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Monfared RV, Abdelkarim S, Derdeyn P, Chen K, Wu H, Leong K, Chang T, Lee J, Versales S, Nauli S, Beier K, Baldi P, Alachkar A. Spatiotemporal Mapping of Brain Cilia Reveals Region-Specific Oscillation of Length and Orientation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546950. [PMID: 37425809 PMCID: PMC10326993 DOI: 10.1101/2023.06.28.546950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In this study, we conducted high-throughput spatiotemporal analysis of primary cilia length and orientation across 22 mouse brain regions. We developed automated image analysis algorithms, which enabled us to examine over 10 million individual cilia, generating the largest spatiotemporal atlas of cilia. We found that cilia length and orientation display substantial variations across different brain regions and exhibit fluctuations over a 24-hour period, with region-specific peaks during light-dark phases. Our analysis revealed unique orientation patterns of cilia at 45 degree intervals, suggesting that cilia orientation within the brain is not random but follows specific patterns. Using BioCycle, we identified circadian rhythms of cilia length in five brain regions: nucleus accumbens core, somatosensory cortex, and three hypothalamic nuclei. Our findings present novel insights into the complex relationship between cilia dynamics, circadian rhythms, and brain function, highlighting cilia crucial role in the brain's response to environmental changes and regulation of time-dependent physiological processes.
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Bernard A, Ojeda Naharros I, Yue X, Mifsud F, Blake A, Bourgain-Guglielmetti F, Ciprin J, Zhang S, McDaid E, Kim K, Nachury MV, Reiter JF, Vaisse C. MRAP2 regulates energy homeostasis by promoting primary cilia localization of MC4R. JCI Insight 2023; 8:e155900. [PMID: 36692018 PMCID: PMC9977312 DOI: 10.1172/jci.insight.155900] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 11/30/2022] [Indexed: 01/24/2023] Open
Abstract
The G protein-coupled receptor melanocortin-4 receptor (MC4R) and its associated protein melanocortin receptor-associated protein 2 (MRAP2) are essential for the regulation of food intake and body weight in humans. MC4R localizes and functions at the neuronal primary cilium, a microtubule-based organelle that senses and relays extracellular signals. Here, we demonstrate that MRAP2 is critical for the weight-regulating function of MC4R neurons and the ciliary localization of MC4R. More generally, our study also reveals that GPCR localization to primary cilia can require specific accessory proteins that may not be present in heterologous cell culture systems. Our findings further demonstrate that targeting of MC4R to neuronal primary cilia is essential for the control of long-term energy homeostasis and suggest that genetic disruption of MC4R ciliary localization may frequently underlie inherited forms of obesity.
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Affiliation(s)
| | | | - Xinyu Yue
- Department of Medicine and The Diabetes Center
| | | | - Abbey Blake
- Department of Medicine and The Diabetes Center
| | | | | | - Sumei Zhang
- Department of Medicine and The Diabetes Center
| | - Erin McDaid
- Department of Medicine and The Diabetes Center
| | - Kellan Kim
- Department of Medicine and The Diabetes Center
| | | | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, UCSF, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Kobayashi Y, Saito Y. Evaluation of ciliary-GPCR dynamics using a validated organotypic brain slice culture method. Methods Cell Biol 2023; 175:69-83. [PMID: 36967146 DOI: 10.1016/bs.mcb.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The primary cilium is a structural organelle present in most mammalian cells. Primary cilia are enriched with a unique protein repertoire distinct from that of the cytosol and the plasma membrane. Such a highly organized microenvironment creates effective machinery for translating extracellular cues into intracellular signals. G protein-coupled receptors (GPCRs) are key receptors in sensing environmental stimuli transmitted via a second messenger into a cellular response. Recent data has demonstrated that a limited number of non-olfactory GPCRs, including melanin-concentrating hormone receptor 1 (MCHR1), are preferentially localized to ciliary membranes of several mammalian cell types, including neuronal cells. Evidence was accumulated to support the functional importance of ciliary-GPCR signaling accompanying ciliary structural changes using cilia-specific cell and molecular biology techniques. Thus, cilia are now considered to function as a unique sensory platform for the integration of GPCR signaling and various cytoplasmic domains. Dissociated neurons expressing ciliary-GPCRs can be a useful tool for examining ciliary dynamics. However, losing preexisting neuronal connectivity may alter neuronal ciliary morphology, such as abnormal elongation. Brain slices prepared under ex vitro conditions are a powerful approach that maintains the cytoarchitecture, enabling researchers to have accurate control over experimental conditions and to study individual cells from subregions of the brain. Here, we present a detailed description of our novel modified method for organotypic culture of rat brain slice and a validated immunostaining protocol to characterize ciliary-GPCR dynamics in coupling with neuropeptides or aminergic activation.
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Affiliation(s)
- Yuki Kobayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yumiko Saito
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.
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Alhassen W, Alhassen S, Chen J, Monfared RV, Alachkar A. Cilia in the Striatum Mediate Timing-Dependent Functions. Mol Neurobiol 2023; 60:545-565. [PMID: 36322337 PMCID: PMC9849326 DOI: 10.1007/s12035-022-03095-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/16/2022] [Indexed: 11/07/2022]
Abstract
Almost all brain cells contain cilia, antennae-like microtubule-based organelles. Yet, the significance of cilia, once considered vestigial organelles, in the higher-order brain functions is unknown. Cilia act as a hub that senses and transduces environmental sensory stimuli to generate an appropriate cellular response. Similarly, the striatum, a brain structure enriched in cilia, functions as a hub that receives and integrates various types of environmental information to drive appropriate motor response. To understand cilia's role in the striatum functions, we used loxP/Cre technology to ablate cilia from the dorsal striatum of male mice and monitored the behavioral consequences. Our results revealed an essential role for striatal cilia in the acquisition and brief storage of information, including learning new motor skills, but not in long-term consolidation of information or maintaining habitual/learned motor skills. A fundamental aspect of all disrupted functions was the "time perception/judgment deficit." Furthermore, the observed behavioral deficits form a cluster pertaining to clinical manifestations overlapping across psychiatric disorders that involve the striatum functions and are known to exhibit timing deficits. Thus, striatal cilia may act as a calibrator of the timing functions of the basal ganglia-cortical circuit by maintaining proper timing perception. Our findings suggest that dysfunctional cilia may contribute to the pathophysiology of neuro-psychiatric disorders, as related to deficits in timing perception.
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Affiliation(s)
- Wedad Alhassen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California-Irvine, 356A Med Surge II, Irvine, CA 92697-4625 USA
| | - Sammy Alhassen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California-Irvine, 356A Med Surge II, Irvine, CA 92697-4625 USA
| | - Jiaqi Chen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California-Irvine, 356A Med Surge II, Irvine, CA 92697-4625 USA
| | - Roudabeh Vakil Monfared
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California-Irvine, 356A Med Surge II, Irvine, CA 92697-4625 USA
| | - Amal Alachkar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California-Irvine, 356A Med Surge II, Irvine, CA 92697-4625 USA ,UC Irvine Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, CA 92697 USA ,Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92697 USA
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5
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Abstract
Cilia sense and transduce sensory stimuli, homeostatic cues and developmental signals by orchestrating signaling reactions. Extracellular vesicles (EVs) that bud from the ciliary membrane have well-studied roles in the disposal of excess ciliary material, most dramatically exemplified by the shedding of micrometer-sized blocks by photoreceptors. Shedding of EVs by cilia also affords cells with a powerful means to shorten cilia. Finally, cilium-derived EVs may enable cell-cell communication in a variety of organisms, ranging from single-cell parasites and algae to nematodes and vertebrates. Mechanistic understanding of EV shedding by cilia is an active area of study, and future progress may open the door to testing the function of ciliary EV shedding in physiological contexts. In this Cell Science at a Glance and the accompanying poster, we discuss the molecular mechanisms that drive the shedding of ciliary material into the extracellular space, the consequences of shedding for the donor cell and the possible roles that ciliary EVs may have in cell non-autonomous contexts.
