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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.
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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
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2
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Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter JF, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nat Struct Mol Biol 2024; 31:667-677. [PMID: 38326651 PMCID: PMC11221913 DOI: 10.1038/s41594-024-01223-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
The orphan G protein-coupled receptor (GPCR) GPR161 plays a central role in development by suppressing Hedgehog signaling. The fundamental basis of how GPR161 is activated remains unclear. Here, we determined a cryogenic-electron microscopy structure of active human GPR161 bound to heterotrimeric Gs. This structure revealed an extracellular loop 2 that occupies the canonical GPCR orthosteric ligand pocket. Furthermore, a sterol that binds adjacent to transmembrane helices 6 and 7 stabilizes a GPR161 conformation required for Gs coupling. Mutations that prevent sterol binding to GPR161 suppress Gs-mediated signaling. These mutants retain the ability to suppress GLI2 transcription factor accumulation in primary cilia, a key function of ciliary GPR161. By contrast, a protein kinase A-binding site in the GPR161 C terminus is critical in suppressing GLI2 ciliary accumulation. Our work highlights how structural features of GPR161 interface with the Hedgehog pathway and sets a foundation to understand the role of GPR161 function in other signaling pathways.
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Affiliation(s)
- Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Simone Harrison
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ziwei Chen
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
| | - Masha Karelina
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vivek R Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samuel P Berry
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Philipp Tschaikner
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Dominik Regele
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Douglas F Covey
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ron O Dror
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Alex S Evers
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
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3
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Kim SE, Kim HY, Wlodarczyk BJ, Finnell RH. The novel linkage between Fuz and Gpr161 genes regulates sonic hedgehog signaling during mouse embryonic development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575263. [PMID: 38260275 PMCID: PMC10802560 DOI: 10.1101/2024.01.11.575263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Sonic hedgehog (Shh) signaling regulates embryonic morphogenesis utilizing primary cilia, the cell antenna acting as a signaling hub. Fuz, an effector of planar cell polarity (PCP) signaling, involves Shh signaling via cilia formation, while the G protein-coupled receptor 161 (Gpr161) is a negative regulator of Shh signaling. The range of phenotypic malformations observed in mice bearing mutations in either of these two genes is similar; however, their functional relations have not been previously explored. This study identified the genetic and biochemical link between Fuz and Gpr161 in mouse embryonic development. Fuz was genetically epistatic to Gpr161 via Shh signaling during mouse embryonic development. The FUZ biochemically interacted with GPR161, and Fuz regulated Gpr161 ciliary trafficking via β-arrestin2. Our study suggested the novel Gpr161-Fuz axis that regulates Shh signaling during mouse embryonic development.
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Affiliation(s)
- Sung-Eun Kim
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin/Dell Medical School, Austin, TX, 78723, USA
| | | | - Bogdan J. Wlodarczyk
- Departments of Molecular and Cellular Biology, Molecular and Human Genetics, and Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard H. Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin/Dell Medical School, Austin, TX, 78723, USA
- Departments of Molecular and Cellular Biology, Molecular and Human Genetics, and Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
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4
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Azzarà A, Cassano I, Lintas C, Bernardini L, Pilato F, Capone F, Di Lazzaro V, Gurrieri F. A new gene for autosomal dominant facial palsy/migraine identified in a family by whole exome sequencing. Eur J Neurol 2024; 31:e16088. [PMID: 37823721 PMCID: PMC11235676 DOI: 10.1111/ene.16088] [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: 03/09/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Facial palsy manifests as unilateral or bilateral weakness and inability to move some of the facial muscles. The aetiology may be different including idiopathic, trauma, infections or brain tumours or it can be associated with chronic neurological diseases. For instance, in recurrent migraine, an increased risk of idiopathic facial palsy (often unilateral) has been observed. Migraine is a neurovascular disorder characterized by mild to severe intensity of headaches, often associated with neuro-ophthalmological symptoms. METHODS A family is reported where five members were affected by facial palsy associated with other clinical features including migraine, diplopia, facial swelling, eye conjunctivitis following a vertical transmission. Whole exome sequencing was performed in three members (two affected and one healthy) in order to identify potential variants causative of their phenotype. RESULTS A missense variant c.304G>A was found leading to the p.(Ala102Thr) substitution in the TRPM8 gene, previously related to migraine by genome wide association studies. This variant was classified as deleterious by several predictor tools, and the mutant residue was predicted to alter the protein structure in terms of flexibility and interactions with the surrounding residues. CONCLUSION These findings suggest that TRPM8 could be a new causative gene further linking migraine and recurrent facial palsy.
