1
|
Pir MS, Begar E, Yenisert F, Demirci HC, Korkmaz ME, Karaman A, Tsiropoulou S, Firat-Karalar EN, Blacque OE, Oner SS, Doluca O, Cevik S, Kaplan OI. CilioGenics: an integrated method and database for predicting novel ciliary genes. Nucleic Acids Res 2024:gkae554. [PMID: 38989623 DOI: 10.1093/nar/gkae554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024] Open
Abstract
Uncovering the full list of human ciliary genes holds enormous promise for the diagnosis of cilia-related human diseases, collectively known as ciliopathies. Currently, genetic diagnoses of many ciliopathies remain incomplete (1-3). While various independent approaches theoretically have the potential to reveal the entire list of ciliary genes, approximately 30% of the genes on the ciliary gene list still stand as ciliary candidates (4,5). These methods, however, have mainly relied on a single strategy to uncover ciliary candidate genes, making the categorization challenging due to variations in quality and distinct capabilities demonstrated by different methodologies. Here, we develop a method called CilioGenics that combines several methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF) network analysis, and text mining) to predict the ciliary capacity of each human gene. Our combined approach provides a CilioGenics score for every human gene that represents the probability that it will become a ciliary gene. Compared to methods that rely on a single method, CilioGenics performs better in its capacity to predict ciliary genes. Our top 500 gene list includes 258 new ciliary candidates, with 31 validated experimentally by us and others. Users may explore the whole list of human genes and CilioGenics scores on the CilioGenics database (https://ciliogenics.com/).
Collapse
Affiliation(s)
- Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Efe Begar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
| | - Ferhan Yenisert
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Hasan C Demirci
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Mustafa E Korkmaz
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Asli Karaman
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
- School of Medicine, Koç University, Istanbul 34450, Turkiye
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sukru S Oner
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkiye
| | - Osman Doluca
- Izmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, Izmir, Turkiye
| | - Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| |
Collapse
|
2
|
Katoh TA, Lange T, Nakajima Y, Yashiro K, Okada Y, Hamada H. BMP4 regulates asymmetric Pkd2 distribution in mouse nodal immotile cilia and ciliary mechanosensing required for left-right determination. Dev Dyn 2024. [PMID: 38984461 DOI: 10.1002/dvdy.727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/18/2024] [Accepted: 06/23/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Mouse nodal immotile cilia mechanically sense the bending direction for left-right (L-R) determination and activate the left-side-specific signaling cascade, leading to increased Nodal activity. Asymmetric distribution of Pkd2, a crucial channel for L-R determination, on immotile cilia has been reported recently. However, the causal relationship between the asymmetric Pkd2 distribution and direction-dependent flow sensing is not well understood. Furthermore, the underlying molecular mechanism directing this asymmetric Pkd2 distribution remains unclear. RESULTS The effects of several recombinant proteins and inhibitors on the Pkd2 distribution were analyzed using super-resolution microscopy. Notably, bone morphogenetic protein 4 (BMP4) affected the Pkd2 distribution. Additionally, three-dimensional manipulation of nodal immotile cilia using optical tweezers revealed that excess BMP4 caused defects in the mechanosensing ability of the cilia. CONCLUSIONS Experimental data together with model calculations suggest that BMP4 regulates the asymmetric distribution of Pkd2 in nodal immotile cilia, thereby affecting the ability of these cilia to sense the bending direction for L-R determination. This study, for the first time, provides insight into the relationship between the asymmetric protein distribution in cilia and their function.
Collapse
Affiliation(s)
- Takanobu A Katoh
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Tim Lange
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yoshiro Nakajima
- Division of Anatomy and Developmental Biology, Department of Anatomy, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenta Yashiro
- Division of Anatomy and Developmental Biology, Department of Anatomy, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Physics, Universal Biology Institute and International Research Center for Neurointelligence, The University of Tokyo, Hongo, Tokyo, Japan
| | - Hiroshi Hamada
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| |
Collapse
|
3
|
Gao H, Huang X, Chen W, Feng Z, Zhao Z, Li P, Tan C, Wang J, Zhuang Q, Gao Y, Min S, Yao Q, Qian M, Ma X, Wu F, Yan W, Sheng W, Huang G. Association of copy number variation in X chromosome-linked PNPLA4 with heterotaxy and congenital heart disease. Chin Med J (Engl) 2024:00029330-990000000-01132. [PMID: 38973237 DOI: 10.1097/cm9.0000000000003192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Heterotaxy (HTX) is a thoracoabdominal organ anomaly syndrome and commonly accompanied by congenital heart disease (CHD). The aim of this study was to analyze rare copy number variations (CNVs) in a HTX/CHD cohort and to examine the potential mechanisms contributing to HTX/CHD. METHODS Chromosome microarray analysis was used to identify rare CNVs in a cohort of 120 unrelated HTX/CHD patients, and available samples from parents were used to confirm the inheritance pattern. Potential candidate genes in CNVs region were prioritized via the DECIPHER database, and PNPLA4 was identified as the leading candidate gene. To validate, we generated PNPLA4-overexpressing human induced pluripotent stem cell lines as well as pnpla4-overexpressing zebrafish model, followed by a series of transcriptomic, biochemical and cellular analyses. RESULTS Seventeen rare CNVs were identified in 15 of the 120 HTX/CHD patients (12.5%). Xp22.31 duplication was one of the inherited CNVs identified in this HTX/CHD cohort, and PNPLA4 in the Xp22.31 was a candidate gene associated with HTX/CHD. PNPLA4 is expressed in the lateral plate mesoderm, which is known to be critical for left/right embryonic patterning as well as cardiomyocyte differentiation, and in the neural crest cell lineage. Through a series of in vivo and in vitro analyses at the molecular and cellular levels, we revealed that the biological function of PNPLA4 is importantly involved in the primary cilia formation and function via its regulation of energy metabolism and mitochondria-mediated ATP production. CONCLUSIONS Our findings demonstrated a significant association between CNVs and HTX/CHD. Our data strongly suggested that an increased genetic dose of PNPLA4 due to Xp22.31 duplication is a disease-causing risk factor for HTX/CHD.
Collapse
Affiliation(s)
- Han Gao
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Xianghui Huang
- Fujian Key Laboratory of Neonatal Diseases, Xiamen Children's Hospital, Xiamen, Fujian 361006, China
| | - Weicheng Chen
- Children's Hospital of Fudan University, Shanghai 201102, China
| | - Zhiyu Feng
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Zhengshan Zhao
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Ping Li
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Chaozhong Tan
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Jinxin Wang
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Quannan Zhuang
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Yuan Gao
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Shaojie Min
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Qinyu Yao
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Maoxiang Qian
- Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaojing Ma
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Feizhen Wu
- Children's Hospital of Fudan University, Shanghai 201102, China
| | - Weili Yan
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
- Research Unit of Early Intervention of Genetically Related Childhood Cardiovascular Diseases, Chinese Academy of Medical Sciences, Shanghai 201102, China
| | - Wei Sheng
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
- Fujian Key Laboratory of Neonatal Diseases, Xiamen Children's Hospital, Xiamen, Fujian 361006, China
- Research Unit of Early Intervention of Genetically Related Childhood Cardiovascular Diseases, Chinese Academy of Medical Sciences, Shanghai 201102, China
| | - Guoying Huang
- Children's Hospital of Fudan University, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
- Fujian Key Laboratory of Neonatal Diseases, Xiamen Children's Hospital, Xiamen, Fujian 361006, China
- Research Unit of Early Intervention of Genetically Related Childhood Cardiovascular Diseases, Chinese Academy of Medical Sciences, Shanghai 201102, China
| |
Collapse
|
4
|
Macarelli V, Harding EC, Gershlick DC, Merkle FT. A Short Sequence Targets Transmembrane Proteins to Primary Cilia. Cells 2024; 13:1156. [PMID: 38995007 PMCID: PMC11240719 DOI: 10.3390/cells13131156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
Primary cilia are finger-like sensory organelles that extend from the bodies of most cell types and have a distinct lipid and protein composition from the plasma membrane. This partitioning is maintained by a diffusion barrier that restricts the entry of non-ciliary proteins, and allows the selective entry of proteins harboring a ciliary targeting sequence (CTS). However, CTSs are not stereotyped and previously reported sequences are insufficient to drive efficient ciliary localisation across diverse cell types. Here, we describe a short peptide sequence that efficiently targets transmembrane proteins to primary cilia in all tested cell types, including human neurons. We generate human-induced pluripotent stem cell (hiPSC) lines stably expressing a transmembrane construct bearing an extracellular HaloTag and intracellular fluorescent protein, which enables the bright, specific labeling of primary cilia in neurons and other cell types to facilitate studies of cilia in health and disease. We demonstrate the utility of this resource by developing an image analysis pipeline for the automated measurement of primary cilia to detect changes in their length associated with altered signaling or disease state.
Collapse
Affiliation(s)
- Viviana Macarelli
- Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Edward C Harding
- Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Florian T Merkle
- Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| |
Collapse
|
5
|
Hilgendorf KI, Myers BR, Reiter JF. Emerging mechanistic understanding of cilia function in cellular signalling. Nat Rev Mol Cell Biol 2024; 25:555-573. [PMID: 38366037 PMCID: PMC11199107 DOI: 10.1038/s41580-023-00698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2023] [Indexed: 02/18/2024]
Abstract
Primary cilia are solitary, immotile sensory organelles present on most cells in the body that participate broadly in human health, physiology and disease. Cilia generate a unique environment for signal transduction with tight control of protein, lipid and second messenger concentrations within a relatively small compartment, enabling reception, transmission and integration of biological information. In this Review, we discuss how cilia function as signalling hubs in cell-cell communication using three signalling pathways as examples: ciliary G-protein-coupled receptors (GPCRs), the Hedgehog (Hh) pathway and polycystin ion channels. We review how defects in these ciliary signalling pathways lead to a heterogeneous group of conditions known as 'ciliopathies', including metabolic syndromes, birth defects and polycystic kidney disease. Emerging understanding of these pathways' transduction mechanisms reveals common themes between these cilia-based signalling pathways that may apply to other pathways as well. These mechanistic insights reveal how cilia orchestrate normal and pathophysiological signalling outputs broadly throughout human biology.
Collapse
Affiliation(s)
- Keren I Hilgendorf
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Benjamin R Myers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
6
|
Patel K, Smith NJ. Primary cilia, A-kinase anchoring proteins and constitutive activity at the orphan G protein-coupled receptor GPR161: A tale about a tail. Br J Pharmacol 2024; 181:2182-2196. [PMID: 36772847 DOI: 10.1111/bph.16053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/22/2022] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
Primary cilia are non-motile antennae-like structures responsible for sensing environmental changes in most mammalian cells. Ciliary signalling is largely mediated by the Sonic Hedgehog (Shh) pathway, which acts as a master regulator of ciliary protein transit and is essential for normal embryonic development. One particularly important player in primary cilia is the orphan G protein-coupled receptor, GPR161. In this review, we introduce GPR161 in the context of Shh signalling and describe the unique features on its C-terminus such as PKA phosphorylation sites and an A-kinase anchoring protein motif, which may influence the function of the receptor, cAMP compartmentalisation and/or trafficking within primary cilia. We discuss the recent putative pairing of GPR161 and spexin-1, highlighting the additional steps needed before GPR161 could be considered 'deorphanised'. Finally, we speculate that the marked constitutive activity and unconventional regulation of GPR161 may indicate that the receptor may not require an endogenous ligand. LINKED ARTICLES: This article is part of a themed issue Therapeutic Targeting of G Protein-Coupled Receptors: hot topics from the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists 2021 Virtual Annual Scientific Meeting. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.14/issuetoc.
