1
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Hellmann C, Wohlgemuth K, Pennekamp P, George S, Dahmer-Heath M, Konrad M, Omran H, König J. Immunofluorescence analyses of respiratory epithelial cells aid the diagnosis of nephronophthisis. Pediatr Nephrol 2024; 39:3471-3483. [PMID: 39098869 DOI: 10.1007/s00467-024-06443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 08/06/2024]
Abstract
BACKGROUND Nephronophthisis (NPH) comprises a heterogeneous group of inherited renal ciliopathies clinically characterized by progressive kidney failure. So far, definite diagnosis is based on molecular testing only. Here, we studied the feasibility of NPHP1 and NPHP4 immunostaining of nasal epithelial cells to secure and accelerate the diagnosis of NPH. METHODS Samples of 86 individuals with genetically determined renal ciliopathies were analyzed for NPHP1 localization using immunofluorescence microscopy (IF). A sub-cohort of 35 individuals was also analyzed for NPHP4 localization. Western blotting was performed to confirm IF results. RESULTS NPHP1 and NPHP4 were both absent in all individuals with disease-causing NPHP1 variants including one with a homozygous missense variant (c.1027G > A; p.Gly343Arg) formerly classified as a "variant of unknown significance." In individuals with an NPHP4 genotype, we observed a complete absence of NPHP4 while NPHP1 was severely reduced. IF results were confirmed by immunoblotting. Variants in other genes related to renal ciliopathies did not show any impact on NPHP1/NPHP4 expression. Aberrant immunostaining in two genetically unsolved individuals gave rise for a further genetic workup resulting in a genetic diagnosis for both with disease-causing variants in NPHP1 and NPHP4, respectively. CONCLUSIONS IF of patient-derived respiratory epithelial cells may help to secure and accelerate the diagnosis of nephronophthisis-both by verifying inconclusive genetic results and by stratifying genetic diagnostic approaches. Furthermore, we provide in vivo evidence for the interaction of NPHP1 and NPHP4 in a functional module.
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Affiliation(s)
- Carlotta Hellmann
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Kai Wohlgemuth
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Petra Pennekamp
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Sebastian George
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Mareike Dahmer-Heath
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Martin Konrad
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Jens König
- Department of General Pediatrics, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany.
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2
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Elsayed MEAA, Ali SM, Gardner C, Kozak I. Novel ocular observations in a child with Joubert syndrome type 6 due to pathogenic variant in TMEM67 gene. Am J Ophthalmol Case Rep 2024; 36:102091. [PMID: 39027323 PMCID: PMC11253217 DOI: 10.1016/j.ajoc.2024.102091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/26/2024] [Accepted: 06/01/2024] [Indexed: 07/20/2024] Open
Abstract
Purpose To describe unique ocular features in a child with Joubert syndrome type 6. Observations A 4-year-old male patient presented with right microphthalmia and non-dilating pupil and left primary position nystagmus. Brain MRI revealed a "molar tooth sign" of the midbrain and a "batwing sign" of the fourth ventricle along with large retroorbital cysts bilaterally. The diagnosis of autosomal recessive Joubert syndrome type 6 due to homozygous pathogenic variant c.725A > G p. (Asn242Ser) in TMEM67 gene was confirmed by whole exome sequencing. Left eye had nystagmus and the left optic nerve and retina showed epipapillary and subretinal fibrosis, respectively. Scleral buckle was performed for left non-rhegmatogenous retinal detachment which then improved and has been stable. Conclusions and Importance We present a rare case of JS with some unique ophthalmic features which expand clinical knowledge on this complex systemic and ocular entity.
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Affiliation(s)
| | - Syed M. Ali
- Moorfields Eye Hospitals UAE, Abu Dhabi, United Arab Emirates
- Danat Al Emarat Hospital, Abu Dhabi, United Arab Emirates
- Mohammed Bin Rashed University, Dubai, United Arab Emirates
| | - Carly Gardner
- Department of Diagnostic Radiology, Cleveland Clinic, Cleveland, OH, USA
| | - Igor Kozak
- Moorfields Eye Hospitals UAE, Abu Dhabi, United Arab Emirates
- Danat Al Emarat Hospital, Abu Dhabi, United Arab Emirates
- Mohammed Bin Rashed University, Dubai, United Arab Emirates
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3
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Kawamura A, Yoshida S, Yoshida K. The diverse functions of DYRK2 in response to cellular stress. Histol Histopathol 2024; 39:1427-1434. [PMID: 38656683 DOI: 10.14670/hh-18-744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
To maintain microenvironmental and cellular homeostasis, cells respond to multiple stresses by activating characteristic cellular mechanisms consisting of receptors, signal transducers, and effectors. Dysfunction of these mechanisms can trigger multiple human diseases as well as cancers. Dual-specificity tyrosine-regulated kinases (DYRKs) are members of the CMGC group and are evolutionarily conserved from yeast to mammals. Previous studies revealed that DYRK2 has important roles in the regulation of the cell cycle and survival in cancer cells. On the other hand, recent studies show that DYRK2 also exhibits significant functions in multiple cellular stress responses and in maintaining cellular homeostasis. Hence, the further elucidation of mechanisms underlying DYRK2's diverse responses to various stresses helps to promote the advancement of innovative clinical therapies and pharmacological drugs. This review summarizes the molecular mechanisms of DYRK2, particularly focusing on cellular stress responses.
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Affiliation(s)
- Akira Kawamura
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
| | - Saishu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kiyotsugu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan.
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4
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Chaya T, Maeda Y, Tsutsumi R, Ando M, Ma Y, Kajimura N, Tanaka T, Furukawa T. Ccrk-Mak/Ick signaling is a ciliary transport regulator essential for retinal photoreceptor survival. Life Sci Alliance 2024; 7:e202402880. [PMID: 39293864 PMCID: PMC11412320 DOI: 10.26508/lsa.202402880] [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: 06/08/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/20/2024] Open
Abstract
Primary cilia are microtubule-based sensory organelles whose dysfunction causes ciliopathies in humans. The formation, function, and maintenance of primary cilia depend crucially on intraflagellar transport (IFT); however, the regulatory mechanisms of IFT at ciliary tips are poorly understood. Here, we identified that the ciliopathy kinase Mak is a ciliary tip-localized IFT regulator that cooperatively acts with the ciliopathy kinase Ick, an IFT regulator. Simultaneous disruption of Mak and Ick resulted in loss of photoreceptor ciliary axonemes and severe retinal degeneration. Gene delivery of Ick and pharmacological inhibition of FGF receptors, Ick negative regulators, ameliorated retinal degeneration in Mak -/- mice. We also identified that Ccrk kinase is an upstream activator of Mak and Ick in retinal photoreceptor cells. Furthermore, the overexpression of Mak, Ick, and Ccrk and pharmacological inhibition of FGF receptors suppressed ciliopathy-related phenotypes caused by cytoplasmic dynein inhibition in cultured cells. Collectively, our results show that the Ccrk-Mak/Ick axis is an IFT regulator essential for retinal photoreceptor maintenance and present activation of Ick as a potential therapeutic approach for retinitis pigmentosa caused by MAK mutations.
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Affiliation(s)
- Taro Chaya
- https://ror.org/035t8zc32 Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yamato Maeda
- https://ror.org/035t8zc32 Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Ryotaro Tsutsumi
- https://ror.org/035t8zc32 Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Makoto Ando
- https://ror.org/035t8zc32 Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yujie Ma
- https://ror.org/035t8zc32 Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Naoko Kajimura
- https://ror.org/035t8zc32 Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Teruyuki Tanaka
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahisa Furukawa
- https://ror.org/035t8zc32 Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
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5
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Gillesse E, Wade A, Parboosingh JS, Au PYB, Bernier FP, Lamont RE, Innes AM. Genome sequencing identifies biallelic variants in SCLT1 in a patient with syndromic nephronophthisis: Reflections on the SCLT1-related ciliopathy spectrum. Am J Med Genet A 2024; 194:e63789. [PMID: 38924217 DOI: 10.1002/ajmg.a.63789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Ciliopathies represent a major category of rare multisystem disease. Arriving at a specific diagnosis for a given patient is challenged by the significant genetic and clinical heterogeneity of these conditions. We report the outcome of the diagnostic odyssey of a child with obesity, renal, and retinal disease. Genome sequencing identified biallelic splice site variants in sodium channel and clathrin linker 1 (SCLT1), an emerging ciliopathy gene. We review the literature on all patients reported with biallelic SCLT1 variants highlighting a frequent clinical presentation that overlaps Bardet-Biedl and Senior-Loken syndromes. We also discuss current concepts in syndrome designation in light of these data.
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Affiliation(s)
- E Gillesse
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - A Wade
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Canada
| | - J S Parboosingh
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - P Y B Au
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
| | - F P Bernier
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
| | - R E Lamont
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - A M Innes
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
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6
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Ganga AK, Sweeney LK, Rubio Ramos A, Wrinn CM, Bishop CS, Hamel V, Guichard P, Breslow DK. A disease-associated PPP2R3C-MAP3K1 phospho-regulatory module controls centrosome function. Curr Biol 2024; 34:4824-4834.e6. [PMID: 39317195 PMCID: PMC11496028 DOI: 10.1016/j.cub.2024.08.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/08/2024] [Accepted: 08/30/2024] [Indexed: 09/26/2024]
Abstract
Centrosomes have critical roles in microtubule organization, ciliogenesis, and cell signaling.1,2,3,4,5,6,7,8 Centrosomal alterations also contribute to diseases, including microcephaly, cancer, and ciliopathies.9,10,11,12,13 To date, over 150 centrosomal proteins have been identified, including several kinases and phosphatases that control centrosome biogenesis, function, and maintenance.2,3,4,5,14,15,16,17,18,19,20,21 However, the regulatory mechanisms that govern centrosome function are not fully defined, and thus how defects in centrosomal regulation contribute to disease is incompletely understood. Using a systems genetics approach, we find here that PPP2R3C, a poorly characterized PP2A phosphatase subunit, is a distal centriole protein and functional partner of centriolar proteins CEP350 and FOP. We further show that a key function of PPP2R3C is to counteract the kinase activity of MAP3K1. In support of this model, MAP3K1 knockout suppresses growth defects caused by PPP2R3C inactivation, and MAP3K1 and PPP2R3C have opposing effects on basal and microtubule stress-induced JNK signaling. Illustrating the importance of balanced MAP3K1 and PPP2R3C activities, acute overexpression of MAP3K1 severely inhibits centrosome function and triggers rapid centriole disintegration. Additionally, inactivating PPP2R3C mutations and activating MAP3K1 mutations both cause congenital syndromes characterized by gonadal dysgenesis.22,23,24,25,26,27,28 As a syndromic PPP2R3C variant is defective in centriolar localization and binding to centriolar protein FOP, we propose that imbalanced activity of this centrosomal kinase-phosphatase pair is the shared cause of these disorders. Thus, our findings reveal a new centrosomal phospho-regulatory module, shed light on disorders of gonadal development, and illustrate the power of systems genetics to identify previously unrecognized gene functions.
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Affiliation(s)
- Anil Kumar Ganga
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Lauren K Sweeney
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Armando Rubio Ramos
- Department of Molecular and Cellular Biology, Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Caitlin M Wrinn
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Cassandra S Bishop
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Paul Guichard
- Department of Molecular and Cellular Biology, Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - David K Breslow
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA.
