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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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Singh S, Nampoothiri S, Narayanan DL, Chaudhry C, Salvankar S, Girisha KM. Biallelic loss of function variants in FUZ result in an orofaciodigital syndrome. Eur J Hum Genet 2024; 32:1022-1026. [PMID: 38702430 PMCID: PMC11291644 DOI: 10.1038/s41431-024-01619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
Orofaciodigital syndrome is a distinctive subtype of skeletal ciliopathies. Disease-causing variants in the genes encoding the CPLANE complex result in a wide variety of skeletal dysplasia with disturbed ciliary functions. The phenotypic spectrum includes orofaciodigital syndrome and short rib polydactyly syndrome. FUZ, as a part of the CPLANE complex, is involved in intraflagellar vesicular trafficking within primary cilia. Previously, the variants, c.98_111+9del and c.851G>T in FUZ were identified in two individuals with a skeletal ciliopathy, manifesting digital anomalies (polydactyly, syndactyly), orofacial cleft, short ribs and cardiac defects. Here, we present two novel variants, c.601G>A and c.625_636del in biallelic state, in two additional subjects exhibiting phenotypic overlap with the previously reported cases. Our findings underscore the association between biallelic loss of function variants in FUZ and skeletal ciliopathy akin to orofaciodigital syndrome.
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Affiliation(s)
- Swati Singh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Kochi, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India.
- Suma Genomics Private Limited, Manipal, India.
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman.
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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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Donato L, Scimone C, Alibrandi S, Vadalà M, Castellucci M, Bonfiglio VME, Scalinci SZ, Abate G, D'Angelo R, Sidoti A. The genomic mosaic of mitochondrial dysfunction: Decoding nuclear and mitochondrial epigenetic contributions to maternally inherited diabetes and deafness pathogenesis. Heliyon 2024; 10:e34756. [PMID: 39148984 PMCID: PMC11324998 DOI: 10.1016/j.heliyon.2024.e34756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024] Open
Abstract
Aims Maternally inherited diabetes and deafness (MIDD) is a complex disorder characterized by multiorgan clinical manifestations, including diabetes, hearing loss, and ophthalmic complications. This pilot study aimed to elucidate the intricate interplay between nuclear and mitochondrial genetics, epigenetic modifications, and their potential implications in the pathogenesis of MIDD. Main methods A comprehensive genomic approach was employed to analyze a Sicilian family affected by clinically characterized MIDD, negative to the only known causative m.3243 A > G variant, integrating whole-exome sequencing and whole-genome bisulfite sequencing of both nuclear and mitochondrial analyses. Key findings Rare and deleterious variants were identified across multiple nuclear genes involved in retinal homeostasis, mitochondrial function, and epigenetic regulation, while complementary mitochondrial DNA analysis revealed a rich tapestry of genetic diversity across genes encoding components of the electron transport chain and ATP synthesis machinery. Epigenetic analyses uncovered significant differentially methylated regions across the genome and within the mitochondrial genome, suggesting a nuanced landscape of epigenetic modulation. Significance The integration of genetic and epigenetic data highlighted the potential crosstalk between nuclear and mitochondrial regulation, with specific mtDNA variants influencing methylation patterns and potentially impacting the expression and regulation of mitochondrial genes. This pilot study provides valuable insights into the complex molecular mechanisms underlying MIDD, emphasizing the interplay between nucleus and mitochondrion, tracing the way for future research into targeted therapeutic interventions and personalized approaches for disease management.
