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Tate HM, Barone V, Schrankel CS, Hamdoun A, Lyons DC. Localization and origins of juvenile skeletogenic cells in the sea urchin Lytechinuspictus. Dev Biol 2024; 514:12-27. [PMID: 38862087 DOI: 10.1016/j.ydbio.2024.05.012] [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: 07/22/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024]
Abstract
The development of the sea urchin larval body plan is well understood from extensive studies of embryonic patterning. However, fewer studies have investigated the late larval stages during which the unique pentaradial adult body plan develops. Previous work on late larval development highlights major tissue changes leading up to metamorphosis, but the location of specific cell types during juvenile development is less understood. Here, we improve on technical limitations by applying highly sensitive hybridization chain reaction fluorescent in situ hybridization (HCR-FISH) to the fast-developing and transparent sea urchin Lytechinus pictus, with a focus on skeletogenic cells. First, we show that HCR-FISH can be used in L. pictus to precisely localize skeletogenic cells in the rudiment. In doing so, we provide a detailed staging scheme for the appearance of skeletogenic cells around the rudiment prior to and during biomineralization and show that many skeletogenic cells unassociated with larval rods localize outside of the rudiment prior to localizing inside. Second, we show that downstream biomineralization genes have similar expression patterns during larval and juvenile skeletogenesis, suggesting some conservation of skeletogenic mechanisms during development between stages. Third, we find co-expression of blastocoelar and skeletogenic cell markers around juvenile skeleton located outside of the rudiment, which is consistent with data showing that cells from the non-skeletogenic mesoderm embryonic lineage contribute to the juvenile skeletogenic cell lineage. This work sets the foundation for subsequent studies of other cell types in the late larva of L. pictus to better understand juvenile body plan development, patterning, and evolution.
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Affiliation(s)
- Heidi M Tate
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Vanessa Barone
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Catherine S Schrankel
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA; San Diego State University, San Diego, CA, USA
| | - Amro Hamdoun
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA.
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2
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Cayrol B, Colella S, Uzest M. Coupling clearing and hybridization chain reaction approaches to investigate gene expression in organs inside intact insect heads. Microsc Res Tech 2024; 87:1926-1932. [PMID: 38558482 DOI: 10.1002/jemt.24561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Detecting RNA molecules within their natural environment inside intact arthropods has long been challenging, particularly in small organisms covered by a tanned and pigmented cuticle. Here, we have developed a methodology that enables high-resolution analysis of the spatial distribution of transcripts of interest without having to dissect tiny organs or tissues, thereby preserving their integrity. We have combined an in situ amplification approach based on hybridization chain reaction, which enhances the signal-to-noise ratio, and a clearing approach that allows the visualization of inner organs beneath the cuticle. We have implemented this methodology for the first time in Hemiptera, mapping two salivary aphid (Acyrthosiphon pisum) transcripts, the effector c002 and the salivary sheath protein SHP. With a multiplex approach, we could simultaneously detect different mRNAs in mounted pea aphid head-thorax samples and show that they were distributed in distinct secretory cells of salivary glands. RESEARCH HIGHLIGHTS: Combining hybridisation chain reaction and clearing allows the detection of transcripts in intact aphids heads. The transcripts of the two salivary proteins c002 and SHP are compartmentalized in distinct secretory cells of the principal glands.
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Affiliation(s)
- Bastien Cayrol
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stefano Colella
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Marilyne Uzest
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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3
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Wang Y, Liu X, Zeng Y, Saka SK, Xie W, Goldaracena I, Kohman RE, Yin P, Church GM. Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. Nucleic Acids Res 2024:gkae592. [PMID: 38966983 DOI: 10.1093/nar/gkae592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Antibodies have long served as vital tools in biological and clinical laboratories for the specific detection of proteins. Conventional methods employ fluorophore or horseradish peroxidase-conjugated antibodies to detect signals. More recently, DNA-conjugated antibodies have emerged as a promising technology, capitalizing on the programmability and amplification capabilities of DNA to enable highly multiplexed and ultrasensitive protein detection. However, the nonspecific binding of DNA-conjugated antibodies has impeded the widespread adoption of this approach. Here, we present a novel DNA-conjugated antibody staining protocol that addresses these challenges and demonstrates superior performance in suppressing nonspecific signals compared to previously published protocols. We further extend the utility of DNA-conjugated antibodies for signal-amplified in situ protein imaging through the hybridization chain reaction (HCR) and design a novel HCR DNA pair to expand the HCR hairpin pool from the previously published 5 pairs to 13, allowing for flexible hairpin selection and higher multiplexing. Finally, we demonstrate highly multiplexed in situ protein imaging using these techniques in both cultured cells and tissue sections.
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Affiliation(s)
- Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Xiaoyu Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yitian Zeng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wenxin Xie
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Goldaracena
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richie E Kohman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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4
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Brooks EC, Han SJY, Bonatto Paese CL, Lewis AA, Aarnio-Peterson M, Brugmann SA. The ciliary protein C2cd3 is required for mandibular musculoskeletal tissue patterning. Differentiation 2024; 138:100782. [PMID: 38810379 PMCID: PMC11227401 DOI: 10.1016/j.diff.2024.100782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
The mandible is composed of several musculoskeletal tissues including bone, cartilage, and tendon that require precise patterning to ensure structural and functional integrity. Interestingly, most of these tissues are derived from one multipotent cell population called cranial neural crest cells (CNCCs). How CNCCs are properly instructed to differentiate into various tissue types remains nebulous. To better understand the mechanisms necessary for the patterning of mandibular musculoskeletal tissues we utilized the avian mutant talpid2 (ta2) which presents with several malformations of the facial skeleton including dysplastic tendons, mispatterned musculature, and bilateral ectopic cartilaginous processes extending off Meckel's cartilage. We found an ectopic epithelial BMP signaling domain in the ta2 mandibular prominence (MNP) that correlated with the subsequent expansion of SOX9+ cartilage precursors. These findings were validated with conditional murine models suggesting an evolutionarily conserved mechanism for CNCC-derived musculoskeletal patterning. Collectively, these data support a model in which cilia are required to define epithelial signal centers essential for proper musculoskeletal patterning of CNCC-derived mesenchyme.
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Affiliation(s)
- Evan C Brooks
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Simon J Y Han
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Medical Scientist Training Program, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Christian Louis Bonatto Paese
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Amya A Lewis
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Megan Aarnio-Peterson
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA; Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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5
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Clarke DN, Formery L, Lowe CJ. See-Star: a versatile hydrogel-based protocol for clearing large, opaque and calcified marine invertebrates. EvoDevo 2024; 15:8. [PMID: 38918798 PMCID: PMC11201320 DOI: 10.1186/s13227-024-00228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Studies of morphology and developmental patterning in adult stages of many invertebrates are hindered by opaque structures, such as shells, skeletal elements, and pigment granules that block or refract light and necessitate sectioning for observation of internal features. An inherent challenge in studies relying on surgical approaches is that cutting tissue is semi-destructive, and delicate structures, such as axonal processes within neural networks, are computationally challenging to reconstruct once disrupted. To address this problem, we developed See-Star, a hydrogel-based tissue clearing protocol to render the bodies of opaque and calcified invertebrates optically transparent while preserving their anatomy in an unperturbed state, facilitating molecular labeling and observation of intact organ systems. The resulting protocol can clear large (> 1 cm3) specimens to enable deep-tissue imaging, and is compatible with molecular techniques, such as immunohistochemistry and in situ hybridization to visualize protein and mRNA localization. To test the utility of this method, we performed a whole-mount imaging study of intact nervous systems in juvenile echinoderms and molluscs and demonstrate that See-Star allows for comparative studies to be extended far into development, facilitating insights into the anatomy of juveniles and adults that are usually not amenable to whole-mount imaging.
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Affiliation(s)
- D N Clarke
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - L Formery
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - C J Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
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6
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André M, Dinvaut S, Castellani V, Falk J. 3D exploration of gene expression in chicken embryos through combined RNA fluorescence in situ hybridization, immunofluorescence, and clearing. BMC Biol 2024; 22:131. [PMID: 38831263 PMCID: PMC11149291 DOI: 10.1186/s12915-024-01922-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Fine characterization of gene expression patterns is crucial to understand many aspects of embryonic development. The chicken embryo is a well-established and valuable animal model for developmental biology. The period spanning from the third to sixth embryonic days (E3 to E6) is critical for many organ developments. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA-FISH) enables multiplex RNA detection in thick samples including embryos of various animal models. However, its use is limited by tissue opacity. RESULTS We optimized HCR RNA-FISH protocol to efficiently label RNAs in whole mount chicken embryos from E3.5 to E5.5 and adapted it to ethyl cinnamate (ECi) tissue clearing. We show that light sheet imaging of HCR RNA-FISH after ECi clearing allows RNA expression analysis within embryonic tissues with good sensitivity and spatial resolution. Finally, whole mount immunofluorescence can be performed after HCR RNA-FISH enabling as exemplified to assay complex spatial relationships between axons and their environment or to monitor GFP electroporated neurons. CONCLUSIONS We could extend the use of HCR RNA-FISH to older chick embryos by optimizing HCR RNA-FISH and combining it with tissue clearing and 3D imaging. The integration of immunostaining makes possible to combine gene expression with classical cell markers, to correlate expressions with morphological differentiation and to depict gene expressions in gain or loss of function contexts. Altogether, this combined procedure further extends the potential of HCR RNA-FISH technique for chicken embryology.
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Affiliation(s)
- Maëlys André
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
| | - Sarah Dinvaut
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Valérie Castellani
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Julien Falk
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
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7
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Kawaguchi A, Wang J, Knapp D, Murawala P, Nowoshilow S, Masselink W, Taniguchi-Sugiura Y, Fei JF, Tanaka EM. A chromatin code for limb segment identity in axolotl limb regeneration. Dev Cell 2024:S1534-5807(24)00300-9. [PMID: 38788714 DOI: 10.1016/j.devcel.2024.05.002] [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: 01/15/2023] [Revised: 07/25/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.
