1
|
Chen S, Jiang Q, Fan J, Cheng H. Nuclear mRNA export. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39243141 DOI: 10.3724/abbs.2024145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2024] Open
Abstract
In eukaryotic cells, gene expression begins with transcription in the nucleus, followed by the maturation of messenger RNAs (mRNAs). These mRNA molecules are then exported to the cytoplasm through the nuclear pore complex (NPC), a process that serves as a critical regulatory phase of gene expression. The export of mRNA is intricately linked to precursor mRNA (pre-mRNA) processing, ensuring that only properly processed mRNA reaches the cytoplasm. This coordination is essential, as recent studies have revealed that mRNA export factors not only assist in transport but also influence upstream processing steps, adding a layer of complexity to gene regulation. Furthermore, the export process competes with RNA processing and degradation pathways, maintaining a delicate balance vital for accurate gene expression. While these mechanisms are generally conserved across eukaryotes, significant differences exist between yeast and higher eukaryotic cells, particularly due to the more genome complexity of the latter. This review delves into the current research on mRNA export in higher eukaryotic cells, focusing on its role in the broader context of gene expression regulation and highlighting how it interacts with other gene expression processes to ensure precise and efficient gene functionality in complex organisms.
Collapse
Affiliation(s)
- Suli Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024, University of Chinese Academy of Sciences, China
| | - Qingyi Jiang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Fan
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Hong Cheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024, University of Chinese Academy of Sciences, China
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
2
|
Colussi C, Bertozzi A, Leone L, Rinaudo M, Sollazzo R, Conte F, Paccosi E, Nardella L, Aceto G, Puma DDL, Ripoli C, Vita MG, Marra C, D'Ascenzo M, Grassi C. Nucleoporin 153 deficiency in adult neural stem cells defines a pathological protein-network signature and defective neurogenesis in a mouse model of AD. Stem Cell Res Ther 2024; 15:275. [PMID: 39227892 PMCID: PMC11373261 DOI: 10.1186/s13287-024-03805-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 06/17/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Reduction of adult hippocampal neurogenesis is an early critical event in Alzheimer's disease (AD), contributing to progressive memory loss and cognitive decline. Reduced levels of the nucleoporin 153 (Nup153), a key epigenetic regulator of NSC stemness, characterize the neural stem cells isolated from a mouse model of AD (3×Tg) (AD-NSCs) and determine their altered plasticity and gene expression. METHODS Nup153-regulated mechanisms contributing to NSC function were investigated: (1) in cultured NSCs isolated from AD and wild type (WT) mice by proteomics; (2) in vivo by lentiviral-mediated delivery of Nup153 or GFP in the hippocampus of AD and control mice analyzing neurogenesis and cognitive function; (3) in human iPSC-derived brain organoids obtained from AD patients and control subjects as a model of neurodevelopment. RESULTS Proteomic approach identified Nup153 interactors in WT- and AD-NSCs potentially implicated in neurogenesis regulation. Gene ontology (GO) analysis showed that Nup153-bound proteins in WT-NSCs were involved in RNA metabolism, nuclear import and epigenetic mechanisms. Nup153-bound proteins in AD-NSCs were involved in pathways of neurodegeneration, mitochondrial dysfunction, proteasomal processing and RNA degradation. Furthermore, recovery of Nup153 levels in AD-NSCs reduced the levels of oxidative stress markers and recovered proteasomal activity. Lentiviral-mediated delivery of Nup153 in the hippocampal niche of AD mice increased the proliferation of early progenitors, marked by BrdU/DCX and BrdU/PSANCAM positivity and, later, the integration of differentiating neurons in the cell granule layer (BrdU/NeuN+ cells) compared with GFP-injected AD mice. Consistently, Nup153-injected AD mice showed an improvement of cognitive performance in comparison to AD-GFP mice at 1 month after virus delivery assessed by Morris Water Maze. To validate the role of Nup153 in neurogenesis we took advantage of brain organoids derived from AD-iPSCs characterized by fewer neuroepithelial progenitor loops and reduced differentiation areas. The upregulation of Nup153 in AD organoids recovered the formation of neural-like tubes and differentiation. CONCLUSIONS Our data suggest that the positive effect of Nup153 on neurogenesis is based on a complex regulatory network orchestrated by Nup153 and that this protein is a valuable disease target.
Collapse
Affiliation(s)
- Claudia Colussi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI) - CNR , National Research Council, Via dei Taurini 19, Rome, 00185, Italy.
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy.
| | - Alessia Bertozzi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI) - CNR , National Research Council, Via dei Taurini 19, Rome, 00185, Italy
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Lucia Leone
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| | - Marco Rinaudo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| | - Raimondo Sollazzo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Federica Conte
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI) - CNR , National Research Council, Via dei Taurini 19, Rome, 00185, Italy
| | - Elena Paccosi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI) - CNR , National Research Council, Via dei Taurini 19, Rome, 00185, Italy
| | - Luca Nardella
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Giuseppe Aceto
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| | - Domenica Donatella Li Puma
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| | - Cristian Ripoli
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| | | | - Camillo Marra
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| | - Marcello D'Ascenzo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, 00168, Italy
| |
Collapse
|
3
|
Kim S, Phan S, Tran HT, Shaw TR, Shahmoradian SH, Ellisman MH, Veatch SL, Barmada SJ, Pappas SS, Dauer WT. TorsinA is essential for neuronal nuclear pore complex localization and maturation. Nat Cell Biol 2024:10.1038/s41556-024-01480-1. [PMID: 39117796 DOI: 10.1038/s41556-024-01480-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/11/2024] [Indexed: 08/10/2024]
Abstract
As lifelong interphase cells, neurons face an array of unique challenges. A key challenge is regulating nuclear pore complex (NPC) biogenesis and localization, the mechanisms of which are largely unknown. Here we identify neuronal maturation as a period of strongly upregulated NPC biogenesis. We demonstrate that the AAA+ protein torsinA, whose dysfunction causes the neurodevelopmental movement disorder DYT-TOR1A dystonia and co-ordinates NPC spatial organization without impacting total NPC density. We generated an endogenous Nup107-HaloTag mouse line to directly visualize NPC organization in developing neurons and find that torsinA is essential for proper NPC localization. In the absence of torsinA, the inner nuclear membrane buds excessively at sites of mislocalized nascent NPCs, and the formation of complete NPCs is delayed. Our work demonstrates that NPC spatial organization and number are independently determined and identifies NPC biogenesis as a process vulnerable to neurodevelopmental disease insults.
Collapse
Affiliation(s)
- Sumin Kim
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hung Tri Tran
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, UT Southwestern, Dallas, TX, USA
| | - Thomas R Shaw
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Program in Applied Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah H Shahmoradian
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, UT Southwestern, Dallas, TX, USA
- Department of Biophysics, UT Southwestern, Dallas, TX, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sarah L Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Program in Applied Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Sami J Barmada
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
| | - Samuel S Pappas
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA.
- Department of Neurology, UT Southwestern, Dallas, TX, USA.
| | - William T Dauer
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA.
- Department of Neurology, UT Southwestern, Dallas, TX, USA.
- Department of Neuroscience, UT Southwestern, Dallas, TX, USA.
| |
Collapse
|
4
|
Li Y, Zhu J, Zhai F, Kong L, Li H, Jin X. Advances in the understanding of nuclear pore complexes in human diseases. J Cancer Res Clin Oncol 2024; 150:374. [PMID: 39080077 PMCID: PMC11289042 DOI: 10.1007/s00432-024-05881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Nuclear pore complexes (NPCs) are sophisticated and dynamic protein structures that straddle the nuclear envelope and act as gatekeepers for transporting molecules between the nucleus and the cytoplasm. NPCs comprise up to 30 different proteins known as nucleoporins (NUPs). However, a growing body of research has suggested that NPCs play important roles in gene regulation, viral infections, cancer, mitosis, genetic diseases, kidney diseases, immune system diseases, and degenerative neurological and muscular pathologies. PURPOSE In this review, we introduce the structure and function of NPCs. Then We described the physiological and pathological effects of each component of NPCs which provide a direction for future clinical applications. METHODS The literatures from PubMed have been reviewed for this article. CONCLUSION This review summarizes current studies on the implications of NPCs in human physiology and pathology, highlighting the mechanistic underpinnings of NPC-associated diseases.
Collapse
Affiliation(s)
- Yuxuan Li
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Jie Zhu
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Fengguang Zhai
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Lili Kong
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Hong Li
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China.
| | - Xiaofeng Jin
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China.
| |
Collapse
|
5
|
Dai W, Liu Z, Yan M, Nian X, Hong F, Zhou Z, Wang C, Fu X, Li X, Jiang M, Zhu Y, Huang Q, Lu X, Hou L, Yan N, Wang Q, Hu J, Mo W, Zhang X, Zhang L. Nucleoporin Seh1 controls murine neocortical development via transcriptional repression of p21 in neural stem cells. Dev Cell 2024; 59:482-495.e6. [PMID: 38272027 DOI: 10.1016/j.devcel.2024.01.002] [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: 11/08/2022] [Revised: 06/21/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024]
Abstract
Mutations or dysregulation of nucleoporins (Nups) are strongly associated with neural developmental diseases, yet the underlying mechanisms remain poorly understood. Here, we show that depletion of Nup Seh1 in radial glial progenitors results in defective neural progenitor proliferation and differentiation that ultimately manifests in impaired neurogenesis and microcephaly. This loss of stem cell proliferation is not associated with defects in the nucleocytoplasmic transport. Rather, transcriptome analysis showed that ablation of Seh1 in neural stem cells derepresses the expression of p21, and knockdown of p21 partially restored self-renewal capacity. Mechanistically, Seh1 cooperates with the NuRD transcription repressor complex at the nuclear periphery to regulate p21 expression. Together, these findings identified that Nups regulate brain development by exerting a chromatin-associated role and affecting neural stem cell proliferation.