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Affiliation(s)
- Irene Ojeda Naharros
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143-3120, USA
| | - Maxence V. Nachury
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143-3120, USA
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Park S, Ma Z, Zarkada G, Papangeli I, Paluri S, Nazo N, Rivera‐Molina F, Toomre D, Rajagopal S, Chun HJ. Endothelial β-arrestins regulate mechanotransduction by the type II bone morphogenetic protein receptor in primary cilia. Pulm Circ 2022; 12:e12167. [PMID: 36532314 PMCID: PMC9751664 DOI: 10.1002/pul2.12167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
Modulation of endothelial cell behavior and phenotype by hemodynamic forces involves many signaling components, including cell surface receptors, intracellular signaling intermediaries, transcription factors, and epigenetic elements. Many of the signaling mechanisms that underlie mechanotransduction by endothelial cells are inadequately defined. Here we sought to better understand how β-arrestins, intracellular proteins that regulate agonist-mediated desensitization and integration of signaling by transmembrane receptors, may be involved in the endothelial cell response to shear stress. We performed both in vitro studies with primary endothelial cells subjected to β-arrestin knockdown, and in vivo studies using mice with endothelial specific deletion of β-arrestin 1 and β-arrestin 2. We found that β-arrestins are localized to primary cilia in endothelial cells, which are present in subpopulations of endothelial cells in relatively low shear states. Recruitment of β-arrestins to cilia involved its interaction with IFT81, a component of the flagellar transport protein complex in the cilia. β-arrestin knockdown led to marked reduction in shear stress response, including induction of NOS3 expression. Within the cilia, β-arrestins were found to associate with the type II bone morphogenetic protein receptor (BMPR-II), whose disruption similarly led to an impaired endothelial shear response. β-arrestins also regulated Smad transcription factor phosphorylation by BMPR-II. Mice with endothelial specific deletion of β-arrestin 1 and β-arrestin 2 were found to have impaired retinal angiogenesis. In conclusion, we have identified a novel role for endothelial β-arrestins as key transducers of ciliary mechanotransduction that play a central role in shear signaling by BMPR-II and contribute to vascular development.
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Affiliation(s)
- Saejeong Park
- Department of Internal MedicineSection of Cardiovascular Medicine, Yale Cardiovascular Research Center, Yale School of MedicineNew HavenConnecticutUSA
| | - Zhiyuan Ma
- Department of MedicineDivision of Cardiology, Duke University School of MedicineDurhamNorth CarolinaUSA
| | - Georgia Zarkada
- Department of Internal MedicineSection of Cardiovascular Medicine, Yale Cardiovascular Research Center, Yale School of MedicineNew HavenConnecticutUSA
| | - Irinna Papangeli
- Department of Internal MedicineSection of Cardiovascular Medicine, Yale Cardiovascular Research Center, Yale School of MedicineNew HavenConnecticutUSA
| | - Sarin Paluri
- Chicago College of Osteopathic MedicineMidwestern UniversityDowners GroveIllinoisUSA
| | - Nour Nazo
- Department of MedicineDivision of Cardiology, Duke University School of MedicineDurhamNorth CarolinaUSA
| | - Felix Rivera‐Molina
- Department of Cell BiologyYale University School of MedicineNew HavenConnecticutUSA
| | - Derek Toomre
- Department of Cell BiologyYale University School of MedicineNew HavenConnecticutUSA
| | - Sudarshan Rajagopal
- Department of MedicineDivision of Cardiology, Duke University School of MedicineDurhamNorth CarolinaUSA
| | - Hyung J. Chun
- Department of Internal MedicineSection of Cardiovascular Medicine, Yale Cardiovascular Research Center, Yale School of MedicineNew HavenConnecticutUSA
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Chaya T, Maeda Y, Sugimura R, Okuzaki D, Watanabe S, Varner LR, Motooka D, Gyoten D, Yamamoto H, Kato H, Furukawa T. Multiple knockout mouse and embryonic stem cell models reveal the role of miR-124a in neuronal maturation. J Biol Chem 2022; 298:102293. [PMID: 35868558 PMCID: PMC9418502 DOI: 10.1016/j.jbc.2022.102293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
MicroRNA-124a (miR-124a) is one of the most abundantly expressed microRNAs in the central nervous system and is encoded in mammals by the three genomic loci miR-124a-1/2/3; however, its in vivo roles in neuronal development and function remain ambiguous. In the present study, we investigated the effect of miR-124a loss on neuronal differentiation in mice and in embryonic stem (ES) cells. Since miR-124a-3 exhibits only background expression levels in the brain and we were unable to obtain miR-124a-1/2/3 triple knockout (TKO) mice by mating, we generated and analyzed miR-124a-1/2 double knockout (DKO) mice. We found that these DKO mice exhibit perinatal lethality. RNA-seq analysis demonstrated that the expression levels of proneural and neuronal marker genes were almost unchanged between the control and miR-124a-1/2 DKO brains; however, genes related to neuronal synaptic formation and function were enriched among downregulated genes in the miR-124a-1/2 DKO brain. In addition, we found the transcription regulator Tardbp/TDP-43, loss of which leads to defects in neuronal maturation and function, was inactivated in the miR-124a-1/2 DKO brain. Furthermore, Tardbp knockdown suppressed neurite extension in cultured neuronal cells. We also generated miR-124a-1/2/3 TKO ES cells using CRISPR-Cas9 as an alternative to TKO mice. Phase-contrast microscopic, immunocytochemical, and gene expression analyses showed that miR-124a-1/2/3 TKO ES cell lines were able to differentiate into neurons. Collectively, these results suggest that miR-124a plays a role in neuronal maturation rather than neurogenesis in vivo and advance our understanding of the functional roles of microRNAs in central nervous system development.
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Affiliation(s)
- Taro Chaya
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yamato Maeda
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Ryo Sugimura
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Satoshi Watanabe
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Leah R. Varner
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daichi Gyoten
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Haruka Yamamoto
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hidemasa Kato
- Department of Functional Histology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan.
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8
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Shimada IS, Kato Y. Ciliary signaling in stem cells in health and disease: Hedgehog pathway and beyond. Semin Cell Dev Biol 2022; 129:115-125. [PMID: 35466055 DOI: 10.1016/j.semcdb.2022.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022]
Abstract
The primary cilium is a hair-like sensory compartment that protrudes from the cellular surface. The primary cilium is enriched in a variety of signaling molecules that regulate cellular activities. Stem cells have primary cilia. They reside in a specialized environment, called the stem cell niche. This niche contains a variety of secreted factors, and some of their receptors are localized in the primary cilia of stem cells. Here, we summarize the current understanding of the function of cilia in compartmentalized signaling in stem cells. We describe how ciliary signaling regulates stem cells and progenitor cells during development, tissue homeostasis and tumorigenesis. We summarize our understanding of cilia regulated signaling -primary involving the hedgehog pathway- in stem cells in diverse settings that include neuroepithelial cells, radial glia, cerebellar granule neuron precursors, hematopoietic stem cells, hair follicle stem cells, bone marrow mesenchymal stem cells and mammary gland stem cells. Overall, our review highlights a variety of roles that ciliary signaling plays in regulating stem cells throughout life.
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Affiliation(s)
- Issei S Shimada
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Azakawasumi, Mizuzho-cho, Mizuho-ku, Nagoya, 467-8601 Aichi, Japan.
| | - Yoichi Kato
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Azakawasumi, Mizuzho-cho, Mizuho-ku, Nagoya, 467-8601 Aichi, Japan.
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9
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Arena DT, Hofer AM. Imaging the cAMP Signaling Microdomain of the Primary Cilium Using Targeted FRET-Based Biosensors. Methods Mol Biol 2022; 2483:77-92. [PMID: 35286670 DOI: 10.1007/978-1-0716-2245-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Optical approaches have revolutionized our view of second messenger signaling in organelles, allowing precise time-resolved assessment of soluble signaling molecules in situ. Among the most challenging of subcellular signaling microdomains to assay is the primary cilium. A petite but visually arresting organelle, the primary cilium extends from the cell surface of most non-dividing cells. Recently, the concept of the primary cilium as an independent cAMP signaling organelle has attracted substantial interest. The cilium sequesters a very specific subset of ciliary cAMP-linked GPCRs in its membrane (e.g., 5-HT6, D1R, MCR4, FFAR4, TGR5), as well as other key components of the cAMP signaling machinery that include adenylyl cyclases, GNAS, phosphodiesterases, PKA holoenzyme, and biologically important PKA targets. Here we provide a practical guide to assessing ciliary cAMP signals in live cells using targeted genetically encoded FRET biosensors. Key experimental difficulties include gathering sufficient signal from such a small, photon-limited volume, and the susceptibility of cilia to movement artifacts. Other challenges are associated with the fidelity of sensor targeting and the difficulties in distinguishing between cAMP signals produced exclusively within the cilium vs. those that emanate from the cell body. Here we describe ratio imaging approaches used in our lab for time-resolved visualization of ciliary cAMP in cultured renal cells. These methods can be readily adapted to other cell types and microscopy platforms according to the needs of the user.
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Affiliation(s)
- Danielle T Arena
- VA Boston Healthcare System and the Department of Surgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Aldebaran M Hofer
- VA Boston Healthcare System and the Department of Surgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.
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10
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Abnormal ciliogenesis in decidual stromal cellsin recurrent miscarriage. J Reprod Immunol 2022; 150:103486. [DOI: 10.1016/j.jri.2022.103486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/29/2021] [Accepted: 01/15/2022] [Indexed: 11/21/2022]
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11
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Hilgendorf KI. Primary Cilia Are Critical Regulators of White Adipose Tissue Expansion. Front Physiol 2021; 12:769367. [PMID: 34759842 PMCID: PMC8573240 DOI: 10.3389/fphys.2021.769367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
The primary cilium is a microtubule-based cellular protrusion found on most mammalian cell types in diverse tissues. It functions as a cellular antenna to sense and transduce a broad range of signals, including odorants, light, mechanical stimuli, and chemical ligands. This diversity in signals requires cilia to display a context and cell type-specific repertoire of receptors. Recently, primary cilia have emerged as critical regulators of metabolism. The importance of primary cilia in metabolic disease is highlighted by the clinical features of human genetic disorders with dysfunctional ciliary signaling, which include obesity and diabetes. This review summarizes the current literature on the role of primary cilia in metabolic disease, focusing on the importance of primary cilia in directing white adipose tissue expansion during obesity.