Collapse
Affiliation(s)
- Kinjal Patel
- Orphan Receptor Laboratory, School of Biomedical Sciences, Faculty of Medicine & Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Nicola J Smith
- Orphan Receptor Laboratory, School of Biomedical Sciences, Faculty of Medicine & Health, UNSW Sydney, Kensington, New South Wales, Australia
| |
Collapse
|
7
|
Rezi CK, Aslanyan MG, Diwan GD, Cheng T, Chamlali M, Junger K, Anvarian Z, Lorentzen E, Pauly KB, Afshar-Bahadori Y, Fernandes EF, Qian F, Tosi S, Christensen ST, Pedersen SF, Strømgaard K, Russell RB, Miner JH, Mahjoub MR, Boldt K, Roepman R, Pedersen LB. DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2. EMBO Rep 2024; 25:3040-3063. [PMID: 38849673 PMCID: PMC11239879 DOI: 10.1038/s44319-024-00170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/08/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney causes ciliary elongation and cystogenesis, and cell-based proximity labeling proteomics and fluorescence microscopy show alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20, and polycystin-2 (PC2) are reduced in the cilia of DLG1-deficient cells compared to control cells. This phenotype is recapitulated in vivo and rescuable by re-expression of wild-type DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggest that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.
Collapse
Affiliation(s)
- Csenge K Rezi
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mariam G Aslanyan
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gaurav D Diwan
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Tao Cheng
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Mohamed Chamlali
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Zeinab Anvarian
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics - Protein Science, Aarhus University, Aarhus, Denmark
| | - Kleo B Pauly
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Eduardo Fa Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sébastien Tosi
- Danish BioImaging Infrastructure Image Analysis Core Facility (DBI-INFRA IACF), University of Copenhagen, Copenhagen, Denmark
| | | | - Stine F Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Robert B Russell
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Jeffrey H Miner
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Moe R Mahjoub
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Ronald Roepman
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
8
|
Reddy Palicharla V, Mukhopadhyay S. Molecular and structural perspectives on protein trafficking to the primary cilium membrane. Biochem Soc Trans 2024; 52:1473-1487. [PMID: 38864436 DOI: 10.1042/bst20231403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024]
Abstract
The primary cilium is a dynamic subcellular compartment templated from the mother centriole or basal body. Cilia are solitary and tiny, but remarkably consequential in cellular pathways regulating proliferation, differentiation, and maintenance. Multiple transmembrane proteins such as G-protein-coupled receptors, channels, enzymes, and membrane-associated lipidated proteins are enriched in the ciliary membrane. The precise regulation of ciliary membrane content is essential for effective signal transduction and maintenance of tissue homeostasis. Surprisingly, a few conserved molecular factors, intraflagellar transport complex A and the tubby family adapter protein TULP3, mediate the transport of most membrane cargoes into cilia. Recent advances in cryogenic electron microscopy provide fundamental insights into these molecular players. Here, we review the molecular players mediating cargo delivery into the ciliary membrane through the lens of structural biology. These mechanistic insights into ciliary transport provide a framework for understanding of disease variants in ciliopathies, enable precise manipulation of cilia-mediated pathways, and provide a platform for the development of targeted therapeutics.
Collapse
Affiliation(s)
- Vivek Reddy Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, U.S.A
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, U.S.A
| |
Collapse
|
9
|
Susa KJ, Bradshaw GA, Eisert RJ, Schilling CM, Kalocsay M, Blacklow SC, Kruse AC. A spatiotemporal map of co-receptor signaling networks underlying B cell activation. Cell Rep 2024; 43:114332. [PMID: 38850533 PMCID: PMC11256977 DOI: 10.1016/j.celrep.2024.114332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/16/2024] [Accepted: 05/23/2024] [Indexed: 06/10/2024] Open
Abstract
The B cell receptor (BCR) signals together with a multi-component co-receptor complex to initiate B cell activation in response to antigen binding. Here, we take advantage of peroxidase-catalyzed proximity labeling combined with quantitative mass spectrometry to track co-receptor signaling dynamics in Raji cells from 10 s to 2 h after BCR stimulation. This approach enables tracking of 2,814 proximity-labeled proteins and 1,394 phosphosites and provides an unbiased and quantitative molecular map of proteins recruited to the vicinity of CD19, the signaling subunit of the co-receptor complex. We detail the recruitment kinetics of signaling effectors to CD19 and identify previously uncharacterized mediators of B cell activation. We show that the glutamate transporter SLC1A1 is responsible for mediating rapid metabolic reprogramming and for maintaining redox homeostasis during B cell activation. This study provides a comprehensive map of BCR signaling and a rich resource for uncovering the complex signaling networks that regulate activation.
Collapse
Affiliation(s)
- Katherine J Susa
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Gary A Bradshaw
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robyn J Eisert
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Charlotte M Schilling
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Marian Kalocsay
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
10
|
Trelford CB, Shepherd TG. LKB1 biology: assessing the therapeutic relevancy of LKB1 inhibitors. Cell Commun Signal 2024; 22:310. [PMID: 38844908 PMCID: PMC11155146 DOI: 10.1186/s12964-024-01689-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024] Open
Abstract
Liver Kinase B1 (LKB1), encoded by Serine-Threonine Kinase 11 (STK11), is a master kinase that regulates cell migration, polarity, proliferation, and metabolism through downstream adenosine monophosphate-activated protein kinase (AMPK) and AMPK-related kinase signalling. Since genetic screens identified STK11 mutations in Peutz-Jeghers Syndrome, STK11 mutants have been implicated in tumourigenesis labelling it as a tumour suppressor. In support of this, several compounds reduce tumour burden through upregulating LKB1 signalling, and LKB1-AMPK agonists are cytotoxic to tumour cells. However, in certain contexts, its role in cancer is paradoxical as LKB1 promotes tumour cell survival by mediating resistance against metabolic and oxidative stressors. LKB1 deficiency has also enhanced the selectivity and cytotoxicity of several cancer therapies. Taken together, there is a need to develop LKB1-specific pharmacological compounds, but prior to developing LKB1 inhibitors, further work is needed to understand LKB1 activity and regulation. However, investigating LKB1 activity is strenuous as cell/tissue type, mutations to the LKB1 signalling pathway, STE-20-related kinase adaptor protein (STRAD) binding, Mouse protein 25-STRAD binding, splicing variants, nucleocytoplasmic shuttling, post-translational modifications, and kinase conformation impact the functional status of LKB1. For these reasons, guidelines to standardize experimental strategies to study LKB1 activity, associate proteins, spliced isoforms, post-translational modifications, and regulation are of upmost importance to the development of LKB1-specific therapies. Therefore, to assess the therapeutic relevancy of LKB1 inhibitors, this review summarizes the importance of LKB1 in cell physiology, highlights contributors to LKB1 activation, and outlines the benefits and risks associated with targeting LKB1.
Collapse
Affiliation(s)
- Charles B Trelford
- The Mary &, John Knight Translational Ovarian Cancer Research Unit, London Regional Cancer Program, 790 Commissioners Road East, Room A4‑921, London, ON, N6A 4L6, Canada.
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
| | - Trevor G Shepherd
- The Mary &, John Knight Translational Ovarian Cancer Research Unit, London Regional Cancer Program, 790 Commissioners Road East, Room A4‑921, London, ON, N6A 4L6, Canada
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Obstetrics and Gynaecology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| |
Collapse
|
11
|
Adamson SE, Hughes JW. Paracrine Signaling by Pancreatic Islet Cilia. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2024; 35:100505. [PMID: 38524256 PMCID: PMC10956557 DOI: 10.1016/j.coemr.2024.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The primary cilium is a sensory and signaling organelle present on most pancreatic islet endocrine cells, where it receives and interprets a wide range of intra-islet chemical cues including hormones, peptides, and neurotransmitters. The ciliary membrane possesses a molecular composition distinct from the plasma membrane, with enrichment of signaling mediators including G protein-coupled receptors (GPCRs), tyrosine kinase family receptors, membrane transporters and others. When activated, these membrane proteins interact with ion channels and adenylyl cyclases to trigger local Ca2+ and cAMP activity and transmit signals to the cell body. Here we review evidence supporting the emerging model in which primary cilia on pancreatic islet cells play a central role in the intra-islet communication network and discuss how changes in cilia-mediated paracrine function in islet cells might lead to diabetes.
Collapse
Affiliation(s)
- Samantha E Adamson
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jing W Hughes
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO, USA
| |
Collapse
|
12
|
Muhamad NA, Masutani K, Furukawa S, Yuri S, Toriyama M, Matsumoto C, Itoh S, Shinagawa Y, Isotani A, Toriyama M, Itoh H. Astrocyte-Specific Inhibition of the Primary Cilium Suppresses C3 Expression in Reactive Astrocyte. Cell Mol Neurobiol 2024; 44:48. [PMID: 38822888 PMCID: PMC11144130 DOI: 10.1007/s10571-024-01482-5] [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] [Received: 11/02/2023] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Abstract
C3-positive reactive astrocytes play a neurotoxic role in various neurodegenerative diseases. However, the mechanisms controlling C3-positive reactive astrocyte induction are largely unknown. We found that the length of the primary cilium, a cellular organelle that receives extracellular signals was increased in C3-positive reactive astrocytes, and the loss or shortening of primary cilium decreased the count of C3-positive reactive astrocytes. Pharmacological experiments suggested that Ca2+ signalling may synergistically promote C3 expression in reactive astrocytes. Conditional knockout (cKO) mice that specifically inhibit primary cilium formation in astrocytes upon drug stimulation exhibited a reduction in the proportions of C3-positive reactive astrocytes and apoptotic cells in the brain even after the injection of lipopolysaccharide (LPS). Additionally, the novel object recognition (NOR) score observed in the cKO mice was higher than that observed in the neuroinflammation model mice. These results suggest that the primary cilium in astrocytes positively regulates C3 expression. We propose that regulating astrocyte-specific primary cilium signalling may be a novel strategy for the suppression of neuroinflammation.