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Affiliation(s)
- Alessia Azzarà
- Research Unit of Medical Genetics, Department of Medicine and SurgeryUniversità Campus Bio‐Medico di RomaRomeItaly
| | - Ilaria Cassano
- Research Unit of Medical Genetics, Department of Medicine and SurgeryUniversità Campus Bio‐Medico di RomaRomeItaly
| | - Carla Lintas
- Research Unit of Medical Genetics, Department of Medicine and SurgeryUniversità Campus Bio‐Medico di RomaRomeItaly
- Operative Research Unit of Medical GeneticsFondazione Policlinico Universitario Campus Bio‐MedicoRomeItaly
| | | | - Fabio Pilato
- Department of Medicine and Surgery, Unit of Neurology, Neurophysiology, Neurobiology and PsichiatryUniversità Campus Bio‐Medico di RomaRomaItaly
- Fondazione Policlinico Universitario Campus Bio‐MedicoRomaItaly
| | - Fioravante Capone
- Department of Medicine and Surgery, Unit of Neurology, Neurophysiology, Neurobiology and PsichiatryUniversità Campus Bio‐Medico di RomaRomaItaly
- Fondazione Policlinico Universitario Campus Bio‐MedicoRomaItaly
| | - Vincenzo Di Lazzaro
- Department of Medicine and Surgery, Unit of Neurology, Neurophysiology, Neurobiology and PsichiatryUniversità Campus Bio‐Medico di RomaRomaItaly
- Fondazione Policlinico Universitario Campus Bio‐MedicoRomaItaly
| | - Fiorella Gurrieri
- Research Unit of Medical Genetics, Department of Medicine and SurgeryUniversità Campus Bio‐Medico di RomaRomeItaly
- Operative Research Unit of Medical GeneticsFondazione Policlinico Universitario Campus Bio‐MedicoRomeItaly
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5
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Kim SE, Chothani PJ, Shaik R, Pollard W, Finnell RH. Pax3 lineage-specific deletion of Gpr161 is associated with spinal neural tube and craniofacial malformations during embryonic development. Dis Model Mech 2023; 16:dmm050277. [PMID: 37885410 PMCID: PMC10694864 DOI: 10.1242/dmm.050277] [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: 05/02/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Sonic hedgehog (Shh) signaling is the morphogen signaling that regulates embryonic craniofacial and neural tube development. G protein-coupled receptor 161 (Gpr161) is a negative regulator of Shh signaling, and its inactivation in mice results in embryo lethality associated with craniofacial defects and neural tube defects. However, the structural defects of later embryonic stages and cell lineages underlying abnormalities have not been well characterized due to the limited lifespan of Gpr161 null mice. We found that embryos with Pax3 lineage-specific deletion of Gpr161 presented with tectal hypertrophy (anterior dorsal neuroepithelium), cranial vault and facial bone hypoplasia (cranial neural crest), vertebral abnormalities (somite) and the closed form of spina bifida (posterior dorsal neuroepithelium). In particular, the closed form of spina bifida was partly due to reduced Pax3 and Cdx4 gene expression in the posterior dorsal neural tubes of Gpr161 mutant embryos with decreased Wnt signaling, whereas Shh signaling was increased. We describe a previously unreported role for Gpr161 in the development of posterior neural tubes and confirm its role in cranial neural crest- and somite-derived skeletogenesis and midbrain morphogenesis in mice.
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Affiliation(s)
- Sung-Eun Kim
- Department of Pediatrics, Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78723, USA
| | - Pooja J. Chothani
- Department of Pediatrics, Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78723, USA
| | - Rehana Shaik
- Department of Pediatrics, Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78723, USA
| | - Westley Pollard
- Department of Pediatrics, Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78723, USA
| | - Richard H. Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78723, USA
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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6
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Kim SE, Chothani PJ, Shaik R, Pollard W, Finnell RH. Pax3 lineage-specific deletion of Gpr161 is associated with spinal neural tube and craniofacial malformations during embryonic development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548129. [PMID: 37461574 PMCID: PMC10350067 DOI: 10.1101/2023.07.07.548129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Shh signaling is the morphogen signaling that regulates embryonic craniofacial and neural tube development. G protein-coupled receptor 161 (Gpr161) is a negative regulator of Shh signaling, and its inactivation in mice results in embryo lethality with craniofacial and neural tube defects (NTDs). However, the structural defects of later embryonic stages in Gpr161 null mice and cell lineages underlying abnormalities were not well characterized due to their limited lifespan. We found the Pax3 lineage-specific deletion of Gpr161 in mice presented with tectal hypertrophy (anterior dorsal neuroepithelium), cranial vault and facial bone hypoplasia (cranial neural crest (CNC)), vertebral abnormalities (somite), and the closed form of spina bifida (posterior dorsal neuroepithelium). In particular, the closed form of spina bifida is partly due to the reduced Pax3 and Cdx4 gene expression of the posterior dorsal neural tubes of Gpr161 mutant embryos involving decreased Wnt signaling whereas Shh signaling was increased. This study provides the novel role of Gpr161 in the posterior neural tube development and confirms its role on CNC- and somite-derived skeletogenesis and midbrain morphogenesis in mice.