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7
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Kubo S, Okada Y, Takada S. Theoretical insights into rotary mechanism of MotAB in the bacterial flagellar motor. Biophys J 2024; 123:3587-3599. [PMID: 39262115 PMCID: PMC11494522 DOI: 10.1016/j.bpj.2024.09.010] [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: 05/15/2024] [Revised: 08/06/2024] [Accepted: 09/09/2024] [Indexed: 09/13/2024] Open
Abstract
Many bacteria enable locomotion by rotating their flagellum. It has been suggested that this rotation is realized by the rotary motion of the stator unit, MotAB, which is driven by proton transfer across the membrane. Recent cryo-electron microscopy studies have revealed a 5:2 MotAB configuration, in which a MotB dimer is encircled by a ring-shaped MotA pentamer. Although the structure implicates the rotary motion of the MotA wheel around the MotB axle, the molecular mechanisms of rotary motion and how they are coupled with proton transfer across the membrane remain elusive. In this study, we built a structure-based computational model for Campylobacter jejuni MotAB, conducted comprehensive protonation-state-dependent molecular dynamics simulations, and revealed a plausible proton-transfer-coupled rotation pathway. The model assumes rotation-dependent proton transfer, in which proton uptake from the periplasmic side to the conserved aspartic acid in MotB is followed by proton hopping to the MotA proton-carrying site, followed by proton export to the CP. We suggest that, by maintaining two of the proton-carrying sites of MotA in the deprotonated state, the MotA pentamer robustly rotates by ∼36° per proton transfer across the membrane. Our results provide a structure-based mechanistic model of the rotary motion of MotAB in bacterial flagellar motors and provide insights into various ion-driven rotary molecular motors.
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Affiliation(s)
- Shintaroh Kubo
- Department of Cell Biology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan; Department of Physics, Graduate School of Science, the University of Tokyo, Tokyo, Japan; Universal Biology Institute and International Research Center for Neurointelligence, the University of Tokyo, Tokyo, Japan; Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research (BDR), RIKEN, Osaka, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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8
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Ferreccio A, Byeon S, Cornell M, Oses-Prieto J, Deshpande A, Weiss LA, Burlingame A, Yadav S. TAOK2 Drives Opposing Cilia Length Deficits in 16p11.2 Deletion and Duplication Carriers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.07.617069. [PMID: 39416068 PMCID: PMC11482803 DOI: 10.1101/2024.10.07.617069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Copy number variation (CNV) in the 16p11.2 (BP4-BP5) genomic locus is strongly associated with autism. Carriers of 16p11.2 deletion and duplication exhibit several common behavioral and social impairments, yet, show opposing brain structural changes and body mass index. To determine cellular mechanisms that might contribute to these opposing phenotypes, we performed quantitative tandem mass tag (TMT) proteomics on human dorsal forebrain neural progenitor cells (NPCs) differentiated from induced pluripotent stem cells (iPSC) derived from 16p11.2 CNV carriers. Differentially phosphorylated proteins between unaffected individuals and 16p11.2 CNV carriers were significantly enriched for centrosomal and cilia proteins. Deletion patient-derived NPCs show increased primary cilium length compared to unaffected individuals, while stunted cilium growth was observed in 16p11.2 duplication NPCs. Through cellular shRNA and overexpression screens in human iPSC derived NPCs, we determined the contribution of genes within the 16p11.2 locus to cilium length. TAOK2, a serine threonine protein kinase, and PPP4C, a protein phosphatase, were found to regulate primary cilia length in a gene dosage-dependent manner. We found TAOK2 was localized at centrosomes and the base of the primary cilium, and NPCs differentiated from TAOK2 knockout iPSCs had longer cilia. In absence of TAOK2, there was increased pericentrin at the basal body, and aberrant accumulation of IFT88 at the ciliary distal tip. Further, pharmacological inhibition of TAO kinase activity led to increased ciliary length, indicating that TAOK2 negatively controls primary cilium length through its catalytic activity. These results implicate aberrant cilia length in the pathophysiology of 16p11.2 CNV, and establish the role of TAOK2 kinase as a regulator of primary cilium length.
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Affiliation(s)
- Amy Ferreccio
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Sujin Byeon
- Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195
| | - Moira Cornell
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Juan Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94195
| | - Aditi Deshpande
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, CA 94195
| | - Lauren A Weiss
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, CA 94195
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94195
| | - Smita Yadav
- Department of Pharmacology, University of Washington, Seattle, WA 98195
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98106
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9
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Li C, Liu Y, Luo S, Yang M, Li L, Sun L. A review of CDKL: An underestimated protein kinase family. Int J Biol Macromol 2024; 277:133604. [PMID: 38964683 DOI: 10.1016/j.ijbiomac.2024.133604] [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: 06/25/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
Cyclin-dependent kinase-like (CDKL) family proteins are serine/threonine protein kinases and is a specific branch of CMGC (including CDK, MAPK, GSK). Its name is due to the sequence similarity with CDK and it consists of 5 members. Their function in protein phosphorylation underpins their important role in cellular activities, including cell cycle, apoptosis, autophagy and microtubule dynamics. CDKL proteins have been demonstrated to regulate the length of primary cilium, which is a dynamic and diverse signaling hub and closely associated with multiple diseases. Furthermore, CDKL proteins have been shown to be involved in the development and progression of several diseases, including cancer, neurodegenerative diseases and kidney disease. In this review, we summarize the structural characteristics and discovered functions of CDKL proteins and their role in diseases, which might be helpful for the development of innovative therapeutic strategies for disease.
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Affiliation(s)
- Chenrui Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Yan Liu
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Shilu Luo
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Ming Yang
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Li Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China.
| | - Lin Sun
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China.
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10
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Van Sciver RE, Caspary T. A prioritization tool for cilia-associated genes and their in vivo resources unveils new avenues for ciliopathy research. Dis Model Mech 2024; 17:dmm052000. [PMID: 39263856 DOI: 10.1242/dmm.052000] [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: 06/19/2024] [Accepted: 09/04/2024] [Indexed: 09/13/2024] Open
Abstract
Defects in ciliary signaling or mutations in proteins that localize to primary cilia lead to a class of human diseases known as ciliopathies. Approximately 10% of mammalian genes encode cilia-associated proteins, and a major gap in the cilia research field is knowing which genes to prioritize to study and finding the in vivo vertebrate mutant alleles and reagents available for their study. Here, we present a unified resource listing the cilia-associated human genes cross referenced to available mouse and zebrafish mutant alleles, and their associated phenotypes, as well as expression data in the kidney and functional data for vertebrate Hedgehog signaling. This resource empowers researchers to easily sort and filter genes based on their own expertise and priorities, cross reference with newly generated -omics datasets, and quickly find in vivo resources and phenotypes associated with a gene of interest.
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Affiliation(s)
- Robert E Van Sciver
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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11
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Gana S, Di Biagio M, Carraro L, Rossetto G, Scarpelli L, Scognamillo I, Valente EM, Signorini S. LZTFL1, a rare cause of Bardet-Biedl syndrome: A new patient with severe short stature and moderate intellectual disability, more than casual associations? Am J Med Genet A 2024; 194:e63723. [PMID: 38801250 DOI: 10.1002/ajmg.a.63723] [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: 02/23/2024] [Revised: 04/24/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Bardet-Biedl syndrome (BBS) is an inherited ciliopathy affecting multiple organs and systems with wide clinical and genetic heterogeneity. To date, biallelic variants of the LZTFL1 gene have been reported only in six patients with BBS. We identified a homozygous LZTFL1 nonsense variant in a boy presenting with classical BBS features. In addition, he showed a more pronounced cognitive impairment than previously reported subjects and severe short stature, matching the phenotype displayed by some other patients with LZTFL1 variants and lztfl1 knock-out mice. This case report contributes to a better understanding of the clinical spectrum associated with LZTFL1 pathogenic variants, and highlights possible genotype-phenotype correlations.
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Affiliation(s)
- Simone Gana
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Marta Di Biagio
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Laura Carraro
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Gloria Rossetto
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Laura Scarpelli
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Ilaria Scognamillo
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Enza Maria Valente
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Sabrina Signorini
- Developmental Neuro-Ophthalmology Unit, IRCCS Mondino Foundation, Pavia, Italy
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12
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Strong A, March ME, Cardinale CJ, Liu Y, Battig MR, Finoti LS, Matsuoka LS, Watson D, Sridhar S, Jarrett JF, Cannon I, Li D, Bhoj E, Zackai EH, Rand EB, Wenger T, Lerman BB, Shikany A, Weaver KN, Hakonarson H. Novel insights into the phenotypic spectrum and pathogenesis of Hardikar syndrome. Genet Med 2024; 26:101222. [PMID: 39045790 PMCID: PMC11456378 DOI: 10.1016/j.gim.2024.101222] [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: 02/01/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
PURPOSE Hardikar syndrome (HS, MIM #301068) is a female-specific multiple congenital anomaly syndrome characterized by retinopathy, orofacial clefting, aortic coarctation, biliary dysgenesis, genitourinary malformations, and intestinal malrotation. We previously showed that heterozygous nonsense and frameshift variants in MED12 cause HS. The phenotypic spectrum of disease and the mechanism by which MED12 variants cause disease is unknown. We aim to expand the phenotypic and molecular landscape of HS and elucidate the mechanism by which MED12 variants cause disease. METHODS We clinically assembled and molecularly characterized a cohort of 11 previously unreported individuals with HS. Additionally, we studied the effect of MED12 deficiency on ciliary biology, hedgehog, and yes-associated protein (YAP) signaling; pathways implicated in diseases with phenotypic overlap with HS. RESULTS We report novel phenotypes associated with HS, including cardiomyopathy, arrhythmia, and vascular anomalies, and expand the molecular landscape of HS to include splice site variants. We additionally demonstrate that MED12 deficiency causes decreased cell ciliation, and impairs hedgehog and YAP signaling. CONCLUSION Our data support updating HS standard-of-care to include regular cardiac imaging, arrhythmia screening, and vascular imaging. We further propose that dysregulation of ciliogenesis and YAP and hedgehog signaling contributes to the pathogenesis of HS.
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Affiliation(s)
- Alanna Strong
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mark R Battig
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Livia Sertori Finoti
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Leticia S Matsuoka
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Deborah Watson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sindura Sridhar
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - James F Jarrett
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - India Cannon
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Elizabeth B Rand
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Gastroenterology and Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Tara Wenger
- Division of Genetic Medicine, University of Washington, Seattle, WA
| | - Bruce B Lerman
- Department of Medicine, Division of Cardiology, Greenberg Institute for Cardiac Electrophysiology, Cornell University Medical Center, New York, NY
| | - Amy Shikany
- Division of Cardiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - K Nicole Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.
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13
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Kim AH, Sakin I, Viviano S, Tuncel G, Aguilera SM, Goles G, Jeffries L, Ji W, Lakhani SA, Kose CC, Silan F, Oner SS, Kaplan OI, Ergoren MC, Mishra-Gorur K, Gunel M, Sag SO, Temel SG, Deniz E. CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow. Life Sci Alliance 2024; 7:e202402708. [PMID: 39168639 PMCID: PMC11339347 DOI: 10.26508/lsa.202402708] [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: 03/11/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Intellectual and developmental disabilities result from abnormal nervous system development. Over a 1,000 genes have been associated with intellectual and developmental disabilities, driving continued efforts toward dissecting variant functionality to enhance our understanding of the disease mechanism. This report identified two novel variants in CC2D1A in a cohort of four patients from two unrelated families. We used multiple model systems for functional analysis, including Xenopus, Drosophila, and patient-derived fibroblasts. Our experiments revealed that cc2d1a is expressed explicitly in a spectrum of ciliated tissues, including the left-right organizer, epidermis, pronephric duct, nephrostomes, and ventricular zone of the brain. In line with this expression pattern, loss of cc2d1a led to cardiac heterotaxy, cystic kidneys, and abnormal CSF circulation via defective ciliogenesis. Interestingly, when we analyzed brain development, mutant tadpoles showed abnormal CSF circulation only in the midbrain region, suggesting abnormal local CSF flow. Furthermore, our analysis of the patient-derived fibroblasts confirmed defective ciliogenesis, further supporting our observations. In summary, we revealed novel insight into the role of CC2D1A by establishing its new critical role in ciliogenesis and CSF circulation.
