102
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Alexandrov T. Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence. Annu Rev Biomed Data Sci 2020; 3:61-87. [PMID: 34056560 DOI: 10.1146/annurev-biodatasci-011420-031537] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spatial metabolomics is an emerging field of omics research that has enabled localizing metabolites, lipids, and drugs in tissue sections, a feat considered impossible just two decades ago. Spatial metabolomics and its enabling technology-imaging mass spectrometry-generate big hyper-spectral imaging data that have motivated the development of tailored computational methods at the intersection of computational metabolomics and image analysis. Experimental and computational developments have recently opened doors to applications of spatial metabolomics in life sciences and biomedicine. At the same time, these advances have coincided with a rapid evolution in machine learning, deep learning, and artificial intelligence, which are transforming our everyday life and promise to revolutionize biology and healthcare. Here, we introduce spatial metabolomics through the eyes of a computational scientist, review the outstanding challenges, provide a look into the future, and discuss opportunities granted by the ongoing convergence of human and artificial intelligence.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA
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103
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Redhai S, Pilgrim C, Gaspar P, Giesen LV, Lopes T, Riabinina O, Grenier T, Milona A, Chanana B, Swadling JB, Wang YF, Dahalan F, Yuan M, Wilsch-Brauninger M, Lin WH, Dennison N, Capriotti P, Lawniczak MKN, Baines RA, Warnecke T, Windbichler N, Leulier F, Bellono NW, Miguel-Aliaga I. An intestinal zinc sensor regulates food intake and developmental growth. Nature 2020; 580:263-268. [PMID: 32269334 PMCID: PMC8833092 DOI: 10.1038/s41586-020-2111-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 02/18/2020] [Indexed: 12/13/2022]
Abstract
In cells, organs and whole organisms, nutrient sensing is key to maintaining homeostasis and adapting to a fluctuating environment1. In many animals, nutrient sensors are found within the enteroendocrine cells of the digestive system; however, less is known about nutrient sensing in their cellular siblings, the absorptive enterocytes1. Here we use a genetic screen in Drosophila melanogaster to identify Hodor, an ionotropic receptor in enterocytes that sustains larval development, particularly in nutrient-scarce conditions. Experiments in Xenopus oocytes and flies indicate that Hodor is a pH-sensitive, zinc-gated chloride channel that mediates a previously unrecognized dietary preference for zinc. Hodor controls systemic growth from a subset of enterocytes-interstitial cells-by promoting food intake and insulin/IGF signalling. Although Hodor sustains gut luminal acidity and restrains microbial loads, its effect on systemic growth results from the modulation of Tor signalling and lysosomal homeostasis within interstitial cells. Hodor-like genes are insect-specific, and may represent targets for the control of disease vectors. Indeed, CRISPR-Cas9 genome editing revealed that the single hodor orthologue in Anopheles gambiae is an essential gene. Our findings highlight the need to consider the instructive contributions of metals-and, more generally, micronutrients-to energy homeostasis.
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Affiliation(s)
- Siamak Redhai
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Clare Pilgrim
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Pedro Gaspar
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Lena van Giesen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Tatiana Lopes
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Olena Riabinina
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Department of Biosciences, Durham University, Durham, UK
| | - Théodore Grenier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, ENS de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Bhavna Chanana
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Jacob B Swadling
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, London, UK
| | - Farah Dahalan
- Department of Life Sciences, Imperial College London, London, UK
- Malaria Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Michaela Yuan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Wei-Hsiang Lin
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Nathan Dennison
- Department of Life Sciences, Imperial College London, London, UK
| | - Paolo Capriotti
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Richard A Baines
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Tobias Warnecke
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | | | - Francois Leulier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, ENS de Lyon, CNRS UMR 5242, Lyon, France
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Irene Miguel-Aliaga
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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105
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The Drosophila Post-mating Response: Gene Expression and Behavioral Changes Reveal Perdurance and Variation in Cross-Tissue Interactions. G3-GENES GENOMES GENETICS 2020; 10:967-983. [PMID: 31907222 PMCID: PMC7056969 DOI: 10.1534/g3.119.400963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Examining cross-tissue interactions is important for understanding physiology and homeostasis. In animals, the female gonad produces signaling molecules that act distally. We examine gene expression in Drosophila melanogaster female head tissues in 1) virgins without a germline compared to virgins with a germline, 2) post-mated females with and without a germline compared to virgins, and 3) post-mated females mated to males with and without a germline compared to virgins. In virgins, the absence of a female germline results in expression changes in genes with known roles in nutrient homeostasis. At one- and three-day(s) post-mating, genes that change expression are enriched with those that function in metabolic pathways, in all conditions. We systematically examine female post-mating impacts on sleep, food preference and re-mating, in the strains and time points used for gene expression analyses and compare to published studies. We show that post-mating, gene expression changes vary by strain, prompting us to examine variation in female re-mating. We perform a genome-wide association study that identifies several DNA polymorphisms, including four in/near Wnt signaling pathway genes. Together, these data reveal how gene expression and behavior in females are influenced by cross-tissue interactions, by examining the impact of mating, fertility, and genotype.
