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Rai M, Li H, Policastro RA, Pepin R, Zentner GE, Nemkov T, D’Alessandro A, Tennessen JM. Glycolytic disruption restricts Drosophila melanogaster larval growth via the cytokine Upd3. PLoS Genet 2025; 21:e1011690. [PMID: 40315265 PMCID: PMC12068724 DOI: 10.1371/journal.pgen.1011690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 05/12/2025] [Accepted: 04/15/2025] [Indexed: 05/04/2025] Open
Abstract
Drosophila larval growth requires efficient conversion of dietary nutrients into biomass. Lactate dehydrogenase (Ldh) and glycerol-3-phosphate dehydrogenase (Gpdh1) support this larval metabolic program by cooperatively promoting glycolytic flux. Consistent with their cooperative functions, the loss of both enzymes, but not either single enzyme alone, induces a developmental arrest. However, Ldh and Gpdh1 exhibit complex and often mutually exclusive expression patterns, suggesting that the lethal phenotypes exhibited by Gpdh1; Ldh double mutants could be mediated non-autonomously. Supporting this possibility, we find that the developmental arrest displayed by double mutants extends beyond simple metabolic disruption and instead stems, in part, from changes in systemic growth factor signaling. Specifically, we demonstrate that the simultaneous loss of Gpdh1 and Ldh results in elevated expression of Upd3, a cytokine involved in Jak/Stat signaling. Furthermore, we show that upd3 loss-of-function mutations suppress the Gpdh1; Ldh larval arrest phenotype, indicating that Upd3 signaling restricts larval development in response to decreased glycolytic flux. Together, our findings reveal a mechanism by which metabolic disruptions can modulate systemic growth factor signaling.
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Affiliation(s)
- Madhulika Rai
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Hongde Li
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Robert A. Policastro
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Robert Pepin
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jason M. Tennessen
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- Member, Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
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2
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Huang K, Miao T, Dantas E, Han M, Hu Y, Wang K, Sanford J, Goncalves M, Perrimon N. Lipid metabolism of hepatocyte-like cells supports intestinal tumor growth by promoting tracheogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.04.647255. [PMID: 40236168 PMCID: PMC11996582 DOI: 10.1101/2025.04.04.647255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Tumors require metabolic adaptations to support their rapid growth, but how they influence lipid metabolism in distant tissues remains poorly understood. Here, we uncover a novel mechanism by which gut tumors in adult flies reprogram lipid metabolism in distal hepatocyte-like cells, known as oenocytes, to promote tracheal development and tumor growth. We show that tumors secrete a PDGF/VEGF-like factor, Pvf1, that activates the TORC1-Hnf4 signaling pathway in oenocytes. This activation enhances the production of specific lipids, including very long-chain fatty acids and wax esters, that are required for tracheal growth surrounding the gut tumor. Importantly, reducing expression in oenocytes of either the transcription factor Hnf4 , or the elongase mElo that generates very long chain fatty acid suppresses tumor growth, tracheogenesis, and associated organ wasting/cachexia-like phenotypes, while extending lifespan. We further demonstrate that this regulatory pathway is conserved in mammals, as VEGF-A stimulates lipid metabolism gene expression in human hepatocytes, and lung tumor-bearing mice show increased hepatic expression of Hnf4 and the lipid elongation gene Elovl7 . Our findings reveal a previously unrecognized tumor-host interaction where tumors non-autonomously reprogram distal lipid metabolism to support their growth. This study not only identifies a novel non-autonomous role of the TORC1-Hnf4 axis in lipid-mediated tumor progression but also highlights potential targets for therapeutic intervention in cancer-associated metabolic disorders.
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3
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Ding G, Li Y, Cheng C, Tan K, Deng Y, Pang H, Wang Z, Dang P, Wu X, Rushworth E, Yuan Y, Yang Z, Song W. A tumor-secreted protein utilizes glucagon release to cause host wasting. Cell Discov 2025; 11:11. [PMID: 39924534 PMCID: PMC11808122 DOI: 10.1038/s41421-024-00762-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 12/23/2024] [Indexed: 02/11/2025] Open
Abstract
Tumor‒host interaction plays a critical role in malignant tumor-induced organ wasting across multiple species. Despite known regulation of regional wasting of individual peripheral organs by tumors, whether and how tumors utilize critical host catabolic hormone(s) to simultaneously induce systemic host wasting, is largely unknown. Using the conserved yki3SA-tumor model in Drosophila, we discovered that tumors increase the production of adipokinetic hormone (Akh), a glucagon-like catabolic hormone, to cause systemic host wasting, including muscle dysfunction, lipid loss, hyperglycemia, and ovary atrophy. We next integrated RNAi screening and Gal4-LexA dual expression system to show that yki3SA-gut tumors secrete Pvf1 to remotely activate its receptor Pvr in Akh-producing cells (APCs), ultimately promoting Akh production. The underlying molecular mechanisms involved the Pvf1-Pvr axis that triggers Mmp2-dependent ECM remodeling of APCs and enhances innervation from the excitatory cholinergic neurons. Interestingly, we also confirmed the similar mechanisms governing tumor-induced glucagon release and organ wasting in mammals. Blockade of either glucagon or PDGFR (homolog of Pvr) action efficiently ameliorated organ wasting in the presence of malignant tumors. Therefore, our results demonstrate that tumors remotely promote neural-associated Akh/glucagon production via Pvf1-Pvr axis to cause systemic host wasting.
