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Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
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Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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2
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Nan Y, Chen W, Chen F, Wei L, Zeng A, Lin X, Zhou W, Yang Y, Li Q. Endosome mediated nucleocytoplasmic trafficking and endomembrane allocation is crucial to polyglutamine toxicity. Cell Biol Toxicol 2024; 40:48. [PMID: 38900277 PMCID: PMC11189978 DOI: 10.1007/s10565-024-09891-4] [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: 12/11/2023] [Accepted: 06/03/2024] [Indexed: 06/21/2024]
Abstract
Aggregation of aberrant proteins is a common pathological hallmark in neurodegeneration such as polyglutamine (polyQ) and other repeat-expansion diseases. Here through overexpression of ataxin3 C-terminal polyQ expansion in Drosophila gut enterocytes, we generated an intestinal obstruction model of spinocerebellar ataxia type3 (SCA3) and reported a new role of nuclear-associated endosomes (NAEs)-the delivery of polyQ to the nucleoplasm. In this model, accompanied by the prominently increased RAB5-positive NAEs are abundant nucleoplasmic reticulum enriched with polyQ, abnormal nuclear envelope invagination, significantly reduced endoplasmic reticulum, indicating dysfunctional nucleocytoplasmic trafficking and impaired endomembrane organization. Consistently, Rab5 but not Rab7 RNAi further decreased polyQ-related NAEs, inhibited endomembrane disorganization, and alleviated disease model. Interestingly, autophagic proteins were enriched in polyQ-related NAEs and played non-canonical autophagic roles as genetic manipulation of autophagic molecules exhibited differential impacts on NAEs and SCA3 toxicity. Namely, the down-regulation of Atg1 or Atg12 mitigated while Atg5 RNAi aggravated the disease phenotypes both in Drosophila intestines and compound eyes. Our findings, therefore, provide new mechanistic insights and underscore the fundamental roles of endosome-centered nucleocytoplasmic trafficking and homeostatic endomembrane allocation in the pathogenesis of polyQ diseases.
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Affiliation(s)
- Yuyu Nan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410000, China
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Wenfeng Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian Province, 350108, China
| | - Fei Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian Province, 350108, China
| | - Lili Wei
- Guangxi Clinical Research Center for Neurological Diseases, Guilin, Guangxi, 541001, China
| | - Aiyuan Zeng
- Department of Neurology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, Guilin, Guangxi, 541004, China
| | - Xiaohui Lin
- Department of Neurology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, Guilin, Guangxi, 541004, China
| | - Wenbin Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Yufeng Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian Province, 350108, China.
| | - Qinghua Li
- Department of Neurology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China.
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, Guilin, Guangxi, 541004, China.
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3
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Guglielmi V, Lam D, D’Angelo MA. Nucleoporin Nup358 drives the differentiation of myeloid-biased multipotent progenitors by modulating HDAC3 nuclear translocation. SCIENCE ADVANCES 2024; 10:eadn8963. [PMID: 38838144 PMCID: PMC11152124 DOI: 10.1126/sciadv.adn8963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Nucleoporins, the components of nuclear pore complexes (NPCs), can play cell type- and tissue-specific functions. Yet, the physiological roles and mechanisms of action for most NPC components have not yet been established. We report that Nup358, a nucleoporin linked to several myeloid disorders, is required for the developmental progression of early myeloid progenitors. We found that Nup358 ablation in mice results in the loss of myeloid-committed progenitors and mature myeloid cells and the accumulation of myeloid-primed multipotent progenitors (MPPs) in bone marrow. Accumulated MPPs in Nup358 knockout mice are greatly restricted to megakaryocyte/erythrocyte-biased MPP2, which fail to progress into committed myeloid progenitors. Mechanistically, we found that Nup358 is required for histone deacetylase 3 (HDAC3) nuclear import and function in MPP2 cells and established that this nucleoporin regulates HDAC3 nuclear translocation in a SUMOylation-independent manner. Our study identifies a critical function for Nup358 in myeloid-primed MPP2 differentiation and uncovers an unexpected role for NPCs in the early steps of myelopoiesis.
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Affiliation(s)
- Valeria Guglielmi
- Cancer Metabolism and Microenvironment Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Davina Lam
- Cancer Metabolism and Microenvironment Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maximiliano A. D’Angelo
- Cancer Metabolism and Microenvironment Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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4
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Mansueto G, Fusco G, Colonna G. A Tiny Viral Protein, SARS-CoV-2-ORF7b: Functional Molecular Mechanisms. Biomolecules 2024; 14:541. [PMID: 38785948 PMCID: PMC11118181 DOI: 10.3390/biom14050541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study presents the interaction with the human host metabolism of SARS-CoV-2 ORF7b protein (43 aa), using a protein-protein interaction network analysis. After pruning, we selected from BioGRID the 51 most significant proteins among 2753 proven interactions and 1708 interactors specific to ORF7b. We used these proteins as functional seeds, and we obtained a significant network of 551 nodes via STRING. We performed topological analysis and calculated topological distributions by Cytoscape. By following a hub-and-spoke network architectural model, we were able to identify seven proteins that ranked high as hubs and an additional seven as bottlenecks. Through this interaction model, we identified significant GO-processes (5057 terms in 15 categories) induced in human metabolism by ORF7b. We discovered high statistical significance processes of dysregulated molecular cell mechanisms caused by acting ORF7b. We detected disease-related human proteins and their involvement in metabolic roles, how they relate in a distorted way to signaling and/or functional systems, in particular intra- and inter-cellular signaling systems, and the molecular mechanisms that supervise programmed cell death, with mechanisms similar to that of cancer metastasis diffusion. A cluster analysis showed 10 compact and significant functional clusters, where two of them overlap in a Giant Connected Component core of 206 total nodes. These two clusters contain most of the high-rank nodes. ORF7b acts through these two clusters, inducing most of the metabolic dysregulation. We conducted a co-regulation and transcriptional analysis by hub and bottleneck proteins. This analysis allowed us to define the transcription factors and miRNAs that control the high-ranking proteins and the dysregulated processes within the limits of the poor knowledge that these sectors still impose.
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Affiliation(s)
- Gelsomina Mansueto
- Dipartimento di Scienze Mediche e Chirurgiche Avanzate, Università della Campania, L. Vanvitelli, 80138 Naples, Italy;
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Giovanni Colonna
- Medical Informatics AOU, Università della Campania, L. Vanvitelli, 80138 Naples, Italy
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Schieweck R, Götz M. Pan-cellular organelles and suborganelles-from common functions to cellular diversity? Genes Dev 2024; 38:98-114. [PMID: 38485267 PMCID: PMC10982711 DOI: 10.1101/gad.351337.123] [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: 04/02/2024]
Abstract
Cell diversification is at the base of increasing multicellular organism complexity in phylogeny achieved during ontogeny. However, there are also functions common to all cells, such as cell division, cell migration, translation, endocytosis, exocytosis, etc. Here we revisit the organelles involved in such common functions, reviewing recent evidence of unexpected differences of proteins at these organelles. For instance, centrosomes or mitochondria differ significantly in their protein composition in different, sometimes closely related, cell types. This has relevance for development and disease. Particularly striking is the high amount and diversity of RNA-binding proteins at these and other organelles, which brings us to review the evidence for RNA at different organelles and suborganelles. We include a discussion about (sub)organelles involved in translation, such as the nucleolus and ribosomes, for which unexpected cell type-specific diversity has also been reported. We propose here that the heterogeneity of these organelles and compartments represents a novel mechanism for regulating cell diversity. One reason is that protein functions can be multiplied by their different contributions in distinct organelles, as also exemplified by proteins with moonlighting function. The specialized organelles still perform pan-cellular functions but in a cell type-specific mode, as discussed here for centrosomes, mitochondria, vesicles, and other organelles. These can serve as regulatory hubs for the storage and transport of specific and functionally important regulators. In this way, they can control cell differentiation, plasticity, and survival. We further include examples highlighting the relevance for disease and propose to examine organelles in many more cell types for their possible differences with functional relevance.
