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Tanaka T, Chung HL. Exploiting fly models to investigate rare human neurological disorders. Neural Regen Res 2025; 20:21-28. [PMID: 38767473 PMCID: PMC11246155 DOI: 10.4103/nrr.nrr-d-23-01847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/05/2024] [Accepted: 03/02/2024] [Indexed: 05/22/2024] Open
Abstract
Rare neurological diseases, while individually are rare, collectively impact millions globally, leading to diverse and often severe neurological symptoms. Often attributed to genetic mutations that disrupt protein function or structure, understanding their genetic basis is crucial for accurate diagnosis and targeted therapies. To investigate the underlying pathogenesis of these conditions, researchers often use non-mammalian model organisms, such as Drosophila (fruit flies), which is valued for their genetic manipulability, cost-efficiency, and preservation of genes and biological functions across evolutionary time. Genetic tools available in Drosophila, including CRISPR-Cas9, offer a means to manipulate gene expression, allowing for a deep exploration of the genetic underpinnings of rare neurological diseases. Drosophila boasts a versatile genetic toolkit, rapid generation turnover, and ease of large-scale experimentation, making it an invaluable resource for identifying potential drug candidates. Researchers can expose flies carrying disease-associated mutations to various compounds, rapidly pinpointing promising therapeutic agents for further investigation in mammalian models and, ultimately, clinical trials. In this comprehensive review, we explore rare neurological diseases where fly research has significantly contributed to our understanding of their genetic basis, pathophysiology, and potential therapeutic implications. We discuss rare diseases associated with both neuron-expressed and glial-expressed genes. Specific cases include mutations in CDK19 resulting in epilepsy and developmental delay, mutations in TIAM1 leading to a neurodevelopmental disorder with seizures and language delay, and mutations in IRF2BPL causing seizures, a neurodevelopmental disorder with regression, loss of speech, and abnormal movements. And we explore mutations in EMC1 related to cerebellar atrophy, visual impairment, psychomotor retardation, and gain-of-function mutations in ACOX1 causing Mitchell syndrome. Loss-of-function mutations in ACOX1 result in ACOX1 deficiency, characterized by very-long-chain fatty acid accumulation and glial degeneration. Notably, this review highlights how modeling these diseases in Drosophila has provided valuable insights into their pathophysiology, offering a platform for the rapid identification of potential therapeutic interventions. Rare neurological diseases involve a wide range of expression systems, and sometimes common phenotypes can be found among different genes that cause abnormalities in neurons or glia. Furthermore, mutations within the same gene may result in varying functional outcomes, such as complete loss of function, partial loss of function, or gain-of-function mutations. The phenotypes observed in patients can differ significantly, underscoring the complexity of these conditions. In conclusion, Drosophila represents an indispensable and cost-effective tool for investigating rare neurological diseases. By facilitating the modeling of these conditions, Drosophila contributes to a deeper understanding of their genetic basis, pathophysiology, and potential therapies. This approach accelerates the discovery of promising drug candidates, ultimately benefiting patients affected by these complex and understudied diseases.
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Affiliation(s)
- Tomomi Tanaka
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, USA
| | - Hyung-Lok Chung
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, USA
- Department of Neurology, Weill Cornell Medical College, New York, NY, USA
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2
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Aguilar G, Bauer M, Vigano MA, Schnider ST, Brügger L, Jiménez-Jiménez C, Guerrero I, Affolter M. Seamless knockins in Drosophila via CRISPR-triggered single-strand annealing. Dev Cell 2024:S1534-5807(24)00383-6. [PMID: 38971155 DOI: 10.1016/j.devcel.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/06/2023] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
CRISPR-Cas greatly facilitated the integration of exogenous sequences into specific loci. However, knockin generation in multicellular animals remains challenging, partially due to the complexity of insertion screening. Here, we describe SEED/Harvest, a method to generate knockins in Drosophila, based on CRISPR-Cas and the single-strand annealing (SSA) repair pathway. In SEED (from "scarless editing by element deletion"), a switchable cassette is first integrated into the target locus. In a subsequent CRISPR-triggered repair event, resolved by SSA, the cassette is seamlessly removed. Germline excision of SEED cassettes allows for fast and robust knockin generation of both fluorescent proteins and short protein tags in tandem. Tissue-specific expression of Cas9 results in somatic cassette excision, conferring spatiotemporal control of protein labeling and the conditional rescue of mutants. Finally, to achieve conditional protein labeling and manipulation of short tag knockins, we developed a genetic toolbox by functionalizing the ALFA nanobody.
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Affiliation(s)
- Gustavo Aguilar
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Milena Bauer
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - M Alessandra Vigano
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Sophie T Schnider
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Lukas Brügger
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Carlos Jiménez-Jiménez
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Isabel Guerrero
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Markus Affolter
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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3
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Peng D, Vangipuram M, Wong J, Leonetti MD. protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in. Nucleic Acids Res 2024:gkae553. [PMID: 38922690 DOI: 10.1093/nar/gkae553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
CRISPR/Cas-mediated knock-in of DNA sequences enables precise genome engineering for research and therapeutic applications. However, designing effective guide RNAs (gRNAs) and homology-directed repair (HDR) donors remains a bottleneck. Here, we present protoSpaceJAM, an open-source algorithm to automate and optimize gRNA and HDR donor design for CRISPR/Cas insertional knock-in experiments, currently supporting SpCas9, SpCas9-VQR and enAsCas12a Cas enzymes. protoSpaceJAM utilizes biological rules to rank gRNAs based on specificity, distance to insertion site, and position relative to regulatory regions. protoSpaceJAM can introduce 'recoding' mutations (silent mutations and mutations in non-coding sequences) in HDR donors to prevent re-cutting and increase knock-in efficiency. Users can customize parameters and design double-stranded or single-stranded donors. We validated protoSpaceJAM's design rules by demonstrating increased knock-in efficiency with recoding mutations and optimal strand selection for single-stranded donors. An additional module enables the design of genotyping primers for deep sequencing of edited alleles. Overall, protoSpaceJAM streamlines and optimizes CRISPR knock-in experimental design in a flexible and modular manner to benefit diverse research and therapeutic applications. protoSpaceJAM is available open-source as an interactive web tool at protospacejam.czbiohub.org or as a standalone Python package at github.com/czbiohub-sf/protoSpaceJAM.
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Affiliation(s)
- Duo Peng
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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4
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Goodman LD, Moulton MJ, Lin G, Bellen HJ. Does glial lipid dysregulation alter sleep in Alzheimer's and Parkinson's disease? Trends Mol Med 2024:S1471-4914(24)00098-4. [PMID: 38755043 DOI: 10.1016/j.molmed.2024.04.010] [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: 02/17/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024]
Abstract
In this opinion article, we discuss potential connections between sleep disturbances observed in Alzheimer's disease (AD) and Parkinson's disease (PD) and the dysregulation of lipids in the brain. Research using Drosophila has highlighted the role of glial-mediated lipid metabolism in sleep and diurnal rhythms. Relevant to AD, the formation of lipid droplets in glia, which occurs in response to elevated neuronal reactive oxygen species (ROS), is required for sleep. In disease models, this process is disrupted, arguing a connection to sleep dysregulation. Relevant to PD, the degradation of neuronally synthesized glucosylceramides by glia requires glucocerebrosidase (GBA, a PD-associated risk factor) and this regulates sleep. Loss of GBA in glia causes an accumulation of glucosylceramides and neurodegeneration. Overall, research primarily using Drosophila has highlighted how dysregulation of glial lipid metabolism may underlie sleep disturbances in neurodegenerative diseases.
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Affiliation(s)
- Lindsey D Goodman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Matthew J Moulton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Guang Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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5
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Bustillo ME, Douthit J, Astigarraga S, Treisman JE. Two distinct mechanisms of Plexin A function in Drosophila optic lobe lamination and morphogenesis. Development 2024; 151:dev202237. [PMID: 38738602 PMCID: PMC11190435 DOI: 10.1242/dev.202237] [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: 08/06/2023] [Accepted: 04/28/2024] [Indexed: 05/14/2024]
Abstract
Visual circuit development is characterized by subdivision of neuropils into layers that house distinct sets of synaptic connections. We find that, in the Drosophila medulla, this layered organization depends on the axon guidance regulator Plexin A. In Plexin A null mutants, synaptic layers of the medulla neuropil and arborizations of individual neurons are wider and less distinct than in controls. Analysis of semaphorin function indicates that Semaphorin 1a, acting in a subset of medulla neurons, is the primary partner for Plexin A in medulla lamination. Removal of the cytoplasmic domain of endogenous Plexin A has little effect on the formation of medulla layers; however, both null and cytoplasmic domain deletion mutations of Plexin A result in an altered overall shape of the medulla neuropil. These data suggest that Plexin A acts as a receptor to mediate morphogenesis of the medulla neuropil, and as a ligand for Semaphorin 1a to subdivide it into layers. Its two independent functions illustrate how a few guidance molecules can organize complex brain structures by each playing multiple roles.
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Affiliation(s)
- Maria E. Bustillo
- Department of Cell Biology, New York University Grossman School of Medicine, 435 E. 30th Street, New York, NY 10016, USA
| | - Jessica Douthit
- Department of Cell Biology, New York University Grossman School of Medicine, 435 E. 30th Street, New York, NY 10016, USA
| | - Sergio Astigarraga
- Department of Cell Biology, New York University Grossman School of Medicine, 435 E. 30th Street, New York, NY 10016, USA
| | - Jessica E. Treisman
- Department of Cell Biology, New York University Grossman School of Medicine, 435 E. 30th Street, New York, NY 10016, USA
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6
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Nguyen TH, Vicidomini R, Choudhury SD, Han TH, Maric D, Brody T, Serpe M. scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development. Dev Cell 2024; 59:1210-1230.e9. [PMID: 38569548 PMCID: PMC11078614 DOI: 10.1016/j.devcel.2024.03.016] [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: 06/27/2023] [Revised: 12/05/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
The Drosophila larval ventral nerve cord (VNC) shares many similarities with the spinal cord of vertebrates and has emerged as a major model for understanding the development and function of motor systems. Here, we use high-quality scRNA-seq, validated by anatomical identification, to create a comprehensive census of larval VNC cell types. We show that the neural lineages that comprise the adult VNC are already defined, but quiescent, at the larval stage. Using fluorescence-activated cell sorting (FACS)-enriched populations, we separate all motor neuron bundles and link individual neuron clusters to morphologically characterized known subtypes. We discovered a glutamate receptor subunit required for basal neurotransmission and homeostasis at the larval neuromuscular junction. We describe larval glia and endorse the general view that glia perform consistent activities throughout development. This census represents an extensive resource and a powerful platform for future discoveries of cellular and molecular mechanisms in repair, regeneration, plasticity, homeostasis, and behavioral coordination.
