1
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Timalsina B, Lee S, Kaang BK. Advances in the labelling and selective manipulation of synapses. Nat Rev Neurosci 2024; 25:668-687. [PMID: 39174832 DOI: 10.1038/s41583-024-00851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Synapses are highly specialized neuronal structures that are essential for neurotransmission, and they are dynamically regulated throughout the lifetime. Although accumulating evidence indicates that these structures are crucial for information processing and storage in the brain, their precise roles beyond neurotransmission are yet to be fully appreciated. Genetically encoded fluorescent tools have deepened our understanding of synaptic structure and function, but developing an ideal methodology to selectively visualize, label and manipulate synapses remains challenging. Here, we provide an overview of currently available synapse labelling techniques and describe their extension to enable synapse manipulation. We categorize these approaches on the basis of their conceptual bases and target molecules, compare their advantages and limitations and propose potential modifications to improve their effectiveness. These methods have broad utility, particularly for investigating mechanisms of synaptic function and synaptopathy.
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Affiliation(s)
- Binod Timalsina
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Bong-Kiun Kaang
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.
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2
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Rojas-Ríos P, Chartier A, Enjolras C, Cremaschi J, Garret C, Boughlita A, Ramat A, Simonelig M. piRNAs are regulators of metabolic reprogramming in stem cells. Nat Commun 2024; 15:8405. [PMID: 39333531 PMCID: PMC11437085 DOI: 10.1038/s41467-024-52709-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Stem cells preferentially use glycolysis instead of oxidative phosphorylation and this metabolic rewiring plays an instructive role in their fate; however, the underlying molecular mechanisms remain largely unexplored. PIWI-interacting RNAs (piRNAs) and PIWI proteins have essential functions in a range of adult stem cells across species. Here, we show that piRNAs and the PIWI protein Aubergine (Aub) are instrumental in activating glycolysis in Drosophila female germline stem cells (GSCs). Higher glycolysis is required for GSC self-renewal and aub loss-of-function induces a metabolic switch in GSCs leading to their differentiation. Aub directly binds glycolytic mRNAs and Enolase mRNA regulation by Aub depends on its 5'UTR. Furthermore, mutations of a piRNA target site in Enolase 5'UTR lead to GSC loss. These data reveal an Aub/piRNA function in translational activation of glycolytic mRNAs in GSCs, and pinpoint a mechanism of regulation of metabolic reprogramming in stem cells based on small RNAs.
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Affiliation(s)
- Patricia Rojas-Ríos
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Aymeric Chartier
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Camille Enjolras
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Julie Cremaschi
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Céline Garret
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Adel Boughlita
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Anne Ramat
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France.
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3
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Teles-Reis J, Jain A, Liu D, Khezri R, Micheli S, Gomez AA, Dillard C, Rusten TE. EyaHOST, a modular genetic system for investigation of intercellular and tumor-host interactions in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.06.611647. [PMID: 39314415 PMCID: PMC11418954 DOI: 10.1101/2024.09.06.611647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Cell biology and genetic analysis of intracellular, intercellular and inter-organ interaction studies in animal models are key for understanding development, physiology, and disease. The MARCM technique can emulate tumor development by simultaneous clonal tumor suppressor loss-of-function generation coupled with GAL4-UAS-driven oncogene and marker expression, but the utility is limited for studying tumor-host interactions due to genetic constraints. To overcome this, we introduce EyaHOST, a novel system that replaces MARCM with the QF2-QUAS binary gene expression system under the eya promoter control, unleashing the fly community genome-wide GAL4-UAS driven tools to manipulate any host cells or tissue at scale. EyaHOST generates epithelial clones in the eye epithelium similar to MARCM. EyaHOST-driven Ras V12 oncogene overexpression coupled with scribble tumor suppressor knockdown recapitulates key cancer features, including systemic catabolic switching and organ wasting. We demonstrate effective tissue-specific manipulation of host compartments such as neighbouring epithelial cells, immune cells, fat body, and muscle using fly avatars with tissue-specific GAL4 drivers. Organ-specific inhibition of autophagy or stimulation of growth-signaling through PTEN knockdown in fat body or muscle prevents cachexia-like wasting. Additionally, we show that Ras V12 , scrib RNAi tumors induce caspase-driven apoptosis in the epithelial microenvironment. Inhibition of apoptosis by p35 expression in the microenvironment promotes tumor growth. EyaHOST offers a versatile modular platform for dissecting tumor-host interactions and other mechanisms involving intercellular and inter-organ communication in Drosophila . Highlights * eyes absent , eye disc-specific enhancer drives clonal KD recombinase flip-out activated QF2 expression in the larval eye epithelium for simultaneous QUAS-driven gain and loss-of-function analysis of gene function. *Clones are visualized by QUAS-tagBFP or QUAS-eGFP facilitating analysis of existing fluorescent reporters.*The GAL4-UAS system and existing genome-wide genetic tools are released to independently manipulate any cell population in the animal for cell biology, intercellular or inter-organ analysis for developmental, physiological, or disease model analysis.*Fly avatars for tumor-host interaction studies with multiple organs allow live monitoring and manipulation of tumors and organs in translucent larva.
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4
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Xu C, Li Z, Lyu C, Hu Y, McLaughlin CN, Wong KKL, Xie Q, Luginbuhl DJ, Li H, Udeshi ND, Svinkina T, Mani DR, Han S, Li T, Li Y, Guajardo R, Ting AY, Carr SA, Li J, Luo L. Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching. Cell 2024; 187:5081-5101.e19. [PMID: 38996528 DOI: 10.1016/j.cell.2024.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/20/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
In developing brains, axons exhibit remarkable precision in selecting synaptic partners among many non-partner cells. Evolutionarily conserved teneurins are transmembrane proteins that instruct synaptic partner matching. However, how intracellular signaling pathways execute teneurins' functions is unclear. Here, we use in situ proximity labeling to obtain the intracellular interactome of a teneurin (Ten-m) in the Drosophila brain. Genetic interaction studies using quantitative partner matching assays in both olfactory receptor neurons (ORNs) and projection neurons (PNs) reveal a common pathway: Ten-m binds to and negatively regulates a RhoGAP, thus activating the Rac1 small GTPases to promote synaptic partner matching. Developmental analyses with single-axon resolution identify the cellular mechanism of synaptic partner matching: Ten-m signaling promotes local F-actin levels and stabilizes ORN axon branches that contact partner PN dendrites. Combining spatial proteomics and high-resolution phenotypic analyses, this study advanced our understanding of both cellular and molecular mechanisms of synaptic partner matching.
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Affiliation(s)
- Chuanyun Xu
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Biology Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Zhuoran Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Biology Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Cheng Lyu
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Yixin Hu
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Biology Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Colleen N McLaughlin
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Kenneth Kin Lam Wong
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Qijing Xie
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Neurosciences Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - David J Luginbuhl
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hongjie Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Namrata D Udeshi
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tanya Svinkina
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shuo Han
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Tongchao Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Yang Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Biology Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Guajardo
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiefu Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Biology Graduate Program, Stanford University, Stanford, CA 94305, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| | - Liqun Luo
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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5
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Walther RF, Lancaster C, Burden JJ, Pichaud F. A dystroglycan-laminin-integrin axis coordinates cell shape remodeling in the developing Drosophila retina. PLoS Biol 2024; 22:e3002783. [PMID: 39226305 PMCID: PMC11398702 DOI: 10.1371/journal.pbio.3002783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/13/2024] [Accepted: 08/03/2024] [Indexed: 09/05/2024] Open
Abstract
Cell shape remodeling is a principal driver of epithelial tissue morphogenesis. While progress continues to be made in our understanding of the pathways that control the apical (top) geometry of epithelial cells, we know comparatively little about those that control cell basal (bottom) geometry. To examine this, we used the Drosophila ommatidium, which is the basic visual unit of the compound eye. The ommatidium is shaped as a hexagonal prism, and generating this 3D structure requires ommatidial cells to adopt specific apical and basal polygonal geometries. Using this model system, we find that generating cell type-specific basal geometries starts with patterning of the basal extracellular matrix, whereby Laminin accumulates at discrete locations across the basal surface of the retina. We find the Dystroglycan receptor complex (DGC) is required for this patterning by promoting localized Laminin accumulation at the basal surface of cells. Moreover, our results reveal that localized accumulation of Laminin and the DGC are required for directing Integrin adhesion. This induces cell basal geometry remodeling by anchoring the basal surface of cells to the extracellular matrix at specific, Laminin-rich locations. We propose that patterning of a basal extracellular matrix by generating discrete Laminin domains can direct Integrin adhesion to induce cell shape remodeling in epithelial morphogenesis.