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Affiliation(s)
- Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dunja Knapp
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Yuka Taniguchi-Sugiura
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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8
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Steyn C, Mishi R, Fillmore S, Verhoog MB, More J, Rohlwink UK, Melvill R, Butler J, Enslin JMN, Jacobs M, Sauka-Spengler T, Greco M, Quiñones S, Dulla CG, Raimondo JV, Figaji A, Hockman D. Cell type-specific gene expression dynamics during human brain maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.29.560114. [PMID: 37808657 PMCID: PMC10557738 DOI: 10.1101/2023.09.29.560114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The human brain undergoes protracted post-natal maturation, guided by dynamic changes in gene expression. Most studies exploring these processes have used bulk tissue analyses, which mask cell type-specific gene expression dynamics. Here, using single nucleus (sn)RNA-seq on temporal lobe tissue, including samples of African ancestry, we build a joint paediatric and adult atlas of 75 cell subtypes, which we verify with spatial transcriptomics. We explore the differences between paediatric and adult cell types, revealing the genes and pathways that change during brain maturation. Our results highlight excitatory neuron subtypes, including the LTK and FREM subtypes, that show elevated expression of genes associated with cognition and synaptic plasticity in paediatric tissue. The new resources we present here improve our understanding of the brain during its development and contribute to global efforts to build an inclusive brain cell map.
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Affiliation(s)
- Christina Steyn
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ruvimbo Mishi
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Stephanie Fillmore
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Matthijs B Verhoog
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Jessica More
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ursula K Rohlwink
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Roger Melvill
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - James Butler
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Johannes M N Enslin
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Muazzam Jacobs
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Immunology, Department of Pathology University of Cape Town
- National Health Laboratory Service, South Africa
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Maria Greco
- Single Cell Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sadi Quiñones
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Graduate School of Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Chris G Dulla
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Joseph V Raimondo
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anthony Figaji
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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Powell GT, Faro A, Zhao Y, Stickney H, Novellasdemunt L, Henriques P, Gestri G, White ER, Ren J, Lu W, Young RM, Hawkins TA, Cavodeassi F, Schwarz Q, Dreosti E, Raible DW, Li VSW, Wright GJ, Jones EY, Wilson SW. Cachd1 interacts with Wnt receptors and regulates neuronal asymmetry in the zebrafish brain. Science 2024; 384:573-579. [PMID: 38696577 PMCID: PMC7615972 DOI: 10.1126/science.ade6970] [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: 09/02/2022] [Accepted: 03/27/2024] [Indexed: 05/04/2024]
Abstract
Neurons on the left and right sides of the nervous system often show asymmetric properties, but how such differences arise is poorly understood. Genetic screening in zebrafish revealed that loss of function of the transmembrane protein Cachd1 resulted in right-sided habenula neurons adopting left-sided identity. Cachd1 is expressed in neuronal progenitors, functions downstream of asymmetric environmental signals, and influences timing of the normally asymmetric patterns of neurogenesis. Biochemical and structural analyses demonstrated that Cachd1 can bind simultaneously to Lrp6 and Frizzled family Wnt co-receptors. Consistent with this, lrp6 mutant zebrafish lose asymmetry in the habenulae, and epistasis experiments support a role for Cachd1 in modulating Wnt pathway activity in the brain. These studies identify Cachd1 as a conserved Wnt receptor-interacting protein that regulates lateralized neuronal identity in the zebrafish brain.
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Affiliation(s)
- Gareth T. Powell
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
- Wellcome Trust Sanger Institute; Cambridge CB10 1SA, UK
| | - Ana Faro
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford; Oxford, OX3 7BN, UK
| | - Heather Stickney
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
- Departments of Otolaryngology-HNS and Biological Structure, University of Washington; Seattle, WA 98195-7420, USA
- Ambry Genetics; Aliso Viejo, CA 92656, USA
| | - Laura Novellasdemunt
- The Francis Crick Institute; London, NW1 1AT, UK
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; 08028, Barcelona, Spain
| | - Pedro Henriques
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
| | - Gaia Gestri
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
| | | | - Jingshan Ren
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford; Oxford, OX3 7BN, UK
| | - Weixian Lu
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford; Oxford, OX3 7BN, UK
| | - Rodrigo M. Young
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
- Institute of Ophthalmology, University College London; London, EC1V 9EL, UK
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor; Camino La Piramide 5750, 8580745, Santiago, Chile
| | - Thomas A. Hawkins
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
| | - Florencia Cavodeassi
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
- St. George’s, University of London; London, SW17 0RE, UK
| | - Quenten Schwarz
- Institute of Ophthalmology, University College London; London, EC1V 9EL, UK
| | - Elena Dreosti
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
| | - David W. Raible
- Departments of Otolaryngology-HNS and Biological Structure, University of Washington; Seattle, WA 98195-7420, USA
| | | | - Gavin J. Wright
- Wellcome Trust Sanger Institute; Cambridge CB10 1SA, UK
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York; York, YO10 5DD, UK
| | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford; Oxford, OX3 7BN, UK
| | - Stephen W. Wilson
- Cell and Developmental Biology, University College London; London, WC1E 6BT, UK
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10
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Tjeerdema E, Lee Y, Metry R, Hamdoun A. Semi-automated, high-content imaging of drug transporter knockout sea urchin (Lytechinus pictus) embryos. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:313-329. [PMID: 38087422 DOI: 10.1002/jez.b.23231] [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: 05/16/2023] [Revised: 11/08/2023] [Accepted: 11/19/2023] [Indexed: 05/01/2024]
Abstract
A defining feature of sea urchins is their extreme fecundity. Urchins produce millions of transparent, synchronously developing embryos, ideal for spatial and temporal analysis of development. This biological feature has been effectively utilized for ensemble measurement of biochemical changes. However, it has been underutilized in imaging studies, where single embryo measurements are used. Here we present an example of how stable genetics and high content imaging, along with machine learning-based image analysis, can be used to exploit the fecundity and synchrony of sea urchins in imaging-based drug screens. Building upon our recently created sea urchin ABCB1 knockout line, we developed a high-throughput assay to probe the role of this drug transporter in embryos. We used high content imaging to compare accumulation and toxicity of canonical substrates and inhibitors of the transporter, including fluorescent molecules and antimitotic cancer drugs, in homozygous knockout and wildtype embryos. To measure responses from the resulting image data, we used a nested convolutional neural network, which rapidly classified embryos according to fluorescence or cell division. This approach identified sea urchin embryos with 99.8% accuracy and determined two-cell and aberrant embryos with 96.3% and 89.1% accuracy, respectively. The results revealed that ABCB1 knockout embryos accumulated the transporter substrate calcein 3.09 times faster than wildtypes. Similarly, knockouts were 4.71 and 3.07 times more sensitive to the mitotic poisons vinblastine and taxol. This study paves the way for large scale pharmacological screens in the sea urchin embryo.
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Affiliation(s)
- Evan Tjeerdema
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Yoon Lee
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Rachel Metry
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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11
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Beaulieu MO, Thomas ED, Raible DW. Transdifferentiation is uncoupled from progenitor pool expansion during hair cell regeneration in the zebrafish inner ear. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588777. [PMID: 38645220 PMCID: PMC11030336 DOI: 10.1101/2024.04.09.588777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Death of mechanosensory hair cells in the inner ear is a common cause of auditory and vestibular impairment in mammals, which have a limited ability to regrow these cells after damage. In contrast, non-mammalian vertebrates including zebrafish can robustly regenerate hair cells following severe organ damage. The zebrafish inner ear provides an understudied model system for understanding hair cell regeneration in organs that are highly conserved with their mammalian counterparts. Here we quantitatively examine hair cell addition during growth and regeneration of the larval zebrafish inner ear. We used a genetically encoded ablation method to induce hair cell death and observed gradual regeneration with correct spatial patterning over two weeks following ablation. Supporting cells, which surround and are a source of new hair cells, divide in response to hair cell ablation, expanding the possible progenitor pool. In parallel, nascent hair cells arise from direct transdifferentiation of progenitor pool cells uncoupled from progenitor division. These findings reveal a previously unrecognized mechanism of hair cell regeneration with implications for how hair cells may be encouraged to regenerate in the mammalian ear.
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Affiliation(s)
- Marielle O. Beaulieu
- Molecular and Cellular Biology Graduate Program, Seattle, WA
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology - Head and Neck Surgery, Seattle, WA
| | - Eric D. Thomas
- Neuroscience Graduate Program, Seattle, WA
- Department of Biological Structure University of Washington, Seattle, WA
| | - David W. Raible
- Molecular and Cellular Biology Graduate Program, Seattle, WA
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology - Head and Neck Surgery, Seattle, WA
- Neuroscience Graduate Program, Seattle, WA
- Department of Biological Structure University of Washington, Seattle, WA
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12
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Truong BT, Shull LC, Zepeda BJ, Lencer E, Artinger KB. Human split hand/foot variants are not as functional as wildtype human PRDM1 in the rescue of craniofacial defects. Birth Defects Res 2024; 116:e2327. [PMID: 38456586 PMCID: PMC10949536 DOI: 10.1002/bdr2.2327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Split hand/foot malformation (SHFM) is a congenital limb disorder presenting with limb anomalies, such as missing, hypoplastic, or fused digits, and often craniofacial defects, including a cleft lip/palate, microdontia, micrognathia, or maxillary hypoplasia. We previously identified three novel variants in the transcription factor, PRDM1, that are associated with SHFM phenotypes. One individual also presented with a high arch palate. Studies in vertebrates indicate that PRDM1 is important for development of the skull; however, prior to our study, human variants in PRDM1 had not been associated with craniofacial anomalies. METHODS Using transient mRNA overexpression assays in prdm1a-/- mutant zebrafish, we tested whether the PRDM1 SHFM variants were functional and could lead to a rescue of the craniofacial defects observed in prdm1a-/- mutants. We also mined previously published CUT&RUN and RNA-seq datasets that sorted EGFP-positive cells from a Tg(Mmu:Prx1-EGFP) transgenic line that labels the pectoral fin, pharyngeal arches, and dorsal part of the head to examine Prdm1a binding and the effect of Prdm1a loss on craniofacial genes. RESULTS The prdm1a-/- mutants exhibit craniofacial defects including a hypoplastic neurocranium, a loss of posterior ceratobranchial arches, a shorter palatoquadrate, and an inverted ceratohyal. Injection of wildtype (WT) hPRDM1 in prdm1a-/- mutants partially rescues the palatoquadrate phenotype. However, injection of each of the three SHFM variants fails to rescue this skeletal defect. Loss of prdm1a leads to a decreased expression of important craniofacial genes by RNA-seq, including emilin3a, confirmed by hybridization chain reaction expression. Other genes including dlx5a/dlx6a, hand2, sox9b, col2a1a, and hoxb genes are also reduced. Validation by real-time quantitative PCR in the anterior half of zebrafish embryos failed to confirm the expression changes suggesting that the differences are enriched in prx1 expressing cells. CONCLUSION These data suggest that the three SHFM variants are likely not functional and may be associated with the craniofacial defects observed in the humans. Finally, they demonstrate how Prdm1a can directly bind and regulate genes involved in craniofacial development.