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Affiliation(s)
| | | | | | | | - Dragan Maric
- Flow and Imaging Cytometry Core, NINDS, NIH, Bethesda, MD 20892, USA
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7
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Atsoniou K, Giannopoulou E, Georganta EM, Skoulakis EMC. Drosophila Contributions towards Understanding Neurofibromatosis 1. Cells 2024; 13:721. [PMID: 38667335 PMCID: PMC11048932 DOI: 10.3390/cells13080721] [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: 03/15/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Neurofibromatosis 1 (NF1) is a multisymptomatic disorder with highly variable presentations, which include short stature, susceptibility to formation of the characteristic benign tumors known as neurofibromas, intense freckling and skin discoloration, and cognitive deficits, which characterize most children with the condition. Attention deficits and Autism Spectrum manifestations augment the compromised learning presented by most patients, leading to behavioral problems and school failure, while fragmented sleep contributes to chronic fatigue and poor quality of life. Neurofibromin (Nf1) is present ubiquitously during human development and postnatally in most neuronal, oligodendrocyte, and Schwann cells. Evidence largely from animal models including Drosophila suggests that the symptomatic variability may reflect distinct cell-type-specific functions of the protein, which emerge upon its loss, or mutations affecting the different functional domains of the protein. This review summarizes the contributions of Drosophila in modeling multiple NF1 manifestations, addressing hypotheses regarding the cell-type-specific functions of the protein and exploring the molecular pathways affected upon loss of the highly conserved fly homolog dNf1. Collectively, work in this model not only has efficiently and expediently modelled multiple aspects of the condition and increased understanding of its behavioral manifestations, but also has led to pharmaceutical strategies towards their amelioration.
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Affiliation(s)
- Kalliopi Atsoniou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Athens, Greece; (K.A.); (E.G.)
- Laboratory of Experimental Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Eleni Giannopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Athens, Greece; (K.A.); (E.G.)
| | - Eirini-Maria Georganta
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Athens, Greece; (K.A.); (E.G.)
| | - Efthimios M. C. Skoulakis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Athens, Greece; (K.A.); (E.G.)
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8
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Webster LJ, Villa-Gomez D, Brown R, Clarke W, Schenk PM. A synthetic biology approach for the treatment of pollutants with microalgae. Front Bioeng Biotechnol 2024; 12:1379301. [PMID: 38646010 PMCID: PMC11032018 DOI: 10.3389/fbioe.2024.1379301] [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] [Received: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.
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Affiliation(s)
- Luke J. Webster
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Denys Villa-Gomez
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Reuben Brown
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - William Clarke
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Peer M. Schenk
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
- Algae Biotechnology, Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD, Australia
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9
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Pan X, Tao AM, Lu S, Ma M, Hannan SB, Slaugh R, Drewes Williams S, O'Grady L, Kanca O, Person R, Carter MT, Platzer K, Schnabel F, Abou Jamra R, Roberts AE, Newburger JW, Revah-Politi A, Granadillo JL, Stegmann APA, Sinnema M, Accogli A, Salpietro V, Capra V, Ghaloul-Gonzalez L, Brueckner M, Simon MEH, Sweetser DA, Glinton KE, Kirk SE, Wangler MF, Yamamoto S, Chung WK, Bellen HJ. De novo variants in FRYL are associated with developmental delay, intellectual disability, and dysmorphic features. Am J Hum Genet 2024; 111:742-760. [PMID: 38479391 PMCID: PMC11023917 DOI: 10.1016/j.ajhg.2024.02.007] [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: 08/23/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 04/07/2024] Open
Abstract
FRY-like transcription coactivator (FRYL) belongs to a Furry protein family that is evolutionarily conserved from yeast to humans. The functions of FRYL in mammals are largely unknown, and variants in FRYL have not previously been associated with a Mendelian disease. Here, we report fourteen individuals with heterozygous variants in FRYL who present with developmental delay, intellectual disability, dysmorphic features, and other congenital anomalies in multiple systems. The variants are confirmed de novo in all individuals except one. Human genetic data suggest that FRYL is intolerant to loss of function (LoF). We find that the fly FRYL ortholog, furry (fry), is expressed in multiple tissues, including the central nervous system where it is present in neurons but not in glia. Homozygous fry LoF mutation is lethal at various developmental stages, and loss of fry in mutant clones causes defects in wings and compound eyes. We next modeled four out of the five missense variants found in affected individuals using fry knockin alleles. One variant behaves as a severe LoF variant, whereas two others behave as partial LoF variants. One variant does not cause any observable defect in flies, and the corresponding human variant is not confirmed to be de novo, suggesting that this is a variant of uncertain significance. In summary, our findings support that fry is required for proper development in flies and that the LoF variants in FRYL cause a dominant disorder with developmental and neurological symptoms due to haploinsufficiency.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Alice M Tao
- Vagelos School of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shabab B Hannan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Sarah Drewes Williams
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Lauren O'Grady
- Division of Medical Genetics & Metabolism, Massachusetts General for Children, Boston, MA, USA; MGH Institute of Health Professions, Charlestown, MA, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | | | - Melissa T Carter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Franziska Schnabel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Amy E Roberts
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Medicine, Division of Genetics, Boston Children's Hospital, Boston, MA, USA
| | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Anya Revah-Politi
- Institute for Genomic Medicine and Precision Genomics Laboratory, Columbia University Irving Medical Center, New York, NY, USA
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Andrea Accogli
- Division of Medical Genetics, Department of Medicine, McGill University Health Center, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, University College London Institute of Neurology, Queen Square, London, UK
| | - Valeria Capra
- Unit of Medical Genetics and Genomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Lina Ghaloul-Gonzalez
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Martina Brueckner
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Marleen E H Simon
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - David A Sweetser
- Division of Medical Genetics & Metabolism, Massachusetts General for Children, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Susan E Kirk
- Section of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Cancer and Hematology Center, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Wendy K Chung
- Departments of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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10
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Zirin J, Jusiak B, Lopes R, Ewen-Campen B, Bosch JA, Risbeck A, Forman C, Villalta C, Hu Y, Perrimon N. Expanding the Drosophila toolkit for dual control of gene expression. eLife 2024; 12:RP94073. [PMID: 38569007 PMCID: PMC10990484 DOI: 10.7554/elife.94073] [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: 04/05/2024] Open
Abstract
The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA system or QF system. Here, we describe a resource of reagents that facilitate combined use of the GAL4/UAS and a second binary system in various Drosophila tissues. Focusing on genes with well-characterized GAL4 expression patterns, we generated a set of more than 40 LexA-GAD and QF2 insertions by CRISPR knock-in and verified their tissue specificity in larvae. We also built constructs that encode QF2 and LexA-GAD transcription factors in a single vector. Following successful integration of this construct into the fly genome, FLP/FRT recombination is used to isolate fly lines that express only QF2 or LexA-GAD. Finally, using new compatible shRNA vectors, we evaluated both LexA and QF systems for in vivo gene knockdown and are generating a library of such RNAi fly lines as a community resource. Together, these LexA and QF system vectors and fly lines will provide a new set of tools for researchers who need to activate or repress two different genes in an orthogonal manner in the same animal.
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Affiliation(s)
- Jonathan Zirin
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Barbara Jusiak
- Department of Physiology and Biophysics, University of California, IrvineIrvineUnited States
| | - Raphael Lopes
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Justin A Bosch
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Corey Forman
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Yanhui Hu
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteBostonUnited States
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11
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Martelli F, Lin J, Mele S, Imlach W, Kanca O, Barlow CK, Paril J, Schittenhelm RB, Christodoulou J, Bellen HJ, Piper MDW, Johnson TK. Identifying potential dietary treatments for inherited metabolic disorders using Drosophila nutrigenomics. Cell Rep 2024; 43:113861. [PMID: 38416643 PMCID: PMC11037929 DOI: 10.1016/j.celrep.2024.113861] [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: 05/16/2023] [Revised: 12/09/2023] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
Inherited metabolic disorders are a group of genetic conditions that can cause severe neurological impairment and child mortality. Uniquely, these disorders respond to dietary treatment; however, this option remains largely unexplored because of low disorder prevalence and the lack of a suitable paradigm for testing diets. Here, we screened 35 Drosophila amino acid disorder models for disease-diet interactions and found 26 with diet-altered development and/or survival. Using a targeted multi-nutrient array, we examine the interaction in a model of isolated sulfite oxidase deficiency, an infant-lethal disorder. We show that dietary cysteine depletion normalizes their metabolic profile and rescues development, neurophysiology, behavior, and lifelong fly survival, thus providing a basis for further study into the pathogenic mechanisms involved in this disorder. Our work highlights the diet-sensitive nature of metabolic disorders and establishes Drosophila as a valuable tool for nutrigenomic studies for informing potential dietary therapies.
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Affiliation(s)
- Felipe Martelli
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Jiayi Lin
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Sarah Mele
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Wendy Imlach
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Oguz Kanca
- Department of Molecular and Human Genetics and Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Christopher K Barlow
- Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Jefferson Paril
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Hugo J Bellen
- Department of Molecular and Human Genetics and Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Matthew D W Piper
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
| | - Travis K Johnson
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Chemistry and La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
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12
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Sanfilippo P, Kim AJ, Bhukel A, Yoo J, Mirshahidi PS, Pandey V, Bevir H, Yuen A, Mirshahidi PS, Guo P, Li HS, Wohlschlegel JA, Aso Y, Zipursky SL. Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome. Neuron 2024; 112:942-958.e13. [PMID: 38262414 PMCID: PMC10957333 DOI: 10.1016/j.neuron.2023.12.014] [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: 08/28/2023] [Revised: 12/03/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024]
Abstract
Neurons express various combinations of neurotransmitter receptor (NR) subunits and receive inputs from multiple neuron types expressing different neurotransmitters. Localizing NR subunits to specific synaptic inputs has been challenging. Here, we use epitope-tagged endogenous NR subunits, expansion light-sheet microscopy, and electron microscopy (EM) connectomics to molecularly characterize synapses in Drosophila. We show that in directionally selective motion-sensitive neurons, different multiple NRs elaborated a highly stereotyped molecular topography with NR localized to specific domains receiving cell-type-specific inputs. Developmental studies suggested that NRs or complexes of them with other membrane proteins determine patterns of synaptic inputs. In support of this model, we identify a transmembrane protein selectively associated with a subset of spatially restricted synapses and demonstrate its requirement for synapse formation through genetic analysis. We propose that mechanisms that regulate the precise spatial distribution of NRs provide a molecular cartography specifying the patterns of synaptic connections onto dendrites.