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Affiliation(s)
- Guangming Ding
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yingge Li
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chen Cheng
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Kai Tan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
| | - Yifei Deng
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
| | - Huiwen Pang
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Zhongyuan Wang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Peixuan Dang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xing Wu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
| | - Elisabeth Rushworth
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China.
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
| | - Zhiyong Yang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China.
| | - Wei Song
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China.
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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4
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Hu Y, Comjean A, Rodiger J, Chen W, Kim AR, Qadiri M, Gao C, Zirin J, Mohr S, Perrimon N. FlyRNAi.org 2025 update-expanded resources for new technologies and species. Nucleic Acids Res 2025; 53:D958-D965. [PMID: 39435987 PMCID: PMC11701652 DOI: 10.1093/nar/gkae917] [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: 08/14/2024] [Revised: 09/18/2024] [Accepted: 10/03/2024] [Indexed: 10/23/2024] Open
Abstract
The design, analysis and mining of large-scale 'omics studies with the goal of advancing biological and biomedical understanding require use of a range of bioinformatics tools, including approaches tailored to needs specific to a given species and/or technology. The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) Functional Genomics Resources (https://fgr.hms.harvard.edu/tools) supports an increasingly broad group of technologies and species. Recently, for example, we expanded the database to include additional new data-centric resources that facilitate mining and analysis of single-cell transcriptomics. In addition, we have applied our approaches to CRISPR reagent and gene-centric bioinformatics approaches in Drosophila to arthropod vectors of infectious diseases. Building on our previous comprehensive reports on the FlyRNAi database, here we focus on new and updated resources with a primary focus on data-centric tools. Altogether, our suite of online resources supports various stages of functional genomics studies for Drosophila and other arthropods, and facilitate a wide range of reagent design, analysis, data mining and analysis approaches by biologists and biomedical experts studying Drosophila, other common genetic model species, arthropod vectors and/or human biology.
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Affiliation(s)
- Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- LifeMine Therapeutics, 30 Acorn Park Dr, Cambridge, MA 02140, USA
| | - Weihang Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ah-Ram Kim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Mujeeb Qadiri
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Chenxi Gao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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5
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Vonolfen MC, Meyer Zu Altenschildesche FL, Nam HJ, Brodesser S, Gyenis A, Buellesbach J, Lam G, Thummel CS, Storelli G. Drosophila HNF4 acts in distinct tissues to direct a switch between lipid storage and export in the gut. Cell Rep 2024; 43:114693. [PMID: 39235946 DOI: 10.1016/j.celrep.2024.114693] [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: 03/26/2024] [Revised: 07/15/2024] [Accepted: 08/13/2024] [Indexed: 09/07/2024] Open
Abstract
Nutrient digestion, absorption, and export must be coordinated in the gut to meet the nutritional needs of the organism. We used the Drosophila intestine to characterize the mechanisms that coordinate the fate of dietary lipids. We identified enterocytes specialized in absorbing and exporting lipids to peripheral organs. Distinct hepatocyte-like cells, called oenocytes, communicate with these enterocytes to adjust intestinal lipid storage and export. A single transcription factor, Drosophila hepatocyte nuclear factor 4 (dHNF4), supports this gut-liver axis. In enterocytes, dHNF4 maximizes dietary lipid export by preventing their sequestration in cytoplasmic lipid droplets. In oenocytes, dHNF4 promotes the expression of the insulin antagonist ImpL2 to activate Foxo and suppress lipid retention in enterocytes. Disruption of this switch between lipid storage and export is associated with intestinal inflammation, suggesting a lipidic origin for inflammatory bowel diseases. These studies establish dHNF4 as a central regulator of intestinal metabolism and inter-organ lipid trafficking.
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Affiliation(s)
- Maximilian C Vonolfen
- University of Cologne, Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Fenja L Meyer Zu Altenschildesche
- University of Cologne, Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Hyuck-Jin Nam
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA
| | - Susanne Brodesser
- University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Akos Gyenis
- University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Jan Buellesbach
- Institute for Evolution & Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany
| | - Geanette Lam
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA
| | - Carl S Thummel
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA
| | - Gilles Storelli
- University of Cologne, Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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6
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Xu J, Liu Y, Yang F, Cao Y, Chen W, Li JSS, Zhang S, Comjean A, Hu Y, Perrimon N. Mechanistic characterization of a Drosophila model of paraneoplastic nephrotic syndrome. Nat Commun 2024; 15:1241. [PMID: 38336808 PMCID: PMC10858251 DOI: 10.1038/s41467-024-45493-8] [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: 04/11/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Paraneoplastic syndromes occur in cancer patients and originate from dysfunction of organs at a distance from the tumor or its metastasis. A wide range of organs can be affected in paraneoplastic syndromes; however, the pathological mechanisms by which tumors influence host organs are poorly understood. Recent studies in the fly uncovered that tumor secreted factors target host organs, leading to pathological effects. In this study, using a Drosophila gut tumor model, we characterize a mechanism of tumor-induced kidney dysfunction. Specifically, we find that Pvf1, a PDGF/VEGF signaling ligand, secreted by gut tumors activates the PvR/JNK/Jra signaling pathway in the principal cells of the kidney, leading to mis-expression of renal genes and paraneoplastic renal syndrome-like phenotypes. Our study describes an important mechanism by which gut tumors perturb the function of the kidney, which might be of clinical relevance for the treatment of paraneoplastic syndromes.