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Affiliation(s)
- Keren I Hilgendorf
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
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12
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Alhassen W, Kobayashi Y, Su J, Robbins B, Nguyen H, Myint T, Yu M, Nauli SM, Saito Y, Alachkar A. Regulation of Brain Primary Cilia Length by MCH Signaling: Evidence from Pharmacological, Genetic, Optogenetic, and Chemogenic Manipulations. Mol Neurobiol 2021; 59:245-265. [PMID: 34665407 DOI: 10.1007/s12035-021-02511-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/29/2021] [Indexed: 12/23/2022]
Abstract
The melanin-concentrating hormone (MCH) system is involved in numerous functions, including energy homeostasis, food intake, sleep, stress, mood, aggression, reward, maternal behavior, social behavior, and cognition. In rodents, MCH acts on MCHR1, a G protein-coupled receptor, which is widely expressed in the brain and abundantly localized to neuronal primary cilia. Cilia act as cells' antennas and play crucial roles in cell signaling to detect and transduce external stimuli to regulate cell differentiation and migration. Cilia are highly dynamic in terms of their length and morphology; however, it is not known if cilia length is causally regulated by MCH system activation in vivo. In the current work, we examined the effects of activation and inactivation of MCH system on cilia lengths by using different experimental models and methodologies, including organotypic brain slice cultures from rat prefrontal cortex (PFC) and caudate-putamen (CPu), in vivo pharmacological (MCHR1 agonist and antagonist GW803430), germline and conditional genetic deletion of MCHR1 and MCH, optogenetic, and chemogenetic (designer receptors exclusively activated by designer drugs (DREADD)) approaches. We found that stimulation of MCH system either directly through MCHR1 activation or indirectly through optogenetic and chemogenetic-mediated excitation of MCH-neuron, caused cilia shortening, detected by the quantification of the presence of ADCY3 protein, a known primary cilia marker. In contrast, inactivation of MCH signaling through pharmacological MCHR1 blockade or through genetic manipulations - germline deletion of MCHR1 and conditional ablation of MCH neurons - induced cilia lengthening. Our study is the first to uncover the causal effects of the MCH system in the regulation of the length of brain neuronal primary cilia. These findings place MCH system at a unique position in the ciliary signaling in physiological and pathological conditions and implicate MCHR1 present at primary cilia as a potential therapeutic target for the treatment of pathological conditions characterized by impaired primary cilia function associated with the modification of its length.
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Affiliation(s)
- Wedad Alhassen
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California, Irvine, CA, 92697, USA
| | - Yuki Kobayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan
| | - Jessica Su
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California, Irvine, CA, 92697, USA
| | - Brianna Robbins
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California, Irvine, CA, 92697, USA
| | - Henry Nguyen
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California, Irvine, CA, 92697, USA
| | - Thant Myint
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California, Irvine, CA, 92697, USA
| | - Micah Yu
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California, Irvine, CA, 92697, USA
| | - Surya M Nauli
- Department of Biomedical and Pharmaceutical Sciences, School of Pharmacy, Chapman University, Health Science Campus, Chapman University, Irvine, CA, 92618, USA
| | - Yumiko Saito
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan
| | - Amal Alachkar
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California, Irvine, CA, 92697, USA. .,Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, 92697, USA.
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13
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Chen S, Alhassen W, Vakil Monfared R, Vachirakorntong B, Nauli SM, Baldi P, Alachkar A. Dynamic Changes of Brain Cilia Transcriptomes across the Human Lifespan. Int J Mol Sci 2021; 22:10387. [PMID: 34638726 PMCID: PMC8509004 DOI: 10.3390/ijms221910387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/27/2022] Open
Abstract
Almost all brain cells contain primary cilia, antennae-like microtubule sensory organelles, on their surface, which play critical roles in brain functions. During neurodevelopmental stages, cilia are essential for brain formation and maturation. In the adult brain, cilia play vital roles as signaling hubs that receive and transduce various signals and regulate cell-to-cell communications. These distinct roles suggest that cilia functions, and probably structures, change throughout the human lifespan. To further understand the age-dependent changes in cilia roles, we identified and analyzed age-dependent patterns of expression of cilia's structural and functional components across the human lifespan. We acquired cilia transcriptomic data for 16 brain regions from the BrainSpan Atlas and analyzed the age-dependent expression patterns using a linear regression model by calculating the regression coefficient. We found that 67% of cilia transcripts were differentially expressed genes with age (DEGAs) in at least one brain region. The age-dependent expression was region-specific, with the highest and lowest numbers of DEGAs expressed in the ventrolateral prefrontal cortex and hippocampus, respectively. The majority of cilia DEGAs displayed upregulation with age in most of the brain regions. The transcripts encoding cilia basal body components formed the majority of cilia DEGAs, and adjacent cerebral cortices exhibited large overlapping pairs of cilia DEGAs. Most remarkably, specific α/β-tubulin subunits (TUBA1A, TUBB2A, and TUBB2B) and SNAP-25 exhibited the highest rates of downregulation and upregulation, respectively, across age in almost all brain regions. α/β-tubulins and SNAP-25 expressions are known to be dysregulated in age-related neurodevelopmental and neurodegenerative disorders. Our results support a role for the high dynamics of cilia structural and functional components across the lifespan in the normal physiology of brain circuits. Furthermore, they suggest a crucial role for cilia signaling in the pathophysiological mechanisms of age-related psychiatric/neurological disorders.
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Affiliation(s)
- Siwei Chen
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92617, USA; (S.C.); (P.B.)
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92617, USA
| | - Wedad Alhassen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA 92617, USA; (W.A.); (R.V.M.); (B.V.)
| | - Roudabeh Vakil Monfared
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA 92617, USA; (W.A.); (R.V.M.); (B.V.)
| | - Benjamin Vachirakorntong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA 92617, USA; (W.A.); (R.V.M.); (B.V.)
| | - Surya M. Nauli
- Department of Biomedical and Pharmaceutical Sciences, School of Pharmacy, Chapman University Rinker Health Science Campus, Irvine, CA 92618, USA;
| | - Pierre Baldi
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92617, USA; (S.C.); (P.B.)
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92617, USA
| | - Amal Alachkar
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92617, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA 92617, USA; (W.A.); (R.V.M.); (B.V.)
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14
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Jana SC, Dutta P, Jain A, Singh A, Adusumilli L, Girotra M, Kumari D, Shirolikar S, Ray K. Kinesin-2 transports Orco into the olfactory cilium of Drosophila melanogaster at specific developmental stages. PLoS Genet 2021; 17:e1009752. [PMID: 34411092 PMCID: PMC8407544 DOI: 10.1371/journal.pgen.1009752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 08/31/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022] Open
Abstract
The cilium, the sensing centre for the cell, displays an extensive repertoire of receptors for various cell signalling processes. The dynamic nature of ciliary signalling indicates that the ciliary entry of receptors and associated proteins must be regulated and conditional. To understand this process, we studied the ciliary localisation of the odour-receptor coreceptor (Orco), a seven-pass transmembrane protein essential for insect olfaction. Little is known about when and how Orco gets into the cilia. Here, using Drosophila melanogaster, we show that the bulk of Orco selectively enters the cilia on adult olfactory sensory neurons in two discrete, one-hour intervals after eclosion. A conditional loss of heterotrimeric kinesin-2 during this period reduces the electrophysiological response to odours and affects olfactory behaviour. We further show that Orco binds to the C-terminal tail fragments of the heterotrimeric kinesin-2 motor, which is required to transfer Orco from the ciliary base to the outer segment and maintain within an approximately four-micron stretch at the distal portion of the ciliary outer-segment. The Orco transport was not affected by the loss of critical intraflagellar transport components, IFT172/Oseg2 and IFT88/NompB, respectively, during the adult stage. These results highlight a novel developmental regulation of seven-pass transmembrane receptor transport into the cilia and indicate that ciliary signalling is both developmentally and temporally regulated.
