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Willsey HR, Seaby EG, Godwin A, Ennis S, Guille M, Grainger RM. Modelling human genetic disorders in Xenopus tropicalis. Dis Model Mech 2024; 17:dmm050754. [PMID: 38832520 DOI: 10.1242/dmm.050754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Recent progress in human disease genetics is leading to rapid advances in understanding pathobiological mechanisms. However, the sheer number of risk-conveying genetic variants being identified demands in vivo model systems that are amenable to functional analyses at scale. Here we provide a practical guide for using the diploid frog species Xenopus tropicalis to study many genes and variants to uncover conserved mechanisms of pathobiology relevant to human disease. We discuss key considerations in modelling human genetic disorders: genetic architecture, conservation, phenotyping strategy and rigour, as well as more complex topics, such as penetrance, expressivity, sex differences and current challenges in the field. As the patient-driven gene discovery field expands significantly, the cost-effective, rapid and higher throughput nature of Xenopus make it an essential member of the model organism armamentarium for understanding gene function in development and in relation to disease.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94518, USA
| | - Eleanor G Seaby
- Genomic Informatics Group, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Annie Godwin
- European Xenopus Resource Centre (EXRC), School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Sarah Ennis
- Genomic Informatics Group, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Matthew Guille
- European Xenopus Resource Centre (EXRC), School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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2
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Jühlen R, Fahrenkrog B. From the sideline: Tissue-specific nucleoporin function in health and disease, an update. FEBS Lett 2023; 597:2750-2768. [PMID: 37873737 DOI: 10.1002/1873-3468.14761] [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: 08/10/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
The subcellular compartmentalisation of eukaryotic cells requires selective exchange between the cytoplasm and the nucleus. Intact nucleocytoplasmic transport is vital for normal cell function and mutations in the executing machinery have been causally linked to human disease. Central players in nucleocytoplasmic exchange are nuclear pore complexes (NPCs), which are built from ~30 distinct proteins collectively termed nucleoporins. Aberrant nucleoporin expression was detected in human cancers and autoimmune diseases since quite some time, while it was through the increasing use of next generation sequencing that mutations in nucleoporin genes associated with mainly rare hereditary diseases were revealed. The number of newly identified mutations is steadily increasing, as is the number of diseases. Mutational hotspots have emerged: mutations in the scaffold nucleoporins seemingly affect primarily inner organs, such as heart, kidney, and ovaries, whereas genetic alterations in peripheral, cytoplasmic nucleoporins affect primarily the central nervous system and development. In this review, we summarise latest insights on altered nucleoporin function in the context of human hereditary disorders, with a focus on those where mechanistic insights are beginning to emerge.
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Affiliation(s)
- Ramona Jühlen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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3
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Chen Y, Zhang Y, Zhou X. Non-classical functions of nuclear pore proteins in ciliopathy. Front Mol Biosci 2023; 10:1278976. [PMID: 37908226 PMCID: PMC10614291 DOI: 10.3389/fmolb.2023.1278976] [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: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Nucleoporins (NUPs) constitute integral nuclear pore protein (NPC) elements. Although traditional NUP functions have been extensively researched, evidence of additional vital non-NPC roles, referred to herein as non-classical NUP functions, is also emerging. Several NUPs localise at the ciliary base. Indeed, Nup188, Nup93 or Nup205 knockdown results in cilia loss, impacting cardiac left-right patterning in models and cell lines. Genetic variants of Nup205 and Nup188 have been identified in patients with congenital heart disease and situs inversus totalis or heterotaxy, a prevalent human ciliopathy. These findings link non-classical NUP functions to human diseases. This mini-review summarises pivotal NUP interactions with NIMA-related kinases or nephronophthisis proteins that regulate ciliary function and explores other NUPs potentially implicated in cilia-related disorders. Overall, elucidating the non-classical roles of NUPs will enhance comprehension of ciliopathy aetiology.