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Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Maria Vadalà
- Department of Biomolecular Strategies, Genetics and Cutting-edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
- Department of Biomedicine, Neuroscience and Advanced Diagnostic (BIND), Ophthalmology Institute, University of Palermo, 90143, Palermo, Italy
| | - Massimo Castellucci
- Department of Biomedicine, Neuroscience and Advanced Diagnostic (BIND), Ophthalmology Institute, University of Palermo, 90143, Palermo, Italy
| | - Vincenza Maria Elena Bonfiglio
- Department of Biomedicine, Neuroscience and Advanced Diagnostic (BIND), Ophthalmology Institute, University of Palermo, 90143, Palermo, Italy
| | | | - Giorgia Abate
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
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5
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Lin WD, Liao WL, Chen WC, Liu TY, Chen YC, Tsai FJ. Genome-wide association study identifies novel susceptible loci and evaluation of polygenic risk score for chronic obstructive pulmonary disease in a Taiwanese population. BMC Genomics 2024; 25:607. [PMID: 38886662 PMCID: PMC11184693 DOI: 10.1186/s12864-024-10526-5] [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: 12/09/2023] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) describes a group of progressive lung diseases causing breathing difficulties. While COPD development typically involves a complex interplay between genetic and environmental factors, genetics play a role in disease susceptibility. This study used genome-wide association studies (GWAS) and polygenic risk score (PRS) to elucidate the genetic basis for COPD in Taiwanese patients. RESULTS GWAS was performed on a Taiwanese COPD case-control cohort with a sample size of 5,442 cases and 17,681 controls. Additionally, the PRS was calculated and assessed in our target groups. GWAS results indicate that although there were no single nucleotide polymorphisms (SNPs) of genome-wide significance, prominent COPD susceptibility loci on or nearby genes such as WWTR1, EXT1, INTU, MAP3K7CL, MAMDC2, BZW1/CLK1, LINC01197, LINC01894, and CFAP95 (C9orf135) were identified, which had not been reported in previous studies. Thirteen susceptibility loci, such as CHRNA4, AFAP1, and DTWD1, previously reported in other populations were replicated and confirmed to be associated with COPD in Taiwanese populations. The PRS was determined in the target groups using the summary statistics from our base group, yielding an effective association with COPD (odds ratio [OR] 1.09, 95% confidence interval [CI] 1.02-1.17, p = 0.011). Furthermore, replication a previous lung function trait PRS model in our target group, showed a significant association of COPD susceptibility with PRS of Forced Expiratory Volume in one second (FEV1)/Forced Vital Capacity (FCV) (OR 0.89, 95% CI 0.83-0.95, p = 0.001). CONCLUSIONS Novel COPD-related genes were identified in the studied Taiwanese population. The PRS model, based on COPD or lung function traits, enables disease risk estimation and enhances prediction before suffering. These results offer new perspectives on the genetics of COPD and serve as a basis for future research.
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Affiliation(s)
- Wei-De Lin
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, 404333, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 404333, Taiwan
- Center for Personalized Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Wei-Cheng Chen
- Department of Internal Medicine, Pulmonary and Critical Care Medicine, China Medical University Hospital, Taichung, 404333, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404327, Taiwan
| | - Ting-Yuan Liu
- Department of Medical Research, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Yu-Chia Chen
- Department of Medical Research, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan.
- School of Chinese Medicine, China Medical University, Taichung, 404333, Taiwan.
- Division of Genetics and Metabolism, China Medical University Children's Hospital, Taichung, 404327, Taiwan.
- Department of Medical Genetics, China Medical University Hospital, Taichung, 404327, Taiwan.
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, 413305, Taiwan.
- Department of Medical Research, China Medical University Hospital, No. 2, Yude Road, North District, Taichung, 404327, Taiwan.
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Hembach S, Schmidt S, Orschmann T, Burtscher I, Lickert H, Giesert F, Weisenhorn DV, Wurst W. Engrailed 1 deficiency induces changes in ciliogenesis during human neuronal differentiation. Neurobiol Dis 2024; 194:106474. [PMID: 38518837 DOI: 10.1016/j.nbd.2024.106474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/24/2024] Open
Abstract
A key pathological feature of Parkinson's Disease (PD) is the progressive degeneration of dopaminergic neurons (DAns) in the substantia nigra pars compacta. Considering the major role of EN1 in the development and maintenance of these DAns and the implications from En1 mouse models, it is highly interesting to study the molecular and protective effect of EN1 also in a human cellular model. Therefore, we generated EN1 knock-out (ko) human induced pluripotent stem cell (hiPSCs) lines and analyzed these during neuronal differentiation. Although the EN1 ko didn't interfere with neuronal differentiation and generation of tyrosine hydroxylase positive (TH+) neurons per se, the neurons exhibited shorter neurites. Furthermore, mitochondrial respiration, as well as mitochondrial complex I abundance was significantly reduced in fully differentiated neurons. To understand the implications of an EN1 ko during differentiation, we performed a transcriptome analysis of human neuronal precursor cells (hNPCs) which unveiled alterations in cilia-associated pathways. Further analysis of ciliary morphology revealed an elongation of primary cilia in EN1-deficient hNPCs. Besides, also Wnt signaling pathways were severely affected. Upon stimulating hNPCs with Wnt which drastically increased EN1 expression in WT lines, the phenotypes concerning mitochondrial function and cilia were exacerbated in EN1 ko hNPCs. They failed to enhance the expression of the complex I subunits NDUFS1 and 3, and now displayed a reduced mitochondrial respiration. Furthermore, Wnt stimulation decreased ciliogenesis in EN1 ko hNPCs but increased ciliary length even further. This further highlights the relevance of primary cilia next to mitochondria for the functionality and correct maintenance of human DAns and provides new possibilities to establish neuroprotective therapies for PD.