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Affiliation(s)
- Jun Xu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Ying Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Fangying Yang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yurou Cao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weihang Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joshua Shing Shun Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shuai Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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7
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Sun C, Shao Y, Iqbal J. Insect Insights at the Single-Cell Level: Technologies and Applications. Cells 2023; 13:91. [PMID: 38201295 PMCID: PMC10777908 DOI: 10.3390/cells13010091] [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: 11/22/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Single-cell techniques are a promising way to unravel the complexity and heterogeneity of transcripts at the cellular level and to reveal the composition of different cell types and functions in a tissue or organ. In recent years, advances in single-cell RNA sequencing (scRNA-seq) have further changed our view of biological systems. The application of scRNA-seq in insects enables the comprehensive characterization of both common and rare cell types and cell states, the discovery of new cell types, and revealing how cell types relate to each other. The recent application of scRNA-seq techniques to insect tissues has led to a number of exciting discoveries. Here we provide an overview of scRNA-seq and its application in insect research, focusing on biological applications, current challenges, and future opportunities to make new discoveries with scRNA-seq in insects.
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Affiliation(s)
- Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Yongqi Shao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junaid Iqbal
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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8
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Aromolaran OT, Isewon I, Adedeji E, Oswald M, Adebiyi E, Koenig R, Oyelade J. Heuristic-enabled active machine learning: A case study of predicting essential developmental stage and immune response genes in Drosophila melanogaster. PLoS One 2023; 18:e0288023. [PMID: 37556452 PMCID: PMC10411809 DOI: 10.1371/journal.pone.0288023] [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: 04/03/2023] [Accepted: 06/18/2023] [Indexed: 08/11/2023] Open
Abstract
Computational prediction of absolute essential genes using machine learning has gained wide attention in recent years. However, essential genes are mostly conditional and not absolute. Experimental techniques provide a reliable approach of identifying conditionally essential genes; however, experimental methods are laborious, time and resource consuming, hence computational techniques have been used to complement the experimental methods. Computational techniques such as supervised machine learning, or flux balance analysis are grossly limited due to the unavailability of required data for training the model or simulating the conditions for gene essentiality. This study developed a heuristic-enabled active machine learning method based on a light gradient boosting model to predict essential immune response and embryonic developmental genes in Drosophila melanogaster. We proposed a new sampling selection technique and introduced a heuristic function which replaces the human component in traditional active learning models. The heuristic function dynamically selects the unlabelled samples to improve the performance of the classifier in the next iteration. Testing the proposed model with four benchmark datasets, the proposed model showed superior performance when compared to traditional active learning models (random sampling and uncertainty sampling). Applying the model to identify conditionally essential genes, four novel essential immune response genes and a list of 48 novel genes that are essential in embryonic developmental condition were identified. We performed functional enrichment analysis of the predicted genes to elucidate their biological processes and the result evidence our predictions. Immune response and embryonic development related processes were significantly enriched in the essential immune response and embryonic developmental genes, respectively. Finally, we propose the predicted essential genes for future experimental studies and use of the developed tool accessible at http://heal.covenantuniversity.edu.ng for conditional essentiality predictions.
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Affiliation(s)
- Olufemi Tony Aromolaran
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Itunu Isewon
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Eunice Adedeji
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum, Jena, Germany
| | - Ezekiel Adebiyi
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Rainer Koenig
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum, Jena, Germany
| | - Jelili Oyelade
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
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9
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Lu TC, Brbić M, Park YJ, Jackson T, Chen J, Kolluru SS, Qi Y, Katheder NS, Cai XT, Lee S, Chen YC, Auld N, Liang CY, Ding SH, Welsch D, D’Souza S, Pisco AO, Jones RC, Leskovec J, Lai EC, Bellen HJ, Luo L, Jasper H, Quake SR, Li H. Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution. Science 2023; 380:eadg0934. [PMID: 37319212 PMCID: PMC10829769 DOI: 10.1126/science.adg0934] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We characterized 163 distinct cell types and performed an in-depth analysis of changes in tissue cell composition, gene expression, and cell identities. We further developed aging clock models to predict fly age and show that ribosomal gene expression is a conserved predictive factor for age. Combining all aging features, we find distinctive cell type-specific aging patterns. This atlas provides a valuable resource for studying fundamental principles of aging in complex organisms.