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Affiliation(s)
- Rico Schieweck
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy;
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Magdalena Götz
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany;
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, 82152 Planegg-Martinsried, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
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6
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Izumi R, Ikeda K, Niihori T, Suzuki N, Shirota M, Funayama R, Nakayama K, Warita H, Tateyama M, Aoki Y, Aoki M. Nuclear pore pathology underlying multisystem proteinopathy type 3-related inclusion body myopathy. Ann Clin Transl Neurol 2024; 11:577-592. [PMID: 38158701 DOI: 10.1002/acn3.51977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024] Open
Abstract
OBJECTIVE Multisystem proteinopathy type 3 (MSP3) is an inherited, pleiotropic degenerative disorder caused by a mutation in heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), which can affect the muscle, bone, and/or nervous system. This study aimed to determine detailed histopathological features and transcriptomic profile of HNRNPA1-mutated skeletal muscles to reveal the core pathomechanism of hereditary inclusion body myopathy (hIBM), a predominant phenotype of MSP3. METHODS Histopathological analyses and RNA sequencing of HNRNPA1-mutated skeletal muscles harboring a c.940G > A (p.D314N) mutation (NM_031157) were performed, and the results were compared with those of HNRNPA1-unlinked hIBM and control muscle tissues. RESULTS RNA sequencing revealed aberrant alternative splicing events that predominantly occurred in myofibril components and mitochondrial respiratory complex. Enrichment analyses identified the nuclear pore complex (NPC) and nucleocytoplasmic transport as suppressed pathways. These two pathways were linked by the hub genes NUP50, NUP98, NUP153, NUP205, and RanBP2. In immunohistochemistry, these nucleoporin proteins (NUPs) were mislocalized to the cytoplasm and aggregated mostly with TAR DNA-binding protein 43 kDa and, to a lesser extent, with hnRNPA1. Based on ultrastructural observation, irregularly shaped myonuclei with deep invaginations were frequently observed in atrophic fibers, consistent with the disorganization of NPCs. Additionally, regarding the expression profiles of overall NUPs, reduced expression of NUP98, NUP153, and RanBP2 was shared with HNRNPA1-unlinked hIBMs. INTERPRETATION The shared subset of altered NUPs in amyotrophic lateral sclerosis (ALS), as demonstrated in prior research, HNRNPA1-mutated, and HNRNPA1-unlinked hIBM muscle tissues may provide evidence regarding the underlying common nuclear pore pathology of hIBM, ALS, and MSP.
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Grants
- KAKENHI (20K16571) Grant-in-Aid for Early-Career Scientists from Japan Society for the Promotion of Science (JSPS)
- KAKENHI (20H03586) Grant-in-Aid for Scientific Research (B) from Japan Society for the Promotion of Science (JSPS)
- KAKENHI (23H02821) Grant-in-Aid for Scientific Research (B) from Japan Society for the Promotion of Science (JSPS)
- KAKENHI (20K07897) Grant-in-Aid for Scientific Research (C) from Japan Society for the Promotion of Science (JSPS)
- 23FC1008 Grants-in-Aid from the Research Committee of CNS Degenerative Diseases, Research on Policy Planning and Evaluation for Rare and Intractable Diseases, Health, Labour and Welfare Sciences Research Grants, the Ministry of Health, Labour and Welfare, Japan
- 23FC1010 Grants-in-Aid from the Research Committee of CNS Degenerative Diseases, Research on Policy Planning and Evaluation for Rare and Intractable Diseases, Health, Labour and Welfare Sciences Research Grants, the Ministry of Health, Labour and Welfare, Japan
- 20FC1036 Grants-in-Aid for Research on Rare and Intractable Diseases from the Ministry of Health, Labour and Welfare of Japan
- 23FC1014 Grants-in-Aid for Research on Rare and Intractable Diseases from the Ministry of Health, Labour and Welfare of Japan
- Haruki ALS Research Foundation
- 2-5 Intramural Research Grant for Neurological and Psychiatric Disorders Provided from National Center of Neurology and Psychiatry of Japan
- 5-6 Intramural Research Grant for Neurological and Psychiatric Disorders Provided from National Center of Neurology and Psychiatry of Japan
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Affiliation(s)
- Rumiko Izumi
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kensuke Ikeda
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoki Suzuki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Science, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hitoshi Warita
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Maki Tateyama
- Department of Neurology, National Hospital Organization Iwate Hospital, Ichinoseki, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
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7
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Bender SWB, Dreisler MW, Zhang M, Kæstel-Hansen J, Hatzakis NS. SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis. Nat Commun 2024; 15:1763. [PMID: 38409214 PMCID: PMC10897458 DOI: 10.1038/s41467-024-46106-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
The morphology of protein assemblies impacts their behaviour and contributes to beneficial and aberrant cellular responses. While single-molecule localization microscopy provides the required spatial resolution to investigate these assemblies, the lack of universal robust analytical tools to extract and quantify underlying structures limits this powerful technique. Here we present SEMORE, a semi-automatic machine learning framework for universal, system- and input-dependent, analysis of super-resolution data. SEMORE implements a multi-layered density-based clustering module to dissect biological assemblies and a morphology fingerprinting module for quantification by multiple geometric and kinetics-based descriptors. We demonstrate SEMORE on simulations and diverse raw super-resolution data: time-resolved insulin aggregates, and published data of dSTORM imaging of nuclear pore complexes, fibroblast growth receptor 1, sptPALM of Syntaxin 1a and dynamic live-cell PALM of ryanodine receptors. SEMORE extracts and quantifies all protein assemblies, their temporal morphology evolution and provides quantitative insights, e.g. classification of heterogeneous insulin aggregation pathways and NPC geometry in minutes. SEMORE is a general analysis platform for super-resolution data, and being a time-aware framework can also support the rise of 4D super-resolution data.
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Affiliation(s)
- Steen W B Bender
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Marcus W Dreisler
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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8
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Jons CK, Cheng D, Dong C, Meany EL, Nassi JJ, Appel EA. AAV eluting lenses for single-step targeted expression of genetically-encoded activity sensors for in vivo microendoscopic calcium imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.09.566491. [PMID: 38014217 PMCID: PMC10680654 DOI: 10.1101/2023.11.09.566491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Optical methods for studying the brain offer powerful approaches for understanding how neural activity underlies complex behavior. These methods typically rely on genetically encoded sensors and actuators to monitor and control neural activity. For microendoscopic calcium imaging, injection of a virus followed by implantation of a lens probe is required to express a calcium sensor and enable optical access to the target brain region. This two-step process poses several challenges, chief among them being the risks associated with mistargeting and/or misalignment between virus expression zone, lens probe and target brain region. Here, we engineer an adeno-associated virus (AAV)-eluting polymer coating for gradient refractive index (GRIN) lenses enabling expression of a genetically encoded calcium indicator (GCaMP) directly within the brain region of interest upon implantation of the lens. This approach requires only one surgical step and guarantees alignment between GCaMP expression and lens in the brain. Additionally, the slow virus release from these coatings increases the working time for surgical implantation, expanding the brain regions and species amenable to this approach. These enhanced capabilities should accelerate neuroscience research utilizing optical methods and advance our understanding of the neural circuit mechanisms underlying brain function and behavior in health and disease. Significance Statement We engineered a polymer coating for gradient refractive index (GRIN) lenses that provides controlled release of adeno-associated viruses (AAVs). This technology enables expression of a genetically encoded calcium indicator (GCaMP) directly at the brain region of interest upon implantation of the lens. Compared to current methods, our coating offers two important improvements. First, it simplifies surgery by combining GCaMP expression and lens placement in one step, saving time and ensuring alignment. Second, controlled release of AAV from these coatings extends the time available for surgery, making it possible to implant lenses in deeper parts of the brain and in more species. These advances accelerate neuroscience research and deepen our understanding of how neural circuits impact both health and disease.
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9
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Baskerville V, Rapuri S, Mehlhop E, Coyne AN. SUN1 facilitates CHMP7 nuclear influx and injury cascades in sporadic amyotrophic lateral sclerosis. Brain 2024; 147:109-121. [PMID: 37639327 PMCID: PMC10766250 DOI: 10.1093/brain/awad291] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/16/2023] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
We have recently identified the aberrant nuclear accumulation of the ESCRT-III protein CHMP7 as an initiating event that leads to a significant injury to the nuclear pore complex (NPC) characterized by the reduction of specific nucleoporins from the neuronal NPC in sporadic amyotrophic lateral sclerosis (sALS) and C9orf72 ALS/frontotemporal dementia (FTD)-induced pluripotent stem cell-derived neurons (iPSNs), a phenomenon also observed in post-mortem patient tissues. Importantly, this NPC injury is sufficient to contribute to TDP-43 dysfunction and mislocalization, a common pathological hallmark of neurodegenerative diseases. However, the molecular mechanisms and events that give rise to increased nuclear translocation and/or retention of CHMP7 to initiate this pathophysiological cascade remain largely unknown. Here, using an iPSN model of sALS, we demonstrate that impaired NPC permeability barrier integrity and interactions with the LINC complex protein SUN1 facilitate CHMP7 nuclear localization and the subsequent 'activation' of NPC injury cascades. Collectively, our data provide mechanistic insights in the pathophysiological underpinnings of ALS/FTD and highlight SUN1 as a potent contributor to and modifier of CHMP7-mediated toxicity in sALS pathogenesis.