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Affiliation(s)
- Sina Hembach
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany; Munich School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Sebastian Schmidt
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany; Neurobiological Engineering, Munich Institute of Biomedical Engineering, TUM School of Natural Sciences, Garching, Germany; Deutsche Zentrum für Psychische Gesundheit (DZPG), Site Munich-Augsburg, Munich, Germany
| | - Tanja Orschmann
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; School of Medicine, Technische Universität München, Munich, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany
| | | | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany; Deutsche Zentrum für Psychische Gesundheit (DZPG), Site Munich-Augsburg, Munich, Germany; Technische Universität München-Weihenstephan, Neuherberg, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.
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7
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Sharma R, Kalot R, Levin Y, Babayeva S, Kachurina N, Chung CF, Liu KJ, Bouchard M, Torban E. The CPLANE protein Fuzzy regulates ciliogenesis by suppressing actin polymerization at the base of the primary cilium via p190A RhoGAP. Development 2024; 151:dev202322. [PMID: 38546045 PMCID: PMC11006408 DOI: 10.1242/dev.202322] [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: 09/04/2023] [Accepted: 02/14/2024] [Indexed: 04/12/2024]
Abstract
The primary cilium decorates most eukaryotic cells and regulates tissue morphogenesis and maintenance. Structural or functional defects of primary cilium result in ciliopathies, congenital human disorders affecting multiple organs. Pathogenic variants in the ciliogenesis and planar cell polarity effectors (CPLANE) genes FUZZY, INTU and WDPCP disturb ciliogenesis, causing severe ciliopathies in humans and mice. Here, we show that the loss of Fuzzy in mice results in defects of primary cilia, accompanied by increased RhoA activity and excessive actin polymerization at the basal body. We discovered that, mechanistically, Fuzzy interacts with and recruits the negative actin regulator ARHGAP35 (also known as p190A RhoGAP) to the basal body. We identified genetic interactions between the two genes and found that a mutant ArhGAP35 allele increases the severity of phenotypic defects observed in Fuzzy-/- mice. Based on our findings, we propose that Fuzzy regulates ciliogenesis by recruiting ARHGAP35 to the basal body, where the latter likely restricts actin polymerization and modifies the actin network. Our study identifies a mechanism whereby CPLANE proteins control both actin polymerization and primary cilium formation.
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Affiliation(s)
- Rhythm Sharma
- Department of Medicine and Department of Physiology, McGill University, Montreal H4A 3J1, QC, Canada
| | - Rita Kalot
- Department of Medicine and Department of Physiology, McGill University, Montreal H4A 3J1, QC, Canada
| | - Yossef Levin
- Department of Medicine and Department of Physiology, McGill University, Montreal H4A 3J1, QC, Canada
| | - Sima Babayeva
- Metabolic Disorders and Complications Program, Research Institute of the McGill University Health Centre, McGill University, Montreal H4A 3J1, QC, Canada
| | - Nadezda Kachurina
- Metabolic Disorders and Complications Program, Research Institute of the McGill University Health Centre, McGill University, Montreal H4A 3J1, QC, Canada
| | - Chen-Feng Chung
- Department of Medicine and Department of Physiology, McGill University, Montreal H4A 3J1, QC, Canada
| | - Karen J. Liu
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Maxime Bouchard
- Rosalind and Morris Goodman Cancer Institute, Department of Medicine of the McGill University,McGill University, Montreal H3A 1A3, QC, Canada
| | - Elena Torban
- Department of Medicine and Department of Physiology, McGill University, Montreal H4A 3J1, QC, Canada
- Metabolic Disorders and Complications Program, Research Institute of the McGill University Health Centre, McGill University, Montreal H4A 3J1, QC, Canada
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8
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Lodge EJ, Barrell WB, Liu KJ, Andoniadou CL. The Fuzzy planar cell polarity protein (FUZ), necessary for primary cilium formation, is essential for pituitary development. J Anat 2024; 244:358-367. [PMID: 37794731 PMCID: PMC10780146 DOI: 10.1111/joa.13961] [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: 08/07/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