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7
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Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter J, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.540554. [PMID: 37292845 PMCID: PMC10245861 DOI: 10.1101/2023.05.23.540554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The orphan G protein-coupled receptor (GPCR) GPR161 is enriched in primary cilia, where it plays a central role in suppressing Hedgehog signaling1. GPR161 mutations lead to developmental defects and cancers2,3,4. The fundamental basis of how GPR161 is activated, including potential endogenous activators and pathway-relevant signal transducers, remains unclear. To elucidate GPR161 function, we determined a cryogenic-electron microscopy structure of active GPR161 bound to the heterotrimeric G protein complex Gs. This structure revealed an extracellular loop 2 that occupies the canonical GPCR orthosteric ligand pocket. Furthermore, we identify a sterol that binds to a conserved extrahelical site adjacent to transmembrane helices 6 and 7 and stabilizes a GPR161 conformation required for Gs coupling. Mutations that prevent sterol binding to GPR161 suppress cAMP pathway activation. Surprisingly, these mutants retain the ability to suppress GLI2 transcription factor accumulation in cilia, a key function of ciliary GPR161 in Hedgehog pathway suppression. By contrast, a protein kinase A-binding site in the GPR161 C-terminus is critical in suppressing GLI2 ciliary accumulation. Our work highlights how unique structural features of GPR161 interface with the Hedgehog pathway and sets a foundation to understand the broader role of GPR161 function in other signaling pathways.
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Affiliation(s)
- Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Simone Harrison
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ziwei Chen
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Taylor Institute for Innovative Psychiatric Research, St. Louis, MO 63110, USA
| | - Masha Karelina
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vivek R. Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samuel P. Berry
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Philipp Tschaikner
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck; Tyrolean Cancer Research Institute (TKFI), Innsbruck 6020, Austria
| | - Dominik Regele
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| | - Douglas F. Covey
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Taylor Institute for Innovative Psychiatric Research, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck; Tyrolean Cancer Research Institute (TKFI), Innsbruck 6020, Austria
| | - Debora S. Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeremy Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94158
| | - Ron O. Dror
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Alex S. Evers
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Taylor Institute for Innovative Psychiatric Research, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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8
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Yan L, Yin H, Mi Y, Wu Y, Zheng Y. Deficiency of Wdr60 and Wdr34 cause distinct neural tube malformation phenotypes in early embryos. Front Cell Dev Biol 2023; 11:1084245. [PMID: 37228654 PMCID: PMC10203710 DOI: 10.3389/fcell.2023.1084245] [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: 11/02/2022] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Cilia are specialized organelles that extend from plasma membrane, functioning as antennas for signal transduction and are involved in embryonic morphogenesis. Dysfunction of cilia lead to many developmental defects, including neural tube defects (NTDs). Heterodimer WDR60-WDR34 (WD repeat domain 60 and 34) are intermediate chains of motor protein dynein-2, which play important roles in ciliary retrograde transport. It has been reported that disruption of Wdr34 in mouse model results in NTDs and defects of Sonic Hedgehog (SHH) signaling. However, no Wdr60 deficiency mouse model has been reported yet. In this study, piggyBac (PB) transposon is used to interfere Wdr60 and Wdr34 expression respectively to establish Wdr60 PB/PB and Wdr34 PB/PB mouse models. We found that the expression of Wdr60 or Wdr34 is significantly decreased in the homozygote mice. Wdr60 homozygote mice die around E13.5 to E14.5, while Wdr34 homozygote mice die around E10.5 to E11.5. WDR60 is highly expressed in the head region at E10.5 and Wdr60 PB/PB embryos have head malformation. RNAseq and qRT-PCR experiments revealed that Sonic Hedgehog signaling is also downregulated in Wdr60 PB/PB head tissue, demonstrating that WDR60 is also required for promoting SHH signaling. Further experiments on mouse embryos also revealed that the expression levels of planar cell polarity (PCP) components such as CELSR1 and downstream signal molecule c-Jun were downregulated in WDR34 homozygotes compared to wildtype littermates. Coincidently, we observed much higher ratio of open cranial and caudal neural tube in Wdr34 PB/PB mice. CO-IP experiment showed that WDR60 and WDR34 both interact with IFT88, but only WDR34 interacts with IFT140. Taken together, WDR60 and WDR34 play overlapped and distinct functions in modulating neural tube development.