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Affiliation(s)
- Brittany T Truong
- Human Medical Genetics & Genomics Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Craniofacial Development, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
| | - Lomeli C Shull
- Department of Craniofacial Development, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bryan J Zepeda
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, Minnesota, USA
| | - Ezra Lencer
- Biology Department, Lafayette College, Easton, Pennsylvania, USA
| | - Kristin B Artinger
- Department of Craniofacial Development, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, Minnesota, USA
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13
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Schulte S, Shin B, Rothenberg EV, Pierce NA. Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction. ACS Chem Biol 2024; 19:280-288. [PMID: 38232374 PMCID: PMC10877569 DOI: 10.1021/acschembio.3c00431] [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: 07/22/2023] [Revised: 11/18/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) facilitates spatial exploration of gene regulatory networks by enabling multiplex, quantitative, high-resolution imaging of RNA and protein targets. Here, we extend these capabilities to the imaging of protein:protein complexes, using proximity-dependent cooperative probes to conditionally generate a single amplified signal if and only if two target proteins are colocalized within the sample. HCR probes and amplifiers combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind nonspecifically in the sample, they will not generate amplified background. We demonstrate protein:protein imaging with a high signal-to-background ratio in human cells, mouse proT cells, and highly autofluorescent formalin-fixed paraffin-embedded (FFPE) human breast tissue sections. Further, we demonstrate multiplex imaging of three different protein:protein complexes simultaneously and validate that HCR enables accurate and precise relative quantitation of protein:protein complexes with subcellular resolution in an anatomical context. Moreover, we establish a unified framework for simultaneous multiplex, quantitative, high-resolution imaging of RNA, protein, and protein:protein targets, with one-step, isothermal, enzyme-free HCR signal amplification performed for all target classes simultaneously.
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Affiliation(s)
- Samuel
J. Schulte
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Boyoung Shin
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Ellen V. Rothenberg
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Niles A. Pierce
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Division
of Engineering and Applied Science, California
Institute of Technology, Pasadena, California 91125, United States
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14
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Schulte SJ, Fornace ME, Hall JK, Shin GJ, Pierce NA. HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples. Development 2024; 151:dev202307. [PMID: 38415752 PMCID: PMC10941662 DOI: 10.1242/dev.202307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/21/2023] [Indexed: 02/29/2024]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) provides a unified framework for multiplex, quantitative, high-resolution imaging of RNA and protein targets in highly autofluorescent samples. With conventional bandpass imaging, multiplexing is typically limited to four or five targets owing to the difficulty in separating signals generated by fluorophores with overlapping spectra. Spectral imaging has offered the conceptual promise of higher levels of multiplexing, but it has been challenging to realize this potential in highly autofluorescent samples, including whole-mount vertebrate embryos. Here, we demonstrate robust HCR spectral imaging with linear unmixing, enabling simultaneous imaging of ten RNA and/or protein targets in whole-mount zebrafish embryos and mouse brain sections. Further, we demonstrate that the amplified and unmixed signal in each of the ten channels is quantitative, enabling accurate and precise relative quantitation of RNA and/or protein targets with subcellular resolution, and RNA absolute quantitation with single-molecule resolution, in the anatomical context of highly autofluorescent samples.
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Affiliation(s)
- Samuel J. Schulte
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark E. Fornace
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John K. Hall
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grace J. Shin
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Niles A. Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
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15
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Schwarz M, Hamburger K. Memory effects of visual and olfactory landmark information in human wayfinding. Cogn Process 2024; 25:37-51. [PMID: 38032500 PMCID: PMC10827900 DOI: 10.1007/s10339-023-01169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Non-human animals are exceptionally good at using smell to find their way through the environment. However, the use of olfactory cues for human navigation is often underestimated. Although the sense of smell is well-known for its distinct connection to memory and emotion, memory effects in human navigation using olfactory landmarks have not been studied yet. Therefore, this article compares wayfinding and recognition performance for visual and olfactory landmarks learned by 52 participants in a virtual maze. Furthermore, it is one of the first empirical studies investigating differences in memory effects on human navigation by using two separate test situations 1 month apart. The experimental task was to find the way through a maze-like virtual environment with either olfactory or visual cues at the intersections that served as decision points. Our descriptive results show that performance was above chance level for both conditions (visual and olfactory landmarks). Wayfinding performance did not decrease 1 month later when using olfactory landmarks. In contrast, when using visual landmarks wayfinding performance decreased significantly, while visual landmarks overall lead to better recognition than olfactory landmarks at both times of testing. The results demonstrate the unique character of human odor memory and support the conclusion that olfactory cues may be used in human spatial orientation. Furthermore, the present study expands the research field of human wayfinding by providing a study that investigates memory for landmark knowledge and route decisions for the visual and olfactory modality. However, more studies are required to put this important research strand forward.
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Affiliation(s)
- Mira Schwarz
- Experimental Psychology and Cognitive Science, Department of Psychology and Sport Science, Justus Liebig University, Otto-Behagel-Str. 10F, 35394, Giessen, Germany.
| | - Kai Hamburger
- Experimental Psychology and Cognitive Science, Department of Psychology and Sport Science, Justus Liebig University, Otto-Behagel-Str. 10F, 35394, Giessen, Germany
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16
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Gautam S, Fenner JL, Wang B, Range RC. Evolutionarily conserved Wnt/Sp5 signaling is critical for anterior-posterior axis patterning in sea urchin embryos. iScience 2024; 27:108616. [PMID: 38179064 PMCID: PMC10765061 DOI: 10.1016/j.isci.2023.108616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/30/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Studies across a diverse group of metazoan embryos indicate that Wnt signaling often activates the transcription factor Sp5, forming a signaling 'cassette' that plays critical roles in many developmental processes. This study explores the role of Wnt/Sp5 signaling during the specification and patterning of the primary germ layers during early anterior-posterior axis formation in the deuterostome sea urchin embryo. Our functional analyses show that Sp5 is critical for endomesoderm specification downstream of Wnt/β-catenin in posterior cells as well as anterior neuroectoderm patterning downstream of non-canonical Wnt/JNK signaling in anterior cells. Interestingly, expression and functional data comparisons show that Wnt/Sp5 signaling often plays similar roles in posterior endomesoderm as well as neuroectoderm patterning along the AP axis of several deuterostome embryos, including vertebrates. Thus, our findings provide strong support for the idea that Wnt-Sp5 signaling cassettes were critical for the establishment of early germ layers in the common deuterostome ancestor.
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Affiliation(s)
- Sujan Gautam
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer L. Fenner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Boyuan Wang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ryan C. Range
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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17
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Rayamajhi D, Ege M, Ukhanov K, Ringers C, Zhang Y, Jung I, D’Gama PP, Li SS, Cosacak MI, Kizil C, Park HC, Yaksi E, Martens JR, Brody SL, Jurisch-Yaksi N, Roy S. The forkhead transcription factor Foxj1 controls vertebrate olfactory cilia biogenesis and sensory neuron differentiation. PLoS Biol 2024; 22:e3002468. [PMID: 38271330 PMCID: PMC10810531 DOI: 10.1371/journal.pbio.3002468] [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: 06/23/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
In vertebrates, olfactory receptors localize on multiple cilia elaborated on dendritic knobs of olfactory sensory neurons (OSNs). Although olfactory cilia dysfunction can cause anosmia, how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1, a forkhead domain-containing transcription factor traditionally linked with motile cilia biogenesis, is expressed in OSNs and required for olfactory epithelium (OE) formation. In keeping with the immotile nature of olfactory cilia, we observed that ciliary motility genes are repressed in zebrafish, mouse, and human OSNs. Strikingly, we also found that besides ciliogenesis, Foxj1 controls the differentiation of the OSNs themselves by regulating their cell type-specific gene expression, such as that of olfactory marker protein (omp) involved in odor-evoked signal transduction. In line with this, response to bile acids, odors detected by OMP-positive OSNs, was significantly diminished in foxj1 mutant zebrafish. Taken together, our findings establish how the canonical Foxj1-mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of immotile olfactory cilia, as well as for the development of the OSNs.
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Affiliation(s)
- Dheeraj Rayamajhi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Mert Ege
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kirill Ukhanov
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida, United States of America
| | - Christa Ringers
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway
| | - Yiliu Zhang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Inyoung Jung
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biomedical Sciences, Korea University, Ansan, South Korea
| | - Percival P. D’Gama
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Summer Shijia Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Dresden, Germany
| | - Caghan Kizil
- Department of Neurology and The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Hae-Chul Park
- Department of Biomedical Sciences, Korea University, Ansan, South Korea
| | - Emre Yaksi
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway
- Koç University Research Center for Translational Medicine, Koç University School of Medicine, Istanbul, Turkey
| | - Jeffrey R. Martens
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida, United States of America
| | - Steven L. Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Nathalie Jurisch-Yaksi
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- Department of Paediatrics, National University of Singapore, Singapore
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18
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Nguyen TT, Mitchell JM, Kiel MD, Kenny CP, Li H, Jones KL, Cornell RA, Williams TJ, Nichols JT, Van Otterloo E. TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. Development 2024; 151:dev202095. [PMID: 38063857 PMCID: PMC10820886 DOI: 10.1242/dev.202095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underlies facial shape variation, yet how those networks in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both TFAP2 family members dysregulates numerous midface GRN components involved in midface morphogenesis, patterning and differentiation. Notably, Alx1, Alx3 and Alx4 (ALX) transcript levels are reduced, whereas ChIP-seq analyses suggest TFAP2 family members directly and positively regulate ALX gene expression. Tfap2a, Tfap2b and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish implies conservation of this regulatory axis across vertebrates. Consistent with this notion, tfap2a zebrafish mutants present with abnormal alx3 expression patterns, Tfap2a binds ALX loci and tfap2a-alx3 genetic interactions are observed. Together, these data demonstrate TFAP2 paralogs regulate vertebrate midfacial development in part by activating expression of ALX transcription factor genes.