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Affiliation(s)
- Victoria Baskerville
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sampath Rapuri
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emma Mehlhop
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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10
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Yang X, Ji C, Liu X, Wei Z, Pang Q, Zhang A. Arabidopsis nucleoporin NUP96 mediates plant salt tolerance by modulating the transcription of salt-responsive genes. PLANTA 2023; 259:34. [PMID: 38160450 DOI: 10.1007/s00425-023-04312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
MAIN CONCLUSION Physiological and molecular tests show that NUP96 plays an important role in the plant response to salt stress, resulting from the reprogramming of transcriptomic profiles, which are likely to be mediated by the influence on the nuclear/cytosol shuttling of the key regulators of salt tolerance. As a key component of the nuclear pore complex (NPC), nucleoporin 96 (NUP96) is critical for modulating plant development and interactions with environmental factors, but whether NUP96 is involved in the salt response is still unknown. Here, we analyzed the role of Arabidopsis NUP96 under salt stress. The loss-of-function mutant nup96 exhibited salt sensitivity in terms of rosette growth and root elongation, and showed attenuated capacity in maintaining ion and ROS homeostasis, which could be compensated for by the overexpression of NUP96. RNA sequencing revealed that many salt-responsive genes were misregulated after NUP96 mutation, and especially NUP96 is required for the expression of a large portion of salt-induced genes. This is likely correlated with the activity in facilitating nuclear/cytosol transport of the underlying regulators in salt tolerance such as the transcription factor ATAP2, targeted by eight downregulated genes in nup96 under salt stress. Our results illustrate that NUP96 plays an important role in the salt response, probably by regulating the nucleocytoplasmic shuttling of key mRNAs or proteins associated with plant salt responsiveness.
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Affiliation(s)
- Xiaomin Yang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Chengcheng Ji
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Xinxin Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Zhaoxin Wei
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Qiuying Pang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Aiqin Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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11
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Rothstein JD, Warlick C, Coyne AN. Highly variable molecular signatures of TDP-43 loss of function are associated with nuclear pore complex injury in a population study of sporadic ALS patient iPSNs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571299. [PMID: 38168312 PMCID: PMC10760028 DOI: 10.1101/2023.12.12.571299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The nuclear depletion and cytoplasmic aggregation of the RNA binding protein TDP-43 is widely considered a pathological hallmark of Amyotrophic Lateral Sclerosis (ALS) and related neurodegenerative diseases. Recent studies have artificially reduced TDP-43 in wildtype human neurons to replicate loss of function associated events. Although this prior work has defined a number of gene expression and mRNA splicing changes that occur in a TDP-43 dependent manner, it is unclear how these alterations relate to authentic ALS where TDP-43 is not depleted from the cell but miscompartmentalized to variable extents. Here, in this population study, we generate ~30,000 qRT-PCR data points spanning 20 genes in induced pluripotent stem cell (iPSC) derived neurons (iPSNs) from >150 control, C9orf72 ALS/FTD, and sALS patients to examine molecular signatures of TDP-43 dysfunction. This data set defines a time dependent and variable profile of individual molecular hallmarks of TDP-43 loss of function within and amongst individual patient lines. Importantly, nearly identical changes are observed in postmortem CNS tissues obtained from a subset of patients whose iPSNs were examined. Notably, these studies provide evidence that induction of nuclear pore complex (NPC) injury via reduction of the transmembrane Nup POM121 in wildtype iPSNs is sufficient to phenocopy disease associated signatured of TDP-43 loss of function thereby directly linking NPC integrity to TDP-43 loss of function. Therapeutically, we demonstrate that the expression of all mRNA species associated with TDP-43 loss of function can be restored in sALS iPSNs via two independent methods to repair NPC injury. Collectively, this data 1) represents a substantial resource for the community to examine TDP-43 loss of function events in authentic sALS patient iPSNs, 2) demonstrates that patient derived iPSNs can accurately reflect actual TDP-43 associated alterations in patient brain, and 3) that targeting NPC injury events can be preclinically and reliably accomplished in an iPSN based platform of a sporadic disease.
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Affiliation(s)
- Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205
| | - Caroline Warlick
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205
| | - Alyssa N. Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205
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12
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Fernández-Jiménez N, Martinez-Garcia M, Varas J, Gil-Dones F, Santos JL, Pradillo M. The scaffold nucleoporins SAR1 and SAR3 are essential for proper meiotic progression in Arabidopsis thaliana. Front Cell Dev Biol 2023; 11:1285695. [PMID: 38111849 PMCID: PMC10725928 DOI: 10.3389/fcell.2023.1285695] [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: 08/30/2023] [Accepted: 11/21/2023] [Indexed: 12/20/2023] Open
Abstract
Nuclear Pore Complexes (NPCs) are embedded in the nuclear envelope (NE), regulating macromolecule transport and physically interacting with chromatin. The NE undergoes dramatic breakdown and reformation during plant cell division. In addition, this structure has a specific meiotic function, anchoring and positioning telomeres to facilitate the pairing of homologous chromosomes. To elucidate a possible function of the structural components of the NPCs in meiosis, we have characterized several Arabidopsis lines with mutations in genes encoding nucleoporins belonging to the outer ring complex. Plants defective for either SUPPRESSOR OF AUXIN RESISTANCE1 (SAR1, also called NUP160) or SAR3 (NUP96) present condensation abnormalities and SPO11-dependent chromosome fragmentation in a fraction of meiocytes, which is increased in the double mutant sar1 sar3. We also observed these meiotic defects in mutants deficient in the outer ring complex protein HOS1, but not in mutants affected in other components of this complex. Furthermore, our findings may suggest defects in the structure of NPCs in sar1 and a potential link between the meiotic role of this nucleoporin and a component of the RUBylation pathway. These results provide the first insights in plants into the role of nucleoporins in meiotic chromosome behavior.
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Affiliation(s)
- Nadia Fernández-Jiménez
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Universidad Complutense de Madrid, Madrid, Spain
| | - Marina Martinez-Garcia
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Félix Gil-Dones
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Luis Santos
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Universidad Complutense de Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Universidad Complutense de Madrid, Madrid, Spain
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13
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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.
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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
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Gusain P, Taketoshi M, Tominaga Y, Tominaga T. Functional Dissection of Ipsilateral and Contralateral Neural Activity Propagation Using Voltage-Sensitive Dye Imaging in Mouse Prefrontal Cortex. eNeuro 2023; 10:ENEURO.0161-23.2023. [PMID: 37977827 DOI: 10.1523/eneuro.0161-23.2023] [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: 05/15/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
Prefrontal cortex (PFC) intrahemispheric activity and the interhemispheric connection have a significant impact on neuropsychiatric disorder pathology. This study aimed to generate a functional map of FC intrahemispheric and interhemispheric connections. Functional dissection of mouse PFCs was performed using the voltage-sensitive dye (VSD) imaging method with high speed (1 ms/frame), high resolution (256 × 256 pixels), and a large field of view (∼10 mm). Acute serial 350 μm slices were prepared from the bregma covering the PFC and numbered 1-5 based on their distance from the bregma (i.e., 1.70, 1.34, 0.98, 0.62, and 0.26 mm) with reference to the Mouse Brain Atlas (Paxinos and Franklin, 2008). The neural response to electrical stimulation was measured at nine sites and then averaged, and a functional map of the propagation patterns was created. Intracortical propagation was observed in slices 3-5, encompassing the anterior cingulate cortex (ACC) and corpus callosum (CC). The activity reached area 33 of the ACC. Direct white matter stimulation activated area 33 in both hemispheres. Similar findings were obtained via DiI staining of the CC. Imaging analysis revealed directional biases in neural signals traveling within the ACC, whereby the signal transmission speed and probability varied based on the signal direction. Specifically, the spread of neural signals from cg2 to cg1 was stronger than that from cingulate cortex area 1(cg1) to cingulate cortex area 2(cg2), which has implications for interhemispheric functional connections. These findings highlight the importance of understanding the PFC functional anatomy in evaluating neuromodulators like serotonin and dopamine, as well as other factors related to neuropsychiatric diseases.
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Affiliation(s)
- Pooja Gusain
- Institute of Neuroscience, Tokushima Bunri University, Sanuki 769-2193, Japan
| | - Makiko Taketoshi
- Institute of Neuroscience, Tokushima Bunri University, Sanuki 769-2193, Japan
| | - Yoko Tominaga
- Institute of Neuroscience, Tokushima Bunri University, Sanuki 769-2193, Japan
| | - Takashi Tominaga
- Institute of Neuroscience, Tokushima Bunri University, Sanuki 769-2193, Japan
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Sanuki 769-2193, Japan
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15
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Gu S, Zhang Z, Li J, Sun J, Cui Z, Li F, Zhuang J, Chen W, Su C, Wu L, Wang X, Guo Z, Xu H, Zhao M, Ma D, Chen W. Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice. PLANT PHYSIOLOGY 2023; 193:2180-2196. [PMID: 37471276 DOI: 10.1093/plphys/kiad420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/17/2023] [Accepted: 06/05/2023] [Indexed: 07/22/2023]
Abstract
Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that 2 functional polymorphisms in O. sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the 2 subspecies O. sativa japonica and O. sativa indica rice, may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for O. sativa metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e. OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.