Collapse
Affiliation(s)
- Wenxiu Dai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Zhixiong Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China; Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai 519031, China
| | - Minbiao Yan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Ximing Nian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Fan Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Zhihao Zhou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Chaomeng Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xing Fu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xuewen Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Mengyun Jiang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Yanqin Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Qiuying Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiaoyun Lu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Lichao Hou
- Department of Anesthesiology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Ning Yan
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qin Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jin Hu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wei Mo
- Sir Run Run Shaw Hospital, Department of Immunology, School of Basic Medical Science, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Hangzhou 311121, China
| | - Xueqin Zhang
- Department of Gynaecology and Obstetrics, Women and Children's Hospital Affiliated to Xiamen University, Xiamen University, Xiamen 361102, Fujian, China
| | - Liang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, Fujian, China; Department of Gynaecology and Obstetrics, Women and Children's Hospital Affiliated to Xiamen University, Xiamen University, Xiamen 361102, Fujian, China.
| |
Collapse
|
6
|
Chintala K, Yandrapally S, Faiz W, Kispotta CR, Sarkar S, Mishra K, Banerjee S. The nuclear pore protein NUP98 impedes LTR-driven basal gene expression of HIV-1, viral propagation, and infectivity. Front Immunol 2024; 15:1330738. [PMID: 38449868 PMCID: PMC10914986 DOI: 10.3389/fimmu.2024.1330738] [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: 10/31/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024] Open
Abstract
Nucleoporins (NUPs) are cellular effectors of human immunodeficiency virus-1 (HIV-1) replication that support nucleocytoplasmic trafficking of viral components. However, these also non-canonically function as positive effectors, promoting proviral DNA integration into the host genome and viral gene transcription, or as negative effectors by associating with HIV-1 restriction factors, such as MX2, inhibiting the replication of HIV-1. Here, we investigated the regulatory role of NUP98 on HIV-1 as we observed a lowering of its endogenous levels upon HIV-1 infection in CD4+ T cells. Using complementary experiments in NUP98 overexpression and knockdown backgrounds, we deciphered that NUP98 negatively affected HIV-1 long terminal repeat (LTR) promoter activity and lowered released virus levels. The negative effect on promoter activity was independent of HIV-1 Tat, suggesting that NUP98 prevents the basal viral gene expression. ChIP-qPCR showed NUP98 to be associated with HIV-1 LTR, with the negative regulatory element (NRE) of HIV-1 LTR playing a dominant role in NUP98-mediated lowering of viral gene transcription. Truncated mutants of NUP98 showed that the attenuation of HIV-1 LTR-driven transcription is primarily contributed by its N-terminal region. Interestingly, the virus generated from the producer cells transiently expressing NUP98 showed lower infectivity, while the virus generated from NUP98 knockdown CD4+ T cells showed higher infectivity as assayed in TZM-bl cells, corroborating the anti-HIV-1 properties of NUP98. Collectively, we show a new non-canonical function of a nucleoporin adding to the list of moonlighting host factors regulating viral infections. Downregulation of NUP98 in a host cell upon HIV-1 infection supports the concept of evolutionary conflicts between viruses and host antiviral factors.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| |
Collapse
|
7
|
Li Y, Bertozzi A, Mann MRW, Kühn B. Interdependent changes of nuclear lamins, nuclear pore complexes, and ploidy regulate cellular regeneration and stress response in the heart. Nucleus 2023; 14:2246310. [PMID: 37606283 PMCID: PMC10446781 DOI: 10.1080/19491034.2023.2246310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
In adult mammals, many heart muscle cells (cardiomyocytes) are polyploid, do not proliferate (post-mitotic), and, consequently, cannot contribute to heart regeneration. In contrast, fetal and neonatal heart muscle cells are diploid, proliferate, and contribute to heart regeneration. We have identified interdependent changes of the nuclear lamina, nuclear pore complexes, and DNA-content (ploidy) in heart muscle cell maturation. These results offer new perspectives on how cells alter their nuclear transport and, with that, their gene regulation in response to extracellular signals. We present how changes of the nuclear lamina alter nuclear pore complexes in heart muscle cells. The consequences of these changes for cellular regeneration and stress response in the heart are discussed.
Collapse
Affiliation(s)
- Yao Li
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alberto Bertozzi
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mellissa RW Mann
- Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Bernhard Kühn
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
8
|
Malik SC, Lin JD, Ziegler-Waldkirch S, Tholen S, Deshpande SS, Schwabenland M, Schilling O, Vlachos A, Meyer-Luehmann M, Schachtrup C. Tpr Misregulation in Hippocampal Neural Stem Cells in Mouse Models of Alzheimer's Disease. Cells 2023; 12:2757. [PMID: 38067185 PMCID: PMC10706632 DOI: 10.3390/cells12232757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Nuclear pore complexes (NPCs) are highly dynamic macromolecular protein structures that facilitate molecular exchange across the nuclear envelope. Aberrant NPC functioning has been implicated in neurodegeneration. The translocated promoter region (Tpr) is a critical scaffolding nucleoporin (Nup) of the nuclear basket, facing the interior of the NPC. However, the role of Tpr in adult neural stem/precursor cells (NSPCs) in Alzheimer's disease (AD) is unknown. Using super-resolution (SR) and electron microscopy, we defined the different subcellular localizations of Tpr and phospho-Tpr (P-Tpr) in NSPCs in vitro and in vivo. Elevated Tpr expression and reduced P-Tpr nuclear localization accompany NSPC differentiation along the neurogenic lineage. In 5xFAD mice, an animal model of AD, increased Tpr expression in DCX+ hippocampal neuroblasts precedes increased neurogenesis at an early stage, before the onset of amyloid-β plaque formation. Whereas nuclear basket Tpr interacts with chromatin modifiers and NSPC-related transcription factors, P-Tpr interacts and co-localizes with cyclin-dependent kinase 1 (Cdk1) at the nuclear chromatin of NSPCs. In hippocampal NSPCs in a mouse model of AD, aberrant Tpr expression was correlated with altered NPC morphology and counts, and Tpr was aberrantly expressed in postmortem human brain samples from patients with AD. Thus, we propose that altered levels and subcellular localization of Tpr in CNS disease affect Tpr functionality, which in turn regulates the architecture and number of NSPC NPCs, possibly leading to aberrant neurogenesis.
Collapse
Affiliation(s)
- Subash C. Malik
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jia-Di Lin
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Stephanie Ziegler-Waldkirch
- Department of Neurology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (S.Z.-W.); (M.M.-L.)
| | - Stefan Tholen
- Institute of Surgical Pathology, Medical Center, University of Freiburg, 79106 Freiburg, Germany; (S.T.); (O.S.)
| | - Sachin S. Deshpande
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marius Schwabenland
- Institute of Neuropathology, University of Freiburg, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Medical Center, University of Freiburg, 79106 Freiburg, Germany; (S.T.); (O.S.)
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
- Center BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
- Center for Basics in Neuromodulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Melanie Meyer-Luehmann
- Department of Neurology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (S.Z.-W.); (M.M.-L.)
- Center for Basics in Neuromodulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Christian Schachtrup
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Center for Basics in Neuromodulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| |
Collapse
|
9
|
Gambadauro A, Mangano GD, Galletta K, Granata F, Riva A, Massella L, Guzzo I, Farello G, Scorrano G, Di Francesco L, Di Donato G, Ianni C, Di Ludovico A, La Bella S, Striano P, Efthymiou S, Houlden H, Nardello R, Chimenz R. NUP85 as a Neurodevelopmental Gene: From Podocyte to Neuron. Genes (Basel) 2023; 14:2143. [PMID: 38136965 PMCID: PMC10743110 DOI: 10.3390/genes14122143] [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: 10/10/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Pathogenic gene variants encoding nuclear pore complex (NPC) proteins were previously implicated in the pathogenesis of steroid-resistant nephrotic syndrome (SRNS). The NUP85 gene, encoding nucleoporin, is related to a very rare form of SRNS with limited genotype-phenotype information. We identified an Italian boy affected with an SRNS associated with severe neurodevelopmental impairment characterized by microcephaly, axial hypotonia, lack of achievement of motor milestones, and refractory seizures with an associated hypsarrhythmic pattern on electroencephalography. Brain magnetic resonance imaging (MRI) showed hypoplasia of the corpus callosum and a simplified gyration of the cerebral cortex. Since the age of 3 years, the boy was followed up at our Pediatric Nephrology Department for an SRNS, with a focal segmental glomerulosclerosis at renal biopsy. The boy died 32 months after SRNS onset, and a Whole-Exome Sequencing analysis revealed a novel compound heterozygous variant in NUP85 (NM_024844.5): 611T>A (p.Val204Glu), c.1904T>G (p.Leu635Arg), inherited from the father and mother, respectively. We delineated the clinical phenotypes of NUP85-related disorders, reviewed the affected individuals so far reported in the literature, and overall expanded both the phenotypic and the molecular spectrum associated with this ultra-rare genetic condition. Our study suggests a potential occurrence of severe neurological phenotypes as part of the NUP85-related clinical spectrum and highlights an important involvement of nucleoporin in brain developmental processes and neurological function.
Collapse
Affiliation(s)
- Antonella Gambadauro
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, University of Messina, Via Consolare Valeria 1, 98124 Messina, Italy; (A.G.); (R.C.)
| | - Giuseppe Donato Mangano
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
| | - Karol Galletta
- Department of Biomedical, Dental Science and Morphological and Functional Images, Neuroradiology Unit, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (K.G.); (F.G.)
| | - Francesca Granata
- Department of Biomedical, Dental Science and Morphological and Functional Images, Neuroradiology Unit, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (K.G.); (F.G.)
| | - Antonella Riva
- Unit of Medical Genetics, IRCSS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; (A.R.); (P.S.)
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Laura Massella
- Division of Nephrology, Department of Pediatric Subspecialties, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00165 Rome, Italy; (L.M.); (I.G.)
| | - Isabella Guzzo
- Division of Nephrology, Department of Pediatric Subspecialties, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00165 Rome, Italy; (L.M.); (I.G.)
| | - Giovanni Farello
- Department of Pediatrics, University of L’Aquila, 67100 L’Aquila, Italy; (G.F.); (G.S.); (L.D.F.); (G.D.D.); (C.I.); (A.D.L.)
| | - Giovanna Scorrano
- Department of Pediatrics, University of L’Aquila, 67100 L’Aquila, Italy; (G.F.); (G.S.); (L.D.F.); (G.D.D.); (C.I.); (A.D.L.)
| | - Ludovica Di Francesco
- Department of Pediatrics, University of L’Aquila, 67100 L’Aquila, Italy; (G.F.); (G.S.); (L.D.F.); (G.D.D.); (C.I.); (A.D.L.)
| | - Giulio Di Donato
- Department of Pediatrics, University of L’Aquila, 67100 L’Aquila, Italy; (G.F.); (G.S.); (L.D.F.); (G.D.D.); (C.I.); (A.D.L.)
| | - Carolina Ianni
- Department of Pediatrics, University of L’Aquila, 67100 L’Aquila, Italy; (G.F.); (G.S.); (L.D.F.); (G.D.D.); (C.I.); (A.D.L.)
| | - Armando Di Ludovico
- Department of Pediatrics, University of L’Aquila, 67100 L’Aquila, Italy; (G.F.); (G.S.); (L.D.F.); (G.D.D.); (C.I.); (A.D.L.)
| | - Saverio La Bella
- Department of Pediatrics, University of L’Aquila, 67100 L’Aquila, Italy; (G.F.); (G.S.); (L.D.F.); (G.D.D.); (C.I.); (A.D.L.)
| | - Pasquale Striano
- Unit of Medical Genetics, IRCSS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; (A.R.); (P.S.)