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Affiliation(s)
- Timothy T. Nguyen
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Jennyfer M. Mitchell
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela D. Kiel
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Colin P. Kenny
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth L. Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Robert A. Cornell
- Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98195, USA
| | - Trevor J. Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James T. Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric Van Otterloo
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
- Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
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19
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Maltby CJ, Krans A, Grudzien SJ, Palacios Y, Muiños J, Suárez A, Asher M, Khurana V, Barmada SJ, Dijkstra AA, Todd PK. AAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571345. [PMID: 38168171 PMCID: PMC10760133 DOI: 10.1101/2023.12.13.571345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by biallelic, non-reference pentameric AAGGG(CCCTT) repeat expansions within the second intron of replication factor complex subunit 1 (RFC1). To investigate how these repeats cause disease, we generated CANVAS patient induced pluripotent stem cell (iPSC) derived neurons (iNeurons) and utilized calcium imaging and transcriptomic analysis to define repeat-elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in CANVAS patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons, and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. These phenotypic deficits were not replicated by knockdown of RFC1 in control neurons and were not rescued by ectopic expression of RFC1. These findings support a repeat-dependent but RFC1-independent cause of neuronal dysfunction in CANVAS, with important implications for therapeutic development in this currently untreatable condition.
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Affiliation(s)
- Connor J. Maltby
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
| | - Samantha J. Grudzien
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yomira Palacios
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Muiños
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- UM SMART Undergraduate Summer Program, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Suárez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Melissa Asher
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Vikram Khurana
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sami J. Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Anke A. Dijkstra
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter K. Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
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20
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Sperling AL, Eves-van den Akker S. Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes. PLANT METHODS 2023; 19:139. [PMID: 38049899 PMCID: PMC10696717 DOI: 10.1186/s13007-023-01112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Plant-parasitic nematodes compromise the agriculture of a wide variety of the most common crops worldwide. Obtaining information on the fundamental biology of these organisms and how they infect the plant has been restricted by the ability to visualize intact nematodes using small molecule stains, antibodies, or in situ hybridization. Consequently, there is limited information available about the internal composition of the nematodes or the biology of the effector molecules they use to reprogram their host plant. RESULTS We present the Sperling prep - a whole mount method for nematode preparation that enables staining with small molecules, antibodies, or in situ hybridization chain reaction. This method does not require specialized apparatus and utilizes typical laboratory equipment and materials. By dissociating the strong cuticle and interior muscle layers, we enabled entry of the small molecule stains into the tissue. After permeabilization, small molecule stains can be used to visualize the nuclei with the DNA stain DAPI and the internal structures of the digestive tract and longitudinal musculature with the filamentous actin stain phalloidin. The permeabilization even allows entry of larger antibodies, albeit with lower efficiency. Finally, this method works exceptionally well with in situ HCR. Using this method, we have visualized effector transcripts specific to the dorsal gland and the subventral grand of the sugar beet cyst nematode, Heterodera schachtii, multiplexed in the same nematode. CONCLUSION We were able to visualize the internal structures of the nematode as well as key effector transcripts that are used during plant infection and parasitism. Therefore, this method provides an important toolkit for studying the biology of plant-parasitic nematodes.
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Affiliation(s)
- Alexis L Sperling
- Department of Plant Sciences, Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, Cambridge, UK
| | - Sebastian Eves-van den Akker
- Department of Plant Sciences, Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, Cambridge, UK.
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21
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Chen Q, Leshkowitz D, Li H, van Impel A, Schulte-Merker S, Amit I, Rizzoti K, Levkowitz G. Neural plate progenitors give rise to both anterior and posterior pituitary cells. Dev Cell 2023; 58:2652-2665.e6. [PMID: 37683631 DOI: 10.1016/j.devcel.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 05/14/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
The pituitary is the master neuroendocrine gland, which regulates body homeostasis. It consists of the anterior pituitary/adenohypophysis harboring hormones producing cells and the posterior pituitary/neurohypophysis, which relays the passage of hormones from the brain to the periphery. It is accepted that the adenohypophysis originates from the oral ectoderm (Rathke's pouch), whereas the neural ectoderm contributes to the neurohypophysis. Single-cell transcriptomics of the zebrafish pituitary showed that cyp26b1-positive astroglial pituicytes of the neurohypophysis and prop1-positive adenohypophyseal progenitors expressed common markers implying lineage relatedness. Genetic tracing identifies that, in contrast to the prevailing dogma, neural plate precursors of zebrafish (her4.3+) and mouse (Sox1+) contribute to both neurohypophyseal and a subset of adenohypophyseal cells. Pituicyte-derived retinoic-acid-degrading enzyme Cyp26b1 fine-tunes differentiation of prop1+ progenitors into hormone-producing cells. These results challenge the notion that adenohypophyseal cells are exclusively derived from non-neural ectoderm and demonstrate that crosstalk between neuro- and adeno-hypophyseal cells affects differentiation of pituitary cells.
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Affiliation(s)
- Qiyu Chen
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Dena Leshkowitz
- Life Science Core Facilities, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Hanjie Li
- Department of Systems Immunology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel; Present address: CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Andreas van Impel
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, Cells-in-Motion Cluster of Excellence, WWU Münster, Münster, Germany
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, Cells-in-Motion Cluster of Excellence, WWU Münster, Münster, Germany
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Karine Rizzoti
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, UK
| | - Gil Levkowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel.
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22
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Huang T, Guillotin B, Rahni R, Birnbaum KD, Wagner D. A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol. PLANT METHODS 2023; 19:131. [PMID: 37993896 PMCID: PMC10666358 DOI: 10.1186/s13007-023-01108-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND In the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported. RESULTS We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol. CONCLUSIONS The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues.
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Affiliation(s)
- Tian Huang
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bruno Guillotin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Ramin Rahni
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kenneth D Birnbaum
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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23
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Kelly JJ, Wen H, Brehm P. Single-cell RNAseq analysis of spinal locomotor circuitry in larval zebrafish. eLife 2023; 12:RP89338. [PMID: 37975797 PMCID: PMC10656102 DOI: 10.7554/elife.89338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish. Electrophysiological studies have shown that in addition to connectivity, understanding of circuitry requires identification of functional specializations among individual circuit components, such as those that regulate levels of transmitter release and neuronal excitability. In this study, we use single-cell RNA sequencing (scRNAseq) to identify the molecular bases for functional distinctions between motoneuron types that are causal to their differential roles in swimming. The primary motoneuron, in particular, expresses high levels of a unique combination of voltage-dependent ion channel types and synaptic proteins termed functional 'cassettes.' The ion channel types are specialized for promoting high-frequency firing of action potentials and augmented transmitter release at the neuromuscular junction, both contributing to greater power generation. Our transcriptional profiling of spinal neurons further assigns expression of this cassette to specific interneuron types also involved in the central circuitry controlling high-speed swimming and escape behaviors. Our analysis highlights the utility of scRNAseq in functional characterization of neuronal circuitry, in addition to providing a gene expression resource for studying cell type diversity.
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Affiliation(s)
- Jimmy J Kelly
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
| | - Hua Wen
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
| | - Paul Brehm
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
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24
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Raji JI, Potter CJ. Hybridization Chain Reaction RNA Whole-Mount Fluorescence In situ Hybridization of Chemosensory Genes in Mosquito Olfactory Appendages. J Vis Exp 2023:10.3791/65933. [PMID: 38047558 PMCID: PMC11099874 DOI: 10.3791/65933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Mosquitoes are effective vectors of deadly diseases and can navigate their chemical environment using chemosensory receptors expressed in their olfactory appendages. Understanding how chemosensory receptors are spatially organized in the peripheral olfactory appendages can offer insights into how odor is encoded in the mosquito olfactory system and inform new ways to combat the spread of mosquito-borne diseases. The emergence of third-generation hybridization chain reaction RNA whole-mount fluorescence in situ hybridization (HCR RNA WM-FISH) allows for spatial mapping and simultaneous expression profiling of multiple chemosensory genes. Here, we describe a stepwise approach for performing HCR RNA WM-FISH on the Anopheles mosquito antenna and maxillary palp. We investigated the sensitivity of this technique by examining the expression profile of ionotropic olfactory receptors. We asked if the HCR WM-FISH technique described was suitable for multiplexed studies by tethering RNA probes to three spectrally distinct fluorophores. Results provided evidence that HCR RNA WM-FISH is robustly sensitive to simultaneously detect multiple chemosensory genes in the antenna and maxillary palp olfactory appendages. Further investigations attest to the suitability of HCR WM-FISH for co-expression profiling of double and triple RNA targets. This technique, when applied with modifications, could be adaptable to localize genes of interest in the olfactory tissues of other insect species or in other appendages.