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Affiliation(s)
- Lu Yan
- Obstetrics and Gynecology Hospital, The Institute of Obstetrics and Gynecology, Fudan University, Shanghai, China
- Department of Cellular and Developmental Biology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hailing Yin
- Obstetrics and Gynecology Hospital, The Institute of Obstetrics and Gynecology, Fudan University, Shanghai, China
- Obstetrics Department of the First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yiwei Mi
- Department of Cellular and Developmental Biology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Wu
- Department of Cellular and Developmental Biology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yufang Zheng
- Obstetrics and Gynecology Hospital, The Institute of Obstetrics and Gynecology, Fudan University, Shanghai, China
- Department of Cellular and Developmental Biology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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9
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Cilia and their role in neural tube development and defects. REPRODUCTIVE AND DEVELOPMENTAL MEDICINE 2022. [DOI: 10.1097/rd9.0000000000000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Wang C, Seltzsam S, Zheng B, Wu CHW, Nicolas-Frank C, Yousef K, Au KS, Mann N, Pantel D, Schneider S, Schierbaum L, Kitzler TM, Connaughton DM, Mao Y, Dai R, Nakayama M, Kari JA, El Desoky S, Shalaby M, Eid LA, Awad HS, Tasic V, Mane SM, Lifton RP, Baum MA, Shril S, Estrada CR, Hildebrandt F. Whole exome sequencing identifies potential candidate genes for spina bifida derived from mouse models. Am J Med Genet A 2022; 188:1355-1367. [PMID: 35040250 PMCID: PMC8995376 DOI: 10.1002/ajmg.a.62644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Spina bifida (SB) is the second most common nonlethal congenital malformation. The existence of monogenic SB mouse models and human monogenic syndromes with SB features indicate that human SB may be caused by monogenic genes. We hypothesized that whole exome sequencing (WES) allows identification of potential candidate genes by (i) generating a list of 136 candidate genes for SB, and (ii) by unbiased exome-wide analysis. We generated a list of 136 potential candidate genes from three categories and evaluated WES data of 50 unrelated SB cases for likely deleterious variants in 136 potential candidate genes, and for potential SB candidate genes exome-wide. We identified 6 likely deleterious variants in 6 of the 136 potential SB candidate genes in 6 of the 50 SB cases, whereof 4 genes were derived from mouse models, 1 gene was derived from human nonsyndromic SB, and 1 gene was derived from candidate genes known to cause human syndromic SB. In addition, by unbiased exome-wide analysis, we identified 12 genes as potential candidates for SB. Identification of these 18 potential candidate genes in larger SB cohorts will help decide which ones can be considered as novel monogenic causes of human SB.
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Affiliation(s)
- Chunyan Wang
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bixia Zheng
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chen-Han Wilfred Wu
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Departments of Urology and Genetics, Case Western Reserve University and University Hospitals, Cleveland, Ohio, USA
| | - Camille Nicolas-Frank
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kirollos Yousef
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Nina Mann
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dalia Pantel
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Sophia Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Schierbaum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas M Kitzler
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dervla M Connaughton
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Youying Mao
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rufeng Dai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Makiko Nakayama
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jameela A Kari
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohammed Shalaby
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos R Estrada
- Department of Urology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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11
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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Proc Natl Acad Sci U S A 2021; 118:2106844118. [PMID: 34916285 PMCID: PMC8713748 DOI: 10.1073/pnas.2106844118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids much of the bias inherent in candidate gene searches that are pervasive in the field. We examine both protein coding and noncoding regions of whole genomes to analyze sequence variants, collapsed by gene or regulatory region, and apply machine learning, gene enrichment, and pathway analyses to elucidate molecular pathways and genes contributing to human SB. Spina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance, and environmental influences that hamper genome-wide association studies approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases versus controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation, and essential transcriptional regulation consistent with their having impact on the pathogenesis of human SB. Additionally, an interrogation of conserved noncoding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to the interrogation of coding and noncoding sequence variant contributions to rare complex genetic disorders.
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12
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Kim SE, Robles-Lopez K, Cao X, Liu K, Chothani PJ, Bhavani N, Rahman L, Mukhopadhyay S, Wlodarczyk BJ, Finnell RH. Wnt1 Lineage Specific Deletion of Gpr161 Results in Embryonic Midbrain Malformation and Failure of Craniofacial Skeletal Development. Front Genet 2021; 12:761418. [PMID: 34887903 PMCID: PMC8650154 DOI: 10.3389/fgene.2021.761418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Sonic hedgehog (Shh) signaling regulates multiple morphogenetic processes during embryonic neurogenesis and craniofacial skeletal development. Gpr161 is a known negative regulator of Shh signaling. Nullizygous Gpr161 mice are embryonic lethal, presenting with structural defects involving the neural tube and the craniofacies. However, the lineage specific role of Gpr161 in later embryonic development has not been thoroughly investigated. We studied the Wnt1-Cre lineage specific role of Gpr161 during mouse embryonic development. We observed three major gross morphological phenotypes in Gpr161 cKO (Gpr161 f/f; Wnt1-Cre) fetuses; protrusive tectum defect, encephalocele, and craniofacial skeletal defect. The overall midbrain tissues were expanded and cell proliferation in ventricular zones of midbrain was increased in Gpr161 cKO fetuses, suggesting that protrusive tectal defects in Gpr161 cKO are secondary to the increased proliferation of midbrain neural progenitor cells. Shh signaling activity as well as upstream Wnt signaling activity were increased in midbrain tissues of Gpr161 cKO fetuses. RNA sequencing further suggested that genes in the Shh, Wnt, Fgf and Notch signaling pathways were differentially regulated in the midbrain of Gpr161 cKO fetuses. Finally, we determined that cranial neural crest derived craniofacial bone formation was significantly inhibited in Gpr161 cKO fetuses, which partly explains the development of encephalocele. Our results suggest that Gpr161 plays a distinct role in midbrain development and in the formation of the craniofacial skeleton during mouse embryogenesis.
