genetic backgrounds in two cohorts. We did find significant variation within some genotypes, though these were much smaller than expected. We also observed that small laboratory changes lead to significant changes in longevity within genotypes, suggesting that longevity repeatability in flies may be difficult. We finally compared our results to previously published longevities and found that reproducibility is similar to what we saw in our own laboratory, further suggesting that stochasticity is a strong component of fruit fly lifespan. Overall, our results suggest that there are still large gaps in our knowledge about the effects of sex and mating, as well as genetic background and laboratory conditions on lifespan reproducibility.
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Affiliation(s)
- Jessica M. Hoffman
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Steven N. Austad
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
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Weller CA, Tilk S, Rajpurohit S, Bergland AO. Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations. G3-GENES GENOMES GENETICS 2021; 11:6156828. [PMID: 33677482 PMCID: PMC8759814 DOI: 10.1093/g3journal/jkab062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/19/2021] [Indexed: 11/27/2022]
Abstract
Genetic association studies seek to uncover the link between genotype and phenotype, and often utilize inbred reference panels as a replicable source of genetic variation. However, inbred reference panels can differ substantially from wild populations in their genotypic distribution, patterns of linkage-disequilibrium, and nucleotide diversity. As a result, associations discovered using inbred reference panels may not reflect the genetic basis of phenotypic variation in natural populations. To address this problem, we evaluated a mapping population design where dozens to hundreds of inbred lines are outbred for few generations, which we call the Hybrid Swarm. The Hybrid Swarm approach has likely remained underutilized relative to pre-sequenced inbred lines due to the costs of genome-wide genotyping. To reduce sequencing costs and make the Hybrid Swarm approach feasible, we developed a computational pipeline that reconstructs accurate whole genomes from ultra-low-coverage (0.05X) sequence data in Hybrid Swarm populations derived from ancestors with phased haplotypes. We evaluate reconstructions using genetic variation from the Drosophila Genetic Reference Panel as well as variation from neutral simulations. We compared the power and precision of Genome-Wide Association Studies using the Hybrid Swarm, inbred lines, recombinant inbred lines (RILs), and highly outbred populations across a range of allele frequencies, effect sizes, and genetic architectures. Our simulations show that these different mapping panels vary in their power and precision, largely depending on the architecture of the trait. The Hybrid Swam and RILs outperform inbred lines for quantitative traits, but not for monogenic ones. Taken together, our results demonstrate the feasibility of the Hybrid Swarm as a cost-effective method of fine-scale genetic mapping.
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Affiliation(s)
- Cory A Weller
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Susanne Tilk
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Subhash Rajpurohit
- Department of Biological and Life Sciences, Ahmedabad University, Ahmedabad 380009, India
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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Patel SP, Talbert ME. Identification of genetic modifiers of lifespan on a high sugar diet in the Drosophila Genetic Reference Panel. Heliyon 2021; 7:e07153. [PMID: 34141921 PMCID: PMC8187823 DOI: 10.1016/j.heliyon.2021.e07153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/12/2021] [Accepted: 05/24/2021] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies (GWAS) have become beneficial in identifying genetic variants underlying susceptibility to various complex diseases and conditions, including obesity. Utilizing the Drosophila Genetic Reference Panel (DGRP), we performed a GWAS of lifespan of 193 genetically distinct lines on a high sugar diet (HSD). The DGRP analysis pipeline determined the most significant lifespan associated polymorphisms were within loci of genes involved in: neural processes, behavior, development, and apoptosis, among other functions. Next, based on the relevance to obesity pathology, and the availability of transgenic RNAi lines targeting the genes we identified, whole-body in vivo knockdown of several candidate genes was performed. We utilized the GAL4-UAS binary expression system to independently validate the impacts of these loci on Drosophila lifespan during HSD. These loci were largely confirmed to affect lifespan in that HSD setting, as well as a normal diet setting. However, we also detected unexpected dietary effects of the HSD, including inconsistent diet effects on lifespan relative to a normal diet and a strong downregulation of feeding quantity.