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Affiliation(s)
- Joshua I Raji
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine
| | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine;
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25
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Schwarz M, Hamburger K. Implicit versus explicit processing of visual, olfactory, and multimodal landmark information in human wayfinding. Front Psychol 2023; 14:1285034. [PMID: 38034279 PMCID: PMC10684750 DOI: 10.3389/fpsyg.2023.1285034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Despite the predominant focus on visual perception in most studies, the role of humans' sense of smell in navigation has often been neglected. Recent research, however, could show that humans are indeed able to use their sense of smell for orientation, particularly when processed implicitly. In this study, we investigate whether implicit perception of olfactory landmarks enhanced wayfinding performance compared to explicit perception. Fifty-two people completed a wayfinding and a recognition task in a virtual maze at two times of testing 1 month apart. Participants either received olfactory, visual, or both cues at the intersections. Wayfinding performance was better for olfactory landmarks, which were not correctly remembered in the recognition task. In contrast, wayfinding performance was better when visual landmarks were correctly remembered. In the multimodal condition, wayfinding performance was better with landmarks being remembered at t1 and remained the same at t2. Our results suggest distinct implicit processing mechanisms within the olfactory system and therefore hold important implications for the nature of spatial odor processing extending beyond explicit odor localization tasks. The study highlights the importance for future studies to develop and employ further experimental methods that capture implicit processing across all of our senses. This is crucial for a comprehensive understanding of consciousness, as olfaction strongly influences our behavior, but remains largely latent unless deliberately honed through practice.
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Affiliation(s)
- Mira Schwarz
- Department of Experimental Psychology and Cognitive Science, Faculty of Psychology and Sport Science, Justus Liebig University Giessen, Giessen, Germany
| | - Kai Hamburger
- Department of Experimental Psychology and Cognitive Science, Faculty of Psychology and Sport Science, Justus Liebig University Giessen, Giessen, Germany
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26
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Banach-Latapy A, Rincheval V, Briand D, Guénal I, Spéder P. Differential adhesion during development establishes individual neural stem cell niches and shapes adult behaviour in Drosophila. PLoS Biol 2023; 21:e3002352. [PMID: 37943883 PMCID: PMC10635556 DOI: 10.1371/journal.pbio.3002352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023] Open
Abstract
Neural stem cells (NSCs) reside in a defined cellular microenvironment, the niche, which supports the generation and integration of newborn neurons. The mechanisms building a sophisticated niche structure around NSCs and their functional relevance for neurogenesis are yet to be understood. In the Drosophila larval brain, the cortex glia (CG) encase individual NSC lineages in membranous chambers, organising the stem cell population and newborn neurons into a stereotypic structure. We first found that CG wrap around lineage-related cells regardless of their identity, showing that lineage information builds CG architecture. We then discovered that a mechanism of temporally controlled differential adhesion using conserved complexes supports the individual encasing of NSC lineages. An intralineage adhesion through homophilic Neuroglian interactions provides strong binding between cells of a same lineage, while a weaker interaction through Neurexin-IV and Wrapper exists between NSC lineages and CG. Loss of Neuroglian results in NSC lineages clumped together and in an altered CG network, while loss of Neurexin-IV/Wrapper generates larger yet defined CG chamber grouping several lineages together. Axonal projections of newborn neurons are also altered in these conditions. Further, we link the loss of these 2 adhesion complexes specifically during development to locomotor hyperactivity in the resulting adults. Altogether, our findings identify a belt of adhesions building a neurogenic niche at the scale of individual stem cell and provide the proof of concept that niche properties during development shape adult behaviour.
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Affiliation(s)
- Agata Banach-Latapy
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
| | | | - David Briand
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
| | - Isabelle Guénal
- Université Paris-Saclay, UVSQ, LGBC, 78000, Versailles, France
| | - Pauline Spéder
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
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27
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Kelly JJ, Wen H, Brehm P. Single cell RNA-seq analysis of spinal locomotor circuitry in larval zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543939. [PMID: 37333232 PMCID: PMC10274715 DOI: 10.1101/2023.06.06.543939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish. Electrophysiological studies have shown that additional to connectivity, understanding of circuitry requires identification of functional specializations among individual circuit components, such as those that regulate levels of transmitter release and neuronal excitability. In this study we use single cell RNA sequencing (scRNAseq) to identify the molecular bases for functional distinctions between motoneuron types that are causal to their differential roles in swimming. The primary motoneuron (PMn) in particular, expresses high levels of a unique combination of voltage-dependent ion channel types and synaptic proteins termed functional 'cassettes'. The ion channel types are specialized for promoting high frequency firing of action potentials and augmented transmitter release at the neuromuscular junction, both contributing to greater power generation. Our transcriptional profiling of spinal neurons further assigns expression of this cassette to specific interneuron types also involved in the central circuitry controlling high speed swimming and escape behaviors. Our analysis highlights the utility of scRNAseq in functional characterization of neuronal circuitry, in addition to providing a gene expression resource for studying cell type diversity.
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Affiliation(s)
- Jimmy J. Kelly
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Hua Wen
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Paul Brehm
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
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28
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Cullen G, Gilligan JB, Guhlin JG, Dearden PK. Germline progenitors and oocyte production in the honeybee queen ovary. Genetics 2023; 225:iyad138. [PMID: 37487025 PMCID: PMC10471204 DOI: 10.1093/genetics/iyad138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023] Open
Abstract
Understanding the reproduction of honeybee queens is crucial to support populations of this economically important insect. Here we examine the structure of the honeybee ovary to determine the nature of the germline progenitors in the ovary. Using a panel of marker genes that mark somatic or germline tissue in other insects we determine which cells in the honeybee ovary are somatic and which germline. We examine patterns of cell division and demonstrate that, unlike Drosophila, there is no evidence of single germline stem cells that provide the germline in honeybees. Germline progenitors are clustered in groups of 8 cells, joined by a polyfusome, and collections of these, in each ovariole, appear to maintain the germline during reproduction. We also show that these 8-cell clusters can divide and that their division occurs such that the numbers of germline progenitors are relatively constant over the reproductive life of queen honeybees. This information helps us to understand the diversity of structures in insect reproduction, and provide information to better support honeybee reproduction.
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Affiliation(s)
- Georgia Cullen
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
| | - Joshua B Gilligan
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
- Biological Heritage National Science Challenge, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
| | - Joseph G Guhlin
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
- Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
| | - Peter K Dearden
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
- Biological Heritage National Science Challenge, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
- Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, 9054, Aotearoa-New Zealand
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29
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Schulte SJ, Fornace ME, Hall JK, Pierce NA. HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555626. [PMID: 37693627 PMCID: PMC10491186 DOI: 10.1101/2023.08.30.555626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) provides a unified framework for multiplex, quantitative, high-resolution imaging of RNA and protein targets in highly autofluorescent samples. With conventional bandpass imaging, multiplexing is typically limited to four or five targets due to the difficulty in separating signals generated by fluorophores with overlapping spectra. Spectral imaging has offered the conceptual promise of higher levels of multiplexing, but it has been challenging to realize this potential in highly autofluorescent samples including whole-mount vertebrate embryos. Here, we demonstrate robust HCR spectral imaging with linear unmixing, enabling simultaneous imaging of 10 RNA and/or protein targets in whole-mount zebrafish embryos and mouse brain sections. Further, we demonstrate that the amplified and unmixed signal in each of 10 channels is quantitative, enabling accurate and precise relative quantitation of RNA and/or protein targets with subcellular resolution, and RNA absolute quantitation with single-molecule resolution, in the anatomical context of highly autofluorescent samples. SUMMARY Spectral imaging with signal amplification based on the mechanism of hybridization chain reaction enables robust 10-plex, quantitative, high-resolution imaging of RNA and protein targets in whole-mount vertebrate embryos and brain sections.
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30
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Ćorić A, Stockinger AW, Schaffer P, Rokvić D, Tessmar-Raible K, Raible F. A Fast And Versatile Method for Simultaneous HCR, Immunohistochemistry And Edu Labeling (SHInE). Integr Comp Biol 2023; 63:372-381. [PMID: 36866518 PMCID: PMC10445416 DOI: 10.1093/icb/icad007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Access to newer, fast, and cheap sequencing techniques, particularly on the single-cell level, have made transcriptomic data of tissues or single cells accessible to many researchers. As a consequence, there is an increased need for in situ visualization of gene expression or encoded proteins to validate, localize, or help interpret such sequencing data, as well as put them in context with cellular proliferation. A particular challenge for labeling and imaging transcripts are complex tissues that are often opaque and/or pigmented, preventing easy visual inspection. Here, we introduce a versatile protocol that combines in situ hybridization chain reaction, immunohistochemistry, and proliferative cell labeling using 5-ethynyl-2'-deoxyuridine, and demonstrate its compatibility with tissue clearing. As a proof-of-concept, we show that our protocol allows for the parallel analysis of cell proliferation, gene expression, and protein localization in bristleworm heads and trunks.
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Affiliation(s)
- Aida Ćorić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Alexander W Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Petra Schaffer
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Dunja Rokvić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Carl-von-Ossietzky University, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
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31
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Subramanian A, Kanzaki LF, Schilling TF. Mechanical force regulates Sox9 expression at the developing enthesis. Development 2023; 150:dev201141. [PMID: 37497608 PMCID: PMC10445799 DOI: 10.1242/dev.201141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Entheses transmit force from tendons and ligaments to the skeleton. Regional organization of enthesis extracellular matrix (ECM) generates differences in stiffness required for force transmission. Two key transcription factors co-expressed in entheseal tenocytes, scleraxis (Scx) and Sox9, directly control production of enthesis ECM components. Formation of embryonic craniofacial entheses in zebrafish coincides with onset of jaw movements, possibly in response to the force of muscle contraction. We show dynamic changes in scxa and sox9a mRNA levels in subsets of entheseal tenocytes that correlate with their roles in force transmission. We also show that transcription of a direct target of Scxa, Col1a, in enthesis ECM is regulated by the ratio of scxa to sox9a expression. Eliminating muscle contraction by paralyzing embryos during early stages of musculoskeletal differentiation alters relative levels of scxa and sox9a in entheses, primarily owing to increased sox9a expression. Force-dependent TGF-β (TGFβ) signaling is required to maintain this balance of scxa and sox9a expression. Thus, force from muscle contraction helps establish a balance of transcription factor expression that controls specialized ECM organization at the tendon enthesis and its ability to transmit force.