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Affiliation(s)
- Swadhin Chandra Jana
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Priya Dutta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Akanksha Jain
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Anjusha Singh
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Lavanya Adusumilli
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Mukul Girotra
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Diksha Kumari
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Seema Shirolikar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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15
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Baldi P, Alhassen W, Chen S, Nguyen H, Khoudari M, Alachkar A. Large-scale analysis reveals spatiotemporal circadian patterns of cilia transcriptomes in the primate brain. J Neurosci Res 2021; 99:2610-2624. [PMID: 34310750 DOI: 10.1002/jnr.24919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 01/13/2023]
Abstract
Cilia are dynamic subcellular systems, with core structural and functional components operating in a highly coordinated manner. Since many environmental stimuli sensed by cilia are circadian in nature, it is reasonable to speculate that genes encoding cilia structural and functional components follow rhythmic circadian patterns of expression. Using computational methods and the largest spatiotemporal gene expression atlas of primates, we identified and analyzed the circadian rhythmic expression of cilia genes across 22 primate brain areas. We found that around 73% of cilia transcripts exhibited circadian rhythmicity across at least one of 22 brain regions. In 12 brain regions, cilia transcriptomes were significantly enriched with circadian oscillating transcripts, as compared to the rest of the transcriptome. The phase of the cilia circadian transcripts deviated from the phase of the majority of the background circadian transcripts, and transcripts coding for cilia basal body components accounted for the majority of cilia circadian transcripts. In addition, adjacent or functionally connected brain nuclei had large overlapping complements of circadian cilia genes. Most remarkably, cilia circadian transcripts shared across the basal ganglia nuclei and the prefrontal cortex peaked in these structures in sequential fashion that is similar to the sequential order of activation of the basal ganglia-cortical circuitry in connection with movement coordination, albeit on completely different timescales. These findings support a role for the circadian spatiotemporal orchestration of cilia gene expression in the normal physiology of the basal ganglia-cortical circuit and motor control. Studying orchestrated cilia rhythmicity in the basal ganglia-cortical circuits and other brain circuits may help develop better functional models, and shed light on the causal effects cilia functions have on these circuits and on the regulation of movement and other behaviors.
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Affiliation(s)
- Pierre Baldi
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA.,Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
| | - Wedad Alhassen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Siwei Chen
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA.,Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
| | - Henry Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Mohammad Khoudari
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Amal Alachkar
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA.,Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
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16
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Alhassen W, Chen S, Vawter M, Robbins BK, Nguyen H, Myint TN, Saito Y, Schulmann A, Nauli SM, Civelli O, Baldi P, Alachkar A. Patterns of cilia gene dysregulations in major psychiatric disorders. Prog Neuropsychopharmacol Biol Psychiatry 2021; 109:110255. [PMID: 33508383 PMCID: PMC9121176 DOI: 10.1016/j.pnpbp.2021.110255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/06/2021] [Accepted: 01/16/2021] [Indexed: 12/15/2022]
Abstract
Primary cilia function as cells' antennas to detect and transduce external stimuli and play crucial roles in cell signaling and communication. The vast majority of cilia genes that are causally linked with ciliopathies are also associated with neurological deficits, such as cognitive impairments. Yet, the roles of cilia dysfunctions in the pathogenesis of psychiatric disorders have not been studied. Our aim is to identify patterns of cilia gene dysregulation in the four major psychiatric disorders: schizophrenia (SCZ), autism spectrum disorder (ASD), bipolar disorder (BP), and major depressive disorder (MDD). For this purpose, we acquired differentially expressed genes (DEGs) from the largest and most recent publicly available databases. We found that 42%, 24%, 17%, and 15% of brain-expressed cilia genes were significantly differentially expressed in SCZ, ASD, BP, and MDD, respectively. Several genes exhibited cross-disorder overlap, suggesting that typical cilia signaling pathways' dysfunctions determine susceptibility to more than one psychiatric disorder or may partially underlie their pathophysiology. Our study revealed that genes encoding proteins of almost all sub-cilia structural and functional compartments were dysregulated in the four psychiatric disorders. Strikingly, the genes of 75% of cilia GPCRs and 50% of the transition zone proteins were differentially expressed in SCZ. The present study is the first to draw associations between cilia and major psychiatric disorders, and is the first step toward understanding the role that cilia components play in their pathophysiological processes, which may lead to novel therapeutic targets for these disorders.
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Affiliation(s)
- Wedad Alhassen
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, CA 92697, USA
| | - Siwei Chen
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92697, USA,Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, CA 92697, USA
| | - Marquis Vawter
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, USA
| | - Brianna Kay Robbins
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, CA 92697, USA
| | - Henry Nguyen
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, CA 92697, USA
| | - Thant Nyi Myint
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, CA 92697, USA
| | - Yumiko Saito
- Graduate School of Integrated Arts and Sciences for Life, Hiroshima University, Japan
| | - Anton Schulmann
- Human Genetics Branch, National Institute of Mental Health, BETHESDA MD 20814, USA
| | - Surya M. Nauli
- Department of Biomedical and Pharmaceutical Sciences, School of Pharmacy, Chapman University, Health Science Campus, Chapman University, Irvine, California 92618, USA
| | - Olivier Civelli
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, CA 92697, USA,Department of Developmental and Cell Biology, School of Biological Sciences, University of California-Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92697, USA,Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, CA 92697, USA
| | - Amal Alachkar
- Departments of Pharmaceutical Sciences, School of Pharmacy, University of California-, Irvine, CA 92697, USA; Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA 92697, USA.
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17
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The linkage of cell cycle and DNA replication with growth difference in female Chinese tongue sole (Cynoglossus semilaevis): Analysis from transcriptomic study and WGCNA. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100833. [PMID: 33848768 DOI: 10.1016/j.cbd.2021.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/19/2021] [Accepted: 04/02/2021] [Indexed: 11/21/2022]
Abstract
In addition to the typical sexual size dimorphism, considerable size differences within the female population of the Chinese tongue sole (Cynoglossus semilaevis) have become a further bottleneck of the improvement of sole aquaculture. To identify the internal mechanism, transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) were employed simultaneously. Transcriptomic analyses of brain, pituitary gland, liver, gonad, and muscle tissues from two female groups with size differences identified 109, 698, 1325, 2299, and 2141 differentially expressed genes (DEGs), respectively. The results of these enrichment analyses suggest that the up-regulation of neuroactive ligand-receptor interaction, cell cycle, DNA replication, and MAPK signaling pathway in the group with larger females may be involved in the regulation of the observed growth differences. WGCNA of DEGs showed that cell cycle and DNA replication might be crucial pathways for accelerating cell growth in the groups with larger females. Finally, a series of hub genes including 6-phosphofructokinase type C (pfkp), ribosome biogenesis protein (wdr12), bleomycin hydrolase (blmh), and semaphorin-3A (sema3a) were recognized by the illustrated network map of modules. The linkage of cell cycle, DNA replication, and hub genes in the growth regulation of C. semilaevis provides further information for a better understanding of growth differences in fish.
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18
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Signal transduction in primary cilia - analyzing and manipulating GPCR and second messenger signaling. Pharmacol Ther 2021; 224:107836. [PMID: 33744260 DOI: 10.1016/j.pharmthera.2021.107836] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022]
Abstract
The primary cilium projects from the surface of most vertebrate cells, where it senses extracellular signals to regulate diverse cellular processes during tissue development and homeostasis. Dysfunction of primary cilia underlies the pathogenesis of severe diseases, commonly referred to as ciliopathies. Primary cilia contain a unique protein repertoire that is distinct from the cell body and the plasma membrane, enabling the spatially controlled transduction of extracellular cues. G-protein coupled receptors (GPCRs) are key in sensing environmental stimuli that are transmitted via second messenger signaling into a cellular response. Here, we will give an overview of the role of GPCR signaling in primary cilia, and how ciliary GPCR signaling can be targeted by pharmacology, chemogenetics, and optogenetics.
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19
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Liu S, Trupiano MX, Simon J, Guo J, Anton ES. The essential role of primary cilia in cerebral cortical development and disorders. Curr Top Dev Biol 2021; 142:99-146. [PMID: 33706927 DOI: 10.1016/bs.ctdb.2020.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Primary cilium, first described in the 19th century in different cell types and organisms by Alexander Ecker, Albert Kolliker, Aleksandr Kowalevsky, Paul Langerhans, and Karl Zimmermann (Ecker, 1844; Kolliker, 1854; Kowalevsky, 1867; Langerhans, 1876; Zimmermann, 1898), play an essential modulatory role in diverse aspects of nervous system development and function. The primary cilium, sometimes referred to as the cell's 'antennae', can receive wide ranging inputs from cellular milieu, including morphogens, growth factors, neuromodulators, and neurotransmitters. Its unique structural and functional organization bequeaths it the capacity to hyper-concentrate signaling machinery in a restricted cellular domain approximately one-thousandth the volume of cell soma. Thus enabling it to act as a signaling hub that integrates diverse developmental and homestatic information from cellular milieu to regulate the development and function of neural cells. Dysfunction of primary cilia contributes to the pathophysiology of several brain malformations, intellectual disabilities, epilepsy, and psychiatric disorders. This review focuses on the most essential contributions of primary cilia to cerebral cortical development and function, in the context of neurodevelopmental disorders and malformations. It highlights the recent progress made in identifying the mechanisms underlying primary cilia's role in cortical progenitors, neurons and glia, in health and disease. A future challenge will be to translate these insights and advances into effective clinical treatments for ciliopathies.