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Stephanie Efthymiou
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK; (S.E.); (H.H.)
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK; (S.E.); (H.H.)
| | - Rosaria Nardello
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
| | - Roberto Chimenz
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, University of Messina, Via Consolare Valeria 1, 98124 Messina, Italy; (A.G.); (R.C.)
| |
Collapse
|
10
|
Penzo A, Palancade B. Puzzling out nuclear pore complex assembly. FEBS Lett 2023; 597:2705-2727. [PMID: 37548888 DOI: 10.1002/1873-3468.14713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Nuclear pore complexes (NPCs) are sophisticated multiprotein assemblies embedded within the nuclear envelope and controlling the exchanges of molecules between the cytoplasm and the nucleus. In this review, we summarize the mechanisms by which these elaborate complexes are built from their subunits, the nucleoporins, based on our ever-growing knowledge of NPC structural organization and on the recent identification of additional features of this process. We present the constraints faced during the production of nucleoporins, their gathering into oligomeric complexes, and the formation of NPCs within nuclear envelopes, and review the cellular strategies at play, from co-translational assembly to the enrolment of a panel of cofactors. Remarkably, the study of NPCs can inform our perception of the biogenesis of multiprotein complexes in general - and vice versa.
Collapse
Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| |
Collapse
|
11
|
Montel F. [Structural and mechanical plasticity of the nuclear pore]. Med Sci (Paris) 2023; 39:625-631. [PMID: 37695152 DOI: 10.1051/medsci/2023096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
The nuclear pore, which can be seen as the gateway to the cell nucleus, is central to many processes including gene regulation. It is a complex and dynamic structure composed of more than 30 proteins present in multiple copies that allows the selective and directional transport of RNA and proteins. As shown by recent studies, it is able to adapt its overall structure to the state of the cell. These results suggest that the structural and mechanical plasticity of the nuclear pore is important for its function but also in the development of cancer or viral infections.
Collapse
Affiliation(s)
- Fabien Montel
- Laboratoire de physique, CNRS UMR 5672, école normale supérieure de Lyon, université de Lyon, F-69342 Lyon, France
| |
Collapse
|
12
|
Ravindran E, Lesca G, Januel L, Goldgruber L, Dickmanns A, Margot H, Kaindl AM. Case report: Compound heterozygous NUP85 variants cause autosomal recessive primary microcephaly. Front Neurol 2023; 14:1124886. [PMID: 36846113 PMCID: PMC9947397 DOI: 10.3389/fneur.2023.1124886] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
Nucleoporin (NUP) 85 is a member of the Y-complex of nuclear pore complex (NPC) that is key for nucleocytoplasmic transport function, regulation of mitosis, transcription, and chromatin organization. Mutations in various nucleoporin genes have been linked to several human diseases. Among them, NUP85 was linked to childhood-onset steroid-resistant nephrotic syndrome (SRNS) in four affected individuals with intellectual disability but no microcephaly. Recently, we broaden the phenotype spectrum of NUP85-associated disease by reporting NUP85 variants in two unrelated individuals with primary autosomal recessive microcephaly (MCPH) and Seckel syndrome (SCKS) spectrum disorders (MCPH-SCKS) without SRNS. In this study, we report compound heterozygous NUP85 variants in an index patient with only MCPH phenotype, but neither Seckel syndrome nor SRNS was reported. We showed that the identified missense variants cause reduced cell viability of patient-derived fibroblasts. Structural simulation analysis of double variants is predicted to alter the structure of NUP85 and its interactions with neighboring NUPs. Our study thereby further expands the phenotypic spectrum of NUP85-associated human disorder and emphasizes the crucial role of NUP85 in the brain development and function.
Collapse
Affiliation(s)
- Ethiraj Ravindran
- Institute of Cell Biology and Neurobiology, Charité – Universitätsmedizin Berlin, Berlin, Germany,Department of Pediatric Neurology, Charité – Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Gaetan Lesca
- Department of Genetics, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France,Institut NeuroMyoGene PNMG, CNRS UMR5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Louis Januel
- Department of Genetics, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
| | - Linus Goldgruber
- Department of Biomedical Engineering, Veterinärmedizinische Universität (Vetmeduni), Vienna, Austria
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Henri Margot
- Department of Medical Genetics, University of Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Bordeaux, France,*Correspondence: Henri Margot ✉
| | - Angela M. Kaindl
- Institute of Cell Biology and Neurobiology, Charité – Universitätsmedizin Berlin, Berlin, Germany,Department of Pediatric Neurology, Charité – Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité – Universitätsmedizin Berlin, Berlin, Germany,Angela M. Kaindl ✉
| |
Collapse
|
13
|
Nuclear envelope assembly and dynamics during development. Semin Cell Dev Biol 2023; 133:96-106. [PMID: 35249812 DOI: 10.1016/j.semcdb.2022.02.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 01/22/2023]
Abstract
The nuclear envelope (NE) protects but also organizes the eukaryotic genome. In this review we will discuss recent literature on how the NE disassembles and reassembles, how it varies in surface area and protein composition and how this translates into chromatin organization and gene expression in the context of animal development.
Collapse
|
14
|
A Nuclear Belt Fastens on Neural Cell Fate. Cells 2022; 11:cells11111761. [PMID: 35681456 PMCID: PMC9179901 DOI: 10.3390/cells11111761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/22/2022] Open
Abstract
Successful embryonic and adult neurogenesis require proliferating neural stem and progenitor cells that are intrinsically and extrinsically guided into a neuronal fate. In turn, migration of new-born neurons underlies the complex cytoarchitecture of the brain. Proliferation and migration are therefore essential for brain development, homeostasis and function in adulthood. Among several tightly regulated processes involved in brain formation and function, recent evidence points to the nuclear envelope (NE) and NE-associated components as critical new contributors. Classically, the NE was thought to merely represent a barrier mediating selective exchange between the cytoplasm and nucleoplasm. However, research over the past two decades has highlighted more sophisticated and diverse roles for NE components in progenitor fate choice and migration of their progeny by tuning gene expression via interactions with chromatin, transcription factors and epigenetic factors. Defects in NE components lead to neurodevelopmental impairments, whereas age-related changes in NE components are proposed to influence neurodegenerative diseases. Thus, understanding the roles of NE components in brain development, maintenance and aging is likely to reveal new pathophysiological mechanisms for intervention. Here, we review recent findings for the previously underrepresented contribution of the NE in neuronal commitment and migration, and envision future avenues for investigation.
Collapse
|
15
|
NUP133 Controls Nuclear Pore Assembly, Transcriptome Composition, and Cytoskeleton Regulation in Podocytes. Cells 2022; 11:cells11081259. [PMID: 35455939 PMCID: PMC9025798 DOI: 10.3390/cells11081259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
Steroid-resistant nephrotic syndrome (SRNS) frequently leads to end-stage renal disease, ultimately requiring kidney replacement therapies. SRNS is often caused by hereditary monogenic mutations, specifically affecting specialized epithelial cells (podocytes) of the glomerular filtration barrier. Mutations in several components of the nuclear pore complex, including NUP133 and NUP107, have been recently identified to cause hereditary SRNS. However, underlying pathomechanisms, eliciting podocyte-specific manifestations of these nucleoporopathies, remained largely elusive. Here, we generated an in vitro model of NUP133-linked nucleoporopathies using CRISPR/Cas9-mediated genome editing in human podocytes. Transcriptome, nuclear pore assembly, and cytoskeleton regulation of NUP133 loss-of-function, mutant, and wild-type podocytes were analyzed. Loss of NUP133 translated into a disruption of the nuclear pore, alterations of the podocyte-specific transcriptome, and impaired cellular protrusion generation. Surprisingly, comparative analysis of the described SRNS-related NUP133 mutations revealed only mild defects. Am impaired protein interaction in the Y-complex and decrease of NUP133 protein levels might be the primary and unifying consequence of mutant variants, leading to a partial loss-of-function phenotype and disease manifestation in susceptible cell types, such as podocytes.
Collapse
|
16
|
Dargemont C. Analysis of Ubiquitylation and SUMOylation of Yeast Nuclear Pore Complex Proteins. Methods Mol Biol 2022; 2502:259-269. [PMID: 35412244 DOI: 10.1007/978-1-0716-2337-4_17] [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: 06/14/2023]
Abstract
Posttranslational modifications and in particular ubiquitylation and SUMOylation of the nuclear pore complex (NPC), have been shown to regulate some of its functions, particularly in response to diverse stress signals.Although proteomic approaches are extremely powerful to identify substrates and modification sites, dissecting specific mechanisms and regulation functions of ubiquitylation and SUMOylation of the diverse NPC proteins, in different genetic backgrounds or cell environmental conditions, requires specific biochemical assays based on purification and precise analysis of 6His-tagged ubiquitylated or SUMOylated protein of interest. Here we describe an approach that can be easily employed without specific equipment. It allowed to successfully analyze yeast NPC proteins but can easily be adapted to the study of the mammalian NPC.
Collapse
Affiliation(s)
- Catherine Dargemont
- Institut de Génétique Humaine, Université de Montpellier, Laboratoire de Virologie Moléculaire CNRS-UMR9002, Montpellier, France.
| |
Collapse
|
17
|
Hamed M, Antonin W. Dunking into the Lipid Bilayer: How Direct Membrane Binding of Nucleoporins Can Contribute to Nuclear Pore Complex Structure and Assembly. Cells 2021; 10:3601. [PMID: 34944108 PMCID: PMC8700311 DOI: 10.3390/cells10123601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 02/07/2023] Open
Abstract
Nuclear pore complexes (NPCs) mediate the selective and highly efficient transport between the cytoplasm and the nucleus. They are embedded in the two membrane structure of the nuclear envelope at sites where these two membranes are fused to pores. A few transmembrane proteins are an integral part of NPCs and thought to anchor these complexes in the nuclear envelope. In addition, a number of nucleoporins without membrane spanning domains interact with the pore membrane. Here we review our current knowledge of how these proteins interact with the membrane and how this interaction can contribute to NPC assembly, stability and function as well as shaping of the pore membrane.
Collapse
Affiliation(s)
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany;
| |
Collapse
|
18
|
Labade AS, Salvi A, Kar S, Karmodiya K, Sengupta K. Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation. J Cell Sci 2021; 134:273378. [PMID: 34746948 DOI: 10.1242/jcs.259307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/30/2021] [Indexed: 11/20/2022] Open
Abstract
Nucleoporins regulate nuclear transport and are also involved in DNA damage, repair, cell cycle, chromatin organization, and gene expression. Here, we studied the role of nucleoporin Nup93 and the chromatin organizer CTCF in regulating HOXA expression during differentiation. ChIP sequencing revealed a significant overlap between Nup93 and CTCF peaks. Interestingly, Nup93 and CTCF are associated with the 3' and 5'HOXA genes respectively. Depletions of Nup93 and CTCF antagonistically modulate expression levels of 3'and 5'HOXA genes in undifferentiated NT2/D1 cells. Nup93 also regulates the localization of the HOXA gene locus, which disengages from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. The dynamic association of Nup93 and CTCF with the HOXA locus during differentiation correlates with its spatial positioning and expression. While Nup93 tethers the HOXA locus to the nuclear periphery, CTCF potentially regulates looping of the HOXA gene cluster in a temporal manner. In summary, Nup93 and CTCF complement one another in modulating the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.
