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Coschiera A, Yoshihara M, Lauter G, Ezer S, Pucci M, Li H, Kavšek A, Riedel CG, Kere J, Swoboda P. Primary cilia promote the differentiation of human neurons through the WNT signaling pathway. BMC Biol 2024; 22:48. [PMID: 38413974 PMCID: PMC10900739 DOI: 10.1186/s12915-024-01845-w] [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: 07/18/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell's immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. RESULTS We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and in RFX2 -/- mutant neurons with altered cilia, we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Experiments in neurons with IFT88 and IFT172 ciliary gene knockdowns, leading to shorter cilia, confirm these results. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. CONCLUSIONS We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
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Affiliation(s)
- Andrea Coschiera
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba, Japan
- Chiba University, Chiba, Japan
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
- Uppsala University, Uppsala, Sweden
| | - Sini Ezer
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Mariangela Pucci
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Bioscience and Technology for Food, Agriculture and Environment, Teramo, Italy
- University of Teramo, Teramo, Italy
| | - Haonan Li
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
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2
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Roux AE, Yuan H, Podshivalova K, Hendrickson D, Kerr R, Kenyon C, Kelley D. Individual cell types in C. elegans age differently and activate distinct cell-protective responses. Cell Rep 2023; 42:112902. [PMID: 37531250 DOI: 10.1016/j.celrep.2023.112902] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023] Open
Abstract
Aging is characterized by a global decline in physiological function. However, by constructing a complete single-cell gene expression atlas, we find that Caenorhabditis elegans aging is not random in nature but instead is characterized by coordinated changes in functionally related metabolic, proteostasis, and stress-response genes in a cell-type-specific fashion, with downregulation of energy metabolism being the only nearly universal change. Similarly, the rates at which cells age differ significantly between cell types. In some cell types, aging is characterized by an increase in cell-to-cell variance, whereas in others, variance actually decreases. Remarkably, multiple resilience-enhancing transcription factors known to extend lifespan are activated across many cell types with age; we discovered new longevity candidates, such as GEI-3, among these. Together, our findings suggest that cells do not age passively but instead react strongly, and individualistically, to events that occur during aging. This atlas can be queried through a public interface.
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Affiliation(s)
| | - Han Yuan
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | - Rex Kerr
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
| | - David Kelley
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
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Brocal-Ruiz R, Esteve-Serrano A, Mora-Martínez C, Franco-Rivadeneira ML, Swoboda P, Tena JJ, Vilar M, Flames N. Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans. eLife 2023; 12:e89702. [PMID: 37449480 PMCID: PMC10393296 DOI: 10.7554/elife.89702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cilia, either motile or non-motile (a.k.a primary or sensory), are complex evolutionarily conserved eukaryotic structures composed of hundreds of proteins required for their assembly, structure and function that are collectively known as the ciliome. Ciliome gene mutations underlie a group of pleiotropic genetic diseases known as ciliopathies. Proper cilium function requires the tight coregulation of ciliome gene transcription, which is only fragmentarily understood. RFX transcription factors (TF) have an evolutionarily conserved role in the direct activation of ciliome genes both in motile and non-motile cilia cell-types. In vertebrates, FoxJ1 and FoxN4 Forkhead (FKH) TFs work with RFX in the direct activation of ciliome genes, exclusively in motile cilia cell-types. No additional TFs have been described to act together with RFX in primary cilia cell-types in any organism. Here we describe FKH-8, a FKH TF, as a direct regulator of the sensory ciliome genes in Caenorhabditis elegans. FKH-8 is expressed in all ciliated neurons in C. elegans, binds the regulatory regions of ciliome genes, regulates ciliome gene expression, cilium morphology and a wide range of behaviors mediated by sensory ciliated neurons. FKH-8 and DAF-19 (C. elegans RFX) physically interact and synergistically regulate ciliome gene expression. C. elegans FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 but not by other members of other mouse FKH subfamilies. In conclusion, RFX and FKH TF families act jointly as direct regulators of ciliome genes also in sensory ciliated cell types suggesting that this regulatory logic could be an ancient trait predating functional cilia sub-specialization.