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Affiliation(s)
- Angelina Haesoo Kim
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Irmak Sakin
- Department of ENT, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Acibadem University School of Medicine, Istanbul, Turkey
| | - Stephen Viviano
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Gulten Tuncel
- https://ror.org/02x8svs93 DESAM Research Institute, Near East University, Nicosia, Cyprus
| | | | - Gizem Goles
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Saquib A Lakhani
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Canan Ceylan Kose
- Canakkale 18 March University, Faculty of Medicine, Department of Medical Genetics, Canakkale, Turkey
| | - Fatma Silan
- Canakkale 18 March University, Faculty of Medicine, Department of Medical Genetics, Canakkale, Turkey
| | - Sukru Sadik Oner
- Department of Pharmacology, Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), Istanbul, Turkey
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Mahmut Cerkez Ergoren
- https://ror.org/02x8svs93 Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Ketu Mishra-Gorur
- https://ror.org/03pnmqc26 Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Murat Gunel
- https://ror.org/03pnmqc26 Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Program in Brain Tumor Research, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
- Department of Histology and Embryology and Health Sciences Institute, Department of Translational Medicine, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Engin Deniz
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
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14
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Dias AP, Rehmani T, Applin BD, Salih M, Tuana B. SLMAP3 is crucial for organogenesis through mechanisms involving primary cilia formation. Open Biol 2024; 14:rsob240206. [PMID: 39417621 PMCID: PMC11484480 DOI: 10.1098/rsob.240206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 10/19/2024] Open
Abstract
SLMAP3 is a constituent of the centrosome and is known to assemble with the striatin-interacting phosphatase and kinase (STRIPAK) complex, where it has been reported to repress Hippo signalling. The global knockout of SLMAP3 in mice results in embryonic/perinatal lethality and stunted growth without changes in the phosphorylation status of YAP. Diverse phenotypes present in the SLMAP3-/- embryos include reduced body axis, small and abnormal organs resembling defects in planar cell polarity (PCP) signalling, while also displaying the notable polycystic kidneys, a known manifestation of ciliopathies. Analysis of cell polarity in primary mouse embryonic fibroblasts (MEFs) including cell migration, orientation and mitotic spindle angle did not reveal any changes due to SLMAP3 loss in these cells, although the expression of DVL3 was significantly reduced. Furthermore, MEFs lacking FGFR1OP2 or STRN3, two other STRIPAK members, did not reveal any significant changes in any of these parameters either. Significant changes in the number of ciliated cells and primary cilium length in SLMAP3 and FGFR1OP2 deficient MEFs were evident, while a reduced primary cilium length was notable in chondrocytes of SLMAP3 deficient embryos. Our findings suggest that SLMAP3 is essential for mouse embryogenesis through novel mechanisms involving the primary cilium/PCP and protein stability independent of Hippo signalling.
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Affiliation(s)
- Ana Paula Dias
- Department of Cellular and Molecular Medicine, University of Ottawa, OttawaK1H 8M5, Canada
| | - Taha Rehmani
- Department of Cellular and Molecular Medicine, University of Ottawa, OttawaK1H 8M5, Canada
| | - Billi Dawn Applin
- Department of Cellular and Molecular Medicine, University of Ottawa, OttawaK1H 8M5, Canada
| | - Maysoon Salih
- Department of Cellular and Molecular Medicine, University of Ottawa, OttawaK1H 8M5, Canada
| | - Balwant Tuana
- Department of Cellular and Molecular Medicine, University of Ottawa, OttawaK1H 8M5, Canada
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15
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Vazquez N, Lee C, Valenzuela I, Phan TP, Derderian C, Chávez M, Mooney NA, Demeter J, Aziz-Zanjani MO, Cusco I, Codina M, Martínez-Gil N, Valverde D, Solarat C, Buel AL, Thauvin-Robinet C, Steichen E, Filges I, Joset P, De Geyter J, Vaidyanathan K, Gardner T, Toriyama M, Marcotte EM, Roberson EC, Jackson PK, Reiter JF, Tizzano EF, Wallingford JB. The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.25.614984. [PMID: 39386566 PMCID: PMC11463498 DOI: 10.1101/2024.09.25.614984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Cilia are essential organelles and variants in genes governing ciliary function result in ciliopathic diseases. The Ciliogenesis and PLANar polarity Effectors (CPLANE) protein complex is essential for ciliogenesis in animals models but remains poorly defined. Notably, all but one subunit of the CPLANE complex have been implicated in human ciliopathy. Here, we identify three families in which variants in the remaining CPLANE subunit CPLANE2/RSG1 also cause ciliopathy. These patients display cleft palate, tongue lobulations and polydactyly, phenotypes characteristic of Oral-Facial-Digital Syndrome. We further show that these alleles disrupt two vital steps of ciliogenesis, basal body docking and recruitment of intraflagellar transport proteins. Moreover, APMS reveals that Rsg1 binds the CPLANE and also the transition zone protein Fam92 in a GTP-dependent manner. Finally, we show that CPLANE is generally required for normal transition zone architecture. Our work demonstrates that CPLANE2/RSG1 is a causative gene for human ciliopathy and also sheds new light on the mechanisms of ciliary transition zone assembly.
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16
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Boldizar H, Friedman A, Stanley T, Padilla M, Galdieri J, Sclar A, Stawicki TM. The role of cilia in the development, survival, and regeneration of hair cells. Biol Open 2024; 13:bio061690. [PMID: 39263863 DOI: 10.1242/bio.061690] [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: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024] Open
Abstract
Mutations impacting cilia genes lead to a class of human diseases known as ciliopathies. This is due to the role of cilia in the development, survival, and regeneration of many cell types. We investigated the extent to which disrupting cilia impacted these processes in lateral line hair cells of zebrafish. We found that mutations in two intraflagellar transport (IFT) genes, ift88 and dync2h1, which lead to the loss of kinocilia, caused increased hair cell apoptosis. IFT gene mutants also have a decreased mitochondrial membrane potential, and blocking the mitochondrial uniporter causes a loss of hair cells in wild-type zebrafish but not mutants, suggesting mitochondria dysfunction may contribute to the apoptosis seen in these mutants. These mutants also showed decreased proliferation during hair cell regeneration but did not show consistent changes in support cell number or proliferation during hair cell development. These results show that the loss of hair cells seen following disruption of cilia through either mutations in anterograde or retrograde IFT genes appears to be due to impacts on hair cell survival but not necessarily development in the zebrafish lateral line.
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Affiliation(s)
- Hope Boldizar
- Neuroscience Program, Lafayette College, Easton, PA 18042, USA
| | - Amanda Friedman
- Neuroscience Program, Lafayette College, Easton, PA 18042, USA
| | - Tess Stanley
- Neuroscience Program, Lafayette College, Easton, PA 18042, USA
| | - María Padilla
- Biology Department, Lafayette College, Easton, PA 18042, USA
| | | | - Arielle Sclar
- Neuroscience Program, Lafayette College, Easton, PA 18042, USA
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17
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Yamaguchi H, Barrell WB, Faisal M, Liu KJ, Komatsu Y. Ciliary and non-ciliary functions of Rab34 during craniofacial bone development. Biochem Biophys Res Commun 2024; 724:150174. [PMID: 38852507 DOI: 10.1016/j.bbrc.2024.150174] [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: 05/22/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
The primary cilium is a hair-like projection that controls cell development and tissue homeostasis. Although accumulated studies identify the molecular link between cilia and cilia-related diseases, the underlying etiology of ciliopathies has not been fully understood. In this paper, we determine the function of Rab34, a small GTPase, as a key regulator for controlling ciliogenesis and type I collagen trafficking in craniofacial development. Mechanistically, Rab34 is required to form cilia that control osteogenic proliferation, survival, and differentiation via cilia-mediated Hedgehog signaling. In addition, Rab34 is indispensable for regulating type I collagen trafficking from the ER to the Golgi. These results demonstrate that Rab34 has both ciliary and non-ciliary functions to regulate osteogenesis. Our study highlights the critical function of Rab34, which may contribute to understanding the novel etiology of ciliopathies that are associated with the dysfunction of RAB34 in humans.
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Affiliation(s)
- Hiroyuki Yamaguchi
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - William B Barrell
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Maryam Faisal
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA; Department of Bioengineering, Rice University George R. Brown School of Engineering, Houston, TX, 77005, USA
| | - Karen J Liu
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Yoshihiro Komatsu
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA; Graduate Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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18
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Li S, Fernandez JJ, Ruehle MD, Howard-Till RA, Fabritius A, Pearson CG, Agard DA, Winey ME. The Structure of Cilium Inner Junctions Revealed by Electron Cryo-tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612100. [PMID: 39314311 PMCID: PMC11419100 DOI: 10.1101/2024.09.09.612100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The cilium is a microtubule-based organelle critical for many cellular functions. Its assembly initiates at a basal body and continues as an axoneme that projects out of the cell to form a functional cilium. This assembly process is tightly regulated. However, our knowledge of the molecular architecture and the mechanism of assembly is limited. By applying electron cryotomography and subtomogram averaging, we obtained subnanometer resolution structures of the inner junction in three distinct regions of the cilium: the proximal region of the basal body, the central core of the basal body, and the flagellar axoneme. The structures allowed us to identify several basal body and axoneme components. While a few proteins are distributed throughout the entire length of the organelle, many are restricted to particular regions of the cilium, forming intricate local interaction networks and bolstering local structural stability. Finally, by knocking out a critical basal body inner junction component Poc1, we found the triplet MT was destabilized, resulting in a defective structure. Surprisingly, several axoneme-specific components were found to "infiltrate" into the mutant basal body. Our findings provide molecular insight into cilium assembly at its inner Junctions, underscoring its precise spatial regulation.
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Affiliation(s)
- Sam Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jose-Jesus Fernandez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Marisa D. Ruehle
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rachel A. Howard-Till
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
| | - Amy Fabritius
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
| | - Chad G. Pearson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Institute for Advanced Biological Imaging, Redwood Shores, CA, USA
| | - Mark E. Winey
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
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19
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Yu K, Chen W, Chen Y, Shen L, Wu B, Zhang Y, Zhou X. De novo and inherited micro-CNV at 16p13.11 in 21 Chinese patients with defective cardiac left-right patterning. Front Genet 2024; 15:1458953. [PMID: 39315310 PMCID: PMC11416941 DOI: 10.3389/fgene.2024.1458953] [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: 07/03/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024] Open
Abstract
Objective Copy number changes at Chromosomal 16p13.11 have been implicated in a variety of human diseases including congenital cardiac abnormalities. The clinical correlation of copy number variants (CNVs) in this region with developmental abnormalities remains controversial as most of the patients inherit the duplication from an unaffected parent. Methods We performed CNV analysis on 164 patients with defective left-right (LR) patterning based on whole genome-exome sequencing (WG-ES) followed by multiplex ligation-dependent probe amplification (MLPA) validation. Most cases were accompanied with complex congenital heart disease (CHD). Results CNVs at 16p13.11 were identified in a total of 21 cases, accounting for 12.80% (21/164) evaluated cases. We observed a marked overrepresentation of chromosome 16p13.11 duplications in cases when compared with healthy controls according to literature reports (15/164, 9.14% versus 0.09% in controls). Notably, in two independent family trios, de novo 16p13.11 micro-duplications were identified in two patients with laterality defects and CHD. Moreover, 16p13.11 micro-duplication was segregated with the disease in a family trio containing 2 affected individuals. Notably, five coding genes, NOMO1, PKD1P3, NPIPA1, PDXDC1, and NTAN1, were potentially affected by micro-CNV at 16p13.11 in these patients. Conclusion Our study provides new family-trio based evidences to support 16p13.11 micro-duplications predispose individuals to defective cardiac left-right patterning and laterality disorder.