Collapse
Affiliation(s)
- Nor Atiqah Muhamad
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Kohei Masutani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Shota Furukawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Shunsuke Yuri
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Michinori Toriyama
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 1 Gakuenuegahara, Sanda, Hyogo, 669-1330, Japan
| | - Chuya Matsumoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Seiya Itoh
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Yuichiro Shinagawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan
| | - Manami Toriyama
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan.
| | - Hiroshi Itoh
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama Cho, Ikoma, Nara, 630-0192, Japan.
| |
Collapse
|
13
|
Lan Q, Li J, Zhang H, Zhou Z, Fang Y, Yang B. Mechanistic complement of autosomal dominant polycystic kidney disease: the role of aquaporins. J Mol Med (Berl) 2024; 102:773-785. [PMID: 38668786 DOI: 10.1007/s00109-024-02446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/21/2024]
Abstract
Autosomal dominant polycystic kidney disease is a genetic kidney disease caused by mutations in the genes PKD1 or PKD2. Its course is characterized by the formation of progressively enlarged cysts in the renal tubules bilaterally. The basic genetic explanation for autosomal dominant polycystic kidney disease is the double-hit theory, and many of its mechanistic issues can be explained by the cilia doctrine. However, the precise molecular mechanisms underpinning this condition's occurrence are still not completely understood. Experimental evidence suggests that aquaporins, a class of transmembrane channel proteins, including aquaporin-1, aquaporin-2, aquaporin-3, and aquaporin-11, are involved in the mechanism of autosomal dominant polycystic kidney disease. Aquaporins are either a potential new target for the treatment of autosomal dominant polycystic kidney disease, and further study into the physiopathological role of aquaporins in autosomal dominant polycystic kidney disease will assist to clarify the disease's pathophysiology and increase the pool of potential treatment options. We primarily cover pertinent findings on aquaporins in autosomal dominant polycystic kidney disease in this review.
Collapse
Affiliation(s)
- Qiumei Lan
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Jie Li
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Hanqing Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Zijun Zhou
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Yaxuan Fang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Bo Yang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China.
- Department of Nephrology, The First Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, No.88, Changling Road, Xiqing District, Tianjin, 300193, China.
| |
Collapse
|
14
|
Jurisch-Yaksi N, Wachten D, Gopalakrishnan J. The neuronal cilium - a highly diverse and dynamic organelle involved in sensory detection and neuromodulation. Trends Neurosci 2024; 47:383-394. [PMID: 38580512 DOI: 10.1016/j.tins.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Cilia are fascinating organelles that act as cellular antennae, sensing the cellular environment. Cilia gained significant attention in the late 1990s after their dysfunction was linked to genetic diseases known as ciliopathies. Since then, several breakthrough discoveries have uncovered the mechanisms underlying cilia biogenesis and function. Like most cells in the animal kingdom, neurons also harbor cilia, which are enriched in neuromodulatory receptors. Yet, how neuronal cilia modulate neuronal physiology and animal behavior remains poorly understood. By comparing ciliary biology between the sensory and central nervous systems (CNS), we provide new perspectives on the functions of cilia in brain physiology.
Collapse
Affiliation(s)
- Nathalie Jurisch-Yaksi
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Science, Norwegian University of Science and Technology, Erling Skalgssons gate 1, 7491 Trondheim, Norway.
| | - Dagmar Wachten
- Department of Biophysical Imaging, Institute of Innate Immunity, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany; Institute for Human Genetics, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, 07740 Jena, Germany
| |
Collapse
|
15
|
Zhang C, Rehman M, Tian X, Pei SLC, Gu J, Bell TA, Dong K, Tham MS, Cai Y, Wei Z, Behrens F, Jetten AM, Zhao H, Lek M, Somlo S. Glis2 is an early effector of polycystin signaling and a target for therapy in polycystic kidney disease. Nat Commun 2024; 15:3698. [PMID: 38693102 PMCID: PMC11063051 DOI: 10.1038/s41467-024-48025-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 04/15/2024] [Indexed: 05/03/2024] Open
Abstract
Mouse models of autosomal dominant polycystic kidney disease (ADPKD) show that intact primary cilia are required for cyst growth following the inactivation of polycystin-1. The signaling pathways underlying this process, termed cilia-dependent cyst activation (CDCA), remain unknown. Using translating ribosome affinity purification RNASeq on mouse kidneys with polycystin-1 and cilia inactivation before cyst formation, we identify the differential 'CDCA pattern' translatome specifically dysregulated in kidney tubule cells destined to form cysts. From this, Glis2 emerges as a candidate functional effector of polycystin signaling and CDCA. In vitro changes in Glis2 expression mirror the polycystin- and cilia-dependent changes observed in kidney tissue, validating Glis2 as a cell culture-based indicator of polycystin function related to cyst formation. Inactivation of Glis2 suppresses polycystic kidney disease in mouse models of ADPKD, and pharmacological targeting of Glis2 with antisense oligonucleotides slows disease progression. Glis2 transcript and protein is a functional target of CDCA and a potential therapeutic target for treating ADPKD.
Collapse
Affiliation(s)
- Chao Zhang
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Michael Rehman
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xin Tian
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Steven Lim Cho Pei
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jianlei Gu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | | | - Ke Dong
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ming Shen Tham
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yiqiang Cai
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Zemeng Wei
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Felix Behrens
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Anton M Jetten
- Cell Biology Section, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Stefan Somlo
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
16
|
Idevall-Hagren O, Incedal Nilsson C, Sanchez G. Keeping pace: the primary cilium as the conducting baton of the islet. Diabetologia 2024; 67:773-782. [PMID: 38353726 PMCID: PMC10955035 DOI: 10.1007/s00125-024-06096-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/03/2024] [Indexed: 03/21/2024]
Abstract
Primary cilia are rod-like sensory organelles that protrude from the surface of most mammalian cells, including the cells of the islet, and mounting evidence supports important roles of these structures in the regulation of beta cell function and insulin secretion. The sensory abilities of the cilium arise from local receptor activation that is coupled to intrinsic signal transduction, and ciliary signals can propagate into the cell and influence cell function. Here, we review recent advances and studies that provide insights into intra-islet cues that trigger primary cilia signalling; how second messenger signals are generated and propagated within cilia; and how ciliary signalling affects beta cell function. We also discuss the potential involvement of primary cilia and ciliary signalling in the development and progression of type 2 diabetes, identify gaps in our current understanding of islet cell cilia function and provide suggestions on how to further our understanding of this intriguing structure.
Collapse
Affiliation(s)
| | | | - Gonzalo Sanchez
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
17
|
Liu X, Yam PT, Schlienger S, Cai E, Zhang J, Chen WJ, Torres Gutierrez O, Jimenez Amilburu V, Ramamurthy V, Ting AY, Branon TC, Cayouette M, Gen R, Marks T, Kong JH, Charron F, Ge X. Numb positively regulates Hedgehog signaling at the ciliary pocket. Nat Commun 2024; 15:3365. [PMID: 38664376 PMCID: PMC11045789 DOI: 10.1038/s41467-024-47244-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Hedgehog (Hh) signaling relies on the primary cilium, a cell surface organelle that serves as a signaling hub for the cell. Using proximity labeling and quantitative proteomics, we identify Numb as a ciliary protein that positively regulates Hh signaling. Numb localizes to the ciliary pocket and acts as an endocytic adaptor to incorporate Ptch1 into clathrin-coated vesicles, thereby promoting Ptch1 exit from the cilium, a key step in Hh signaling activation. Numb loss impedes Sonic hedgehog (Shh)-induced Ptch1 exit from the cilium, resulting in reduced Hh signaling. Numb loss in spinal neural progenitors reduces Shh-induced differentiation into cell fates reliant on high Hh activity. Genetic ablation of Numb in the developing cerebellum impairs the proliferation of granule cell precursors, a Hh-dependent process, resulting in reduced cerebellar size. This study highlights Numb as a regulator of ciliary Ptch1 levels during Hh signal activation and demonstrates the key role of ciliary pocket-mediated endocytosis in cell signaling.
Collapse
Affiliation(s)
- Xiaoliang Liu
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | - Patricia T Yam
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Sabrina Schlienger
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 0G4, Canada
| | - Eva Cai
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | - Jingyi Zhang
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | - Wei-Ju Chen
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
- Department of Biology, McGill University, Montreal, QC, H3A 0G4, Canada
| | - Oscar Torres Gutierrez
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | | | - Vasanth Ramamurthy
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Alice Y Ting
- Departments of Genetics, of Biology, and by courtesy, of Chemistry, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Tess C Branon
- Departments of Genetics, of Biology, and by courtesy, of Chemistry, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Interline Therapeutics, South San Francisco, CA, USA
| | - Michel Cayouette
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, University of Montreal, Montreal, QC, H3T 1J4, Canada
| | - Risako Gen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Tessa Marks
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Jennifer H Kong
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Frédéric Charron
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada.
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 0G4, Canada.
- Department of Medicine, University of Montreal, Montreal, QC, H3T 1J4, Canada.
| | - Xuecai Ge
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA.
| |
Collapse
|
18
|
Walker MF, Zhang J, Steiner W, Ku PI, Zhu JF, Michaelson Z, Yen YC, Lee A, Long AB, Casey MJ, Poddar A, Nelson IB, Arveseth CD, Nagel F, Clough R, LaPotin S, Kwan KM, Schulz S, Stewart RA, Tesmer JJG, Caspary T, Subramanian R, Ge X, Myers BR. GRK2 Kinases in the Primary Cilium Initiate SMOOTHENED-PKA Signaling in the Hedgehog Cascade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.10.540226. [PMID: 37214942 PMCID: PMC10197709 DOI: 10.1101/2023.05.10.540226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
During Hedgehog (Hh) signal transduction in development and disease, the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO) communicates with GLI transcription factors by binding the protein kinase A catalytic subunit (PKA-C) and physically blocking its enzymatic activity. Here we show that GPCR kinase 2 (GRK2) orchestrates this process during endogenous Hh pathway activation in the vertebrate primary cilium. Upon SMO activation, GRK2 rapidly relocalizes from the ciliary base to the shaft, triggering SMO phosphorylation and PKA-C interaction. Reconstitution studies reveal that GRK2 phosphorylation enables active SMO to bind PKA-C directly. Lastly, the SMO-GRK2-PKA pathway underlies Hh signal transduction in a range of cellular and in vivo models. Thus, GRK2 phosphorylation of ciliary SMO, and the ensuing PKA-C binding and inactivation, are critical initiating events for the intracellular steps in Hh signaling. More broadly, our study suggests an expanded role for GRKs in enabling direct GPCR interactions with diverse intracellular effectors.
Collapse
|
19
|
Rezi CK, Aslanyan MG, Diwan GD, Cheng T, Chamlali M, Junger K, Anvarian Z, Lorentzen E, Pauly KB, Afshar-Bahadori Y, Fernandes EFA, Qian F, Tosi S, Christensen ST, Pedersen SF, Strømgaard K, Russell RB, Miner JH, Mahjoub MR, Boldt K, Roepman R, Pedersen LB. DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.10.566524. [PMID: 37987012 PMCID: PMC10659422 DOI: 10.1101/2023.11.10.566524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney caused ciliary elongation and cystogenesis, and cell-based proximity labelling proteomics and fluorescence microscopy showed alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20 and polycystin-2 (PC2) were reduced in cilia of DLG1 deficient cells compared to control cells. This phenotype was recapitulated in vivo and rescuable by re-expression of wildtype DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggested that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.