The primary cilium is an essential organelle that is important for normal cell signalling during development and homeostasis but its role in pituitary development has not been reported. The primary cilium facilitates signal transduction for multiple pathways, the best-characterised being the SHH pathway, which is known to be necessary for correct pituitary gland development. FUZ is a planar cell polarity (PCP) effector that is essential for normal ciliogenesis, where the primary cilia of Fuz-/- mutants are shorter or non-functional. FUZ is part of a group of proteins required for recruiting retrograde intraflagellar transport proteins to the base of the organelle. Previous work has reported ciliopathy phenotypes in Fuz-/- homozygous null mouse mutants, including neural tube defects, craniofacial abnormalities, and polydactyly, alongside PCP defects including kinked/curly tails and heart defects. Interestingly, the pituitary gland was reported to be missing in Fuz-/- mutants at 14.5 dpc but the mechanisms underlying this phenotype were not investigated. Here, we have analysed the pituitary development of Fuz-/- mutants. Histological analyses reveal that Rathke's pouch (RP) is initially induced normally but is not specified and fails to express LHX3, resulting in hypoplasia and apoptosis. Characterisation of SHH signalling reveals reduced pathway activation in Fuz-/- mutant relative to control embryos, leading to deficient specification of anterior pituitary fate. Analyses of the key developmental signals FGF8 and BMP4, which are influenced by SHH, reveal abnormal patterning in the ventral diencephalon, contributing further to abnormal RP development. Taken together, our analyses suggest that primary cilia are required for normal pituitary specification through SHH signalling.
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Affiliation(s)
- Emily J. Lodge
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonUK
| | - William B. Barrell
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonUK
| | - Karen J. Liu
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonUK
| | - Cynthia L. Andoniadou
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonUK
- Department of Medicine IIIUniversity Hospital Carl Gustav Carus, Technische Universität DresdenDresdenGermany
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9
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Nawaz H, Khan SA, Bibi F, Waqas A, Bari A, Khan N, Muhammad N, Khan A, Paracha SA, Alam Q, Kamal MA, Rafeeq MM, Muhammad N, Haq FU, Khan S, Mahmood A, Khan S, Umair M. Biallelic Variants in Seven Different Genes Associated with Clinically Suspected Bardet-Biedl Syndrome. Genes (Basel) 2023; 14:genes14051113. [PMID: 37239474 DOI: 10.3390/genes14051113] [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: 04/08/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare clinically and genetically heterogeneous autosomal recessive multi-systemic disorder with 22 known genes. The primary clinical and diagnostic features include six different hallmarks, such as rod-cone dystrophy, learning difficulties, renal abnormalities, male hypogonadism, post-axial polydactyly, and obesity. Here, we report nine consanguineous families and a non-consanguineous family with several affected individuals presenting typical clinical features of BBS. In the present study, 10 BBS Pakistani families were subjected to whole exome sequencing (WES), which revealed novel/recurrent gene variants, including a homozygous nonsense mutation (c.94C>T; p.Gln32Ter) in the IFT27 (NM_006860.5) gene in family A, a homozygous nonsense mutation (c.160A>T; p.Lys54Ter) in the BBIP1 (NM_001195306.1) gene in family B, a homozygous nonsense variant (c.720C>A; p.Cys240Ter) in the WDPCP (NM_015910.7) in family C, a homozygous nonsense variant (c.505A>T; p.Lys169Ter) in the LZTFL1 (NM_020347.4) in family D, pathogenic homozygous 1 bp deletion (c.775delA; p.Thr259Leufs*21) in the MKKS/BBS5 (NM_170784.3) gene in family E, a pathogenic homozygous missense variant (c.1339G>A; p.Ala447Thr) in BBS1 (NM_024649.4) in families F and G, a pathogenic homozygous donor splice site variant (c.951+1G>A; p?) in BBS1 (NM_024649.4) in family H, a pathogenic bi-allelic nonsense variant in MKKS (NM_170784.3) (c.119C>G; p.Ser40*) in family I, and homozygous pathogenic frameshift variants (c.196delA; p.Arg66Glufs*12) in BBS5 (NM_152384.3) in family J. Our findings extend the mutation and phenotypic spectrum of four different types of ciliopathies causing BBS and also support the importance of these genes in the development of multi-systemic human genetic disorders.