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Affiliation(s)
- Rhian F Walther
- Cell Biology of Tissue Architecture and Physiology. Laboratory for Molecular Cell Biology (LMCB), University College London, London, United Kingdom
| | - Courtney Lancaster
- Cell Biology of Tissue Architecture and Physiology. Laboratory for Molecular Cell Biology (LMCB), University College London, London, United Kingdom
| | - Jemima J Burden
- Cell Biology of Tissue Architecture and Physiology. Laboratory for Molecular Cell Biology (LMCB), University College London, London, United Kingdom
| | - Franck Pichaud
- Cell Biology of Tissue Architecture and Physiology. Laboratory for Molecular Cell Biology (LMCB), University College London, London, United Kingdom
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6
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Zhu J, Boivin JC, Garner A, Ning J, Zhao YQ, Ohyama T. Feedback inhibition by a descending GABAergic neuron regulates timing of escape behavior in Drosophila larvae. eLife 2024; 13:RP93978. [PMID: 39196635 DOI: 10.7554/elife.93978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
Escape behaviors help animals avoid harm from predators and other threats in the environment. Successful escape relies on integrating information from multiple stimulus modalities (of external or internal origin) to compute trajectories toward safe locations, choose between actions that satisfy competing motivations, and execute other strategies that ensure survival. To this end, escape behaviors must be adaptive. When a Drosophila melanogaster larva encounters a noxious stimulus, such as the focal pressure a parasitic wasp applies to the larval cuticle via its ovipositor, it initiates a characteristic escape response. The escape sequence consists of an initial abrupt bending, lateral rolling, and finally rapid crawling. Previous work has shown that the detection of noxious stimuli primarily relies on class IV multi-dendritic arborization neurons (Class IV neurons) located beneath the body wall, and more recent studies have identified several important components in the nociceptive neural circuitry involved in rolling. However, the neural mechanisms that underlie the rolling-escape sequence remain unclear. Here, we present both functional and anatomical evidence suggesting that bilateral descending neurons within the subesophageal zone of D. melanogaster larva play a crucial role in regulating the termination of rolling and subsequent transition to escape crawling. We demonstrate that these descending neurons (designated SeIN128) are inhibitory and receive inputs from a second-order interneuron upstream (Basin-2) and an ascending neuron downstream of Basin-2 (A00c). Together with optogenetic experiments showing that co-activation of SeIN128 neurons and Basin-2 influence the temporal dynamics of rolling, our findings collectively suggest that the ensemble of SeIN128, Basin-2, and A00c neurons forms a GABAergic feedback loop onto Basin-2, which inhibits rolling and thereby facilitates the shift to escape crawling.
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Affiliation(s)
- Jiayi Zhu
- Department of Biology, McGill University, Montreal, Canada
- Integrated Program of Neuroscience, McGill University, Montreal, Canada
| | - Jean-Christophe Boivin
- Department of Biology, McGill University, Montreal, Canada
- Integrated Program of Neuroscience, McGill University, Montreal, Canada
| | - Alastair Garner
- Department of Biology, McGill University, Montreal, Canada
- Integrated Program of Neuroscience, McGill University, Montreal, Canada
| | - Jing Ning
- Department of Biology, McGill University, Montreal, Canada
| | - Yi Q Zhao
- Department of Biology, McGill University, Montreal, Canada
| | - Tomoko Ohyama
- Department of Biology, McGill University, Montreal, Canada
- Alan Edwards Center for Research on Pain, McGill University, Montreal, Canada
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7
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Lyu C, Li Z, Xu C, Wong KKL, Luginbuhl DJ, McLaughlin CN, Xie Q, Li T, Li H, Luo L. Dimensionality reduction simplifies synaptic partner matching in an olfactory circuit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609939. [PMID: 39253519 PMCID: PMC11383009 DOI: 10.1101/2024.08.27.609939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
The distribution of postsynaptic partners in three-dimensional (3D) space presents complex choices for a navigating axon. Here, we discovered a dimensionality reduction principle in establishing the 3D glomerular map in the fly antennal lobe. Olfactory receptor neuron (ORN) axons first contact partner projection neuron (PN) dendrites at the 2D spherical surface of the antennal lobe during development, regardless of whether the adult glomeruli are at the surface or interior of the antennal lobe. Along the antennal lobe surface, axons of each ORN type take a specific 1D arc-shaped trajectory that precisely intersects with their partner PN dendrites. Altering axon trajectories compromises synaptic partner matching. Thus, a 3D search problem is reduced to 1D, which simplifies synaptic partner matching and may generalize to the wiring process of more complex brains.
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Affiliation(s)
- Cheng Lyu
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Zhuoran Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Biology Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Chuanyun Xu
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Biology Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Kenneth Kin Lam Wong
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David J. Luginbuhl
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Colleen N. McLaughlin
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Qijing Xie
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Neurosciences Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Tongchao Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Present address: Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou 311121, China
| | - Hongjie Li
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Present address: Huffington Center on Aging, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liqun Luo
- Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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8
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Nitta Y, Osaka J, Maki R, Hakeda-Suzuki S, Suzuki E, Ueki S, Suzuki T, Sugie A. Drosophila model to clarify the pathological significance of OPA1 in autosomal dominant optic atrophy. eLife 2024; 12:RP87880. [PMID: 39177028 PMCID: PMC11343565 DOI: 10.7554/elife.87880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Abstract
Autosomal dominant optic atrophy (DOA) is a progressive form of blindness caused by degeneration of retinal ganglion cells and their axons, mainly caused by mutations in the OPA1 mitochondrial dynamin like GTPase (OPA1) gene. OPA1 encodes a dynamin-like GTPase present in the mitochondrial inner membrane. When associated with OPA1 mutations, DOA can present not only ocular symptoms but also multi-organ symptoms (DOA plus). DOA plus often results from point mutations in the GTPase domain, which are assumed to have dominant-negative effects. However, the presence of mutations in the GTPase domain does not always result in DOA plus. Therefore, an experimental system to distinguish between DOA and DOA plus is needed. In this study, we found that loss-of-function mutations of the dOPA1 gene in Drosophila can imitate the pathology of optic nerve degeneration observed in DOA. We successfully rescued this degeneration by expressing the human OPA1 (hOPA1) gene, indicating that hOPA1 is functionally interchangeable with dOPA1 in the fly system. However, mutations previously identified did not ameliorate the dOPA1 deficiency phenotype. By expressing both WT and DOA plus mutant hOPA1 forms in the optic nerve of dOPA1 mutants, we observed that DOA plus mutations suppressed the rescue, facilitating the distinction between loss-of-function and dominant-negative mutations in hOPA1. This fly model aids in distinguishing DOA from DOA plus and guides initial hOPA1 mutation treatment strategies.
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Affiliation(s)
- Yohei Nitta
- Brain Research Institute, Niigata UniversityNiigataJapan
| | - Jiro Osaka
- Brain Research Institute, Niigata UniversityNiigataJapan
- School of Life Science and Technology, Tokyo Institute of TechnologyYokohamaJapan
| | - Ryuto Maki
- School of Life Science and Technology, Tokyo Institute of TechnologyYokohamaJapan
| | - Satoko Hakeda-Suzuki
- School of Life Science and Technology, Tokyo Institute of TechnologyYokohamaJapan
- Research Initiatives and Promotion Organization, Yokohama National UniversityYokohamaJapan
| | - Emiko Suzuki
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan UniversityHachiojiJapan
- Department of Gene Function and Phenomics, National Institute of GeneticsMishimaJapan
| | - Satoshi Ueki
- Division of Ophthalmology and Visual Science, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigataJapan
| | - Takashi Suzuki
- School of Life Science and Technology, Tokyo Institute of TechnologyYokohamaJapan
| | - Atsushi Sugie
- Brain Research Institute, Niigata UniversityNiigataJapan
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9
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Lee H, Langseth CM, Salas SM, Sariyar S, Metousis A, Rueda-Alaña E, Bekiari C, Lundberg E, Garcı A-Moreno F, Grillo M, Nilsson M. Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology. Development 2024; 151:dev202448. [PMID: 39099456 PMCID: PMC11385644 DOI: 10.1242/dev.202448] [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: 10/19/2023] [Accepted: 07/19/2024] [Indexed: 08/06/2024]
Abstract
Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
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Affiliation(s)
- Hower Lee
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | | | - Sergio Marco Salas
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Sanem Sariyar
- Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 17165Stockholm, Sweden
| | - Andreas Metousis
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Eneritz Rueda-Alaña
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Christina Bekiari
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 17165Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Fernando Garcı A-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
| | - Marco Grillo
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
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10
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Chen W, Choi J, Li X, Nathans JF, Martin B, Yang W, Hamazaki N, Qiu C, Lalanne JB, Regalado S, Kim H, Agarwal V, Nichols E, Leith A, Lee C, Shendure J. Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature 2024; 632:1073-1081. [PMID: 39020177 PMCID: PMC11357993 DOI: 10.1038/s41586-024-07706-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter1, we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems.
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Affiliation(s)
- Wei Chen
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
| | - Junhong Choi
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Jenny F Nathans
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Wei Yang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | | | - Samuel Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Haedong Kim
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Eva Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Anh Leith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
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11
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Sui L, Dahmann C. A cellular tilting mechanism important for dynamic tissue shape changes and cell differentiation in Drosophila. Dev Cell 2024; 59:1794-1808.e5. [PMID: 38692272 DOI: 10.1016/j.devcel.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 12/15/2023] [Accepted: 04/11/2024] [Indexed: 05/03/2024]
Abstract
Dynamic changes in three-dimensional cell shape are important for tissue form and function. In the developing Drosophila eye, photoreceptor differentiation requires the progression across the tissue of an epithelial fold known as the morphogenetic furrow. Morphogenetic furrow progression involves apical cell constriction and movement of apical cell edges. Here, we show that cells progressing through the morphogenetic furrow move their basal edges in opposite direction to their apical edges, resulting in a cellular tilting movement. We further demonstrate that cells generate, at their basal side, oriented, force-generating protrusions. Knockdown of the protein kinase Src42A or photoactivation of a dominant-negative form of the small GTPase Rac1 reduces protrusion formation. Impaired protrusion formation stalls basal cell movement and slows down morphogenetic furrow progression and photoreceptor differentiation. This work identifies a cellular tilting mechanism important for the generation of dynamic tissue shape changes and cell differentiation.