Collapse
Affiliation(s)
- Csenge K. Rezi
- Department of Biology, University of Copenhagen, Denmark
| | - Mariam G. Aslanyan
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Gaurav D. Diwan
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Tao Cheng
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | | | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | | | - Esben Lorentzen
- Department of Molecular Biology and Genetics - Protein Science, Aarhus University, Denmark
| | - Kleo B. Pauly
- Department of Biology, University of Copenhagen, Denmark
| | | | - Eduardo F. A. Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sébastien Tosi
- Danish BioImaging Infrastructure Image Analysis Core Facility (DBI-INFRA IACF), University of Copenhagen, Denmark
| | | | | | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Robert B. Russell
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Jeffrey H. Miner
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Moe R. Mahjoub
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | |
Collapse
|
20
|
Niedziółka SM, Datta S, Uśpieński T, Baran B, Skarżyńska W, Humke EW, Rohatgi R, Niewiadomski P. The exocyst complex and intracellular vesicles mediate soluble protein trafficking to the primary cilium. Commun Biol 2024; 7:213. [PMID: 38378792 PMCID: PMC10879184 DOI: 10.1038/s42003-024-05817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 01/15/2024] [Indexed: 02/22/2024] Open
Abstract
The efficient transport of proteins into the primary cilium is a crucial step for many signaling pathways. Dysfunction of this process can lead to the disruption of signaling cascades or cilium assembly, resulting in developmental disorders and cancer. Previous studies on the protein delivery to the cilium were mostly focused on the membrane-embedded receptors. In contrast, how soluble proteins are delivered into the cilium is poorly understood. In our work, we identify the exocyst complex as a key player in the ciliary trafficking of soluble Gli transcription factors. In line with the known function of the exocyst in intracellular vesicle transport, we demonstrate that soluble proteins, including Gli2/3 and Lkb1, can use the endosome recycling machinery for their delivery to the primary cilium. Finally, we identify GTPases: Rab14, Rab18, Rab23, and Arf4 that are involved in vesicle-mediated Gli protein ciliary trafficking. Our data pave the way for a better understanding of ciliary transport and uncover transport mechanisms inside the cell.
Collapse
Affiliation(s)
- S M Niedziółka
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - S Datta
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - T Uśpieński
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - B Baran
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - W Skarżyńska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - E W Humke
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- IGM Biosciences, Inc, Mountain View, CA, USA
| | - R Rohatgi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - P Niewiadomski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
21
|
Bartholow T, Burroughs PW, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Photoproximity Labeling from Single Catalyst Sites Allows Calibration and Increased Resolution for Carbene Labeling of Protein Partners In Vitro and on Cells. ACS CENTRAL SCIENCE 2024; 10:199-208. [PMID: 38292613 PMCID: PMC10823516 DOI: 10.1021/acscentsci.3c01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
The cell surface proteome (surfaceome) plays a pivotal role in virtually all extracellular biology, and yet we are only beginning to understand the protein complexes formed in this crowded environment. Recently, a high-resolution approach (μMap) was described that utilizes multiple iridium-photocatalysts attached to a secondary antibody, directed to a primary antibody of a protein of interest, to identify proximal neighbors by light-activated conversion of a biotin-diazirine to a highly reactive carbene followed by LC/MS (Geri, J. B.; Oakley, J. V.; Reyes-Robles, T.; Wang, T.; McCarver, S. J.; White, C. H.; Rodriguez-Rivera, F. P.; Parker, D. L.; Hett, E. C.; Fadeyi, O. O.; Oslund, R. C.; MacMillan, D. W. C. Science2020, 367, 1091-1097). Here we calibrated the spatial resolution for carbene labeling using site-specific conjugation of a single photocatalyst to a primary antibody drug, trastuzumab (Traz), in complex with its structurally well-characterized oncogene target, HER2. We observed relatively uniform carbene labeling across all amino acids, and a maximum distance of ∼110 Å from the fixed photocatalyst. When targeting HER2 overexpression cells, we identified 20 highly enriched HER2 neighbors, compared to a nonspecific membrane tethered catalyst. These studies identify new HER2 interactors and calibrate the radius of carbene photoprobe labeling for the surfaceome.
Collapse
Affiliation(s)
- Thomas
G. Bartholow
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Paul W.W. Burroughs
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Susanna K. Elledge
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James R. Byrnes
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Lisa L. Kirkemo
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Virginia Garda
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Kevin K. Leung
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
- Department
of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
22
|
Wu JY, Cho SJ, Descant K, Li PH, Shapson-Coe A, Januszewski M, Berger DR, Meyer C, Casingal C, Huda A, Liu J, Ghashghaei T, Brenman M, Jiang M, Scarborough J, Pope A, Jain V, Stein JL, Guo J, Yasuda R, Lichtman JW, Anton ES. Mapping of neuronal and glial primary cilia contactome and connectome in the human cerebral cortex. Neuron 2024; 112:41-55.e3. [PMID: 37898123 PMCID: PMC10841524 DOI: 10.1016/j.neuron.2023.09.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 07/25/2023] [Accepted: 09/22/2023] [Indexed: 10/30/2023]
Abstract
Primary cilia act as antenna receivers of environmental signals and enable effective neuronal or glial responses. Disruption of their function is associated with circuit disorders. To understand the signals these cilia receive, we comprehensively mapped cilia's contacts within the human cortical connectome using serial-section EM reconstruction of a 1 mm3 cortical volume, spanning the entire cortical thickness. We mapped the "contactome" of cilia emerging from neurons and astrocytes in every cortical layer. Depending on the layer and cell type, cilia make distinct patterns of contact. Primary cilia display cell-type- and layer-specific variations in size, shape, and microtubule axoneme core, which may affect their signaling competencies. Neuronal cilia are intrinsic components of a subset of cortical synapses and thus a part of the connectome. This diversity in the structure, contactome, and connectome of primary cilia endows each neuron or glial cell with a unique barcode of access to the surrounding neural circuitry.
Collapse
Affiliation(s)
- Jun Yao Wu
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Su-Ji Cho
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Katherine Descant
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Peter H Li
- Google Research, Mountain View, CA 94043, USA
| | - Alexander Shapson-Coe
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Daniel R Berger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cailyn Meyer
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Cristine Casingal
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ariba Huda
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jiaqi Liu
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tina Ghashghaei
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mikayla Brenman
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Michelle Jiang
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Joseph Scarborough
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Art Pope
- Google Research, Mountain View, CA 94043, USA
| | - Viren Jain
- Google Research, Mountain View, CA 94043, USA
| | - Jason L Stein
- UNC Neuroscience Center and the Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jiami Guo
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA.
| | - Jeff W Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - E S Anton
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| |
Collapse
|
23
|
Turan FB, Ercan ME, Firat-Karalar EN. A Chemically Inducible Organelle Rerouting Assay to Probe Primary Cilium Assembly, Maintenance, and Disassembly in Cultured Cells. Methods Mol Biol 2024; 2725:55-78. [PMID: 37856017 DOI: 10.1007/978-1-0716-3507-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
The primary cilium is a conserved, microtubule-based organelle that protrudes from the surface of most vertebrate cells as well as sensory cells of many organisms. It transduces extracellular chemical and mechanical cues to regulate diverse cellular processes during development and physiology. Loss-of-function studies via RNA interference and CRISPR/Cas9-mediated gene knockouts have been the main tool for elucidating the functions of proteins, protein complexes, and organelles implicated in cilium biology. However, these methods are limited in studying acute spatiotemporal functions of proteins as well as the connection between their cellular positioning and functions. A powerful approach based on inducible recruitment of plus or minus end-directed molecular motors to the protein of interest enables fast and precise control of protein activity in time and in space. In this chapter, we present a chemically inducible heterodimerization method for functional perturbation of centriolar satellites, an emerging membrane-less organelle involved in cilium biogenesis and function. The method we present is based on rerouting of centriolar satellites to the cell center or the periphery in mammalian epithelial cells. We also describe how this method can be applied to study the temporal functions of centriolar satellites during primary cilium assembly, maintenance, and disassembly.
Collapse
Affiliation(s)
- F Basak Turan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - M Erdem Ercan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.
- Koc University School of Medicine, Istanbul, Turkey.
| |
Collapse
|
24
|
Chae S, Park TJ, Kwon T. Convergent differentiation of multiciliated cells. Sci Rep 2023; 13:23028. [PMID: 38155158 PMCID: PMC10754865 DOI: 10.1038/s41598-023-50077-5] [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] [Received: 09/22/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Multiciliated cells (MCCs) are epithelial cells that control body fluid flow and contribute to the clearance of pathogenic microbes and other particles from the airways, egg transport in oviducts, and circulation of cerebrospinal fluid in the central nervous system. Although MCCs have shared functions to control fluid flow via coordinated motility of multiple ciliary structures, they are found in multiple mammalian tissues originating from distinct germ layers and differentiate via distinct developmental pathways. To understand the similarities and differences of MCCs in multiple tissues, we investigated single-cell transcriptome data of nasal epithelial cells, bronchial tubes, fallopian tubes, and ependymal cells in the subventricular zone from humans and mice by cross-species data integration. Expression of cilia-associated genes was indistinguishable between these MCCs, although cell populations had unique properties by the species and tissue, demonstrating that they share the same final differentiation status for ciliary functions. We further analyzed the final differentiation step of MCCs from their distinctive progenitors and confirmed their convergent gene set expression for ciliogenesis at the final step. These results may provide new insight into understanding ciliogenesis during the developmental process.
Collapse
Affiliation(s)
- Shinhyeok Chae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tae Joo Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| |
Collapse
|
25
|
Loukil A, Ebright E, Uezu A, Gao Y, Soderling SH, Goetz SC. Identification of new ciliary signaling pathways in the brain and insights into neurological disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572700. [PMID: 38187761 PMCID: PMC10769350 DOI: 10.1101/2023.12.20.572700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Primary cilia are conserved sensory hubs essential for signaling transduction and embryonic development. Ciliary dysfunction causes a variety of developmental syndromes with neurological features and cognitive impairment, whose basis mostly remains unknown. Despite connections to neural function, the primary cilium remains an overlooked organelle in the brain. Most neurons have a primary cilium; however, it is still unclear how this organelle modulates brain architecture and function, given the lack of any systemic dissection of neuronal ciliary signaling. Here, we present the first in vivo glance at the molecular composition of cilia in the mouse brain. We have adapted in vivo BioID (iBioID), targeting the biotin ligase BioID2 to primary cilia in neurons. We identified tissue-specific signaling networks enriched in neuronal cilia, including Eph/Ephrin and GABA receptor signaling pathways. Our iBioID ciliary network presents a wealth of neural ciliary hits that provides new insights into neurological disorders. Our findings are a promising first step in defining the fundamentals of ciliary signaling and their roles in shaping neural circuits and behavior. This work can be extended to pathological conditions of the brain, aiming to identify the molecular pathways disrupted in the brain cilium. Hence, finding novel therapeutic strategies will help uncover and leverage the therapeutic potential of the neuronal cilium.
Collapse
Affiliation(s)
- Abdelhalim Loukil
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Emma Ebright
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Akiyoshi Uezu
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Yudong Gao
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Sarah C. Goetz
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
26
|
Deretic J, Odabasi E, Firat-Karalar EN. The multifaceted roles of microtubule-associated proteins in the primary cilium and ciliopathies. J Cell Sci 2023; 136:jcs261148. [PMID: 38095645 DOI: 10.1242/jcs.261148] [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: 12/18/2023] Open
Abstract
The primary cilium is a conserved microtubule-based organelle that is critical for transducing developmental, sensory and homeostatic signaling pathways. It comprises an axoneme with nine parallel doublet microtubules extending from the basal body, surrounded by the ciliary membrane. The axoneme exhibits remarkable stability, serving as the skeleton of the cilium in order to maintain its shape and provide tracks to ciliary trafficking complexes. Although ciliary trafficking and signaling have been exhaustively characterized over the years, less is known about the unique structural and functional complexities of the axoneme. Recent work has yielded new insights into the mechanisms by which the axoneme is built with its proper length and architecture, particularly regarding the activity of microtubule-associated proteins (MAPs). In this Review, we first summarize current knowledge about the architecture, composition and specialized compartments of the primary cilium. Next, we discuss the mechanistic underpinnings of how a functional cilium is assembled, maintained and disassembled through the regulation of its axonemal microtubules. We conclude by examining the diverse localizations and functions of ciliary MAPs for the pathobiology of ciliary diseases.