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Affiliation(s)
- Piero Sanfilippo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander J Kim
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anuradha Bhukel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Juyoun Yoo
- Neuroscience Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pegah S Mirshahidi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Vijaya Pandey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Harry Bevir
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ashley Yuen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Parmis S Mirshahidi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Peiyi Guo
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hong-Sheng Li
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - S Lawrence Zipursky
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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13
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Zhu H, Ludington WB, Spradling AC. Cellular and molecular organization of the Drosophila foregut. Proc Natl Acad Sci U S A 2024; 121:e2318760121. [PMID: 38442150 PMCID: PMC10945768 DOI: 10.1073/pnas.2318760121] [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: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024] Open
Abstract
The animal foregut is the first tissue to encounter ingested food, bacteria, and viruses. We characterized the adult Drosophila foregut using transcriptomics to better understand how it triages consumed items for digestion or immune response and manages resources. Cell types were assigned and validated using GFP-tagged and Gal4 reporter lines. Foregut-associated neuroendocrine cells play a major integrative role by coordinating gut activity with nutrition, the microbiome, and circadian cycles; some express clock genes. Multiple epithelial cell types comprise the proventriculus, the central foregut organ that secretes the peritrophic matrix (PM) lining the gut. Analyzing cell types synthesizing individual PM layers revealed abundant mucin production close to enterocytes, similar to the mammalian intestinal mucosa. The esophagus and salivary gland express secreted proteins likely to line the esophageal surface, some of which may generate a foregut commensal niche housing specific gut microbiome species. Overall, our results imply that the foregut coordinates dietary sensing, hormonal regulation, and immunity in a manner that has been conserved during animal evolution.
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Affiliation(s)
- Haolong Zhu
- Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD21218
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
| | - William B. Ludington
- Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD21218
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
| | - Allan C. Spradling
- Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD21218
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
- HHMI, Baltimore, MD21218
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14
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Thorpe HJ, Owings KG, Aziz MC, Haller M, Coelho E, Chow CY. Drosophila models of phosphatidylinositol glycan biosynthesis class A congenital disorder of glycosylation (PIGA-CDG) mirror patient phenotypes. G3 (BETHESDA, MD.) 2024; 14:jkad291. [PMID: 38124489 PMCID: PMC10917494 DOI: 10.1093/g3journal/jkad291] [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: 10/30/2023] [Revised: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Mutations in the phosphatidylinositol glycan biosynthesis class A (PIGA) gene cause a rare, X-linked recessive congenital disorder of glycosylation. Phosphatidylinositol glycan biosynthesis class A congenital disorder of glycosylation (PIGA-CDG) is characterized by seizures, intellectual and developmental delay, and congenital malformations. The PIGA gene encodes an enzyme involved in the first step of glycosylphosphatidylinositol (GPI) anchor biosynthesis. There are over 100 GPI-anchored proteins that attach to the cell surface and are involved in cell signaling, immunity, and adhesion. Little is known about the pathophysiology of PIGA-CDG. Here, we describe the first Drosophila model of PIGA-CDG and demonstrate that loss of PIG-A function in Drosophila accurately models the human disease. As expected, complete loss of PIG-A function is larval lethal. Heterozygous null animals appear healthy but, when challenged, have a seizure phenotype similar to what is observed in patients. To identify the cell-type specific contributions to disease, we generated neuron- and glia-specific knockdown of PIG-A. Neuron-specific knockdown resulted in reduced lifespan and a number of neurological phenotypes but no seizure phenotype. Glia-knockdown also reduced lifespan and, notably, resulted in a very strong seizure phenotype. RNA sequencing analyses demonstrated that there are fundamentally different molecular processes that are disrupted when PIG-A function is eliminated in different cell types. In particular, loss of PIG-A in neurons resulted in upregulation of glycolysis, but loss of PIG-A in glia resulted in upregulation of protein translation machinery. Here, we demonstrate that Drosophila is a good model of PIGA-CDG and provide new data resources for future study of PIGA-CDG and other GPI anchor disorders.
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Affiliation(s)
- Holly J Thorpe
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Katie G Owings
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Miriam C Aziz
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Madelyn Haller
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Emily Coelho
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
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15
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Zirin J, Jusiak B, Lopes R, Ewen-Campen B, Bosch JA, Risbeck A, Forman C, Villalta C, Hu Y, Perrimon N. Expanding the Drosophila toolkit for dual control of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.15.553399. [PMID: 37645802 PMCID: PMC10461983 DOI: 10.1101/2023.08.15.553399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA-system or QF-system. Here, we describe a resource of reagents that facilitate combined use of the GAL4/UAS and a second binary system in various Drosophila tissues. Focusing on genes with well-characterizsed GAL4 expression patterns, we generated a set of more than 40 LexA-GAD and QF2 insertions by CRISPR knock-in and verified their tissue-specificity in larvae. We also built constructs that encode QF2 and LexA-GAD transcription factors in a single vector. Following successful integration of this construct into the fly genome, FLP/FRT recombination is used to isolate fly lines that express only QF2 or LexA-GAD. Finally, using new compatible shRNA vectors, we evaluated both LexA and QF systems for in vivo gene knockdown and are generating a library of such RNAi fly lines as a community resource. Together, these LexA and QF system vectors and fly lines will provide a new set of tools for researchers who need to activate or repress two different genes in an orthogonal manner in the same animal.
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16
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Stinchfield MJ, Weasner BP, Weasner BM, Zhitomersky D, Kumar JP, O’Connor MB, Newfeld SJ. Fourth Chromosome Resource Project: a comprehensive resource for genetic analysis in Drosophila that includes humanized stocks. Genetics 2024; 226:iyad201. [PMID: 37981656 PMCID: PMC10847715 DOI: 10.1093/genetics/iyad201] [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: 10/11/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
The fourth chromosome is the final frontier for genetic analysis in Drosophila. Small, heterochromatic, and devoid of recombination the fourth has long been ignored. Nevertheless, its long arm contains 79 protein-coding genes. The Fourth Chromosome Resource Project (FCRP) has a goal of facilitating the investigation of genes on this neglected chromosome. The project has 446 stocks publicly available at the Bloomington and Kyoto stock centers with phenotypic data curated by the FlyBase and FlyPush resources. Four of the five stock sets are nearly complete: (1) UAS.fly cDNAs, (2) UAS.human homolog cDNAs, (3) gene trap mutants and protein traps, and (4) stocks promoting meiotic and mitotic recombination on the fourth. Ongoing is mutagenesis of each fourth gene on a new FRT-bearing chromosome for marked single-cell clones. Beyond flies, FCRP facilitates the creation and analysis of humanized fly stocks. These provide opportunities to apply Drosophila genetics to the analysis of human gene interaction and function. In addition, the FCRP provides investigators with confidence through stock validation and an incentive via phenotyping to tackle genes on the fourth that have never been studied. Taken together, FCRP stocks will facilitate all manner of genetic and molecular studies. The resource is readily available to researchers to enhance our understanding of metazoan biology, including conserved molecular mechanisms underlying health and disease.
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Affiliation(s)
| | | | - Bonnie M Weasner
- Department Biology, Indiana University, Bloomington, IN 47405, USA
| | - David Zhitomersky
- Department Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Justin P Kumar
- Department Biology, Indiana University, Bloomington, IN 47405, USA
| | - Michael B O’Connor
- Department Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stuart J Newfeld
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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17
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Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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18
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Bonanno SL, Sanfilippo P, Eamani A, Sampson MM, Binu K, Li K, Burns GD, Makar ME, Zipursky SL, Krantz DE. Constitutive and conditional epitope-tagging of endogenous G protein coupled receptors in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573472. [PMID: 38234787 PMCID: PMC10793450 DOI: 10.1101/2023.12.27.573472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
To visualize the cellular and subcellular localization of neuromodulatory G-protein coupled receptors (GPCRs) in Drosophila , we implement a molecular strategy recently used to add epitope tags to ionotropic receptors at their endogenous loci. Leveraging evolutionary conservation to identify sites more likely to permit insertion of a tag, we generated constitutive and conditional tagged alleles for Drosophila 5-HT1A, 5-HT2A, 5-HT2B, Octβ1R, Octβ2R, two isoforms of OAMB, and mGluR. The conditional alleles allow for the restricted expression of tagged receptor in specific cell types, an option not available for any previous reagents to label these proteins. We show that 5-HT1A and 5-HT2B localize to the mushroom bodies and central complex respectively, as predicted by their roles in sleep. By contrast, the unexpected enrichment of Octβ1R in the central complex and of 5-HT1A and 5-HT2A to nerve terminals in lobular columnar cells in the visual system suggest new hypotheses about their function at these sites. Using an additional tagged allele of the serotonin transporter, a marker of serotonergic tracts, we demonstrate diverse spatial relationships between postsynaptic 5-HT receptors and presynaptic 5-HT neurons, consistent with the importance of both synaptic and volume transmission. Finally, we use the conditional allele of 5-HT1A to show that it localizes to distinct sites within the mushroom bodies as both a postsynaptic receptor in Kenyon cells and a presynaptic autoreceptor. Significance Statement In Drosophila , despite remarkable advances in both connectomic and genomic studies, antibodies to many aminergic GPCRs are not available. We have overcome this obstacle using evolutionary conservation to identify loci in GPCRs amenable to epitope-tagging, and CRISPR/Cas9 genome editing to generated eight novel lines. This method also may be applied to other GPCRs and allows cell-specific expression of the tagged locus. We have used the tagged alleles we generated to address several questions that remain poorly understood. These include the relationship between pre- and post-synaptic sites that express the same receptor, and the use of relatively distant targets by pre-synaptic release sites that may employ volume transmission as well as standard synaptic signaling.