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Affiliation(s)
- Liyuan Sui
- School of Science, Technische Universität Dresden, 01062 Dresden, Germany
| | - Christian Dahmann
- School of Science, Technische Universität Dresden, 01062 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany.
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12
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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13
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Hiraiwa S, Takeshita S, Terano T, Hayashi R, Suzuki K, Tajiri R, Kojima T. Unveiling the cell dynamics during the final shape formation of the tarsus in Drosophila adult leg by live imaging. Dev Genes Evol 2024:10.1007/s00427-024-00719-z. [PMID: 38977431 DOI: 10.1007/s00427-024-00719-z] [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: 03/01/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
Organisms display a remarkable diversity in their shapes. Although substantial progress has been made in unraveling the mechanisms that govern cell fate determination during development, the mechanisms by which fate-determined cells give rise to the final shapes of organisms remain largely unknown. This study describes in detail the process of the final shape formation of the tarsus, which is near the distal tip of the adult leg, during the pupal stage in Drosophila melanogaster. Days-long live imaging revealed unexpectedly complicated cellular dynamics. The epithelial cells transiently form the intriguing structure, which we named the Parthenon-like structure. The basal surface of the epithelial cells and localization of the basement membrane protein initially show a mesh-like structure and rapidly shrink into the membranous structure during the formation and disappearance of the Parthenon-like structure. Furthermore, macrophage-like cells are observed moving around actively in the Parthenon-like structure and engulfing epithelial cells. The findings in this research are expected to significantly contribute to our understanding of the mechanisms involved in shaping the final structure of the adult tarsus.
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Affiliation(s)
- Shotaro Hiraiwa
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Biosciences Building 501, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Shumpei Takeshita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Biosciences Building 501, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Tensho Terano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Biosciences Building 501, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Ryuhei Hayashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Biosciences Building 501, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Koyo Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Biosciences Building 501, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Reiko Tajiri
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Biosciences Building 501, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
- Present address: Laboratory for Extracellular Morphogenesis, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - Tetsuya Kojima
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Biosciences Building 501, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan.
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14
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Mao R, Yu J, Deng B, Dai X, Du Y, Du S, Zhang W, Rao Y. Conditional chemoconnectomics (cCCTomics) as a strategy for efficient and conditional targeting of chemical transmission. eLife 2024; 12:RP91927. [PMID: 38686992 PMCID: PMC11060718 DOI: 10.7554/elife.91927] [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: 05/02/2024] Open
Abstract
Dissection of neural circuitry underlying behaviors is a central theme in neurobiology. We have previously proposed the concept of chemoconnectome (CCT) to cover the entire chemical transmission between neurons and target cells in an organism and created tools for studying it (CCTomics) by targeting all genes related to the CCT in Drosophila. Here we have created lines targeting the CCT in a conditional manner after modifying GFP RNA interference, Flp-out, and CRISPR/Cas9 technologies. All three strategies have been validated to be highly effective, with the best using chromatin-peptide fused Cas9 variants and scaffold optimized sgRNAs. As a proof of principle, we conducted a comprehensive intersection analysis of CCT genes expression profiles in the clock neurons, uncovering 43 CCT genes present in clock neurons. Specific elimination of each from clock neurons revealed that loss of the neuropeptide CNMa in two posterior dorsal clock neurons (DN1ps) or its receptor (CNMaR) caused advanced morning activity, indicating a suppressive role of CNMa-CNMaR on morning anticipation, opposite to the promoting role of PDF-PDFR on morning anticipation. These results demonstrate the effectiveness of conditional CCTomics and its tools created here and establish an antagonistic relationship between CNMa-CNMaR and PDF-PDFR signaling in regulating morning anticipation.
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Affiliation(s)
- Renbo Mao
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
- National Institute of Biological Sciences, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Jianjun Yu
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Bowen Deng
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Xihuimin Dai
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Yuyao Du
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Sujie Du
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Wenxia Zhang
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Yi Rao
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
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15
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Castaneda AN, Huda A, Whitaker IBM, Reilly JE, Shelby GS, Bai H, Ni L. Functional labeling of individualized postsynaptic neurons using optogenetics and trans-Tango in Drosophila (FLIPSOT). PLoS Genet 2024; 20:e1011190. [PMID: 38483970 PMCID: PMC10965055 DOI: 10.1371/journal.pgen.1011190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 03/26/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
A population of neurons interconnected by synapses constitutes a neural circuit, which performs specific functions upon activation. It is essential to identify both anatomical and functional entities of neural circuits to comprehend the components and processes necessary for healthy brain function and the changes that characterize brain disorders. To date, few methods are available to study these two aspects of a neural circuit simultaneously. In this study, we developed FLIPSOT, or functional labeling of individualized postsynaptic neurons using optogenetics and trans-Tango. FLIPSOT uses (1) trans-Tango to access postsynaptic neurons genetically, (2) optogenetic approaches to activate (FLIPSOTa) or inhibit (FLIPSOTi) postsynaptic neurons in a random and sparse manner, and (3) fluorescence markers tagged with optogenetic genes to visualize these neurons. Therefore, FLIPSOT allows using a presynaptic driver to identify the behavioral function of individual postsynaptic neurons. It is readily applied to identify functions of individual postsynaptic neurons and has the potential to be adapted for use in mammalian circuits.
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Affiliation(s)
- Allison N. Castaneda
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Ainul Huda
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Iona B. M. Whitaker
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Julianne E. Reilly
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Grace S. Shelby
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Hua Bai
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Lina Ni
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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16
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Zhang M, Lui KO, Zhou B. Application of New Lineage Tracing Techniques in Cardiovascular Development and Physiology. Circ Res 2024; 134:445-458. [PMID: 38359092 DOI: 10.1161/circresaha.123.323179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cardiovascular disease has been the leading cause of mortality and morbidity worldwide in the past 3 decades. Multiple cell lineages undergo dynamic alternations in gene expression, cell state determination, and cell fate conversion to contribute, adapt, and even modulate the pathophysiological processes during disease progression. There is an urgent need to understand the intricate cellular and molecular underpinnings of cardiovascular cell development in homeostasis and pathogenesis. Recent strides in lineage tracing methodologies have revolutionized our understanding of cardiovascular biology with the identification of new cellular origins, fates, plasticity, and heterogeneity within the cardiomyocyte, endothelial, and mesenchymal cell populations. In this review, we introduce the new technologies for lineage tracing of cardiovascular cells and summarize their applications in studying cardiovascular development, diseases, repair, and regeneration.
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Affiliation(s)
- MingJun Zhang
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, China (M.J., B.Z.)
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, China (K.O.L.)
| | - Bin Zhou
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, China (M.J., B.Z.)
- School of Life Science and Technology, ShanghaiTech University, China (B.Z.)
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, China (B.Z.)
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17
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Guo L, Yang G. Pioneering DNA assembling techniques and their applications in eukaryotic microalgae. Biotechnol Adv 2024; 70:108301. [PMID: 38101551 DOI: 10.1016/j.biotechadv.2023.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/12/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.
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Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China; Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; MoE Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao 266003, China.
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18
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Cachoux VML, Balakireva M, Gracia M, Bosveld F, López-Gay JM, Maugarny A, Gaugué I, di Pietro F, Rigaud SU, Noiret L, Guirao B, Bellaïche Y. Epithelial apoptotic pattern emerges from global and local regulation by cell apical area. Curr Biol 2023; 33:4807-4826.e6. [PMID: 37827152 PMCID: PMC10681125 DOI: 10.1016/j.cub.2023.09.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Geometry is a fundamental attribute of biological systems, and it underlies cell and tissue dynamics. Cell geometry controls cell-cycle progression and mitosis and thus modulates tissue development and homeostasis. In sharp contrast and despite the extensive characterization of the genetic mechanisms of caspase activation, we know little about whether and how cell geometry controls apoptosis commitment in developing tissues. Here, we combined multiscale time-lapse microscopy of developing Drosophila epithelium, quantitative characterization of cell behaviors, and genetic and mechanical perturbations to determine how apoptosis is controlled during epithelial tissue development. We found that early in cell lives and well before extrusion, apoptosis commitment is linked to two distinct geometric features: a small apical area compared with other cells within the tissue and a small relative apical area with respect to the immediate neighboring cells. We showed that these global and local geometric characteristics are sufficient to recapitulate the tissue-scale apoptotic pattern. Furthermore, we established that the coupling between these two geometric features and apoptotic cells is dependent on the Hippo/YAP and Notch pathways. Overall, by exploring the links between cell geometry and apoptosis commitment, our work provides important insights into the spatial regulation of cell death in tissues and improves our understanding of the mechanisms that control cell number and tissue size.
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Affiliation(s)
- Victoire M L Cachoux
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Maria Balakireva
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Mélanie Gracia
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Floris Bosveld
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Jesús M López-Gay
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Aude Maugarny
- 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
| | - Florencia di Pietro
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Stéphane U Rigaud
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Lorette Noiret
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Boris Guirao
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France.
| | - Yohanns Bellaïche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France.