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Affiliation(s)
- Sung-Eun Kim
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX, United States
| | - Karla Robles-Lopez
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX, United States.,Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Xuanye Cao
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Kristyn Liu
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX, United States
| | - Pooja J Chothani
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX, United States
| | - Nikitha Bhavani
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX, United States
| | - Lauren Rahman
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX, United States
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Bogdan J Wlodarczyk
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Richard H Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX, United States.,Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States.,Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX, United States
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13
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Chou CH, Wang HK, Lin YC, Tsai DH, Lu MT, Ho CT, Hseu YC, Yang HL, Way TD. Bisdemethoxycurcumin Promotes Apoptosis and Inhibits the Epithelial-Mesenchymal Transition through the Inhibition of the G-Protein-Coupled Receptor 161/Mammalian Target of Rapamycin Signaling Pathway in Triple Negative Breast Cancer Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14557-14567. [PMID: 34813306 DOI: 10.1021/acs.jafc.1c05585] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Triple negative breast cancer (TNBC) is one of the leading causes of cancer death in the world and lacks an effective targeted therapy. G-protein-coupled receptor 161 (GPR161) has been demonstrated to perform the functional regulations on TNBC progression and might be a potential new target for TNBC therapy. This study showed the effects of bisdemethoxycurcumin (BDMC) on GPR161 regulation, indicating that BDMC effectively inhibited GPR161 expression and downregulated GPR161-driven signaling. BDMC showed the potent inhibitory effects on TNBC proliferation through suppressing GPR161-mediated mammalian target of rapamycin (mTOR)/70 kDa ribosomal protein S6 kinase (p70S6K) activation. Besides, in this study, we discover the mechanism of GPR161-driven TNBC metastasis, linking to GPR161-mediated twist-related protein 1 (Twist1)/matrix metallopeptidase 9 (MMP9) contributing to the epithelial-mesenchymal transition (EMT). BDMC effectively repressed GPR161-mediated TNBC metastasis via inhibiting Twist1/MMP9-induced EMT. The three-dimensional invasion assay also showed that BDMC significantly inhibited TNBC invasion. The combination treatment of BDMC and rapamycin enhanced the inhibition of TNBC proliferation and metastasis through increasing the blockage of mTOR activation. Furthermore, this study also observed that BDMC activated the caspase 3/9 signaling pathway to induce TNBC apoptosis. Therefore, BDMC could be applicable to anticancer therapy, especially targeting on the GPR161-driven cancer type.
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Affiliation(s)
- Chun-Hung Chou
- Ph.D. Program for Biotechnology Industry, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
| | - Hao-Kuang Wang
- Department of Neurosurgery, E-Da Hospital/I-Shou University, Kaohsiung 84001, Taiwan
- School of Medicine, I-Shou University, Kaohsiung 84001, Taiwan
| | - Ying-Chao Lin
- Division of Neurosurgery, Buddhist Tzu Chi General Hospital, Taichung Branch, Taichung 427, Taiwan
- School of Medicine, Tzu Chi University, Hualien 970, Taiwan
- Department of Medical Imaging and Radiological Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan
| | - Dai-Hua Tsai
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Meng-Tien Lu
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chi-Tang Ho
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - You-Cheng Hseu
- Department of Cosmeceutics, College of Pharmacy, China Medical University, Taichung 406040, Taiwan
| | - Hsin-Ling Yang
- Institute of Nutrition, College of Health Care, China Medical University, Taichung 406040, Taiwan
| | - Tzong-Der Way
- Ph.D. Program for Biotechnology Industry, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
- Department of Health and Nutrition Biotechnology, College of Health Science, Asia University, Taichung 41354, Taiwan
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14
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Hwang SH, Somatilaka BN, White K, Mukhopadhyay S. Ciliary and extraciliary Gpr161 pools repress hedgehog signaling in a tissue-specific manner. eLife 2021; 10:67121. [PMID: 34346313 PMCID: PMC8378848 DOI: 10.7554/elife.67121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
The role of compartmentalized signaling in primary cilia during tissue morphogenesis is not well understood. The cilia localized G protein-coupled receptor, Gpr161, represses hedgehog pathway via cAMP signaling. We engineered a knock-in at the Gpr161 locus in mice to generate a variant (Gpr161mut1), which was ciliary localization defective but cAMP signaling competent. Tissue phenotypes from hedgehog signaling depend on downstream bifunctional Gli transcriptional factors functioning as activators or repressors. Compared to knockout (ko), Gpr161mut1/ko had delayed embryonic lethality, moderately increased hedgehog targets, and partially down-regulated Gli3 repressor. Unlike ko, the Gpr161mut1/ko neural tube did not show Gli2 activator-dependent expansion of ventral-most progenitors. Instead, the intermediate neural tube showed progenitor expansion that depends on loss of Gli3 repressor. Increased extraciliary receptor levels in Gpr161mut1/mut1 prevented ventralization. Morphogenesis in limb buds and midface requires Gli repressor; these tissues in Gpr161mut1/mut1 manifested hedgehog hyperactivation phenotypes—polydactyly and midfacial widening. Thus, ciliary and extraciliary Gpr161 pools likely establish tissue-specific Gli repressor thresholds in determining morpho-phenotypic outcomes.