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Affiliation(s)
- Arul Subramanian
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Lauren F. Kanzaki
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
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32
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Mar KB, Wells AI, Caballero Van Dyke MC, Lopez AH, Eitson JL, Fan W, Hanners NW, Evers BM, Shelton JM, Schoggins JW. LY6E is a pan-coronavirus restriction factor in the respiratory tract. Nat Microbiol 2023; 8:1587-1599. [PMID: 37443277 PMCID: PMC11234902 DOI: 10.1038/s41564-023-01431-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
LY6E is an antiviral restriction factor that inhibits coronavirus spike-mediated fusion, but the cell types in vivo that require LY6E for protection from respiratory coronavirus infection are unknown. Here we used a panel of seven conditional Ly6e knockout mice to define which Ly6e-expressing cells confer control of airway infection by murine coronavirus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Loss of Ly6e in Lyz2-expressing cells, radioresistant Vav1-expressing cells and non-haematopoietic cells increased susceptibility to murine coronavirus. Global conditional loss of Ly6e expression resulted in clinical disease and higher viral burden after SARS-CoV-2 infection, but little evidence of immunopathology. We show that Ly6e expression protected secretory club and ciliated cells from SARS-CoV-2 infection and prevented virus-induced loss of an epithelial cell transcriptomic signature in the lung. Our study demonstrates that lineage confined rather than broad expression of Ly6e sufficiently confers resistance to disease caused by murine and human coronaviruses.
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Affiliation(s)
- Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alexandra I Wells
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Alexandra H Lopez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wenchun Fan
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Natasha W Hanners
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bret M Evers
- Departments of Pathology and Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John M Shelton
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Kozol RA, Conith AJ, Yuiska A, Cree-Newman A, Tolentino B, Benesh K, Paz A, Lloyd E, Kowalko JE, Keene AC, Albertson C, Duboue ER. A brain-wide analysis maps structural evolution to distinct anatomical module. eLife 2023; 12:e80777. [PMID: 37498318 PMCID: PMC10435234 DOI: 10.7554/elife.80777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
The vertebrate brain is highly conserved topologically, but less is known about neuroanatomical variation between individual brain regions. Neuroanatomical variation at the regional level is hypothesized to provide functional expansion, building upon ancestral anatomy needed for basic functions. Classically, animal models used to study evolution have lacked tools for detailed anatomical analysis that are widely used in zebrafish and mice, presenting a barrier to studying brain evolution at fine scales. In this study, we sought to investigate the evolution of brain anatomy using a single species of fish consisting of divergent surface and cave morphs, that permits functional genetic testing of regional volume and shape across the entire brain. We generated a high-resolution brain atlas for the blind Mexican cavefish Astyanax mexicanus and coupled the atlas with automated computational tools to directly assess variability in brain region shape and volume across all populations. We measured the volume and shape of every grossly defined neuroanatomical region of the brain and assessed correlations between anatomical regions in surface fish, cavefish, and surface × cave F2 hybrids, whose phenotypes span the range of surface to cave. We find that dorsal regions of the brain are contracted, while ventral regions have expanded, with F2 hybrid data providing support for developmental constraint along the dorsal-ventral axis. Furthermore, these dorsal-ventral relationships in anatomical variation show similar patterns for both volume and shape, suggesting that the anatomical evolution captured by these two parameters could be driven by similar developmental mechanisms. Together, these data demonstrate that A. mexicanus is a powerful system for functionally determining basic principles of brain evolution and will permit testing how genes influence early patterning events to drive brain-wide anatomical evolution.
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Affiliation(s)
- Robert A Kozol
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Andrew J Conith
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Anders Yuiska
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexia Cree-Newman
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Bernadeth Tolentino
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Kasey Benesh
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexandra Paz
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Evan Lloyd
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh UniversityBethlehemUnited States
| | - Alex C Keene
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Craig Albertson
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
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34
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Bronchain O, Ducos B, Putzer H, Delagrange M, Laalami S, Philippe-Caraty L, Saroul K, Ciapa B. Natural antisense transcription of presenilin in sea urchin reveals a possible role for natural antisense transcription in the general control of gene expression during development. J Cell Sci 2023; 136:jcs261284. [PMID: 37345489 DOI: 10.1242/jcs.261284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
One presenilin gene (PSEN) is expressed in the sea urchin embryo, in the vegetal pole of the gastrula and then mainly in cilia cells located around the digestive system of the pluteus, as we recently have reported. PSEN expression must be accurately regulated for correct execution of these two steps of development. While investigating PSEN expression changes in embryos after expansion of endoderm with LiCl or of ectoderm with Zn2+ by whole-mount in situ hybridization (WISH) and quantitative PCR (qPCR), we detected natural antisense transcription of PSEN. We then found that Endo16 and Wnt5, markers of endo-mesoderm, and of Hnf6 and Gsc, markers of ectoderm, are also sense and antisense transcribed. We discuss that general gene expression could depend on both sense and antisense transcription. This mechanism, together with the PSEN gene, should be included in gene regulatory networks (GRNs) that theorize diverse processes in this species. We suggest that it would also be relevant to investigate natural antisense transcription of PSEN in the field of Alzheimer's disease (AD) where the role of human PSEN1 and PSEN2 is well known.
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Affiliation(s)
- Odile Bronchain
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Harald Putzer
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Marine Delagrange
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Soumaya Laalami
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Laetitia Philippe-Caraty
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Krystel Saroul
- Institut CURIE, Université Paris-Saclay, INSERM U932, Immunité et Cancer, 91400 Orsay, France
| | - Brigitte Ciapa
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
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35
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Nguyen TT, Mitchell JM, Kiel MD, Jones KL, Williams TJ, Nichols JT, Van Otterloo E. TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545376. [PMID: 37398373 PMCID: PMC10312788 DOI: 10.1101/2023.06.16.545376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest even during the late migratory phase results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both Tfap2 members dysregulated numerous midface GRN components involved in midface fusion, patterning, and differentiation. Notably, Alx1/3/4 (Alx) transcript levels are reduced, while ChIP-seq analyses suggest TFAP2 directly and positively regulates Alx gene expression. TFAP2 and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish further implies conservation of this regulatory axis across vertebrates. Consistent with this notion, tfap2a mutant zebrafish present abnormal alx3 expression patterns, and the two genes display a genetic interaction in this species. Together, these data demonstrate a critical role for TFAP2 in regulating vertebrate midfacial development in part through ALX transcription factor gene expression.
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Affiliation(s)
- Timothy T Nguyen
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
| | - Jennyfer M Mitchell
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela D Kiel
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - James T Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric Van Otterloo
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
- Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA, 52242, USA
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36
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McNulty R, Sritharan D, Pahng SH, Meisch JP, Liu S, Brennan MA, Saxer G, Hormoz S, Rosenthal AZ. Probe-based bacterial single-cell RNA sequencing predicts toxin regulation. Nat Microbiol 2023; 8:934-945. [PMID: 37012420 PMCID: PMC10159851 DOI: 10.1038/s41564-023-01348-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/25/2023] [Indexed: 04/05/2023]
Abstract
Clonal bacterial populations rely on transcriptional variation across individual cells to produce specialized states that increase fitness. Understanding all cell states requires studying isogenic bacterial populations at the single-cell level. Here we developed probe-based bacterial sequencing (ProBac-seq), a method that uses libraries of DNA probes and an existing commercial microfluidic platform to conduct bacterial single-cell RNA sequencing. We sequenced the transcriptome of thousands of individual bacterial cells per experiment, detecting several hundred transcripts per cell on average. Applied to Bacillus subtilis and Escherichia coli, ProBac-seq correctly identifies known cell states and uncovers previously unreported transcriptional heterogeneity. In the context of bacterial pathogenesis, application of the approach to Clostridium perfringens reveals heterogeneous expression of toxin by a subpopulation that can be controlled by acetate, a short-chain fatty acid highly prevalent in the gut. Overall, ProBac-seq can be used to uncover heterogeneity in isogenic microbial populations and identify perturbations that affect pathogenicity.
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Affiliation(s)
- Ryan McNulty
- IFF Health and Biosciences, Wilmington, DE, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Duluxan Sritharan
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Seong Ho Pahng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Shichen Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Gerda Saxer
- IFF Health and Biosciences, Wilmington, DE, USA
| | - Sahand Hormoz
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Adam Z Rosenthal
- IFF Health and Biosciences, Wilmington, DE, USA.
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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37
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Truong BT, Shull LC, Lencer E, Bend EG, Field M, Blue EE, Bamshad MJ, Skinner C, Everman D, Schwartz CE, Flanagan-Steet H, Artinger KB. PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in split hand/foot malformation. Dis Model Mech 2023; 16:dmm049977. [PMID: 37083955 PMCID: PMC10151829 DOI: 10.1242/dmm.049977] [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: 11/10/2022] [Accepted: 03/09/2023] [Indexed: 04/22/2023] Open
Abstract
Split hand/foot malformation (SHFM) is a rare limb abnormality with clefting of the fingers and/or toes. For many individuals, the genetic etiology is unknown. Through whole-exome and targeted sequencing, we detected three novel variants in a gene encoding a transcription factor, PRDM1, that arose de novo in families with SHFM or segregated with the phenotype. PRDM1 is required for limb development; however, its role is not well understood and it is unclear how the PRDM1 variants affect protein function. Using transient and stable overexpression rescue experiments in zebrafish, we show that the variants disrupt the proline/serine-rich and DNA-binding zinc finger domains, resulting in a dominant-negative effect. Through gene expression assays, RNA sequencing, and CUT&RUN in isolated pectoral fin cells, we demonstrate that Prdm1a directly binds to and regulates genes required for fin induction, outgrowth and anterior/posterior patterning, such as fgfr1a, dlx5a, dlx6a and smo. Taken together, these results improve our understanding of the role of PRDM1 in the limb gene regulatory network and identified novel PRDM1 variants that link to SHFM in humans.