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19
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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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20
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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: 5] [Impact Index Per Article: 5.0] [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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21
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Benner L, Muron S, Oliver B. Female germline expression of OVO transcription factor bridges Drosophila generations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554887. [PMID: 37662231 PMCID: PMC10473757 DOI: 10.1101/2023.08.25.554887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
OVO is required for karyotypically female germ cell viability but has no known function in the male germline in Drosophila. ovo is autoregulated by two antagonistic isoforms, OVO-A and OVO-B. All ovo- alleles were created as partial revertants of the antimorphic ovoD1 allele. Creation of new targeted alleles in an ovo+ background indicated that disrupting the germline-specific exon extension of ovo-B leads to an arrested egg chamber phenotype, rather than germ cell death. RNA-seq analysis, including >1K full length cDNAs, indicates that ovo utilizes a number of unannotated splice variations in the extended exon and a minor population of ovo-B transcripts utilizes an alternative splice. This indicates that classical ovo alleles such as ovoD1rv23, are not truly null for ovo, and are likely to be weak antimorphs. To generate bonafide nulls, we deleted the ovo-A and ovo-B promoters showing that only ovo-B is required for female germ cell viability and there is an early and polyphasic developmental requirement for ovo-B in the female germline. To visualize OVO expression and localization, we endogenously tagged ovo and found nuclear OVO in all differentiating female germ cells throughout oogenesis in adults. We also found that OVO is maternally deposited into the embryo, where it showed nuclear localization in newly formed pole cells. Maternal OVO persisted in embryonic germ cells until zygotic OVO expression was detectable, suggesting that there is continuous nuclear OVO expression in the female germline in the transition from one generation to the next.
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Affiliation(s)
- Leif Benner
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Savannah Muron
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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22
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Migunova E, Rajamani S, Bonanni S, Wang F, Zhou C, Dubrovsky EB. Cardiac RNase Z edited via CRISPR-Cas9 drives heart hypertrophy in Drosophila. PLoS One 2023; 18:e0286214. [PMID: 37228086 PMCID: PMC10212119 DOI: 10.1371/journal.pone.0286214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Cardiomyopathy (CM) is a group of diseases distinguished by morphological and functional abnormalities in the myocardium. It is etiologically heterogeneous and may develop via cell autonomous and/or non-autonomous mechanisms. One of the most severe forms of CM has been linked to the deficiency of the ubiquitously expressed RNase Z endoribonuclease. RNase Z cleaves off the 3'-trailer of both nuclear and mitochondrial primary tRNA (pre-tRNA) transcripts. Cells mutant for RNase Z accumulate unprocessed pre-tRNA molecules. Patients carrying RNase Z variants with reduced enzymatic activity display a plethora of symptoms including muscular hypotonia, microcephaly and severe heart hypertrophy; still, they die primarily due to acute heart decompensation. Determining whether the underlying mechanism of heart malfunction is cell autonomous or not will provide an opportunity to develop novel strategies of more efficient treatments for these patients. In this study, we used CRISPR-TRiM technology to create Drosophila models that carry cardiomyopathy-linked alleles of RNase Z only in the cardiomyocytes. We found that this modification is sufficient for flies to develop heart hypertrophy and systolic dysfunction. These observations support the idea that the RNase Z linked CM is driven by cell autonomous mechanisms.
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Affiliation(s)
- Ekaterina Migunova
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Saathvika Rajamani
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Stefania Bonanni
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Fei Wang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Chao Zhou
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Edward B. Dubrovsky
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
- Center for Cancer, Genetic Diseases, and Gene Regulation, Fordham University, Bronx, NY, United States of America
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23
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Pierini G, Dahmann C. Hedgehog morphogen gradient is robust towards variations in tissue morphology in Drosophila. Sci Rep 2023; 13:8454. [PMID: 37231029 DOI: 10.1038/s41598-023-34632-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/04/2023] [Indexed: 05/27/2023] Open
Abstract
During tissue development, gradients of secreted signaling molecules known as morphogens provide cells with positional information. The mechanisms underlying morphogen spreading have been widely studied, however, it remains largely unexplored whether the shape of morphogen gradients is influenced by tissue morphology. Here, we developed an analysis pipeline to quantify the distribution of proteins within a curved tissue. We applied it to the Hedgehog morphogen gradient in the Drosophila wing and eye-antennal imaginal discs, which are flat and curved tissues, respectively. Despite a different expression profile, the slope of the Hedgehog gradient was comparable between the two tissues. Moreover, inducing ectopic folds in wing imaginal discs did not affect the slope of the Hedgehog gradient. Suppressing curvature in the eye-antennal imaginal disc also did not alter the Hedgehog gradient slope but led to ectopic Hedgehog expression. In conclusion, through the development of an analysis pipeline that allows quantifying protein distribution in curved tissues, we show that the Hedgehog gradient is robust towards variations in tissue morphology.
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Affiliation(s)
- Giulia Pierini
- School of Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Christian Dahmann
- School of Science, Technische Universität Dresden, 01062, Dresden, Germany.
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062, Dresden, Germany.
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24
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Parisi MJ, Aimino MA, Mosca TJ. A conditional strategy for cell-type-specific labeling of endogenous excitatory synapses in Drosophila. CELL REPORTS METHODS 2023; 3:100477. [PMID: 37323572 PMCID: PMC10261928 DOI: 10.1016/j.crmeth.2023.100477] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/28/2023] [Accepted: 04/19/2023] [Indexed: 06/17/2023]
Abstract
Chemical neurotransmission occurs at specialized contacts where neurotransmitter release machinery apposes neurotransmitter receptors to underlie circuit function. A series of complex events underlies pre- and postsynaptic protein recruitment to neuronal connections. To better study synaptic development in individual neurons, we need cell-type-specific strategies to visualize endogenous synaptic proteins. Although presynaptic strategies exist, postsynaptic proteins remain less studied because of a paucity of cell-type-specific reagents. To study excitatory postsynapses with cell-type specificity, we engineered dlg1[4K], a conditionally labeled marker of Drosophila excitatory postsynaptic densities. With binary expression systems, dlg1[4K] labels central and peripheral postsynapses in larvae and adults. Using dlg1[4K], we find that distinct rules govern postsynaptic organization in adult neurons, multiple binary expression systems can concurrently label pre- and postsynapse in a cell-type-specific manner, and neuronal DLG1 can sometimes localize presynaptically. These results validate our strategy for conditional postsynaptic labeling and demonstrate principles of synaptic organization.
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Affiliation(s)
- Michael J. Parisi
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA 19107, USA
| | - Michael A. Aimino
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA 19107, USA
| | - Timothy J. Mosca
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA 19107, USA
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25
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Singh C, Kumar R, Sehgal H, Bhati S, Singhal T, Gayacharan, Nimmy MS, Yadav R, Gupta SK, Abdallah NA, Hamwieh A, Kumar R. Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat. Front Genet 2023; 14:1085024. [PMID: 37144131 PMCID: PMC10153629 DOI: 10.3389/fgene.2023.1085024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/24/2023] [Indexed: 09/09/2023] Open
Abstract
Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.
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Affiliation(s)
- Charul Singh
- USBT, Guru Govind Singh Indraprastha University, Delhi, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad Prayagraj, Prayagraj, India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Sharmista Bhati
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gayacharan
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. S. Nimmy
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Aladdin Hamwieh
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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26
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Spratt SJ, Mizuguchi T, Akaboshi H, Kosakamoto H, Okada R, Obata F, Ozeki Y. Imaging the uptake of deuterated methionine in Drosophila with stimulated Raman scattering. Front Chem 2023; 11:1141920. [PMID: 37065821 PMCID: PMC10090404 DOI: 10.3389/fchem.2023.1141920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
Introduction: Visualizing small individual biomolecules at subcellular resolution in live cells and tissues can provide valuable insights into metabolic activity in heterogeneous cells, but is challenging.Methods: Here, we used stimulated Raman scattering (SRS) microscopy to image deuterated methionine (d-Met) incorporated into Drosophila tissues in vivo.Results: Our results demonstrate that SRS can detect a range of previously uncharacterized cell-to-cell differences in d-Met distribution within a tissue at the subcellular level.Discussion: These results demonstrate the potential of SRS microscopy for metabolic imaging of less abundant but important amino acids such as methionine in tissue.
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Affiliation(s)
- Spencer J. Spratt
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Takaha Mizuguchi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hikaru Akaboshi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hina Kosakamoto
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Rina Okada
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Fumiaki Obata
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yasuyuki Ozeki,
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27
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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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28
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Karuparti S, Yeung AT, Wang B, Guicardi PF, Han C. A toolkit for converting Gal4 into LexA and Flippase transgenes in Drosophila. G3 (BETHESDA, MD.) 2023; 13:jkad003. [PMID: 36617215 PMCID: PMC9997562 DOI: 10.1093/g3journal/jkad003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/01/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023]
Abstract
Drosophila has been a powerful model system for biological studies due to the wide range of genetic tools established for it. Among these tools, Gal4 is the most abundant, offering unparalleled tissue and developmental stage specificity for gene manipulation. In comparison, other genetic reagents are far fewer in choices. Here we present a genetic toolkit for converting Gal4 strains into LexA and Flippase transgenes through simple genetic crosses and fluorescence screening. We demonstrate the proof-of-principle by converting ten Gal4 lines that exhibit diverse tissue specificities and examined the activity patterns of the converted LexA and Flippase lines. Gal4-to-LexA and Flp conversion is fast and convenient and should greatly expand the choices of LexA and Flp for binary expression and FRT-based mosaic analysis, respectively, in Drosophila.