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Affiliation(s)
- Siling Liu
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Mia X Trupiano
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Jeremy Simon
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Jiami Guo
- Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, and the Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - E S Anton
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States.
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20
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Kobayashi Y, Hamamoto A, Saito Y. Analysis of ciliary status via G-protein-coupled receptors localized on primary cilia. Microscopy (Oxf) 2020; 69:277-285. [PMID: 32627821 DOI: 10.1093/jmicro/dfaa035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/20/2020] [Accepted: 07/02/2020] [Indexed: 11/14/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) comprise the largest and most diverse cell surface receptor family, with more than 800 known GPCRs identified in the human genome. Binding of an extracellular cue to a GPCR results in intracellular G protein activation, after which a sequence of events, can be amplified and optimized by selective binding partners and downstream effectors in spatially discrete cellular environments. Because GPCRs are widely expressed in the body, they help to regulate an incredible range of physiological processes from sensation to growth to hormone responses. Indeed, it is estimated that ∼ 30% of all clinically approved drugs act by binding to GPCRs. The primary cilium is a sensory organelle composed of a microtubule axoneme that extends from the basal body. The ciliary membrane is highly enriched in specific signaling components, allowing the primary cilium to efficiently convey signaling cascades in a highly ordered microenvironment. Recent data demonstrated that a limited number of non-olfactory GPCRs, including somatostatin receptor 3 and melanin-concentrating hormone receptor 1 (MCHR1), are selectively localized to cilia on several mammalian cell types including neuronal cells. Utilizing cilia-specific cell biological and molecular biological approaches, evidence has accumulated to support the biological importance of ciliary GPCR signaling followed by cilia structural changes. Thus, cilia are now considered a unique sensory platform for integration of GPCR signaling toward juxtaposed cytoplasmic structures. Herein, we review ciliary GPCRs and focus on a novel role of MCHR1 in ciliary length control that will impact ciliary signaling capacity and neuronal function.
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Affiliation(s)
- Yuki Kobayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Akie Hamamoto
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, Gifu 502-0857, Japan
| | - Yumiko Saito
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
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21
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Regulation and function of calcium in the cilium. CURRENT OPINION IN PHYSIOLOGY 2020; 17:278-283. [DOI: 10.1016/j.cophys.2020.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Kobayashi Y. New perspectives on GPCRs: GPCR heterodimer formation (melanocortin receptor) and GPCR on primary cilia (melanin concentrating hormone receptor). Gen Comp Endocrinol 2020; 293:113474. [PMID: 32240710 DOI: 10.1016/j.ygcen.2020.113474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/18/2020] [Accepted: 03/28/2020] [Indexed: 11/13/2022]
Abstract
GPCRs are the largest family of receptors accounting for about 30% of the current drug targets. However, it is difficult to fully elucidate the mechanisms regulating intracellular GPCR signal regulation. It is thus important to consider and investigate GPCRs with respect to endogenous situations. Our group has been investigating GPCRs involved in body color (teleost and amphibian) and eating (vertebrate). Here, I review two independent GPCR systems (heterodimer formation and primary ciliated GPCR) that can be breakthroughs in GPCR research. In teleosts, MCRs form heterodimers, which significantly reduce their affinity for acetylated ligands. In mammals, MCHR1 is localized in the ciliary membrane and shortens the length of the primary cilia through a unique signal from the ciliary membrane. Considering these two new GPCR concepts is expected to advance the overall view of the GPCR system.
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Affiliation(s)
- Yuki Kobayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan.
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23
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Primary Cilia Signaling Promotes Axonal Tract Development and Is Disrupted in Joubert Syndrome-Related Disorders Models. Dev Cell 2020; 51:759-774.e5. [PMID: 31846650 DOI: 10.1016/j.devcel.2019.11.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/08/2019] [Accepted: 11/10/2019] [Indexed: 12/18/2022]
Abstract
Appropriate axonal growth and connectivity are essential for functional wiring of the brain. Joubert syndrome-related disorders (JSRD), a group of ciliopathies in which mutations disrupt primary cilia function, are characterized by axonal tract malformations. However, little is known about how cilia-driven signaling regulates axonal growth and connectivity. We demonstrate that the deletion of related JSRD genes, Arl13b and Inpp5e, in projection neurons leads to de-fasciculated and misoriented axonal tracts. Arl13b deletion disrupts the function of its downstream effector, Inpp5e, and deregulates ciliary-PI3K/AKT signaling. Chemogenetic activation of ciliary GPCR signaling and cilia-specific optogenetic modulation of downstream second messenger cascades (PI3K, AKT, and AC3) commonly regulated by ciliary signaling receptors induce rapid changes in axonal dynamics. Further, Arl13b deletion leads to changes in transcriptional landscape associated with dysregulated PI3K/AKT signaling. These data suggest that ciliary signaling acts to modulate axonal connectivity and that impaired primary cilia signaling underlies axonal tract defects in JSRD.
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24
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Yang S, Bahl K, Chou HT, Woodsmith J, Stelzl U, Walz T, Nachury MV. Near-atomic structures of the BBSome reveal the basis for BBSome activation and binding to GPCR cargoes. eLife 2020; 9:55954. [PMID: 32510327 PMCID: PMC7311171 DOI: 10.7554/elife.55954] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Dynamic trafficking of G protein-coupled receptors (GPCRs) out of cilia is mediated by the BBSome. In concert with its membrane recruitment factor, the small GTPase ARL6/BBS3, the BBSome ferries GPCRs across the transition zone, a diffusion barrier at the base of cilia. Here, we present the near-atomic structures of the BBSome by itself and in complex with ARL6GTP, and we describe the changes in BBSome conformation induced by ARL6GTP binding. Modeling the interactions of the BBSome with membranes and the GPCR Smoothened (SMO) reveals that SMO, and likely also other GPCR cargoes, must release their amphipathic helix 8 from the membrane to be recognized by the BBSome.
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Affiliation(s)
- Shuang Yang
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Kriti Bahl
- Department of Ophthalmology, University of California San Francisco, San Francisco, United States
| | - Hui-Ting Chou
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Jonathan Woodsmith
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Graz, Austria
| | - Ulrich Stelzl
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Graz, Austria
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Maxence V Nachury
- Department of Ophthalmology, University of California San Francisco, San Francisco, United States
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Abstract
Primary cilia project in a single copy from the surface of most vertebrate cell types; they detect and transmit extracellular cues to regulate diverse cellular processes during development and to maintain tissue homeostasis. The sensory capacity of primary cilia relies on the coordinated trafficking and temporal localization of specific receptors and associated signal transduction modules in the cilium. The canonical Hedgehog (HH) pathway, for example, is a bona fide ciliary signalling system that regulates cell fate and self-renewal in development and tissue homeostasis. Specific receptors and associated signal transduction proteins can also localize to primary cilia in a cell type-dependent manner; available evidence suggests that the ciliary constellation of these proteins can temporally change to allow the cell to adapt to specific developmental and homeostatic cues. Consistent with important roles for primary cilia in signalling, mutations that lead to their dysfunction underlie a pleiotropic group of diseases and syndromic disorders termed ciliopathies, which affect many different tissues and organs of the body. In this Review, we highlight central mechanisms by which primary cilia coordinate HH, G protein-coupled receptor, WNT, receptor tyrosine kinase and transforming growth factor-β (TGFβ)/bone morphogenetic protein (BMP) signalling and illustrate how defects in the balanced output of ciliary signalling events are coupled to developmental disorders and disease progression.
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26
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Direct visualization of cAMP signaling in primary cilia reveals up-regulation of ciliary GPCR activity following Hedgehog activation. Proc Natl Acad Sci U S A 2019; 116:12066-12071. [PMID: 31142652 DOI: 10.1073/pnas.1819730116] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The primary cilium permits compartmentalization of specific signaling pathways, including elements of the Hedgehog (Hh) pathway. Hh transcriptional activity is thought to be negatively regulated by constitutively high ciliary cAMP maintained by the Gα(s)-coupled GPCR, GPR161. However, cilia also sequester many other Gα(s)-coupled GPCRs with unknown potential to regulate Hh. Here we used biosensors optimized for ciliary cAMP and strategies to isolate signals in the cilium from the cell body and neighboring cells. We found that ciliary cAMP was not elevated relative to cellular cAMP, inconsistent with constitutive cAMP production. Gα(s)-coupled GPCRs (e.g., the 5-HT6 serotonin and D1R dopamine receptor) had reduced ability to generate cAMP upon trafficking to the ciliary membrane. However, activation of the Hh pathway restored or amplified GPCR function to permit cAMP elevation selectively in the cilium. Hh therefore enables its own local GPCR-dependent cAMP regulatory circuit. Considering that GPCRs comprise much of the druggable genome, these data suggest alternative strategies to modify Hh signaling.