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Affiliation(s)
- Shuang Gu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Zhang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Strube Research GmbH & Co. KG, Söllingen 38387, Germany
| | - Jian Sun
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhibo Cui
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Fengcheng Li
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Jia Zhuang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Wanchun Chen
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Chang Su
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Lian Wu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoliang Wang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhifu Guo
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Hai Xu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Minghui Zhao
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | | | - Wenfu Chen
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
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16
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Padilla‐Mejia NE, Field MC. Evolutionary, structural and functional insights in nuclear organisation and nucleocytoplasmic transport in trypanosomes. FEBS Lett 2023; 597:2501-2518. [PMID: 37789516 PMCID: PMC10953052 DOI: 10.1002/1873-3468.14747] [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: 06/27/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
One of the remarkable features of eukaryotes is the nucleus, delimited by the nuclear envelope (NE), a complex structure and home to the nuclear lamina and nuclear pore complex (NPC). For decades, these structures were believed to be mainly architectural elements and, in the case of the NPC, simply facilitating nucleocytoplasmic trafficking. More recently, the critical roles of the lamina, NPC and other NE constituents in genome organisation, maintaining chromosomal domains and regulating gene expression have been recognised. Importantly, mutations in genes encoding lamina and NPC components lead to pathogenesis in humans, while pathogenic protozoa disrupt the progression of normal development and expression of pathogenesis-related genes. Here, we review features of the lamina and NPC across eukaryotes and discuss how these elements are structured in trypanosomes, protozoa of high medical and veterinary importance, highlighting lineage-specific and conserved aspects of nuclear organisation.
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Affiliation(s)
| | - Mark C. Field
- School of Life SciencesUniversity of DundeeUK
- Institute of Parasitology, Biology CentreCzech Academy of SciencesČeské BudějoviceCzechia
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17
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Desgraupes S, Etienne L, Arhel NJ. RANBP2 evolution and human disease. FEBS Lett 2023; 597:2519-2533. [PMID: 37795679 DOI: 10.1002/1873-3468.14749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
Ran-binding protein 2 (RANBP2)/Nup358 is a nucleoporin and a key component of the nuclear pore complex. Through its multiple functions (e.g., SUMOylation, regulation of nucleocytoplasmic transport) and subcellular localizations (e.g., at the nuclear envelope, kinetochores, annulate lamellae), it is involved in many cellular processes. RANBP2 dysregulation or mutation leads to the development of human pathologies, such as acute necrotizing encephalopathy 1, cancer, neurodegenerative diseases, and it is also involved in viral infections. The chromosomal region containing the RANBP2 gene is highly dynamic, with high structural variation and recombination events that led to the appearance of a gene family called RANBP2 and GCC2 Protein Domains (RGPD), with multiple gene loss/duplication events during ape evolution. Although RGPD homoplasy and maintenance during evolution suggest they might confer an advantage to their hosts, their functions are still unknown and understudied. In this review, we discuss the appearance and importance of RANBP2 in metazoans and its function-related pathologies, caused by an alteration of its expression levels (through promotor activity, post-transcriptional, or post-translational modifications), its localization, or genetic mutations.
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Affiliation(s)
- Sophie Desgraupes
- Institut de Recherche en Infectiologie de Montpellier (IRIM), University of Montpellier, France
| | - Lucie Etienne
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR 5308, ENS de Lyon, Université de Lyon, France
| | - Nathalie J Arhel
- Institut de Recherche en Infectiologie de Montpellier (IRIM), University of Montpellier, France
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18
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [PMID: 37974978 PMCID: PMC10643749 DOI: 10.1007/s12551-023-01136-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 11/19/2023] Open
Abstract
Nuclear cytoplasmic transport is mediated by many receptors that recognize specific nuclear localization signals on proteins and RNA and transport these substrates through nuclear pore complexes. Facilitated diffusion through nuclear pore complexes requires the attachment of transport receptors. Despite the relatively large tunnel diameter, some even small proteins (less than 20-30 kDa), such as histones, pass through the nuclear pore complex only with transport receptors. Over several decades, considerable material has been accumulated on the structure, architecture, and amino acid composition of the proteins included in this complex and the sequence of many receptors. We consider the data available in the literature on the structure of the nuclear pore complex and possible mechanisms of nuclear-cytoplasmic transport, applying the theory of electrostatic interactions in the context of our data on changes in the electrokinetic potential of nuclei and our previously proposed physical model of the mechanism of facilitated diffusion through the nuclear pore complex (NPC). According to our data, the main contribution to the charge of the nuclear membrane is made by anionic phospholipids, which are part of both the nuclear membrane and the nuclear matrix, which creates a potential difference between them. The nuclear membrane is a four-layer phospholipid dielectric, so the potential vector can only pass through the NPC, creating an electrostatic funnel that "pulls in" the positively charged load-NLS-NTR trigger complexes. Considering the newly obtained data, an improved model of the previously proposed physical model of the mechanism of nuclear-cytoplasmic transport is proposed. This model considers the contribution of electrostatic fields to the transportation speed when changing the membrane's thickness in the NPC basket at a higher load.
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Affiliation(s)
- Liya A. Minasbekyan
- Scientific Research Institute of Biology, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
| | - Hamlet G. Badalyan
- Chair of General Physics, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
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19
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Cristi AC, Rapuri S, Coyne AN. Nuclear pore complex and nucleocytoplasmic transport disruption in neurodegeneration. FEBS Lett 2023; 597:2546-2566. [PMID: 37657945 PMCID: PMC10612469 DOI: 10.1002/1873-3468.14729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/29/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Nuclear pore complexes (NPCs) play a critical role in maintaining the equilibrium between the nucleus and cytoplasm, enabling bidirectional transport across the nuclear envelope, and are essential for proper nuclear organization and gene regulation. Perturbations in the regulatory mechanisms governing NPCs and nuclear envelope homeostasis have been implicated in the pathogenesis of several neurodegenerative diseases. The ESCRT-III pathway emerges as a critical player in the surveillance and preservation of well-assembled, functional NPCs, as well as nuclear envelope sealing. Recent studies have provided insights into the involvement of nuclear ESCRT-III in the selective reduction of specific nucleoporins associated with neurodegenerative pathologies. Thus, maintaining quality control of the nuclear envelope and NPCs represents a pivotal element in the pathological cascade leading to neurodegenerative diseases. This review describes the constituents of the nuclear-cytoplasmic transport machinery, encompassing the nuclear envelope, NPC, and ESCRT proteins, and how their structural and functional alterations contribute to the development of neurodegenerative diseases.
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Affiliation(s)
- América Chandía Cristi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Sampath Rapuri
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
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20
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [DOI: https:/doi.org/10.1007/s12551-023-01136-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 02/27/2024] Open
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21
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Chen S, Cao R, Xiang L, Li Z, Chen H, Zhang J, Feng X. Research progress in nucleus-targeted tumor therapy. Biomater Sci 2023; 11:6436-6456. [PMID: 37609783 DOI: 10.1039/d3bm01116j] [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: 08/24/2023]
Abstract
The nucleus is considered the most important organelle in the cell as it plays a central role in controlling cell reproduction, metabolism, and the cell cycle. The successful delivery of drugs into the nucleus can achieve excellent therapeutic effects, which reveals the potential of nucleus-targeted therapy in precision medicine. However, the transportation of therapeutics into the nucleus remains a significant challenge due to various biological barriers. Herein, we summarize the recent progress in the nucleus-targeted drug delivery system (NDDS). The structures of the nucleus and nuclear envelope are first described in order to understand the mechanisms by which drugs cross the nuclear envelope. Then, various drug delivery strategies based on the mechanisms and their applications are discussed. Finally, the challenges and solutions in the field of nucleus-targeted drug delivery are raised for developing a more efficient NDDS and promoting its clinical transformation.
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Affiliation(s)
- Shaofeng Chen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.
| | - Rumeng Cao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.
| | - Ling Xiang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.
| | - Ziyi Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.
| | - Hui Chen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.
| | - Jiumeng Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xuli Feng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.
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22
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Bensidoun P, Zenklusen D, Oeffinger M. Differential affinity purification and mass spectrometry analysis of two nuclear pore complex isoforms in yeast S. cerevisiae. STAR Protoc 2023; 4:102359. [PMID: 37327111 PMCID: PMC10300402 DOI: 10.1016/j.xpro.2023.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/03/2023] [Accepted: 05/16/2023] [Indexed: 06/18/2023] Open
Abstract
Two isoforms of the nuclear pore complex (NPC) have been identified in the yeast S. cerevisiae, which coexist at the periphery of the nucleus and differ by the presence or absence of a nuclear basket. Here, we present a protocol to isolate the two types of NPCs from the same cell extract and dissect their interactomes. We describe steps for powder preparation and magnetic bead conjunction and detail differential affinity purification and outcome evaluation through SDS-PAGE, silver staining, and mass spectrometry analysis. For complete details on the use and execution of this protocol, please refer to Bensidoun et al.1.