Collapse
Affiliation(s)
- Ajay S Labade
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Adwait Salvi
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Saswati Kar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Kundan Sengupta
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| |
Collapse
|
19
|
Targa A, Larrimore KE, Wong CK, Chong YL, Fung R, Lee J, Choi H, Rancati G. Non-genetic and genetic rewiring underlie adaptation to hypomorphic alleles of an essential gene. EMBO J 2021; 40:e107839. [PMID: 34528284 PMCID: PMC8561638 DOI: 10.15252/embj.2021107839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptive evolution to cellular stress is a process implicated in a wide range of biological and clinical phenomena. Two major routes of adaptation have been identified: non-genetic changes, which allow expression of different phenotypes in novel environments, and genetic variation achieved by selection of fitter phenotypes. While these processes are broadly accepted, their temporal and epistatic features in the context of cellular evolution and emerging drug resistance are contentious. In this manuscript, we generated hypomorphic alleles of the essential nuclear pore complex (NPC) gene NUP58. By dissecting early and long-term mechanisms of adaptation in independent clones, we observed that early physiological adaptation correlated with transcriptome rewiring and upregulation of genes known to interact with the NPC; long-term adaptation and fitness recovery instead occurred via focal amplification of NUP58 and restoration of mutant protein expression. These data support the concept that early phenotypic plasticity allows later acquisition of genetic adaptations to a specific impairment. We propose this approach as a genetic model to mimic targeted drug therapy in human cells and to dissect mechanisms of adaptation.
Collapse
Affiliation(s)
- Altea Targa
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Katherine E Larrimore
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Cheng Kit Wong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yu Lin Chong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Ronald Fung
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Joseph Lee
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Hyungwon Choi
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| |
Collapse
|
20
|
Semmelink MFW, Steen A, Veenhoff LM. Measuring and Interpreting Nuclear Transport in Neurodegenerative Disease-The Example of C9orf72 ALS. Int J Mol Sci 2021; 22:9217. [PMID: 34502125 PMCID: PMC8431710 DOI: 10.3390/ijms22179217] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
Transport from and into the nucleus is essential to all eukaryotic life and occurs through the nuclear pore complex (NPC). There are a multitude of data supporting a role for nuclear transport in neurodegenerative diseases, but actual transport assays in disease models have provided diverse outcomes. In this review, we summarize how nuclear transport works, which transport assays are available, and what matters complicate the interpretation of their results. Taking a specific type of ALS caused by mutations in C9orf72 as an example, we illustrate these complications, and discuss how the current data do not firmly answer whether the kinetics of nucleocytoplasmic transport are altered. Answering this open question has far-reaching implications, because a positive answer would imply that widespread mislocalization of proteins occurs, far beyond the reported mislocalization of transport reporters, and specific proteins such as FUS, or TDP43, and thus presents a challenge for future research.
Collapse
Affiliation(s)
| | | | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands; (M.F.W.S.); (A.S.)
| |
Collapse
|
21
|
Colussi C, Grassi C. Epigenetic regulation of neural stem cells: The emerging role of nucleoporins. STEM CELLS (DAYTON, OHIO) 2021; 39:1601-1614. [PMID: 34399020 PMCID: PMC9290943 DOI: 10.1002/stem.3444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/28/2021] [Indexed: 11/06/2022]
Abstract
Nucleoporins (Nups) are components of the nuclear pore complex that, besides regulating nucleus-cytoplasmic transport, emerged as a hub for chromatin interaction and gene expression modulation. Specifically, Nups act in a dynamic manner both at specific gene level and in the topological organization of chromatin domains. As such, they play a fundamental role during development and determination of stemness/differentiation balance in stem cells. An increasing number of reports indicate the implication of Nups in many central nervous system functions with great impact on neurogenesis, neurophysiology, and neurological disorders. Nevertheless, the role of Nup-mediated epigenetic regulation in embryonic and adult neural stem cells (NSCs) is a field largely unexplored and the comprehension of their mechanisms of action is only beginning to be unveiled. After a brief overview of epigenetic mechanisms, we will present and discuss the emerging role of Nups as new effectors of neuroepigenetics and as dynamic platform for chromatin function with specific reference to the biology of NSCs.
Collapse
Affiliation(s)
- Claudia Colussi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI)-CNR, Rome, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| |
Collapse
|
22
|
Gonzalez-Estevez A, Verrico A, Orniacki C, Reina-San-Martin B, Doye V. Integrity of the short arm of the nuclear pore Y-complex is required for mouse embryonic stem cell growth and differentiation. J Cell Sci 2021; 134:268378. [PMID: 34037234 DOI: 10.1242/jcs.258340] [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: 12/21/2020] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Many cellular processes, ranging from cell division to differentiation, are controlled by nuclear pore complexes (NPCs). However, studying the contributions of individual NPC subunits to these processes in vertebrates has long been impeded by their complexity and the lack of efficient genetic tools. Here, we use genome editing in mouse embryonic stem cells (mESCs) to characterize the role of NPC structural components, focusing on the short arm of the Y-complex that comprises Nup85, Seh1 and Nup43. We show that Seh1 and Nup43, although dispensable in pluripotent mESCs, are required for their normal cell growth rates, their viability upon differentiation and for the maintenance of proper NPC density. mESCs with an N-terminally truncated Nup85 mutation (in which interaction with Seh1 is greatly impaired) feature a similar reduction of NPC density. However, their proliferation and differentiation are unaltered, indicating that it is the integrity of the Y-complex, rather than the number of NPCs, that is critical to ensure these processes.
Collapse
Affiliation(s)
- Alba Gonzalez-Estevez
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
| | - Annalisa Verrico
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France
| | - Clarisse Orniacki
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France.,Inserm U 1258, Illkirch 67404, France.,Centre National de la Recherche Scientifique UMR (Unité Mixte de Recherche) 7104, Illkirch 67404, France.,Université de Strasbourg, Illkirch 67404, France
| | - Valérie Doye
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
| |
Collapse
|
23
|
Pathak RU, Soujanya M, Mishra RK. Deterioration of nuclear morphology and architecture: A hallmark of senescence and aging. Ageing Res Rev 2021; 67:101264. [PMID: 33540043 DOI: 10.1016/j.arr.2021.101264] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
The metazoan nucleus is a highly structured organelle containing several well-defined sub-organelles. It is the largest organelle inside a cell taking up from one tenth to half of entire cell volume. This makes it one of the easiest organelles to identify and study under the microscope. Abnormalities in the nuclear morphology and architecture are commonly observed in an aged and senescent cell. For example, the nuclei enlarge, loose their shape, appear lobulated, harbour nuclear membrane invaginations, carry enlarged/fragmented nucleolus, loose heterochromatin, etc. In this review we discuss about the age-related changes in nuclear features and elaborate upon the molecular reasons driving the change. Many of these changes can be easily imaged under a microscope and analysed in silico. Thus, computational image analysis of nuclear features appears to be a promising tool to evaluate physiological age of a cell and offers to be a legitimate biomarker. It can be used to examine progression of age-related diseases and evaluate therapies.
Collapse
Affiliation(s)
| | - Mamilla Soujanya
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India
| | - Rakesh Kumar Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India.
| |
Collapse
|
24
|
Hachiya N, Sochocka M, Brzecka A, Shimizu T, Gąsiorowski K, Szczechowiak K, Leszek J. Nuclear Envelope and Nuclear Pore Complexes in Neurodegenerative Diseases-New Perspectives for Therapeutic Interventions. Mol Neurobiol 2021; 58:983-995. [PMID: 33067781 PMCID: PMC7878205 DOI: 10.1007/s12035-020-02168-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022]
Abstract
Transport of proteins, transcription factors, and other signaling molecules between the nucleus and cytoplasm is necessary for signal transduction. The study of these transport phenomena is particularly challenging in neurons because of their highly polarized structure. The bidirectional exchange of molecular cargoes across the nuclear envelope (NE) occurs through nuclear pore complexes (NPCs), which are aqueous channels embedded in the nuclear envelope. The NE and NPCs regulate nuclear transport but are also emerging as relevant regulators of chromatin organization and gene expression. The alterations in nuclear transport are regularly identified in affected neurons associated with human neurodegenerative diseases. This review presents insights into the roles played by nuclear transport defects in neurodegenerative disease, focusing primarily on NE proteins and NPCs. The subcellular mislocalization of proteins might be a very desirable means of therapeutic intervention in neurodegenerative disorders.
Collapse
Affiliation(s)
- Naomi Hachiya
- Tokyo Metropolitan Industrial Technology Research Institute, Tokyo, Japan
| | - Marta Sochocka
- Laboratory of Virology, Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anna Brzecka
- Department of Pulmonology and Lung Cancer, Wroclaw Medical University, Wroclaw, Poland
| | - Takuto Shimizu
- Tokyo Metropolitan Industrial Technology Research Institute, Tokyo, Japan
- Laboratory of Biochemistry, School of Veterinary Medicine, Azabu University, Sagamihara, Japan
| | | | | | - Jerzy Leszek
- Department of Psychiatry, Wroclaw Medical University, Wybrzeże L. Pasteura 10, 50-367, Wroclaw, Poland.
| |
Collapse
|
25
|
The nuclear pore complex and the genome: organizing and regulatory principles. Curr Opin Genet Dev 2021; 67:142-150. [PMID: 33556822 DOI: 10.1016/j.gde.2021.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/29/2022]
Abstract
The nuclear pore complex (NPC) is a massive nuclear envelope-embedded protein complex, the canonical function of which is to mediate selective nucleocytoplasmic transport. In addition to its transport function, the NPC has been shown to interact with the underlying chromatin and to influence both activating and repressive gene regulatory processes, contributing to the establishment and the epigenetic maintenance of cell identity. In this review, we discuss diverse gene regulatory functions of NPC components and emerging mechanisms underlying these functions, including roles in genome architecture, transcription complex assembly, chromatin remodeling, and coordination of transcription and mRNA export. These functional roles highlight the importance of the NPC as a nuclear scaffold directing genome organization and function.
