1
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Ding J, Liqian, Lin Y, Zheng X, Huang C, Hong J, Chen C, Fei Z. Baseline SUVmax is correlated with tumor hypoxia and patient outcomes in nasopharyngeal carcinoma. Sci Rep 2024; 14:20157. [PMID: 39215035 PMCID: PMC11364769 DOI: 10.1038/s41598-024-71191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
To evaluate the prognostic significance of the maximum standardized uptake value (SUVmax) in nasopharyngeal carcinoma (NPC), establish a gene signature that correlates with SUVmax, and explore the underlying biological behaviors associated with these correlations for the prediction of clinical outcomes. A cohort of 726 patients with NPC was examined to identify correlations between SUVmax and various clinical variables. RNA sequencing was performed to identify genes related to SUVmax, and these genes were used to develop an SUV signature. Additionally, transcriptome enrichment analysis was conducted to investigate the potential biological behaviors underlying the observed correlations. Higher SUVmax was associated with an increased tumor burden and worse prognosis. The SUV signature, which consisted of 10 genes, was positively correlated with SUVmax, and it predicted worse survival outcomes. This signature was highly expressed in malignant epithelial cells and associated with hypoxia and resistance to radiotherapy. Additionally, the signature was negatively correlated with immune function. SUVmax is a valuable prognostic indicator in NPC, with higher values predicting worse outcomes. The SUV signature offers further prognostic insights, linking glucose metabolism to tumor aggressiveness, treatment resistance, and immune function, and it could represent a potential biomarker for NPC.
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Affiliation(s)
- Jianming Ding
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Liqian
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Yuhao Lin
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Xiaobing Zheng
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Chaoxiong Huang
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Jiabiao Hong
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Chuanben Chen
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China.
| | - Zhaodong Fei
- Department of Radiation Oncology, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China.
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2
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Li Y, Zhu J, Zhai F, Kong L, Li H, Jin X. Advances in the understanding of nuclear pore complexes in human diseases. J Cancer Res Clin Oncol 2024; 150:374. [PMID: 39080077 PMCID: PMC11289042 DOI: 10.1007/s00432-024-05881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Nuclear pore complexes (NPCs) are sophisticated and dynamic protein structures that straddle the nuclear envelope and act as gatekeepers for transporting molecules between the nucleus and the cytoplasm. NPCs comprise up to 30 different proteins known as nucleoporins (NUPs). However, a growing body of research has suggested that NPCs play important roles in gene regulation, viral infections, cancer, mitosis, genetic diseases, kidney diseases, immune system diseases, and degenerative neurological and muscular pathologies. PURPOSE In this review, we introduce the structure and function of NPCs. Then We described the physiological and pathological effects of each component of NPCs which provide a direction for future clinical applications. METHODS The literatures from PubMed have been reviewed for this article. CONCLUSION This review summarizes current studies on the implications of NPCs in human physiology and pathology, highlighting the mechanistic underpinnings of NPC-associated diseases.
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Affiliation(s)
- Yuxuan Li
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Jie Zhu
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Fengguang Zhai
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Lili Kong
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Hong Li
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China.
| | - Xiaofeng Jin
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China.
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3
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Yeo WH, Zhang Y, Neely AE, Bao X, Sun C, Zhang HF. Investigating Uncertainties in Single-Molecule Localization Microscopy Using Experimentally Informed Monte Carlo Simulation. NANO LETTERS 2023; 23:7253-7259. [PMID: 37463268 PMCID: PMC10528527 DOI: 10.1021/acs.nanolett.3c00852] [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] [Indexed: 07/20/2023]
Abstract
Single-molecule localization microscopy (SMLM) enables the visualization of cellular nanostructures in vitro with sub-20 nm resolution. While substructures can generally be imaged with SMLM, the structural understanding of the images remains elusive. To better understand the link between SMLM images and the underlying structure, we developed a Monte Carlo (MC) simulation based on experimental imaging parameters and geometric information to generate synthetic SMLM images. We chose the nuclear pore complex (NPC), a nanosized channel on the nuclear membrane which gates nucleo-cytoplasmic transport of biomolecules, as a test geometry for testing our MC model. Using the MC model to simulate SMLM images, we first optimized our clustering algorithm to separate >106 molecular localizations of fluorescently labeled NPC proteins into hundreds of individual NPCs in each cell. We then illustrated using our MC model to generate cellular substructures with different angles of labeling to inform our structural understanding through the SMLM images obtained.