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Affiliation(s)
- Pierre Bensidoun
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
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23
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Ikliptikawati DK, Hirai N, Makiyama K, Sabit H, Kinoshita M, Matsumoto K, Lim K, Meguro-Horike M, Horike SI, Hazawa M, Nakada M, Wong RW. Nuclear transport surveillance of p53 by nuclear pores in glioblastoma. Cell Rep 2023; 42:112882. [PMID: 37552992 DOI: 10.1016/j.celrep.2023.112882] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/30/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the central apparatus of nucleocytoplasmic transport. Disease-specific alterations of NPCs contribute to the pathogenesis of many cancers; however, the roles of NPCs in glioblastoma (GBM) are unknown. In this study, we report genomic amplification of NUP107, a component of NPCs, in GBM and show that NUP107 is overexpressed simultaneously with MDM2, a critical E3 ligase that mediates p53 degradation. Depletion of NUP107 inhibits the growth of GBM cell lines through p53 protein stabilization. Mechanistically, NPCs establish a p53 degradation platform via an export pathway coupled with 26S proteasome tethering. NUP107 is the keystone for NPC assembly; the loss of NUP107 affects the integrity of the NPC structure, and thus the proportion of 26S proteasome in the vicinity of nuclear pores significantly decreases. Together, our findings establish roles of NPCs in transport surveillance and provide insights into p53 inactivation in GBM.
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Affiliation(s)
- Dini Kurnia Ikliptikawati
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan; Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan; WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 9201192, Japan
| | - Nozomi Hirai
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 9208641, Japan; Department of Neurosurgery, Toho University Ohashi Medical Center, Tokyo 1538515, Japan
| | - Kei Makiyama
- Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan
| | - Hemragul Sabit
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 9208641, Japan
| | - Masashi Kinoshita
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 9208641, Japan
| | - Koki Matsumoto
- Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan
| | - Keesiang Lim
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 9201192, Japan
| | - Makiko Meguro-Horike
- Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shin-Ichi Horike
- Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan; Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan; WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 9201192, Japan.
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 9208641, Japan.
| | - Richard W Wong
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan; Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 9201192, Japan; WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 9201192, Japan.
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24
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Kong SH, Ma L, Yuan Q, Liu X, Han Y, Xiang W, Liu DX, Zhang Y, Lu J. Inhibition of EZH2 alleviates SAHA-induced senescence-associated secretion phenotype in small cell lung cancer cells. Cell Death Discov 2023; 9:289. [PMID: 37543653 PMCID: PMC10404275 DOI: 10.1038/s41420-023-01591-y] [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: 02/06/2023] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023] Open
Abstract
Chemotherapy has been widely used in small cell lung cancer (SCLC) treatment in the past decades. However, SCLC is easy to recur after chemotherapy. The senescence of cancer cells during chemotherapy is one of the effective therapeutic strategies to inhibit the progression of cancer. Nevertheless, the senescence-associated secretion phenotype (SASP) promotes chronic inflammation of the cancer microenvironment and further accelerates the progression of tumors. Therefore, inducing the senescence of cancer cells and inhibiting the production of SASP factors during anticancer treatment have become effective therapeutic strategies to improve the anticancer effect of drugs. Here we reported that SCLC cells treated with an FDA-approved HDAC inhibitor SAHA underwent senescence and displayed remarkable SASP. In particular, SAHA promoted the formation of cytoplasmic chromatin fragments (CCFs) in SCLC cells. The increased CCFs in SAHA-treated SCLC cells were related to nuclear porin Tpr, which activated the cGAS-STING pathway, and promoted the secretion of SASP in cancer cells. Inhibition of EZH2 suppressed the increase of CCFs in SAHA-treated SCLC cells, weakened the production of SASP, and increased the antiproliferative effect of SAHA. Overall, our work affords new insight into the secretion of SASP in SCLC and establishes a foundation for constructing a new therapeutic strategy for SCLC patients.
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Affiliation(s)
- Sun-Hyok Kong
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Life Science, University of Science, Pyongyang, 999091, Democratic People's Republic of Korea
| | - Lie Ma
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Qingxia Yuan
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiangxiang Liu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Yu Han
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Weifang Xiang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Dong-Xu Liu
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, 1010, New Zealand
| | - Yu Zhang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Jun Lu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China.
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25
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Curnutte HA, Lan X, Sargen M, Ao Ieong SM, Campbell D, Kim H, Liao Y, Lazar SB, Trcek T. Proteins rather than mRNAs regulate nucleation and persistence of Oskar germ granules in Drosophila. Cell Rep 2023; 42:112723. [PMID: 37384531 PMCID: PMC10439980 DOI: 10.1016/j.celrep.2023.112723] [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: 12/09/2022] [Revised: 04/24/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
RNA granules are membraneless condensates that provide functional compartmentalization within cells. The mechanisms by which RNA granules form are under intense investigation. Here, we characterize the role of mRNAs and proteins in the formation of germ granules in Drosophila. Super-resolution microscopy reveals that the number, size, and distribution of germ granules is precisely controlled. Surprisingly, germ granule mRNAs are not required for the nucleation or the persistence of germ granules but instead control their size and composition. Using an RNAi screen, we determine that RNA regulators, helicases, and mitochondrial proteins regulate germ granule number and size, while the proteins of the endoplasmic reticulum, nuclear pore complex, and cytoskeleton control their distribution. Therefore, the protein-driven formation of Drosophila germ granules is mechanistically distinct from the RNA-dependent condensation observed for other RNA granules such as stress granules and P-bodies.
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Affiliation(s)
- Harrison A Curnutte
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Xinyue Lan
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Manuel Sargen
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Si Man Ao Ieong
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Dylan Campbell
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Hyosik Kim
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Yijun Liao
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Sarah Bailah Lazar
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Tatjana Trcek
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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26
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Huang P, Hu YD, Liu YJ, Li JP, Zhang YH. An Analysis Regarding the Association Between the Nuclear Pore Complex (NPC) and Hepatocellular Carcinoma (HCC). J Hepatocell Carcinoma 2023; 10:959-978. [PMID: 37377841 PMCID: PMC10292625 DOI: 10.2147/jhc.s417501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Background The nuclear pore complex (NPC) is the main mediator of nuclear and cytoplasmic communication, and delaying or blocking nuclear RNA export and protein shuttling can inhibit cell proliferation and induce apoptosis. Although NPC is a research hotspot in structural biology, relevant studies in hepatocellular carcinoma are scarce, especially in terms of translation into clinical practice. Methods This study used a bioinformatics approach combining validation experiments to investigate the biological mechanisms that may be related with NPC. A series of experiments performed to explore the function of the Targeting protein for Xenopus kinesin-like protein 2 (TPX2) in HCC. Results Patients with HCC can be divided into two NPC clusters. Patients with high NPC levels (C1) had a shorter survival time than those with low NPC levels (C2) and are characterised by high levels of proliferative signals. We demonstrated that TPX2 regulates HCC growth and inhibits apoptosis in an NPC-dependent manner and contributes to the maintenance of HCC stemness. We developed the NPCScore to predict the prognosis and degree of differentiation in HCC patients. Conclusion NPC plays an important role in the malignant proliferation of HCC. Assessing NPC expression patterns could help enhance our understanding of tumor cell proliferation and could guide more effective chemotherapeutic strategies.
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Affiliation(s)
- Pan Huang
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
| | - Yi-dou Hu
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
| | - Yuan-jie Liu
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
| | - Jie-pin Li
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Key Laboratory of Tumor System Biology of Traditional Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
| | - Yong-hua Zhang
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
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27
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Xu AF, Molinuevo R, Fazzari E, Tom H, Zhang Z, Menendez J, Casey KM, Ruggero D, Hinck L, Pritchard JK, Barna M. Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates. eLife 2023; 12:e78695. [PMID: 37306301 PMCID: PMC10313321 DOI: 10.7554/elife.78695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/09/2023] [Indexed: 06/13/2023] Open
Abstract
The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.