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Affiliation(s)
- Yan Chen
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| | - Yuan Zhang
- Department of Assisted Reproduction, 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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4
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Soon HR, Gaunt JR, Bansal VA, Lenherr C, Sze SK, Ch’ng TH. Seizure enhances SUMOylation and zinc-finger transcriptional repression in neuronal nuclei. iScience 2023; 26:107707. [PMID: 37694138 PMCID: PMC10483055 DOI: 10.1016/j.isci.2023.107707] [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: 04/10/2023] [Revised: 05/29/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
A single episode of pilocarpine-induced status epilepticus can trigger the development of spontaneous recurrent seizures in a rodent model for epilepsy. The initial seizure-induced events in neuronal nuclei that lead to long-term changes in gene expression and cellular responses likely contribute toward epileptogenesis. Using a transgenic mouse model to specifically isolate excitatory neuronal nuclei, we profiled the seizure-induced nuclear proteome via tandem mass tag mass spectrometry and observed robust enrichment of nuclear proteins associated with the SUMOylation pathway. In parallel with nuclear proteome, we characterized nuclear gene expression by RNA sequencing which provided insights into seizure-driven transcriptional regulation and dynamics. Strikingly, we saw widespread downregulation of zinc-finger transcription factors, specifically proteins that harbor Krüppel-associated box (KRAB) domains. Our results provide a detailed snapshot of nuclear events induced by seizure activity and demonstrate a robust method for cell-type-specific nuclear profiling that can be applied to other cell types and models.
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Affiliation(s)
- Hui Rong Soon
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
| | - Jessica Ruth Gaunt
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Vibhavari Aysha Bansal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Clara Lenherr
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Centre for Discovery Brain Science, The University of Edinburgh, Edinburgh, UK
| | - Siu Kwan Sze
- Faculty of Applied Health Sciences, Brock University, St. Catherines, ON, Canada
| | - Toh Hean Ch’ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
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5
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Marquez J, Aslam F, Khokha MK. Expanding EMC foldopathies: Topogenesis deficits alter the neural crest. Genesis 2023; 61:e23520. [PMID: 37318954 PMCID: PMC10524326 DOI: 10.1002/dvg.23520] [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: 06/23/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is essential for the insertion of a wide variety of transmembrane proteins into the plasma membrane across cell types. Each EMC is composed of Emc1-7, Emc10, and either Emc8 or Emc9. Recent human genetics studies have implicated variants in EMC genes as the basis for a group of human congenital diseases. The patient phenotypes are varied but appear to affect a subset of tissues more prominently than others. Namely, craniofacial development seems to be commonly affected. We previously developed an array of assays in Xenopus tropicalis to assess the effects of emc1 depletion on the neural crest, craniofacial cartilage, and neuromuscular function. We sought to extend this approach to additional EMC components identified in patients with congenital malformations. Through this approach, we determine that EMC9 and EMC10 are important for neural crest development and the development of craniofacial structures. The phenotypes observed in patients and our Xenopus model phenotypes similar to EMC1 loss of function likely due to a similar mechanism of dysfunction in transmembrane protein topogenesis.
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Affiliation(s)
- Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Faiza Aslam
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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Chen S, Jin Q, Hou S, Li M, Zhang Y, Guan L, Pan W, Ge J, Zhou D. Identification of recurrent variants implicated in disease in bicuspid aortic valve patients through whole-exome sequencing. Hum Genomics 2022; 16:36. [PMID: 36071494 PMCID: PMC9450445 DOI: 10.1186/s40246-022-00405-z] [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: 04/27/2022] [Accepted: 08/06/2022] [Indexed: 11/10/2022] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect in human beings, with an estimated prevalence in the general population of between 0.5 and 2%. Moreover, BAV is the most common cause of aortic stenosis in the pediatric population. Patients with BAV may have no symptoms for life, and some of them may progress to aortic stenosis. Genetic factors increase the susceptibility and development of BAV. However, the pathogenesis and BAV are still unclear, and more genetic variants are still needed for elucidating the molecular mechanism and stratification of patients. The present study carried out screening of variants implicated in disease in BAV patients. The whole-exome sequencing (WES) was performed in 20 BAV patients and identified 40 different heterozygous missense mutations in 36 genes (MIB2, FAAH, S100A1, RGS16, MAP3K19, NEB, TTN, TNS1, CAND2, CCK, KALRN, ATP10D, SLIT3, ROS1, FABP7, NUP205, IL11RA, NPR2, COL5A1, CUBN, JMJD1C, ANXA7, TRIM8, LGR4, TPCN2, APOA5, GPR84, LRP1, NCOR2, AKAP11, ESRRB, NGB, AKAP13, WWOX, KCNJ12, ARHGEF1). The mutations in these genes were identified as recurrent variants implicated in disease by in silico prediction tool analysis. Nine genes (MIB2, S100A1, TTN, CCK, NUP205, LGR4, NCOR2, ESRRB, and WWOX) among the 36 genes were identified as variants implicated in disease via unanimous agreement of in silico prediction tool analysis and sequenced in an independent cohort of 137 BAV patients to validate the results of WES. BAV patients carrying these variants demonstrated reduced left ventricular ejection fractions (LVEF) (63.8 ± 7.5% vs. 58.4 ± 5.2%, P < 0.001) and larger calcification volume [(1129.3 ± 154) mm3 vs. (1261.8 ± 123) mm3, P < 0.001]. The variants in TTN, NUP205 and NCOR2 genes are significantly associated with reduced LVEF, and the variants in S100A1, LGR4, ESRRB, and WWOX genes are significantly associated with larger calcification volume. We identified a panel of recurrent variants implicated in disease in genes related to the pathogenesis of BAV. Our data speculate that these variants are promising markers for risk stratification of BAV patients with increased susceptibility to aortic stenosis.