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Affiliation(s)
- Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Ainara Esteve-Serrano
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | | | - Peter Swoboda
- Department of Biosciences and Nutrition. Karolinska Institute. Campus FlemingsbergStockholmSweden
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de OlavideSevilleSpain
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
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4
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Kaulich E, McCubbin PTN, Schafer WR, Walker DS. Physiological insight into the conserved properties of Caenorhabditis elegans acid-sensing degenerin/epithelial sodium channels. J Physiol 2023; 601:1625-1653. [PMID: 36200489 PMCID: PMC10424705 DOI: 10.1113/jp283238] [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: 04/30/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are members of the diverse family of degenerin/epithelial sodium channels (DEG/ENaCs). They perform a wide range of physiological roles in healthy organisms, including in gut function and synaptic transmission, but also play important roles in disease, as acidosis is a hallmark of painful inflammatory and ischaemic conditions. We performed a screen for acid sensitivity on all 30 subunits of the Caenorhabditis elegans DEG/ENaC family using two-electrode voltage clamp in Xenopus oocytes. We found two groups of acid-sensitive DEG/ENaCs characterised by being either inhibited or activated by increasing proton concentrations. Three of these acid-sensitive C. elegans DEG/ENaCs were activated by acidic pH, making them functionally similar to the vertebrate ASICs. We also identified three new members of the acid-inhibited DEG/ENaC group, giving a total of seven additional acid-sensitive channels. We observed sensitivity to the anti-hypertensive drug amiloride as well as modulation by the trace element zinc. Acid-sensitive DEG/ENaCs were found to be expressed in both neurons and non-neuronal tissue, highlighting the likely functional diversity of these channels. Our findings provide a framework to exploit the C. elegans channels as models to study the function of these acid-sensing channels in vivo, as well as to study them as potential targets for anti-helminthic drugs. KEY POINTS: Acidosis plays many roles in healthy physiology, including synaptic transmission and gut function, but is also a key feature of inflammatory pain, ischaemia and many other conditions. Cells monitor acidosis of their surroundings via pH-sensing channels, including the acid-sensing ion channels (ASICs). These are members of the degenerin/epithelial sodium channel (DEG/ENaC) family, along with, as the name suggests, vertebrate ENaCs and degenerins of the roundworm Caenorhabditis elegans. By screening all 30 C. elegans DEG/ENaCs for pH dependence, we describe, for the first time, three acid-activated members, as well as three additional acid-inhibited channels. We surveyed both groups for sensitivity to amiloride and zinc; like their mammalian counterparts, their currents can be blocked, enhanced or unaffected by these modulators. Likewise, they exhibit diverse ion selectivity. Our findings underline the diversity of acid-sensitive DEG/ENaCs across species and provide a comparative resource for better understanding the molecular basis of their function.
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Affiliation(s)
- Eva Kaulich
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
| | | | - William R. Schafer
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
- Department of BiologyKU LeuvenLeuvenBelgium
| | - Denise S. Walker
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
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5
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Ahn S, Yang H, Son S, Lee HS, Park D, Yim H, Choi HJ, Swoboda P, Lee J. The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Rep 2022; 39:110661. [PMID: 35417689 DOI: 10.1016/j.celrep.2022.110661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Cilia are important for the interaction with environments and the proper function of tissues. While the basic structure of cilia is well conserved, ciliated cells have various functions. To understand the distinctive identities of ciliated cells, the identification of cell-specific proteins and its regulation is essential. Here, we report the mechanism that confers a specific identity on IL2 neurons in Caenorhabditis elegans, neurons important for the dauer larva-specific nictation behavior. We show that DAF-19M, an isoform of the sole C. elegans RFX transcription factor DAF-19, heads a regulatory subroutine, regulating target genes through an X-box motif variant under the control of terminal selector proteins UNC-86 and CFI-1 in IL2 neurons. Considering the conservation of DAF-19M module in IL2 neurons for nictation and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature "recognizing the environment."
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Affiliation(s)
- Soungyub Ahn
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Sangwon Son
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyun Sik Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dongjun Park
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
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6
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Moreno E, Lenuzzi M, Rödelsperger C, Prabh N, Witte H, Roeseler W, Riebesell M, Sommer RJ. DAF‐19/RFX controls ciliogenesis and influences oxygen‐induced social behaviors in
Pristionchus pacificus. Evol Dev 2018; 20:233-243. [DOI: 10.1111/ede.12271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Eduardo Moreno
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Maša Lenuzzi
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Neel Prabh
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Hanh Witte
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Waltraud Roeseler
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Metta Riebesell
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
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7
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Holbrook RI, Mortimer B. Vibration sensitivity found in Caenorhabditis elegans. ACTA ACUST UNITED AC 2018; 221:jeb.178947. [PMID: 29903836 DOI: 10.1242/jeb.178947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/11/2018] [Indexed: 01/10/2023]
Abstract
Mechanical sensing is important for all organisms, but is the least understood of the senses. As mechanical stimuli come in diverse forms, organisms often have sensors or sensory systems that specialise in a form of mechanical stimuli, such as touch or vibration. Here, we tested the hypothesis that the nematode worm Caenorhabditis elegans exhibits a behavioural response to vibration that is distinct from its responses to touch. We show that wild-type strain worms respond to sustained low-frequency vibration in a manner distinct from the known responses to non-localised mechanical stimuli. Furthermore, the behavioural responses of mutant strains suggest different roles for ciliated versus non-ciliated neurons in mediating the response. Although further study is required to identify the vibration-sensing pathway, our data support that C. elegans can sense substrate-borne vibrations using cells distinct from those used in gentle touch.
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Affiliation(s)
- Robert I Holbrook
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,School of Computing, Faculty of Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - Beth Mortimer
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK .,Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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