Collapse
|
26
|
Expression of NR5A2, NUP153, HNF4A, USP15 and FNDC3B is consistent with their use as novel biomarkers for bovine mammary stem/progenitor cells. J Mol Histol 2021; 52:289-300. [PMID: 33400051 DOI: 10.1007/s10735-020-09948-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/18/2020] [Indexed: 12/19/2022]
Abstract
Mammary stem cells (MaSC) are essential for growth and maintenance of mammary epithelium. Previous studies have utilized morphological characteristics or retention of bromodeoxyuridine (BrdU) label to identify MaSC and progenitor cells, these approaches may not be feasible or may not identify all resident stem cells. Alternatively, these special cells may be identified by assessing protein and mRNA expression of appropriate markers. The focus of this study was to assess the staining patterns and in situ quantification of novel candidate markers for bovine MaSC/progenitor cells. The candidate markers for MaSC/progenitor cells for immunohistochemical analysis were: NR5A2, NUP153, HNF4A, USP15 and FNDC3B and for in situ transcripts quantification were HNF4A and NUP153. We also evaluated protein expression pattern of presumptive MaSC markers known from the literature namely, ALDH1, MSI1 and Notch3. We found that NR5A2, NUP153, HNF4A and USP15-labeled cells represented 2.5-6% of epithelial cells prepubertally and were distributed in a fashion consistent with the location and abundance of MaSC/progenitor cells. A transient increase (10-37%) in expression of these markers was observed at peak lactation. FNDC3B was localized mainly in the nucleus prepubertally and in the cytoplasm of myoepithelial cells and nuclei of a limited number of alveolar cells during lactation. Abundant expression (~ 48%) and luminal localization of ALDH1 precludes its use as a bovine MaSC marker but may include transamplifying progenitor cells. MSI1 staining was consistent with MaSC localization. Onset of lumen formation in mammary ducts of prepubertal gland was associated with Notch 3 expression in the apical surface of luminal cells. RNAscope analysis of HNF4A and NUP153 transcripts in calf mammary gland showed very low copy numbers in a few epithelial cells, supporting the idea that these markers are expressed by fewer cells of epithelial origin. This study suggests that NR5A2, NUP153, HNF4A, USP15 and FNDC3B are likely markers for bovine MaSC/progenitor cells. Quantification of RNA transcripts of HNF4A and NUP153 in bovine MEC as potential MaSC markers are novel. Further studies to correlate protein expression of these markers with their transcripts level using single cell analysis in larger samples in lactating cow at different physiological stages are warranted.
Collapse
|
27
|
Pulupa J, Prior H, Johnson DS, Simon SM. Conformation of the nuclear pore in living cells is modulated by transport state. eLife 2020; 9:e60654. [PMID: 33346731 PMCID: PMC7752133 DOI: 10.7554/elife.60654] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
While the static structure of the nuclear pore complex (NPC) continues to be refined with cryo-EM and x-ray crystallography, in vivo conformational changes of the NPC remain under-explored. We developed sensors that report on the orientation of NPC components by rigidly conjugating mEGFP to different NPC proteins. Our studies show conformational changes to select domains of nucleoporins (Nups) within the inner ring (Nup54, Nup58, Nup62) when transport through the NPC is perturbed and no conformational changes to Nups elsewhere in the NPC. Our results suggest that select components of the NPC are flexible and undergo conformational changes upon engaging with cargo.
Collapse
Affiliation(s)
- Joan Pulupa
- Laboratory of Cellular Biophysics, Rockefeller UniversityNew YorkUnited States
| | - Harriet Prior
- Laboratory of Cellular Biophysics, Rockefeller UniversityNew YorkUnited States
| | - Daniel S Johnson
- Department of Physics and Astronomy, Hofstra UniversityHempsteadUnited States
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller UniversityNew YorkUnited States
| |
Collapse
|
28
|
Abstract
Nuclear pore complexes are multiprotein channels that span the nuclear envelope, which connects the nucleus to the cytoplasm. In addition to their main role in the regulation of nucleocytoplasmic molecule exchange, it has become evident that nuclear pore complexes and their components also have multiple transport-independent functions. In recent years, an increasing number of studies have reported the involvement of nuclear pore complex components in embryogenesis, cell differentiation and tissue-specific processes. Here, we review the findings that highlight the dynamic nature of nuclear pore complexes and their roles in many cell type-specific functions during development and tissue homeostasis.
Collapse
Affiliation(s)
- Valeria Guglielmi
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Maximiliano A D'Angelo
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| |
Collapse
|
29
|
A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure. Nat Commun 2020; 11:6179. [PMID: 33268786 PMCID: PMC7710722 DOI: 10.1038/s41467-020-19884-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working in S. cerevisiae, and to study the assembly of these two essential subcomplexes, we here develop a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite in S. cerevisiae detect accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.
Collapse
|
30
|
Sunny DE, Hammer E, Strempel S, Joseph C, Manchanda H, Ittermann T, Hübner S, Weiss FU, Völker U, Heckmann M. Nup133 and ERα mediate the differential effects of hyperoxia-induced damage in male and female OPCs. Mol Cell Pediatr 2020; 7:10. [PMID: 32844334 PMCID: PMC7447710 DOI: 10.1186/s40348-020-00102-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023] Open
Abstract
Background Hyperoxia is a well-known cause of cerebral white matter injury in preterm infants with male sex being an independent and critical risk factor for poor neurodevelopmental outcome. Sex is therefore being widely considered as one of the major decisive factors for prognosis and treatment of these infants. But unfortunately, we still lack a clear view of the molecular mechanisms that lead to such a profound difference. Hence, using mouse-derived primary oligodendrocyte progenitor cells (OPCs), we investigated the molecular factors and underlying mechanisms behind the differential response of male and female cells towards oxidative stress. Results We demonstrate that oxidative stress severely affects cellular functions related to energy metabolism, stress response, and maturation in the male-derived OPCs, whereas the female cells remain largely unaffected. CNPase protein level was found to decline following hyperoxia in male but not in female cells. This impairment of maturation was accompanied by the downregulation of nucleoporin and nuclear lamina proteins in the male cells. We identify Nup133 as a novel target protein affected by hyperoxia, whose inverse regulation may mediate this differential response in the male and female cells. Nup133 protein level declined following hyperoxia in male but not in female cells. We show that nuclear respiratory factor 1 (Nrf1) is a direct downstream target of Nup133 and that Nrf1 mRNA declines following hyperoxia in male but not in female cells. The female cells may be rendered resistant due to synergistic protection via the estrogen receptor alpha (ERα) which was upregulated following hyperoxia in female but not in male cells. Both Nup133 and ERα regulate mitochondrial function and oxidative stress response by transcriptional regulation of Nrf1. Conclusions These findings from a basic cell culture model establish prominent sex-based differences and suggest a novel mechanism involved in the differential response of OPCs towards oxidative stress. It conveys a strong message supporting the need to study how complex cellular processes are regulated differently in male and female brains during development and for a better understanding of how the brain copes up with different forms of stress after preterm birth.
Collapse
Affiliation(s)
- Donna Elizabeth Sunny
- Department of Neonatology and Pediatric Intensive Care, University of Medicine Greifswald, Ferdinand-Sauerbruchstrasse, 17475, Greifswald, Germany.
| | - Elke Hammer
- Department of Functional Genomics, University of Medicine Greifswald, Greifswald, Germany
| | | | - Christy Joseph
- Department of Pharmacology, Center of Drug Absorption and Transport (C_DAT), University of Medicine Greifswald, Greifswald, Germany
| | - Himanshu Manchanda
- Department of Bioinformatics, University of Medicine Greifswald, Greifswald, Germany
| | - Till Ittermann
- Institute for Community Medicine, University of Medicine Greifswald, Greifswald, Germany
| | - Stephanie Hübner
- Department of Neonatology and Pediatric Intensive Care, University of Medicine Greifswald, Ferdinand-Sauerbruchstrasse, 17475, Greifswald, Germany
| | - Frank Ulrich Weiss
- Department of Internal Medicine A, University of Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, University of Medicine Greifswald, Greifswald, Germany
| | - Matthias Heckmann
- Department of Neonatology and Pediatric Intensive Care, University of Medicine Greifswald, Ferdinand-Sauerbruchstrasse, 17475, Greifswald, Germany
| |
Collapse
|
31
|
Zhang A, Wang S, Kim J, Yan J, Yan X, Pang Q, Hua J. Nuclear pore complex components have temperature-influenced roles in plant growth and immunity. PLANT, CELL & ENVIRONMENT 2020; 43:1452-1466. [PMID: 32022936 DOI: 10.1111/pce.13741] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/19/2020] [Accepted: 02/01/2020] [Indexed: 05/28/2023]
Abstract
Nuclear pore complexes (NPCs) are main channels controlling nucleocytoplasmic transport and are composed of approximately 30 nucleoporins (NUPs). Emerging evidence suggests that some NUP genes have specialized functions that challenge the traditional view of NPCs as structures of uniform composition. Here, we analysed the role of six outer-ring components of NPC at normal and warm growth temperatures by examining their loss-of-function mutants in Arabidopsis thaliana. All six NUP subunits, NUP85, NUP96, NUP 133, NUP 160, SEH1 and HOS1, have a non-redundant temperature-influenced function in one or more of the processes, including rosette growth, leaf architecture and intracellular immune receptor-mediated disease resistance. At the molecular level, NUP85 and NUP133 are required for mRNA export only at warm temperature and play a larger role in the localization of transcription factor at warm temperature. In addition, NUP96 and HOS1 are essential for the expression of high temperature-responsive genes, which is correlated with their larger activity in facilitating nuclear accumulation of the transcription factor PIF4 at warm temperature. Our results show that subunits of NPC have differential roles at different temperatures, suggesting the existence of temperature-influenced NPC complexes and activities.
Collapse
Affiliation(s)
- Aiqin Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| | - Shuai Wang
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jitae Kim
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| | - Jiapei Yan
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| | - Xiufeng Yan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Qiuying Pang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Jian Hua
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| |
Collapse
|
32
|
Khan AU, Qu R, Ouyang J, Dai J. Role of Nucleoporins and Transport Receptors in Cell Differentiation. Front Physiol 2020; 11:239. [PMID: 32308628 PMCID: PMC7145948 DOI: 10.3389/fphys.2020.00239] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
Bidirectional molecular movements between the nucleus and cytoplasm take place through nuclear pore complexes (NPCs) embedded in the nuclear membrane. These macromolecular structures are composed of several nucleoporins, which form seven different subcomplexes based on their biochemical affinity. These nucleoporins are integral components of the complex, not only allowing passive transport but also interacting with importin, exportin, and other molecules that are required for transport of protein in various cellular processes. Transport of different proteins is carried out either dependently or independently on transport receptors. As well as facilitating nucleocytoplasmic transport, nucleoporins also play an important role in cell differentiation, possibly by their direct gene interaction. This review will cover the general role of nucleoporins (whether its dependent or independent) and nucleocytoplasmic transport receptors in cell differentiation.
