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Wu F, Sun G, Nai Y, Shi X, Ma Y, Cao H. NUP43 promotes PD-L1/nPD-L1/PD-L1 feedback loop via TM4SF1/JAK/STAT3 pathway in colorectal cancer progression and metastatsis. Cell Death Discov 2024; 10:241. [PMID: 38762481 PMCID: PMC11102480 DOI: 10.1038/s41420-024-02025-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024] Open
Abstract
Programmed cell death-ligand 1 (PD-L1) has a significant role in tumor progression and metastasis, facilitating tumor cell evasion from immune surveillance. PD-L1 can be detected in the tumor cell nucleus and exert an oncogenic effect by nuclear translocation. Colorectal cancer (CRC) progression and liver metastasis (CCLM) are among the most lethal diseases worldwide, but the mechanism of PD-L1 nuclear translocation in CRC and CCLM remains to be fully understood. In this study, using CRISPR-Cas9-based genome-wide screening combined with RNA-seq, we found that the oncogenic factor NUP43 impacted the process of PD-L1 nuclear translocation by regulating the expression level of the PD-L1 chaperone protein IPO5. Subsequent investigation revealed that this process could stimulate the expression of tumor-promoting factor TM4SF1 and further activate the JAK/STAT3 signaling pathway, which ultimately enhanced the transcription of PD-L1, thus establishing a PD-L1-nPD-L1-PD-L1 feedback loop that ultimately promoted CRC progression and CCLM. In conclusion, our study reveals a novel role for nPD-L1 in CRC, identifies the PD-L1-nPD-L1-PD-L1 feedback loop in CRC, and provides a therapeutic strategy for CRC patients.
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Affiliation(s)
- Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guoqiang Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Yongjun Nai
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuesong Shi
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Yong Ma
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
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2
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Pennacchio FA, Poli A, Pramotton FM, Lavore S, Rancati I, Cinquanta M, Vorselen D, Prina E, Romano OM, Ferrari A, Piel M, Cosentino Lagomarsino M, Maiuri P. N2FXm, a method for joint nuclear and cytoplasmic volume measurements, unravels the osmo-mechanical regulation of nuclear volume in mammalian cells. Nat Commun 2024; 15:1070. [PMID: 38326317 PMCID: PMC10850064 DOI: 10.1038/s41467-024-45168-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
In eukaryotes, cytoplasmic and nuclear volumes are tightly regulated to ensure proper cell homeostasis. However, current methods to measure cytoplasmic and nuclear volumes, including confocal 3D reconstruction, have limitations, such as relying on two-dimensional projections or poor vertical resolution. Here, to overcome these limitations, we describe a method, N2FXm, to jointly measure cytoplasmic and nuclear volumes in single cultured adhering human cells, in real time, and across cell cycles. We find that this method accurately provides joint size over dynamic measurements and at different time resolutions. Moreover, by combining several experimental perturbations and analyzing a mathematical model including osmotic effects and tension, we show that N2FXm can give relevant insights on how mechanical forces exerted by the cytoskeleton on the nuclear envelope can affect the growth of nucleus volume by biasing nuclear import. Our method, by allowing for accurate joint nuclear and cytoplasmic volume dynamic measurements at different time resolutions, highlights the non-constancy of the nucleus/cytoplasm ratio along the cell cycle.
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Affiliation(s)
- Fabrizio A Pennacchio
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Alessandro Poli
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Francesca Michela Pramotton
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, CH-8092, Switzerland
| | - Stefania Lavore
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Ilaria Rancati
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mario Cinquanta
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Daan Vorselen
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98105, USA
| | - Elisabetta Prina
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Orso Maria Romano
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Aldo Ferrari
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, CH-8092, Switzerland
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Marco Cosentino Lagomarsino
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, and I.N.F.N., Via Celoria 16, 20133, Milan, Italy
| | - Paolo Maiuri
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131, Naples, Italy.