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Saito M, Sato T. [Current situation of researches on a sensor organelle, primary cilium, to understand the pathogenesis of ciliopathy]. Nihon Yakurigaku Zasshi 2019; 153:117-123. [PMID: 30867380 DOI: 10.1254/fpj.153.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Primary cilium is a membrane-protruding immotile sensory organelle. It had been supposed that the cilium was a static organelle for long periods. However, recent studies have uncovered that the cilium is dynamically organized organelle in a cell cycle-dependent manner; it is formed during G0/G1 phase and resorbed when the cells enter cell division cycle. Despite the primary cilium is very short and its surface area is extremely small, the cilium possesses a few kinds of G protein-coupled receptors, growth factor receptors and ion channels. Therefore, it can function as a signaling receptor for selective bioactive ligands and mechanical stresses. Dysregulation of the ciliary dynamics is linked with hereditary disorders, so called "ciliopathy", with clinical manifestations of microcephaly, polycystic kidney, situs inversus, polydactyly, and so on. No effective medical treatment for the ciliopathies has been available. Increasing evidences about the molecular mechanisms of ciliary dynamics and ciliary functions have revealed that enormous number of molecules regulate a cycle of ciliogenesis, cilium-derived signaling, ciliary resorption and elimination. However, it is a fact that research progress is far inferior to the full disclosure of the molecular mechanisms. Further studies are required to clarify the pathogenesis of the cilipathies. Moreover, efficient medical treatments are expected to be developed by pharmacological approaches.
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Affiliation(s)
- Masaki Saito
- Department of Molecular Pharmacology, Tohoku University School of Medicine
| | - Takeya Sato
- Department of Molecular Pharmacology, Tohoku University School of Medicine
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Saito Y, Hamamoto A, Kobayashi Y. [Selective signaling pathway via feeding-related ciliary GPCR, melanin-concentrating hormone receptor 1]. Nihon Yakurigaku Zasshi 2019; 154:179-185. [PMID: 31597896 DOI: 10.1254/fpj.154.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
G-protein-coupled receptors (GPCRs), which constitute a highly diverse family of seven transmembrane receptors, respond to external signals and regulate a variety of cellular and physiological processes. GPCRs are encoded by about 800 different genes in human and they represent the largest family of drug targets in clinical trials, which accounts for about 30% of approved drugs acting on 108 unique GPCRs. Signaling through GPCRs can be optimized by enriching receptors, selective binding partners, and downstream effectors in discrete cellular environment. The primary cilium is a ubiquitous organelle that functions as a sensory antenna for surrounding physical and chemical stimuli. Primary cilium's compartment is as little as 1/10,000th of the total cell volume. Therefore, the ciliary membrane is highly enriched for specific signaling molecules, allowing the primary cilium to organize signaling in a highly ordered microenvironment. Recently, a set of non-olfactory GPCRs such as somatostatin receptor 3 and melanin-concentrating hormone receptor 1 (MCHR1) have been found to be selectively targeted to cilia on several mammalian cell types including neuronal cells both in vitro and in vivo approaches. Moreover, investigations into the pathophysiology have implicated GPCR ciliary signaling in a number of developmental and cellular pathways. Thus, cilia are now considered as an increasingly important connection for GPCR signaling. This review summarizes our current understanding of the signaling pathways though ciliary GPCR, especially feeding- and mood-related GPCR MCHR1, along with specific biological phenomenon as cilia length shortening.
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Affiliation(s)
- Yumiko Saito
- Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Akie Hamamoto
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University
| | - Yuki Kobayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University
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29
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Saternos HC, AbouAlaiwi WA. Signaling interplay between primary cilia and nitric oxide: A mini review. Nitric Oxide 2018; 80:108-112. [PMID: 30099097 DOI: 10.1016/j.niox.2018.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/01/2018] [Accepted: 08/06/2018] [Indexed: 01/12/2023]
Abstract
New discoveries into the functional role of primary cilia are on the rise. In little more than 20 years, research has shown the once vestigial organelle is a signaling powerhouse involved in a vast number of essential cellular processes. In the same decade that interest in primary cilia was burgeoning, nitric oxide won molecule of the year and a Nobel prize for its role as a near ubiquitous signaling molecule. Although primary cilia and nitric oxide are both involved in signaling, a direct relationship has not been investigated; however, after a quick review of the literature, parallels between their functions can be drawn. This review aims to suggest a possible interplay between primary cilia and nitric oxide signaling especially in the areas of vascular tissue homeostasis and cellular proliferation.
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Affiliation(s)
- Hannah C Saternos
- University of Toledo, College of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology and Experimental Therapeutics, USA
| | - Wissam A AbouAlaiwi
- University of Toledo, College of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology and Experimental Therapeutics, USA.
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30
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Klink BU, Zent E, Juneja P, Kuhlee A, Raunser S, Wittinghofer A. A recombinant BBSome core complex and how it interacts with ciliary cargo. eLife 2017; 6. [PMID: 29168691 PMCID: PMC5700813 DOI: 10.7554/elife.27434] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/03/2017] [Indexed: 01/07/2023] Open
Abstract
Cilia are small, antenna-like structures on the surface of eukaryotic cells that harbor a unique set of sensory proteins, including GPCRs and other membrane proteins. The transport of these proteins involves the BBSome, an eight-membered protein complex that is recruited to ciliary membranes by the G-protein Arl6. BBSome malfunction leads to Bardet-Biedl syndrome, a ciliopathy with severe consequences. Short ciliary targeting sequences (CTS) have been identified that trigger the transport of ciliary proteins. However, mechanistic studies that relate ciliary targeting to BBSome binding are missing. Here we used heterologously expressed BBSome subcomplexes to analyze the complex architecture and to investigate the binding of GPCRs and other receptors to the BBSome. A stable heterohexameric complex was identified that binds to GPCRs with interactions that only partially overlap with previously described CTS, indicating a more complex recognition than anticipated. Arl6•GTP does not affect these interactions, suggesting no direct involvement in cargo loading/unloading.
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Affiliation(s)
- Björn Udo Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Eldar Zent
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Puneet Juneja
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Anne Kuhlee
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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Guo J, Otis JM, Higginbotham H, Monckton C, Cheng J, Asokan A, Mykytyn K, Caspary T, Stuber GD, Anton ES. Primary Cilia Signaling Shapes the Development of Interneuronal Connectivity. Dev Cell 2017; 42:286-300.e4. [PMID: 28787594 DOI: 10.1016/j.devcel.2017.07.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 05/18/2017] [Accepted: 07/12/2017] [Indexed: 01/06/2023]
Abstract
Appropriate growth and synaptic integration of GABAergic inhibitory interneurons are essential for functional neural circuits in the brain. Here, we demonstrate that disruption of primary cilia function following the selective loss of ciliary GTPase Arl13b in interneurons impairs interneuronal morphology and synaptic connectivity, leading to altered excitatory/inhibitory activity balance. The altered morphology and connectivity of cilia mutant interneurons and the functional deficits are rescued by either chemogenetic activation of ciliary G-protein-coupled receptor (GPCR) signaling or the selective induction of Sstr3, a ciliary GPCR, in Arl13b-deficient cilia. Our results thus define a specific requirement for primary cilia-mediated GPCR signaling in interneuronal connectivity and inhibitory circuit formation.
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Affiliation(s)
- Jiami Guo
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - James M Otis
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Holden Higginbotham
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Chase Monckton
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - JrGang Cheng
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Aravind Asokan
- Department of Genetics and Gene Therapy Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Kirk Mykytyn
- Department of Biological Chemistry and Pharmacology, Neuroscience Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Garret D Stuber
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - E S Anton
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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Mykytyn K, Askwith C. G-Protein-Coupled Receptor Signaling in Cilia. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028183. [PMID: 28159877 DOI: 10.1101/cshperspect.a028183] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most versatile family of signaling receptors in humans. They respond to diverse external signals, such as photons, proteins, peptides, chemicals, hormones, lipids, and sugars, and mediate a myriad of functions in the human body. Signaling through GPCRs can be optimized by enriching receptors and downstream effectors in discrete cellular domains. Many GPCRs have been found to be selectively targeted to cilia on numerous mammalian cell types. Moreover, investigations into the pathophysiology of human ciliopathies have implicated GPCR ciliary signaling in a number of developmental and cellular pathways. Thus, cilia are now appreciated as an increasingly important nexus for GPCR signaling. Yet, we are just beginning to understand the precise signaling pathways mediated by most ciliary GPCRs and how they impact cellular function and mammalian physiology.