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Affiliation(s)
- Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Bandarigoda N Somatilaka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kevin White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
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15
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Azzarà A, Rendeli C, Crivello AM, Brugnoletti F, Rumore R, Ausili E, Sangiorgi E, Gurrieri F. Identification of new candidate genes for spina bifida through exome sequencing. Childs Nerv Syst 2021; 37:2589-2596. [PMID: 33855610 DOI: 10.1007/s00381-021-05153-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022]
Abstract
PURPOSE Neural tube defects are a group of birth defects caused by failure of neural tube closure during development. The etiology of NTD, requiring a complex interaction between environmental and genetic factors, is not well understood. METHODS We performed whole-exome sequencing (WES) in six trios, with a single affected proband with spina bifida, to identify rare/novel variants as potential causes of the NTD. RESULTS Our analysis identified four de novo and ten X-linked recessive variants in four of the six probands, all of them in genes previously never implicated in NTD. Among the 14 variants, we ruled out six of them, based on different criteria and pursued the evaluation of eight potential candidates in the following genes: RXRγ, DTX1, COL15A1, ARHGAP36, TKTL1, AMOT, GPR50, and NKRF. The de novo variants where located in the RXRγ, DTX1, and COL15A1 genes while ARHGAP36, TKTL1, AMOT, GPR50, and NKRF carry X-linked recessive variants. This analysis also revealed that four patients presented multiple variants, while we were unable to identify any significant variant in two patients. CONCLUSIONS Our preliminary conclusion support a major role for the de novo variants with respect to the X-linked recessive variants where the X-linked could represent a contribution to the phenotype in an oligogenic model.
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Affiliation(s)
- Alessia Azzarà
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia. .,Unità di Genetica Medica, Università Campus Bio-Medico, Roma, Italia.
| | - Claudia Rendeli
- Spina Bifida Center, Dipartimento di Scienze della Vita e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Anna Maria Crivello
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Fulvia Brugnoletti
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Roberto Rumore
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Emanuele Ausili
- Spina Bifida Center, Dipartimento di Scienze della Vita e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Eugenio Sangiorgi
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Fiorella Gurrieri
- Unità di Genetica Medica, Università Campus Bio-Medico, Roma, Italia
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16
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Tamkeen N, AlOmar SY, Alqahtani SAM, Al-Jurayyan A, Farooqui A, Tazyeen S, Ahmad N, Ishrat R. Identification of the Key Regulators of Spina Bifida Through Graph-Theoretical Approach. Front Genet 2021; 12:597983. [PMID: 33889172 PMCID: PMC8056047 DOI: 10.3389/fgene.2021.597983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
Spina Bifida (SB) is a congenital spinal cord malformation. Efforts to discern the key regulators (KRs) of the SB protein-protein interaction (PPI) network are requisite for developing its successful interventions. The architecture of the SB network, constructed from 117 manually curated genes was found to self-organize into a scale-free fractal state having a weak hierarchical organization. We identified three modules/motifs consisting of ten KRs, namely, TNIP1, TNF, TRAF1, TNRC6B, KMT2C, KMT2D, NCOA3, TRDMT1, DICER1, and HDAC1. These KRs serve as the backbone of the network, they propagate signals through the different hierarchical levels of the network to conserve the network’s stability while maintaining low popularity in the network. We also observed that the SB network exhibits a rich-club organization, the formation of which is attributed to our key regulators also except for TNIP1 and TRDMT1. The KRs that were found to ally with each other and emerge in the same motif, open up a new dimension of research of studying these KRs together. Owing to the multiple etiology and mechanisms of SB, a combination of several biomarkers is expected to have higher diagnostic accuracy for SB as compared to using a single biomarker. So, if all the KRs present in a single module/motif are targetted together, they can serve as biomarkers for the diagnosis of SB. Our study puts forward some novel SB-related genes that need further experimental validation to be considered as reliable future biomarkers and therapeutic targets.