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Affiliation(s)
- Brittany T. Truong
- Human Medical Genetics & Genomics Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lomeli C. Shull
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ezra Lencer
- Biology Department, Lafayette College, Easton, PA 18042, USA
| | - Eric G. Bend
- Greenwood Genetics Center, Greenwood, SC 29646, USA
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, AUS
| | - Elizabeth E. Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | - Kristin B. Artinger
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
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38
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Fuiten AM, Yoshimoto Y, Shukunami C, Stadler HS. Digits in a dish: An in vitro system to assess the molecular genetics of hand/foot development at single-cell resolution. Front Cell Dev Biol 2023; 11:1135025. [PMID: 36994104 PMCID: PMC10040768 DOI: 10.3389/fcell.2023.1135025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
In vitro models allow for the study of developmental processes outside of the embryo. To gain access to the cells mediating digit and joint development, we identified a unique property of undifferentiated mesenchyme isolated from the distal early autopod to autonomously re-assemble forming multiple autopod structures including: digits, interdigital tissues, joints, muscles and tendons. Single-cell transcriptomic analysis of these developing structures revealed distinct cell clusters that express canonical markers of distal limb development including: Col2a1, Col10a1, and Sp7 (phalanx formation), Thbs2 and Col1a1 (perichondrium), Gdf5, Wnt5a, and Jun (joint interzone), Aldh1a2 and Msx1 (interdigital tissues), Myod1 (muscle progenitors), Prg4 (articular perichondrium/articular cartilage), and Scx and Tnmd (tenocytes/tendons). Analysis of the gene expression patterns for these signature genes indicates that developmental timing and tissue-specific localization were also recapitulated in a manner similar to the initiation and maturation of the developing murine autopod. Finally, the in vitro digit system also recapitulates congenital malformations associated with genetic mutations as in vitro cultures of Hoxa13 mutant mesenchyme produced defects present in Hoxa13 mutant autopods including digit fusions, reduced phalangeal segment numbers, and poor mesenchymal condensation. These findings demonstrate the robustness of the in vitro digit system to recapitulate digit and joint development. As an in vitro model of murine digit and joint development, this innovative system will provide access to the developing limb tissues facilitating studies to discern how digit and articular joint formation is initiated and how undifferentiated mesenchyme is patterned to establish individual digit morphologies. The in vitro digit system also provides a platform to rapidly evaluate treatments aimed at stimulating the repair or regeneration of mammalian digits impacted by congenital malformation, injury, or disease.
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Affiliation(s)
- Allison M. Fuiten
- Research Center, Shriners Children’s, Portland, OR, United States
- Department of Orthopaedics and Rehabilitation, Oregon Health and Science University, Portland, OR, United States
| | - Yuki Yoshimoto
- Department of Molecular Biology and Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Chisa Shukunami
- Department of Molecular Biology and Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - H. Scott Stadler
- Research Center, Shriners Children’s, Portland, OR, United States
- Department of Orthopaedics and Rehabilitation, Oregon Health and Science University, Portland, OR, United States
- *Correspondence: H. Scott Stadler,
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39
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Schulte S, Huang J, Pierce NA. Hybridization Chain Reaction Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing. ACS Infect Dis 2023; 9:450-458. [PMID: 36735927 PMCID: PMC9924079 DOI: 10.1021/acsinfecdis.2c00472] [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: 09/18/2022] [Indexed: 02/05/2023]
Abstract
The lateral flow assay format enables rapid, instrument-free, at-home testing for SARS-CoV-2. Due to the absence of signal amplification, this simplicity comes at a cost in sensitivity. Here, we enhance sensitivity by developing an amplified lateral flow assay that incorporates isothermal, enzyme-free signal amplification based on the mechanism of hybridization chain reaction (HCR). The simplicity of the user experience is maintained using a disposable 3-channel lateral flow device to automatically deliver reagents to the test region in three successive stages without user interaction. To perform a test, the user loads the sample, closes the device, and reads the result by eye after 60 min. Detecting gamma-irradiated SARS-CoV-2 virions in a mixture of saliva and extraction buffer, the current amplified HCR lateral flow assay achieves a limit of detection of 200 copies/μL using available antibodies to target the SARS-CoV-2 nucleocapsid protein. By comparison, five commercial unamplified lateral flow assays that use proprietary antibodies exhibit limits of detection of 500 copies/μL, 1000 copies/μL, 2000 copies/μL, 2000 copies/μL, and 20,000 copies/μL. By swapping out antibody probes to target different pathogens, amplified HCR lateral flow assays offer a platform for simple, rapid, and sensitive at-home testing for infectious diseases. As an alternative to viral protein detection, we further introduce an HCR lateral flow assay for viral RNA detection.
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Affiliation(s)
- Samuel
J. Schulte
- Division
of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jining Huang
- Division
of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Niles A. Pierce
- Division
of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division
of Engineering & Applied Science, California
Institute of Technology, Pasadena, California 91125, United States
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40
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Inwood SN, Harrop TWR, Dearden PK. The venom composition and parthenogenesis mechanism of the parasitoid wasp Microctonus hyperodae, a declining biocontrol agent. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 153:103897. [PMID: 36584929 DOI: 10.1016/j.ibmb.2022.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
A biocontrol system in New Zealand using the endoparasitoid Microctonus hyperodae is failing, despite once being one of the most successful examples of classical biocontrol worldwide. Though it is of significant economic importance as a control agent, little is known about the genetics of M. hyperodae. In this study, RNA-seq was used to characterise two key traits of M. hyperodae in this system, the venom, critical for the initial success of biocontrol, and the asexual reproduction mode, which influenced biocontrol decline. Expanded characterisation of M. hyperodae venom revealed candidates involved in manipulating the host environment to source nutrition for the parasitoid egg, preventing a host immune response against the egg, as well as two components that may stimulate the host's innate immune system. Notably lacking from the venom-specific expression list was calreticulin, as it also had high expression in the ovaries. In-situ hybridisation revealed this ovarian expression was localised to the follicle cells, which may result in the deposition of calreticulin into the egg exochorion. Investigating the asexual reproduction of M. hyperodae revealed core meiosis-specific genes had conserved expression patterns with the highest expression in the ovaries, suggesting M. hyperodae parthenogenesis involves meiosis and that the potential for sexual reproduction may have been retained. Upregulation of genes involved in endoreduplication provides a potential mechanism for the restoration of diploidy in eggs after meiosis.
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Affiliation(s)
- Sarah N Inwood
- Bioprotection Aotearoa, Genomics Aotearoa, and the Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Thomas W R Harrop
- Bioprotection Aotearoa, Genomics Aotearoa, and the Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand; Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter K Dearden
- Bioprotection Aotearoa, Genomics Aotearoa, and the Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand.
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41
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McMahon NP, Jones JA, Anderson AN, Dietz MS, Wong MH, Gibbs SL. Flexible Cyclic Immunofluorescence (cyCIF) Using Oligonucleotide Barcoded Antibodies. Cancers (Basel) 2023; 15:827. [PMID: 36765785 PMCID: PMC9913741 DOI: 10.3390/cancers15030827] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Advances in our understanding of the complex, multifaceted interactions between tumor epithelia, immune infiltrate, and tumor microenvironmental cells have been driven by highly multiplexed imaging technologies. These techniques are capable of labeling many more biomarkers than conventional immunostaining methods. However, multiplexed imaging techniques suffer from low detection sensitivity, cell loss-particularly in fragile samples-, and challenges with antibody labeling. Herein, we developed and optimized an oligonucleotide antibody barcoding strategy for cyclic immunofluorescence (cyCIF) that can be amplified to increase the detection efficiency of low-abundance antigens. Stained fluorescence signals can be readily removed using ultraviolet light treatment, preserving tissue and fragile cell sample integrity. We also extended the oligonucleotide barcoding strategy to secondary antibodies to enable the inclusion of difficult-to-label primary antibodies in a cyCIF panel. Using both the amplification oligonucleotides to label DNA barcoded antibodies and in situ hybridization of multiple fluorescently labeled oligonucleotides resulted in signal amplification and increased signal-to-background ratios. This procedure was optimized through the examination of staining parameters including staining oligonucleotide concentration, staining temperature, and oligonucleotide sequence design, resulting in a robust amplification technique. As a proof-of-concept, we demonstrate the flexibility of our cyCIF strategy by simultaneously imaging with the original oligonucleotide conjugated antibody (Ab-oligo) cyCIF strategy, the novel Ab-oligo cyCIF amplification strategy, as well as direct and indirect immunofluorescence to generate highly multiplexed images.
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Affiliation(s)
- Nathan P. McMahon
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Jocelyn A. Jones
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Ashley N. Anderson
- Department of Cell, Development & Cancer Biology Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Matthew S. Dietz
- Department of Cell, Development & Cancer Biology Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Melissa H. Wong
- Department of Cell, Development & Cancer Biology Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Summer L. Gibbs
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
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42
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Wang X, Yang C, Wang X, Miao J, Chen W, Zhou Y, Xu Y, An Y, Cheng A, Ye W, Chen M, Song D, Yuan X, Wang J, Qian P, Ruohao Wu A, Zhang ZY, Liu K. Driving axon regeneration by orchestrating neuronal and non-neuronal innate immune responses via the IFNγ-cGAS-STING axis. Neuron 2023; 111:236-255.e7. [PMID: 36370710 PMCID: PMC9851977 DOI: 10.1016/j.neuron.2022.10.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/20/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
The coordination mechanism of neural innate immune responses for axon regeneration is not well understood. Here, we showed that neuronal deletion of protein tyrosine phosphatase non-receptor type 2 sustains the IFNγ-STAT1 activity in retinal ganglion cells (RGCs) to promote axon regeneration after injury, independent of mTOR or STAT3. DNA-damage-induced cGAMP synthase (cGAS)-stimulator of interferon genes (STINGs) activation is the functional downstream signaling. Directly activating neuronal STING by cGAMP promotes axon regeneration. In contrast to the central axons, IFNγ is locally translated in the injured peripheral axons and upregulates cGAS expression in Schwann cells and infiltrating blood cells to produce cGAMP, which promotes spontaneous axon regeneration as an immunotransmitter. Our study demonstrates that injured peripheral nervous system (PNS) axons can direct the environmental innate immune response for self-repair and that the neural antiviral mechanism can be harnessed to promote axon regeneration in the central nervous system (CNS).
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Affiliation(s)
- Xu Wang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong 518057, China,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou 510515, China,These authors contributed equally
| | - Chao Yang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong 518057, China,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou 510515, China,These authors contributed equally
| | - Xuejie Wang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Jinmin Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research and Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA
| | - Weitao Chen
- Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Yiren Zhou
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ying Xu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yongyan An
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Aifang Cheng
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wenkang Ye
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Mengxian Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Dong Song
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xue Yuan
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Jiguang Wang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Angela Ruohao Wu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China,Center for Aging Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research and Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA
| | - Kai Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China; Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong 518057, China; Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou 510515, China.