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Affiliation(s)
- Adele Francis Xu
- Department of Genetics, Stanford UniversityStanfordUnited States
- Medical Scientist Training Program, Stanford School of MedicineStanfordUnited States
| | - Rut Molinuevo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Elisa Fazzari
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Harrison Tom
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Zijian Zhang
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Julien Menendez
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Kerriann M Casey
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Comparative Medicine, Stanford School of MedicineStanfordUnited States
| | - Davide Ruggero
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Lindsay Hinck
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | | | - Maria Barna
- Department of Genetics, Stanford UniversityStanfordUnited States
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28
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Zentella R, Wang Y, Zahn E, Hu J, Jiang L, Shabanowitz J, Hunt DF, Sun TP. SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants. PLANT PHYSIOLOGY 2023; 191:1546-1560. [PMID: 36740243 PMCID: PMC10022643 DOI: 10.1093/plphys/kiad011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/12/2022] [Indexed: 05/28/2023]
Abstract
SPINDLY (SPY) is a novel nucleocytoplasmic protein O-fucosyltransferase that regulates target protein activity or stability via O-fucosylation of specific Ser/Thr residues. Previous genetic studies indicate that AtSPY regulates plant development during vegetative and reproductive growth by modulating gibberellin and cytokinin responses. AtSPY also regulates the circadian clock and plant responses to biotic and abiotic stresses. The pleiotropic phenotypes of spy mutants point to the likely role of AtSPY in regulating key proteins functioning in diverse cellular pathways. However, very few AtSPY targets are known. Here, we identified 88 SPY targets from Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana via the purification of O-fucosylated peptides using Aleuria aurantia lectin followed by electron transfer dissociation-MS/MS analysis. Most AtSPY targets were nuclear proteins that function in DNA repair, transcription, RNA splicing, and nucleocytoplasmic transport. Cytoplasmic AtSPY targets were involved in microtubule-mediated cell division/growth and protein folding. A comparison with the published O-linked-N-acetylglucosamine (O-GlcNAc) proteome revealed that 30% of AtSPY targets were also O-GlcNAcylated, indicating that these distinct glycosylations could co-regulate many protein functions. This study unveiled the roles of O-fucosylation in modulating many key nuclear and cytoplasmic proteins and provided a valuable resource for elucidating the regulatory mechanisms involved.
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Affiliation(s)
- Rodolfo Zentella
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Yan Wang
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Emily Zahn
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Jianhong Hu
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Liang Jiang
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia 22903, USA
| | - Tai-ping Sun
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
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29
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Raval PK, Garg SG, Gould SB. Endosymbiotic selective pressure at the origin of eukaryotic cell biology. eLife 2022; 11:e81033. [PMID: 36355038 PMCID: PMC9648965 DOI: 10.7554/elife.81033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
The dichotomy that separates prokaryotic from eukaryotic cells runs deep. The transition from pro- to eukaryote evolution is poorly understood due to a lack of reliable intermediate forms and definitions regarding the nature of the first host that could no longer be considered a prokaryote, the first eukaryotic common ancestor, FECA. The last eukaryotic common ancestor, LECA, was a complex cell that united all traits characterising eukaryotic biology including a mitochondrion. The role of the endosymbiotic organelle in this radical transition towards complex life forms is, however, sometimes questioned. In particular the discovery of the asgard archaea has stimulated discussions regarding the pre-endosymbiotic complexity of FECA. Here we review differences and similarities among models that view eukaryotic traits as isolated coincidental events in asgard archaeal evolution or, on the contrary, as a result of and in response to endosymbiosis. Inspecting eukaryotic traits from the perspective of the endosymbiont uncovers that eukaryotic cell biology can be explained as having evolved as a solution to housing a semi-autonomous organelle and why the addition of another endosymbiont, the plastid, added no extra compartments. Mitochondria provided the selective pressures for the origin (and continued maintenance) of eukaryotic cell complexity. Moreover, they also provided the energetic benefit throughout eukaryogenesis for evolving thousands of gene families unique to eukaryotes. Hence, a synthesis of the current data lets us conclude that traits such as the Golgi apparatus, the nucleus, autophagosomes, and meiosis and sex evolved as a response to the selective pressures an endosymbiont imposes.
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Affiliation(s)
- Parth K Raval
- Institute for Molecular Evolution, Heinrich-Heine-University DüsseldorfDusseldorfGermany
| | - Sriram G Garg
- Evolutionary Biochemistry Group, Max-Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine-University DüsseldorfDusseldorfGermany
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30
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Han L, Mich-Basso JD, Li Y, Ammanamanchi N, Xu J, Bargaje AP, Liu H, Wu L, Jeong JH, Franks J, Stolz DB, Wu YL, Rajasundaram D, Liu Y, Kühn B. Changes in nuclear pore numbers control nuclear import and stress response of mouse hearts. Dev Cell 2022; 57:2397-2411.e9. [PMID: 36283391 PMCID: PMC9614572 DOI: 10.1016/j.devcel.2022.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/24/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022]
Abstract
Nuclear pores are essential for nuclear-cytoplasmic transport. Whether and how cells change nuclear pores to alter nuclear transport and cellular function is unknown. Here, we show that rat heart muscle cells (cardiomyocytes) undergo a 63% decrease in nuclear pore numbers during maturation, and this changes their responses to extracellular signals. The maturation-associated decline in nuclear pore numbers is associated with lower nuclear import of signaling proteins such as mitogen-activated protein kinase (MAPK). Experimental reduction of nuclear pore numbers decreased nuclear import of signaling proteins, resulting in decreased expression of immediate-early genes. In a mouse model of high blood pressure, reduction of nuclear pore numbers improved adverse heart remodeling and reduced progression to lethal heart failure. The decrease in nuclear pore numbers in cardiomyocyte maturation and resulting functional changes demonstrate how terminally differentiated cells permanently alter their handling of information flux across the nuclear envelope and, with that, their behavior.
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Affiliation(s)
- Lu Han
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jocelyn D Mich-Basso
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Yao Li
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Niyatie Ammanamanchi
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jianquan Xu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anita P Bargaje
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Honghai Liu
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Liwen Wu
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jong-Hyeon Jeong
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jonathan Franks
- Center for Biologic Imaging, Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Donna B Stolz
- Center for Biologic Imaging, Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yijen L Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Yang Liu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bernhard Kühn
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219-3110, USA.
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31
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Bensidoun P, Reiter T, Montpetit B, Zenklusen D, Oeffinger M. Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast. Mol Cell 2022; 82:3856-3871.e6. [PMID: 36220102 PMCID: PMC10300651 DOI: 10.1016/j.molcel.2022.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/24/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022]
Abstract
To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly.
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Affiliation(s)
- Pierre Bensidoun
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Taylor Reiter
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Daniel Zenklusen
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada.
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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32
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Adrenal histological and functional changes after hepatic encephalopathy: From mice model to an integrative bioinformatics analysis. Acta Histochem 2022; 124:151960. [DOI: 10.1016/j.acthis.2022.151960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/28/2022] [Indexed: 11/15/2022]
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33
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Genetic modification, intercellular communication, and epigenetic regulation in plants: An outlook. Biochem Biophys Res Commun 2022; 633:92-95. [DOI: 10.1016/j.bbrc.2022.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/23/2022]
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34
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Up-regulation of POM121 is linked to prostate cancer aggressiveness and serves as a prognostic biomarker. Urol Oncol 2022; 40:380.e11-380.e18. [DOI: 10.1016/j.urolonc.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/13/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022]
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35
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Regulating Phase Transition in Neurodegenerative Diseases by Nuclear Import Receptors. BIOLOGY 2022; 11:biology11071009. [PMID: 36101390 PMCID: PMC9311884 DOI: 10.3390/biology11071009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
RNA-binding proteins (RBPs) with a low-complexity prion-like domain (PLD) can undergo aberrant phase transitions and have been implicated in neurodegenerative diseases such as ALS and FTD. Several nuclear RBPs mislocalize to cytoplasmic inclusions in disease conditions. Impairment in nucleocytoplasmic transport is another major event observed in ageing and in neurodegenerative disorders. Nuclear import receptors (NIRs) regulate the nucleocytoplasmic transport of different RBPs bearing a nuclear localization signal by restoring their nuclear localization. NIRs can also specifically dissolve or prevent the aggregation and liquid–liquid phase separation of wild-type or disease-linked mutant RBPs, due to their chaperoning activity. This review focuses on the LLPS of intrinsically disordered proteins and the role of NIRs in regulating LLPS in neurodegeneration. This review also discusses the implication of NIRs as therapeutic agents in neurogenerative diseases.
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36
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Aomine Y, Sakurai K, Macpherson T, Ozawa T, Miyamoto Y, Yoneda Y, Oka M, Hikida T. Importin α3 (KPNA3) Deficiency Augments Effortful Reward-Seeking Behavior in Mice. Front Neurosci 2022; 16:905991. [PMID: 35844217 PMCID: PMC9279672 DOI: 10.3389/fnins.2022.905991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Importin α3 (Gene: Kpna3, the ortholog of human Importin α4) is a member of the importin α family and participates in nucleocytoplasmic transport by forming trimeric complexes between cargo proteins and importin β1. Evidence from human studies has indicated that single nucleotide polymorphisms (SNP) in the KPNA3 gene are associated with the occurrence of several psychiatric disorders accompanied by abnormal reward-related behavior, including schizophrenia, major depression, and substance addiction. However, the precise roles of importin α3 in controlling reward processing and motivation are still unclear. In this study, we evaluated the behavioral effects of Kpna3 knockout (KO) in mice on performance in touchscreen operant chamber-based tasks evaluating simple (fixed-ratio) and effortful (progressive-ratio) reward-seeking behaviors. While Kpna3 KO mice showed no significant differences in operant reward learning on a fixed-ratio schedule, they demonstrated significantly increased motivation (increased break point) to instrumentally respond for sucrose on a progressive-ratio schedule. We additionally measured the number of c-Fos-positive cells, a marker of neural activity, in 20 regions of the brain and identified a network of brain regions based on their interregional correlation coefficients. Network and graph-theoretic analyses suggested that Kpna3 deficiency enhanced overall interregional functional connectivity. These findings suggest the importance of Kpna3 in motivational control and indicate that Kpna3 KO mice may be an attractive line for modeling motivational abnormalities associated with several psychiatric disorders.