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Affiliation(s)
- Naaila Tamkeen
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Suliman Yousef AlOmar
- Doping Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Abdullah Al-Jurayyan
- Immunology and HLA Section, Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Anam Farooqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nadeem Ahmad
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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17
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Kopinke D, Norris AM, Mukhopadhyay S. Developmental and regenerative paradigms of cilia regulated hedgehog signaling. Semin Cell Dev Biol 2021; 110:89-103. [PMID: 32540122 PMCID: PMC7736055 DOI: 10.1016/j.semcdb.2020.05.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 01/08/2023]
Abstract
Primary cilia are immotile appendages that have evolved to receive and interpret a variety of different extracellular cues. Cilia play crucial roles in intercellular communication during development and defects in cilia affect multiple tissues accounting for a heterogeneous group of human diseases called ciliopathies. The Hedgehog (Hh) signaling pathway is one of these cues and displays a unique and symbiotic relationship with cilia. Not only does Hh signaling require cilia for its function but the majority of the Hh signaling machinery is physically located within the cilium-centrosome complex. More specifically, cilia are required for both repressing and activating Hh signaling by modifying bifunctional Gli transcription factors into repressors or activators. Defects in balancing, interpreting or establishing these repressor/activator gradients in Hh signaling either require cilia or phenocopy disruption of cilia. Here, we will summarize the current knowledge on how spatiotemporal control of the molecular machinery of the cilium allows for a tight control of basal repression and activation states of the Hh pathway. We will then discuss several paradigms on how cilia influence Hh pathway activity in tissue morphogenesis during development. Last, we will touch on how cilia and Hh signaling are being reactivated and repurposed during adult tissue regeneration. More specifically, we will focus on mesenchymal stem cells within the connective tissue and discuss the similarities and differences of how cilia and ciliary Hh signaling control the formation of fibrotic scar and adipose tissue during fatty fibrosis of several tissues.
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Affiliation(s)
- Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA.
| | - Alessandra M Norris
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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18
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Schöneberg T, Liebscher I. Mutations in G Protein-Coupled Receptors: Mechanisms, Pathophysiology and Potential Therapeutic Approaches. Pharmacol Rev 2020; 73:89-119. [PMID: 33219147 DOI: 10.1124/pharmrev.120.000011] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There are approximately 800 annotated G protein-coupled receptor (GPCR) genes, making these membrane receptors members of the most abundant gene family in the human genome. Besides being involved in manifold physiologic functions and serving as important pharmacotherapeutic targets, mutations in 55 GPCR genes cause about 66 inherited monogenic diseases in humans. Alterations of nine GPCR genes are causatively involved in inherited digenic diseases. In addition to classic gain- and loss-of-function variants, other aspects, such as biased signaling, trans-signaling, ectopic expression, allele variants of GPCRs, pseudogenes, gene fusion, and gene dosage, contribute to the repertoire of GPCR dysfunctions. However, the spectrum of alterations and GPCR involvement is probably much larger because an additional 91 GPCR genes contain homozygous or hemizygous loss-of-function mutations in human individuals with currently unidentified phenotypes. This review highlights the complexity of genomic alteration of GPCR genes as well as their functional consequences and discusses derived therapeutic approaches. SIGNIFICANCE STATEMENT: With the advent of new transgenic and sequencing technologies, the number of monogenic diseases related to G protein-coupled receptor (GPCR) mutants has significantly increased, and our understanding of the functional impact of certain kinds of mutations has substantially improved. Besides the classical gain- and loss-of-function alterations, additional aspects, such as biased signaling, trans-signaling, ectopic expression, allele variants of GPCRs, uniparental disomy, pseudogenes, gene fusion, and gene dosage, need to be elaborated in light of GPCR dysfunctions and possible therapeutic strategies.
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Affiliation(s)
- Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig, Germany
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19
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Somatilaka BN, Hwang SH, Palicharla VR, White KA, Badgandi H, Shelton JM, Mukhopadhyay S. Ankmy2 Prevents Smoothened-Independent Hyperactivation of the Hedgehog Pathway via Cilia-Regulated Adenylyl Cyclase Signaling. Dev Cell 2020; 54:710-726.e8. [PMID: 32702291 PMCID: PMC9042708 DOI: 10.1016/j.devcel.2020.06.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 04/12/2020] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
The mechanisms underlying subcellular targeting of cAMP-generating adenylyl cyclases and processes regulated by their compartmentalization are poorly understood. Here, we identify Ankmy2 as a repressor of the Hedgehog pathway via adenylyl cyclase targeting. Ankmy2 binds to multiple adenylyl cyclases, determining their maturation and trafficking to primary cilia. Mice lacking Ankmy2 are mid-embryonic lethal. Knockout embryos have increased Hedgehog signaling and completely open neural tubes showing co-expansion of all ventral neuroprogenitor markers, comparable to the loss of the Hedgehog receptor Patched1. Ventralization in Ankmy2 knockout is completely independent of the Hedgehog pathway transducer Smoothened. Instead, ventralization results from the reduced formation of Gli2 and Gli3 repressors and early depletion of adenylyl cyclase III in neuroepithelial cilia, implicating deficient pathway repression. Ventralization in Ankmy2 knockout requires both cilia and Gli2 activation. These findings indicate that cilia-dependent adenylyl cyclase signaling represses the Hedgehog pathway and promotes morphogenetic patterning.