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Affiliation(s)
- Sasidhar Karuparti
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ann T Yeung
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Pedro F Guicardi
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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29
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Mendaluk A, Caussinus E, Boutros M, Lehner CF. A genome-wide RNAi screen for genes important for proliferation of cultured Drosophila cells at low temperature identifies the Ball/VRK protein kinase. Chromosoma 2023; 132:31-53. [PMID: 36746786 PMCID: PMC9981717 DOI: 10.1007/s00412-023-00787-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
A change in ambient temperature is predicted to disrupt cellular homeostasis by affecting all cellular processes in an albeit non-uniform manner. Diffusion is generally less temperature-sensitive than enzymes, for example, and each enzyme has a characteristic individual temperature profile. The actual effects of temperature variation on cells are still poorly understood at the molecular level. Towards an improved understanding, we have performed a genome-wide RNA interference screen with S2R + cells. This Drosophila cell line proliferates over a temperature range comparable to that tolerated by the parental ectothermic organism. Based on effects on cell counts and cell cycle profile after knockdown at 27 and 17 °C, respectively, genes were identified with an apparent greater physiological significance at one or the other temperature. While 27 °C is close to the temperature optimum, the substantially lower 17 °C was chosen to identify genes important at low temperatures, which have received less attention compared to the heat shock response. Among a substantial number of screen hits, we validated a set successfully in cell culture and selected ballchen for further evaluation in the organism. This gene encodes the conserved metazoan VRK protein kinase that is crucial for the release of chromosomes from the nuclear envelope during mitosis. Our analyses in early embryos and larval wing imaginal discs confirmed a higher requirement for ballchen function at temperatures below the optimum. Overall, our experiments validate the genome-wide screen as a basis for future characterizations of genes with increased physiological significance at the lower end of the readily tolerated temperature range.
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Affiliation(s)
- Anna Mendaluk
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
| | - Emmanuel Caussinus
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, BioQuant, Heidelberg, Germany
| | - Christian F Lehner
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland.
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30
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Villedieu A, Alpar L, Gaugué I, Joudat A, Graner F, Bosveld F, Bellaïche Y. Homeotic compartment curvature and tension control spatiotemporal folding dynamics. Nat Commun 2023; 14:594. [PMID: 36737611 PMCID: PMC9898526 DOI: 10.1038/s41467-023-36305-6] [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: 04/08/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Shape is a conspicuous and fundamental property of biological systems entailing the function of organs and tissues. While much emphasis has been put on how tissue tension and mechanical properties drive shape changes, whether and how a given tissue geometry influences subsequent morphogenesis remains poorly characterized. Here, we explored how curvature, a key descriptor of tissue geometry, impinges on the dynamics of epithelial tissue invagination. We found that the morphogenesis of the fold separating the adult Drosophila head and thorax segments is driven by the invagination of the Deformed (Dfd) homeotic compartment. Dfd controls invagination by modulating actomyosin organization and in-plane epithelial tension via the Tollo and Dystroglycan receptors. By experimentally introducing curvature heterogeneity within the homeotic compartment, we established that a curved tissue geometry converts the Dfd-dependent in-plane tension into an inward force driving folding. Accordingly, the interplay between in-plane tension and tissue curvature quantitatively explains the spatiotemporal folding dynamics. Collectively, our work highlights how genetic patterning and tissue geometry provide a simple design principle driving folding morphogenesis during development.
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Affiliation(s)
- Aurélien Villedieu
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - Lale Alpar
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - Isabelle Gaugué
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - Amina Joudat
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - François Graner
- Université Paris Cité, CNRS, Matière et Systèmes Complexes, F-75006, Paris, France
| | - Floris Bosveld
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France.
| | - Yohanns Bellaïche
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France.
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31
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Soriano A, Petit C, Ryan S, Jemc JC. Tracking Follicle Cell Development. Methods Mol Biol 2023; 2626:151-177. [PMID: 36715904 DOI: 10.1007/978-1-0716-2970-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Somatic follicle cells are critical support cells for Drosophila oogenesis, as they provide signals and molecules needed to produce a mature egg. Throughout this process, the follicle cells differentiate into multiple subpopulations and transition between three different cell cycle programs to support nurse cell and oocyte development. The follicle cells are mitotic in early egg chamber development, as they cover the germline cyst. In mid-oogenesis, follicle cells switch from mitosis to endocycling, increasing their ploidy from 2C to 16C. Finally, in late oogenesis, cells transition from endocycling to gene amplification, increasing the copy number of a small subset of genes, including the genes encoding proteins required for egg maturation. In order to explore the genetic regulation of these cell cycle switches and follicle cell development and specification, clonal analysis and the GAL4/UAS system are used frequently to reduce or increase expression of genes of interest. These genetic approaches combined with immunohistochemistry and in situ hybridization are powerful tools for characterizing the mechanisms regulating follicle cell development and the mitosis/endocycle and endocycle/gene amplification transitions. This chapter describes the genetic tools available to manipulate gene expression in follicle cells, as well as the methods and reagents that can be utilized to explore gene expression throughout follicle cell development.
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Affiliation(s)
- Adrianna Soriano
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Houston Baptist University, Houston, TX, USA
| | | | - Savannah Ryan
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Jennifer C Jemc
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.
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32
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Hajirnis N, Pandey S, Mishra RK. CRISPR/Cas9 and FLP-FRT mediated regulatory dissection of the BX-C of Drosophila melanogaster. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:7. [PMID: 36719476 DOI: 10.1007/s10577-023-09716-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 02/01/2023]
Abstract
The homeotic genes or Hox define the anterior-posterior (AP) body axis formation in bilaterians and are often present on the chromosome in an order collinear to their function across the AP axis. However, there are many cases wherein the Hox are not collinear, but their expression pattern is conserved across the AP axis. The expression pattern of Hox is attributed to the cis-regulatory modules (CRMs) consisting of enhancers, initiators, or repressor elements that regulate the genes in a segment-specific manner. In the Drosophila melanogaster Hox complex, the bithorax complex (BX-C) and even the CRMs are organized in an order that is collinear to their function in the thoracic and abdominal segments. In the present study, the regulatorily inert regions were targeted using CRISPR/Cas9 to generate a series of transgenic lines with the insertion of FRT sequences. These FRT lines are repurposed to shuffle the CRMs associated with Abd-B to generate modular deletion, duplication, or inversion of multiple CRMs. The rearrangements yielded entirely novel phenotypes in the fly suggesting the requirement of such complex manipulations to address the significance of higher order arrangement of the CRMs. The functional map and the transgenic flies generated in this study are important resources to decipher the collective ability of multiple regulatory elements in the eukaryotic genome to function as complex modules.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Anatomy and Neurobiology, University of Maryland, Baltimore, USA
| | | | - Rakesh K Mishra
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India. .,AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India. .,Tata Institute for Genetics and Society (TIGS), Bangalore, India.
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33
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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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34
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Phipps DN, Powell AM, Ables ET. Utilizing the FLP-Out System for Clonal RNAi Analysis in the Adult Drosophila Ovary. Methods Mol Biol 2023; 2626:69-87. [PMID: 36715900 PMCID: PMC10044525 DOI: 10.1007/978-1-0716-2970-3_4] [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: 01/31/2023]
Abstract
The ability to conduct spatially controlled RNA interference (RNAi) for gene knockdown using the UAS/Gal4 system is among the most appealing techniques available for analysis of gene function in the Drosophila ovary. While gene knockdown experiments in somatic cells in the developing organism (i.e., embryos and larvae) are effectively and commonly performed, the use of RNAi in adult ovarian cells can be hampered by the unintended deleterious effects of Gal4 expression in "off-target" developing tissues. Mosaic analysis overcomes these problems by imparting temporal and spatial control over gene manipulation, providing a useful tool to compare manipulated cells with wild-type cells in the same tissue. Here, we provide a method to utilize the UAS/Gal4 system in combination with the Flippase (FLP)-Flippase Recognition Target (FRT) system to generate positively labeled "FLP-Out" clones expressing a chosen RNAi in both the germline and the soma in the Drosophila ovary. This protocol outlines each step of the generation of clones and the selection of appropriate fly stocks and reagents, providing a guide to this powerful tool in the Drosophila genetic toolbox. These techniques allow for RNAi analysis within a specific cell type, providing an opportunity to study a variety of unique aspects of cell function that would not be possible in more traditional RNAi-based experiments.
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Affiliation(s)
- Daniel N Phipps
- Department of Biology, East Carolina University, Greenville, NC, USA
- Biomedical Sciences Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Amanda M Powell
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Elizabeth T Ables
- Department of Biology, East Carolina University, Greenville, NC, USA.
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35
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Moore SL, Adamini FC, Coopes ES, Godoy D, Northington SJ, Stewart JM, Tillett RL, Bieser KL, Kagey JD. Patched and Costal-2 mutations lead to differences in tissue overgrowth autonomy. Fly (Austin) 2022; 16:176-189. [PMID: 35468034 PMCID: PMC9045829 DOI: 10.1080/19336934.2022.2062991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 02/03/2023] Open
Abstract
Genetic screens are used in Drosophila melanogaster to identify genes key in the regulation of organismal development and growth. These screens have defined signalling pathways necessary for tissue and organismal development, which are evolutionarily conserved across species, including Drosophila. Here, we have used an FLP/FRT mosaic system to screen for conditional regulators of cell growth and cell division in the Drosophila eye. The conditional nature of this screen utilizes a block in the apoptotic pathway to prohibit the mosaic mutant cells from dying via apoptosis. From this screen, we identified two different mutants that mapped to the Hedgehog signalling pathway. Previously, we described a novel Ptc mutation and here we add to the understanding of disrupting the Hh pathway with a novel allele of Cos2. Both of these Hh components are negative regulators of the pathway, yet they depict mutant differences in the type of overgrowth created. Ptc mutations lead to overgrowth consisting of almost entirely wild-type tissue (non-autonomous overgrowth), while the Cos2 mutation results in tissue that is overgrown in both the mutant and wild-type clones (both autonomous and non-autonomous). These differences in tissue overgrowth are consistent in the Drosophila eye and wing. The observed difference is correlated with different deregulation patterns of pMad, the downstream effector of DPP signalling. This finding provides insight into pathway-specific differences that help to better understand intricacies of developmental processes and human diseases that result from deregulated Hedgehog signalling, such as basal cell carcinoma.