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19
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Mohr SE, Kim AR, Hu Y, Perrimon N. Finding information about uncharacterized Drosophila melanogaster genes. Genetics 2023; 225:iyad187. [PMID: 37933691 PMCID: PMC10697813 DOI: 10.1093/genetics/iyad187] [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: 07/31/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023] Open
Abstract
Genes that have been identified in the genome but remain uncharacterized with regards to function offer an opportunity to uncover novel biological information. Novelty is exciting but can also be a barrier. If nothing is known, how does one start planning and executing experiments? Here, we provide a recommended information-mining workflow and a corresponding guide to accessing information about uncharacterized Drosophila melanogaster genes, such as those assigned only a systematic coding gene identifier. The available information can provide insights into where and when the gene is expressed, what the function of the gene might be, whether there are similar genes in other species, whether there are known relationships to other genes, and whether any other features have already been determined. In addition, available information about relevant reagents can inspire and facilitate experimental studies. Altogether, mining available information can help prioritize genes for further study, as well as provide starting points for experimental assays and other analyses.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, 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
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, 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
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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20
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Nil Z, Deshwar AR, Huang Y, Barish S, Zhang X, Choufani S, Le Quesne Stabej P, Hayes I, Yap P, Haldeman-Englert C, Wilson C, Prescott T, Tveten K, Vøllo A, Haynes D, Wheeler PG, Zon J, Cytrynbaum C, Jobling R, Blyth M, Banka S, Afenjar A, Mignot C, Robin-Renaldo F, Keren B, Kanca O, Mao X, Wegner DJ, Sisco K, Shinawi M, Wangler MF, Weksberg R, Yamamoto S, Costain G, Bellen HJ. Rare de novo gain-of-function missense variants in DOT1L are associated with developmental delay and congenital anomalies. Am J Hum Genet 2023; 110:1919-1937. [PMID: 37827158 PMCID: PMC10645550 DOI: 10.1016/j.ajhg.2023.09.009] [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: 05/25/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Abstract
Misregulation of histone lysine methylation is associated with several human cancers and with human developmental disorders. DOT1L is an evolutionarily conserved gene encoding a lysine methyltransferase (KMT) that methylates histone 3 lysine-79 (H3K79) and was not previously associated with a Mendelian disease in OMIM. We have identified nine unrelated individuals with seven different de novo heterozygous missense variants in DOT1L through the Undiagnosed Disease Network (UDN), the SickKids Complex Care genomics project, and GeneMatcher. All probands had some degree of global developmental delay/intellectual disability, and most had one or more major congenital anomalies. To assess the pathogenicity of the DOT1L variants, functional studies were performed in Drosophila and human cells. The fruit fly DOT1L ortholog, grappa, is expressed in most cells including neurons in the central nervous system. The identified DOT1L variants behave as gain-of-function alleles in flies and lead to increased H3K79 methylation levels in flies and human cells. Our results show that human DOT1L and fly grappa are required for proper development and that de novo heterozygous variants in DOT1L are associated with a Mendelian disease.
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Affiliation(s)
- Zelha Nil
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ashish R Deshwar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China; National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410005, China
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, the University of Auckland, Auckland, New Zealand
| | - Ian Hayes
- Genetic Health Service New Zealand- Northern Hub, Auckland District Health Board, Auckland, New Zealand
| | - Patrick Yap
- Genetic Health Service New Zealand- Northern Hub, Auckland District Health Board, Auckland, New Zealand
| | | | - Carolyn Wilson
- Mission Fullerton Genetics Center, Asheville, NC 28803, USA
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Arve Vøllo
- Department of Pediatrics, Hospital of Østfold, 1714 Grålum, Norway
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children - Orlando Health, Orlando, FL, USA; Clinical Genetics Service, Guy's Hospital, Guy's and St Thomas' NHS Trust, London, England, UK
| | - Patricia G Wheeler
- Division of Genetics, Arnold Palmer Hospital for Children - Orlando Health, Orlando, FL, USA
| | - Jessica Zon
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Moira Blyth
- North of Scotland Regional Genetics Service, Clinical Genetics Centre, Ashgrove House, Foresterhill, Aberdeen, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, M13 9WL Manchester, UK
| | - Alexandra Afenjar
- Service de génétique, CRMR des malformations et maladies congénitales du cervelet et CRMR déficience intellectuelle, hôpital Trousseau, AP-HP, Paris, France
| | - Cyril Mignot
- Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, Paris, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | | | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, 75013 Paris, France
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xiao Mao
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410005, China; Clinical Research Center for Placental Medicine in Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410005, China
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathleen Sisco
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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21
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Thorpe HJ, Owings KG, Aziz MC, Haller M, Coelho E, Chow CY. Drosophila models of PIGA-CDG mirror patient phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564441. [PMID: 37961693 PMCID: PMC10634882 DOI: 10.1101/2023.10.27.564441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Mutations in the phosphatidylinositol glycan biosynthesis class A (PIGA) gene cause a rare, X-linked recessive congenital disorder of glycosylation (CDG). PIGA-CDG is characterized by seizures, intellectual and developmental delay, and congenital malformations. The PIGA gene encodes an enzyme involved in the first step of GPI anchor biosynthesis. There are over 100 GPI anchored proteins that attach to the cell surface and are involved in cell signaling, immunity, and adhesion. Little is known about the pathophysiology of PIGA-CDG. Here we describe the first Drosophila model of PIGA-CDG and demonstrate that loss of PIG-A function in Drosophila accurately models the human disease. As expected, complete loss of PIG-A function is larval lethal. Heterozygous null animals appear healthy, but when challenged, have a seizure phenotype similar to what is observed in patients. To identify the cell-type specific contributions to disease, we generated neuron- and glia-specific knockdown of PIG-A. Neuron-specific knockdown resulted in reduced lifespan and a number of neurological phenotypes, but no seizure phenotype. Glia-knockdown also reduced lifespan and, notably, resulted in a very strong seizure phenotype. RNAseq analyses demonstrated that there are fundamentally different molecular processes that are disrupted when PIG-A function is eliminated in different cell types. In particular, loss of PIG-A in neurons resulted in upregulation of glycolysis, but loss of PIG-A in glia resulted in upregulation of protein translation machinery. Here we demonstrate that Drosophila is a good model of PIGA-CDG and provide new data resources for future study of PIGA-CDG and other GPI anchor disorders.
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Affiliation(s)
| | | | | | - Madelyn Haller
- Department of Human Genetics, University of Utah School of Medicine
| | - Emily Coelho
- Department of Human Genetics, University of Utah School of Medicine
| | - Clement Y. Chow
- Department of Human Genetics, University of Utah School of Medicine
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22
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Sanfilippo P, Kim AJ, Bhukel A, Yoo J, Mirshahidi PS, Pandey V, Bevir H, Yuen A, Mirshahidi PS, Guo P, Li HS, Wohlschlegel JA, Aso Y, Zipursky SL. Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560011. [PMID: 37873314 PMCID: PMC10592863 DOI: 10.1101/2023.10.02.560011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Neurons express different combinations of neurotransmitter receptor (NR) subunits and receive inputs from multiple neuron types expressing different neurotransmitters. Localizing NR subunits to specific synaptic inputs has been challenging. Here we use epitope tagged endogenous NR subunits, expansion light-sheet microscopy, and EM connectomics to molecularly characterize synapses in Drosophila. We show that in directionally selective motion sensitive neurons, different multiple NRs elaborated a highly stereotyped molecular topography with NR localized to specific domains receiving cell-type specific inputs. Developmental studies suggested that NRs or complexes of them with other membrane proteins determines patterns of synaptic inputs. In support of this model, we identify a transmembrane protein associated selectively with a subset of spatially restricted synapses and demonstrate through genetic analysis its requirement for synapse formation. We propose that mechanisms which regulate the precise spatial distribution of NRs provide a molecular cartography specifying the patterns of synaptic connections onto dendrites.
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Affiliation(s)
- Piero Sanfilippo
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexander J Kim
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Anuradha Bhukel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Juyoun Yoo
- Neuroscience Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Pegah S Mirshahidi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Vijaya Pandey
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Harry Bevir
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Ashley Yuen
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Parmis S Mirshahidi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Peiyi Guo
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hong-Sheng Li
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - S Lawrence Zipursky
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Lead Contact
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23
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Loehlin DW, McClain GL, Xu M, Kedia R, Root E. Demonstration of in vivo engineered tandem duplications of varying sizes using CRISPR and recombinases in Drosophila melanogaster. G3 (BETHESDA, MD.) 2023; 13:jkad155. [PMID: 37462278 PMCID: PMC10542505 DOI: 10.1093/g3journal/jkad155] [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: 01/08/2023] [Revised: 01/08/2023] [Accepted: 06/09/2023] [Indexed: 07/28/2023]
Abstract
Tandem gene duplicates are important parts of eukaryotic genome structure, yet the phenotypic effects of new tandem duplications are not well-understood, in part owing to a lack of techniques to build and modify them. We introduce a method, Recombinase-Mediated Tandem Duplication, to engineer specific tandem duplications in vivo using CRISPR and recombinases. We describe construction of four different tandem duplications of the Alcohol Dehydrogenase (Adh) gene in Drosophila melanogaster, with duplicated block sizes ranging from 4.2 to 20.7 kb. Flies with the Adh duplications show elevated ADH enzyme activity over unduplicated single copies. This approach to engineering duplications is combinatoric, opening the door to systematic study of the relationship between the structure of tandem duplications and their effects on expression.
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Affiliation(s)
- David W Loehlin
- Biology Department, Williams College, Williamstown, MA 01267, USA
| | | | - Manting Xu
- Biology Department, Williams College, Williamstown, MA 01267, USA
| | - Ria Kedia
- Biology Department, Williams College, Williamstown, MA 01267, USA
| | - Elise Root
- Biology Department, Williams College, Williamstown, MA 01267, USA
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24
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Dutta D, Kanca O, Byeon SK, Marcogliese PC, Zuo Z, Shridharan RV, Park JH, Lin G, Ge M, Heimer G, Kohler JN, Wheeler MT, Kaipparettu BA, Pandey A, Bellen HJ. A defect in mitochondrial fatty acid synthesis impairs iron metabolism and causes elevated ceramide levels. Nat Metab 2023; 5:1595-1614. [PMID: 37653044 PMCID: PMC11151872 DOI: 10.1038/s42255-023-00873-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
In most eukaryotic cells, fatty acid synthesis (FAS) occurs in the cytoplasm and in mitochondria. However, the relative contribution of mitochondrial FAS (mtFAS) to the cellular lipidome is not well defined. Here we show that loss of function of Drosophila mitochondrial enoyl coenzyme A reductase (Mecr), which is the enzyme required for the last step of mtFAS, causes lethality, while neuronal loss of Mecr leads to progressive neurodegeneration. We observe a defect in Fe-S cluster biogenesis and increased iron levels in flies lacking mecr, leading to elevated ceramide levels. Reducing the levels of either iron or ceramide suppresses the neurodegenerative phenotypes, indicating an interplay between ceramide and iron metabolism. Mutations in human MECR cause pediatric-onset neurodegeneration, and we show that human-derived fibroblasts display similar elevated ceramide levels and impaired iron homeostasis. In summary, this study identifies a role of mecr/MECR in ceramide and iron metabolism, providing a mechanistic link between mtFAS and neurodegeneration.