Collapse
|
33
|
Mehta SJK, Kumar V, Mishra RK. Drosophila ELYS regulates Dorsal dynamics during development. J Biol Chem 2020; 295:2421-2437. [PMID: 31941789 DOI: 10.1074/jbc.ra119.009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 01/13/2020] [Indexed: 11/06/2022] Open
Abstract
Embryonic large molecule derived from yolk sac (ELYS) is a constituent protein of nuclear pores. It initiates assembly of nuclear pore complexes into functional nuclear pores toward the end of mitosis. Using cellular, molecular, and genetic tools, including fluorescence and Electron microscopy, quantitative PCR, and RNAi-mediated depletion, we report here that the ELYS ortholog (dElys) plays critical roles during Drosophila development. dElys localized to the nuclear rim in interphase cells, but during mitosis it was absent from kinetochores and enveloped chromatin. We observed that RNAi-mediated dElys depletion leads to aberrant development and, at the cellular level, to defects in the nuclear pore and nuclear lamina assembly. Further genetic analyses indicated that dElys depletion re-activates the Dorsal (NF-κB) pathway during late larval stages. Re-activated Dorsal caused untimely expression of the Dorsal target genes in the post-embryonic stages. We also demonstrate that activated Dorsal triggers apoptosis during later developmental stages by up-regulating the pro-apoptotic genes reaper and hid The apoptosis induced by Reaper and Hid was probably the underlying cause for developmental abnormalities observed upon dElys depletion. Moreover, we noted that dElys has conserved structural features, but contains a noncanonical AT-hook-like motif through which it strongly binds to DNA. Together, our results uncover a novel epistatic interaction that regulates Dorsal dynamics by dElys during development.
Collapse
Affiliation(s)
- Saurabh Jayesh Kumar Mehta
- Nups and SUMO Biology Group, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India
| | - Vimlesh Kumar
- Laboratory of Neurogenetics, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India
| | - Ram Kumar Mishra
- Nups and SUMO Biology Group, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India.
| |
Collapse
|
34
|
Gomar-Alba M, Mendoza M. Modulation of Cell Identity by Modification of Nuclear Pore Complexes. Front Genet 2020; 10:1301. [PMID: 31969901 PMCID: PMC6960265 DOI: 10.3389/fgene.2019.01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/26/2019] [Indexed: 11/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) are protein assemblies that form channels across the nuclear envelope to mediate communication between the nucleus and the cytoplasm. Additionally, NPCs interact with chromatin and influence the position and expression of multiple genes. Interestingly, the composition of NPCs can vary in different cell-types, tissues, and developmental states. Here, we review recent findings suggesting that modifications of NPC composition, including post-translational modifications, play an instructive role in cell fate establishment. In particular, we focus on the role of cell-specific NPC deacetylation in asymmetrically dividing budding yeast, which modulates transport-dependent and transport-independent NPC functions to determine the time of commitment to a new division cycle in daughter cells. By modulating protein localization and gene expression, NPCs are therefore emerging as central regulators of cell identity.
Collapse
Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| |
Collapse
|
35
|
Abstract
Increasing evidence points to nuclear pore complexes as important regulators of cell fate and tissue homeostasis. A recent report by Liu et al. (2019) in this issue of Neuron uncovers that nucleoporin Seh1 is required for the expression of genes critical for oligodendrocyte differentiation and myelination.
Collapse
|
36
|
Loss of SMPD4 Causes a Developmental Disorder Characterized by Microcephaly and Congenital Arthrogryposis. Am J Hum Genet 2019; 105:689-705. [PMID: 31495489 DOI: 10.1016/j.ajhg.2019.08.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Sphingomyelinases generate ceramide from sphingomyelin as a second messenger in intracellular signaling pathways involved in cell proliferation, differentiation, or apoptosis. Children from 12 unrelated families presented with microcephaly, simplified gyral pattern of the cortex, hypomyelination, cerebellar hypoplasia, congenital arthrogryposis, and early fetal/postnatal demise. Genomic analysis revealed bi-allelic loss-of-function variants in SMPD4, coding for the neutral sphingomyelinase-3 (nSMase-3/SMPD4). Overexpression of human Myc-tagged SMPD4 showed localization both to the outer nuclear envelope and the ER and additionally revealed interactions with several nuclear pore complex proteins by proteomics analysis. Fibroblasts from affected individuals showed ER cisternae abnormalities, suspected for increased autophagy, and were more susceptible to apoptosis under stress conditions, while treatment with siSMPD4 caused delayed cell cycle progression. Our data show that SMPD4 links homeostasis of membrane sphingolipids to cell fate by regulating the cross-talk between the ER and the outer nuclear envelope, while its loss reveals a pathogenic mechanism in microcephaly.
Collapse
|
37
|
Khalaf B, Roncador A, Pischedda F, Casini A, Thomas S, Piccoli G, Kiebler M, Macchi P. Ankyrin-G induces nucleoporin Nup358 to associate with the axon initial segment of neurons. J Cell Sci 2019; 132:jcs.222802. [PMID: 31427429 DOI: 10.1242/jcs.222802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/12/2019] [Indexed: 12/11/2022] Open
Abstract
Nup358 (also known as RanBP2) is a member of the large nucleoporin family that constitutes the nuclear pore complex. Depending on the cell type and the physiological state, Nup358 interacts with specific partner proteins and influences distinct mechanisms independent of its role in nucleocytoplasmic transport. Here, we provide evidence that Nup358 associates selectively with the axon initial segment (AIS) of mature neurons, mediated by the AIS scaffold protein ankyrin-G (AnkG, also known as Ank3). The N-terminus of Nup358 is demonstrated to be sufficient for its localization at the AIS. Further, we show that Nup358 is expressed as two isoforms, one full-length and another shorter form of Nup358. These isoforms differ in their subcellular distribution in neurons and expression level during neuronal development. Overall, the present study highlights an unprecedented localization of Nup358 within the AIS and suggests its involvement in neuronal function.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Bouchra Khalaf
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Alessandro Roncador
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Francesca Pischedda
- Dulbecco Telethon Laboratory of Biology of Synapses, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Antonio Casini
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Sabine Thomas
- Department for Cell Biology, Biomedical Center, Medical Faculty, Ludwig-Maximilian University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Giovanni Piccoli
- Dulbecco Telethon Laboratory of Biology of Synapses, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Michael Kiebler
- Department for Cell Biology, Biomedical Center, Medical Faculty, Ludwig-Maximilian University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| |
Collapse
|
38
|
Chen X, Shen WB, Yang P, Dong D, Sun W, Yang P. High Glucose Inhibits Neural Stem Cell Differentiation Through Oxidative Stress and Endoplasmic Reticulum Stress. Stem Cells Dev 2019; 27:745-755. [PMID: 29695191 DOI: 10.1089/scd.2017.0203] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Maternal diabetes induces neural tube defects by suppressing neurogenesis in the developing neuroepithelium. Our recent study further revealed that high glucose inhibited embryonic stem cell differentiation into neural lineage cells. However, the mechanism whereby high glucose suppresses neural differentiation is unclear. To investigate whether high glucose-induced oxidative stress and endoplasmic reticulum (ER) stress lead to the inhibition of neural differentiation, the effect of high glucose on neural stem cell (the C17.2 cell line) differentiation was examined. Neural stem cells were cultured in normal glucose (5 mM) or high glucose (25 mM) differentiation medium for 3, 5, and 7 days. High glucose suppressed neural stem cell differentiation by significantly decreasing the expression of the neuron marker Tuj1 and the glial cell marker GFAP and the numbers of Tuj1+ and GFAP+ cells. The antioxidant enzyme superoxide dismutase mimetic Tempol reversed high glucose-decreased Tuj1 and GFAP expression and restored the numbers of neurons and glial cells differentiated from neural stem cells. Hydrogen peroxide treatment imitated the inhibitory effect of high glucose on neural stem cell differentiation. Both high glucose and hydrogen peroxide triggered ER stress, whereas Tempol blocked high glucose-induced ER stress. The ER stress inhibitor, 4-phenylbutyrate, abolished the inhibition of high glucose or hydrogen peroxide on neural stem cell differentiation. Thus, oxidative stress and its resultant ER stress mediate the inhibitory effect of high glucose on neural stem cell differentiation.
Collapse
Affiliation(s)
- Xi Chen
- 1 Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine , Baltimore, Maryland
| | - Wei-Bin Shen
- 1 Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine , Baltimore, Maryland
| | - Penghua Yang
- 1 Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine , Baltimore, Maryland
| | - Daoyin Dong
- 1 Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine , Baltimore, Maryland
| | - Winny Sun
- 1 Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine , Baltimore, Maryland.,2 Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland
| | - Peixin Yang
- 1 Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine , Baltimore, Maryland.,2 Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland
| |
Collapse
|
39
|
Capitanchik C, Dixon CR, Swanson SK, Florens L, Kerr ARW, Schirmer EC. Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins. Nucleus 2019; 9:410-430. [PMID: 29912636 PMCID: PMC7000147 DOI: 10.1080/19491034.2018.1469351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Laminopathies yield tissue-specific pathologies, yet arise from mutation of ubiquitously-expressed genes. A little investigated hypothesis to explain this is that the mutated proteins or their partners have tissue-specific splice variants. To test this, we analyzed RNA-Seq datasets, finding novel isoforms or isoform tissue-specificity for: Lap2, linked to cardiomyopathy; Nesprin 2, linked to Emery-Dreifuss muscular dystrophy and Lmo7, that regulates the Emery-Dreifuss muscular dystrophy linked emerin gene. Interestingly, the muscle-specific Lmo7 exon is rich in serine phosphorylation motifs, suggesting regulatory function. Muscle-specific splice variants in non-nuclear envelope proteins linked to other muscular dystrophies were also found. Nucleoporins tissue-specific variants were found for Nup54, Nup133, Nup153 and Nup358/RanBP2. RT-PCR confirmed novel Lmo7 and RanBP2 variants and specific knockdown of the Lmo7 variantreduced myogenic index. Nuclear envelope proteins were enriched for tissue-specific splice variants compared to the rest of the genome, suggesting that splice variants contribute to its tissue-specific functions.
Collapse
Affiliation(s)
- Charlotte Capitanchik
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Charles R Dixon
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Selene K Swanson
- b Stowers Institute for Medical Research , Kansas City , MO , USA
| | - Laurence Florens
- b Stowers Institute for Medical Research , Kansas City , MO , USA
| | - Alastair R W Kerr
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Eric C Schirmer
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| |
Collapse
|
40
|
Abstract
Nuclear pore complexes (NPCs), the channels connecting the nucleus with the cytoplasm, are the largest protein structures of the nuclear envelope. In addition to their role in regulating nucleocytoplasmic transport, increasing evidence shows that these multiprotein structures play central roles in the regulation of gene activity. In light of recent discoveries, NPCs are emerging as scaffolds that mediate the regulation of specific gene sets at the nuclear periphery. The function of NPCs as genome organizers and hubs for transcriptional regulation provides additional evidence that the compartmentalization of genes and transcriptional regulators within the nuclear space is an important mechanism of gene expression regulation.