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43
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Shi T, Beaulieu MO, Saunders LM, Fabian P, Trapnell C, Segil N, Crump JG, Raible DW. Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes. eLife 2023; 12:82978. [PMID: 36598134 PMCID: PMC9851615 DOI: 10.7554/elife.82978] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/04/2023] [Indexed: 01/05/2023] Open
Abstract
A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non-mammalian vertebrates such as zebrafish, regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability, the degree to which the inner ears of fish and mammals share common hair cells and supporting cell types remains unresolved. Here, we perform single-cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair cells and non-sensory supporting cells. We identify a putative progenitor population for hair cells and supporting cells, as well as distinct hair and supporting cell types in the maculae versus cristae. The hair cell and supporting cell types differ from those described for the lateral line system, a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae, we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the three macular organs, the utricle, saccule, and lagena, consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals validate zebrafish as a relevant model for understanding inner ear-specific hair cell function and regeneration.
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Affiliation(s)
- Tuo Shi
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Marielle O Beaulieu
- Department of Otolaryngology-Head and Neck Surgery, University of WashingtonSeattleUnited States
| | - Lauren M Saunders
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Peter Fabian
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Cole Trapnell
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - David W Raible
- Department of Otolaryngology-Head and Neck Surgery, University of WashingtonSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Biological Structure, University of WashingtonSeattleUnited States
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44
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Rodríguez-Sastre N, Shapiro N, Hawkins DY, Lion AT, Peyreau M, Correa AE, Dionne K, Bradham CA. Ethanol exposure perturbs sea urchin development and disrupts developmental timing. Dev Biol 2023; 493:89-102. [PMID: 36368523 DOI: 10.1016/j.ydbio.2022.11.001] [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: 07/04/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Ethanol is a known vertebrate teratogen that causes craniofacial defects as a component of fetal alcohol syndrome (FAS). Our results show that sea urchin embryos treated with ethanol similarly show broad skeletal patterning defects, potentially analogous to the defects associated with FAS. The sea urchin larval skeleton is a simple patterning system that involves only two cell types: the primary mesenchymal cells (PMCs) that secrete the calcium carbonate skeleton and the ectodermal cells that provide migratory, positional, and differentiation cues for the PMCs. Perturbations in RA biosynthesis and Hh signaling pathways are thought to be causal for the FAS phenotype in vertebrates. Surprisingly, our results indicate that these pathways are not functionally relevant for the teratogenic effects of ethanol in developing sea urchins. We found that developmental morphology as well as the expression of some ectodermal and PMC genes was delayed by ethanol exposure. Temporal transcriptome analysis revealed significant impacts of ethanol on signaling and metabolic gene expression, and a disruption in the timing of GRN gene expression that includes both delayed and precocious gene expression throughout the specification network. We conclude that the skeletal patterning perturbations in ethanol-treated embryos likely arise from a loss of temporal synchrony within and between the instructive and responsive tissues.
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Affiliation(s)
| | | | | | - Alexandra T Lion
- Biology Department, Boston University, Boston, MA, USA; MCBB Program, Boston University, Boston, MA, USA
| | | | - Andrea E Correa
- Universidad de Puerto Rico-Recinto Aguadilla, Puerto Rico, USA
| | | | - Cynthia A Bradham
- Biology Department, Boston University, Boston, MA, USA; MCBB Program, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA.
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45
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D'Gama PP, Jurisch-Yaksi N. Methods to study motile ciliated cell types in the zebrafish brain. Methods Cell Biol 2023; 176:103-123. [PMID: 37164533 DOI: 10.1016/bs.mcb.2023.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Cilia are well conserved hair-like structures that have diverse sensory and motile functions. In the brain, motile ciliated cells, known as ependymal cells, line the cerebrospinal fluid (CSF) filled ventricles, where their beating contribute to fluid movement. Ependymal cells have gathered increasing interest since they are associated with hydrocephalus, a neurological condition with ventricular enlargement. In this article, we highlight methods to identify and characterize motile ciliated ependymal lineage in the brain of zebrafish using histological staining and transgenic reporter lines.
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46
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Duruz J, Sprecher M, Kaldun JC, Al-Soudy AS, Lischer HEL, van Geest G, Nicholson P, Bruggmann R, Sprecher SG. Molecular characterization of cell types in the squid Loligo vulgaris. eLife 2023; 12:80670. [PMID: 36594460 PMCID: PMC9839350 DOI: 10.7554/elife.80670] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary distance that separates vertebrates from cephalopods, it is evident that higher cognitive features have evolved separately in these clades despite the similarities that they share. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Despite significant progress in genome and transcriptome sequencing, the molecular identities of cell types in cephalopods remain largely unknown. We here combine single-cell transcriptomics with in situ gene expression analysis to uncover cell type diversity in the European squid Loligo vulgaris. We describe cell types that are conserved with other phyla such as neurons, muscles, or connective tissues but also cephalopod-specific cells, such as chromatophores or sucker cells. Moreover, we investigate major components of the squid nervous system including progenitor and developing cells, differentiated cells of the brain and optic lobes, as well as sensory systems of the head. Our study provides a molecular assessment for conserved and novel cell types in cephalopods and a framework for mapping the nervous system of L. vulgaris.
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Affiliation(s)
- Jules Duruz
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Marta Sprecher
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Jenifer C Kaldun
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Al-Sayed Al-Soudy
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Heidi EL Lischer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | - Geert van Geest
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | - Simon G Sprecher
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
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47
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Bui M, Dalla Benetta E, Dong Y, Zhao Y, Yang T, Li M, Antoshechkin IA, Buchman A, Bottino-Rojas V, James AA, Perry MW, Dimopoulos G, Akbari OS. CRISPR mediated transactivation in the human disease vector Aedes aegypti. PLoS Pathog 2023; 19:e1010842. [PMID: 36656895 PMCID: PMC9888728 DOI: 10.1371/journal.ppat.1010842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/31/2023] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
As a major insect vector of multiple arboviruses, Aedes aegypti poses a significant global health and economic burden. A number of genetic engineering tools have been exploited to understand its biology with the goal of reducing its impact. For example, current tools have focused on knocking-down RNA transcripts, inducing loss-of-function mutations, or expressing exogenous DNA. However, methods for transactivating endogenous genes have not been developed. To fill this void, here we developed a CRISPR activation (CRISPRa) system in Ae. aegypti to transactivate target gene expression. Gene expression is activated through pairing a catalytically-inactive ('dead') Cas9 (dCas9) with a highly-active tripartite activator, VP64-p65-Rta (VPR) and synthetic guide RNA (sgRNA) complementary to a user defined target-gene promoter region. As a proof of concept, we demonstrate that engineered Ae. aegypti mosquitoes harboring a binary CRISPRa system can be used to effectively overexpress two developmental genes, even-skipped (eve) and hedgehog (hh), resulting in observable morphological phenotypes. We also used this system to overexpress the positive transcriptional regulator of the Toll immune pathway known as AaRel1, which resulted in a significant suppression of dengue virus serotype 2 (DENV2) titers in the mosquito. This system provides a versatile tool for research pathways not previously possible in Ae. aegypti, such as programmed overexpression of endogenous genes, and may aid in gene characterization studies and the development of innovative vector control tools.
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Affiliation(s)
- Michelle Bui
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Elena Dalla Benetta
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yunchong Zhao
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Ting Yang
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Ming Li
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Igor A. Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Anna Buchman
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Vanessa Bottino-Rojas
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Anthony A. James
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California, United States of America
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Michael W. Perry
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Omar S. Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
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48
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Clark E, Battistara M, Benton MA. A timer gene network is spatially regulated by the terminal system in the Drosophila embryo. eLife 2022; 11:e78902. [PMID: 36524728 PMCID: PMC10065802 DOI: 10.7554/elife.78902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the 'timer' genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small 'tail' region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.
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Affiliation(s)
- Erik Clark
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Margherita Battistara
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Matthew A Benton
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Developmental Biology Unit, EMBLHeidelbergGermany
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49
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Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022; 5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.
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Affiliation(s)
- Oana Pelea
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Address correspondence to: Oana Pelea, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
| | - Tudor A. Fulga
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Address correspondence to: Tatjana Sauka-Spengler, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
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50
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Prasad AR, Lago-Baldaia I, Bostock MP, Housseini Z, Fernandes VM. Differentiation signals from glia are fine-tuned to set neuronal numbers during development. eLife 2022; 11:78092. [PMID: 36094172 PMCID: PMC9507125 DOI: 10.7554/elife.78092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/11/2022] [Indexed: 11/13/2022] Open
Abstract
Neural circuit formation and function require that diverse neurons are specified in appropriate numbers. Known strategies for controlling neuronal numbers involve regulating either cell proliferation or survival. We used the Drosophila visual system to probe how neuronal numbers are set. Photoreceptors from the eye-disc induce their target field, the lamina, such that for every unit eye there is a corresponding lamina unit (column). Although each column initially contains ~6 post-mitotic lamina precursors, only 5 differentiate into neurons, called L1-L5; the 'extra' precursor, which is invariantly positioned above the L5 neuron in each column, undergoes apoptosis. Here, we showed that a glial population called the outer chiasm giant glia (xgO), which resides below the lamina, secretes multiple ligands to induce L5 differentiation in response to EGF from photoreceptors. By forcing neuronal differentiation in the lamina, we uncovered that though fated to die, the 'extra' precursor is specified as an L5. Therefore, two precursors are specified as L5s but only one differentiates during normal development. We found that the row of precursors nearest to xgO differentiate into L5s and, in turn, antagonise differentiation signalling to prevent the 'extra' precursors from differentiating, resulting in their death. Thus, an intricate interplay of glial signals and feedback from differentiating neurons defines an invariant and stereotyped pattern of neuronal differentiation and programmed cell death to ensure that lamina columns each contain exactly one L5 neuron.
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Affiliation(s)
- Anadika R Prasad
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Inês Lago-Baldaia
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Matthew P Bostock
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Zaynab Housseini
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Vilaiwan M Fernandes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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