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Affiliation(s)
- Yoshiatsu Aomine
- Laboratory for Advanced Brain Functions, Institute for Protein Research, Osaka University, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Koki Sakurai
- Laboratory for Advanced Brain Functions, Institute for Protein Research, Osaka University, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Tom Macpherson
- Laboratory for Advanced Brain Functions, Institute for Protein Research, Osaka University, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Takaaki Ozawa
- Laboratory for Advanced Brain Functions, Institute for Protein Research, Osaka University, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - Yoshihiro Yoneda
- National Institutes for Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - Masahiro Oka
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - Takatoshi Hikida
- Laboratory for Advanced Brain Functions, Institute for Protein Research, Osaka University, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
- *Correspondence: Takatoshi Hikida,
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37
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Heinemann D, Zabic M, Terakawa M, Boch J. Laser-based molecular delivery and its applications in plant science. PLANT METHODS 2022; 18:82. [PMID: 35690858 PMCID: PMC9188231 DOI: 10.1186/s13007-022-00908-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 05/14/2023]
Abstract
Lasers enable modification of living and non-living matter with submicron precision in a contact-free manner which has raised the interest of researchers for decades. Accordingly, laser technologies have drawn interest across disciplines. They have been established as a valuable tool to permeabilize cellular membranes for molecular delivery in a process termed photoinjection. Laser-based molecular delivery was first reported in 1984, when normal kidney cells were successfully transfected with a frequency-multiplied Nd:YAG laser. Due to the rapid development of optical technologies, far more sophisticated laser platforms have become available. In particular, near infrared femtosecond (NIR fs) laser sources enable an increasing progress of laser-based molecular delivery procedures and opened up multiple variations and applications of this technique.This review is intended to provide a plant science audience with the physical principles as well as the application potentials of laser-based molecular delivery. The historical origins and technical development of laser-based molecular delivery are summarized and the principle physical processes involved in these approaches and their implications for practical use are introduced. Successful cases of laser-based molecular delivery in plant science will be reviewed in detail, and the specific hurdles that plant materials pose will be discussed. Finally, we will give an outlook on current limitations and possible future applications of laser-based molecular delivery in the field of plant science.
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Affiliation(s)
- Dag Heinemann
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany.
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1, 30167, Hannover, Germany.
| | - Miroslav Zabic
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Mitsuhiro Terakawa
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Jens Boch
- Institute of Plant Genetics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Coyne AN, Rothstein JD. Nuclear pore complexes - a doorway to neural injury in neurodegeneration. Nat Rev Neurol 2022; 18:348-362. [PMID: 35488039 PMCID: PMC10015220 DOI: 10.1038/s41582-022-00653-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings and end-stage pathological hallmarks of neurodegenerative diseases are increasingly well defined, but the cellular pathophysiology of disease initiation and propagation remains poorly understood, especially in sporadic forms of these diseases. Altered nucleocytoplasmic transport is emerging as a prominent pathomechanism of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer disease, frontotemporal dementia and Huntington disease. The nuclear pore complex (NPC) and interactions between its individual nucleoporin components and nuclear transport receptors regulate nucleocytoplasmic transport, as well as genome organization and gene expression. Specific nucleoporin abnormalities have been identified in sporadic and familial forms of neurodegenerative disease, and these alterations are thought to contribute to disrupted nucleocytoplasmic transport. The specific nucleoporins and nucleocytoplasmic transport proteins that have been linked to different neurodegenerative diseases are partially distinct, suggesting that NPC injury contributes to the cellular specificity of neurodegenerative disease and could be an early initiator of the pathophysiological cascades that underlie neurodegenerative disease. This concept is consistent with the fact that rare genetic mutations in some nucleoporins cause cell-type-specific neurological disease. In this Review, we discuss nucleoporin and NPC disruptions and consider their impact on cellular function and the pathophysiology of neurodegenerative disease.
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Affiliation(s)
- Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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39
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Li M, Zhao H. Bioinformatics analysis of the expression and clinical significance of the NUP210 Gene in acute myeloid leukaemia. Hematology 2022; 27:456-462. [PMID: 35413221 DOI: 10.1080/16078454.2022.2061107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
: Nucleoporin 210 (NUP210) is a membrane-spanning nuclear protein known to be involved in the development of solid tumours; however, its role in haematological cancers has not been investigated. This study aimed to assess the expression and prognostic potential of NUP210 gene expression in patients with acute myeloid leukaemia (AML). : In this study, we assessed the expression and prognostic potential of NUP210 gene expression in patients with AML through bioinformatics analysis of The Cancer Genome Atlas and Genotype-Tissue Expression databases. :The expression of NUP210 mRNA in bone marrow was significantly increased in patients with AML compared to that in healthy individuals and was correlated with AML subtypes according to French-American-British classification as well as with bone marrow blast counts and patient sex (P < 0.05). The high NUP210 expression level was an independent biomarker of poor prognosis in the total AML population (P < 0.05) and separately in female but not male patients. : Our results of NUP210 mRNA analyses revealed, for the first time, that NUP210 transcription was upregulated in patients with AML and positively associated with unfavourable AML prognosis, suggesting that NUP210 expression can be used as guidance in patient stratification for targeted therapy.
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Affiliation(s)
- Mengqi Li
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - He Zhao
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
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40
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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.
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41
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Li Z, Chen S, Zhao L, Huang G, Pi X, Sun S, Wang P, Sui SF. Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex. Cell Res 2022; 32:437-450. [PMID: 35301440 PMCID: PMC9061825 DOI: 10.1038/s41422-022-00632-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their huge size and highly dynamic nature. Here we determined the structure of the asymmetric unit of the inner ring (IR monomer) at 3.73 Å resolution by single-particle cryo-electron microscopy, and created an atomic model of the intact IR consisting of 192 molecules of 8 nucleoporins. In each IR monomer, the Z-shaped Nup188–Nup192 complex in the middle layer is sandwiched by two approximately parallel rhomboidal structures in the inner and outer layers, while Nup188, Nup192 and Nic96 link all subunits to constitute a relatively stable IR monomer. In contrast, the intact IR is assembled by loose and instable interactions between IR monomers. These structures, together with previously reported structural information of IR, reveal two distinct interaction modes between IR monomers and extensive flexible connections in IR assembly, providing a structural basis for the stability and malleability of IR.
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Affiliation(s)
- Zongqiang Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shuaijiabin Chen
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Liang Zhao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Guoqiang Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Xiong Pi
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peiyi Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China.,Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China. .,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China. .,Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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42
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Raices M, D'Angelo MA. Structure, Maintenance, and Regulation of Nuclear Pore Complexes: The Gatekeepers of the Eukaryotic Genome. Cold Spring Harb Perspect Biol 2022; 14:a040691. [PMID: 34312247 PMCID: PMC8789946 DOI: 10.1101/cshperspect.a040691] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the genetic material is segregated inside the nucleus. This compartmentalization of the genome requires a transport system that allows cells to move molecules across the nuclear envelope, the membrane-based barrier that surrounds the chromosomes. Nuclear pore complexes (NPCs) are the central component of the nuclear transport machinery. These large protein channels penetrate the nuclear envelope, creating a passage between the nucleus and the cytoplasm through which nucleocytoplasmic molecule exchange occurs. NPCs are one of the largest protein assemblies of eukaryotic cells and, in addition to their critical function in nuclear transport, these structures also play key roles in many cellular processes in a transport-independent manner. Here we will review the current knowledge of the NPC structure, the cellular mechanisms that regulate their formation and maintenance, and we will provide a brief description of a variety of processes that NPCs regulate.
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Affiliation(s)
- Marcela Raices
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Maximiliano A D'Angelo
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
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43
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Lauw MI, Qi Z, Eversmeyer L, Prakash S, Wen KW, Yu J, Monaghan SA, Aggarwal N, Wang L. Distinct Pathologic Feature of Myeloid Neoplasm with t(v;11p15); NUP98 Rearrangement. Hum Pathol 2022; 123:11-19. [DOI: 10.1016/j.humpath.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/30/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
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44
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Liashkovich I, Rosso G, Shahin V. Atomic Force Microscopy for Structural and Biophysical Investigations on Nuclear Pore Complexes. Methods Mol Biol 2022; 2502:299-310. [PMID: 35412247 DOI: 10.1007/978-1-0716-2337-4_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Atomic force microscopy (AFM) enables simultaneous generation of topographical and biophysical maps of surfaces of biological samples at nanoresolution in physiologically relevant environments. Here, we describe the application of AFM to study nuclear pore complexes from structural and biophysical aspects.