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Affiliation(s)
- Kun Yu
- The Fourth Affiliated Hospital of Soochow University, Suzhou Dushu Lake Hospital, Soochow, China
| | - Weicheng Chen
- Pediatric Cardiovascular Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Yan Chen
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| | - Libing Shen
- International Human Phenome Institutes (IHPI), Shanghai, China
| | - Boxuan Wu
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| | - Yuan Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiangyu Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
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20
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Huang Y, Dong X, Sun SY, Lim TK, Lin Q, He CY. ARL3 GTPases facilitate ODA16 unloading from IFT in motile cilia. SCIENCE ADVANCES 2024; 10:eadq2950. [PMID: 39231220 PMCID: PMC11373600 DOI: 10.1126/sciadv.adq2950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
Eukaryotic cilia and flagella are essential for cell motility and sensory functions. Their biogenesis and maintenance rely on the intraflagellar transport (IFT). Several cargo adapters have been identified to aid IFT cargo transport, but how ciliary cargos are discharged from the IFT remains largely unknown. During our explorations of small GTPases ARL13 and ARL3 in Trypanosoma brucei, we found that ODA16, a known IFT cargo adapter present exclusively in motile cilia, is a specific effector of ARL3. In the cilia, active ARL3 GTPases bind to ODA16 and dissociate ODA16 from the IFT complex. Depletion of ARL3 GTPases stabilizes ODA16 interaction with the IFT, leading to ODA16 accumulation in cilia and defects in axonemal assembly. The interactions between human ODA16 homolog HsDAW1 and ARL GTPases are conserved, and these interactions are altered in HsDAW1 disease variants. These findings revealed a conserved function of ARL GTPases in IFT transport of motile ciliary components, and a mechanism of cargo unloading from the IFT.
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Affiliation(s)
- Yameng Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Xiaoduo Dong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Stella Y Sun
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Teck-Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- The Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
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21
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Maraval J, Delahaye-Duriez A, Racine C, Bruel AL, Denommé-Pichon AS, Gaudillat L, Thauvin-Robinet C, Lucain M, Satre V, Coutton C, de Sainte Agathe JM, Keren B, Faivre L. Expanding MNS1 Heterotaxy Phenotype. Am J Med Genet A 2024:e63862. [PMID: 39233552 DOI: 10.1002/ajmg.a.63862] [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: 04/02/2024] [Revised: 07/30/2024] [Accepted: 08/18/2024] [Indexed: 09/06/2024]
Abstract
MNS1 (meiosis-specific nuclear structural protein-1 gene) encodes a structural protein implicated in motile ciliary function and sperm flagella assembly. To date, two different homozygous MNS1 variants have been associated with autosomal recessive visceral heterotaxy (MIM#618948). A French individual was identified with compound heterozygous variants in the MNS1 gene. A collaborative call was proposed via GeneMatcher to describe new cases with this rare syndrome, leading to the identification of another family. The first patient was a female presenting complete situs inversus and unusual symptoms, including severe myopia and dental agenesis of 10 permanent teeth. She was found to carry compound heterozygous frameshift and nonsense variants in MNS1. The second and third patients were sibling fetuses with homozygous in-frame deletion variants in MNS1 and homozygous missense variants in GLDN. Autopsies revealed a complex prenatal malformation syndrome. We add here new cases with the ultra-rare MNS1-related disorder and provide a review of all published individuals.
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Affiliation(s)
- Julien Maraval
- Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs, Dijon, France
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
| | - Andrée Delahaye-Duriez
- Hôpitaux Universitaires de Paris Seine-Saint-Denis-APHP, UF de médecine génomique et génétique Clinique, Hôpital Jean Verdier, Bondy, France
- UFR Santé Médecine et Biologie Humaine, Université Sorbonne Paris Nord, Bobigny, France
- Inserm UMR1141 NeuroDiderot, Université Paris Cité, Paris, France
| | - Caroline Racine
- Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs, Dijon, France
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
| | - Ange-Line Bruel
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
| | - Léa Gaudillat
- Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs, Dijon, France
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
| | - Christel Thauvin-Robinet
- Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs, Dijon, France
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
| | - Marie Lucain
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
| | - Véronique Satre
- Laboratoire de Biologie Médicale Multi-Sites AURAGEN, CHU Grenoble, Grenoble, France
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR2309, Université Grenoble Alpes, Genetic Epigenetic and Therapies of Infertility Team, Grenoble, France
- GCS AURAGEN, Lyon, France
| | - Charles Coutton
- Laboratoire de Biologie Médicale Multi-Sites AURAGEN, CHU Grenoble, Grenoble, France
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR2309, Université Grenoble Alpes, Genetic Epigenetic and Therapies of Infertility Team, Grenoble, France
- GCS AURAGEN, Lyon, France
| | | | - Boris Keren
- Hôpital la Pitié-Salpêtrière, Département de Génétique Médicale, APHP Sorbonne Université, Paris, France
| | - Laurence Faivre
- Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs, Dijon, France
- Inserm UMR1231 GAD, Université Bourgogne-Franche Comté, Dijon, France
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22
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Dumoulin A, Wilson NH, Tucker KL, Stoeckli ET. A cell-autonomous role for primary cilium-mediated signaling in long-range commissural axon guidance. Development 2024; 151:dev202788. [PMID: 39157903 PMCID: PMC11423920 DOI: 10.1242/dev.202788] [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: 02/23/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024]
Abstract
Ciliopathies are characterized by the absence or dysfunction of primary cilia. Despite the fact that cognitive impairments are a common feature of ciliopathies, how cilia dysfunction affects neuronal development has not been characterized in detail. Here, we show that primary cilium-mediated signaling is required cell-autonomously by neurons during neural circuit formation. In particular, a functional primary cilium is crucial during axonal pathfinding for the switch in responsiveness of axons at a choice point or intermediate target. Using different animal models and in vivo, ex vivo and in vitro experiments, we provide evidence for a crucial role of primary cilium-mediated signaling in long-range axon guidance. The primary cilium on the cell body of commissural neurons transduces long-range guidance signals sensed by growth cones navigating an intermediate target. In extension of our finding that Shh is required for the rostral turn of post-crossing commissural axons, we suggest a model implicating the primary cilium in Shh signaling upstream of a transcriptional change of axon guidance receptors, which in turn mediate the repulsive response to floorplate-derived Shh shown by post-crossing commissural axons.
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Affiliation(s)
- Alexandre Dumoulin
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nicole H Wilson
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kerry L Tucker
- University of New England, College of Osteopathic Medicine, Department of Biomedical Sciences, Center for Excellence in the Neurosciences, Biddeford, ME 04005, USA
| | - Esther T Stoeckli
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- University Research Priority Program 'Adaptive Brain Circuits in Development and Learning' (URPP AdaBD), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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23
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Sekar T, Sebire NJ. Renal Pathology of Ciliopathies. Pediatr Dev Pathol 2024; 27:411-425. [PMID: 38616607 DOI: 10.1177/10935266241242173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Renal ciliopathies are a group of genetic disorders that affect the function of the primary cilium in the kidney, as well as other organs. Since primary cilia are important for regulation of cell signaling pathways, ciliary dysfunction results in a range of clinical manifestations, including renal failure, cyst formation, and hypertension. We summarize the current understanding of the pathophysiological and pathological features of renal ciliopathies in childhood, including autosomal dominant and recessive polycystic kidney disease, nephronophthisis, and Bardet-Biedl syndrome, as well as skeletal dysplasia associated renal ciliopathies. The genetic basis of these disorders is now well-established in many cases, with mutations in a large number of cilia-related genes such as PKD1, PKD2, BBS, MKS, and NPHP being responsible for the majority of cases. Renal ciliopathies are broadly characterized by development of interstitial fibrosis and formation of multiple renal cysts which gradually enlarge and replace normal renal tissue, with each condition demonstrating subtle differences in the degree, location, and age-related development of cysts and fibrosis. Presentation varies from prenatal diagnosis of congenital multisystem syndromes to an asymptomatic childhood with development of complications in later adulthood and therefore clinicopathological correlation is important, including increasing use of targeted genetic testing or whole genome sequencing, allowing greater understanding of genetic pathophysiological mechanisms.
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Affiliation(s)
- Thivya Sekar
- Histopathology Department, Level 3 CBL Labs, Great Ormond Street Hospital, London, UK
| | - Neil J Sebire
- Histopathology Department, Level 3 CBL Labs, Great Ormond Street Hospital, London, UK
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24
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Balasubramaniam K, He T, Chen H, Lin Z, He CY. Cytoplasmic preassembly of the flagellar outer dynein arm complex in Trypanosoma brucei. Mol Biol Cell 2024; 35:br16. [PMID: 39024276 PMCID: PMC11449384 DOI: 10.1091/mbc.e24-06-0263] [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: 06/17/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The outer dynein arm (ODA) is a large, multimeric protein complex essential for ciliary motility. The composition and assembly of ODA are best characterized in the green algae Chlamydomonas reinhardtii, where individual ODA subunits are synthesized and preassembled into a mature complex in the cytosol prior to ciliary import. The single-cellular parasite Trypanosoma brucei contains a motile flagellum essential for cell locomotion and pathogenesis. Similar to human motile cilia, T. brucei flagellum contains a two-headed ODA complex arranged at 24 nm intervals along the axonemal microtubule doublets. The subunit composition and the preassembly of the ODA complex in T. brucei, however, have not been investigated. In this study, we affinity-purified the ODA complex from T. brucei cytoplasmic extract. Proteomic analyses revealed the presence of two heavy chains (ODAα and ODAβ), two intermediate chains (IC1and IC2) and several light chains. We showed that both heavy chains and both intermediate chains are indispensable for flagellar ODA assembly. Our study also provided biochemical evidence supporting the presence of a cytoplasmic, preassembly pathway for T. brucei ODA.
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Affiliation(s)
- Karthika Balasubramaniam
- Department of Biological Science, The Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543
| | - Tingting He
- Department of Biological Science, The Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543
| | - Helen Chen
- Department of Biological Science, The Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543
| | - Zhewang Lin
- Department of Biological Science, The Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543
| | - Cynthia Y. He
- Department of Biological Science, The Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543
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25
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Vinay L, Hess RA, Belleannée C. Human efferent ductules and epididymis display unique cell lineages with motile and primary cilia. Andrology 2024. [PMID: 39212979 DOI: 10.1111/andr.13732] [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: 06/14/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Previous research has illustrated the role of cilia as mechanical and sensory antennae in various organs within the mammalian male reproductive system across different developmental stages. Despite their significance in both organ development and homeostasis, primary cilia in the human male reproductive excurrent duct have been overlooked due to limited access to human specimens. OBJECTIVE This study aimed to characterize the unique cellular composition of human efferent and epididymal ducts, with a focus on their association with primary cilia. MATERIALS AND METHODS Human efferent ductules/epididymides from five donors aged 32-47 years, were obtained through our local organ transplant program. Cell lineage specificity and primary cilia features were examined by immunofluorescent staining and confocal microscopy in the efferent ductules and the distinct segments of the epididymis. RESULTS The epithelium of the human efferent duct exhibited estrogen receptor-positive cells with primary cilia, FoxJ1-positive multiciliated cells with numerous motile cilia, and non-ciliated intraepithelial immune cells. Notably, intraluminal macrophages, identified by CD163/CD68 positivity, were observed to engage in sperm phagocytosis. In all three segments of the human epididymis, primary cilia were found on the surface of principal and basal cells. DISCUSSION AND CONCLUSIONS Our research indicates that the human efferent ductules create a distinct environment, characterized by the presence of two types of ciliated cells that are in contact with immune cells. The discovery of sensory primary cilia exposed on the surface of reabsorptive cells in the efferent ductules, as well as on basal and principal cells in the epididymis, lays the foundation for complementary functional studies. This research uncovers novel characteristics exclusive to human efferent ductules and epididymides, providing a basis for exploring innovative approaches to male contraception and infertility treatment.