Collapse
Affiliation(s)
- Maximiliano A D'Angelo
- a Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, NCI-Designated Cancer Center , 10901 N. Torrey Pines Road, La Jolla , CA , United States
| |
Collapse
|
41
|
Fujita A, Tsukaguchi H, Koshimizu E, Nakazato H, Itoh K, Kuraoka S, Komohara Y, Shiina M, Nakamura S, Kitajima M, Tsurusaki Y, Miyatake S, Ogata K, Iijima K, Matsumoto N, Miyake N. Homozygous splicing mutation in NUP133 causes Galloway-Mowat syndrome. Ann Neurol 2019; 84:814-828. [PMID: 30427554 DOI: 10.1002/ana.25370] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Galloway-Mowat syndrome (GAMOS) is a neural and renal disorder, characterized by microcephaly, brain anomalies, and early onset nephrotic syndrome. Biallelic mutations in WDR73 and the 4 subunit genes of the KEOPS complex are reported to cause GAMOS. Furthermore, an identical homozygous NUP107 (nucleoporin 107kDa) mutation was identified in 4 GAMOS-like families, although biallelic NUP107 mutations were originally identified in steroid-resistant nephrotic syndrome. NUP107 and NUP133 (nucleoporin 133kDa) are interacting subunits of the nuclear pore complex in the nuclear envelope during interphase, and these proteins are also involved in centrosome positioning and spindle assembly during mitosis. METHODS Linkage analysis and whole exome sequencing were performed in a previously reported GAMOS family with brain atrophy and steroid-resistant nephrotic syndrome. RESULTS We identified a homozygous NUP133 mutation, c.3335-11T>A, which results in the insertion of 9bp of intronic sequence between exons 25 and 26 in the mutant transcript. NUP133 and NUP107 interaction was impaired by the NUP133 mutation based on an immunoprecipitation assay. Importantly, focal cortical dysplasia type IIa was recognized in the brain of an autopsied patient and focal segmental glomerulosclerosis was confirmed in the kidneys of the 3 examined patients. A nup133-knockdown zebrafish model exhibited microcephaly, fewer neuronal cells, underdeveloped glomeruli, and fusion of the foot processes of the podocytes, which mimicked human GAMOS features. nup133 morphants could be rescued by human wild-type NUP133 mRNA but not by mutant mRNA. INTERPRETATION These data indicate that the biallelic NUP133 loss-of-function mutation causes GAMOS. Ann Neurol 2018;84:814-828.
Collapse
Affiliation(s)
- Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama
| | | | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama
| | - Hitoshi Nakazato
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto
| | - Shohei Kuraoka
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto
| | - Yoshihiro Komohara
- Department of Cell Pathology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto
| | - Masaaki Shiina
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama
| | - Shohei Nakamura
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama
| | - Mika Kitajima
- Department of Diagnostic Radiology, Faculty of Life Sciences, Kumamoto University, Kumamoto
| | | | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama
| |
Collapse
|
42
|
Buchwalter A, Kaneshiro JM, Hetzer MW. Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet 2019; 20:39-50. [PMID: 30356165 DOI: 10.1038/s41576-018-0063-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing.
Collapse
Affiliation(s)
- Abigail Buchwalter
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Jeanae M Kaneshiro
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
43
|
Lucas T, Kohwi M. From insects to mammals: regulation of genome architecture in neural development. Curr Opin Neurobiol 2019; 59:146-156. [PMID: 31299459 DOI: 10.1016/j.conb.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
One of the hallmarks of the metazoan genome is that genes are non-randomly positioned within the cell nucleus; in fact, the entire genome is packaged in a highly organized manner to orchestrate proper gene expression for each cell type. This is an especially daunting task for the development of the brain, which consists of an incredibly diverse population of neural cells. How genome architecture is established, maintained, and regulated to promote diverse cell fates and functions are fascinating questions with important implications in development and disease. The explosion in various biochemical and imaging techniques to analyze chromatin is now making it possible to interrogate the genome at an unprecedented resolution. Here we will focus on current advances in understanding genome architecture and gene regulation in the context of neural development.
Collapse
Affiliation(s)
- Tanguy Lucas
- Department of Neuroscience, Mortimer B. Zuckerman Institute for Mind Brain Behavior, Kavli Institute for Brain Sciences, Columbia University, New York, NY, United States
| | - Minoree Kohwi
- Department of Neuroscience, Mortimer B. Zuckerman Institute for Mind Brain Behavior, Kavli Institute for Brain Sciences, Columbia University, New York, NY, United States.
| |
Collapse
|
44
|
Cipollini M, Luisi S, Piomboni P, Luddi A, Landi D, Melaiu O, Figlioli G, Garritano S, Cappelli V, Viganò P, Gemignani F, Petraglia F, Landi S. Functional polymorphism within NUP210 encoding for nucleoporin GP210 is associated with the risk of endometriosis. Fertil Steril 2019; 112:343-352.e1. [PMID: 31256999 DOI: 10.1016/j.fertnstert.2019.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To investigate whether nucleoporin 210 (GP210, encoded by NUP210 gene) is involved in endometriosis. DESIGN Immunohistofluorescence analysis for assessing whether GP210 is expressed in endometrial tissues from patients and controls; genotyping and case-control study for assessing the association between rs354476 within NUP210 and risk of endometriosis; in vitro luciferase assay for assessing the functional activity of rs354476. SETTING University. PATIENT(S) Histologically diagnosed cases (n = 175) of endometriosis: minimal or mild (stage I-II) in 48 cases (28%), moderate (stage III) in 69 cases (39%), and severe (stage IV) in 58 cases (33%). Controls (n = 557) were female blood donors collected at Meyer Hospital of Florence. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) GP210 tissue expression; genotype distribution and risk of endometriosis; in vitro gene expression measurements. RESULT(S) GP210 had positive nuclear immunohistofluorescence staining in endometrial glandular epithelium. Carriers of the variant allele were associated with increased risks: C/T, odds ratio (OR) 1.83, 95% confidence interval (CI) 1.04-3.21; T/T, OR 2.55, 95% CI 1.36-4.80. In vitro, luciferase assay showed that rs354476 is a bona fide target for hsa-miR-125b-5p. CONCLUSION(S) Nucleoporin GP210 is involved in endometriosis. Rs354476 polymorphism affects the regulation of NUP210 gene expression by altering the binding with hsa-miR-125b-5p, a microRNA already known as playing an important role for endometriosis. This provides the rationale for the observed increased risk of endometriosis in carriers of the variant allele.
Collapse
Affiliation(s)
| | - Stefano Luisi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Paola Piomboni
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Alice Luddi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Debora Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | | | | | - Sonia Garritano
- Centre for Integrated Biology, University of Trento, Trento, Italy
| | - Valentina Cappelli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Paola Viganò
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | | | - Felice Petraglia
- Obstetrics and Gynecology, Department of Biomedical, Experimental and Clinical Sciences "Mario Serio" University of Florence, Florence, Italy
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| |
Collapse
|
45
|
Cianciolo Cosentino C, Berto A, Pelletier S, Hari M, Loffing J, Neuhauss SCF, Doye V. Moderate Nucleoporin 133 deficiency leads to glomerular damage in zebrafish. Sci Rep 2019; 9:4750. [PMID: 30894603 PMCID: PMC6426968 DOI: 10.1038/s41598-019-41202-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 02/26/2019] [Indexed: 01/13/2023] Open
Abstract
Although structural nuclear pore proteins (nucleoporins) are seemingly required in every cell type to assemble a functional nuclear transport machinery, mutations or deregulation of a subset of them have been associated with specific human hereditary diseases. In particular, previous genetic studies of patients with nephrotic syndrome identified mutations in Nup107 that impaired the expression or the localization of its direct partner at nuclear pores, Nup133. In the present study, we characterized the zebrafish nup133 orthologous gene and its expression pattern during larval development. Using a morpholino-mediated gene knockdown, we show that partial depletion of Nup133 in zebrafish larvae leads to the formation of kidney cysts, a phenotype that can be rescued by co-injection of wild type mRNA. Analysis of different markers for tubular and glomerular development shows that the overall kidney development is not affected by nup133 knockdown. Likewise, no gross defect in nuclear pore complex assembly was observed in these nup133 morphants. On the other hand, nup133 downregulation results in proteinuria and moderate foot process effacement, mimicking some of the abnormalities typically featured by patients with nephrotic syndrome. These data indicate that nup133 is a new gene required for proper glomerular structure and function in zebrafish.
Collapse
Affiliation(s)
- Chiara Cianciolo Cosentino
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Institute of Anatomy, University of Zurich, Zurich, Switzerland.,Fondazione RiMED, Palermo, Italy
| | - Alessandro Berto
- Institut Jacques Monod, UMR7592 CNRS-Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France.,Ecole Doctorale SDSV, Université Paris Sud, F-91405, Orsay, France
| | - Stéphane Pelletier
- Institut Jacques Monod, UMR7592 CNRS-Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Michelle Hari
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | | | - Valérie Doye
- Institut Jacques Monod, UMR7592 CNRS-Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France.
| |
Collapse
|
46
|
Liu Z, Yan M, Liang Y, Liu M, Zhang K, Shao D, Jiang R, Li L, Wang C, Nussenzveig DR, Zhang K, Chen S, Zhong C, Mo W, Fontoura BMA, Zhang L. Nucleoporin Seh1 Interacts with Olig2/Brd7 to Promote Oligodendrocyte Differentiation and Myelination. Neuron 2019; 102:587-601.e7. [PMID: 30876848 DOI: 10.1016/j.neuron.2019.02.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/12/2019] [Accepted: 02/13/2019] [Indexed: 01/10/2023]
Abstract
Nucleoporins (Nups) are involved in neural development, and alterations in Nup genes are linked to human neurological diseases. However, physiological functions of specific Nups and the underlying mechanisms involved in these processes remain elusive. Here, we show that tissue-specific depletion of the nucleoporin Seh1 causes dramatic myelination defects in the CNS. Although proliferation is not altered in Seh1-deficient oligodendrocyte progenitor cells (OPCs), they fail to differentiate into mature oligodendrocytes, which impairs myelin production and remyelination after demyelinating injury. Genome-wide analyses show that Seh1 regulates a core myelinogenic regulatory network and establishes an accessible chromatin landscape. Mechanistically, Seh1 regulates OPCs differentiation by assembling Olig2 and Brd7 into a transcription complex at nuclear periphery. Together, our results reveal that Seh1 is required for oligodendrocyte differentiation and myelination by promoting assembly of an Olig2-dependent transcription complex and define a nucleoporin as a key player in the CNS.