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Affiliation(s)
- Hamed Nawaz
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Farhana Bibi
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Ahmed Waqas
- Department Zoology, Division of Science and Technology, University of Education, Lahore 54782, Pakistan
| | - Abdul Bari
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Niamatullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Amjad Khan
- Faculty of Science, Department of Biological Sciences (Zoology), University of Lakki Marwat, Lakki Marwat 28420, Pakistan
| | - Sohail Aziz Paracha
- Department of Anatomy, KMU Institute of Medical Sciences (KIMS), Kohat 26000, Pakistan
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Block Zinj, Manama 359, Bahrain
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi Arabia
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Fayaz Ul Haq
- Department of Radiological Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 12271, Saudi Arabia
| | - Shazia Khan
- Hafeez Institute of Medical Sciences, Islamabad 44000, Pakistan
- Department of Biological Sciences, International Islamic University Islamabad, H-10, Islamabad 44000, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh 12271, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore 14611, Pakistan
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Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ, Bosch F, Braun RE, Brown SDM, Chin HJG, Dickinson ME, Hsu CW, Dobbie M, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Mammano F, Nutter LMJ, Parkinson H, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, Brooks B, McKerlie C, Lloyd KCK, Westerberg H, Moshiri A. Genome-wide screening reveals the genetic basis of mammalian embryonic eye development. BMC Biol 2023; 21:22. [PMID: 36737727 PMCID: PMC9898963 DOI: 10.1186/s12915-022-01475-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/23/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.
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Affiliation(s)
- Justine M Chee
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Dave Clary
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Kendall Higgins
- University of Miami: Miller School of Medicine, Miami, FL, USA
| | - Lynette Bower
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Ann Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Ruolin Guo
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fatima Bosch
- Centre of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Steve D M Brown
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - H-J Genie Chin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), Taipei City, Taiwan
| | - Mary E Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chih-Wei Hsu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael Dobbie
- Phenomics Australia, The John Curtin School of Medical Research, Canberra, Australia
| | - Xiang Gao
- Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Sanjeev Galande
- Indian Institutes of Science Education and Research, Pune, India
| | - Anne Grobler
- Faculty of Health Sciences, PCDDP North-West University, Potchefstroom, South Africa
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Monterotondo Scalo, Italy
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Parkinson
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Chuan Qin
- National Laboratory Animal Center, National Applied Research Laboratories, Beijing, China
| | | | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - J-K Seong
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Ying Xu
- CAM-SU Genomic Resource Center, Soochow University, Suzhou, China
| | - Brian Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Colin McKerlie
- The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, CA, USA
| | - Henrik Westerberg
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, University of California Davis, Sacramento, CA, USA.
- UC Davis Eye Center, 4860 Y St., Ste. 2400, Sacramento, CA, 95817, USA.
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11
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Platova S, Poliushkevich L, Kulakova M, Nesterenko M, Starunov V, Novikova E. Gotta Go Slow: Two Evolutionarily Distinct Annelids Retain a Common Hedgehog Pathway Composition, Outlining Its Pan-Bilaterian Core. Int J Mol Sci 2022; 23:ijms232214312. [PMID: 36430788 PMCID: PMC9695228 DOI: 10.3390/ijms232214312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022] Open
Abstract
Hedgehog signaling is one of the key regulators of morphogenesis, cell differentiation, and regeneration. While the Hh pathway is present in all bilaterians, it has mainly been studied in model animals such as Drosophila and vertebrates. Despite the conservatism of its core components, mechanisms of signal transduction and additional components vary in Ecdysozoa and Deuterostomia. Vertebrates have multiple copies of the pathway members, which complicates signaling implementation, whereas model ecdysozoans appear to have lost some components due to fast evolution rates. To shed light on the ancestral state of Hh signaling, models from the third clade, Spiralia, are needed. In our research, we analyzed the transcriptomes of two spiralian animals, errantial annelid Platynereis dumerilii (Nereididae) and sedentarian annelid Pygospio elegans (Spionidae). We found that both annelids express almost all Hh pathway components present in Drosophila and mouse. We performed a phylogenetic analysis of the core pathway components and built multiple sequence alignments of the additional key members. Our results imply that the Hh pathway compositions of both annelids share more similarities with vertebrates than with the fruit fly. Possessing an almost complete set of single-copy Hh pathway members, lophotrochozoan signaling composition may reflect the ancestral features of all three bilaterian branches.