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Affiliation(s)
- Shannon L. Moore
- Biology Department, University of Detroit Mercy, Detroit, Michigan, USA
| | - Frank C. Adamini
- Biology Department, University of Detroit Mercy, Detroit, Michigan, USA
| | - Erik S. Coopes
- Biology Department, University of Detroit Mercy, Detroit, Michigan, USA
| | - Dustin Godoy
- Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada, USA
| | - Shyra J. Northington
- Biology Department, University of Detroit Mercy, Detroit, Michigan, USA
- ReBUILDetroit, University of Detroit Mercy, Detroit, Michigan, USA
| | - Jordan M. Stewart
- Biology Department, University of Detroit Mercy, Detroit, Michigan, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Nevada, USA
| | - Kayla L. Bieser
- Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada, USA
| | - Jacob D. Kagey
- Biology Department, University of Detroit Mercy, Detroit, Michigan, USA
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36
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Fernandez-Acosta M, Romero JI, Bernabó G, Velázquez-Campos GM, Gonzalez N, Mares ML, Werbajh S, Avendaño-Vázquez LA, Rechberger GN, Kühnlein RP, Marino-Buslje C, Cantera R, Rezaval C, Ceriani MF. orsai, the Drosophila homolog of human ETFRF1, links lipid catabolism to growth control. BMC Biol 2022; 20:233. [PMID: 36266680 PMCID: PMC9585818 DOI: 10.1186/s12915-022-01417-w] [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: 10/28/2021] [Accepted: 09/26/2022] [Indexed: 11/24/2022] Open
Abstract
Background Lipid homeostasis is an evolutionarily conserved process that is crucial for energy production, storage and consumption. Drosophila larvae feed continuously to achieve the roughly 200-fold increase in size and accumulate sufficient reserves to provide all energy and nutrients necessary for the development of the adult fly. The mechanisms controlling this metabolic program are poorly understood. Results Herein we identified a highly conserved gene, orsai (osi), as a key player in lipid metabolism in Drosophila. Lack of osi function in the larval fat body, the regulatory hub of lipid homeostasis, reduces lipid reserves and energy output, evidenced by decreased ATP production and increased ROS levels. Metabolic defects due to reduced Orsai (Osi) in time trigger defective food-seeking behavior and lethality. Further, we demonstrate that downregulation of Lipase 3, a fat body-specific lipase involved in lipid catabolism in response to starvation, rescues the reduced lipid droplet size associated with defective orsai. Finally, we show that osi-related phenotypes are rescued through the expression of its human ortholog ETFRF1/LYRm5, known to modulate the entry of β-oxidation products into the electron transport chain; moreover, knocking down electron transport flavoproteins EtfQ0 and walrus/ETFA rescues osi-related phenotypes, further supporting this mode of action. Conclusions These findings suggest that Osi may act in concert with the ETF complex to coordinate lipid homeostasis in the fat body in response to stage-specific demands, supporting cellular functions that in turn result in an adaptive behavioral response. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01417-w.
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Affiliation(s)
- Magdalena Fernandez-Acosta
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - Juan I Romero
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - Guillermo Bernabó
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina.,Present Address: Innovid, Buenos Aires, Argentina
| | - Giovanna M Velázquez-Campos
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - Nerina Gonzalez
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - M Lucía Mares
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - Santiago Werbajh
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina.,Present Address: Fundación Cassará, Buenos Aires, Argentina
| | - L Amaranta Avendaño-Vázquez
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina.,Present Address: IFIBYNE-CONICET, Buenos Aires, Argentina
| | - Gerald N Rechberger
- Institute for Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Ronald P Kühnlein
- Institute for Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Cristina Marino-Buslje
- Laboratorio de Bioinformática Estructural, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - Rafael Cantera
- Departamento de Biología del Neurodesarrollo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.,Zoology Department, Stockholm University, Stockholm, Sweden
| | - Carolina Rezaval
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina.,Present Address: School of Biosciences, University of Birmingham, Birmingham, UK
| | - M Fernanda Ceriani
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina.
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37
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Tian A, Morejon V, Kohoutek S, Huang Y, Deng W, Jiang J. Damage-induced regeneration of the intestinal stem cell pool through enteroblast mitosis in the Drosophila midgut. EMBO J 2022; 41:e110834. [PMID: 35950466 PMCID: PMC9531297 DOI: 10.15252/embj.2022110834] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/09/2022] Open
Abstract
Many adult tissues and organs including the intestine rely on resident stem cells to maintain homeostasis and regeneration. In mammals, the progenies of intestinal stem cells (ISCs) can dedifferentiate to generate ISCs upon ablation of resident stem cells. However, whether and how mature tissue cells generate ISCs under physiological conditions remains unknown. Here, we show that infection of the Drosophila melanogaster intestine with pathogenic bacteria induces entry of enteroblasts (EBs), which are ISC progenies, into the mitotic cycle through upregulation of epidermal growth factor receptor (EGFR)-Ras signaling. We also show that ectopic activation of EGFR-Ras signaling in EBs is sufficient to drive enteroblast mitosis cell autonomously. Furthermore, we find that the dividing enteroblasts do not gain ISC identity as a prerequisite to divide, and the regenerative ISCs are produced through EB mitosis. Taken together, our work uncovers a new role for EGFR-Ras signaling in driving EB mitosis and replenishing the ISC pool during fly intestinal regeneration, which may have important implications for tissue homeostasis and tumorigenesis in vertebrates.
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Affiliation(s)
- Aiguo Tian
- Department of Biochemistry and Molecular Biology, Tulane University School of MedicineLouisiana Cancer Research CenterNew OrleansLAUSA
- Tulane Aging CenterTulane University School of MedicineNew OrleansLAUSA
| | - Virginia Morejon
- Department of Biochemistry and Molecular Biology, Tulane University School of MedicineLouisiana Cancer Research CenterNew OrleansLAUSA
| | - Sarah Kohoutek
- Department of Biochemistry and Molecular Biology, Tulane University School of MedicineLouisiana Cancer Research CenterNew OrleansLAUSA
| | - Yi‐Chun Huang
- Department of Biochemistry and Molecular Biology, Tulane University School of MedicineLouisiana Cancer Research CenterNew OrleansLAUSA
| | - Wu‐Min Deng
- Department of Biochemistry and Molecular Biology, Tulane University School of MedicineLouisiana Cancer Research CenterNew OrleansLAUSA
| | - Jin Jiang
- Department of Molecular Biology and Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
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38
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Ribeiro IMA, Eßbauer W, Kutlesa R, Borst A. Spatial and temporal control of expression with light-gated LOV-LexA. G3 GENES|GENOMES|GENETICS 2022; 12:6649684. [PMID: 35876796 PMCID: PMC9526042 DOI: 10.1093/g3journal/jkac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022]
Abstract
The ability to drive expression of exogenous genes in different tissues and cell types, under the control of specific enhancers, has been crucial for discovery in biology. While many enhancers drive expression broadly, several genetic tools were developed to obtain access to isolated cell types. Studies of spatially organized neuropiles in the central nervous system of fruit flies have raised the need for a system that targets subsets of cells within a single neuronal type, a feat currently dependent on stochastic flip-out methods. To access the same cells within a given expression pattern consistently across fruit flies, we developed the light-gated expression system LOV-LexA. We combined the bacterial LexA transcription factor with the plant-derived light, oxygen, or voltage photosensitive domain and a fluorescent protein. Exposure to blue light uncages a nuclear localizing signal in the C-terminal of the light, oxygen, or voltage domain and leads to the translocation of LOV-LexA to the nucleus, with the subsequent initiation of transcription. LOV-LexA enables spatial and temporal control of expression of transgenes under LexAop sequences in larval fat body and pupal and adult neurons with blue light. The LOV-LexA tool is ready to use with GAL4 and Split-GAL4 drivers in its current form and constitutes another layer of intersectional genetics that provides light-controlled genetic access to specific cells across flies.