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Affiliation(s)
| | - Sun-Hee Hwang
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vivek Reddy Palicharla
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin Andrew White
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hemant Badgandi
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Michael Shelton
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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20
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Closing in on Mechanisms of Open Neural Tube Defects. Trends Neurosci 2020; 43:519-532. [PMID: 32423763 DOI: 10.1016/j.tins.2020.04.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/02/2020] [Accepted: 04/22/2020] [Indexed: 11/24/2022]
Abstract
Neural tube defects (NTDs) represent a failure of the neural plate to complete the developmental transition to a neural tube. NTDs are the most common birth anomaly of the CNS. Following mandatory folic acid fortification of dietary grains, a dramatic reduction in the incidence of NTDs was observed in areas where the policy was implemented, yet the genetic drivers of NTDs in humans, and the mechanisms by which folic acid prevents disease, remain disputed. Here, we discuss current understanding of human NTD genetics, recent advances regarding potential mechanisms by which folic acid might modify risk through effects on the epigenome and transcriptome, and new approaches to study refined phenotypes for a greater appreciation of the developmental and genetic causes of NTDs.
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Abstract
During embryonic development, the central nervous system forms as the neural plate and then rolls into a tube in a complex morphogenetic process known as neurulation. Neural tube defects (NTDs) occur when neurulation fails and are among the most common structural birth defects in humans. The frequency of NTDs varies greatly anywhere from 0.5 to 10 in 1000 live births, depending on the genetic background of the population, as well as a variety of environmental factors. The prognosis varies depending on the size and placement of the lesion and ranges from death to severe or moderate disability, and some NTDs are asymptomatic. This chapter reviews how mouse models have contributed to the elucidation of the genetic, molecular, and cellular basis of neural tube closure, as well as to our understanding of the causes and prevention of this devastating birth defect.
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Affiliation(s)
- Irene E Zohn
- Center for Genetic Medicine, Children's Research Institute, Children's National Medical Center, Washington, DC, USA.
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22
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Abstract
PURPOSE OF REVIEW An update is presented regarding neural tube defects (NTDs) including spina bifida and anencephaly, which are among the most common serious birth defects world-wide. Decades of research suggest that no single factor is responsible for neurulation failure, but rather NTDs arise from a complex interplay of disrupted gene regulatory networks, environmental influences and epigenetic regulation. A comprehensive understanding of these dynamics is critical to advance NTD research and prevention. RECENT FINDINGS Next-generation sequencing has ushered in a new era of genomic insight toward NTD pathophysiology, implicating novel gene associations with human NTD risk. Ongoing research is moving from a candidate gene approach toward genome-wide, systems-based investigations that are starting to uncover genetic and epigenetic complexities that underlie NTD manifestation. SUMMARY Neural tube closure is critical for the formation of the human brain and spinal cord. Broader, more all-inclusive perspectives are emerging to identify the genetic determinants of human NTDs.
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Affiliation(s)
- Paul Wolujewicz
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
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23
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Wang L, Ren A, Tian T, Li N, Cao X, Zhang P, Jin L, Li Z, Shen Y, Zhang B, Finnell RH, Lei Y. Whole-Exome Sequencing Identifies Damaging de novo Variants in Anencephalic Cases. Front Neurosci 2019; 13:1285. [PMID: 31849593 PMCID: PMC6896715 DOI: 10.3389/fnins.2019.01285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Anencephaly is a lethal neural tube defect (NTD). Although variants in several genes have been implicated in the development of anencephaly, a more complete picture of variants in the genome, especially de novo variants (DNVs), remains unresolved. We aim to identify DNVs that play an important role in the development of anencephaly by performing whole-exome DNA sequencing (WES) of proband-parent trios. RESULTS A total of 13 DNVs were identified in 8 anencephaly trios by WES, including two loss of function (LoF) variants detected in pLI > 0.9 genes (SPHKAP, c.2629_2633del, and NCOR1, p.Y1907X). Damaging DNVs were identified in 61.5% (8/13) of the anencephalic cases. Independent validation was conducted in an additional 502 NTD cases. Gene inactivation using targeted morpholino antisense oligomers and rescue assays were conducted in zebrafish, and transfection expression in HEK293T cells. Four DNVs in four cases were identified and predicted to alter protein function, including p.R328Q in WD repeat domain phosphoinositide-interacting 1 (WIPI1). Three variants, p.G313R, p.T418M, and p.L406P, in the WIPI1 gene were identified from the independent replication cohort consisting of 502 cases. Functional analysis suggested that the wipi1 p.L406P and p.R328Q variants most likely displayed loss-of-function effects during embryonic development. CONCLUSION De novo damaging variants are the main culprit for majority of anencephalic cases. Missense variants in WIPI1 may play a role in the genetic etiology of anencephaly, and LoF variants in SPHKAP and NCOR1 may also contribute to anencephaly. These findings add to our existing understanding of the genetic mechanisms of NTD formation.
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Affiliation(s)
- Linlin Wang
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Aiguo Ren
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Tian Tian
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Nan Li
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Xuanye Cao
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Peng Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei Jin
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Zhiwen Li
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Yan Shen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Richard H. Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
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Targeted panel sequencing establishes the implication of planar cell polarity pathway and involves new candidate genes in neural tube defect disorders. Hum Genet 2019; 138:363-374. [DOI: 10.1007/s00439-019-01993-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/26/2019] [Indexed: 01/18/2023]
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