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Affiliation(s)
- Shasha Chen
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Qinchun Jin
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Shiqiang Hou
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Mingfei Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Yuan Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Lihua Guan
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Wenzhi Pan
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China.,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China.,National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Daxin Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, No. 180 of Road Fenglin, District Xuhui, Shanghai, 200032, China. .,Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, China. .,National Clinical Research Center for Interventional Medicine, Shanghai, China.
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Wells JR, Padua MB, Ware SM. The genetic landscape of cardiovascular left-right patterning defects. Curr Opin Genet Dev 2022; 75:101937. [PMID: 35777348 PMCID: PMC10698510 DOI: 10.1016/j.gde.2022.101937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/11/2022] [Accepted: 05/19/2022] [Indexed: 11/26/2022]
Abstract
Heterotaxy is a disorder with complex congenital heart defects and diverse left-right (LR) patterning defects in other organ systems. Despite evidence suggesting a strong genetic component in heterotaxy, the majority of molecular causes remain unknown. Established genes often involve a ciliated, embryonic structure known as the left-right organizer (LRO). Herein, we focus on genetic discoveries in heterotaxy in the past two years. These include complex genetic architecture, novel mechanisms regulating cilia formation, and evidence for conservation of LR patterning between distant species. We feature new insights regarding established LR signaling pathways, bring attention to heterotaxy candidate genes in novel pathways, and provide an extensive overview of genes previously associated with laterality phenotypes in humans.
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Affiliation(s)
- John R Wells
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Maria B Padua
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
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Najafi M, Riedhammer KM, Rad A, Torbati PN, Berutti R, Schüle I, Schroda S, Meitinger T, Ćomić J, Bojd SS, Baranzehi T, Shojaei A, Azarfar A, Khazaei MR, Köttgen A, Backofen R, Karimiani EG, Hoefele J, Schmidts M. High detection rate for disease-causing variants in a cohort of 30 Iranian pediatric steroid resistant nephrotic syndrome cases. Front Pediatr 2022; 10:974840. [PMID: 36245711 PMCID: PMC9555279 DOI: 10.3389/fped.2022.974840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Steroid resistant nephrotic syndrome (SRNS) represents a significant renal disease burden in childhood and adolescence. In contrast to steroid sensitive nephrotic syndrome (SSNS), renal outcomes are significantly poorer in SRNS. Over the past decade, extensive genetic heterogeneity has become evident while disease-causing variants are still only identified in 30% of cases in previously reported studies with proportion and type of variants identified differing depending on the age of onset and ethnical background of probands. A genetic diagnosis however can have implications regarding clinical management, including kidney transplantation, extrarenal disease manifestations, and, in some cases, even causal therapy. Genetic diagnostics therefore play an important role for the clinical care of SRNS affected individuals. METHODOLOGY AND RESULTS Here, we performed NPHS2 Sanger sequencing and subsequent exome sequencing in 30 consanguineous Iranian families with a child affected by SRNS with a mean age of onset of 16 months. We identified disease-causing variants and one variant of uncertain significance in 22 families (73%), including variants in NPHS1 (30%), followed by NPHS2 (20%), WT1 (7%) as well as in NUP205, COQ6, ARHGDIA, SGPL1, and NPHP1 in single cases. Eight of these variants have not previously been reported as disease-causing, including four NPHS1 variants and one variant in NPHS2, ARHGDIA, SGPL1, and NPHP1 each. CONCLUSION In line with previous studies in non-Iranian subjects, we most frequently identified disease-causing variants in NPHS1 and NPHS2. While Sanger sequencing of NPHS2 can be considered as first diagnostic step in non-congenital cases, the genetic heterogeneity underlying SRNS renders next-generation sequencing based diagnostics as the most efficient genetic screening method. In accordance with the mainly autosomal recessive inheritance pattern, diagnostic yield can be significantly higher in consanguineous than in outbred populations.