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Affiliation(s)
- Inês M A Ribeiro
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Wolfgang Eßbauer
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Romina Kutlesa
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Alexander Borst
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
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39
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Brittle A, Warrington SJ, Strutt H, Manning E, Tan SE, Strutt D. Distinct mechanisms of planar polarization by the core and Fat-Dachsous planar polarity pathways in the Drosophila wing. Cell Rep 2022; 40:111419. [PMID: 36170824 PMCID: PMC9631118 DOI: 10.1016/j.celrep.2022.111419] [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: 04/18/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Planar polarity describes the coordinated polarization of cells within a tissue plane, and in animals can be determined by the “core” or Fat-Dachsous pathways. Current models for planar polarity establishment involve two components: tissue-level “global” cues that determine the overall axis of polarity and cell-level feedback-mediated cellular polarity amplification. Here, we investigate the contributions of global cues versus cellular feedback amplification in the core and Fat-Dachsous pathways during Drosophila pupal wing development. We present evidence that these pathways generate planar polarity via distinct mechanisms. Core pathway function is consistent with strong feedback capable of self-organizing cell polarity, which can then be aligned with the tissue axis via weak or transient global cues. Conversely, generation of cell polarity by the Ft-Ds pathway depends on strong global cues in the form of graded patterns of gene expression, which can then be amplified by weak feedback mechanisms. The core and Fat-Dachsous planar polarity pathways function via distinct mechanisms The core can self-organize planar polarity and be oriented by weak upstream cues Fat-Dachsous are oriented by strong gradient cues but show poor self-organization
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Affiliation(s)
- Amy Brittle
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | | | - Helen Strutt
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Elizabeth Manning
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Su Ee Tan
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David Strutt
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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40
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Williams AM, Donoughe S, Munro E, Horne-Badovinac S. Fat2 polarizes the WAVE complex in trans to align cell protrusions for collective migration. eLife 2022; 11:e78343. [PMID: 36154691 PMCID: PMC9576270 DOI: 10.7554/elife.78343] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/11/2022] [Indexed: 11/13/2022] Open
Abstract
For a group of cells to migrate together, each cell must couple the polarity of its migratory machinery with that of the other cells in the cohort. Although collective cell migrations are common in animal development, little is known about how protrusions are coherently polarized among groups of migrating epithelial cells. We address this problem in the collective migration of the follicular epithelial cells in Drosophila melanogaster. In this epithelium, the cadherin Fat2 localizes to the trailing edge of each cell and promotes the formation of F-actin-rich protrusions at the leading edge of the cell behind. We show that Fat2 performs this function by acting in trans to concentrate the activity of the WASP family verprolin homolog regulatory complex (WAVE complex) at one long-lived region along each cell's leading edge. Without Fat2, the WAVE complex distribution expands around the cell perimeter and fluctuates over time, and protrusive activity is reduced and unpolarized. We further show that Fat2's influence is very local, with sub-micron-scale puncta of Fat2 enriching the WAVE complex in corresponding puncta just across the leading-trailing cell-cell interface. These findings demonstrate that a trans interaction between Fat2 and the WAVE complex creates stable regions of protrusive activity in each cell and aligns the cells' protrusions across the epithelium for directionally persistent collective migration.
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Affiliation(s)
- Audrey Miller Williams
- Department of Molecular Genetics and Cell Biology, University of ChicagoChicagoUnited States
| | - Seth Donoughe
- Department of Molecular Genetics and Cell Biology, University of ChicagoChicagoUnited States
| | - Edwin Munro
- Department of Molecular Genetics and Cell Biology, University of ChicagoChicagoUnited States
- Committee on Development, Regeneration, and Stem Cell Biology, University of ChicagoChicagoUnited States
- Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Sally Horne-Badovinac
- Department of Molecular Genetics and Cell Biology, University of ChicagoChicagoUnited States
- Committee on Development, Regeneration, and Stem Cell Biology, University of ChicagoChicagoUnited States
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41
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Predictive model for cytoneme guidance in Hedgehog signaling based on Ihog- Glypicans interaction. Nat Commun 2022; 13:5647. [PMID: 36163184 PMCID: PMC9512826 DOI: 10.1038/s41467-022-33262-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 09/09/2022] [Indexed: 11/28/2022] Open
Abstract
During embryonic development, cell-cell communication is crucial to coordinate cell behavior, especially in the generation of differentiation patterns via morphogen gradients. Morphogens are signaling molecules secreted by a source of cells that elicit concentration-dependent responses in target cells. For several morphogens, cell-cell contact via filopodia-like-structures (cytonemes) has been proposed as a mechanism for their gradient formation. Despite of the advances on cytoneme signaling, little is known about how cytonemes navigate through the extracellular matrix and how they orient to find their target. For the Hedgehog (Hh) signaling pathway in Drosophila, Hh co-receptor and adhesion protein Interference hedgehog (Ihog) and the glypicans Dally and Dally-like-protein (Dlp) interact affecting the cytoneme behavior. Here, we describe that differences in the cytoneme stabilization and orientation depend on the relative levels of Ihog and glypicans, suggesting a mechanism for cytoneme guidance. Furthermore, we have developed a mathematical model to study and corroborate this cytoneme guiding mechanism. Cytonemes are specialized filopodia-like structures known to be involved in signal transduction. Here they propose a new predictive model for cytoneme guidance in Hedgehog signaling, which is based on Ihog, Dally, and Dlp protein levels.
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42
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Jia D, Jevitt A, Huang YC, Ramos B, Deng WM. Developmental regulation of epithelial cell cuboidal-to-squamous transition in Drosophila follicle cells. Dev Biol 2022; 491:113-125. [PMID: 36100084 DOI: 10.1016/j.ydbio.2022.09.001] [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: 01/18/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022]
Abstract
Epithelial cells form continuous membranous structures for organ formation, and these cells are classified into three major morphological categories: cuboidal, columnar, and squamous. It is crucial that cells transition between these shapes during the morphogenetic events of organogenesis, yet this process remains poorly understood. All three epithelial cell shapes can be found in the follicular epithelium of Drosophila egg chamber during oogenesis. Squamous cells (SCs) are initially restricted to the anterior terminus in cuboidal shape. They then rapidly become flattened to assume squamous shape by stretching and expansion in 12 h during midoogenesis. Previously, we reported that Notch signaling activated a zinc-finger transcription factor Broad (Br) at the end of early oogenesis. Here we report that ecdysone and JAK/STAT pathways subsequently converge on Br to serve as an important spatiotemporal regulator of this dramatic morphological change of SCs. The early uniform pattern of Br in the follicular epithelium is directly established by Notch signaling at stage 5 of oogenesis. Later, ecdysone and JAK/STAT signaling activities synergize to suppress Br in SCs from stage 8 to 10a, contributing to proper SC squamous shape. During this process, ecdysone signaling is essential for SC stretching, while JAK/STAT regulates SC clustering and cell fate determination. This study reveals an inhibitory role of ecdysone signaling in suppressing Br in epithelial cell remodeling. In this study we also used single-cell RNA sequencing data to highlight the shift in gene expression which occurs as Br is suppressed and cells become flattened.
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Affiliation(s)
- Dongyu Jia
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA; Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
| | - Allison Jevitt
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA; Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Yi-Chun Huang
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Belen Ramos
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA; Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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Abstract
In Darwin's and Mendel's times, researchers investigated a wealth of organisms, chosen to solve particular problems for which they seemed especially well suited. Later, a focus on a few organisms, which are accessible to systematic genetic investigations, resulted in larger repertoires of methods and applications in these few species. Genetic animal model organisms with large research communities are the nematode Caenorhabditis elegans, the fly Drosophila melanogaster, the zebrafish Danio rerio, and the mouse Mus musculus. Due to their specific strengths, these model organisms have their strongest impacts in rather different areas of biology. C. elegans is unbeatable in the analysis of cell-to-cell contacts by saturation mutagenesis, as worms can be grown very fast in very high numbers. In Drosophila, a rich pattern is generated in the embryo as well as in adults that is used to unravel the underlying mechanisms of morphogenesis. The transparent larvae of zebrafish are uniquely suited to study organ development in a vertebrate, and the superb versatility of reverse genetics in the mouse made it the model organism to study human physiology and diseases. The combination of these models allows the in-depth genetic analysis of many fundamental biological processes using a plethora of different methods, finally providing many specific approaches to combat human diseases. The plant model Arabidopsis thaliana provides an understanding of many aspects of plant biology that might ultimately be useful for breeding crops.
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Herrmann KA, Liu Y, Llobet-Rosell A, McLaughlin CN, Neukomm LJ, Coutinho-Budd JC, Broihier HT. Divergent signaling requirements of dSARM in injury-induced degeneration and developmental glial phagocytosis. PLoS Genet 2022; 18:e1010257. [PMID: 35737721 PMCID: PMC9223396 DOI: 10.1371/journal.pgen.1010257] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
Elucidating signal transduction mechanisms of innate immune pathways is essential to defining how they elicit distinct cellular responses. Toll-like receptors (TLR) signal through their cytoplasmic TIR domains which bind other TIR domain-containing adaptors. dSARM/SARM1 is one such TIR domain adaptor best known for its role as the central axon degeneration trigger after injury. In degeneration, SARM1's domains have been assigned unique functions: the ARM domain is auto-inhibitory, SAM-SAM domain interactions mediate multimerization, and the TIR domain has intrinsic NAD+ hydrolase activity that precipitates axonal demise. Whether and how these distinct functions contribute to TLR signaling is unknown. Here we show divergent signaling requirements for dSARM in injury-induced axon degeneration and TLR-mediated developmental glial phagocytosis through analysis of new knock-in domain and point mutations. We demonstrate intragenic complementation between reciprocal pairs of domain mutants during development, providing evidence for separability of dSARM functional domains in TLR signaling. Surprisingly, dSARM's NAD+ hydrolase activity is strictly required for both degenerative and developmental signaling, demonstrating that TLR signal transduction requires dSARM's enzymatic activity. In contrast, while SAM domain-mediated dSARM multimerization is important for axon degeneration, it is dispensable for TLR signaling. Finally, dSARM functions in a linear genetic pathway with the MAP3K Ask1 during development but not in degenerating axons. Thus, we propose that dSARM exists in distinct signaling states in developmental and pathological contexts.