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Affiliation(s)
- Ludovic Vinay
- Faculty of Medicine, Department of Obstetrics, Gynecology and Reproduction, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Canada
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle, Quebec City, Canada
| | - Rex A Hess
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Clémence Belleannée
- Faculty of Medicine, Department of Obstetrics, Gynecology and Reproduction, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Canada
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle, Quebec City, Canada
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26
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Tian X, Zhang K, Hong R, Wang H, Dong X, Zhou J, Yang Y, Liu M. Primary cilia restrict autoinflammation by mediating PD-L1 expression. Sci Bull (Beijing) 2024; 69:2505-2508. [PMID: 38553347 DOI: 10.1016/j.scib.2024.03.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 08/27/2024]
Affiliation(s)
- Xiaoyu Tian
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Haihe Laboratory of Cell Ecosystem, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Kaiyue Zhang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Haihe Laboratory of Cell Ecosystem, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Renjie Hong
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hanyu Wang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Haihe Laboratory of Cell Ecosystem, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Xifeng Dong
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Haihe Laboratory of Cell Ecosystem, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China; State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yunfan Yang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.
| | - Min Liu
- Laboratory of Tissue Homeostasis, Haihe Laboratory of Cell Ecosystem, Tianjin 300462, China.
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27
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Lewis TR, Castillo CM, Klementieva NV, Hsu Y, Hao Y, Spencer WJ, Drack AV, Pazour GJ, Arshavsky VY. Contribution of intraflagellar transport to compartmentalization and maintenance of the photoreceptor cell. Proc Natl Acad Sci U S A 2024; 121:e2408551121. [PMID: 39145934 PMCID: PMC11348033 DOI: 10.1073/pnas.2408551121] [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: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
The first steps of vision take place in the ciliary outer segment compartment of photoreceptor cells. The protein composition of outer segments is uniquely suited to perform this function. The most abundant among these proteins is the visual pigment, rhodopsin, whose outer segment trafficking involves intraflagellar transport (IFT). Here, we report three major findings from the analysis of mice in which ciliary transport was acutely impaired by conditional knockouts of IFT-B subunits. First, we demonstrate the existence of a sorting mechanism whereby mislocalized rhodopsin is recruited to and concentrated in extracellular vesicles prior to their release, presumably to protect the cell from adverse effects of protein mislocalization. Second, reducing rhodopsin expression significantly delays photoreceptor degeneration caused by IFT disruption, suggesting that controlling rhodopsin levels may be an effective therapy for some cases of retinal degenerative disease. Last, the loss of IFT-B subunits does not recapitulate a phenotype observed in mutants of the BBSome (another ciliary transport protein complex relying on IFT) in which non-ciliary proteins accumulate in the outer segment. Whereas it is widely thought that the role of the BBSome is to primarily participate in ciliary transport, our data suggest that the BBSome has another major function independent of IFT and possibly related to maintaining the diffusion barrier of the ciliary transition zone.
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Affiliation(s)
- Tylor R. Lewis
- Department of Ophthalmology, Duke University Medical Center, Durham, NC27710
| | - Carson M. Castillo
- Department of Ophthalmology, Duke University Medical Center, Durham, NC27710
| | | | - Ying Hsu
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA52242
| | - Ying Hao
- Department of Ophthalmology, Duke University Medical Center, Durham, NC27710
| | - William J. Spencer
- Department of Ophthalmology, Duke University Medical Center, Durham, NC27710
| | - Arlene V. Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA52242
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA01605
| | - Vadim Y. Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, NC27710
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC27710
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28
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Huang XX, Wang YM, Xie MY, Sun YQ, Zhao XH, Chen YH, Chen JQ, Han SY, Zhou MW, Sun XD. Publication trends of Leber congenital amaurosis researches: a bibliometric study during 2002-2022. Int J Ophthalmol 2024; 17:1501-1509. [PMID: 39156783 PMCID: PMC11286431 DOI: 10.18240/ijo.2024.08.17] [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: 02/03/2024] [Accepted: 04/12/2024] [Indexed: 08/20/2024] Open
Abstract
AIM To analyze the changes in scientific output relating to Leber congenital amaurosis (LCA) and forecast the study trends in this field. METHODS All of the publications in the field of LCA from 2002 to 2022 were collected from Web of Science (WOS) database. We analyzed the quantity (number of publications), quality (citation and H-index) and development trends (relative research interest, RRI) of published LCA research over the last two decades. Moreover, VOSviewer software was applied to define the co-occurrence network of keywords in this field. RESULTS A total of 2158 publications were ultimately examined. We found that the focus on LCA kept rising and peaked in 2015 and 2018, which is consistent with the development trend of gene therapy. The USA has contributed most to this field with 1162 publications, 56 674 citations and the highest H-index value (116). The keywords analysis was divided into five clusters to show the hotspots in the field of LCA, namely mechanism-related, genotype-related, local phenotype-related, system phenotype-related, and therapy-related. We also identified gene therapy and anti-retinal degeneration therapy as a major focus in recent years. CONCLUSION Our study illustrates historical research process and future development trends in LCA field. This may help to guide the orientation for further clinical diagnosis, treatment and scientific research.
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Affiliation(s)
- Xiao-Xu Huang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Disease, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
| | - Yi-Min Wang
- Department of Ophthalmology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Min-Yue Xie
- Beijing Tongren Hospital, Capital Medical University, Beijing 100054, China
| | - Yi-Qing Sun
- Eberly College of Science, Penn State University, University Park 16802-1503, United States
| | - Xiao-Huan Zhao
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Disease, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
| | - Yu-Hong Chen
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Disease, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
| | - Jie-Qiong Chen
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Disease, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
| | - Si-Yang Han
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Disease, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
| | - Min-Wen Zhou
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Disease, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
| | - Xiao-Dong Sun
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Disease, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
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29
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Yuan J, Shao Z, Lv M, Li K, Wei Z. Identification of deleterious variants in nine polycystic kidney disease affected families. Gene 2024; 919:148505. [PMID: 38670396 DOI: 10.1016/j.gene.2024.148505] [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: 12/08/2023] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Polycystic kidney disease (PKD) is common genetic renal disorder. In present study, we performed WES to identify pathogenic variant in nine families including 26 patients with PKD and 19 unaffected members. The eight pathogenic variants were identified in known PKD associated genes including PKD1 (n = 6), PKD2 (n = 1), and OFD1 (n = 1) in eight families. There is one missense, one stopgain, two non-frameshifts, two canonical splicing variants, three frameshift variants and one potential non-canonical splicing variant (NCSV) in 8 families. The six variants were novel variants and not reported in ClinVar database. In addition, the compound heterozygous variants in PKHD1 were identified including one frameshift variants (PKHD1: NM_138694.4, c.9841del, p.S3281Lfs*4) and one non-canonical splicing variant (PKHD1: NM_138694.4, c.6332 + 40A > G) which were defined as deleterious variant by four splicing prediction tools (CADD-splice, SpliceAI, Spliceogen, Squirl). We used the minigene method to validate whether the prioritized potential NSCVs disrupt the typical mRNA splicing process and found abnormally larger PCR production of minigene carrying potential NCSV comparing to wild-type minigene. Sanger sequencing confirmed the 39-bp insertion of intron 38 between exon 38 and exon 39, which results in non-frameshift and 13 amino acid insertions. In conclusion, our study expands the variant spectrum and highlight the important role of non-canonical splicing variant in PKD.
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Affiliation(s)
- Jing Yuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhongmei Shao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Mingrong Lv
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Kuokuo Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China.
| | - Zhaolian Wei
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China.
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30
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Dai X, Xu R, Li N. The Interplay between Airway Cilia and Coronavirus Infection, Implications for Prevention and Control of Airway Viral Infections. Cells 2024; 13:1353. [PMID: 39195243 DOI: 10.3390/cells13161353] [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: 07/23/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
Coronaviruses (CoVs) are a class of respiratory viruses with the potential to cause severe respiratory diseases by infecting cells of the upper respiratory tract, bronchial epithelium, and lung. The airway cilia are distributed on the surface of respiratory epithelial cells, forming the first point of contact between the host and the inhaled coronaviruses. The function of the airway cilia is to oscillate and sense, thereby defending against and removing pathogens to maintain the cleanliness and patency of the respiratory tract. Following infection of the respiratory tract, coronaviruses exploit the cilia to invade and replicate in epithelial cells while also damaging the cilia to facilitate the spread and exacerbation of respiratory diseases. It is therefore imperative to investigate the interactions between coronaviruses and respiratory cilia, as well as to elucidate the functional mechanism of respiratory cilia following coronavirus invasion, in order to develop effective strategies for the prevention and treatment of respiratory viral infections. This review commences with an overview of the fundamental characteristics of airway cilia, and then, based on the interplay between airway cilia and coronavirus infection, we propose that ciliary protection and restoration may represent potential therapeutic approaches in emerging and re-emerging coronavirus pandemics.
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Affiliation(s)
- Xuyao Dai
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ruodan Xu
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ning Li
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
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31
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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; 52:8127-8145. [PMID: 38989623 DOI: 10.1093/nar/gkae554] [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: 04/11/2023] [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/).
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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
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Maddirevula S, Shagrani M, Ji AR, Horne CR, Young SN, Mather LJ, Alqahtani M, McKerlie C, Wood G, Potter PK, Abdulwahab F, AlSheddi T, van der Woerd WL, van Gassen KLI, AlBogami D, Kumar K, Muhammad Akhtar AS, Binomar H, Almanea H, Faqeih E, Fuchs SA, Scott JW, Murphy JM, Alkuraya FS. Large-scale genomic investigation of pediatric cholestasis reveals a novel hepatorenal ciliopathy caused by PSKH1 mutations. Genet Med 2024; 26:101231. [PMID: 39132680 DOI: 10.1016/j.gim.2024.101231] [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: 02/10/2024] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024] Open
Abstract
PURPOSE Pediatric cholestasis is the phenotypic expression of clinically and genetically heterogeneous disorders of bile acid synthesis and flow. Although a growing number of monogenic causes of pediatric cholestasis have been identified, the majority of cases remain undiagnosed molecularly. METHODS In a cohort of 299 pediatric participants (279 families) with intrahepatic cholestasis, we performed exome sequencing as a first-tier diagnostic test. RESULTS A likely causal variant was identified in 135 families (48.56%). These comprise 135 families that harbor variants spanning 37 genes with established or tentative links to cholestasis. In addition, we propose a novel candidate gene (PSKH1) (HGNC:9529) in 4 families. PSKH1 was particularly compelling because of strong linkage in 3 consanguineous families who shared a novel hepatorenal ciliopathy phenotype. Two of the 4 families shared a founder homozygous variant, whereas the third and fourth had different homozygous variants in PSKH1. PSKH1 encodes a putative protein serine kinase of unknown function. Patient fibroblasts displayed abnormal cilia that are long and show abnormal transport. A homozygous Pskh1 mutant mouse faithfully recapitulated the human phenotype and displayed abnormally long cilia. The phenotype could be rationalized by the loss of catalytic activity observed for each recombinant PSKH1 variant using in vitro kinase assays. CONCLUSION Our results support the use of genomics in the workup of pediatric cholestasis and reveal PSKH1-related hepatorenal ciliopathy as a novel candidate monogenic form.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammad Shagrani
- Pediatric Transplant Gastro & Hepatology, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ae-Ri Ji
- Translational Medicine Research Program, The Hospital for Sick Children, Toronto, ON, Canada; The Centre for Phenogenomics, Toronto, ON, Canada
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Victoria, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Lucy J Mather
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Colin McKerlie
- Translational Medicine Research Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Geoffrey Wood
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Paul K Potter
- Department of Biomedical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa AlSheddi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wendy L van der Woerd
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dalal AlBogami
- Pediatric Transplant Gastro & Hepatology, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Kishwer Kumar
- Pediatric Transplant Gastro & Hepatology, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ali Syed Muhammad Akhtar
- Pediatric Transplant Gastro & Hepatology, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hiba Binomar
- Pediatric Transplant Gastro & Hepatology, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hadeel Almanea
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, Department of Pediatric Subspecialties, Children Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Sabine A Fuchs
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - John W Scott
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Victoria, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia; St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Victoria, Australia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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Rutter GA, Gresch A, Delgadillo Silva L, Benninger RKP. Exploring pancreatic beta-cell subgroups and their connectivity. Nat Metab 2024:10.1038/s42255-024-01097-6. [PMID: 39117960 DOI: 10.1038/s42255-024-01097-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024]
Abstract
Functional pancreatic islet beta cells are essential to ensure glucose homeostasis across species from zebrafish to humans. These cells show significant heterogeneity, and emerging studies have revealed that connectivity across a hierarchical network is required for normal insulin release. Here, we discuss current thinking and areas of debate around intra-islet connectivity, cellular hierarchies and potential "controlling" beta-cell populations. We focus on methodologies, including comparisons of different cell preparations as well as in vitro and in vivo approaches to imaging and controlling the activity of human and rodent islet preparations. We also discuss the analytical approaches that can be applied to live-cell data to identify and study critical subgroups of cells with a disproportionate role in control Ca2+ dynamics and thus insulin secretion (such as "first responders", "leaders" and "hubs", as defined by Ca2+ responses to glucose stimulation). Possible mechanisms by which this hierarchy is achieved, its physiological relevance and how its loss may contribute to islet failure in diabetes mellitus are also considered. A glossary of terms and links to computational resources are provided.