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Genotype and Trait Specific Responses to Rapamycin Intake in Drosophila melanogaster. INSECTS 2021; 12:insects12050474. [PMID: 34065203 PMCID: PMC8161023 DOI: 10.3390/insects12050474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022]
Abstract
Simple Summary Rapamycin is commonly used as an immunosuppressant, but also as an anti-aging medicine. Despite its widespread use, results suggest that there is large variability in drug efficiency among patients, and limited knowledge exists about potential side-effects. In the present study, we investigated the effects of rapamycin using the common fruit fly as model organism. Six genetically distinct lines were exposed to rapamycin, and the phenotypic consequence on fecundity, longevity and heat stress tolerance was quantified. Flies exposed to rapamycin had increased longevity and heat stress tolerance, however a side effect in the form of decreased fecundity was also observed. Our data clearly show that the costs and benefits of rapamycin treatment is strongly genotype dependent. These observations are important as they imply that a ‘one size fits all’ approach when it comes to rapamycin treatment is not advisable. Future studies should address the underlying genetic component that drive the drug response variability. Abstract Rapamycin is a powerful inhibitor of the TOR (Target of Rapamycin) pathway, which is an evolutionarily conserved protein kinase, that plays a central role in plants and animals. Rapamycin is used globally as an immunosuppressant and as an anti-aging medicine. Despite widespread use, treatment efficiency varies considerably across patients, and little is known about potential side effects. Here we seek to investigate the effects of rapamycin by using Drosophila melanogaster as model system. Six isogenic D. melanogaster lines were assessed for their fecundity, male longevity and male heat stress tolerance with or without rapamycin treatment. The results showed increased longevity and heat stress tolerance for male flies treated with rapamycin. Conversely, the fecundity of rapamycin-exposed individuals was lower than for flies from the non-treated group, suggesting unwanted side effects of the drug in D. melanogaster. We found strong evidence for genotype-by-treatment interactions suggesting that a ‘one size fits all’ approach when it comes to treatment with rapamycin is not recommendable. The beneficial responses to rapamycin exposure for stress tolerance and longevity are in agreement with previous findings, however, the unexpected effects on reproduction are worrying and need further investigation and question common believes that rapamycin constitutes a harmless drug.
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Hoffmann AA, Miller AD, Weeks AR. Genetic mixing for population management: From genetic rescue to provenancing. Evol Appl 2021; 14:634-652. [PMID: 33767740 PMCID: PMC7980264 DOI: 10.1111/eva.13154] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/10/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.
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Affiliation(s)
- Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityWarrnamboolVic.Australia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | - Andrew R. Weeks
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
- cesar Pty LtdParkvilleVic.Australia
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Bird KA. No support for the hereditarian hypothesis of the Black-White achievement gap using polygenic scores and tests for divergent selection. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:465-476. [PMID: 33529393 DOI: 10.1002/ajpa.24216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/27/2020] [Accepted: 12/20/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Debate about the cause of IQ score gaps between Black and White populations has persisted within genetics, anthropology, and psychology. Recently, authors claimed polygenic scores provide evidence that a significant portion of differences in cognitive performance between Black and White populations are caused by genetic differences due to natural selection, the "hereditarian hypothesis." This study aims to show conceptual and methodological flaws of past studies supporting the hereditarian hypothesis. MATERIALS AND METHODS Polygenic scores for educational attainment were constructed for African and European samples of the 1000 Genomes Project. Evidence for selection was evaluated using an excess variance test. Education associated variants were further evaluated for signals of selection by testing for excess genetic differentiation (Fst ). Expected mean difference in IQ for populations was calculated under a neutral evolutionary scenario and contrasted to hereditarian claims. RESULTS Tests for selection using polygenic scores failed to find evidence of natural selection when the less biased within-family GWAS effect sizes were used. Tests for selection using Fst values did not find evidence of natural selection. Expected mean difference in IQ was substantially smaller than postulated by hereditarians, even under unrealistic assumptions that overestimate genetic contribution. CONCLUSION Given these results, hereditarian claims are not supported in the least. Cognitive performance does not appear to have been under diversifying selection in Europeans and Africans. In the absence of diversifying selection, the best case estimate for genetic contributions to group differences in cognitive performance is substantially smaller than hereditarians claim and is consistent with genetic differences contributing little to the Black-White gap.