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Affiliation(s)
- Kelsey A. Herrmann
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Yizhou Liu
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Arnau Llobet-Rosell
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Colleen N. McLaughlin
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Lukas J. Neukomm
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Jaeda C. Coutinho-Budd
- Department of Neuroscience, University of Virginia, Charlottesville, Virginia, United States of America
| | - Heather T. Broihier
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail:
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Downregulation of glob1 mitigates human tau mediated neurotoxicity by restricting heterochromatin loss and elevating the autophagic response in drosophila. Mol Biol Rep 2022; 49:6581-6590. [PMID: 35633418 DOI: 10.1007/s11033-022-07498-8] [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: 02/17/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Human neuronal tauopathies are typically characterized by the accumulation of hyperphosphorylated tau in the forms of paired helical filaments and/or neurofibrillary tangles in the brain neurons. Tau-mediated heterochromatin loss and subsequent global transcriptional upsurge have been demonstrated as one of the key factors that promotes tau toxicity. We have reported earlier that expression of human tau-transgene in Drosophila induces the expression of glob1, and its restored level restricts tau etiology by regulating tau hyperphosphorylation and ROS generation via GSK-3β/p-Akt and Nrf2-keap1-ARE pathways, respectively. In view of this noted capability of glob1 in regulation of oxidative stress, and involvement of ROS in chromatin remodeling; we investigate if downregulation of glob1 restores tau-mediated heterochromatin loss in order to alleviate neurotoxicity. METHODS AND RESULTS The tauV337M transgene was expressed in Drosophila eye by utilizing GAL4/UAS system. Expression of glob1 was depleted in tauV337M expressing tissues by co-expressing an UAS-glob1RNAi transgene by GMR-Gal4 driver. Immunostaining and wstern blot analysis suggested that tissue-specific downregulation of glob1 restores the cellular level of CBP and minimizes tau-mediated heterochromatin loss. It also assists in mounting an improved protective autophagic response to alleviate the human tau-induced neurotoxicity in Drosophila tauopathy models. CONCLUSIONS Our study unfolds a novel aspect of the multitasking globin protein in restricting the pathogenesis of neuronal tauopathies. Interestingly, due to notable similarities between Drosophila glob1 and human globin gene(s), our findings may be helpful in developing novel therapeutic approaches against tauopathies.
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Xie Q, Li J, Li H, Udeshi ND, Svinkina T, Orlin D, Kohani S, Guajardo R, Mani DR, Xu C, Li T, Han S, Wei W, Shuster SA, Luginbuhl DJ, Quake SR, Murthy SE, Ting AY, Carr SA, Luo L. Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code. Neuron 2022; 110:2299-2314.e8. [PMID: 35613619 DOI: 10.1016/j.neuron.2022.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/11/2022] [Accepted: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains, and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combined expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.
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Affiliation(s)
- Qijing Xie
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Neurosciences Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Jiefu Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hongjie Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Namrata D Udeshi
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tanya Svinkina
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Orlin
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sayeh Kohani
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Guajardo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chuanyun Xu
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Tongchao Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Shuo Han
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Wei Wei
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - S Andrew Shuster
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Neurosciences Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - David J Luginbuhl
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Swetha E Murthy
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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47
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Pan D. The unfolding of the Hippo signaling pathway. Dev Biol 2022; 487:1-9. [PMID: 35405135 DOI: 10.1016/j.ydbio.2022.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 12/15/2022]
Abstract
The development of a functional organ requires not only patterning mechanisms that confer proper identities to individual cells, but also growth-regulatory mechanisms that specify the final size of the organ. At the turn of the 21st century, comprehensive genetic screens in model organisms had successfully uncovered the major signaling pathways that mediate pattern formation in metazoans. In contrast, signaling pathways dedicated to growth control were less explored. The past two decades has witnessed the emergence of the Hippo signaling pathway as a central mediator of organ size control through coordinated regulation of cell proliferation and apoptosis. Here I reflect on the early discoveries in Drosophila that elucidated the core kinase cascade and transcriptional machinery of the Hippo pathway, highlight its deep evolutionary conservation from humans to unicellular relatives of metazoan, and discuss the complex regulation of Hippo signaling by upstream inputs. This historical perspective underscores the importance of model organisms in uncovering fundamental and universal mechanisms of life processes.
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Affiliation(s)
- Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9040, USA.
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48
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The great small organisms of developmental genetics: Caenorhabditis elegans and Drosophila melanogaster. Dev Biol 2022; 485:93-122. [PMID: 35247454 PMCID: PMC9092520 DOI: 10.1016/j.ydbio.2022.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/30/2022]
Abstract
Experimental embryologists working at the turn of the 19th century suggested fundamental mechanisms of development, such as localized cytoplasmic determinants and tissue induction. However, the molecular basis underlying these processes proved intractable for a long time, despite concerted efforts in many developmental systems to isolate factors with a biological role. That road block was overcome by combining developmental biology with genetics. This powerful approach used unbiased genome-wide screens to isolate mutants with developmental defects and to thereby identify genes encoding key determinants and regulatory pathways that govern development. Two small invertebrates were the pioneers: the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. Their modes of development differ in many ways, but the two together led the way to unraveling the molecular mechanisms of many fundamental developmental processes. The discovery of the grand homologies between key players in development throughout the animal kingdom underscored the usefulness of studying these small invertebrate models for animal development and even human disease. We describe developmental genetics in Drosophila and C. elegans up to the rise of genomics at the beginning of the 21st Century. Finally, we discuss themes that emerge from the histories of such distinct organisms and prospects of this approach for the future.
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49
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Yang S, Wu X, Daoutidou EI, Zhang Y, Shimell M, Chuang KH, Peterson AJ, O'Connor MB, Zheng X. The NDNF-like factor Nord is a Hedgehog-induced extracellular BMP modulator that regulates Drosophila wing patterning and growth. eLife 2022; 11:e73357. [PMID: 35037619 PMCID: PMC8856659 DOI: 10.7554/elife.73357] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/15/2022] [Indexed: 11/23/2022] Open
Abstract
Hedgehog (Hh) and Bone Morphogenetic Proteins (BMPs) pattern the developing Drosophila wing by functioning as short- and long-range morphogens, respectively. Here, we show that a previously unknown Hh-dependent mechanism fine-tunes the activity of BMPs. Through genome-wide expression profiling of the Drosophila wing imaginal discs, we identify nord as a novel target gene of the Hh signaling pathway. Nord is related to the vertebrate Neuron-Derived Neurotrophic Factor (NDNF) involved in congenital hypogonadotropic hypogonadism and several types of cancer. Loss- and gain-of-function analyses implicate Nord in the regulation of wing growth and proper crossvein patterning. At the molecular level, we present biochemical evidence that Nord is a secreted BMP-binding protein and localizes to the extracellular matrix. Nord binds to Decapentaplegic (Dpp) or the heterodimer Dpp-Glass-bottom boat (Gbb) to modulate their release and activity. Furthermore, we demonstrate that Nord is a dosage-dependent BMP modulator, where low levels of Nord promote and high levels inhibit BMP signaling. Taken together, we propose that Hh-induced Nord expression fine-tunes both the range and strength of BMP signaling in the developing Drosophila wing.
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Affiliation(s)
- Shu Yang
- Department of Anatomy and Cell Biology and the GW Cancer Center, George Washington University School of Medicine and Health SciencesWashingtonUnited States
| | - Xuefeng Wu
- Department of Anatomy and Cell Biology and the GW Cancer Center, George Washington University School of Medicine and Health SciencesWashingtonUnited States
| | - Euphrosyne I Daoutidou
- Department of Genetics, Cell Biology & Development and the Developmental Biology Center, University of MinnesotaMinneapolisUnited States
| | - Ya Zhang
- Department of Anatomy and Cell Biology and the GW Cancer Center, George Washington University School of Medicine and Health SciencesWashingtonUnited States
| | - MaryJane Shimell
- Department of Genetics, Cell Biology & Development and the Developmental Biology Center, University of MinnesotaMinneapolisUnited States
| | - Kun-Han Chuang
- Department of Anatomy and Cell Biology and the GW Cancer Center, George Washington University School of Medicine and Health SciencesWashingtonUnited States
| | - Aidan J Peterson
- Department of Genetics, Cell Biology & Development and the Developmental Biology Center, University of MinnesotaMinneapolisUnited States
| | - Michael B O'Connor
- Department of Genetics, Cell Biology & Development and the Developmental Biology Center, University of MinnesotaMinneapolisUnited States
| | - Xiaoyan Zheng
- Department of Anatomy and Cell Biology and the GW Cancer Center, George Washington University School of Medicine and Health SciencesWashingtonUnited States
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50
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Hill EM, Chen CY, Del Viso F, Ellington LR, He S, Karabulut A, Paulson A, Gibson MC. Manipulation of Gene Activity in the Regenerative Model Sea Anemone, Nematostella vectensis. Methods Mol Biol 2022; 2450:437-465. [PMID: 35359322 PMCID: PMC9761902 DOI: 10.1007/978-1-0716-2172-1_23] [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: 06/14/2023]
Abstract
With a surprisingly complex genome and an ever-expanding genetic toolkit, the sea anemone Nematostella vectensis has become a powerful model system for the study of both development and whole-body regeneration. Here we provide the most current protocols for short-hairpin RNA (shRNA )-mediated gene knockdown and CRISPR/Cas9-targeted mutagenesis in this system. We further show that a simple Klenow reaction followed by in vitro transcription allows for the production of gene-specific shRNAs and single guide RNAs (sgRNAs) in a fast, affordable, and readily scalable manner. Together, shRNA knockdown and CRISPR/Cas9-targeted mutagenesis allow for rapid screens of gene function as well as the production of stable mutant lines that enable functional genetic analysis throughout the Nematostella life cycle.
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Affiliation(s)
- Eric M Hill
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Cheng-Yi Chen
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Ahmet Karabulut
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, USA.
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