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Affiliation(s)
- Guy A Rutter
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada.
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | - Anne Gresch
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Luis Delgadillo Silva
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada
| | - Richard K P Benninger
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Fujii T, Liang L, Nakayama K, Katoh Y. Defects in diffusion barrier function of ciliary transition zone caused by ciliopathy variations of TMEM218. Hum Mol Genet 2024; 33:1442-1453. [PMID: 38751342 DOI: 10.1093/hmg/ddae083] [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: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 08/09/2024] Open
Abstract
Primary cilia are antenna-like structures protruding from the surface of various eukaryotic cells, and have distinct protein compositions in their membranes. This distinct protein composition is maintained by the presence of the transition zone (TZ) at the ciliary base, which acts as a diffusion barrier between the ciliary and plasma membranes. Defects in cilia and the TZ are known to cause a group of disorders collectively called the ciliopathies, which demonstrate a broad spectrum of clinical features, such as perinatally lethal Meckel syndrome (MKS), relatively mild Joubert syndrome (JBTS), and nonsyndromic nephronophthisis (NPHP). Proteins constituting the TZ can be grouped into the MKS and NPHP modules. The MKS module is composed of several transmembrane proteins and three soluble proteins. TMEM218 was recently reported to be mutated in individuals diagnosed as MKS and JBTS. However, little is known about how TMEM218 mutations found in MKS and JBTS affect the functions of cilia. In this study, we found that ciliary membrane proteins were not localized to cilia in TMEM218-knockout cells, indicating impaired barrier function of the TZ. Furthermore, the exogenous expression of JBTS-associated TMEM218 variants but not MKS-associated variants in TMEM218-knockout cells restored the localization of ciliary membrane proteins. In particular, when expressed in TMEM218-knockout cells, the TMEM218(R115H) variant found in JBTS was able to restore the barrier function of cells, whereas the MKS variant TMEM218(R115C) could not. Thus, the severity of symptoms of MKS and JBTS individuals appears to correlate with the degree of their ciliary defects at the cellular level.
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Affiliation(s)
- Taiju Fujii
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Luxiaoxue Liang
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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35
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Zhang Q, Huang Y, Gao S, Ding Y, Zhang H, Chang G, Wang X. Obesity-Related Ciliopathies: Focus on Advances of Biomarkers. Int J Mol Sci 2024; 25:8484. [PMID: 39126056 PMCID: PMC11312664 DOI: 10.3390/ijms25158484] [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: 06/30/2024] [Revised: 07/27/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Obesity-related ciliopathies, as a group of ciliopathies including Alström Syndrome and Bardet-Biedl Syndrome, exhibit distinct genetic and phenotypic variability. The understanding of these diseases is highly significant for understanding the functions of primary cilia in the human body, particularly regarding the relationship between obesity and primary cilia. The diagnosis of these diseases primarily relies on clinical presentation and genetic testing. However, there is a significant lack of research on biomarkers to elucidate the variability in clinical manifestations, disease progression, prognosis, and treatment responses. Through an extensive literature review, the paper focuses on obesity-related ciliopathies, reviewing the advancements in the field and highlighting the potential roles of biomarkers in the clinical presentation, diagnosis, and prognosis of these diseases.
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Affiliation(s)
- Qianwen Zhang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (Q.Z.); (Y.H.); (S.G.); (Y.D.)
| | - Yiguo Huang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (Q.Z.); (Y.H.); (S.G.); (Y.D.)
| | - Shiyang Gao
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (Q.Z.); (Y.H.); (S.G.); (Y.D.)
| | - Yu Ding
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (Q.Z.); (Y.H.); (S.G.); (Y.D.)
| | - Hao Zhang
- Heart Center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, National Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
| | - Guoying Chang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (Q.Z.); (Y.H.); (S.G.); (Y.D.)
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (Q.Z.); (Y.H.); (S.G.); (Y.D.)
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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. PLoS Biol 2024; 22:e3002685. [PMID: 39138140 PMCID: PMC11322411 DOI: 10.1371/journal.pbio.3002685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 05/21/2024] [Indexed: 08/15/2024] Open
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 mouse and zebrafish Hh pathway activation in the 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.
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Affiliation(s)
- Madison F. Walker
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Jingyi Zhang
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, California, United States of America
| | - William Steiner
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Pei-I Ku
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ju-Fen Zhu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Zachary Michaelson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Annabel Lee
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Alyssa B. Long
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Mattie J. Casey
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Abhishek Poddar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac B. Nelson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Corvin D. Arveseth
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | | | - Ryan Clough
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Sarah LaPotin
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Kristen M. Kwan
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Stefan Schulz
- 7TM Antibodies GmbH, Jena, Germany
- Institute of Pharmacology and Toxicology, University Hospital Jena, Jena, Germany
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - John J. G. Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xuecai Ge
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, California, United States of America
| | - Benjamin R. Myers
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
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Wang M, Pan B, Hu Y, Gao J, Hou L, Yu Z, Li M, Zhao Z. STIL facilitates the development and malignant progression of triple-negative breast cancer through activation of Fanconi anemia pathway via interacting with KLF16. Transl Oncol 2024; 46:102010. [PMID: 38823260 PMCID: PMC11177054 DOI: 10.1016/j.tranon.2024.102010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 05/08/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND STIL is an important cell cycle-regulating protein specifically recruited to the mitotic centrosome to promote the replication of centrioles in dividing cells. However, the potential role of STIL in the regulation of the biological functions of triple-negative breast cancer remains still unclear. METHODS We screened for differentially expressed STIL in the Cancer Genome Atlas database. The expression of STIL protein in 10 pairs of breast cancer tissues and adjacent normal tissues was further assessed by western blotting. Functionally, the knockdown and overexpression of STIL have been used to explore the effects of STIL on breast cancer cell proliferation, migration, and invasion. Mechanistically, RNA-seq, dual-luciferase reporter assay, chromatin immunoprecipitation assay, mass spectrometry, immunoprecipitation assay, and DNA pull-down assay were performed. RESULTS Breast cancer tissues and cells have higher STIL expression than normal tissues and cells. STIL knockdown impairs breast cancer cell growth, migration, and invasion, whereas STIL overexpression accelerates these processes. STIL promotes breast cancer progression by regulating FANCD2 expression, and exploration of its molecular mechanism demonstrated that STIL interacts with KLF16 to regulate the expression of FANCD2. CONCLUSIONS Collectively, our findings identified STIL as a critical promoter of breast cancer progression that interacts with KLF16 to regulate Fanconi anemia pathway protein FANCD2. In summary, STIL is a potential novel biomarker and therapeutic target for breast cancer.
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Affiliation(s)
- Meiling Wang
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Bo Pan
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Ye Hu
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Jiyue Gao
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Lu Hou
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Zhenlong Yu
- College of Pharmacy, Dalian Medical University, Dalian, China.
| | - Man Li
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China.
| | - Zuowei Zhao
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China.
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Mostafazadeh N, Resnick A, Young YN, Peng Z. Microstructure-based modeling of primary cilia mechanics. Cytoskeleton (Hoboken) 2024; 81:369-381. [PMID: 38676536 DOI: 10.1002/cm.21860] [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: 01/10/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
A primary cilium, made of nine microtubule doublets enclosed in a cilium membrane, is a mechanosensing organelle that bends under an external mechanical load and sends an intracellular signal through transmembrane proteins activated by cilium bending. The nine microtubule doublets are the main load-bearing structural component, while the transmembrane proteins on the cilium membrane are the main sensing component. No distinction was made between these two components in all existing models, where the stress calculated from the structural component (nine microtubule doublets) was used to explain the sensing location, which may be totally misleading. For the first time, we developed a microstructure-based primary cilium model by considering these two components separately. First, we refined the analytical solution of bending an orthotropic cylindrical shell for individual microtubule, and obtained excellent agreement between finite element simulations and the theoretical predictions of a microtubule bending as a validation of the structural component in the model. Second, by integrating the cilium membrane with nine microtubule doublets and simulating the tip-anchored optical tweezer experiment on our computational model, we found that the microtubule doublets may twist significantly as the whole cilium bends. Third, besides being cilium-length-dependent, we found the mechanical properties of the cilium are also highly deformation-dependent. More important, we found that the cilium membrane near the base is not under pure in-plane tension or compression as previously thought, but has significant local bending stress. This challenges the traditional model of cilium mechanosensing, indicating that transmembrane proteins may be activated more by membrane curvature than membrane stretching. Finally, we incorporated imaging data of primary cilia into our microstructure-based cilium model, and found that comparing to the ideal model with uniform microtubule length, the imaging-informed model shows the nine microtubule doublets interact more evenly with the cilium membrane, and their contact locations can cause even higher bending curvature in the cilium membrane than near the base.
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Affiliation(s)
- Nima Mostafazadeh
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
| | - Andrew Resnick
- Department of Physics and Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, USA
| | - Y-N Young
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Zhangli Peng
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
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39
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Gabriel GC, Ganapathiraju M, Lo CW. The Role of Cilia and the Complex Genetics of Congenital Heart Disease. Annu Rev Genomics Hum Genet 2024; 25:309-327. [PMID: 38724024 DOI: 10.1146/annurev-genom-121222-105345] [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: 08/29/2024]
Abstract
Congenital heart disease (CHD) can affect up to 1% of live births, and despite abundant evidence of a genetic etiology, the genetic landscape of CHD is still not well understood. A large-scale mouse chemical mutagenesis screen for mutations causing CHD yielded a preponderance of cilia-related genes, pointing to a central role for cilia in CHD pathogenesis. The genes uncovered by the screen included genes that regulate ciliogenesis and cilia-transduced cell signaling as well as many that mediate endocytic trafficking, a cell process critical for both ciliogenesis and cell signaling. The clinical relevance of these findings is supported by whole-exome sequencing analysis of CHD patients that showed enrichment for pathogenic variants in ciliome genes. Surprisingly, among the ciliome CHD genes recovered were many that encoded direct protein-protein interactors. Assembly of the CHD genes into a protein-protein interaction network yielded a tight interactome that suggested this protein-protein interaction may have functional importance and that its disruption could contribute to the pathogenesis of CHD. In light of these and other findings, we propose that an interactome enriched for ciliome genes may provide the genomic context for the complex genetics of CHD and its often-observed incomplete penetrance and variable expressivity.