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3
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Ester L, Cabrita I, Ventzke M, Kieckhöfer E, Christodoulou M, Mandel AM, Diefenhardt P, Fabretti F, Benzing T, Habbig S, Schermer B. The role of the FSGS disease gene product and nuclear pore protein NUP205 in regulating nuclear localization and activity of transcriptional regulators YAP and TAZ. Hum Mol Genet 2023; 32:3153-3165. [PMID: 37565816 PMCID: PMC10630254 DOI: 10.1093/hmg/ddad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
Mutations in genes encoding nuclear pore proteins (NUPs) lead to the development of steroid-resistant nephrotic syndrome and focal segmental glomerulosclerosis (FSGS). However, the precise molecular mechanisms by which NUP dysfunction contributes to podocyte injury preceding FSGS remain unclear. The tightly regulated activity of Yes-associated protein (YAP) and WW-domain-containing transcription regulator 1 (TAZ), the transcriptional effectors of the Hippo pathway, is crucial for podocytes and the maintenance of the glomerular filter. In this study, we investigate the impact of NUPs on the regulation of YAP/TAZ nuclear import and activity in podocytes. In unbiased interactome studies using quantitative label-free mass spectrometry, we identify the FSGS disease gene products NUP107, NUP133, NUP205, and Exportin-5 (XPO5) as components of YAP and TAZ protein complexes in podocytes. Moreover, we demonstrate that NUP205 is essential for YAP/TAZ nuclear import. Consistently, both the nuclear interaction of YAP/TAZ with TEA domain transcription factor 1 and their transcriptional activity were dependent on NUP205 expression. Additionally, we elucidate a regulatory feedback mechanism whereby YAP activity is modulated in response to TAZ-mediated NUP205 expression. In conclusion, this study establishes a connection between the FSGS disease protein NUP205 and the activity of the transcriptional regulators and Hippo effectors YAP and TAZ and it proposes a potential pathological role of YAP/TAZ dysregulation in podocytes of patients with pathogenic NUP205 variants.
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Affiliation(s)
- Lioba Ester
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Inês Cabrita
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Michel Ventzke
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Emilia Kieckhöfer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Marita Christodoulou
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Amrei M Mandel
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Paul Diefenhardt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Sandra Habbig
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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4
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Li H, Zhu D, Yang Y, Ma Y, Chen Y, Xue P, Chen J, Qin M, Xu D, Cai C, Cheng H. Restricted tRNA methylation by intermolecular disulfide bonds in DNMT2/TRDMT1. Int J Biol Macromol 2023; 251:126310. [PMID: 37579906 DOI: 10.1016/j.ijbiomac.2023.126310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Reportedly, DNMT2/TRDMT1 mainly methylates tRNAs at C38 and prevents them from the cleavage under stress. It also plays an essential role in the survival and physiological homeostasis of organisms. Nevertheless, DNMT2/TRDMT1 exhibits much weaker tRNA methylation activity in vitro than other tRNA methyltransferases, TrmD and Trm5. Here, we explored the restricted tRNA methylation mechanism by DNMT2/TRDMT1. In the current study, the optimized buffer C at 37 °C was the best condition for DNMT2/TRDMT1 activation. Of note, Dithiothreitol (DTT) was an indispensable component for this enzyme catalysis. Moreover, reductants took similar effects on the conformation change and oligomeric formation of DNMT2/TRDMT1. Ultimately, LC-MS/MS result revealed that C292-C292 and C292-C287 were predominant intermolecular disulfide bonds in recombinant DNMT2/TRDMT1. Notably, DNMT2/TRDMT1 existed primarily as dimers via intermolecular disulfide bonds C79-C24, C292-C292, and C222-C24 in HEK293T cells. GSSG stress enhanced tRNA methylation level in the early stage of stress, whereas the DNMT2/TRDMT1 activity might be unfavorable along with this enzyme accumulation in the nucleus. Excitingly, GSH stress downregulated the DNMT2/TRDMT1 expression and promoted tRNA methylation in cells, probably through breaking intermolecular disulfide bonds in this enzyme. Thus, our findings demonstrated restricted tRNA methylation by disulfide bonds in DNMT2/TRDMT1, and will provide important implications for redox stress related-diseases.
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Affiliation(s)
- Huari Li
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China.