Collapse
Affiliation(s)
- Jovana Deretic
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Ezgi Odabasi
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
- School of Medicine, Koç University, Istanbul 34450, Turkey
| |
Collapse
|
27
|
Hoffmann F, Bolz S, Junger K, Klose F, Stehle IF, Ueffing M, Boldt K, Beyer T. Paralog-specific TTC30 regulation of Sonic hedgehog signaling. Front Mol Biosci 2023; 10:1268722. [PMID: 38074101 PMCID: PMC10701685 DOI: 10.3389/fmolb.2023.1268722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024] Open
Abstract
The intraflagellar transport (IFT) machinery is essential for cilia assembly, maintenance, and trans-localization of signaling proteins. The IFT machinery consists of two large multiprotein complexes, one of which is the IFT-B. TTC30A and TTC30B are integral components of this complex and were previously shown to have redundant functions in the context of IFT, preventing the disruption of IFT-B and, thus, having a severe ciliogenesis defect upon loss of one paralog. In this study, we re-analyzed the paralog-specific protein complexes and discovered a potential involvement of TTC30A or TTC30B in ciliary signaling. Specifically, we investigated a TTC30A-specific interaction with protein kinase A catalytic subunit α, a negative regulator of Sonic hedgehog (Shh) signaling. Defects in this ciliary signaling pathway are often correlated to synpolydactyly, which, intriguingly, is also linked to a rare TTC30 variant. For an in-depth analysis of this unique interaction and the influence on Shh, TTC30A or B single- and double-knockout hTERT-RPE1 were employed, as well as rescue cells harboring wildtype TTC30 or the corresponding mutation. We could show that mutant TTC30A inhibits the ciliary localization of Smoothened. This observed effect is independent of Patched1 but associated with a distinct phosphorylated PKA substrate accumulation upon treatment with forskolin. This rather prominent phenotype was attenuated in mutant TTC30B. Mass spectrometry analysis of wildtype versus mutated TTC30A or TTC30B uncovered differences in protein complex patterns and identified an impaired TTC30A-IFT57 interaction as the possible link leading to synpolydactyly. We could observe no impact on cilia assembly, leading to the hypothesis that a slight decrease in IFT-B binding can be compensated, but mild phenotypes, like synpolydactyly, can be induced by subtle signaling changes. Our systematic approach revealed the paralog-specific influence of TTC30A KO and mutated TTC30A on the activity of PRKACA and the uptake of Smoothened into the cilium, resulting in a downregulation of Shh. This downregulation, combined with interactome alterations, suggests a potential mechanism of how mutant TTC30A is linked to synpolydactyly.
Collapse
Affiliation(s)
- Felix Hoffmann
- Institute for Ophthalmic Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | | | | | | | | | | | | | - Tina Beyer
- *Correspondence: Felix Hoffmann, ; Tina Beyer,
| |
Collapse
|
28
|
Park S, Wang X, Li X, Huang X, Fong KC, Yu C, Tran AA, Scipioni L, Dai Z, Huang L, Shi X. Proximity Labeling Expansion Microscopy (PL-ExM) resolves structure of the interactome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566477. [PMID: 38014020 PMCID: PMC10680661 DOI: 10.1101/2023.11.09.566477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Elucidating the spatial relationships within the protein interactome is pivotal to understanding the organization and regulation of protein-protein interactions. However, capturing the 3D architecture of the interactome presents a dual challenge: precise interactome labeling and super-resolution imaging. To bridge this gap, we present the Proximity Labeling Expansion Microscopy (PL-ExM). This innovation combines proximity labeling (PL) to spatially biotinylate interacting proteins with expansion microscopy (ExM) to increase imaging resolution by physically enlarging cells. PL-ExM unveils intricate details of the 3D interactome's spatial layout in cells using standard microscopes, including confocal and Airyscan. Multiplexing PL-ExM imaging was achieved by pairing the PL with immunofluorescence staining. These multicolor images directly visualize how interactome structures position specific proteins in the protein-protein interaction network. Furthermore, PL-ExM stands out as an assessment method to gauge the labeling radius and efficiency of different PL techniques. The accuracy of PL-ExM is validated by our proteomic results from PL mass spectrometry. Thus, PL-ExM is an accessible solution for 3D mapping of the interactome structure and an accurate tool to access PL quality.
Collapse
|
29
|
Yuan F, Li Y, Zhou X, Meng P, Zou P. Spatially resolved mapping of proteome turnover dynamics with subcellular precision. Nat Commun 2023; 14:7217. [PMID: 37940635 PMCID: PMC10632371 DOI: 10.1038/s41467-023-42861-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
Cellular activities are commonly associated with dynamic proteomic changes at the subcellular level. Although several techniques are available to quantify whole-cell protein turnover dynamics, such measurements often lack sufficient spatial resolution at the subcellular level. Herein, we report the development of prox-SILAC method that combines proximity-dependent protein labeling (APEX2/HRP) with metabolic incorporation of stable isotopes (pulse-SILAC) to map newly synthesized proteins with subcellular spatial resolution. We apply prox-SILAC to investigate proteome dynamics in the mitochondrial matrix and the endoplasmic reticulum (ER) lumen. Our analysis reveals a highly heterogeneous distribution in protein turnover dynamics within macromolecular machineries such as the mitochondrial ribosome and respiratory complexes I-V, thus shedding light on their mechanism of hierarchical assembly. Furthermore, we investigate the dynamic changes of ER proteome when cells are challenged with stress or undergoing stimulated differentiation, identifying subsets of proteins with unique patterns of turnover dynamics, which may play key regulatory roles in alleviating stress or promoting differentiation. We envision that prox-SILAC could be broadly applied to profile protein turnover at various subcellular compartments, under both physiological and pathological conditions.
Collapse
Affiliation(s)
- Feng Yuan
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China
| | - Yi Li
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xinyue Zhou
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China
| | - Peiyuan Meng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Peng Zou
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China.
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China.
- Chinese Institute for Brain Research (CIBR), Beijing, 102206, China.
| |
Collapse
|
30
|
Gopalakrishnan J, Feistel K, Friedrich BM, Grapin‐Botton A, Jurisch‐Yaksi N, Mass E, Mick DU, Müller R, May‐Simera H, Schermer B, Schmidts M, Walentek P, Wachten D. Emerging principles of primary cilia dynamics in controlling tissue organization and function. EMBO J 2023; 42:e113891. [PMID: 37743763 PMCID: PMC10620770 DOI: 10.15252/embj.2023113891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/07/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Primary cilia project from the surface of most vertebrate cells and are key in sensing extracellular signals and locally transducing this information into a cellular response. Recent findings show that primary cilia are not merely static organelles with a distinct lipid and protein composition. Instead, the function of primary cilia relies on the dynamic composition of molecules within the cilium, the context-dependent sensing and processing of extracellular stimuli, and cycles of assembly and disassembly in a cell- and tissue-specific manner. Thereby, primary cilia dynamically integrate different cellular inputs and control cell fate and function during tissue development. Here, we review the recently emerging concept of primary cilia dynamics in tissue development, organization, remodeling, and function.
Collapse
Affiliation(s)
- Jay Gopalakrishnan
- Institute for Human Genetics, Heinrich‐Heine‐UniversitätUniversitätsklinikum DüsseldorfDüsseldorfGermany
| | - Kerstin Feistel
- Department of Zoology, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | | | - Anne Grapin‐Botton
- Cluster of Excellence Physics of Life, TU DresdenDresdenGermany
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at The University Hospital Carl Gustav Carus and Faculty of Medicine of the TU DresdenDresdenGermany
| | - Nathalie Jurisch‐Yaksi
- Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
| | - Elvira Mass
- Life and Medical Sciences Institute, Developmental Biology of the Immune SystemUniversity of BonnBonnGermany
| | - David U Mick
- Center for Molecular Signaling (PZMS), Center of Human and Molecular Biology (ZHMB)Saarland School of MedicineHomburgGermany
| | - Roman‐Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Helen May‐Simera
- Institute of Molecular PhysiologyJohannes Gutenberg‐UniversityMainzGermany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Miriam Schmidts
- Pediatric Genetics Division, Center for Pediatrics and Adolescent MedicineUniversity Hospital FreiburgFreiburgGermany
- CIBSS‐Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
| | - Peter Walentek
- CIBSS‐Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
- Renal Division, Internal Medicine IV, Medical CenterUniversity of FreiburgFreiburgGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical FacultyUniversity of BonnBonnGermany
| |
Collapse
|
31
|
Jung HJ, Dixon EE, Coleman R, Watnick T, Reiter JF, Outeda P, Cebotaru V, Woodward OM, Welling PA. Polycystin-2-dependent transcriptome reveals early response of autosomal dominant polycystic kidney disease. Physiol Genomics 2023; 55:565-577. [PMID: 37720991 PMCID: PMC11178268 DOI: 10.1152/physiolgenomics.00040.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in polycystin genes, Pkd1 and Pkd2, but the underlying pathogenic mechanisms are poorly understood. To identify genes and pathways that operate downstream of polycystin-2 (PC2), a comprehensive gene expression database was created, cataloging changes in the transcriptome immediately following PC2 protein depletion. To explore cyst initiation processes, an immortalized mouse inner medullary collecting duct line was developed with the ability to knock out the Pkd2 gene conditionally. Genome-wide transcriptome profiling was performed using RNA sequencing in the cells immediately after PC2 was depleted and compared with isogenic control cells. Differentially expressed genes were identified, and a bioinformatic analysis pipeline was implemented. Altered expression of candidate cystogenic genes was validated in Pkd2 knockout mice. The expression of nearly 900 genes changed upon PC2 depletion. Differentially expressed genes were enriched for genes encoding components of the primary cilia, the canonical Wnt pathway, and MAPK signaling. Among the PC2-dependent ciliary genes, the transcription factor Glis3 was significantly downregulated. MAPK signaling formed a key node at the epicenter of PC2-dependent signaling networks. Activation of Wnt and MAPK signaling, concomitant with the downregulation of Glis3, was corroborated in Pkd2 knockout mice. The data identify a PC2 cilia-to-nucleus signaling axis and dysregulation of the Gli-similar subfamily of transcription factors as a potential initiator of cyst formation in ADPKD. The catalog of PC2-regulated genes should provide a valuable resource for future ADPKD research and new opportunities for drug development.NEW & NOTEWORTHY Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease. Mutations in polycystin genes cause the disease, but the underlying mechanisms of cystogenesis are unknown. To help fill this knowledge gap, we created an inducible cell model of ADPKD and assembled a catalog of genes that respond in immediate proximity to polycystin-2 depletion using transcriptomic profiling. The catalog unveils a ciliary signaling-to-nucleus axis proximal to polycystin-2 dysfunction, highlighting Glis, Wnt, and MAPK signaling.