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Affiliation(s)
- Sofia Platova
- Faculty of Biology, St. Petersburg State University, Saint Petersburg 199034, Russia
- Zoological Institute RAS, Saint Petersburg 199034, Russia
| | | | - Milana Kulakova
- Faculty of Biology, St. Petersburg State University, Saint Petersburg 199034, Russia
- Zoological Institute RAS, Saint Petersburg 199034, Russia
- Correspondence: (M.K.); (E.N.)
| | | | - Viktor Starunov
- Faculty of Biology, St. Petersburg State University, Saint Petersburg 199034, Russia
- Zoological Institute RAS, Saint Petersburg 199034, Russia
| | - Elena Novikova
- Faculty of Biology, St. Petersburg State University, Saint Petersburg 199034, Russia
- Zoological Institute RAS, Saint Petersburg 199034, Russia
- Correspondence: (M.K.); (E.N.)
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12
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Tsitsiridis G, Steinkamp R, Giurgiu M, Brauner B, Fobo G, Frishman G, Montrone C, Ruepp A. CORUM: the comprehensive resource of mammalian protein complexes-2022. Nucleic Acids Res 2022; 51:D539-D545. [PMID: 36382402 PMCID: PMC9825459 DOI: 10.1093/nar/gkac1015] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The CORUM database has been providing comprehensive reference information about experimentally characterized, mammalian protein complexes and their associated biological and biomedical properties since 2007. Given that most catalytic and regulatory functions of the cell are carried out by protein complexes, their composition and characterization is of greatest importance in basic and disease biology. The new CORUM 4.0 release encompasses 5204 protein complexes offering the largest and most comprehensive publicly available dataset of manually curated mammalian protein complexes. The CORUM dataset is built from 5299 different genes, representing 26% of the protein coding genes in humans. Complex information from 3354 scientific articles is mainly obtained from human (70%), mouse (16%) and rat (9%) cells and tissues. Recent curation work includes sets of protein complexes, Functional Complex Groups, that offer comprehensive collections of published data in specific biological processes and molecular functions. In addition, a new graphical analysis tool was implemented that displays co-expression data from the subunits of protein complexes. CORUM is freely accessible at http://mips.helmholtz-muenchen.de/corum/.
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Affiliation(s)
- George Tsitsiridis
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Ralph Steinkamp
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Madalina Giurgiu
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité Universitätsmedizin Berlin, Berlin 13125, Germany
| | - Barbara Brauner
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Gisela Fobo
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Goar Frishman
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Corinna Montrone
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Andreas Ruepp
- To whom correspondence should be addressed. Tel: +49 89 3187 3189; Fax: +49 89 3187 3500;
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13
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Ge R, Cao M, Chen M, Liu M, Xie S. Cytoskeletal networks in primary cilia: Current knowledge and perspectives. J Cell Physiol 2022; 237:3975-3983. [PMID: 36000703 DOI: 10.1002/jcp.30865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/08/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022]
Abstract
Primary cilia, microtubule-based protrusions present on the surface of most mammalian cells, function as sensory organelles that monitor extracellular signals and transduce them into intracellular biochemical responses. There is renewed research interest in primary cilia due to their essential roles in development, tissue homeostasis, and human diseases. Primary cilia dysfunction causes a large spectrum of human diseases, collectively known as ciliopathies. Despite significant advances in our understanding of primary cilia, there are still no effective agents for treating ciliopathies. Primary ciliogenesis is a highly ordered process involving membrane trafficking, basal body maturation, vesicle docking and fusion, transition zone assembly, and axoneme extension, in which actin and microtubule networks play critical and multiple roles. Actin and microtubule network architecture, isotropy, and dynamics are tightly controlled by cytoskeleton-associated proteins, a growing number of which are now recognized as responsible for cilium formation and maintenance. Here we summarize the roles of actin and microtubules and their associated proteins in primary ciliogenesis and maintenance. In doing so, we highlight that targeting cytoskeleton-associated proteins may be a promising therapeutic strategy for the treatment of ciliopathies.
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Affiliation(s)
- Ruixin Ge
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China
| | - Minghui Cao
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China
| | - Miao Chen
- Department of Bioscience, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Min Liu
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China
| | - Songbo Xie
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China.,Department of Bioscience, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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