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Affiliation(s)
- Wei-Hong Yeo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Yang Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Currently with Molecular Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering, Chemistry and Science, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Amy E Neely
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department of Dermatology, Northwestern University, Chicago, Illinois 60611, United States
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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4
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Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis. FISHES 2022. [DOI: 10.3390/fishes7030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3, pomc, npy, npb, sst, rln3, crh, gh, and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2, seh1l, kdm6a, arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3, dlx3, dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk, slc13a2_3_5, ndufa5, and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic and serine-type peptidase activity pathways were significantly enriched in the SL stage. These results provide a more detailed understanding of the processes of early development of clearhead icefish.
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Yamada C, Morooka A, Miyazaki S, Nagai M, Mase S, Iemura K, Tasnin MN, Takuma T, Nakamura S, Morshed S, Koike N, Mostofa MG, Rahman MA, Sharmin T, Katsuta H, Ohara K, Tanaka K, Ushimaru T. TORC1 inactivation promotes APC/C-dependent mitotic slippage in yeast and human cells. iScience 2022; 25:103675. [PMID: 35141499 PMCID: PMC8814761 DOI: 10.1016/j.isci.2021.103675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 10/20/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Unsatisfied kinetochore-microtubule attachment activates the spindle assembly checkpoint to inhibit the metaphase-anaphase transition. However, some cells eventually override mitotic arrest by mitotic slippage. Here, we show that inactivation of TORC1 kinase elicits mitotic slippage in budding yeast and human cells. Yeast mitotic slippage was accompanied with aberrant aspects, such as degradation of the nucleolar protein Net1, release of phosphatase Cdc14, and anaphase-promoting complex/cyclosome (APC/C)-Cdh1-dependent degradation of securin and cyclin B in metaphase. This mitotic slippage caused chromosome instability. In human cells, mammalian TORC1 (mTORC1) inactivation also invoked mitotic slippage, indicating that TORC1 inactivation-induced mitotic slippage is conserved from yeast to mammalian cells. However, the invoked mitotic slippage in human cells was not dependent on APC/C-Cdh1. This study revealed an unexpected involvement of TORC1 in mitosis and provides information on undesirable side effects of the use of TORC1 inhibitors as immunosuppressants and anti-tumor drugs. Yeast TORC1 inhibition promotes Net1 degradation and Cdc14 release Yeast TORC1 inhibition invokes mitotic slippage in an APC/C-Cdh1-dependent manner Human mTORC1 inhibition also elicits mitotic slippage
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Affiliation(s)
- Chihiro Yamada
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Aya Morooka
- Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Seira Miyazaki
- Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Masayoshi Nagai
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan.,Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Satoru Mase
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Kenji Iemura
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tsuneyuki Takuma
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Shotaro Nakamura
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Shamsul Morshed
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Naoki Koike
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Md Golam Mostofa
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Muhammad Arifur Rahman
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tasnuva Sharmin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Haruko Katsuta
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Kotaro Ohara
- Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Takashi Ushimaru
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan.,Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.,Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
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6
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Yu Z, Yang Z, Ren G, Wang Y, Luo X, Zhu F, Yu S, Jia L, Chen M, Worley PF, Xiao B. GATOR2 complex-mediated amino acid signaling regulates brain myelination. Proc Natl Acad Sci U S A 2022; 119:e2110917119. [PMID: 35022234 PMCID: PMC8784133 DOI: 10.1073/pnas.2110917119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/16/2021] [Indexed: 02/05/2023] Open
Abstract
Amino acids are essential for cell growth and metabolism. Amino acid and growth factor signaling pathways coordinately regulate the mechanistic target of rapamycin complex 1 (mTORC1) kinase in cell growth and organ development. While major components of amino acid signaling mechanisms have been identified, their biological functions in organ development are unclear. We aimed to understand the functions of the critically positioned amino acid signaling complex GAP activity towards Rags 2 (GATOR2) in brain development. GATOR2 mediates amino acid signaling to mTORC1 by directly linking the amino acid sensors for arginine and leucine to downstream signaling complexes. Now, we report a role of GATOR2 in oligodendrocyte myelination in postnatal brain development. We show that the disruption of GATOR2 complex by genetic deletion of meiosis regulator for oocyte development (Mios, encoding a component of GATOR2) selectively impairs the formation of myelinating oligodendrocytes, thus brain myelination, without apparent effects on the formation of neurons and astrocytes. The loss of Mios impairs cell cycle progression of oligodendrocyte precursor cells, leading to their reduced proliferation and differentiation. Mios deletion manifests a cell type-dependent effect on mTORC1 in the brain, with oligodendroglial mTORC1 selectively affected. However, the role of Mios/GATOR2 in oligodendrocyte formation and myelination involves mTORC1-independent function. This study suggests that GATOR2 coordinates amino acid and growth factor signaling to regulate oligodendrocyte myelination.