Collapse
Affiliation(s)
- Hyun Jun Jung
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Eryn E Dixon
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland, United States
| | - Richard Coleman
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Terry Watnick
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Patricia Outeda
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States
| | - Valeriu Cebotaru
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States
| | - Owen M Woodward
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland, United States
| | - Paul A Welling
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| |
Collapse
|
32
|
Hoi KK, Xia W, Wei MM, Ulloa Navas MJ, Garcia Verdugo JM, Nachury MV, Reiter JF, Fancy SPJ. Primary cilia control oligodendrocyte precursor cell proliferation in white matter injury via Hedgehog-independent CREB signaling. Cell Rep 2023; 42:113272. [PMID: 37858465 PMCID: PMC10715572 DOI: 10.1016/j.celrep.2023.113272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/30/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
Remyelination after white matter injury (WMI) often fails in diseases such as multiple sclerosis because of improper recruitment and repopulation of oligodendrocyte precursor cells (OPCs) in lesions. How OPCs elicit specific intracellular programs in response to a chemically and mechanically diverse environment to properly regenerate myelin remains unclear. OPCs construct primary cilia, specialized signaling compartments that transduce Hedgehog (Hh) and G-protein-coupled receptor (GPCR) signals. We investigated the role of primary cilia in the OPC response to WMI. Removing cilia from OPCs genetically via deletion of Ift88 results in OPCs failing to repopulate WMI lesions because of reduced proliferation. Interestingly, loss of cilia does not affect Hh signaling in OPCs or their responsiveness to Hh signals but instead leads to dysfunctional cyclic AMP (cAMP)-dependent cAMP response element-binding protein (CREB)-mediated transcription. Because inhibition of CREB activity in OPCs reduces proliferation, we propose that a GPCR/cAMP/CREB signaling axis initiated at OPC cilia orchestrates OPC proliferation during development and in response to WMI.
Collapse
Affiliation(s)
- Kimberly K Hoi
- Departments of Neurology and Pediatrics, Division of Neuroimmunology and Glial Biology, Newborn Brain Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wenlong Xia
- Departments of Neurology and Pediatrics, Division of Neuroimmunology and Glial Biology, Newborn Brain Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ming Ming Wei
- Departments of Neurology and Pediatrics, Division of Neuroimmunology and Glial Biology, Newborn Brain Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Maria Jose Ulloa Navas
- Laboratorio de Neurobiología Comparada, Instituto Cavanilles, Universidad de Valencia, CIBERNED, 46980 Paterna, Spain
| | - Jose-Manuel Garcia Verdugo
- Laboratorio de Neurobiología Comparada, Instituto Cavanilles, Universidad de Valencia, CIBERNED, 46980 Paterna, Spain
| | - Maxence V Nachury
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Stephen P J Fancy
- Departments of Neurology and Pediatrics, Division of Neuroimmunology and Glial Biology, Newborn Brain Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
33
|
Ali RQ, Meyer-Miner A, David-Rachel M, Lee FJH, Wilkins BJ, Karpen SJ, Ciruna B, Ghanekar A, Kamath BM. Loss of zebrafish pkd1l1 causes biliary defects that have implications for biliary atresia splenic malformation. Dis Model Mech 2023; 16:dmm049326. [PMID: 37675454 PMCID: PMC10581383 DOI: 10.1242/dmm.049326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/15/2023] [Indexed: 09/08/2023] Open
Abstract
Biliary atresia is a fibroinflammatory neonatal disease with no effective therapies. A subset of cases (10-20%) is associated with laterality defects - labeled biliary atresia splenic malformation (BASM) syndrome. Recently, whole-exome sequencing of patients with BASM identified deleterious variants in PKD1L1. PKD1L1 is involved in left-right axis determination; however, its role in cholangiocytes is unknown. We generated the pkd1l1hsc117 allele using CRISPR/Cas9 mutagenesis in zebrafish to determine the role of Pkd1l1 in biliary development and function. Wild-type and mutant larvae were assessed for laterality defects, biliary function and biliary tree architecture at 5 days post fertilization. pkd1l1hsc117 mutant larvae exhibited early left-right patterning defects. The gallbladder was positioned on the left in 47% of mutants compared to 4% of wild-type larvae. Accumulation of PED6 in the gallbladder, an indicator of hepatobiliary function, was significantly reduced in pkd1l1hsc117 mutants (46%) compared to wild-type larvae (4%). pkd1l1hsc117 larvae exhibited fewer biliary epithelial cells and reduced density of the intrahepatic biliary network compared to those in wild-type larvae. These data highlight the essential role of pkd1l1 in normal development and function of the zebrafish biliary system, supporting a role for this gene as a cause of BASM.
Collapse
Affiliation(s)
- Rouknuddin Q. Ali
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Anne Meyer-Miner
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Marie David-Rachel
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Fiona J. H. Lee
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Saul J. Karpen
- Department of Pediatrics Emory, University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Brian Ciruna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anand Ghanekar
- Division of General Surgery, University Health Network, Toronto, ON M5C 2C4, Canada
- Department of Surgery, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
| | - Binita M. Kamath
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| |
Collapse
|
34
|
Tasaki K, Zhou Z, Ishida Y, Katoh Y, Nakayama K. Compound heterozygous IFT81 variations in a skeletal ciliopathy patient cause Bardet-Biedl syndrome-like ciliary defects. Hum Mol Genet 2023; 32:2887-2900. [PMID: 37427975 DOI: 10.1093/hmg/ddad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023] Open
Abstract
Owing to their crucial roles in development and homeostasis, defects in cilia cause ciliopathies with diverse clinical manifestations. The intraflagellar transport (IFT) machinery, containing the IFT-A and IFT-B complexes, mediates not only the intraciliary bidirectional trafficking but also import and export of ciliary proteins together with the kinesin-2 and dynein-2 motor complexes. The BBSome, containing eight subunits encoded by causative genes of Bardet-Biedl syndrome (BBS), connects the IFT machinery to ciliary membrane proteins to mediate their export from cilia. Although mutations in subunits of the IFT-A and dynein-2 complexes cause skeletal ciliopathies, mutations in some IFT-B subunits are also known to cause skeletal ciliopathies. We here show that compound heterozygous variations of an IFT-B subunit, IFT81, found in a patient with skeletal ciliopathy cause defects in its interactions with other IFT-B subunits, and in ciliogenesis and ciliary protein trafficking when one of the two variants was expressed in IFT81-knockout (KO) cells. Notably, we found that IFT81-KO cells expressing IFT81(Δ490-519), which lacks the binding site for the IFT25-IFT27 dimer, causes ciliary defects reminiscent of those found in BBS cells and those in IFT74-KO cells expressing a BBS variant of IFT74, which forms a heterodimer with IFT81. In addition, IFT81-KO cells expressing IFT81(Δ490-519) in combination with the other variant, IFT81 (L645*), which mimics the cellular conditions of the above skeletal ciliopathy patient, demonstrated essentially the same phenotype as those expressing only IFT81(Δ490-519). Thus, our data indicate that BBS-like defects can be caused by skeletal ciliopathy variants of IFT81.
Collapse
Affiliation(s)
- Koshi Tasaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Zhuang Zhou
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| |
Collapse
|
35
|
Jung M, Zimmermann R. Quantitative Mass Spectrometry Characterizes Client Spectra of Components for Targeting of Membrane Proteins to and Their Insertion into the Membrane of the Human ER. Int J Mol Sci 2023; 24:14166. [PMID: 37762469 PMCID: PMC10532041 DOI: 10.3390/ijms241814166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
To elucidate the redundancy in the components for the targeting of membrane proteins to the endoplasmic reticulum (ER) and/or their insertion into the ER membrane under physiological conditions, we previously analyzed different human cells by label-free quantitative mass spectrometry. The HeLa and HEK293 cells had been depleted of a certain component by siRNA or CRISPR/Cas9 treatment or were deficient patient fibroblasts and compared to the respective control cells by differential protein abundance analysis. In addition to clients of the SRP and Sec61 complex, we identified membrane protein clients of components of the TRC/GET, SND, and PEX3 pathways for ER targeting, and Sec62, Sec63, TRAM1, and TRAP as putative auxiliary components of the Sec61 complex. Here, a comprehensive evaluation of these previously described differential protein abundance analyses, as well as similar analyses on the Sec61-co-operating EMC and the characteristics of the topogenic sequences of the various membrane protein clients, i.e., the client spectra of the components, are reported. As expected, the analysis characterized membrane protein precursors with cleavable amino-terminal signal peptides or amino-terminal transmembrane helices as predominant clients of SRP, as well as the Sec61 complex, while precursors with more central or even carboxy-terminal ones were found to dominate the client spectra of the SND and TRC/GET pathways for membrane targeting. For membrane protein insertion, the auxiliary Sec61 channel components indeed share the client spectra of the Sec61 complex to a large extent. However, we also detected some unexpected differences, particularly related to EMC, TRAP, and TRAM1. The possible mechanistic implications for membrane protein biogenesis at the human ER are discussed and can be expected to eventually advance our understanding of the mechanisms that are involved in the so-called Sec61-channelopathies, resulting from deficient ER protein import.
Collapse
Affiliation(s)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
| |
Collapse
|
36
|
Tanaka Y, Morozumi A, Hirokawa N. Nodal flow transfers polycystin to determine mouse left-right asymmetry. Dev Cell 2023; 58:1447-1461.e6. [PMID: 37413993 DOI: 10.1016/j.devcel.2023.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/30/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Left-dominant [Ca2+]i elevation on the left margin of the ventral node furnishes the initial laterality of mouse embryos. It depends on extracellular leftward fluid flow (nodal flow), fibroblast growth factor receptor (FGFR)/sonic hedgehog (Shh) signaling, and the PKD1L1 polycystin subunit, of which interrelationship is still elusive. Here, we show that leftward nodal flow directs PKD1L1-containing fibrous strands and facilitates Nodal-mediated [Ca2+]i elevation on the left margin. We generate KikGR-PKD1L1 knockin mice in order to monitor protein dynamics with a photoconvertible fluorescence protein tag. By imaging those embryos, we have identified fragile meshwork being gradually transferred leftward involving pleiomorphic extracellular events. A portion of the meshwork finally bridges over the left nodal crown cells in an FGFR/Shh-dependent manner. As PKD1L1 N-term is predominantly associated with Nodal on the left margin and that PKD1L1/PKD2 overexpression significantly augments cellular Nodal sensitivity, we propose that leftward transfer of polycystin-containing fibrous strands determines left-right asymmetry in developing embryos.