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Affiliation(s)
- Kirk Mykytyn
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Ohio 43210.,Neuroscience Research Institute, The Ohio State University, Ohio 43210
| | - Candice Askwith
- Neuroscience Research Institute, The Ohio State University, Ohio 43210.,Department of Neuroscience, The Ohio State University, Ohio 43210
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Kresovich JK, Zheng Y, Cardenas A, Joyce BT, Rifas-Shiman SL, Oken E, Gillman MW, Hivert MF, Baccarelli AA, Hou L. Cord blood DNA methylation and adiposity measures in early and mid-childhood. Clin Epigenetics 2017; 9:86. [PMID: 28814982 PMCID: PMC5558655 DOI: 10.1186/s13148-017-0384-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/07/2017] [Indexed: 12/22/2022] Open
Abstract
Background Excess adiposity in childhood is associated with numerous adverse health outcomes. As this condition is difficult to treat once present, identification of risk early in life can help inform and implement strategies to prevent the onset of the condition. We performed an epigenome-wide association study to prospectively investigate the relationship between cord blood DNA methylation and adiposity measurements in childhood. Methods We measured genome-wide DNA methylation from 478 children in cord blood and measured overall and central adiposity via skinfold caliper measurements in early (range 3.1–3.3 years) and mid-childhood (age range 7.3–8.3 years) and via dual X-ray absorptiometry (DXA) in mid-childhood. Final models were adjusted for maternal age at enrollment, pre-pregnancy body mass index, education, folate intake during pregnancy, smoking during pregnancy, and gestational weight gain, and child sex, race/ethnicity, current age, and cord blood cell composition. Results We identified four promoter proximal CpG sites that were associated with adiposity as measured by subscapular (SS) and triceps (TR) ratio (SS:TR) in early childhood, in the genes KPRP, SCL9A10, MYLK2, and PRLHR. We additionally identified one gene body CpG site associated with early childhood SS + TR on PPAPDC1A; this site was nominally associated with SS + TR in mid-childhood. Higher methylation at one promoter proximal CpG site in MMP25 was also associated with SS:TR in mid-childhood. In regional analyses, methylation at an exonal region of GFPT2 was positively associated with SS:TR in early childhood. Finally, we identified regions of two long, non-coding RNAs which were associated with SS:TR (LOC100049716) and fat-free mass index (LOC102723493) in mid-childhood. Conclusion This analysis identified novel CpG loci associated with adiposity outcomes. However, our results suggest little consistency across the various adiposity outcomes tested, particularly among the more accurate DXA measurements of body composition. We recommend using caution when interpreting these associations. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0384-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacob K Kresovich
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL USA.,Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University, Chicago, IL USA
| | - Yinan Zheng
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University, Chicago, IL USA
| | - Andres Cardenas
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Brian T Joyce
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University, Chicago, IL USA
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Matthew W Gillman
- Environmental Influences on Child Health Outcomes (ECHO) Program, Office of the Director, National Institutes of Health, Bethesda, MD USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Andrea A Baccarelli
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY USA
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University, Chicago, IL USA
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Shimada IS, Badgandi H, Somatilaka BN, Mukhopadhyay S. Using Primary Neurosphere Cultures to Study Primary Cilia. J Vis Exp 2017. [PMID: 28448009 DOI: 10.3791/55315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The primary cilium is fundamentally important for the proliferation of neural stem/progenitor cells and for neuronal differentiation during embryonic, postnatal, and adult life. In addition, most differentiated neurons possess primary cilia that house signaling receptors, such as G-protein-coupled receptors, and signaling molecules, such as adenylyl cyclases. The primary cilium determines the activity of multiple developmental pathways, including the sonic hedgehog pathway during embryonic neuronal development, and also functions in promoting compartmentalized subcellular signaling during adult neuronal function. Unsurprisingly, defects in primary cilium biogenesis and function have been linked to developmental anomalies of the brain, central obesity, and learning and memory deficits. Thus, it is imperative to study primary cilium biogenesis and ciliary trafficking in the context of neural stem/progenitor cells and differentiated neurons. However, culturing methods for primary neurons require considerable expertise and are not amenable to freeze-thaw cycles. In this protocol, we discuss culturing methods for mixed populations of neural stem/progenitor cells using primary neurospheres. The neurosphere-based culturing methods provide the combined benefits of studying primary neural stem/progenitor cells: amenability to multiple passages and freeze-thaw cycles, differentiation potential into neurons/glia, and transfectability. Importantly, we determined that neurosphere-derived neural stem/progenitor cells and differentiated neurons are ciliated in culture and localize signaling molecules relevant to ciliary function in these compartments. Utilizing these cultures, we further describe methods to study ciliogenesis and ciliary trafficking in neural stem/progenitor cells and differentiated neurons. These neurosphere-based methods allow us to study cilia-regulated cellular pathways, including G-protein-coupled receptor and sonic hedgehog signaling, in the context of neural stem/progenitor cells and differentiated neurons.
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Affiliation(s)
- Issei S Shimada
- Department of Cell Biology, University of Texas Southwestern Medical Center;
| | - Hemant Badgandi
- Department of Cell Biology, University of Texas Southwestern Medical Center
| | | | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center;
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Badgandi HB, Hwang SH, Shimada IS, Loriot E, Mukhopadhyay S. Tubby family proteins are adapters for ciliary trafficking of integral membrane proteins. J Cell Biol 2017; 216:743-760. [PMID: 28154160 PMCID: PMC5350516 DOI: 10.1083/jcb.201607095] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/25/2016] [Accepted: 01/09/2017] [Indexed: 01/19/2023] Open
Abstract
Trafficking of integral membrane proteins to cilia is poorly understood. Badgandi et al. show that tubby family proteins TULP3 and TUB act as general adapters for ciliary trafficking of structurally diverse integral membrane cargo like GCPRs and the polycystin 1/2 complex. The primary cilium is a paradigmatic organelle for studying compartmentalized signaling; however, unlike soluble protein trafficking, processes targeting integral membrane proteins to cilia are poorly understood. In this study, we determine that the tubby family protein TULP3 functions as a general adapter for ciliary trafficking of structurally diverse integral membrane cargo, including multiple reported and novel rhodopsin family G protein–coupled receptors (GPCRs) and the polycystic kidney disease–causing polycystin 1/2 complex. The founding tubby family member TUB also localizes to cilia similar to TULP3 and determines trafficking of a subset of these GPCRs to neuronal cilia. Using minimal ciliary localization sequences from GPCRs and fibrocystin (also implicated in polycystic kidney disease), we demonstrate these motifs to be sufficient and TULP3 dependent for ciliary trafficking. We propose a three-step model for TULP3/TUB-mediated ciliary trafficking, including the capture of diverse membrane cargo by the tubby domain in a phosphoinositide 4,5-bisphosphate (PI(4,5)P2)-dependent manner, ciliary delivery by intraflagellar transport complex A binding to the TULP3/TUB N terminus, and subsequent release into PI(4,5)P2-deficient ciliary membrane.
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Affiliation(s)
- Hemant B Badgandi
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Issei S Shimada
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Evan Loriot
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390.,STARS Program, University of Texas Southwestern Medical Center, Dallas, TX 75390.,Jesuit College Preparatory School of Dallas, Dallas, TX 75244
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Agnati LF, Marcoli M, Maura G, Fuxe K, Guidolin D. The multi-facet aspects of cell sentience and their relevance for the integrative brain actions: role of membrane protein energy landscape. Rev Neurosci 2016; 27:347-63. [DOI: 10.1515/revneuro-2015-0049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/11/2015] [Indexed: 12/14/2022]
Abstract
AbstractSeveral ion channels can be randomly and spontaneously in an open state, allowing the exchange of ion fluxes between extracellular and intracellular environments. We propose that the random changes in the state of ion channels could be also due to proteins exploring their energy landscapes. Indeed, proteins can modify their steric conformation under the effects of the physicochemical parameters of the environments with which they are in contact, namely, the extracellular, intramembrane and intracellular environments. In particular, it is proposed that the random walk of proteins in their energy landscape is towards attractors that can favor the open or close condition of the ion channels and/or intrinsic activity of G-protein-coupled receptors. The main aspect of the present proposal is that some relevant physicochemical parameters of the environments (e.g. molecular composition, temperature, electrical fields) with which some signaling-involved plasma membrane proteins are in contact alter their conformations. In turn, these changes can modify their information handling via a modulatory action on their random walk towards suitable attractors of their energy landscape. Thus, spontaneous and/or signal-triggered electrical activities of neurons occur that can have emergent properties capable of influencing the integrative actions of brain networks. Against this background, Cook’s hypothesis on ‘cell sentience’ is developed by proposing that physicochemical parameters of the environments with which the plasma-membrane proteins of complex cellular networks are in contact fulfill a fundamental role in their spontaneous and/or signal-triggered activity. Furthermore, it is proposed that a specialized organelle, the primary cilium, which is present in most cells (also neurons and astrocytes), could be of peculiar importance to pick up chemical signals such as ions and transmitters and to detect physical signals such as pressure waves, thermal gradients, and local field potentials.