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Affiliation(s)
- Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Seul Kee Byeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Rishi V Shridharan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Guang Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Ming Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Gali Heimer
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jennefer N Kohler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew T Wheeler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Benny A Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Manipal Academy of Higher Education, Manipal, India
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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25
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Sun R, Raban R, Akbari OS. CRISPR-Cas9 Methods and Key Considerations in the Production of Aedes aegypti Mutant Strains. Cold Spring Harb Protoc 2023; 2023:607-613. [PMID: 36931732 PMCID: PMC10901255 DOI: 10.1101/pdb.top107693] [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] [Indexed: 03/19/2023]
Abstract
Since the characterization of the CRISPR-Cas9 system in prokaryotes, it has become the prime choice in gene editing because of its exceptional flexibility, ease of use, high efficiency, and superior specificity. As a result, CRISPR-Cas9-mediated gene-editing technologies have enabled researchers not only to engineer transgenic animal strains with site-directed insertions more efficiently but also to generate desired mutants for previously intractable species. One such species is the invasive yellow fever mosquito, Aedes aegypti, which is notorious for its ability to transmit many blood-borne human pathogens. Methods for developing new transgenic strains of the yellow fever mosquito may aid in the effort to control its populations and provide significant benefits for the public. Here, we provide an overview of injection and noninjection methods for generating transgenic mosquitoes and also highlight important experimental design features.
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Affiliation(s)
- Ruichen Sun
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093, USA
| | - Robyn Raban
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093, USA
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26
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Eroglu M, Yu B, Derry WB. Efficient CRISPR/Cas9 mediated large insertions using long single-stranded oligonucleotide donors in C. elegans. FEBS J 2023; 290:4429-4439. [PMID: 37254814 DOI: 10.1111/febs.16876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/05/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Highly efficient generation of deletions, substitutions, and small insertions (up to ~ 150 bp) into the Caenorhabditis elegans genome by CRISPR/Cas9 has been facilitated by the use of single-stranded oligonucleotide donors as repair templates. However, insertion of larger sequences such as fluorescent markers and other functional domains remains challenging due to uncertainty of optimal performance between single-stranded or double-stranded repair templates and labor-intensive as well as inefficient protocols for their preparations. Here, we simplify the generation of long ssDNA as donors in CRISPR/Cas9. High yields of ssDNA can be rapidly generated using a standard PCR followed by a single enzymatic digest with lambda exonuclease. Comparison of long ssDNA donors obtained using this method to dsDNA demonstrates orders of magnitude increased insertion frequency for ssDNA donors. This can be leveraged to simultaneously generate multiple large insertions as well as successful edits without the use of selection or co-conversion (co-CRISPR) markers when necessary. Our approach complements the CRISPR/Cas9 toolkit for C. elegans to enable highly efficient insertion of longer sequences with a simple, standardized, and labor-minimal protocol.
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Affiliation(s)
- Matthew Eroglu
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Canada
| | - Bin Yu
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - W Brent Derry
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Canada
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27
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Guichard A, Lu S, Kanca O, Bressan D, Huang Y, Ma M, Sanz Juste S, Andrews JC, Jay KL, Sneider M, Schwartz R, Huang MC, Bei D, Pan H, Ma L, Lin WW, Auradkar A, Bhagwat P, Park S, Wan KH, Ohsako T, Takano-Shimizu T, Celniker SE, Wangler MF, Yamamoto S, Bellen HJ, Bier E. A comprehensive Drosophila resource to identify key functional interactions between SARS-CoV-2 factors and host proteins. Cell Rep 2023; 42:112842. [PMID: 37480566 PMCID: PMC10962759 DOI: 10.1016/j.celrep.2023.112842] [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: 02/21/2023] [Revised: 05/18/2023] [Accepted: 07/05/2023] [Indexed: 07/24/2023] Open
Abstract
Development of effective therapies against SARS-CoV-2 infections relies on mechanistic knowledge of virus-host interface. Abundant physical interactions between viral and host proteins have been identified, but few have been functionally characterized. Harnessing the power of fly genetics, we develop a comprehensive Drosophila COVID-19 resource (DCR) consisting of publicly available strains for conditional tissue-specific expression of all SARS-CoV-2 encoded proteins, UAS-human cDNA transgenic lines encoding established host-viral interacting factors, and GAL4 insertion lines disrupting fly homologs of SARS-CoV-2 human interacting proteins. We demonstrate the utility of the DCR to functionally assess SARS-CoV-2 genes and candidate human binding partners. We show that NSP8 engages in strong genetic interactions with several human candidates, most prominently with the ATE1 arginyltransferase to induce actin arginylation and cytoskeletal disorganization, and that two ATE1 inhibitors can reverse NSP8 phenotypes. The DCR enables parallel global-scale functional analysis of SARS-CoV-2 components in a prime genetic model system.
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Affiliation(s)
- Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Daniel Bressan
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Sara Sanz Juste
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Department of Epigenetics & Molecular Carcinogenesis at MD Anderson, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan C Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Kristy L Jay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Marketta Sneider
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Ruth Schwartz
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Mei-Chu Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Liwen Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Wen-Wen Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Pranjali Bhagwat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Soo Park
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kenneth H Wan
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Takashi Ohsako
- Advanced Technology Center, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Toshiyuki Takano-Shimizu
- Kyoto Drosophila Stock Center and Faculty of Applied Biology, Kyoto Institute of Technology, Kyoto 616-8354, Japan
| | - Susan E Celniker
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Tata Institute for Genetics and Society - UCSD, La Jolla, CA 92093, USA.
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28
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Bustillo ME, Douthit J, Astigarraga S, Treisman JE. Two distinct mechanisms of Plexin A function in Drosophila optic lobe lamination and morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552282. [PMID: 37609142 PMCID: PMC10441316 DOI: 10.1101/2023.08.07.552282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Visual circuit development is characterized by subdivision of neuropils into layers that house distinct sets of synaptic connections. We find that in the Drosophila medulla, this layered organization depends on the axon guidance regulator Plexin A. In plexin A null mutants, synaptic layers of the medulla neuropil and arborizations of individual neurons are wider and less distinct than in controls. Analysis of Semaphorin function indicates that Semaphorin 1a, provided by cells that include Tm5 neurons, is the primary partner for Plexin A in medulla lamination. Removal of the cytoplasmic domain of endogenous Plexin A does not disrupt the formation of medulla layers; however, both null and cytoplasmic domain deletion mutations of plexin A result in an altered overall shape of the medulla neuropil. These data suggest that Plexin A acts as a receptor to mediate morphogenesis of the medulla neuropil, and as a ligand for Semaphorin 1a to subdivide it into layers. Its two independent functions illustrate how a few guidance molecules can organize complex brain structures by each playing multiple roles. Summary statement The axon guidance molecule Plexin A has two functions in Drosophila medulla development; morphogenesis of the neuropil requires its cytoplasmic domain, but establishing synaptic layers through Semaphorin 1a does not.
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29
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Abruzzi KC, Ratner C, Rosbash M. Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells. RNA (NEW YORK, N.Y.) 2023; 29:1230-1242. [PMID: 37169395 PMCID: PMC10351885 DOI: 10.1261/rna.079608.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/28/2023] [Indexed: 05/13/2023]
Abstract
RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to an RBP. When the RBP binds to an mRNA, ADAR catalyzes A to G modifications in the target mRNA that can be easily identified in standard RNA sequencing. In STAMP, the concept is the same except the ADARcd is replaced by the RNA editing enzyme APOBEC. Here we compared TRIBE and STAMP side-by-side in human and Drosophila cells. The goal is to learn the pros and cons of each method so that researchers can choose the method best suited to their RBP and system. In human cells, TRIBE and STAMP were performed using the RBP TDP-43. Although they both identified TDP-43 target mRNAs, combining the two methods more successfully identified high-confidence targets. In Drosophila cells, RBP-APOBEC fusions generated only low numbers of editing sites, comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (Drosophila EIF4E-BP), indicating that STAMP does not work well in Drosophila.
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Affiliation(s)
- Katharine C Abruzzi
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Corrie Ratner
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
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30
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Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, White BH, Perrimon N. split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80. Proc Natl Acad Sci U S A 2023; 120:e2304730120. [PMID: 37276389 PMCID: PMC10268248 DOI: 10.1073/pnas.2304730120] [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: 03/22/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Abstract
The split-Gal4 system allows for intersectional genetic labeling of highly specific cell types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell type-specific genetic drivers based on in silico predictions generated by single-cell RNAseq (scRNAseq) datasets, and we describe an algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible.
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Affiliation(s)
- Ben Ewen-Campen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Haojiang Luan
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD20892
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Rohit Singh
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Neha Joshi
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Tanuj Thakkar
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02143
| | - Benjamin H. White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD20892
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- HHMI, Boston, MA02115
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31
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Han W, Li Z, Guo Y, He K, Li W, Xu C, Ge L, He M, Yin X, Zhou J, Li C, Yao D, Bao J, Liang H. Efficient precise integration of large DNA sequences with 3'-overhang dsDNA donors using CRISPR/Cas9. Proc Natl Acad Sci U S A 2023; 120:e2221127120. [PMID: 37216515 PMCID: PMC10235934 DOI: 10.1073/pnas.2221127120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
CRISPR/Cas9 genome-editing tools have tremendously boosted our capability of manipulating the eukaryotic genomes in biomedical research and innovative biotechnologies. However, the current approaches that allow precise integration of gene-sized large DNA fragments generally suffer from low efficiency and high cost. Herein, we developed a versatile and efficient approach, termed LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in), by utilizing specially designed 3'-overhang double-stranded DNA (odsDNA) donors harboring 50-nt homology arm. The length of the 3'-overhangs of odsDNA is specified by the five consecutive phosphorothioate modifications. Compared with existing methods, LOCK allows highly efficient targeted insertion of kilobase-sized DNA fragments into the mammalian genomes with low cost and low off-target effects, yielding >fivefold higher knock-in frequencies than conventional homologous recombination-based approaches. This newly designed LOCK approach based on homology-directed repair is a powerful tool suitable for gene-sized fragment integration that is urgently needed for genetic engineering, gene therapies, and synthetic biology.
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Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Yijun Guo
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Kaining He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Wenqing Li
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Caoling Xu
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Lishuang Ge
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Chengxu Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Jianqiang Bao
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
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32
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Chung HL, Ye Q, Park YJ, Zuo Z, Mok JW, Kanca O, Tattikota SG, Lu S, Perrimon N, Lee HK, Bellen HJ. Very-long-chain fatty acids induce glial-derived sphingosine-1-phosphate synthesis, secretion, and neuroinflammation. Cell Metab 2023; 35:855-874.e5. [PMID: 37084732 PMCID: PMC10160010 DOI: 10.1016/j.cmet.2023.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 01/10/2023] [Accepted: 03/29/2023] [Indexed: 04/23/2023]
Abstract
VLCFAs (very-long-chain fatty acids) are the most abundant fatty acids in myelin. Hence, during demyelination or aging, glia are exposed to higher levels of VLCFA than normal. We report that glia convert these VLCFA into sphingosine-1-phosphate (S1P) via a glial-specific S1P pathway. Excess S1P causes neuroinflammation, NF-κB activation, and macrophage infiltration into the CNS. Suppressing the function of S1P in fly glia or neurons, or administration of Fingolimod, an S1P receptor antagonist, strongly attenuates the phenotypes caused by excess VLCFAs. In contrast, elevating the VLCFA levels in glia and immune cells exacerbates these phenotypes. Elevated VLCFA and S1P are also toxic in vertebrates based on a mouse model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE). Indeed, reducing VLCFA with bezafibrate ameliorates the phenotypes. Moreover, simultaneous use of bezafibrate and fingolimod synergizes to improve EAE, suggesting that lowering VLCFA and S1P is a treatment avenue for MS.