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Affiliation(s)
- Zongyan Yu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, People's Republic of China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, People's Republic of China
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen 518000, People's Republic of China
| | - Zhiwen Yang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, People's Republic of China
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen 518000, People's Republic of China
| | - Guoru Ren
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, People's Republic of China
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen 518000, People's Republic of China
| | - Yingjie Wang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, People's Republic of China
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen 518000, People's Republic of China
| | - Xiang Luo
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, People's Republic of China
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen 518000, People's Republic of China
| | - Feiyan Zhu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, People's Republic of China
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen 518000, People's Republic of China
| | - Shouyang Yu
- Neuroscience & Metabolism Research, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, People's Republic of China
| | - Lanlan Jia
- Neuroscience & Metabolism Research, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, People's Republic of China
| | - Mina Chen
- Neuroscience & Metabolism Research, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, People's Republic of China
| | - Paul F Worley
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bo Xiao
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, People's Republic of China;
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen 518000, People's Republic of China
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7
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Loissell-Baltazar YA, Dokudovskaya S. SEA and GATOR 10 Years Later. Cells 2021; 10:cells10102689. [PMID: 34685669 PMCID: PMC8534245 DOI: 10.3390/cells10102689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 12/17/2022] Open
Abstract
The SEA complex was described for the first time in yeast Saccharomyces cerevisiae ten years ago, and its human homologue GATOR complex two years later. During the past decade, many advances on the SEA/GATOR biology in different organisms have been made that allowed its role as an essential upstream regulator of the mTORC1 pathway to be defined. In this review, we describe these advances in relation to the identification of multiple functions of the SEA/GATOR complex in nutrient response and beyond and highlight the consequence of GATOR mutations in cancer and neurodegenerative diseases.
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8
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Evolution and diversification of the nuclear pore complex. Biochem Soc Trans 2021; 49:1601-1619. [PMID: 34282823 PMCID: PMC8421043 DOI: 10.1042/bst20200570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022]
Abstract
The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.
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9
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Yu J, Liu TT, Liang LL, Liu J, Cai HQ, Zeng J, Wang TT, Li J, Xiu L, Li N, Wu LY. Identification and validation of a novel glycolysis-related gene signature for predicting the prognosis in ovarian cancer. Cancer Cell Int 2021; 21:353. [PMID: 34229669 PMCID: PMC8258938 DOI: 10.1186/s12935-021-02045-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/24/2021] [Indexed: 01/10/2023] Open
Abstract
Background Ovarian cancer (OC) is the most lethal gynaecological tumor. Changes in glycolysis have been proven to play an important role in OC progression. We aimed to identify a novel glycolysis-related gene signature to better predict the prognosis of patients with OC. Methods mRNA and clinical data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Genotype Tissue Expression (GTEx) database. The “limma” R package was used to identify glycolysis-related differentially expressed genes (DEGs). Then, a multivariate Cox proportional regression model and survival analysis were used to develop a glycolysis-related gene signature. Furthermore, the TCGA training set was divided into two internal test sets for validation, while the ICGC dataset was used as an external test set. A nomogram was constructed in the training set, and the relative proportions of 22 types of tumor-infiltrating immune cells were evaluated using the “CIBERSORT” R package. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined by single-sample gene set enrichment analysis (ssGSEA) with the “GSVA” R package. Finally, the expression and function of the unreported signature genes ISG20 and SEH1L were explored using immunohistochemistry, western blotting, qRT-PCR, proliferation, migration, invasion and xenograft tumor assays. Results A five-gene signature comprising ANGPTL4, PYGB, ISG20, SEH1L and IRS2 was constructed. This signature could predict prognosis independent of clinical factors. A nomogram incorporating the signature and three clinical features was constructed, and the calibration plot suggested that the nomogram could accurately predict the survival rate. According to ssGSEA, the signature was associated with KEGG pathways related to axon guidance, mTOR signalling, tight junctions, etc. The proportions of tumor-infiltrating immune cells differed significantly between the high-risk group and the low-risk group. The expression levels of ISG20 and SEH1L were lower in tumor tissues than in normal tissues. Overexpression of ISG20 or SEH1L suppressed the proliferation, migration and invasion of Caov3 cells in vitro and the growth of xenograft tumors in vivo. Conclusion Five glycolysis-related genes were identified and incorporated into a novel risk signature that can effectively assess the prognosis and guide the treatment of OC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02045-0.