Collapse
Affiliation(s)
- Yosuke Tanaka
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Ai Morozumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Nobutaka Hirokawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Juntendo Advanced Research Institute for Health Science, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
| |
Collapse
|
37
|
Clearman KR, Haycraft CJ, Croyle MJ, Collawn JF, Yoder BK. Functions of the primary cilium in the kidney and its connection with renal diseases. Curr Top Dev Biol 2023; 155:39-94. [PMID: 38043952 DOI: 10.1016/bs.ctdb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The nonmotile primary cilium is a sensory structure found on most mammalian cell types that integrates multiple signaling pathways involved in tissue development and postnatal function. As such, mutations disrupting cilia activities cause a group of disorders referred to as ciliopathies. These disorders exhibit a wide spectrum of phenotypes impacting nearly every tissue. In the kidney, primary cilia dysfunction caused by mutations in polycystin 1 (Pkd1), polycystin 2 (Pkd2), or polycystic kidney and hepatic disease 1 (Pkhd1), result in polycystic kidney disease (PKD), a progressive disorder causing renal functional decline and end-stage renal disease. PKD affects nearly 1 in 1000 individuals and as there is no cure for PKD, patients frequently require dialysis or renal transplantation. Pkd1, Pkd2, and Pkhd1 encode membrane proteins that all localize in the cilium. Pkd1 and Pkd2 function as a nonselective cation channel complex while Pkhd1 protein function remains uncertain. Data indicate that the cilium may act as a mechanosensor to detect fluid movement through renal tubules. Other functions proposed for the cilium and PKD proteins in cyst development involve regulation of cell cycle and oriented division, regulation of renal inflammation and repair processes, maintenance of epithelial cell differentiation, and regulation of mitochondrial structure and metabolism. However, how loss of cilia or cilia function leads to cyst development remains elusive. Studies directed at understanding the roles of Pkd1, Pkd2, and Pkhd1 in the cilium and other locations within the cell will be important for developing therapeutic strategies to slow cyst progression.
Collapse
Affiliation(s)
- Kelsey R Clearman
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney J Haycraft
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mandy J Croyle
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bradley K Yoder
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States.
| |
Collapse
|
38
|
Cevik S, Peng X, Beyer T, Pir MS, Yenisert F, Woerz F, Hoffmann F, Altunkaynak B, Pir B, Boldt K, Karaman A, Cakiroglu M, Oner SS, Cao Y, Ueffing M, Kaplan OI. WDR31 displays functional redundancy with GTPase-activating proteins (GAPs) ELMOD and RP2 in regulating IFT complex and recruiting the BBSome to cilium. Life Sci Alliance 2023; 6:e202201844. [PMID: 37208194 PMCID: PMC10200814 DOI: 10.26508/lsa.202201844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023] Open
Abstract
The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caenorhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumulations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into the cilia and exit from the cilia are impacted. Furthermore, anterograde IFT in the middle segment travels at increased speed in wdr-31;rpi-2;elmd-1 Remarkably, a non-ciliary protein leaks into the cilia of wdr-31;rpi-2;elmd-1, possibly because of IFT defects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.
Collapse
Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Xiaoyu Peng
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Tina Beyer
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Ferhan Yenisert
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Franziska Woerz
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Felix Hoffmann
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Betul Altunkaynak
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Betul Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Karsten Boldt
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Asli Karaman
- Science and Advanced Technology Application and Research Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - Miray Cakiroglu
- Science and Advanced Technology Application and Research Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - S Sadik Oner
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
- Science and Advanced Technology Application and Research Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - Ying Cao
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Marius Ueffing
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| |
Collapse
|
39
|
Awoniyi LO, Cunha DM, Sarapulov AV, Hernández-Pérez S, Runsala M, Tejeda-González B, Šuštar V, Balci MÖ, Petrov P, Mattila PK. B cell receptor-induced protein dynamics and the emerging role of SUMOylation revealed by proximity proteomics. J Cell Sci 2023; 136:jcs261119. [PMID: 37417469 PMCID: PMC10445728 DOI: 10.1242/jcs.261119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023] Open
Abstract
Successful B cell activation, which is critical for high-affinity antibody production, is controlled by the B cell antigen receptor (BCR). However, we still lack a comprehensive protein-level view of the very dynamic multi-branched cellular events triggered by antigen binding. Here, we employed APEX2 proximity biotinylation to study antigen-induced changes, 5-15 min after receptor activation, at the vicinity of the plasma membrane lipid rafts, wherein BCR enriches upon activation. The data reveals dynamics of signaling proteins, as well as various players linked to the subsequent processes, such as actin cytoskeleton remodeling and endocytosis. Interestingly, our differential expression analysis identified dynamic responses in various proteins previously not linked to early B cell activation. We demonstrate active SUMOylation at the sites of BCR activation in various conditions and report its functional role in BCR signaling through the AKT and ERK1/2 axes.
Collapse
Affiliation(s)
- Luqman O. Awoniyi
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Diogo M. Cunha
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Alexey V. Sarapulov
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Sara Hernández-Pérez
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Marika Runsala
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Blanca Tejeda-González
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Vid Šuštar
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - M. Özge Balci
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Petar Petrov
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Pieta K. Mattila
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| |
Collapse
|
40
|
Yao Y, Li T, Yu T, Yang X, Wang Y, Cai J, Cheng SY, Liu C, Yue S. Hedgehog signal activates AMPK via Smoothened to promote autophagy and lipid degradation in hepatocytes. Biochem Cell Biol 2023; 101:284-293. [PMID: 36821837 DOI: 10.1139/bcb-2022-0345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Studies in the past decade have shown that lipid droplets stored in liver cells under starvation are encapsulated by autophagosomes and fused to lysosomes via the endocytic system. Autophagy responds to a variety of environmental factors inside and outside the cell, so it has a complex signal regulation network. To this end, we first explored the role of Hedgehog (Hh) in autophagy and lipid metabolism. Treatment of normal mouse liver cells with SAG and GDC-0449 revealed elevated phosphorylation of AMP-activated protein kinase (AMPK) and increased lipidation of LC3. SAG, and GDC-0449 were agonist and antagonist of Smoothened (Smo) in canonical Hh pathway, respectively, but they played a consistent role in the regulation of autophagy in hepatocytes. Moreover, SAG and GDC-0449 did not affect the expression of glioma-associated oncogene (Gli1) and patched 1, suggesting the absence of canonical Hh signaling in hepatocytes. We further knocked down the Smo and found that the effects of SAG and GDC-0449 disappeared, indicating that the non-canonical Smo pathway was involved in the regulation of autophagy in hepatocytes. In addition, SAG and GDC-0449 promoted lipid degradation and inhibited lipid production signals. Knockdown of Smo slowed down the rate of lipid degradation rather than Sufu or Gli1, indicating that Hh signaling regulated the lipid metabolism via Smo. In summary, activates AMPK via Smo to promote autophagy and lipid degradation.
Collapse
Affiliation(s)
- Yixing Yao
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
- Department of Pathology, Suzhou Ninth People's Hospital, Suzhou 215200, China
| | - Tianyuan Li
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Tingting Yu
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Xin Yang
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Yue Wang
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Jing Cai
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Steven Y Cheng
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Chen Liu
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Shen Yue
- Department of Medical Genetics, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| |
Collapse
|
41
|
Bartholow TG, Burroughs P, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Site-specific proximity labeling at single residue resolution for identification of protein partners in vitro and on cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550738. [PMID: 37546992 PMCID: PMC10402114 DOI: 10.1101/2023.07.27.550738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The cell surface proteome, or surfaceome, is encoded by more than 4000 genes, but we are only beginning to understand the complexes they form. Rapid proximity labeling around specific membrane targets allows for capturing weak and transient interactions expected in the crowded and dynamic environment of the surfaceome. Recently, a high-resolution approach called μMap has been described (Geri, J. B., Oakley, J. V., Reyes-Robles, T., Wang, T., McCarver, S. J., White, C. H., Rodriguez-Rivera, F. P., Parker, D. L., Hett, E. C., Fadeyi, O. O., Oslund, R. C., and MacMillan, D. W. C. (2020) Science 367 , 1091-1097) in which an iridium (Ir)-based photocatalyst is attached to a specific antibody to target labeling of neighbors utilizing light-activated generation of carbenes from diazirine compounds via Dexter Energy Transfer (DET). Here we studied and optimized the spatial resolution for the method using an oncoprotein complex between the antibody drug, trastuzumab (Traz), and its target HER2. A set of eight single site-specific Ir-catalytic centers were engineered into Traz to study intra- and inter-molecular labeling in vitro and on cells by mass spectrometry. From this structurally well-characterized complex we observed a maximum distance of ∼110 Å for labeling. Labeling occurred almost uniformly over the full range of amino acids, unlike the residue specific labeling of other techniques. To examine on cell labeling that is specific to HER2 as opposed to simply being on the membrane, we compared the labeling patterns for the eight Traz-catalyst species to random labeling of membrane proteins using a metabolically integrated fatty acid catalyst. Our results identified 20 high confidence HER2 neighbors, many novel, that were more than 6-fold enriched compared to the non-specific membrane tethered catalyst. These studies define distance labeling parameters from single-site catalysts placed directly on the membrane target of interest, and more accurately compare to non-specific labeling to identify membrane complexes with higher confidence.
Collapse
|
42
|
Mill P, Christensen ST, Pedersen LB. Primary cilia as dynamic and diverse signalling hubs in development and disease. Nat Rev Genet 2023; 24:421-441. [PMID: 37072495 PMCID: PMC7615029 DOI: 10.1038/s41576-023-00587-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 04/20/2023]
Abstract
Primary cilia, antenna-like sensory organelles protruding from the surface of most vertebrate cell types, are essential for regulating signalling pathways during development and adult homeostasis. Mutations in genes affecting cilia cause an overlapping spectrum of >30 human diseases and syndromes, the ciliopathies. Given the immense structural and functional diversity of the mammalian cilia repertoire, there is a growing disconnect between patient genotype and associated phenotypes, with variable severity and expressivity characteristic of the ciliopathies as a group. Recent technological developments are rapidly advancing our understanding of the complex mechanisms that control biogenesis and function of primary cilia across a range of cell types and are starting to tackle this diversity. Here, we examine the structural and functional diversity of primary cilia, their dynamic regulation in different cellular and developmental contexts and their disruption in disease.
Collapse
Affiliation(s)
- Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | | | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
43
|
Shim S, Goyal R, Panoutsopoulos AA, Balashova OA, Lee D, Borodinsky LN. Calcium dynamics at the neural cell primary cilium regulate Hedgehog signaling-dependent neurogenesis in the embryonic neural tube. Proc Natl Acad Sci U S A 2023; 120:e2220037120. [PMID: 37252980 PMCID: PMC10266006 DOI: 10.1073/pnas.2220037120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/18/2023] [Indexed: 06/01/2023] Open
Abstract
The balance between neural stem cell proliferation and neuronal differentiation is paramount for the appropriate development of the nervous system. Sonic hedgehog (Shh) is known to sequentially promote cell proliferation and specification of neuronal phenotypes, but the signaling mechanisms responsible for the developmental switch from mitogenic to neurogenic have remained unclear. Here, we show that Shh enhances Ca2+ activity at the neural cell primary cilium of developing Xenopus laevis embryos through Ca2+ influx via transient receptor potential cation channel subfamily C member 3 (TRPC3) and release from intracellular stores in a developmental stage-dependent manner. This ciliary Ca2+ activity in turn antagonizes canonical, proliferative Shh signaling in neural stem cells by down-regulating Sox2 expression and up-regulating expression of neurogenic genes, enabling neuronal differentiation. These discoveries indicate that the Shh-Ca2+-dependent switch in neural cell ciliary signaling triggers the switch in Shh action from canonical-mitogenic to neurogenic. The molecular mechanisms identified in this neurogenic signaling axis are potential targets for the treatment of brain tumors and neurodevelopmental disorders.