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106
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Belmonte RL, Corbally MK, Duneau DF, Regan JC. Sexual Dimorphisms in Innate Immunity and Responses to Infection in Drosophila melanogaster. Front Immunol 2020; 10:3075. [PMID: 32076419 PMCID: PMC7006818 DOI: 10.3389/fimmu.2019.03075] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/16/2019] [Indexed: 12/20/2022] Open
Abstract
The sexes show profound differences in responses to infection and the development of autoimmunity. Dimorphisms in immune responses are ubiquitous across taxa, from arthropods to vertebrates. Drosophila melanogaster shows strong sex dimorphisms in immune system responses at baseline, upon pathogenic challenge, and over aging. We have performed an exhaustive survey of peer-reviewed literature on Drosophila immunity, and present a database of publications indicating the sex(es) analyzed in each study. While we found a growing interest in the community in adult immunity and in reporting both sexes, the main body of work in this field uses only one sex, or does not stratify by sex. We synthesize evidence for sexually dimorphic responses to bacterial, viral, and fungal infections. Dimorphisms may be mediated by distinct immune compartments, and we review work on sex differences in behavioral, epithelial, cellular, and systemic (fat body-mediated) immunity. Emerging work on sexually dimorphic aging of immune tissues, immune senescence, and inflammation are examined. We consider evolutionary drivers for sex differences in immune investment, highlight the features of Drosophila biology that make it particularly amenable to studies of immune dimorphisms, and discuss areas for future exploration.
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Affiliation(s)
- Rebecca L. Belmonte
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Mary-Kate Corbally
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | - David F. Duneau
- Laboratoire Evolution & Diversite Biologique, UMR5174 EDB, CNRS, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Jennifer C. Regan
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, United Kingdom
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107
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Vásquez-Procopio J, Osorio B, Cortés-Martínez L, Hernández-Hernández F, Medina-Contreras O, Ríos-Castro E, Comjean A, Li F, Hu Y, Mohr S, Perrimon N, Missirlis F. Intestinal response to dietary manganese depletion inDrosophila. Metallomics 2020; 12:218-240. [DOI: 10.1039/c9mt00218a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metabolic adaptations to manganese deficiency.
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108
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Mohr SE, Perrimon N. Drosophila melanogaster: a simple system for understanding complexity. Dis Model Mech 2019; 12:12/10/dmm041871. [PMID: 31562251 PMCID: PMC6826030 DOI: 10.1242/dmm.041871] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Understanding human gene function is fundamental to understanding and treating diseases. Research using the model organism Drosophila melanogaster benefits from a wealth of molecular genetic resources and information useful for efficient invivo experimentation. Moreover, Drosophila offers a balance as a relatively simple organism that nonetheless exhibits complex multicellular activities. Recent examples demonstrate the power and continued promise of Drosophila research to further our understanding of conserved gene functions. Summary: This Editorial outlines how research in Drosophila has and continues to help answer complex research questions in genetics, highlighting the value of this relatively simple model organism.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Drosophila RNAi Screening Center, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA .,Drosophila RNAi Screening Center, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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