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Affiliation(s)
- Ivan Liashkovich
- Institute of Physiology II, University of Münster, Münster, Germany
| | - Gonzalo Rosso
- Institute of Physiology II, University of Münster, Münster, Germany
| | - Victor Shahin
- Institute of Physiology II, University of Münster, Münster, Germany.
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45
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Bindra D, Mishra RK. In Pursuit of Distinctiveness: Transmembrane Nucleoporins and Their Disease Associations. Front Oncol 2022; 11:784319. [PMID: 34970494 PMCID: PMC8712647 DOI: 10.3389/fonc.2021.784319] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
The bi-directional nucleocytoplasmic shuttling of macromolecules like molecular signals, transcription factors, regulatory proteins, and RNAs occurs exclusively through Nuclear Pore Complex (NPC) residing in the nuclear membrane. This magnanimous complex is essentially a congregation of ~32 conserved proteins termed Nucleoporins (Nups) present in multiple copies and mostly arranged as subcomplexes to constitute a functional NPC. Nups participate in ancillary functions such as chromatin organization, transcription regulation, DNA damage repair, genome stabilization, and cell cycle control, apart from their central role as nucleocytoplasmic conduits. Thus, Nups exert a role in the maintenance of cellular homeostasis. In mammals, precisely three nucleoporins traverse the nuclear membrane, are called transmembrane Nups (TM-Nups), and are involved in multiple cellular functions. Owing to their vital roles in cellular processes and homeostasis, dysregulation of nucleoporin function is implicated in various diseases. The deregulated functioning of TM-Nups can thus act as an opportune window for the development of diseases. Indeed, mounting evidence exhibits a strong association of TM-Nups in cancer and numerous other physiological disorders. These findings have provided much-needed insights into the novel mechanisms of disease progression. While nucleoporin’s functions have often been summarized in the disease context, a focus on TM-Nups has always lacked. This review emphasizes the elucidation of distinct canonical and non-canonical functions of mammalian TM-Nups and the underlying mechanisms of their disease association.
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Affiliation(s)
- Divya Bindra
- Nups and SUMO Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Ram Kumar Mishra
- Nups and SUMO Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
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46
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Ansar R, Saqib S, Mukhtar A, Niazi MBK, Shahid M, Jahan Z, Kakar SJ, Uzair B, Mubashir M, Ullah S, Khoo KS, Lim HR, Show PL. Challenges and recent trends with the development of hydrogel fiber for biomedical applications. CHEMOSPHERE 2022; 287:131956. [PMID: 34523459 DOI: 10.1016/j.chemosphere.2021.131956] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Hydrogel is the most emblematic soft material which possesses significantly tunable and programmable characteristics. Polymer hydrogels possess significant advantages including, biocompatible, simple, reliable and low cost. Therefore, research on the development of hydrogel for biomedical applications has been grown intensely. However, hydrogel development is challenging and required significant effort before the application at an industrial scale. Therefore, the current work focused on evaluating recent trends and issues with hydrogel development for biomedical applications. In addition, the hydrogel's development methodology, physicochemical properties, and biomedical applications are evaluated and benchmarked against the reported literature. Later, biomedical applications of the nano-cellulose-based hydrogel are considered and critically discussed. Based on a detailed review, it has been found that the surface energy, intermolecular interactions, and interactions of hydrogel adhesion forces are major challenges that contribute to the development of hydrogel. In addition, compared to other hydrogels, nanocellulose hydrogels demonstrated higher potential for drug delivery, 3D cell culture, diagnostics, tissue engineering, tissue therapies and gene therapies. Overall, nanocellulose hydrogel has the potential for commercialization for different biomedical applications.
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Affiliation(s)
- Reema Ansar
- Department of Chemical Engineering, University of Gujrat, 50700, Pakistan.
| | - Sidra Saqib
- Department of Chemical Engineering, COMSATS University Islamabad, Lahore Campus, 54000, Lahore, Pakistan.
| | - Ahmad Mukhtar
- Department of Chemical Engineering, NFC Institute of Engineering and Fertilizer Research, Jaranwala Road, 38000, Faisalabad, Pakistan.
| | - Muhammad Bilal Khan Niazi
- School of Chemical and Materials Engineering, National University of Sciences and Technology, Islamabad, Pakistan.
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan.
| | - Zaib Jahan
- School of Chemical and Materials Engineering, National University of Sciences and Technology, Islamabad, Pakistan.
| | - Salik Javed Kakar
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, Pakistan.
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan.
| | - Muhammad Mubashir
- Department of Petroleum Engineering, School of Engineering, Asia Pacific University of Technology and Innovation, 57000, Kuala Lumpur, Malaysia.
| | - Sami Ullah
- Department of Chemistry, College of Science, King Khalid University, Abha, Saudi Arabia.
| | - Kuan Shiong Khoo
- Department of Chemical and Environmental Engineering, Faculty Science and Engineering, University of Nottingham, Malaysia, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Hooi Ren Lim
- Department of Chemical and Environmental Engineering, Faculty Science and Engineering, University of Nottingham, Malaysia, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty Science and Engineering, University of Nottingham, Malaysia, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
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Sakuma S, Zhu EY, Raices M, Zhang P, Murad R, D'Angelo MA. Loss of Nup210 results in muscle repair delays and age-associated alterations in muscle integrity. Life Sci Alliance 2021; 5:5/3/e202101216. [PMID: 34911810 PMCID: PMC8711851 DOI: 10.26508/lsa.202101216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022] Open
Abstract
This study describes the the role of a nuclear pore complex protein in mammalian in skeletal muscle maintenance, repair, and function. Nuclear pore complexes, the channels connecting the nucleus with the cytoplasm, are built by multiple copies of ∼30 proteins called nucleoporins. Recent evidence has exposed that nucleoporins can play cell type-specific functions. Despite novel discoveries into the cellular functions of nucleoporins, their role in the regulation of mammalian tissue physiology remains mostly unexplored because of a limited number of nucleoporin mouse models. Here we show that ablation of Nup210/Gp210, a nucleoporin previously identified to play a role in myoblast differentiation and Zebrafish muscle maturation, is dispensable for skeletal muscle formation and growth in mice. We found that although primary satellite cells from Nup210 knockout mice can differentiate, these animals show delayed muscle repair after injury. Moreover, Nup210 knockout mice display an increased percentage of centrally nucleated fibers and abnormal fiber type distribution as they age. Muscle function experiments also exposed that Nup210 is required for muscle endurance during voluntary running. Our findings indicate that in mammals, Nup210 is important for the maintenance of skeletal muscle integrity and for proper muscle function providing novel insights into the in vivo roles of nuclear pore complex components.
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Affiliation(s)
- Stephen Sakuma
- Cell and Molecular Biology of Cancer Program, National Cancer Institute (NCI)-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Ethan Ys Zhu
- Cell and Molecular Biology of Cancer Program, National Cancer Institute (NCI)-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marcela Raices
- Cell and Molecular Biology of Cancer Program, National Cancer Institute (NCI)-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Pan Zhang
- Bioinformatics Core, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Rabi Murad
- Bioinformatics Core, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maximiliano A D'Angelo
- Cell and Molecular Biology of Cancer Program, National Cancer Institute (NCI)-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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Romanauska A. Seeing fat inside the nucleus. Science 2021; 374:1066. [PMID: 34822281 DOI: 10.1126/science.abm8139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ, Iorio F. CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens. BMC Genomics 2021; 22:828. [PMID: 34789150 PMCID: PMC8597285 DOI: 10.1186/s12864-021-08129-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 10/28/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 genome-wide screens are being increasingly performed, allowing systematic explorations of cancer dependencies at unprecedented accuracy and scale. One of the major computational challenges when analysing data derived from such screens is to identify genes that are essential for cell survival invariantly across tissues, conditions, and genomic-contexts (core-fitness genes), and to distinguish them from context-specific essential genes. This is of paramount importance to assess the safety profile of candidate therapeutic targets and for elucidating mechanisms involved in tissue-specific genetic diseases. RESULTS We have developed CoRe: an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens. We demonstrate, through a fully reproducible benchmarking pipeline, that CoRe outperforms state-of-the-art tools, yielding more reliable and biologically relevant sets of core-fitness genes. CONCLUSIONS CoRe offers a flexible pipeline, compatible with many pre-processing methods for the analysis of CRISPR data, which can be tailored onto different use-cases. The CoRe package can be used for the identification of high-confidence novel core-fitness genes, as well as a means to filter out potentially cytotoxic hits while analysing cancer dependency datasets for identifying and prioritising novel selective therapeutic targets.
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Affiliation(s)
| | - Emre Karakoc
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Clare Pacini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Francesco Iorio
- Human Technopole, Milan, Italy.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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50
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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.
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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
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