Collapse
Affiliation(s)
- Sangwoo Shim
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Raman Goyal
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Alexios A. Panoutsopoulos
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Olga A. Balashova
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - David Lee
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Laura N. Borodinsky
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| |
Collapse
|
44
|
Gerlach GF, Imseis ZH, Cooper SL, Santos AN, O’Brien LL. Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process. Front Cell Dev Biol 2023; 11:1195037. [PMID: 37325559 PMCID: PMC10262054 DOI: 10.3389/fcell.2023.1195037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: The unique architecture of glomerular podocytes is integral to kidney filtration. Interdigitating foot processes extend from the podocyte cell body, wrap around fenestrated capillaries, and form specialized junctional complexes termed slit diaphragms to create a molecular sieve. However, the full complement of proteins which maintain foot process integrity, and how this localized proteome changes with disease, remain to be elucidated. Methods: Proximity-dependent biotin identification (BioID) enables the identification of spatially localized proteomes. To this end, we developed a novel in vivo BioID knock-in mouse model. We utilized the slit diaphragm protein podocin (Nphs2) to create a podocin-BioID fusion. Podocin-BioID localizes to the slit diaphragm, and biotin injection leads to podocyte-specific protein biotinylation. We isolated the biotinylated proteins and performed mass spectrometry to identify proximal interactors. Results and Discussion: Gene ontology analysis of 54 proteins specifically enriched in our podocin-BioID sample revealed 'cell junctions,' 'actin binding,' and 'cytoskeleton organization' as top terms. Known foot process components were identified, and we further uncovered two novel proteins: the tricellular junctional protein Ildr2 and the CDC42 and N-WASP interactor Fnbp1l. We confirmed that Ildr2 and Fnbp1l are expressed by podocytes and partially colocalize with podocin. Finally, we investigated how this proteome changes with age and uncovered a significant increase in Ildr2. This was confirmed by immunofluorescence on human kidney samples and suggests altered junctional composition may preserve podocyte integrity. Together, these assays have led to new insights into podocyte biology and support the efficacy of utilizing BioID in vivo to interrogate spatially localized proteomes in health, aging, and disease.
Collapse
Affiliation(s)
| | | | | | | | - Lori L. O’Brien
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
45
|
Zheng F, Yu C, Zhou X, Zou P. Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome. Nat Commun 2023; 14:2978. [PMID: 37221179 PMCID: PMC10205723 DOI: 10.1038/s41467-023-38565-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 477 mitochondrial proteins with 94% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum (ER). The temporal control of RinID enables pulse-chase labeling of ER proteome in HeLa cells, which reveals substantially higher clearance rate for secreted proteins than ER resident proteins.
Collapse
Affiliation(s)
- Fu Zheng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Chenxin Yu
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Xinyue Zhou
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China.
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
- Chinese Institute for Brain Research (CIBR), Beijing, 102206, China.
| |
Collapse
|
46
|
Gao G, Li X, Jiang Z, Osorio L, Tang YL, Yu X, Jin G, Zhou Z. Isthmin-1 (Ism1) modulates renal branching morphogenesis and mesenchyme condensation during early kidney development. Nat Commun 2023; 14:2378. [PMID: 37185772 PMCID: PMC10130008 DOI: 10.1038/s41467-023-37992-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
The outgrowth of epithelial bud followed by reiterated bifurcations during renal development is driven by the ligand-receptor interactions between the epithelium and the surrounding mesenchyme. Here, by exploring ligand-receptor interactions in E10.5 and E11.5 kidneys by single cell RNA-seq, we find that Isthmin1 (Ism1), a secreted protein, resembles Gdnf expression and modulates kidney branching morphogenesis. Mice deficient for Ism1 exhibit defective ureteric bud bifurcation and impaired metanephric mesenchyme condensation in E11.5 embryos, attributable to the compromised Gdnf/Ret signaling, ultimately leading to renal agenesis and hypoplasia/dysplasia. By HRP-induced proximity labelling, we further identify integrin α8β1 as a receptor of Ism1 in E11.5 kidney and demonstrate that Ism1 promoted cell-cell adhesion through interacting with Integrin α8β1, the receptor whose activation is responsible for Gdnf expression and mesenchyme condensation. Taken together, our work reveals Ism1 as a critical regulator of cell-cell interaction that modulates Gdnf/Ret signaling during early kidney development.
Collapse
Affiliation(s)
- Ge Gao
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, China
- School of Biomedical Sciences, LKS Faculty of medicine, The University of Hong Kong, Hong Kong, China
| | - Xiaoping Li
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, 510630, Guangdong, China
| | - Zhixin Jiang
- School of Biomedical Sciences, LKS Faculty of medicine, The University of Hong Kong, Hong Kong, China
| | - Liliana Osorio
- School of Biomedical Sciences, LKS Faculty of medicine, The University of Hong Kong, Hong Kong, China
| | - Ying Lam Tang
- School of Biomedical Sciences, LKS Faculty of medicine, The University of Hong Kong, Hong Kong, China
| | - Xueqing Yu
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, China
| | - Guoxiang Jin
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, China
| | - Zhongjun Zhou
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, China.
- School of Biomedical Sciences, LKS Faculty of medicine, The University of Hong Kong, Hong Kong, China.
- Reproductive Medical Center, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.
| |
Collapse
|
47
|
Shinde SR, Mick DU, Aoki E, Rodrigues RB, Gygi SP, Nachury MV. The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia. Dev Cell 2023; 58:677-693.e9. [PMID: 37019113 PMCID: PMC10133032 DOI: 10.1016/j.devcel.2023.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/19/2022] [Accepted: 03/07/2023] [Indexed: 04/07/2023]
Abstract
Many G protein-coupled receptors (GPCRs) reside within cilia of mammalian cells and must undergo regulated exit from cilia for the appropriate transduction of signals such as hedgehog morphogens. Lysine 63-linked ubiquitin (UbK63) chains mark GPCRs for regulated removal from cilia, but the molecular basis of UbK63 recognition inside cilia remains elusive. Here, we show that the BBSome-the trafficking complex in charge of retrieving GPCRs from cilia-engages the ancestral endosomal sorting factor target of Myb1-like 2 (TOM1L2) to recognize UbK63 chains within cilia of human and mouse cells. TOM1L2 directly binds to UbK63 chains and the BBSome, and targeted disruption of the TOM1L2/BBSome interaction results in the accumulation of TOM1L2, ubiquitin, and the GPCRs SSTR3, Smoothened, and GPR161 inside cilia. Furthermore, the single-cell alga Chlamydomonas also requires its TOM1L2 ortholog in order to clear ubiquitinated proteins from cilia. We conclude that TOM1L2 broadly enables the retrieval of UbK63-tagged proteins by the ciliary trafficking machinery.
Collapse
Affiliation(s)
- Swapnil Rohidas Shinde
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David U Mick
- Center of Human and Molecular Biology and Center for Molecular Signaling, Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - Erika Aoki
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rachel B Rodrigues
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Maxence V Nachury
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
48
|
Elliott KH, Balchand SK, Bonatto Paese CL, Chang CF, Yang Y, Brown KM, Rasicci DT, He H, Thorner K, Chaturvedi P, Murray SA, Chen J, Porollo A, Peterson KA, Brugmann SA. Identification of a heterogeneous and dynamic ciliome during embryonic development and cell differentiation. Development 2023; 150:dev201237. [PMID: 36971348 PMCID: PMC10163354 DOI: 10.1242/dev.201237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
Primary cilia are nearly ubiquitous organelles that transduce molecular and mechanical signals. Although the basic structure of the cilium and the cadre of genes that contribute to ciliary formation and function (the ciliome) are believed to be evolutionarily conserved, the presentation of ciliopathies with narrow, tissue-specific phenotypes and distinct molecular readouts suggests that an unappreciated heterogeneity exists within this organelle. Here, we provide a searchable transcriptomic resource for a curated primary ciliome, detailing various subgroups of differentially expressed genes within the ciliome that display tissue and temporal specificity. Genes within the differentially expressed ciliome exhibited a lower level of functional constraint across species, suggesting organism and cell-specific function adaptation. The biological relevance of ciliary heterogeneity was functionally validated by using Cas9 gene-editing to disrupt ciliary genes that displayed dynamic gene expression profiles during osteogenic differentiation of multipotent neural crest cells. Collectively, this novel primary cilia-focused resource will allow researchers to explore longstanding questions related to how tissue and cell-type specific functions and ciliary heterogeneity may contribute to the range of phenotypes associated with ciliopathies.
Collapse
Affiliation(s)
- Kelsey H. Elliott
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Sai K. Balchand
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Christian Louis Bonatto Paese
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Ching-Fang Chang
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Yanfen Yang
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Kari M. Brown
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | | | - Hao He
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Konrad Thorner
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | - Praneet Chaturvedi
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | | | - Jing Chen
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | - Aleksey Porollo
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | | | - Samantha A. Brugmann
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| |
Collapse
|
49
|
Kubo S, Black CS, Joachimiak E, Yang SK, Legal T, Peri K, Khalifa AAZ, Ghanaeian A, McCafferty CL, Valente-Paterno M, De Bellis C, Huynh PM, Fan Z, Marcotte EM, Wloga D, Bui KH. Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins. Nat Commun 2023; 14:2168. [PMID: 37061538 PMCID: PMC10105768 DOI: 10.1038/s41467-023-37868-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 42 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation.
Collapse
Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Corbin S Black
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Shun Kai Yang
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Thibault Legal
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Katya Peri
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Ahmad Abdelzaher Zaki Khalifa
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Avrin Ghanaeian
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Caitlyn L McCafferty
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Melissa Valente-Paterno
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Chelsea De Bellis
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Phuong M Huynh
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Zhe Fan
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093, Warsaw, Poland.
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada.
| |
Collapse
|
50
|
Susa KJ, Bradshaw GA, Eisert RJ, Schilling CM, Kalocsay M, Blacklow SC, Kruse AC. A Spatiotemporal Map of Co-Receptor Signaling Networks Underlying B Cell Activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533227. [PMID: 36993395 PMCID: PMC10055206 DOI: 10.1101/2023.03.17.533227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The B cell receptor (BCR) signals together with a multi-component co-receptor complex to initiate B cell activation in response to antigen binding. This process underlies nearly every aspect of proper B cell function. Here, we take advantage of peroxidase-catalyzed proximity labeling combined with quantitative mass spectrometry to track B cell co-receptor signaling dynamics from 10 seconds to 2 hours after BCR stimulation. This approach enables tracking of 2,814 proximity-labeled proteins and 1,394 quantified phosphosites and provides an unbiased and quantitative molecular map of proteins recruited to the vicinity of CD19, the key signaling subunit of the co-receptor complex. We detail the recruitment kinetics of essential signaling effectors to CD19 following activation, and then identify new mediators of B cell activation. In particular, we show that the glutamate transporter SLC1A1 is responsible for mediating rapid metabolic reprogramming immediately downstream of BCR stimulation and for maintaining redox homeostasis during B cell activation. This study provides a comprehensive map of the BCR signaling pathway and a rich resource for uncovering the complex signaling networks that regulate B cell activation.
Collapse
Affiliation(s)
- Katherine J. Susa
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Current address: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Gary A. Bradshaw
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robyn J. Eisert
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Charlotte M. Schilling
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Marian Kalocsay
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Lead contact
| |
Collapse
|