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Affiliation(s)
- Tzu-Chiao Lu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ye-Jin Park
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Tyler Jackson
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Cancer Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiaye Chen
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sai Saroja Kolluru
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Yanyan Qi
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Xiaoyu Tracy Cai
- Regenerative Medicine, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, New York, NY 10065, USA
| | - Yen-Chung Chen
- Department of Biology, New York University, New York, NY 10013, USA
| | - Niccole Auld
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Cancer Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chung-Yi Liang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Sophia H. Ding
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Doug Welsch
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Robert C. Jones
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, New York, NY 10065, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Heinrich Jasper
- Regenerative Medicine, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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10
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Ghosh AC, Hu Y, Tattikota SG, Liu Y, Comjean A, Perrimon N. Modeling exercise using optogenetically contractible Drosophila larvae. BMC Genomics 2022; 23:623. [PMID: 36042416 PMCID: PMC9425970 DOI: 10.1186/s12864-022-08845-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
The pathophysiological effects of a number of metabolic and age-related disorders can be prevented to some extent by exercise and increased physical activity. However, the molecular mechanisms that contribute to the beneficial effects of muscle activity remain poorly explored. Availability of a fast, inexpensive, and genetically tractable model system for muscle activity and exercise will allow the rapid identification and characterization of molecular mechanisms that mediate the beneficial effects of exercise. Here, we report the development and characterization of an optogenetically-inducible muscle contraction (OMC) model in Drosophila larvae that we used to study acute exercise-like physiological responses. To characterize muscle-specific transcriptional responses to acute exercise, we performed bulk mRNA-sequencing, revealing striking similarities between acute exercise-induced genes in flies and those previously identified in humans. Our larval muscle contraction model opens a path for rapid identification and characterization of exercise-induced factors.
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Affiliation(s)
- Arpan C Ghosh
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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11
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Deshpande R, Lee B, Grewal SS. Enteric bacterial infection in Drosophila induces whole-body alterations in metabolic gene expression independently of the immune deficiency signaling pathway. G3 GENES|GENOMES|GENETICS 2022; 12:6628587. [PMID: 35781508 PMCID: PMC9635644 DOI: 10.1093/g3journal/jkac163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022]
Abstract
When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden and also to alter host physiology and behavior to promote infection tolerance, and they are often mediated through alterations in host gene expression. Here, we have used transcriptome profiling to examine gene expression changes induced by enteric infection with the Gram-negative bacteria Pseudomonas entomophila in adult female Drosophila. We find that infection induces a strong upregulation of metabolic gene expression, including gut and fat body-enriched genes involved in lipid transport, lipolysis, and beta-oxidation, as well as glucose and amino acid metabolism genes. Furthermore, we find that the classic innate immune deficiency (Imd)/Relish/NF-KappaB pathway is not required for, and in some cases limits, these infection-mediated increases in metabolic gene expression. We also see that enteric infection with Pseudomonas entomophila downregulates the expression of many transcription factors and cell–cell signaling molecules, particularly those previously shown to be involved in gut-to-brain and neuronal signaling. Moreover, as with the metabolic genes, these changes occurred largely independent of the Imd pathway. Together, our study identifies many metabolic, signaling, and transcription factor gene expression changes that may contribute to organismal physiological and behavioral responses to enteric pathogen infection.
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Affiliation(s)
- Rujuta Deshpande
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Alberta Children’s Hospital Research Institute, University of Calgary , Alberta T2N 4N1, Canada
- Department of Biochemistry and Molecular Biology Calgary, University of Calgary , Alberta T2N 4N1, Canada
| | - Byoungchun Lee
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Alberta Children’s Hospital Research Institute, University of Calgary , Alberta T2N 4N1, Canada
- Department of Biochemistry and Molecular Biology Calgary, University of Calgary , Alberta T2N 4N1, Canada
| | - Savraj S Grewal
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Alberta Children’s Hospital Research Institute, University of Calgary , Alberta T2N 4N1, Canada
- Department of Biochemistry and Molecular Biology Calgary, University of Calgary , Alberta T2N 4N1, Canada
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12
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Li Y, Du Y, Xu Z, He Y, Yao R, Jiang H, Ju W, Qiao J, Xu K, Liu TM, Zeng L. Intravital lipid droplet labeling and imaging reveals the phenotypes and functions of individual macrophages in vivo. J Lipid Res 2022; 63:100207. [PMID: 35398040 PMCID: PMC9117931 DOI: 10.1016/j.jlr.2022.100207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/06/2023] Open
Abstract
Macrophages play pivotal roles in the maintenance of tissue homeostasis. However, the reactivation of macrophages toward proinflammatory states correlates with a plethora of inflammatory diseases, including atherosclerosis, obesity, neurodegeneration, and bone marrow (BM) failure syndromes. The lack of methods to reveal macrophage phenotype and function in vivo impedes the translational research of these diseases. Here, we found that proinflammatory macrophages accumulate intracellular lipid droplets (LDs) relative to resting or noninflammatory macrophages both in vitro and in vivo, indicating that LD accumulation serves as a structural biomarker for macrophage phenotyping. To realize the staining and imaging of macrophage LDs in vivo, we developed a fluorescent fatty acid analog-loaded poly(lactic-co-glycolic acid) nanoparticle to label macrophages in mice with high efficiency and specificity. Using these novel nanoparticles, we achieved in situ functional identification of single macrophages in BM, liver, lung, and adipose tissues under conditions of acute or chronic inflammation. Moreover, with this intravital imaging platform, we further realized in vivo phenotyping of individual macrophages in the calvarial BM of mice under systemic inflammation. In conclusion, we established an efficient in vivo LD labeling and imaging system for single macrophage phenotyping, which will aid in the development of diagnostics and therapeutic monitoring. Moreover, this method also provides new avenues for the study of lipid trafficking and dynamics in vivo.