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Affiliation(s)
- George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
| | - Madhavi Ganapathiraju
- Carnegie Mellon University in Qatar, Doha, Qatar
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA;
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
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Ha K, Mundt-Machado N, Bisignano P, Pinedo A, Raleigh DR, Loeb G, Reiter JF, Cao E, Delling M. Cilia-enriched oxysterol 7β,27-DHC is required for polycystin ion channel activation. Nat Commun 2024; 15:6468. [PMID: 39085216 PMCID: PMC11291729 DOI: 10.1038/s41467-024-50318-9] [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: 09/13/2023] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Polycystin-1 (PC-1) and PC-2 form a heteromeric ion channel complex that is abundantly expressed in primary cilia of renal epithelial cells. This complex functions as a non-selective cation channel, and mutations within the polycystin complex cause autosomal dominant polycystic kidney disease (ADPKD). The spatial and temporal regulation of the polycystin complex within the ciliary membrane remains poorly understood. Using both whole-cell and ciliary patch-clamp recordings, we identify a cilia-enriched oxysterol, 7β,27-dihydroxycholesterol (DHC), that serves as a necessary activator of the polycystin complex. We further identify an oxysterol-binding pocket within PC-2 and showed that mutations within this binding pocket disrupt 7β,27-DHC-dependent polycystin activation. Pharmacologic and genetic inhibition of oxysterol synthesis reduces channel activity in primary cilia. In summary, our findings reveal a regulator of the polycystin complex. This oxysterol-binding pocket in PC-2 may provide a specific target for potential ADPKD therapeutics.
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Affiliation(s)
- Kodaji Ha
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Nadine Mundt-Machado
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Paola Bisignano
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Aide Pinedo
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel Loeb
- Department of Medicine, University of California, San Francisco, CA, 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
| | - Erhu Cao
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Markus Delling
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.
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Limerick A, McCabe EA, Turner JS, Kuang KW, Brautigan DL, Hao Y, Chu CY, Fu SH, Ahmadi S, Xu W, Fu Z. An Epilepsy-Associated CILK1 Variant Compromises KATNIP Regulation and Impairs Primary Cilia and Hedgehog Signaling. Cells 2024; 13:1258. [PMID: 39120290 PMCID: PMC11311665 DOI: 10.3390/cells13151258] [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: 05/30/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
Mutations in human CILK1 (ciliogenesis associated kinase 1) are linked to ciliopathies and epilepsy. Homozygous point and nonsense mutations that extinguish kinase activity impair primary cilia function, whereas mutations outside the kinase domain are not well understood. Here, we produced a knock-in mouse equivalent to the human CILK1 A615T variant identified in juvenile myoclonic epilepsy (JME). This residue is in the intrinsically disordered C-terminal region of CILK1 separate from the kinase domain. Mouse embryo fibroblasts (MEFs) with either heterozygous or homozygous A612T mutant alleles exhibited a higher ciliation rate, shorter individual cilia, and upregulation of ciliary Hedgehog signaling. Thus, a single A612T mutant allele was sufficient to impair primary cilia and ciliary signaling in MEFs. Gene expression profiles of wild-type versus mutant MEFs revealed profound changes in cilia-related molecular functions and biological processes. The CILK1 A615T mutant protein was not increased to the same level as the wild-type protein when co-expressed with scaffold protein KATNIP (katanin-interacting protein). Our data show that KATNIP regulation of a JME-associated single-residue variant of CILK1 is compromised, and this impairs the maintenance of primary cilia and Hedgehog signaling.
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Affiliation(s)
- Ana Limerick
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
| | - Ellie A. McCabe
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
| | - Jacob S. Turner
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
| | - Kevin W. Kuang
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
| | - David L. Brautigan
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA; (D.L.B.); (W.X.)
| | - Yi Hao
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA;
| | - Cheuk Ying Chu
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
| | - Sean H. Fu
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
| | - Sean Ahmadi
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
| | - Wenhao Xu
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA; (D.L.B.); (W.X.)
| | - Zheng Fu
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (A.L.); (E.A.M.); (J.S.T.); (K.W.K.); (C.Y.C.); (S.H.F.); (S.A.)
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Power KM, Barr MM. osm-5p- driven fluorophores are differentially expressed in ccpp-1Δ and nekl-4Δ mutant ciliated neurons. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001245. [PMID: 39135985 PMCID: PMC11318990 DOI: 10.17912/micropub.biology.001245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/12/2024] [Accepted: 07/22/2024] [Indexed: 08/15/2024]
Abstract
Intraflagellar transport (IFT) involves the coordinated transport of molecular motors and other proteins and is required for ciliogenesis and ciliary maintenance. The C. elegans IFT protein OSM-5 /IFT88 is expressed in a majority of the ciliated neurons in the animal, and osm-5 mutants exhibit structurally defective cilia. The osm-5 promoter is commonly used to express genetic constructs in the ciliated neurons. In this study, we show that brightness of osm-5p- driven constructs is altered in mutants of the tubulin deglutamylase ccpp-1 and the NIMA-related kinase nekl-4 . This raises the possibility that osm-5 expression levels may be regulated by ccpp-1 and nekl-4 .
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Affiliation(s)
- Kaiden M Power
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States
| | - Maureen M Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States
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Liu L, Sun P, Zhang W. A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics. Brief Bioinform 2024; 25:bbae376. [PMID: 39082645 PMCID: PMC11289681 DOI: 10.1093/bib/bbae376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/26/2024] [Accepted: 07/17/2024] [Indexed: 08/03/2024] Open
Abstract
3'UTR-APAs have been extensively studied, but intronic polyadenylations (IPAs) remain largely unexplored. We characterized the profiles of 22 260 IPAs in 9679 patient samples across 32 cancer types from the Cancer Genome Atlas cohort. By comparing tumor and paired normal tissues, we identified 180 ~ 4645 dysregulated IPAs in 132 ~ 2249 genes in each of 690 patient tumors from 22 cancer types that showed consistent patterns within individual cancer types. We selected 2741 genes that showed consistently patterns across cancer types, including 1834 pan-cancer tumor-enriched and 907 tumor-depleted IPA genes; the former were amply represented in the functional pathways such as deoxyribonucleic acid damage repair. Expression of IPA isoforms was associated with tumor mutation burden and patient characteristics (e.g. sex, race, cancer stages, and subtypes) in cancer-specific and feature-specific manners, and could be a more accurate prognostic marker than gene expression (summary of all isoforms). In summary, our study reveals the roles and the clinical relevance of tumor-associated IPAs.
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Affiliation(s)
- Liang Liu
- Department of Cancer Biology, Wake Forest University School of Medicine, Medical Center Blvd, Winston-Salem, NC 27157, United States
- Center for Cancer Genomics and Precision Oncology, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Medical Center Blvd, Winston-Salem, NC 27157, United States
| | - Peiqing Sun
- Department of Cancer Biology, Wake Forest University School of Medicine, Medical Center Blvd, Winston-Salem, NC 27157, United States
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest University School of Medicine, Medical Center Blvd, Winston-Salem, NC 27157, United States
- Center for Cancer Genomics and Precision Oncology, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Medical Center Blvd, Winston-Salem, NC 27157, United States
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Deconte D, Diniz BL, Hartmann JK, de Souza MA, Zottis LFF, Zen PRG, Rosa RFM, Fiegenbaum M. Expanding the Phenotypic Spectrum of Pathogenic KIAA0586 Variants: From Joubert Syndrome to Hydrolethalus Syndrome. Int J Mol Sci 2024; 25:7900. [PMID: 39063141 PMCID: PMC11277298 DOI: 10.3390/ijms25147900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
KIAA0586 variants have been associated with a wide range of ciliopathies, mainly Joubert syndrome (JS, OMIM #616490) and short-rib thoracic dysplasia syndrome (SRTD, OMIM #616546). However, the hypothesis that this gene is involved with hydrolethalus syndrome (HSL, OMIM #614120) and orofaciodigital syndrome IV (OMIM #258860) has already been raised. Ciliopathies' clinical features are often overlapped despite differing in phenotype severity. Besides KIAA0586, HYLS1 and KIF7 are also known for being causative of ciliopathies, indicating that all three genes may have similar or converging genomic pathways. Overall, the genotypic and phenotypic spectrum of ciliopathies becomes wider and conflicting while more and more new variants are added to this group of disorders' molecular pot. In this case report we discuss the first Brazilian individual clinically diagnosed with hydrolethalus syndrome and molecular findings that demonstrate the role of KIAA0586 as a causative gene of a group of genetic disorders. Also, recent reports on individuals with intronic and exonic variants combined leading to ciliopathies support our patient's molecular diagnosis. At the same time, we discuss variable expressivity and overlapping features in ciliopathies.
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Affiliation(s)
- Desirée Deconte
- Programa de Pós-Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil; (D.D.); (B.L.D.)
| | - Bruna Lixinski Diniz
- Programa de Pós-Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil; (D.D.); (B.L.D.)
| | - Jéssica K. Hartmann
- Faculty of Medicine, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil; (J.K.H.); (M.A.d.S.); (L.F.F.Z.)
| | - Mateus A. de Souza
- Faculty of Medicine, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil; (J.K.H.); (M.A.d.S.); (L.F.F.Z.)
| | - Laira F. F. Zottis
- Faculty of Medicine, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil; (J.K.H.); (M.A.d.S.); (L.F.F.Z.)
| | - Paulo Ricardo Gazzola Zen
- Departamento de Clínica Médica, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil; (P.R.G.Z.)
| | - Rafael F. M. Rosa
- Departamento de Clínica Médica, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil; (P.R.G.Z.)
| | - Marilu Fiegenbaum
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, Brazil
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Nowak-Ciołek M, Ciołek M, Tomaszewska A, Hildebrandt F, Kitzler T, Deutsch K, Lemberg K, Shril S, Szczepańska M, Zachurzok A. Collaborative effort: managing Bardet-Biedl syndrome in pediatric patients. Case series and a literature review. Front Endocrinol (Lausanne) 2024; 15:1424819. [PMID: 39092285 PMCID: PMC11291331 DOI: 10.3389/fendo.2024.1424819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
Bardet-Biedl Syndrome (BBS) is an autosomal recessive non-motile ciliopathy, caused by mutations in more than twenty genes. Their expression leads to the production of BBSome-building proteins or chaperon-like proteins supporting its structure. The prevalence of the disease is estimated at 1: 140,000 - 160,000 of life births. Its main clinical features are retinal dystrophy, polydactyly, obesity, cognitive impairment, hypogonadism, genitourinary malformations, and kidney disease. BBS is characterized by heterogeneous clinical manifestation and the variable onset of signs and symptoms. We present a case series of eight pediatric patients with BBS (6 boys and 2 girls) observed in one clinical center including two pairs of siblings. The patients' age varies between 2 to 13 years (average age of diagnosis: 22 months). At presentation kidney disorders were observed in seven patients, polydactyly in six patients' obesity, and psychomotor development delay in two patients. In two patients with kidney disorders, the genetic tests were ordered at the age of 1 and 6 months due to the presence of symptoms suggesting BBS and having an older sibling with the diagnosis of the syndrome. The mutations in the following genes were confirmed: BBS10, MKKS, BBS7/BBS10, BBS7, BBS9. All described patients developed symptoms related to the urinary system and kidney-function impairment. Other most common symptoms are polydactyly and obesity. In one patient the obesity class 3 was diagnosed with multiple metabolic disorders. In six patients the developmental delay was diagnosed. The retinopathy was observed only in one, the oldest patient. Despite having the same mutations (siblings) or having mutations in the same gene, the phenotypes of the patients are different. We aimed to addresses gaps in understanding BBS by comparing our data and existing literature through a narrative review. This research includes longitudinal data and explores genotype-phenotype correlations of children with BBS. BBS exhibits diverse clinical features and genetic mutations, making diagnosis challenging despite defined criteria. Same mutations can result in different phenotypes. Children with constellations of polydactyly and/or kidney disorders and/or early-onset obesity should be managed towards BBS. Early diagnosis is crucial for effective monitoring and intervention to manage the multisystemic dysfunctions associated with BBS.