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Affiliation(s)
- Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, Netherlands.,Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Aboulfazl Rad
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, Netherlands.,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | | | - Riccardo Berutti
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Isabel Schüle
- Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany
| | - Sophie Schroda
- Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Jasmina Ćomić
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Simin Sadeghi Bojd
- Children and Adolescents Health Research Center, Research Institute of Cellular and Molecular Science in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Tayebeh Baranzehi
- Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran
| | - Azadeh Shojaei
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Anoush Azarfar
- Pediatric Nephrology, Kidney Transplantation Complications Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmood Reza Khazaei
- Department of Pediatrics, Faculty of Medicine, Mashhad Medical Sciences, Islamic Azad University, Mashhad, Iran
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Center for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany.,Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Ehsan Ghayoor Karimiani
- Next Generation Genetic Polyclinic, Mashhad, Iran.,Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University, London, United Kingdom
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, Netherlands.,Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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10
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Nuclear pore complex maintenance and implications for age-related diseases. Trends Cell Biol 2021; 32:216-227. [PMID: 34782239 DOI: 10.1016/j.tcb.2021.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022]
Abstract
Nuclear pore complexes (NPCs) bridge the nucleus and the cytoplasm and are indispensable for crucial cellular activities, such as bidirectional molecular trafficking and gene transcription regulation. The discovery of long-lived proteins (LLPs) in NPCs from postmitotic cells raises the exciting possibility that the maintenance of NPC integrity might play an inherent role in lifelong cell function. Age-dependent deterioration of NPCs and loss of nuclear integrity have been linked to age-related decline in postmitotic cell function and degenerative diseases. In this review, we discuss our current understanding of NPC maintenance in proliferating and postmitotic cells, and how malfunction of nucleoporins (Nups) might contribute to the pathogenesis of various neurodegenerative and cardiovascular diseases.
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11
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Evolution and diversification of the nuclear pore complex. Biochem Soc Trans 2021; 49:1601-1619. [PMID: 34282823 PMCID: PMC8421043 DOI: 10.1042/bst20200570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022]
Abstract
The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.
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Abstract
Congenital birth defects result from an abnormal development of an embryo and have detrimental effects on children's health. Specifically, congenital heart malformations are a leading cause of death among pediatric patients and often require surgical interventions within the first year of life. Increased efforts to navigate the human genome provide an opportunity to discover multiple candidate genes in patients suffering from birth defects. These efforts, however, fail to provide an explanation regarding the mechanisms of disease pathogenesis and emphasize the need for an efficient platform to screen candidate genes. Xenopus is a rapid, cost effective, high-throughput vertebrate organism to model the mechanisms behind human disease. This review provides numerous examples describing the successful use of Xenopus to investigate the contribution of patient mutations to complex phenotypes including congenital heart disease and heterotaxy. Moreover, we describe a variety of unique methods that allow us to rapidly recapitulate patients' phenotypes in frogs: gene knockout and knockdown strategies, the use of fate maps for targeted manipulations, and novel imaging modalities. The combination of patient genomics data and the functional studies in Xenopus will provide necessary answers to the patients suffering from birth defects. Furthermore, it will allow for the development of better diagnostic methods to ensure early detection and intervention. Finally, with better understanding of disease pathogenesis, new treatment methods can be tailored specifically to address patient's phenotype and genotype.
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Affiliation(s)
- Valentyna Kostiuk
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, United States.
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Baluška F, Lyons S. Archaeal Origins of Eukaryotic Cell and Nucleus. Biosystems 2021; 203:104375. [PMID: 33549602 DOI: 10.1016/j.biosystems.2021.104375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 01/12/2023]
Abstract
Symbiosis is a major evolutionary force, especially at the cellular level. Here we discuss several older and new discoveries suggesting that besides mitochondria and plastids, eukaryotic nuclei also have symbiotic origins. We propose an archaea-archaea scenario for the evolutionary origin of the eukaryotic cells. We suggest that two ancient archaea-like cells, one based on the actin cytoskeleton and another one based on the tubulin-centrin cytoskeleton, merged together to form the first nucleated eukaryotic cell. This archaeal endosymbiotic origin of eukaryotic cells and their nuclei explains several features of eukaryotic cells which are incompatible with the currently preferred autogenous scenarios of eukaryogenesis.
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Affiliation(s)
| | - Sherrie Lyons
- Union College, 130 N. College, St. - Schenectady, NY, 12305, USA.
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