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13
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Huang K, Liu Y, Perrimon N. Roles of Insect Oenocytes in Physiology and Their Relevance to Human Metabolic Diseases. FRONTIERS IN INSECT SCIENCE 2022; 2:859847. [PMID: 38468774 PMCID: PMC10926422 DOI: 10.3389/finsc.2022.859847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/14/2022] [Indexed: 03/13/2024]
Abstract
Oenocytes are large secretory cells present in the abdomen of insects known to synthesize very-long-chain fatty acids to produce hydrocarbons and pheromones that mediate courtship behavior in adult flies. In recent years, oenocytes have been implicated in the regulation of energy metabolism. These hepatocyte-like cells accumulate lipid droplets under starvation and can non-autonomously regulate tracheal waterproofing and adipocyte lipid composition. Here, we summarize evidence, mostly from Drosophila, establishing that oenocytes perform liver-like functions. We also compare the functional differences in oenocytes and the fat body, another lipid storage tissue which also performs liver-like functions. Lastly, we examine signaling pathways that regulate oenocyte metabolism derived from other metabolic tissues, as well as oenocyte-derived signals that regulate energy homeostasis.
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Affiliation(s)
- Kerui Huang
- Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Ying Liu
- Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
- Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, United States
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14
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Abstract
Cachexia, a wasting syndrome that is often associated with cancer, is one of the primary causes of death in cancer patients. Cancer cachexia occurs largely due to systemic metabolic alterations stimulated by tumors. Despite the prevalence of cachexia, our understanding of how tumors interact with host tissues and how they affect metabolism is limited. Among the challenges of studying tumor-host tissue crosstalk are the complexity of cancer itself and our insufficient knowledge of the factors that tumors release into the blood. Drosophila is emerging as a powerful model in which to identify tumor-derived factors that influence systemic metabolism and tissue wasting. Strikingly, studies that are characterizing factors derived from different fly tumor cachexia models are identifying both common and distinct cachectic molecules, suggesting that cachexia is more than one disease and that fly models can help identify these differences. Here, we review what has been learned from studies of tumor-induced organ wasting in Drosophila and discuss the open questions.
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Affiliation(s)
- Ying Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Pedro Saavedra
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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15
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Parra-Peralbo E, Talamillo A, Barrio R. Origin and Development of the Adipose Tissue, a Key Organ in Physiology and Disease. Front Cell Dev Biol 2022; 9:786129. [PMID: 34993199 PMCID: PMC8724577 DOI: 10.3389/fcell.2021.786129] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022] Open
Abstract
Adipose tissue is a dynamic organ, well known for its function in energy storage and mobilization according to nutrient availability and body needs, in charge of keeping the energetic balance of the organism. During the last decades, adipose tissue has emerged as the largest endocrine organ in the human body, being able to secrete hormones as well as inflammatory molecules and having an important impact in multiple processes such as adipogenesis, metabolism and chronic inflammation. However, the cellular progenitors, development, homeostasis and metabolism of the different types of adipose tissue are not fully known. During the last decade, Drosophila melanogaster has demonstrated to be an excellent model to tackle some of the open questions in the field of metabolism and development of endocrine/metabolic organs. Discoveries ranged from new hormones regulating obesity to subcellular mechanisms that regulate lipogenesis and lipolysis. Here, we review the available evidences on the development, types and functions of adipose tissue in Drosophila and identify some gaps for future research. This may help to understand the cellular and molecular mechanism underlying the pathophysiology of this fascinating key tissue, contributing to establish this organ as a therapeutic target.
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Affiliation(s)
| | - Ana Talamillo
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
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16
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Yousefian S, Musillo MJ, Bageritz J. Analysis of Single-Cell Transcriptome Data in Drosophila. Methods Mol Biol 2022; 2540:93-111. [PMID: 35980574 DOI: 10.1007/978-1-0716-2541-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The fly Drosophila is a versatile model organism that has led to fascinating biological discoveries. In the past few years, Drosophila researchers have used single-cell RNA-sequencing (scRNA-seq) to gain insights into the cellular composition, and developmental processes of various tissues and organs. Given the success of single-cell technologies a variety of computational tools and software packages were developed to enable and facilitate the analysis of scRNA-seq data. In this book chapter we want to give guidance on analyzing droplet-based scRNA-seq data from Drosophila. We will initially describe the preprocessing commonly done for Drosophila, point out possible downstream analyses, and finally highlight computational methods developed using Drosophila scRNA-seq data.