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Affiliation(s)
- Maria Nowak-Ciołek
- Students’ Scientific Association at the Department of Pediatrics, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Michał Ciołek
- Students’ Scientific Association at the Department of Psychiatry and Psychotherapy of Developmental Age, Medical University of Silesia in Katowice, Katowice, Poland
| | | | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Thomas Kitzler
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Konstantin Deutsch
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Katharina Lemberg
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Maria Szczepańska
- Department of Pediatrics, Faculty of Medical Sciences, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Agnieszka Zachurzok
- Department of Pediatrics, Faculty of Medical Sciences, Medical University of Silesia in Katowice, Zabrze, Poland
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Li F, Tan Z, Chen H, Gao Y, Xia J, Huang T, Liang L, Zhang J, Zhang X, Shi X, Chen Q, Shu Q, Yu L. Integrative analysis of bulk and single-cell RNA sequencing reveals the gene expression profile and the critical signaling pathways of type II CPAM. Cell Biosci 2024; 14:94. [PMID: 39026356 PMCID: PMC11264590 DOI: 10.1186/s13578-024-01276-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUD Type II congenital pulmonary airway malformation (CPAM) is a rare pulmonary microcystic developmental malformation. Surgical excision is the primary treatment for CPAM, although maternal steroids and betamethasone have proven effective in reducing microcystic CPAM. Disturbed intercellular communication may contribute to the development of CPAM. This study aims to investigate the expression profile and analyze intercellular communication networks to identify genes potentially associated with type II CPAM pathogenesis and therapeutic targets. METHODS RNA sequencing (RNA-seq) was performed on samples extracted from both the cystic area and the adjacent normal tissue post-surgery in CPAM patients. Iterative weighted gene correlation network analysis (iWGCNA) was used to identify genes specifically expressed in type II CPAM. Single-cell RNA-seq (scRNA-seq) was integrated to unveil the heterogeneity in cell populations and analyze the communication and interaction within epithelial cell sub-populations. RESULTS A total of 2,618 differentially expressed genes were identified, primarily enriched in cilium-related biological process and inflammatory response process. Key genes such as EDN1, GPR17, FPR2, and CHRM1, involved in the G protein-coupled receptor (GPCR) signaling pathway and playing roles in cell differentiation, apoptosis, calcium homeostasis, and the immune response, were highlighted based on the protein-protein interaction network. Type II CPAM-associated modules, including ciliary function-related genes, were identified using iWGCNA. By integrating scRNA-seq data, AGR3 (related to calcium homeostasis) and SLC11A1 (immune related) were identified as the only two differently expressed genes in epithelial cells of CPAM. Cell communication analysis revealed that alveolar type 1 (AT1) and alveolar type 2 (AT2) cells were the predominant communication cells for outgoing and incoming signals in epithelial cells. The ligands and receptors between epithelial cell subtypes included COLLAGEN genes enriched in PI3K-AKT singaling and involved in epithelial to mesenchymal transition. CONCLUSIONS In summary, by integrating bulk RNA-seq data of type II CPAM with scRNA-seq data, the gene expression profile and critical signaling pathways such as GPCR signaling and PI3K-AKT signaling pathways were revealed. Abnormally expressed genes in these pathways may disrupt epithelial-mesenchymal transition and contribute to the development of CPAM. Given the effectiveness of prenatal treatments of microcystic CPAM using maternal steroids and maternal betamethasone administration, targeting the genes and signaling pathways involved in the development of CPAM presents a promising therapeutic strategy.
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Affiliation(s)
- Fengxia Li
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Zheng Tan
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Hongyu Chen
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Yue Gao
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jie Xia
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Ting Huang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Liang Liang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jian Zhang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xianghong Zhang
- Department of Cardiac Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xucong Shi
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Qiang Chen
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Jiangxi, China.
| | - Qiang Shu
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Lan Yu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
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Yoshida S, Kawamura A, Aoki K, Wiriyasermkul P, Sugimoto S, Tomiyoshi J, Tajima A, Ishida Y, Katoh Y, Tsukada T, Tsuneoka Y, Yamada K, Nagamori S, Nakayama K, Yoshida K. Positive regulation of Hedgehog signaling via phosphorylation of GLI2/GLI3 by DYRK2 kinase. Proc Natl Acad Sci U S A 2024; 121:e2320070121. [PMID: 38968120 PMCID: PMC11252808 DOI: 10.1073/pnas.2320070121] [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: 11/16/2023] [Accepted: 06/02/2024] [Indexed: 07/07/2024] Open
Abstract
Hedgehog (Hh) signaling, an evolutionarily conserved pathway, plays an essential role in development and tumorigenesis, making it a promising drug target. Multiple negative regulators are known to govern Hh signaling; however, how activated Smoothened (SMO) participates in the activation of downstream GLI2 and GLI3 remains unclear. Herein, we identified the ciliary kinase DYRK2 as a positive regulator of the GLI2 and GLI3 transcription factors for Hh signaling. Transcriptome and interactome analyses demonstrated that DYRK2 phosphorylates GLI2 and GLI3 on evolutionarily conserved serine residues at the ciliary base, in response to activation of the Hh pathway. This phosphorylation induces the dissociation of GLI2/GLI3 from suppressor, SUFU, and their translocation into the nucleus. Loss of Dyrk2 in mice causes skeletal malformation, but neural tube development remains normal. Notably, DYRK2-mediated phosphorylation orchestrates limb development by controlling cell proliferation. Taken together, the ciliary kinase DYRK2 governs the activation of Hh signaling through the regulation of two processes: phosphorylation of GLI2 and GLI3 downstream of SMO and cilia formation. Thus, our findings of a unique regulatory mechanism of Hh signaling expand understanding of the control of Hh-associated diseases.
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Affiliation(s)
- Saishu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Akira Kawamura
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Katsuhiko Aoki
- Radioisotope Research Facilities, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Pattama Wiriyasermkul
- Center for Stable Isotope Medical Research, The Jikei University School of Medicine, Tokyo105-8461, Japan
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, Tokyo105-8461, Japan
- Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo105-8461, Japan
- Laboratory of Amyloid Regulation, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Junnosuke Tomiyoshi
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Ayasa Tajima
- Center for Stable Isotope Medical Research, The Jikei University School of Medicine, Tokyo105-8461, Japan
- Department of Molecular Biology, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan
| | - Takehiro Tsukada
- Department of Biomolecular Science, Toho University, Chiba274-8510, Japan
| | - Yousuke Tsuneoka
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo143-8540, Japan
| | - Kohji Yamada
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Shushi Nagamori
- Center for Stable Isotope Medical Research, The Jikei University School of Medicine, Tokyo105-8461, Japan
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo105-8461, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan
| | - Kiyotsugu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo105-8461, Japan
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48
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Hufft-Martinez BM, Wang HH, Saadi I, Tran PV. Actin cytoskeletal regulation of ciliogenesis in development and disease. Dev Dyn 2024. [PMID: 38958410 DOI: 10.1002/dvdy.724] [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: 04/07/2024] [Revised: 05/29/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024] Open
Abstract
Primary cilia are antenna-like sensory organelles that are evolutionarily conserved in nearly all modern eukaryotes, from the single-celled green alga, Chlamydomonas reinhardtii, to vertebrates and mammals. Cilia are microtubule-based cellular projections that have adapted to perform a broad range of species-specific functions, from cell motility to detection of light and the transduction of extracellular mechanical and chemical signals. These functions render cilia essential for organismal development and survival. The high conservation of cilia has allowed for discoveries in C. reinhardtii to inform our understanding of the basic biology of mammalian primary cilia, and to provide insight into the genetic etiology of ciliopathies. Over the last two decades, a growing number of studies has revealed that multiple aspects of ciliary homeostasis are regulated by the actin cytoskeleton, including centrosome migration and positioning, vesicle transport to the basal body, ectocytosis, and ciliary-mediated signaling. Here, we review actin regulation of ciliary homeostasis, and highlight conserved and divergent mechanisms in C. reinhardtii and mammalian cells. Further, we compare the disease manifestations of patients with ciliopathies to those with mutations in actin and actin-associated genes, and propose that primary cilia defects caused by genetic alteration of the actin cytoskeleton may underlie certain birth defects.
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Affiliation(s)
- Brittany M Hufft-Martinez
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Henry H Wang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Irfan Saadi
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute of Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Pamela V Tran
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas, USA
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49
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Shao S, Chen Y, Deng H, Pan J. Quantitative proteomics reveals insights into the assembly of IFT trains and ciliary assembly. J Cell Sci 2024; 137:jcs262152. [PMID: 38853670 DOI: 10.1242/jcs.262152] [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: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024] Open
Abstract
Intraflagellar transport (IFT) is required for ciliary assembly. The IFT machinery comprises the IFT motors kinesin-2 and IFT dynein plus IFT-A and IFT-B complexes, which assemble into IFT trains in cilia. To gain mechanistic understanding of IFT and ciliary assembly, here, we performed an absolute quantification of IFT machinery in Chlamydomonas reinhardtii cilium. There are ∼756, ∼532, ∼276 and ∼350 molecules of IFT-B, IFT-A, IFT dynein and kinesin-2, respectively, per cilium. The amount of IFT-B is sufficient to sustain rapid ciliary growth in terms of tubulin delivery. The stoichiometric ratio of IFT-B:IFT-A:dynein is ∼3:2:1 whereas the IFT-B:IFT-A ratio in an IFT dynein mutant is 2:1, suggesting that there is a plastic interaction between IFT-A and IFT-B that can be influenced by IFT dynein. Considering diffusion of kinesin-2 during retrograde IFT, it is estimated that one kinesin-2 molecule drives eight molecules of IFT-B during anterograde IFT. These data provide new insights into the assembly of IFT trains and ciliary assembly.
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Affiliation(s)
- Shangjin Shao
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province 266000, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Core Facility Center for Biomedical Analysis, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Core Facility Center for Biomedical Analysis, Tsinghua University, Beijing 100084, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province 266000, China
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50
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Nagayama S, Takahashi H, Hasegawa F, Hori A, Kizami S, Furukawa R, Horie K, Ogoyama M, Hata K, Fujiwara H. A novel variant in IFT122 associated with a severe phenotype of cranioectodermal dysplasia. Congenit Anom (Kyoto) 2024; 64:177-181. [PMID: 38637985 DOI: 10.1111/cga.12569] [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: 11/07/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024]
Abstract
A 27-year-old multiparous woman conceived her fetus naturally. Early second-trimester ultrasound showed short extremities with systemic subcutaneous edema. The pregnancy was artificially terminated at 19 weeks of gestation because of the abnormalities based on the parents' wishes. The parents desired whole-exome sequencing to detect a causative gene using the umbilical cord and the parents' saliva. Compound heterozygous variants (NC_000003.11(NM_052989.3):c.230 T > G/NC_000003.11(NM_052985.4):c.1178A > T) were identified. We described a fetus with a novel compound heterozygous variant in IFT122. The phenotype of this case was severer than of other types of cranioectodermal dysplasia.
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Affiliation(s)
- Shiho Nagayama
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, Japan
| | - Hironori Takahashi
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, Japan
| | - Fuyuki Hasegawa
- Department of Clinical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Asuka Hori
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Sho Kizami
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, Japan
| | - Rieko Furukawa
- Department of Radiology, Jichi Medical University, Shimotsuke, Japan
| | - Kenji Horie
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, Japan
| | - Manabu Ogoyama
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Biology, Gunma University, Maebashi, Japan
| | - Hiroyuki Fujiwara
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, Japan
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