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Affiliation(s)
- Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA.,Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, Michigan, USA
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Marderstein AR, Davenport ER, Kulm S, Van Hout CV, Elemento O, Clark AG. Leveraging phenotypic variability to identify genetic interactions in human phenotypes. Am J Hum Genet 2021; 108:49-67. [PMID: 33326753 PMCID: PMC7820920 DOI: 10.1016/j.ajhg.2020.11.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Although thousands of loci have been associated with human phenotypes, the role of gene-environment (GxE) interactions in determining individual risk of human diseases remains unclear. This is partly because of the severe erosion of statistical power resulting from the massive number of statistical tests required to detect such interactions. Here, we focus on improving the power of GxE tests by developing a statistical framework for assessing quantitative trait loci (QTLs) associated with the trait means and/or trait variances. When applying this framework to body mass index (BMI), we find that GxE discovery and replication rates are significantly higher when prioritizing genetic variants associated with the variance of the phenotype (vQTLs) compared to when assessing all genetic variants. Moreover, we find that vQTLs are enriched for associations with other non-BMI phenotypes having strong environmental influences, such as diabetes or ulcerative colitis. We show that GxE effects first identified in quantitative traits such as BMI can be used for GxE discovery in disease phenotypes such as diabetes. A clear conclusion is that strong GxE interactions mediate the genetic contribution to body weight and diabetes risk.
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Affiliation(s)
- Andrew R Marderstein
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Emily R Davenport
- Department of Biology, Huck Institutes of the Life Sciences, Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Scott Kulm
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA.
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Parker GA, Kohn N, Spirina A, McMillen A, Huang W, Mackay TFC. Genetic Basis of Increased Lifespan and Postponed Senescence in Drosophila melanogaster. G3 (BETHESDA, MD.) 2020; 10:1087-1098. [PMID: 31969430 PMCID: PMC7056975 DOI: 10.1534/g3.120.401041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/21/2020] [Indexed: 01/14/2023]
Abstract
Limited lifespan and senescence are near-universal phenomena. These quantitative traits exhibit variation in natural populations due to the segregation of many interacting loci and from environmental effects. Due to the complexity of the genetic control of lifespan and senescence, our understanding of the genetic basis of variation in these traits is incomplete. Here, we analyzed the pattern of genetic divergence between long-lived (O) Drosophila melanogaster lines selected for postponed reproductive senescence and unselected control (B) lines. We quantified the productivity of the O and B lines and found that reproductive senescence is maternally controlled. We therefore chose 57 candidate genes that are expressed in ovaries, 49 of which have human orthologs, and assessed the effects of RNA interference in ovaries and accessary glands on lifespan and reproduction. All but one candidate gene affected at least one life history trait in one sex or productivity week. In addition, 23 genes had antagonistic pleiotropic effects on lifespan and productivity. Identifying evolutionarily conserved genes affecting increased lifespan and delayed reproductive senescence is the first step toward understanding the evolutionary forces that maintain segregating variation at these loci in nature and may provide potential targets for therapeutic intervention to delay senescence while increasing lifespan.
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Affiliation(s)
- Grace A Parker
- Department of Biological Sciences
- Program in Genetics
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, 27695 and
| | | | | | | | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, Michigan, 48824
| | - Trudy F C Mackay
- Department of Biological Sciences,
- Program in Genetics
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, 27695 and
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