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Affiliation(s)
- Schayan Yousefian
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Jelena Musillo
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany
| | - Josephine Bageritz
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany.
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17
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Liu Y, Li JSS, Rodiger J, Comjean A, Attrill H, Antonazzo G, Brown NH, Hu Y, Perrimon N. FlyPhoneDB: an integrated web-based resource for cell-cell communication prediction in Drosophila. Genetics 2021; 220:6491251. [PMID: 35100387 PMCID: PMC9176295 DOI: 10.1093/genetics/iyab235] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/20/2021] [Indexed: 01/02/2023] Open
Abstract
Multicellular organisms rely on cell-cell communication to exchange information necessary for developmental processes and metabolic homeostasis. Cell-cell communication pathways can be inferred from transcriptomic datasets based on ligand-receptor expression. Recently, data generated from single-cell RNA sequencing have enabled ligand-receptor interaction predictions at an unprecedented resolution. While computational methods are available to infer cell-cell communication in vertebrates such a tool does not yet exist for Drosophila. Here, we generated a high-confidence list of ligand-receptor pairs for the major fly signaling pathways and developed FlyPhoneDB, a quantification algorithm that calculates interaction scores to predict ligand-receptor interactions between cells. At the FlyPhoneDB user interface, results are presented in a variety of tabular and graphical formats to facilitate biological interpretation. To illustrate that FlyPhoneDB can effectively identify active ligands and receptors to uncover cell-cell communication events, we applied FlyPhoneDB to Drosophila single-cell RNA sequencing data sets from adult midgut, abdomen, and blood, and demonstrate that FlyPhoneDB can readily identify previously characterized cell-cell communication pathways. Altogether, FlyPhoneDB is an easy-to-use framework that can be used to predict cell-cell communication between cell types from single-cell RNA sequencing data in Drosophila.
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Affiliation(s)
- Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA,Corresponding author: Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA. ; Corresponding author: Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
| | - Joshua Shing Shun Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Nicholas H Brown
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA,Howard Hughes Medical Institute, Boston, MA 02138, USA,Corresponding author: Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA. ; Corresponding author: Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
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18
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Moraes KCM, Montagne J. Drosophila melanogaster: A Powerful Tiny Animal Model for the Study of Metabolic Hepatic Diseases. Front Physiol 2021; 12:728407. [PMID: 34603083 PMCID: PMC8481879 DOI: 10.3389/fphys.2021.728407] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022] Open
Abstract
Animal experimentation is limited by unethical procedures, time-consuming protocols, and high cost. Thus, the development of innovative approaches for disease treatment based on alternative models in a fast, safe, and economic manner is an important, yet challenging goal. In this paradigm, the fruit-fly Drosophila melanogaster has become a powerful model for biomedical research, considering its short life cycle and low-cost maintenance. In addition, biological processes are conserved and homologs of ∼75% of human disease-related genes are found in the fruit-fly. Therefore, this model has been used in innovative approaches to evaluate and validate the functional activities of candidate molecules identified via in vitro large-scale analyses, as putative agents to treat or reverse pathological conditions. In this context, Drosophila offers a powerful alternative to investigate the molecular aspects of liver diseases, since no effective therapies are available for those pathologies. Non-alcoholic fatty liver disease is the most common form of chronic hepatic dysfunctions, which may progress to the development of chronic hepatitis and ultimately to cirrhosis, thereby increasing the risk for hepatocellular carcinoma (HCC). This deleterious situation reinforces the use of the Drosophila model to accelerate functional research aimed at deciphering the mechanisms that sustain the disease. In this short review, we illustrate the relevance of using the fruit-fly to address aspects of liver pathologies to contribute to the biomedical area.
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Affiliation(s)
- Karen C M Moraes
- Laboratório de Sinalização Celular e Expressão Gênica, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, Brazil
| | - Jacques Montagne
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
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19
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Li H. Single-cell RNA sequencing in Drosophila: Technologies and applications. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2021; 10:e396. [PMID: 32940008 PMCID: PMC7960577 DOI: 10.1002/wdev.396] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cell states and functions at the single-cell level. It has greatly revolutionized transcriptomic studies in many life science research fields, such as neurobiology, immunology, and developmental biology. With the fast development of both experimental platforms and bioinformatics approaches over the past decade, scRNA-seq is becoming economically feasible and experimentally practical for many biomedical laboratories. Drosophila has served as an excellent model organism for dissecting cellular and molecular mechanisms that underlie tissue development, adult cell function, disease, and aging. The recent application of scRNA-seq methods to Drosophila tissues has led to a number of exciting discoveries. In this review, I will provide a summary of recent scRNA-seq studies in Drosophila, focusing on technical approaches and biological applications. I will also discuss current challenges and future opportunities of making new discoveries using scRNA-seq in Drosophila. This article is categorized under: Technologies > Analysis of the Transcriptome.