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Affiliation(s)
- Jing Yu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ting-Ting Liu
- Department of Blood Grouping, Beijing Red Cross Blood Center, Beijing, 100088, China
| | - Lei-Lei Liang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jing Liu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hong-Qing Cai
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jia Zeng
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tian-Tian Wang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Xiu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ning Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Ling-Ying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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10
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Gonzalez-Estevez A, Verrico A, Orniacki C, Reina-San-Martin B, Doye V. Integrity of the short arm of the nuclear pore Y-complex is required for mouse embryonic stem cell growth and differentiation. J Cell Sci 2021; 134:268378. [PMID: 34037234 DOI: 10.1242/jcs.258340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Many cellular processes, ranging from cell division to differentiation, are controlled by nuclear pore complexes (NPCs). However, studying the contributions of individual NPC subunits to these processes in vertebrates has long been impeded by their complexity and the lack of efficient genetic tools. Here, we use genome editing in mouse embryonic stem cells (mESCs) to characterize the role of NPC structural components, focusing on the short arm of the Y-complex that comprises Nup85, Seh1 and Nup43. We show that Seh1 and Nup43, although dispensable in pluripotent mESCs, are required for their normal cell growth rates, their viability upon differentiation and for the maintenance of proper NPC density. mESCs with an N-terminally truncated Nup85 mutation (in which interaction with Seh1 is greatly impaired) feature a similar reduction of NPC density. However, their proliferation and differentiation are unaltered, indicating that it is the integrity of the Y-complex, rather than the number of NPCs, that is critical to ensure these processes.
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Affiliation(s)
- Alba Gonzalez-Estevez
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
| | - Annalisa Verrico
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France
| | - Clarisse Orniacki
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France.,Inserm U 1258, Illkirch 67404, France.,Centre National de la Recherche Scientifique UMR (Unité Mixte de Recherche) 7104, Illkirch 67404, France.,Université de Strasbourg, Illkirch 67404, France
| | - Valérie Doye
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
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11
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Barrera-Conde M, Ausin K, Lachén-Montes M, Fernández-Irigoyen J, Galindo L, Cuenca-Royo A, Fernández-Avilés C, Pérez V, de la Torre R, Santamaría E, Robledo P. Cannabis Use Induces Distinctive Proteomic Alterations in Olfactory Neuroepithelial Cells of Schizophrenia Patients. J Pers Med 2021; 11:jpm11030160. [PMID: 33668817 PMCID: PMC7996288 DOI: 10.3390/jpm11030160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 12/19/2022] Open
Abstract
A close epidemiological link has been reported between cannabis use and schizophrenia (SCZ). However, biochemical markers in living humans related to the impact of cannabis in this disease are still missing. Olfactory neuroepithelium (ON) cells express neural features and offer a unique advantage to study biomarkers of psychiatric diseases. The aim of our study was to find exclusively deregulated proteins in ON cells of SCZ patients with and without a history of cannabis use. Thus, we compared the proteomic profiles of SCZ non-cannabis users (SCZ/nc) and SCZ cannabis users (SCZ/c) with control subjects non-cannabis users (C/nc) and control cannabis users (C/c). The results revealed that the main cascades affected in SCZ/nc were cell cycle, DNA replication, signal transduction and protein localization. Conversely, cannabis use in SCZ patients induced specific alterations in metabolism of RNA and metabolism of proteins. The levels of targeted proteins in each population were then correlated with cognitive performance and clinical scores. In SCZ/c, the expression levels of 2 proteins involved in the metabolism of RNA (MTREX and ZNF326) correlated with several cognitive markers and clinical signs. Moreover, use duration of cannabis negatively correlated with ZNF326 expression. These findings indicate that RNA-related proteins might be relevant to understand the influence of cannabis use on SCZ.