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Affiliation(s)
| | - Manuela Marcoli
- 3University of Genova, Department of Pharmacy and Center of Excellence for Biomedical Research, Viale Cembrano 4, I-16148 Genova, Italy
| | - Guido Maura
- 3University of Genova, Department of Pharmacy and Center of Excellence for Biomedical Research, Viale Cembrano 4, I-16148 Genova, Italy
| | - Kjell Fuxe
- 2Karolinska Institutet, Department of Neuroscience, S-17177 Stockholm, Sweden
| | - Diego Guidolin
- 4University of Padova, Department of Molecular Medicine, I-35122 Padova, Italy
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Pal K, Hwang SH, Somatilaka B, Badgandi H, Jackson PK, DeFea K, Mukhopadhyay S. Smoothened determines β-arrestin-mediated removal of the G protein-coupled receptor Gpr161 from the primary cilium. J Cell Biol 2016; 212:861-75. [PMID: 27002170 PMCID: PMC4810300 DOI: 10.1083/jcb.201506132] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/11/2016] [Indexed: 02/08/2023] Open
Abstract
Dynamic changes in membrane protein composition of the primary cilium are central to development and homeostasis, but we know little about mechanisms regulating membrane protein flux. Stimulation of the sonic hedgehog (Shh) pathway in vertebrates results in accumulation and activation of the effector Smoothened within cilia and concomitant disappearance of a negative regulator, the orphan G protein-coupled receptor (GPCR), Gpr161. Here, we describe a two-step process determining removal of Gpr161 from cilia. The first step involves β-arrestin recruitment by the signaling competent receptor, which is facilitated by the GPCR kinase Grk2. An essential factor here is the ciliary trafficking and activation of Smoothened, which by increasing Gpr161-β-arrestin binding promotes Gpr161 removal, both during resting conditions and upon Shh pathway activation. The second step involves clathrin-mediated endocytosis, which functions outside of the ciliary compartment in coordinating Gpr161 removal. Mechanisms determining dynamic compartmentalization of Gpr161 in cilia define a new paradigm for down-regulation of GPCRs during developmental signaling from a specialized subcellular compartment.
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Affiliation(s)
- Kasturi Pal
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Bandarigoda Somatilaka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hemant Badgandi
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Peter K Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Kathryn DeFea
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Hilgendorf KI, Johnson CT, Jackson PK. The primary cilium as a cellular receiver: organizing ciliary GPCR signaling. Curr Opin Cell Biol 2016; 39:84-92. [PMID: 26926036 DOI: 10.1016/j.ceb.2016.02.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/12/2022]
Abstract
The primary cilium is an antenna-like cellular protrusion mediating sensory and neuroendocrine signaling. Its localization within tissue architecture and a growing list of cilia-localized receptors, in particular G-protein-coupled receptors, determine a host of crucial physiologies, which are disrupted in human ciliopathies. Here, we discuss recent advances in the identification and characterization of ciliary signaling components and pathways. Recent studies have highlighted the unique signaling environment of the primary cilium and we are just beginning to understand how this design allows for highly amplified and regulated signaling.
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Affiliation(s)
- Keren I Hilgendorf
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carl T Johnson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stem Cell and Regenerative Medicine PhD Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Abstract
In the last decade highly conserved cellular appendages called cilia have enjoyed a renewed interest from basic, biomedical scientists, and clinicians alike. This interest has grown upon the elucidation that cilia throughout the body serve as important sensory and signaling centers in both development and adult homeostasis. Furthermore, the identification of several rare genetic disorders associated with cilia dysfunction has broadened the field. However, even though their potential role in human health and disease is now recognized many basic questions about their functions remain. This chapter seeks to explore the trafficking of cilia-specific G protein-coupled receptors (GPCRs) and discusses several model systems in which this has been explored. We open the chapter by briefly discussing cilia and GPCRs then begin discussing some aspects of rhodopsin trafficking, arguably the most well studied of cilia GPCRs. We continue with sections on neuronal cilia and olfactory cilia receptor trafficking. Finally, we conclude with the emerging area of dynamic ciliary GPCR trafficking and speculate about future directions and some of the questions that remain for ciliary GPCRs.
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Affiliation(s)
- Jeremy C McIntyre
- Department of Neuroscience, University of Florida, Gainesville, FL, USA; Center for Smell and Taste, University of Florida, Gainesville, FL, USA
| | - Mellisa M Hege
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Nicolas F Berbari
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
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Pembroke WG, Babbs A, Davies KE, Ponting CP, Oliver PL. Temporal transcriptomics suggest that twin-peaking genes reset the clock. eLife 2015; 4. [PMID: 26523393 PMCID: PMC4718813 DOI: 10.7554/elife.10518] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/01/2015] [Indexed: 01/08/2023] Open
Abstract
The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior and physiology, yet a detailed understanding of its coordinated transcriptional programmes is lacking. To reveal the finer details of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection (LCM) and RNA-seq over a 24 hr light / dark cycle. We show that 7-times more genes exhibited a classic sinusoidal expression signature than previously observed in the SCN. Another group of 766 genes unexpectedly peaked twice, near both the start and end of the dark phase; this twin-peaking group is significantly enriched for synaptic transmission genes that are crucial for light-induced phase shifting of the circadian clock. 341 intergenic non-coding RNAs, together with novel exons of annotated protein-coding genes, including Cry1, also show specific circadian expression variation. Overall, our data provide an important chronobiological resource (www.wgpembroke.com/shiny/SCNseq/) and allow us to propose that transcriptional timing in the SCN is gating clock resetting mechanisms. DOI:http://dx.doi.org/10.7554/eLife.10518.001 The daily cycles of life in mammals are driven by a small region of the brain called the suprachiasmatic nucleus (or SCN). The SCN receives signals from sunlight and other environmental factors to help coordinate most aspects of daily biological activity and behaviour. To work correctly, it is essential that the SCN switches certain genes on and off at exactly the right time. However, many questions remain over the identity of these genes and how their levels of activity change during a 24-hour period. When a gene is active (or “being expressed”), it is used as a template to build the molecules of RNA that are needed to make proteins and to help to control how cells work. Pembroke et al. have now sequenced the RNA molecules made in the SCN of mice (which plays the same role as the equivalent human brain region) over a 24-hour period. The mice spent half of each day in the light, and half in the dark. This revealed that the expression levels of over a quarter of all the genes that are found in the SCN fluctuate over a 24-hour period. One particular group of genes peak in activity twice a day; Pembroke et al. suggest that these genes are important for controlling how an animal can adjust its body clock to light. Further research is now needed to find out which of the newly discovered fluctuating genes play the most important roles in daily activity rhythms, and which might play a part in disease. DOI:http://dx.doi.org/10.7554/eLife.10518.002
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Affiliation(s)
- William G Pembroke
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Arran Babbs
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Kay E Davies
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter L Oliver
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Schou KB, Pedersen LB, Christensen ST. Ins and outs of GPCR signaling in primary cilia. EMBO Rep 2015; 16:1099-113. [PMID: 26297609 DOI: 10.15252/embr.201540530] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/01/2015] [Indexed: 12/17/2022] Open
Abstract
Primary cilia are specialized microtubule-based signaling organelles that convey extracellular signals into a cellular response in most vertebrate cell types. The physiological significance of primary cilia is underscored by the fact that defects in assembly or function of these organelles lead to a range of severe diseases and developmental disorders. In most cell types of the human body, signaling by primary cilia involves different G protein-coupled receptors (GPCRs), which transmit specific signals to the cell through G proteins to regulate diverse cellular and physiological events. Here, we provide an overview of GPCR signaling in primary cilia, with main focus on the rhodopsin-like (class A) and the smoothened/frizzled (class F) GPCRs. We describe how such receptors dynamically traffic into and out of the ciliary compartment and how they interact with other classes of ciliary GPCRs, such as class B receptors, to control ciliary function and various physiological and behavioral processes. Finally, we discuss future avenues for developing GPCR-targeted drug strategies for the treatment of ciliopathies.
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Novas R, Cardenas-Rodriguez M, Irigoín F, Badano JL. Bardet-Biedl syndrome: Is it only cilia dysfunction? FEBS Lett 2015; 589:3479-91. [PMID: 26231314 DOI: 10.1016/j.febslet.2015.07.031] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 01/12/2023]
Abstract
Bardet-Biedl syndrome (BBS) is a genetically heterogeneous, pleiotropic disorder, characterized by both congenital and late onset defects. From the analysis of the mutational burden in patients to the functional characterization of the BBS proteins, this syndrome has become a model for both understanding oligogenic patterns of inheritance and the biology of a particular cellular organelle: the primary cilium. Here we briefly review the genetics of BBS to then focus on the function of the BBS proteins, not only in the context of the cilium but also highlighting potential extra-ciliary roles that could be relevant to the etiology of the disorder. Finally, we provide an overview of how the study of this rare syndrome has contributed to the understanding of cilia biology and how this knowledge has informed on the cellular basis of different clinical manifestations that characterize BBS and the ciliopathies.
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Affiliation(s)
- Rossina Novas
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | | | - Florencia Irigoín
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay; Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Montevideo, Gral. Flores 2125, Montevideo CP11800, Uruguay
| | - Jose L Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay.
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