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Affiliation(s)
- Hongjie Li
- Department of Biology, Stanford University, Stanford, California, USA
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20
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Cable J, Pourquié O, Wellen KE, Finley LWS, Aulehla A, Gould AP, Teleman A, Tu WB, Garrett WS, Miguel-Aliaga I, Perrimon N, Hooper LV, Walhout AJM, Wei W, Alexandrov T, Erez A, Ralser M, Rabinowitz JD, Hemalatha A, Gutiérrez-Pérez P, Chandel NS, Rutter J, Locasale JW, Landoni JC, Christofk H. Metabolic decisions in development and disease-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:55-73. [PMID: 34414571 DOI: 10.1111/nyas.14678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 07/31/2021] [Indexed: 12/11/2022]
Abstract
There is an increasing appreciation for the role of metabolism in cell signaling and cell decision making. Precise metabolic control is essential in development, as evident by the disorders caused by mutations in metabolic enzymes. The metabolic profile of cells is often cell-type specific, changing as cells differentiate or during tumorigenesis. Recent evidence has shown that changes in metabolism are not merely a consequence of changes in cell state but that metabolites can serve to promote and/or inhibit these changes. Metabolites can link metabolic pathways with cell signaling pathways via several mechanisms, for example, by serving as substrates for protein post-translational modifications, by affecting enzyme activity via allosteric mechanisms, or by altering epigenetic markers. Unraveling the complex interactions governing metabolism, gene expression, and protein activity that ultimately govern a cell's fate will require new tools and interactions across disciplines. On March 24 and 25, 2021, experts in cell metabolism, developmental biology, and human disease met virtually for the Keystone eSymposium, "Metabolic Decisions in Development and Disease." The discussions explored how metabolites impact cellular and developmental decisions in a diverse range of model systems used to investigate normal development, developmental disorders, dietary effects, and cancer-mediated changes in metabolism.
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Affiliation(s)
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Stem Cell Institute, Boston, Massachusetts
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lydia W S Finley
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Aurelio Teleman
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - William B Tu
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Wendy Sarah Garrett
- Harvard T. H. Chan School of Public Health and Dana-Farber Cancer, Boston, Massachusetts
| | - Irene Miguel-Aliaga
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Howard Hughes Institute, Boston, Massachusetts
| | - Lora V Hooper
- Department of Immunology and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - A J Marian Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, California.,Department of Biology and Stanford ChEM-H, Stanford University, Stanford, California
| | - Theodore Alexandrov
- Structural and Computational Biology Unit and Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Joshua D Rabinowitz
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Anupama Hemalatha
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Paula Gutiérrez-Pérez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Navdeep S Chandel
- Department of Medicine, Robert H. Lurie Cancer Center, Chicago, Illinois.,Department of Biochemistry and Molecular Genetics, Robert H. Lurie Cancer Center Metabolomics Core, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jared Rutter
- Department of Biochemistry and Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Juan C Landoni
- Research Program in Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Heather Christofk
- Departments of Biological Chemistry and Molecular & Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California
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21
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Gillette CM, Tennessen JM, Reis T. Balancing energy expenditure and storage with growth and biosynthesis during Drosophila development. Dev Biol 2021; 475:234-244. [DOI: 10.1016/j.ydbio.2021.01.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 12/15/2022]
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22
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Heier C, Klishch S, Stilbytska O, Semaniuk U, Lushchak O. The Drosophila model to interrogate triacylglycerol biology. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158924. [PMID: 33716135 DOI: 10.1016/j.bbalip.2021.158924] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 12/21/2022]
Abstract
The deposition of storage fat in the form of triacylglycerol (TAG) is an evolutionarily conserved strategy to cope with fluctuations in energy availability and metabolic stress. Organismal TAG storage in specialized adipose tissues provides animals a metabolic reserve that sustains survival during development and starvation. On the other hand, excessive accumulation of adipose TAG, defined as obesity, is associated with an increasing prevalence of human metabolic diseases. During the past decade, the fruit fly Drosophila melanogaster, traditionally used in genetics and developmental biology, has been established as a versatile model system to study TAG metabolism and the etiology of lipid-associated metabolic diseases. Similar to humans, Drosophila TAG homeostasis relies on the interplay of organ systems specialized in lipid uptake, synthesis, and processing, which are integrated by an endocrine network of hormones and messenger molecules. Enzymatic formation of TAG from sugar or dietary lipid, its storage in lipid droplets, and its mobilization by lipolysis occur via mechanisms largely conserved between Drosophila and humans. Notably, dysfunctional Drosophila TAG homeostasis occurs in the context of aging, overnutrition, or defective gene function, and entails tissue-specific and organismal pathologies that resemble human disease. In this review, we summarize the physiology and biochemistry of TAG in Drosophila and outline the potential of this organism as a model system to understand the genetic and dietary basis of TAG storage and TAG-related metabolic disorders.