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Affiliation(s)
- Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Qi Ye
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ye-Jin Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jung-Wan Mok
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Nobert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hyun Kyoung Lee
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
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Yarnall MTN, Ioannidi EI, Schmitt-Ulms C, Krajeski RN, Lim J, Villiger L, Zhou W, Jiang K, Garushyants SK, Roberts N, Zhang L, Vakulskas CA, Walker JA, Kadina AP, Zepeda AE, Holden K, Ma H, Xie J, Gao G, Foquet L, Bial G, Donnelly SK, Miyata Y, Radiloff DR, Henderson JM, Ujita A, Abudayyeh OO, Gootenberg JS. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat Biotechnol 2023; 41:500-512. [PMID: 36424489 PMCID: PMC10257351 DOI: 10.1038/s41587-022-01527-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022]
Abstract
Programmable genome integration of large, diverse DNA cargo without DNA repair of exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We present programmable addition via site-specific targeting elements (PASTE), which uses a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase for targeted genomic recruitment and integration of desired payloads. We demonstrate integration of sequences as large as ~36 kilobases at multiple genomic loci across three human cell lines, primary T cells and non-dividing primary human hepatocytes. To augment PASTE, we discovered 25,614 serine integrases and cognate attachment sites from metagenomes and engineered orthologs with higher activity and shorter recognition sequences for efficient programmable integration. PASTE has editing efficiencies similar to or exceeding those of homology-directed repair and non-homologous end joining-based methods, with activity in non-dividing cells and in vivo with fewer detectable off-target events. PASTE expands the capabilities of genome editing by allowing large, multiplexed gene insertion without reliance on DNA repair pathways.
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Affiliation(s)
- Matthew T N Yarnall
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eleonora I Ioannidi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- ETH Zürich, Zürich, Switzerland
| | - Cian Schmitt-Ulms
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Justin Lim
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Liyang Zhang
- Integrated DNA Technologies, Coralville, IA, USA
| | | | | | | | | | | | - Hong Ma
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jun Xie
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Guangping Gao
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Greg Bial
- Yecuris Corporation, Tualatin, OR, USA
| | | | | | | | | | | | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
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34
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Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, White BH, Perrimon N. split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534001. [PMID: 36993523 PMCID: PMC10055387 DOI: 10.1101/2023.03.24.534001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
The split-Gal4 system allows for intersectional genetic labeling of highly specific cell-types and tissues in Drosophila . However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a new split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is fully repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell-type specific genetic drivers based on in silico predictions generated by single cell RNAseq (scRNAseq) datasets, and we describe a new algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible. Significance statement The split-Gal4 system allows Drosophila researchers to drive transgene expression with extraordinary cell type specificity. However, the existing split-Gal4 system cannot be controlled temporally, and therefore cannot be applied to many important areas of research. Here, we present a new split-Gal4 system based on a self-excising split-intein, which is fully controllable by Gal80, as well as a related drug-inducible split GeneSwitch system. This approach can both leverage and inform single-cell RNAseq datasets, and we introduce an algorithm to identify pairs of genes that precisely and narrowly mark a desired cell cluster. Our split-intein Gal4 system will be of value to the Drosophila research community, and allow for the creation of highly specific genetic drivers that are also inducible/repressible.
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Affiliation(s)
- Ben Ewen-Campen
- These authors contributed equally
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Haojiang Luan
- These authors contributed equally
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Jun Xu
- These authors contributed equally
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, China
| | - Rohit Singh
- These authors contributed equally
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Neha Joshi
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tanuj Thakkar
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge MA 02143
| | - Benjamin H White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- HHMI, Boston, MA 02115, USA
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35
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di Pietro F, Osswald M, De Las Heras JM, Cristo I, López-Gay J, Wang Z, Pelletier S, Gaugué I, Leroy A, Martin C, Morais-de-Sá E, Bellaïche Y. Systematic analysis of RhoGEF/GAP localizations uncovers regulators of mechanosensing and junction formation during epithelial cell division. Curr Biol 2023; 33:858-874.e7. [PMID: 36917931 PMCID: PMC10017266 DOI: 10.1016/j.cub.2023.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 02/17/2023]
Abstract
Cell proliferation is central to epithelial tissue development, repair, and homeostasis. During cell division, small RhoGTPases control both actomyosin dynamics and cell-cell junction remodeling to faithfully segregate the genome while maintaining tissue polarity and integrity. To decipher the mechanisms of RhoGTPase spatiotemporal regulation during epithelial cell division, we generated a transgenic fluorescently tagged library for the 48 Drosophila Rho guanine exchange factors (RhoGEFs) and GTPase-activating proteins (GAPs), and we systematically characterized their endogenous distributions by time-lapse microscopy. Therefore, we unveiled candidate regulators of the interplay between actomyosin and junctional dynamics during epithelial cell division. Building on these findings, we established that the conserved RhoGEF Cysts and RhoGEF4 play sequential and distinct roles to couple cytokinesis with de novo junction formation. During ring contraction, Cysts via Rho1 participates in the neighbor mechanosensing response, promoting daughter-daughter cell membrane juxtaposition in preparation to de novo junction formation. Subsequently and upon midbody formation, RhoGEF4 via Rac acts in the dividing cell to ensure the withdrawal of the neighboring cell membranes, thus controlling de novo junction length and cell-cell arrangements upon cytokinesis. Altogether, our findings delineate how the RhoGTPases Rho and Rac are locally and temporally activated during epithelial cytokinesis, highlighting the RhoGEF/GAP library as a key resource to understand the broad range of biological processes regulated by RhoGTPases.
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Affiliation(s)
- Florencia di Pietro
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Mariana Osswald
- IBMC - Instituto de Biologia Molecular e Celular; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - José M De Las Heras
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Inês Cristo
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Jesús López-Gay
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Zhimin Wang
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Stéphane Pelletier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Isabelle Gaugué
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Adrien Leroy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Charlotte Martin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Eurico Morais-de-Sá
- IBMC - Instituto de Biologia Molecular e Celular; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Yohanns Bellaïche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France.
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36
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Richardson C, Kelsh RN, J. Richardson R. New advances in CRISPR/Cas-mediated precise gene-editing techniques. Dis Model Mech 2023; 16:dmm049874. [PMID: 36847161 PMCID: PMC10003097 DOI: 10.1242/dmm.049874] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutations in a variety of model organisms, from Escherichia coli to zebrafish, rodents and large mammals. CRISPR/Cas-based gene editing effectively generates insertions or deletions (indels), which allow for rapid gene disruption. However, a large proportion of human genetic diseases are caused by single-base-pair substitutions, which result in more subtle alterations to protein function, and which require more complex and precise editing to recreate in model systems. Precise genome editing (PGE) methods, however, typically have efficiencies of less than a tenth of those that generate less-specific indels, and so there has been a great deal of effort to improve PGE efficiency. Such optimisations include optimal guide RNA and mutation-bearing donor DNA template design, modulation of DNA repair pathways that underpin how edits result from Cas-induced cuts, and the development of Cas9 fusion proteins that introduce edits via alternative mechanisms. In this Review, we provide an overview of the recent progress in optimising PGE methods and their potential for generating models of human genetic disease.
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Affiliation(s)
- Chris Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Rebecca J. Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
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Loehlin DW, McClain GL, Xu M, Kedia R, Root E. Demonstration of in vivo engineered tandem duplications of varying sizes using CRISPR and recombinases in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.08.523181. [PMID: 36711585 PMCID: PMC9881931 DOI: 10.1101/2023.01.08.523181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Tandem gene duplicates are important parts of eukaryotic genome structure, yet the phenotypic effects of new tandem duplications are not well-understood, in part owing to a lack of techniques to build and modify them. We introduce a method, Recombinase-Mediated Tandem Duplication (RMTD), to engineer specific tandem duplications in vivo using CRISPR and recombinases. We describe construction of four different tandem duplications of the Alcohol Dehydrogenase ( Adh ) gene in Drosophila melanogaster , with duplicated block sizes ranging from 4.2 kb to 20.7 kb. Flies with the Adh duplications show elevated ADH enzyme activity over unduplicated single copies. This approach to engineering duplications is combinatoric, opening the door to systematic study of the relationship between the structure of tandem duplications and their effects on expression.
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Affiliation(s)
| | | | - Manting Xu
- Biology Department, Williams College, Williamstown, MA 01267
| | - Ria Kedia
- Biology Department, Williams College, Williamstown, MA 01267
| | - Elise Root
- Biology Department, Williams College, Williamstown, MA 01267
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38
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Pan X, Dutta D, Lu S, Bellen HJ. Sphingolipids in neurodegenerative diseases. Front Neurosci 2023; 17:1137893. [PMID: 36875645 PMCID: PMC9978793 DOI: 10.3389/fnins.2023.1137893] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/27/2023] [Indexed: 02/18/2023] Open
Abstract
Neurodegenerative Diseases (NDDs) are a group of disorders that cause progressive deficits of neuronal function. Recent evidence argues that sphingolipid metabolism is affected in a surprisingly broad set of NDDs. These include some lysosomal storage diseases (LSDs), hereditary sensory and autonomous neuropathy (HSAN), hereditary spastic paraplegia (HSP), infantile neuroaxonal dystrophy (INAD), Friedreich's ataxia (FRDA), as well as some forms of amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD). Many of these diseases have been modeled in Drosophila melanogaster and are associated with elevated levels of ceramides. Similar changes have also been reported in vertebrate cells and mouse models. Here, we summarize studies using fly models and/or patient samples which demonstrate the nature of the defects in sphingolipid metabolism, the organelles that are implicated, the cell types that are initially affected, and potential therapeutics for these diseases.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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39
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Kim AR, Xu J, Cheloha R, Mohr SE, Zirin J, Ploegh HL, Perrimon N. NanoTag Nanobody Tools for Drosophila In Vitro and In Vivo Studies. Curr Protoc 2022; 2:e628. [PMID: 36571722 PMCID: PMC9811555 DOI: 10.1002/cpz1.628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nanobodies have emerged as powerful protein-binding tools to uncover protein functions. Using functionalized protein binders, proteins of interest can be visualized, degraded, delocalized, or post-translationally modified in vivo. We recently reported the use of two short peptide tags, 10-aa 127D01 and 14-aa VHH05, and their corresponding nanobodies, Nb127D01 and NbVHH05, for both in vitro and in vivo studies in Drosophila. Here, we provide detailed protocols for nanobody production and for visualization of proteins of interest in either fixed or live samples. In addition, we include protocols for endogenous protein tagging using CRISPR-mediated genome engineering. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Nanobody production in S2 cells Basic Protocol 2: Nanobody expression and purification in bacterial cells Basic Protocol 3: Immunostaining with nanobodies Basic Protocol 4: Immunoblotting with nanobodies Basic Protocol 5: Immunoprecipitation with nanobodies prepared from S2 cells Basic Protocol 6: Immunoprecipitation with nanobodies prepared from bacteria Basic Protocol 7: NbVHH05 and Nb127D01 used as chromobodies Basic Protocol 8: NanoTag trap as a method to alter protein localization Support Protocol: CRISPR-mediated tagging of endogenous genes with NanoTags.