Collapse
Affiliation(s)
- Zhixiong Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, China
| | - Minbiao Yan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, China
| | - Yaoji Liang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102, China; XMU School of Pharmaceutical Sciences-Amogene Joint R&D Center for Genetic Diagnostics, Amogene Biotech, Xiamen, Fujian 361102, China; The First Affiliated Hospital, Medical College, Xiamen University, Xiamen, Fujian 361102, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Kun Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Dandan Shao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Rencai Jiang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Li Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Chaomeng Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Daniel R Nussenzveig
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA; Veterans Affairs North Texas Health Care System: Dallas VA Medical Center, Dallas, TX 75216, USA
| | - Kunkun Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Shaoxuan Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Chuanqi Zhong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Wei Mo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Liang Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, China.
| |
Collapse
|
47
|
Shamseldin HE, Makhseed N, Ibrahim N, Al-Sheddi T, Alobeid E, Abdulwahab F, Alkuraya FS. NUP214 deficiency causes severe encephalopathy and microcephaly in humans. Hum Genet 2019; 138:221-229. [PMID: 30758658 DOI: 10.1007/s00439-019-01979-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
Abstract
Nuclear pore complex (NPC) is a fundamental component of the nuclear envelope and is key to the nucleocytoplasmic transport. Mutations in several NUP genes that encode individual components of NPC known as nucleoporins have been identified in recent years among patients with static encephalopathies characterized by developmental delay and microcephaly. We describe a multiplex consanguineous family in which four affected members presented with severe neonatal hypotonia, profound global developmental delay, progressive microcephaly and early death. Autozygome and linkage analysis revealed that this phenotype is linked to a founder disease haplotype (chr9:127,113,732-135,288,807) in which whole exome sequencing revealed the presence of a novel homozygous missense variant in NUP214. Functional analysis of patient-derived fibroblasts recapitulated the dysmorphic phenotype of nuclei that was previously described in NUP214 knockdown cells. In addition, the typical rim staining of NUP214 is largely displaced, further supporting the deleterious effect of the variant. Our data expand the list of NUP genes that are mutated in encephalopathy disorders in humans.
Collapse
Affiliation(s)
- Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nawal Makhseed
- Department of Pediatrics, Al-Jahra Hospital, Kuwait City, Kuwait
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Al-Sheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| |
Collapse
|
48
|
Braun DA, Lovric S, Schapiro D, Schneider R, Marquez J, Asif M, Hussain MS, Daga A, Widmeier E, Rao J, Ashraf S, Tan W, Lusk CP, Kolb A, Jobst-Schwan T, Schmidt JM, Hoogstraten CA, Eddy K, Kitzler TM, Shril S, Moawia A, Schrage K, Khayyat AIA, Lawson JA, Gee HY, Warejko JK, Hermle T, Majmundar AJ, Hugo H, Budde B, Motameny S, Altmüller J, Noegel AA, Fathy HM, Gale DP, Waseem SS, Khan A, Kerecuk L, Hashmi S, Mohebbi N, Ettenger R, Serdaroğlu E, Alhasan KA, Hashem M, Goncalves S, Ariceta G, Ubetagoyena M, Antonin W, Baig SM, Alkuraya FS, Shen Q, Xu H, Antignac C, Lifton RP, Mane S, Nürnberg P, Khokha MK, Hildebrandt F. Mutations in multiple components of the nuclear pore complex cause nephrotic syndrome. J Clin Invest 2018; 128:4313-4328. [PMID: 30179222 PMCID: PMC6159964 DOI: 10.1172/jci98688] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 07/24/2018] [Indexed: 01/08/2023] Open
Abstract
Steroid-resistant nephrotic syndrome (SRNS) almost invariably progresses to end-stage renal disease. Although more than 50 monogenic causes of SRNS have been described, a large proportion of SRNS remains unexplained. Recently, it was discovered that mutations of NUP93 and NUP205, encoding 2 proteins of the inner ring subunit of the nuclear pore complex (NPC), cause SRNS. Here, we describe mutations in genes encoding 4 components of the outer rings of the NPC, namely NUP107, NUP85, NUP133, and NUP160, in 13 families with SRNS. Using coimmunoprecipitation experiments, we showed that certain pathogenic alleles weakened the interaction between neighboring NPC subunits. We demonstrated that morpholino knockdown of nup107, nup85, or nup133 in Xenopus disrupted glomerulogenesis. Re-expression of WT mRNA, but not of mRNA reflecting mutations from SRNS patients, mitigated this phenotype. We furthermore found that CRISPR/Cas9 knockout of NUP107, NUP85, or NUP133 in podocytes activated Cdc42, an important effector of SRNS pathogenesis. CRISPR/Cas9 knockout of nup107 or nup85 in zebrafish caused developmental anomalies and early lethality. In contrast, an in-frame mutation of nup107 did not affect survival, thus mimicking the allelic effects seen in humans. In conclusion, we discovered here that mutations in 4 genes encoding components of the outer ring subunits of the NPC cause SRNS and thereby provide further evidence that specific hypomorphic mutations in these essential genes cause a distinct, organ-specific phenotype.
Collapse
Affiliation(s)
- Daniela A. Braun
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Internal Medicine D, University Hospital of Münster, Münster, Germany
| | - Svjetlana Lovric
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Schapiro
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ronen Schneider
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Maria Asif
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Ankana Daga
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jia Rao
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Shazia Ashraf
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Weizhen Tan
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - C. Patrick Lusk
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Amy Kolb
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Johanna Magdalena Schmidt
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte A. Hoogstraten
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn Eddy
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas M. Kitzler
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Abubakar Moawia
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Kathrin Schrage
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Arwa Ishaq A. Khayyat
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- Biochemistry Department, King Saud University, Riyadh, Saudi Arabia
| | - Jennifer A. Lawson
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K. Warejko
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias Hermle
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amar J. Majmundar
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hannah Hugo
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Birgit Budde
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Susanne Motameny
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Angelika Anna Noegel
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Hanan M. Fathy
- Pediatric Nephrology Unit, Alexandria Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Daniel P. Gale
- Centre for Nephrology, University College London, Royal Free Hospital, London, United Kingdom
| | - Syeda Seema Waseem
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Ayaz Khan
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Larissa Kerecuk
- Birmingham Children’s Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Seema Hashmi
- Department of Pediatric Nephrology, Sindh Institute of Urology and Transplantation, Karachi, Pakistan
| | - Nilufar Mohebbi
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Robert Ettenger
- Department of Pediatrics, University of California, Los Angeles, California
| | - Erkin Serdaroğlu
- Department of Pediatric Nephrology, Dr. Behçet Uz Children’s Hospital, Izmir, Turkey
| | - Khalid A. Alhasan
- Pediatric Department, College of Medicine, King Saud University and King Khalid University Hospital, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sara Goncalves
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes–Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Gema Ariceta
- Universitat Autonoma de Barcelona, Hospital Universitari Vall d’Hebron, Pediatric Nephrology, Barcelona, Spain
| | - Mercedes Ubetagoyena
- Hospital Universitario Donostia, Pediatric Nephrology, Donostia–San Sebastian, Spain
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Qian Shen
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes–Sorbonne Paris Cité, Imagine Institute, Paris, France
- Department of Genetics, Necker Hospital, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
49
|
van Nieuwenhuijze A, Burton O, Lemaitre P, Denton AE, Cascalho A, Goodchild RE, Malengier-Devlies B, Cauwe B, Linterman MA, Humblet-Baron S, Liston A. Mice Deficient in Nucleoporin Nup210 Develop Peripheral T Cell Alterations. Front Immunol 2018; 9:2234. [PMID: 30323813 PMCID: PMC6173157 DOI: 10.3389/fimmu.2018.02234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022] Open
Abstract
The nucleopore is an essential structure of the eukaryotic cell, regulating passage between the nucleus and cytoplasm. While individual functions of core nucleopore proteins have been identified, the role of other components, such as Nup210, are poorly defined. Here, through the use of an unbiased ENU mutagenesis screen for mutations effecting the peripheral T cell compartment, we identified a Nup210 mutation in a mouse strain with altered CD4/CD8 T cell ratios. Through the generation of Nup210 knockout mice we identified Nup210 as having a T cell-intrinsic function in the peripheral homeostasis of T cells. Remarkably, despite the deep evolutionary conservation of this key nucleopore complex member, no other major phenotypes developed, with viable and healthy knockout mice. These results identify Nup210 as an important nucleopore complex component for peripheral T cells, and raise further questions of why this nucleopore component shows deep evolutionary conservation despite seemingly redundant functions in most cell types.
Collapse
Affiliation(s)
- Annemarie van Nieuwenhuijze
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Oliver Burton
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Pierre Lemaitre
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Alice E Denton
- Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Ana Cascalho
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Neurosciences, University of Leuven, Leuven, Belgium
| | - Rose E Goodchild
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Neurosciences, University of Leuven, Leuven, Belgium
| | - Bert Malengier-Devlies
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Bénédicte Cauwe
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | | | - Stephanie Humblet-Baron
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Adrian Liston
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| |
Collapse
|
50
|
Kane M, Rebensburg SV, Takata MA, Zang TM, Yamashita M, Kvaratskhelia M, Bieniasz PD. Nuclear pore heterogeneity influences HIV-1 infection and the antiviral activity of MX2. eLife 2018; 7:e35738. [PMID: 30084827 PMCID: PMC6101944 DOI: 10.7554/elife.35738] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
HIV-1 accesses the nuclear DNA of interphase cells via a poorly defined process involving functional interactions between the capsid protein (CA) and nucleoporins (Nups). Here, we show that HIV-1 CA can bind multiple Nups, and that both natural and manipulated variation in Nup levels impacts HIV-1 infection in a manner that is strikingly dependent on cell-type, cell-cycle, and cyclophilin A (CypA). We also show that Nups mediate the function of the antiviral protein MX2, and that MX2 can variably inhibit non-viral NLS function. Remarkably, both enhancing and inhibiting effects of cyclophilin A and MX2 on various HIV-1 CA mutants could be induced or abolished by manipulating levels of the Nup93 subcomplex, the Nup62 subcomplex, NUP88, NUP214, RANBP2, or NUP153. Our findings suggest that several Nup-dependent 'pathways' are variably exploited by HIV-1 to target host DNA in a cell-type, cell-cycle, CypA and CA-sequence dependent manner, and are differentially inhibited by MX2.
Collapse
Affiliation(s)
- Melissa Kane
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Stephanie V Rebensburg
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Matthew A Takata
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Trinity M Zang
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Mamuka Kvaratskhelia
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Paul D Bieniasz
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| |
Collapse
|