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Affiliation(s)
- Christoph Heier
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Humboldtstrasse 50, A-8010 Graz, Austria; BioTechMed-Graz, Graz, Austria.
| | - Svitlana Klishch
- Department of Biochemistry and Biotechnology, Department Biochemistry 1, Faculty of Natural Sciences, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str, Ivano-Frankivsk 76018, Ukraine
| | - Olha Stilbytska
- Department of Biochemistry and Biotechnology, Department Biochemistry 1, Faculty of Natural Sciences, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str, Ivano-Frankivsk 76018, Ukraine
| | - Uliana Semaniuk
- Department of Biochemistry and Biotechnology, Department Biochemistry 1, Faculty of Natural Sciences, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str, Ivano-Frankivsk 76018, Ukraine
| | - Oleh Lushchak
- Department of Biochemistry and Biotechnology, Department Biochemistry 1, Faculty of Natural Sciences, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str, Ivano-Frankivsk 76018, Ukraine.
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23
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Mohr SE, Tattikota SG, Xu J, Zirin J, Hu Y, Perrimon N. Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila. Genetics 2021; 217:6156631. [PMID: 33713129 DOI: 10.1093/genetics/iyab019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 01/26/2023] Open
Abstract
Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify clusters of cells that share common gene expression signatures. A major challenge in scRNAseq studies is to map the clusters to specific anatomical regions along the body and within tissues. Existing data, such as information obtained from large-scale in situ RNA hybridization studies, cell type specific transcriptomics, gene expression reporters, antibody stainings, and fluorescent tagged proteins, can help to map clusters to anatomy. However, in many cases, additional validation is needed to precisely map the spatial location of cells in clusters. Several approaches are available for spatial resolution in Drosophila, including mining of existing datasets, and use of existing or new tools for direct or indirect detection of RNA, or direct detection of proteins. Here, we review available resources and emerging technologies that will facilitate spatial mapping of scRNAseq clusters at high resolution in Drosophila. Importantly, we discuss the need, available approaches, and reagents for multiplexing gene expression detection in situ, as in most cases scRNAseq clusters are defined by the unique coexpression of sets of genes.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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24
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Diaz AV, Reis T. Muscle signals to the rescue. eLife 2020; 9:64587. [PMID: 33345778 PMCID: PMC7752131 DOI: 10.7554/elife.64587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
The skeletal muscle of fruit flies communicates with other organs to prevent the accumulation of too much fat and to protect adults against obesity.
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Affiliation(s)
- Arely V Diaz
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Tânia Reis
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States
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25
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Ghosh AC, Tattikota SG, Liu Y, Comjean A, Hu Y, Barrera V, Ho Sui SJ, Perrimon N. Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity. eLife 2020; 9:56969. [PMID: 33107824 PMCID: PMC7752135 DOI: 10.7554/elife.56969] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/26/2020] [Indexed: 12/21/2022] Open
Abstract
PDGF/VEGF ligands regulate a plethora of biological processes in multicellular organisms via autocrine, paracrine, and endocrine mechanisms. We investigated organ-specific metabolic roles of Drosophila PDGF/VEGF-like factors (Pvfs). We combine genetic approaches and single-nuclei sequencing to demonstrate that muscle-derived Pvf1 signals to the Drosophila hepatocyte-like cells/oenocytes to suppress lipid synthesis by activating the Pi3K/Akt1/TOR signaling cascade in the oenocytes. Functionally, this signaling axis regulates expansion of adipose tissue lipid stores in newly eclosed flies. Flies emerge after pupation with limited adipose tissue lipid stores and lipid level is progressively accumulated via lipid synthesis. We find that adult muscle-specific expression of pvf1 increases rapidly during this stage and that muscle-to-oenocyte Pvf1 signaling inhibits expansion of adipose tissue lipid stores as the process reaches completion. Our findings provide the first evidence in a metazoan of a PDGF/VEGF ligand acting as a myokine that regulates systemic lipid homeostasis by activating TOR in hepatocyte-like cells.
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Affiliation(s)
- Arpan C Ghosh
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Victor Barrera
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Shannan J Ho Sui
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Boston, United States
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26
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Bretscher H, O’Connor MB. The Role of Muscle in Insect Energy Homeostasis. Front Physiol 2020; 11:580687. [PMID: 33192587 PMCID: PMC7649811 DOI: 10.3389/fphys.2020.580687] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 12/16/2022] Open
Abstract
Maintaining energy homeostasis is critical for ensuring proper growth and maximizing survival potential of all organisms. Here we review the role of somatic muscle in regulating energy homeostasis in insects. The muscle is not only a large consumer of energy, it also plays a crucial role in regulating metabolic signaling pathways and energy stores of the organism. We examine the metabolic pathways required to supply the muscle with energy, as well as muscle-derived signals that regulate metabolic energy homeostasis.
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Affiliation(s)
| | - Michael B. O’Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
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