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Affiliation(s)
- Ah-Ram Kim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- 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, China
| | - Ross Cheloha
- Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Hidde L Ploegh
- Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
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40
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NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks. Commun Biol 2022; 5:1282. [PMID: 36418514 PMCID: PMC9684490 DOI: 10.1038/s42003-022-04226-7] [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] [Received: 08/23/2021] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
The inference of Gene Regulatory Networks (GRNs) is one of the key challenges in systems biology. Leading algorithms utilize, in addition to gene expression, prior knowledge such as Transcription Factor (TF) DNA binding motifs or results of TF binding experiments. However, such prior knowledge is typically incomplete, therefore, integrating it with gene expression to infer GRNs remains difficult. To address this challenge, we introduce NetREX-CF-Regulatory Network Reconstruction using EXpression and Collaborative Filtering-a GRN reconstruction approach that brings together Collaborative Filtering to address the incompleteness of the prior knowledge and a biologically justified model of gene expression (sparse Network Component Analysis based model). We validated the NetREX-CF using Yeast data and then used it to construct the GRN for Drosophila Schneider 2 (S2) cells. To corroborate the GRN, we performed a large-scale RNA-Seq analysis followed by a high-throughput RNAi treatment against all 465 expressed TFs in the cell line. Our knockdown result has not only extensively validated the GRN we built, but also provides a benchmark that our community can use for evaluating GRNs. Finally, we demonstrate that NetREX-CF can infer GRNs using single-cell RNA-Seq, and outperforms other methods, by using previously published human data.
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41
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Huang Y, Lemire G, Briere LC, Liu F, Wessels MW, Wang X, Osmond M, Kanca O, Lu S, High FA, Walker MA, Rodan LH, Kernohan KD, Sweetser DA, Boycott KM, Bellen HJ. The recurrent de novo c.2011C>T missense variant in MTSS2 causes syndromic intellectual disability. Am J Hum Genet 2022; 109:1923-1931. [PMID: 36067766 PMCID: PMC9606386 DOI: 10.1016/j.ajhg.2022.08.011] [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: 06/01/2022] [Accepted: 08/12/2022] [Indexed: 01/25/2023] Open
Abstract
MTSS2, also known as MTSS1L, binds to plasma membranes and modulates their bending. MTSS2 is highly expressed in the central nervous system (CNS) and appears to be involved in activity-dependent synaptic plasticity. Variants in MTSS2 have not yet been associated with a human phenotype in OMIM. Here we report five individuals with the same heterozygous de novo variant in MTSS2 (GenBank: NM_138383.2: c.2011C>T [p.Arg671Trp]) identified by exome sequencing. The individuals present with global developmental delay, mild intellectual disability, ophthalmological anomalies, microcephaly or relative microcephaly, and shared mild facial dysmorphisms. Immunoblots of fibroblasts from two affected individuals revealed that the variant does not significantly alter MTSS2 levels. We modeled the variant in Drosophila and showed that the fly ortholog missing-in-metastasis (mim) was widely expressed in most neurons and a subset of glia of the CNS. Loss of mim led to a reduction in lifespan, impaired locomotor behavior, and reduced synaptic transmission in adult flies. Expression of the human MTSS2 reference cDNA rescued the mim loss-of-function (LoF) phenotypes, whereas the c.2011C>T variant had decreased rescue ability compared to the reference, suggesting it is a partial LoF allele. However, elevated expression of the variant, but not the reference MTSS2 cDNA, led to similar defects as observed by mim LoF, suggesting that the variant is toxic and may act as a dominant-negative allele when expressed in flies. In summary, our findings support that mim is important for appropriate neural function, and that the MTSS2 c.2011C>T variant causes a syndromic form of intellectual disability.
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Affiliation(s)
- Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lauren C Briere
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fang Liu
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang 050082, Hebei, China
| | - Marja W Wessels
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Xueqi Wang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Frances A High
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Melissa A Walker
- Department of Neurology, Division of Neurogenetics, Child Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lance H Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - David A Sweetser
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA.
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42
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Zhang JL, Chen SJ, Liu XY, Moczek AP, Xu HJ. The transcription factor Zfh1 acts as a wing-morph switch in planthoppers. Nat Commun 2022; 13:5670. [PMID: 36167844 PMCID: PMC9515195 DOI: 10.1038/s41467-022-33422-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Insect wing polyphenism is characterized by its ability to produce two or more distinct wing morphs from a single genotype in response to changing environments. However, the molecular basis of this phenomenon remains poorly understood. Here, we identified a zinc finger homeodomain transcription factor Zfh1 that acts as an upstream regulator for the development of long-winged (LW) or shorted-winged (SW) morphs in planthoppers. Knockdown of Zfh1 directs SW-destined nymphs to develop into LW morphs by down-regulating the transcriptional level of FoxO, a prominent downstream effector of the insulin/IGF signaling (IIS) pathway. The balance between transcriptional regulation via the Zfh1-FoxO cascade and post-translational regulation via the IIS-FoxO cascade provides a flexible regulatory mechanism for the development of alternative wing morphs. These findings help us understand how phenotypic diversity is generated by altering the activity of conserved proteins, and provide an extended framework for the evolution of wing morphological diversity in insects.
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Affiliation(s)
- Jin-Li Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China
| | - Sun-Jie Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China
| | - Xin-Yang Liu
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China
| | - Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN, 47405, USA
| | - Hai-Jun Xu
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China.
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43
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Cheng KC, Burdine RD, Dickinson ME, Ekker SC, Lin AY, Lloyd KCK, Lutz CM, MacRae CA, Morrison JH, O'Connor DH, Postlethwait JH, Rogers CD, Sanchez S, Simpson JH, Talbot WS, Wallace DC, Weimer JM, Bellen HJ. Promoting validation and cross-phylogenetic integration in model organism research. Dis Model Mech 2022; 15:276675. [PMID: 36125045 PMCID: PMC9531892 DOI: 10.1242/dmm.049600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Model organism (MO) research provides a basic understanding of biology and disease due to the evolutionary conservation of the molecular and cellular language of life. MOs have been used to identify and understand the function of orthologous genes, proteins, cells and tissues involved in biological processes, to develop and evaluate techniques and methods, and to perform whole-organism-based chemical screens to test drug efficacy and toxicity. However, a growing richness of datasets and the rising power of computation raise an important question: How do we maximize the value of MOs? In-depth discussions in over 50 virtual presentations organized by the National Institutes of Health across more than 10 weeks yielded important suggestions for improving the rigor, validation, reproducibility and translatability of MO research. The effort clarified challenges and opportunities for developing and integrating tools and resources. Maintenance of critical existing infrastructure and the implementation of suggested improvements will play important roles in maintaining productivity and facilitating the validation of animal models of human biology and disease.
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Affiliation(s)
- Keith C Cheng
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.,Institute for Computational and Data Sciences, Pennsylvania State University, Park, PA 16802, USA
| | - Rebecca D Burdine
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77007, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77007, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55906, USA
| | - Alex Y Lin
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - K C Kent Lloyd
- Mouse Biology Program, School of Medicinel, University of California Davis, Davis, CA 95618, USA.,Department of Surgery, School of Medicine, University of California Davis, Davis, CA 95618, USA
| | - Cathleen M Lutz
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME 04609, USA
| | - Calum A MacRae
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 360 Longwood Avenue, Boston, MA 02215, USA
| | - John H Morrison
- California National Primate Research Center, University of California Davis, Davis, CA 95616, USA.,Department of Neurology, University of California Davis, Davis, CA 95616, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University ofWisconsin-Madison, Madison, WI 53711, USA
| | | | - Crystal D Rogers
- School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA
| | - Julie H Simpson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA 93117, USA
| | - William S Talbot
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Douglas C Wallace
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jill M Weimer
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Neurological Research Institute (TCH), Baylor College of Medicine, Houston, TX 77007, USA
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44
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Huang Y, Ma M, Mao X, Pehlivan D, Kanca O, Un-Candan F, Shu L, Akay G, Mitani T, Lu S, Candan S, Wang H, Xiao B, Lupski JR, Bellen HJ. Novel dominant and recessive variants in human ROBO1 cause distinct neurodevelopmental defects through different mechanisms. Hum Mol Genet 2022; 31:2751-2765. [PMID: 35348658 PMCID: PMC9402236 DOI: 10.1093/hmg/ddac070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 07/27/2023] Open
Abstract
The Roundabout (Robo) receptors, located on growth cones of neurons, induce axon repulsion in response to the extracellular ligand Slit. The Robo family of proteins controls midline crossing of commissural neurons during development in flies. Mono- and bi-allelic variants in human ROBO1 (HGNC: 10249) have been associated with incomplete penetrance and variable expressivity for a breath of phenotypes, including neurodevelopmental defects such as strabismus, pituitary defects, intellectual impairment, as well as defects in heart and kidney. Here, we report two novel ROBO1 variants associated with very distinct phenotypes. A homozygous missense p.S1522L variant in three affected siblings with nystagmus; and a monoallelic de novo p.D422G variant in a proband who presented with early-onset epileptic encephalopathy. We modeled these variants in Drosophila and first generated a null allele by inserting a CRIMIC T2A-GAL4 in an intron. Flies that lack robo1 exhibit reduced viability but have very severe midline crossing defects in the central nervous system. The fly wild-type cDNA driven by T2A-Gal4 partially rescues both defects. Overexpression of the human reference ROBO1 with T2A-GAL4 is toxic and reduces viability, whereas the recessive p.S1522L variant is less toxic, suggesting that it is a partial loss-of-function allele. In contrast, the dominant variant in fly robo1 (p.D413G) affects protein localization, impairs axonal guidance activity and induces mild phototransduction defects, suggesting that it is a neomorphic allele. In summary, our studies expand the phenotypic spectrum associated with ROBO1 variant alleles.