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yapeng Yang
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yunfei Ma
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yong Chen
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Pingfang Xue
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Juan Chen
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Mian Qin
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Dandan Xu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Chao Cai
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Hongjing Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
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5
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Cisneros B, García-Aguirre I, De Ita M, Arrieta-Cruz I, Rosas-Vargas H. Hutchinson-Gilford Progeria Syndrome: Cellular Mechanisms and Therapeutic Perspectives. Arch Med Res 2023; 54:102837. [PMID: 37390702 DOI: 10.1016/j.arcmed.2023.06.002] [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: 01/09/2023] [Revised: 05/26/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023]
Abstract
In humans, aging is characterized by a gradual decline of physical and psychological functions, with the concomitant onset of chronic-degenerative diseases, which ultimately lead to death. The study of Hutchinson-Gilford progeria syndrome (HGPS), a premature aging disorder that recapitulates several features of natural aging, has provided important insights into deciphering the aging process. The genetic origin of HGPS is a de novo point mutation in the LMNA gene that drives the synthesis of progerin, mutant version of lamin A. Progerin is aberrantly anchored to the nuclear envelope disrupting a plethora of molecular processes; nonetheless, how progerin exerts a cascade of deleterious alterations at the cellular and systemic levels is not fully understood. Over the past decade, the use of different cellular and animal models for HGPS has allowed the identification of the molecular mechanisms underlying HGPS, paving the way towards the development of therapeutic treatments against the disease. In this review, we present an updated overview of the biology of HGPS, including its clinical features, description of key cellular processes affected by progerin (nuclear morphology and function, nucleolar activity, mitochondrial function, protein nucleocytoplasmic trafficking and telomere homeostasis), as well as discussion of the therapeutic strategies under development.
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Affiliation(s)
- Bulmaro Cisneros
- Genetics and Molecular Biology Department, Research and Advanced Studies Center, National Polytechnical Institute, Mexico City, Mexico
| | - Ian García-Aguirre
- Genetics and Molecular Biology Department, Research and Advanced Studies Center, National Polytechnical Institute, Mexico City, Mexico; Bioengineering Department, School of Engineering and Sciences, Tecnológico de Monterrey, Mexico City, Mexico
| | - Marlon De Ita
- Genetics and Molecular Biology Department, Research and Advanced Studies Center, National Polytechnical Institute, Mexico City, Mexico; Medical Research Unit in Human Genetics, Pediatrics Hospital, 21st Century National Medical Center, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Isabel Arrieta-Cruz
- Basic Research Department, Research Direction, National Institute of Geriatrics, Ministry of Health, Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Medical Research Unit in Human Genetics, Pediatrics Hospital, 21st Century National Medical Center, Instituto Mexicano del Seguro Social, Mexico City, Mexico.
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6
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Udi Y, Zhang W, Stein ME, Ricardo-Lax I, Pasolli HA, Chait BT, Rout MP. A general method for quantitative fractionation of mammalian cells. J Cell Biol 2023; 222:213941. [PMID: 36920247 PMCID: PMC10040634 DOI: 10.1083/jcb.202209062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.
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Affiliation(s)
- Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University , New York, NY, USA
| | - Hilda A Pasolli
- Electron Microscopy Resource Center, The Rockefeller University , New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
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7
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Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans 2023; 51:871-886. [PMID: 37099395 PMCID: PMC10212546 DOI: 10.1042/bst20220494] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo-EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a 'restrained concentrate' which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid on- and off-rates among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, ageing, viral diseases, and neurodegeneration.
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Affiliation(s)
- David Cowburn
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, U.S.A
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8
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Zheng T, Zilman A. Self-regulation of the nuclear pore complex enables clogging-free crowded transport. Proc Natl Acad Sci U S A 2023; 120:e2212874120. [PMID: 36757893 PMCID: PMC9963888 DOI: 10.1073/pnas.2212874120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the main conduits for macromolecular transport into and out of the nucleus of eukaryotic cells. The central component of the NPC transport mechanism is an assembly of intrinsically disordered proteins (IDPs) that fills the NPC channel. The channel interior is further crowded by large numbers of simultaneously translocating cargo-carrying and free transport proteins. How the NPC can efficiently, rapidly, and selectively transport varied cargoes in such crowded conditions remains ill understood. Past experimental results suggest that the NPC is surprisingly resistant to clogging and that transport may even become faster and more efficient as the concentration of transport protein increases. To understand the mechanisms behind these puzzling observations, we construct a computational model of the NPC comprising only a minimal set of commonly accepted consensus features. This model qualitatively reproduces the previous experimental results and identifies self-regulating mechanisms that relieve crowding. We show that some of the crowding-alleviating mechanisms-such as preventing saturation of the bulk flux-are "robust" and rely on very general properties of crowded dynamics in confined channels, pertaining to a broad class of selective transport nanopores. By contrast, the counterintuitive ability of the NPC to leverage crowding to achieve more efficient single-molecule translocation is "fine-tuned" and relies on the particular spatial architecture of the IDP assembly in the NPC channel.
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Affiliation(s)
- Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
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9
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Herceg S, Janoštiak R. Diagnostic and Prognostic Profiling of Nucleocytoplasmic Shuttling Genes in Hepatocellular Carcinoma. Folia Biol (Praha) 2023; 69:133-148. [PMID: 38410971 DOI: 10.14712/fb2023069040133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
One of the key features of eukaryotic cells is the separation of nuclear and cytoplasmic compartments by a double-layer nuclear envelope. This separation is crucial for timely regulation of gene expression, mRNA biogenesis, cell cycle, and differentiation. Since transcription takes place in the nucleus and the major part of translation in the cytoplasm, proper distribution of biomolecules between these two compartments is ensured by nucleocytoplasmic shuttling proteins - karyopherins. Karyopherins transport biomolecules through nuclear pores bidirectionally in collaboration with Ran GTPases and utilize GTP as the source of energy. Different karyopherins transport different cargo molecules that play important roles in the regulation of cell physiology. In cancer cells, this nucleocytoplasmic transport is significantly dysregulated to support increased demands for the import of cell cycle-promoting biomolecules and export of cell cycle inhibitors and mRNAs. Here, we analysed genomic, transcriptomic and proteomic data from published datasets to comprehensively profile karyopherin genes in hepatocellular carcinoma. We have found out that expression of multiple karyopherin genes is increased in hepatocellular carcinoma in comparison to the normal liver, with importin subunit α-1, exportin 2, importin subunit β-1 and importin 9 being the most over-expressed. More-over, we have found that increased expression of these genes is associated with higher neoplasm grade as well as significantly worse overall survival of liver cancer patients. Taken together, our bioinformatic data-mining analysis provides a comprehensive geno-mic and transcriptomic landscape of karyopherins in hepatocellular carcinoma and identifies potential members that could be targeted in order to develop new treatment regimens.
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Affiliation(s)
- Samuel Herceg
- BIOCEV - First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Radoslav Janoštiak
- BIOCEV - First Faculty of Medicine, Charles University, Prague, Czech Republic.
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10
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Tough Way In, Tough Way Out: The Complex Interplay of Host and Viral Factors in Nucleocytoplasmic Trafficking during HIV-1 Infection. Viruses 2022; 14:v14112503. [PMID: 36423112 PMCID: PMC9696704 DOI: 10.3390/v14112503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) is a retrovirus that integrates its reverse-transcribed genome as proviral DNA into the host genome to establish a successful infection. The viral genome integration requires safeguarding the subviral complexes, reverse transcription complex (RTC) and preintegration complex (PIC), in the cytosol from degradation, presumably effectively secured by the capsid surrounding these complexes. An intact capsid, however, is a large structure, which raises concerns about its translocation from cytoplasm to nucleus crossing the nuclear membrane, guarded by complex nuclear pore structures, which do not allow non-specific transport of large molecules. In addition, the generation of new virions requires the export of incompletely processed viral RNA from the nucleus to the cytoplasm, an event conventionally not permitted through mammalian nuclear membranes. HIV-1 has evolved multiple mechanisms involving redundant host pathways by liaison with the cell's nucleocytoplasmic trafficking system, failure of which would lead to the collapse of the infection cycle. This review aims to assemble the current developments in temporal and spatial events governing nucleocytoplasmic transport of HIV-1 factors. Discoveries are anticipated to serve as the foundation for devising host-directed therapies involving selective abolishment of the critical interactomes between viral proteins and their host equivalents.