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Affiliation(s)
- Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao Mao
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feride Un-Candan
- Department of Neuroloy, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Li Shu
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sukru Candan
- Department of Medical Genetics, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Hua Wang
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Bo Xiao
- Neurology Department, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
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45
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Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [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: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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46
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Shekhar C, Maeda T. A simple approach for random genomic insertion-deletions using ambiguous sequences in Escherichia coli. J Basic Microbiol 2022; 62:948-962. [PMID: 35739617 DOI: 10.1002/jobm.202100636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/20/2022] [Accepted: 06/11/2022] [Indexed: 11/07/2022]
Abstract
Escherichia coli K-12, being one of the best understood and thoroughly analyzed organisms, is the preferred platform for genetic and biochemical research. Among all genetic engineering approaches applied on E. coli, the homologous recombination approach is versatile and precise, which allows engineering genes or large segments of the chromosome directly by using polymerase chain reaction (PCR) products or synthetic oligonucleotides. The previously explained approaches for random insertion and deletions were reported as technically not easy and laborious. This study, first, finds the minimum length of homology extension that is efficient and accurate for homologous recombination, as 30 nt. Second, proposes an approach utilizing PCR products flanking ambiguous NNN-sequence (30-nt) extensions, which facilitate the homologous recombination to recombine them at multiple regions on the genome and generate insertion-deletion mutations. Further analysis found that these mutations were varying in number, that is, multiple genomic regions were deleted. Moreover, evaluation of the phenotype of all the multiple random insertion-deletion mutants demonstrated no significant changes in the normal metabolism of bacteria. This study not only presents the efficiency of ambiguous sequences in making random deletion mutations, but also demonstrates their further applicability in genomics.
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Affiliation(s)
- Chandra Shekhar
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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47
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Kanca O, Zirin J, Hu Y, Tepe B, Dutta D, Lin WW, Ma L, Ge M, Zuo Z, Liu LP, Levis RW, Perrimon N, Bellen HJ. An expanded toolkit for Drosophila gene tagging using synthesized homology donor constructs for CRISPR-mediated homologous recombination. eLife 2022; 11:e76077. [PMID: 35723254 PMCID: PMC9239680 DOI: 10.7554/elife.76077] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/19/2022] [Indexed: 11/13/2022] Open
Abstract
Previously, we described a large collection of Drosophila strains that each carry an artificial exon containing a T2AGAL4 cassette inserted in an intron of a target gene based on CRISPR-mediated homologous recombination. These alleles permit numerous applications and have proven to be very useful. Initially, the homologous recombination-based donor constructs had long homology arms (>500 bps) to promote precise integration of large constructs (>5 kb). Recently, we showed that in vivo linearization of the donor constructs enables insertion of large artificial exons in introns using short homology arms (100-200 bps). Shorter homology arms make it feasible to commercially synthesize homology donors and minimize the cloning steps for donor construct generation. Unfortunately, about 58% of Drosophila genes lack a suitable coding intron for integration of artificial exons in all of the annotated isoforms. Here, we report the development of new set of constructs that allow the replacement of the coding region of genes that lack suitable introns with a KozakGAL4 cassette, generating a knock-out/knock-in allele that expresses GAL4 similarly as the targeted gene. We also developed custom vector backbones to further facilitate and improve transgenesis. Synthesis of homology donor constructs in custom plasmid backbones that contain the target gene sgRNA obviates the need to inject a separate sgRNA plasmid and significantly increases the transgenesis efficiency. These upgrades will enable the targeting of nearly every fly gene, regardless of exon-intron structure, with a 70-80% success rate.
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Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Duncan Neurological Research Institute, Texas Children HospitalHoustonUnited States
| | - Jonathan Zirin
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Yanhui Hu
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Burak Tepe
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Duncan Neurological Research Institute, Texas Children HospitalHoustonUnited States
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Duncan Neurological Research Institute, Texas Children HospitalHoustonUnited States
| | - Wen-Wen Lin
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Duncan Neurological Research Institute, Texas Children HospitalHoustonUnited States
| | - Liwen Ma
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Duncan Neurological Research Institute, Texas Children HospitalHoustonUnited States
| | - Ming Ge
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Duncan Neurological Research Institute, Texas Children HospitalHoustonUnited States
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Duncan Neurological Research Institute, Texas Children HospitalHoustonUnited States
| | - Lu-Ping Liu
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Robert W Levis
- Department of Embryology, Carnegie Institution for ScienceBaltimoreUnited States
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
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48
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Hillen AEJ, Hruzova M, Rothgangl T, Breur M, Bugiani M, van der Knaap MS, Schwank G, Heine VM. In vivo targeting of a variant causing vanishing white matter using CRISPR/Cas9. Mol Ther Methods Clin Dev 2022; 25:17-25. [PMID: 35317047 PMCID: PMC8917273 DOI: 10.1016/j.omtm.2022.02.006] [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: 08/27/2021] [Accepted: 02/19/2022] [Indexed: 11/17/2022]
Abstract
Vanishing white matter (VWM) is a leukodystrophy caused by recessive variants in subunits of eIF2B. At present, no curative treatment is available and patients often die at young age. Due to its monogenic nature, VWM is a promising candidate for the development of CRISPR/Cas9-mediated gene therapy. Here we tested a dual-AAV approach in VWM mice encoding CRISPR/Cas9 and a DNA donor template to correct a pathogenic variant in Eif2b5. We performed sequencing analysis to assess gene correction rates and examined effects on the VWM phenotype, including motor behavior. Sequence analysis demonstrated that over 90% of CRISPR/Cas9-induced edits at the targeted locus are insertion or deletion (indel) mutations, rather than precise corrections from the DNA donor template by homology-directed repair. Around half of the CRISPR/Cas9-treated animals died prematurely. VWM mice showed no improvement in motor skills, weight, or neurological scores at 7 months of age, and CRISPR/Cas9-treated controls displayed an induced VWM phenotype. In conclusion, CRISPR/Cas9-induced DNA double-strand breaks (DSBs) at the Eif2b5 locus did not lead to sufficient correction of the VWM variant. Moreover, indel formation in Eif2b5 induced an exacerbated VWM phenotype. Therefore, DSB-independent strategies like base- or prime editing might better suited for VWM correction.
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Affiliation(s)
- Anne E J Hillen
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Marjolein Breur
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marianna Bugiani
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
| | - Gerald Schwank
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vivi M Heine
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands.,Department of Child and Adolescence Psychiatry, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
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49
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Wang Y, Lobb-Rabe M, Ashley J, Chatterjee P, Anand V, Bellen HJ, Kanca O, Carrillo RA. Systematic expression profiling of Dpr and DIP genes reveals cell surface codes in Drosophila larval motor and sensory neurons. Development 2022; 149:dev200355. [PMID: 35502740 PMCID: PMC9188756 DOI: 10.1242/dev.200355] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/20/2022] [Indexed: 07/26/2023]
Abstract
In complex nervous systems, neurons must identify their correct partners to form synaptic connections. The prevailing model to ensure correct recognition posits that cell-surface proteins (CSPs) in individual neurons act as identification tags. Thus, knowing what cells express which CSPs would provide insights into neural development, synaptic connectivity, and nervous system evolution. Here, we investigated expression of Dpr and DIP genes, two CSP subfamilies belonging to the immunoglobulin superfamily, in Drosophila larval motor neurons (MNs), muscles, glia and sensory neurons (SNs) using a collection of GAL4 driver lines. We found that Dpr genes are more broadly expressed than DIP genes in MNs and SNs, and each examined neuron expresses a unique combination of Dpr and DIP genes. Interestingly, many Dpr and DIP genes are not robustly expressed, but are found instead in gradient and temporal expression patterns. In addition, the unique expression patterns of Dpr and DIP genes revealed three uncharacterized MNs. This study sets the stage for exploring the functions of Dpr and DIP genes in Drosophila MNs and SNs and provides genetic access to subsets of neurons.
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Affiliation(s)
- Yupu Wang
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Meike Lobb-Rabe
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - James Ashley
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
| | - Purujit Chatterjee
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
| | - Veera Anand
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics and Jan and Dan Duncan Neurobiological Research Institute, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Department of Neuroscience and Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics and Jan and Dan Duncan Neurobiological Research Institute, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Robert A. Carrillo
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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50
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Task D, Lin CC, Vulpe A, Afify A, Ballou S, Brbic M, Schlegel P, Raji J, Jefferis GSXE, Li H, Menuz K, Potter CJ. Chemoreceptor co-expression in Drosophila melanogaster olfactory neurons. eLife 2022; 11:e72599. [PMID: 35442190 PMCID: PMC9020824 DOI: 10.7554/elife.72599] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
Drosophila melanogaster olfactory neurons have long been thought to express only one chemosensory receptor gene family. There are two main olfactory receptor gene families in Drosophila, the odorant receptors (ORs) and the ionotropic receptors (IRs). The dozens of odorant-binding receptors in each family require at least one co-receptor gene in order to function: Orco for ORs, and Ir25a, Ir8a, and Ir76b for IRs. Using a new genetic knock-in strategy, we targeted the four co-receptors representing the main chemosensory families in D. melanogaster (Orco, Ir8a, Ir76b, Ir25a). Co-receptor knock-in expression patterns were verified as accurate representations of endogenous expression. We find extensive overlap in expression among the different co-receptors. As defined by innervation into antennal lobe glomeruli, Ir25a is broadly expressed in 88% of all olfactory sensory neuron classes and is co-expressed in 82% of Orco+ neuron classes, including all neuron classes in the maxillary palp. Orco, Ir8a, and Ir76b expression patterns are also more expansive than previously assumed. Single sensillum recordings from Orco-expressing Ir25a mutant antennal and palpal neurons identify changes in olfactory responses. We also find co-expression of Orco and Ir25a in Drosophila sechellia and Anopheles coluzzii olfactory neurons. These results suggest that co-expression of chemosensory receptors is common in insect olfactory neurons. Together, our data present the first comprehensive map of chemosensory co-receptor expression and reveal their unexpected widespread co-expression in the fly olfactory system.
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Affiliation(s)
- Darya Task
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Chun-Chieh Lin
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Mortimer B. Zuckermann Mind Brain Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Alina Vulpe
- Physiology & Neurobiology Department, University of ConnecticutMansfieldUnited States
| | - Ali Afify
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Sydney Ballou
- Physiology & Neurobiology Department, University of ConnecticutMansfieldUnited States
| | - Maria Brbic
- Department of Computer Science, Stanford UniversityStanfordUnited States
| | - Philipp Schlegel
- Drosophila Connectomics Group, Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Joshua Raji
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Gregory SXE Jefferis
- Drosophila Connectomics Group, Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Neurobiology Division, MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Hongjie Li
- Department of Biology, Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Karen Menuz
- Physiology & Neurobiology Department, University of ConnecticutMansfieldUnited States
| | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
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