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Damizia M, Altieri L, Lavia P. Non-transport roles of nuclear import receptors: In need of the right balance. Front Cell Dev Biol 2022; 10:1041938. [PMID: 36438555 PMCID: PMC9686011 DOI: 10.3389/fcell.2022.1041938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2023] Open
Abstract
Nuclear import receptors ensure the recognition and transport of proteins across the nuclear envelope into the nucleus. In addition, as diverse processes as mitosis, post-translational modifications at mitotic exit, ciliogenesis, and phase separation, all share a common need for regulation by nuclear import receptors - particularly importin beta-1 and importin beta-2/transportin - independent on nuclear import. In particular, 1) nuclear import receptors regulate the mitotic spindle after nuclear envelope breakdown, 2) they shield cargoes from unscheduled ubiquitination, regulating their timely proteolysis; 3) they regulate ciliary factors, crucial to cell communications and tissue architecture during development; and 4) they prevent phase separation of toxic proteins aggregates in neurons. The balance of nuclear import receptors to cargoes is critical in all these processes, albeit in opposite directions: overexpression of import receptors, as often found in cancer, inhibits cargoes and impairs downstream processes, motivating the therapeutic design of specific inhibitors. On the contrary, elevated expression is beneficial in neuronal contexts, where nuclear import receptors are regarded as potential therapeutic tools in counteracting the formation of aggregates that may cause neurodegeneration. This paradox demonstrates the amplitude of nuclear import receptors-dependent functions in different contexts and adds complexity in considering their therapeutic implications.
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Affiliation(s)
- Michela Damizia
- Department of Cellular, Computational and Integrated Biology (CIBIO), University of Trento, Trento, Italy
| | - Ludovica Altieri
- Institute of Molecular Biology and Pathology (IBPM), CNR National Research Council of Italy, Sapienza University of Rome, Rome, Italy
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Patrizia Lavia
- Institute of Molecular Biology and Pathology (IBPM), CNR National Research Council of Italy, Sapienza University of Rome, Rome, Italy
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
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Wu X, Han J, Guo C. Function of Nuclear Pore Complexes in Regulation of Plant Defense Signaling. Int J Mol Sci 2022; 23:ijms23063031. [PMID: 35328452 PMCID: PMC8953349 DOI: 10.3390/ijms23063031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
In eukaryotes, the nucleus is the regulatory center of cytogenetics and metabolism, and it is critical for fundamental biological processes, including DNA replication and transcription, protein synthesis, and biological macromolecule transportation. The eukaryotic nucleus is surrounded by a lipid bilayer called the nuclear envelope (NE), which creates a microenvironment for sophisticated cellular processes. The NE is perforated by the nuclear pore complex (NPC), which is the channel for biological macromolecule bi-directional transport between the nucleus and cytoplasm. It is well known that NPC is the spatial designer of the genome and the manager of genomic function. Moreover, the NPC is considered to be a platform for the continual adaptation and evolution of eukaryotes. So far, a number of nucleoporins required for plant-defense processes have been identified. Here, we first provide an overview of NPC organization in plants, and then discuss recent findings in the plant NPC to elaborate on and dissect the distinct defensive functions of different NPC subcomponents in plant immune defense, growth and development, hormone signaling, and temperature response. Nucleoporins located in different components of NPC have their unique functions, and the link between the NPC and nucleocytoplasmic trafficking promotes crosstalk of different defense signals in plants. It is necessary to explore appropriate components of the NPC as potential targets for the breeding of high-quality and broad spectrum resistance crop varieties.
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Affiliation(s)
- Xi Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
| | - Junyou Han
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
- Correspondence: (J.H.); (C.G.)
| | - Changkui Guo
- Laboratory of Plant Molecular and Developmental Biology, Zhejiang A & F University, Hangzhou 311300, China
- Correspondence: (J.H.); (C.G.)
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