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Affiliation(s)
- Marta Barrera-Conde
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain;
| | - Karina Ausin
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Liliana Galindo
- Department of Psychiatry, University of Cambridge, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge CB2 1TN, UK;
- Neuropsychiatry and Addictions Institute (INAD) of Parc de Salut Mar, 08003 Barcelona and CIBER de Salud Mental, Spain;
| | - Aida Cuenca-Royo
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
| | | | - Víctor Pérez
- Neuropsychiatry and Addictions Institute (INAD) of Parc de Salut Mar, 08003 Barcelona and CIBER de Salud Mental, Spain;
- Department of Psychiatry and Legal Medicine, Autonomous University of Barcelona, 08193 Barcelona, Spain
| | - Rafael de la Torre
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Patricia Robledo
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain;
- Correspondence: ; Tel.: +34-93-316-0455
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12
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Burdine RD, Preston CC, Leonard RJ, Bradley TA, Faustino RS. Nucleoporins in cardiovascular disease. J Mol Cell Cardiol 2020; 141:43-52. [PMID: 32209327 DOI: 10.1016/j.yjmcc.2020.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 01/01/2023]
Abstract
Cardiovascular disease is a pressing health problem with significant global health, societal, and financial burdens. Understanding the molecular basis of polygenic cardiac pathology is thus essential to devising novel approaches for management and treatment. Recent identification of uncharacterized regulatory functions for a class of nuclear envelope proteins called nucleoporins offers the opportunity to understand novel putative mechanisms of cardiac disease development and progression. Consistent reports of nucleoporin deregulation associated with ischemic and dilated cardiomyopathies, arrhythmias and valvular disorders suggests that nucleoporin impairment may be a significant but understudied variable in cardiopathologic disorders. This review discusses and converges existing literature regarding nuclear pore complex proteins and their association with cardiac pathologies, and proposes a role for nucleoporins as facilitators of cardiac disease.
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Affiliation(s)
- Ryan D Burdine
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; School of Health Sciences, University of South Dakota, 414 E Clark St, Vermillion, SD 57069, United States of America
| | - Claudia C Preston
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Riley J Leonard
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Tyler A Bradley
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Randolph S Faustino
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, 1400 W. 22(nd) Street, Sioux Falls, SD 57105, United States of America.
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13
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Nespolo RF, Gaitan-Espitia JD, Quintero-Galvis JF, Fernandez FV, Silva AX, Molina C, Storey KB, Bozinovic F. A functional transcriptomic analysis in the relict marsupial Dromiciops gliroides
reveals adaptive regulation of protective functions during hibernation. Mol Ecol 2018; 27:4489-4500. [DOI: 10.1111/mec.14876] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Roberto F. Nespolo
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
- Departamento de Ecología; Center of Applied Ecology and Sustainability (CAPES); Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
- Millennium Institute for Integrative Biology (iBio); Santiago Chile
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences; The University of Hong Kong; Hong Kong SAR China
- CSIRO Oceans & Atmosphere; Hobart Tasmania Australia
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Fernanda V. Fernandez
- Instituto de Fisiología; Facultad de Medicina; Universidad Austral de Chile; Valdivia Chile
| | - Andrea X. Silva
- AUSTRALomics, Vicerrectoría de Investigación, Desarrollo y Creación Artística; Universidad Austral de Chile; Valdivia Chile
| | - Cristian Molina
- AUSTRALomics, Vicerrectoría de Investigación, Desarrollo y Creación Artística; Universidad Austral de Chile; Valdivia Chile
| | - Kenneth B. Storey
- Department of Biology and Institute of Biochemistry; Carleton University; Ottawa Ontario Canada
| | - Francisco Bozinovic
- Departamento de Ecología; Center of Applied Ecology and Sustainability (CAPES); Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
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14
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Abstract
In metazoans, the assembly of kinetochores on centrometric chromatin and the dismantling of nuclear pore complexes are processes that have to be tightly coordinated to ensure the proper assembly of the mitotic spindle and a successful mitosis. It is therefore noteworthy that these two macromolecular assemblies share a subset of constituents. One of these multifaceted components is Cenp-F, a protein implicated in cancer and developmental pathologies. During the cell cycle, Cenp-F localizes in multiple cellular structures including the nuclear envelope in late G2/early prophase and kinetochores throughout mitosis. We recently characterized the molecular determinants of Cenp-F interaction with Nup133, a structural nuclear pore constituent. In parallel with two other independent studies, we further elucidated the mechanisms governing Cenp-F kinetochore recruitment that mainly relies on its interaction with Bub1, with redundant contribution of Cenp-E upon acute microtubule depolymerisation. Here we synthesize the current literature regarding the dual location of Cenp-F at nuclear pores and kinetochores and extend our discussion to the regulation of these NPC and kinetochore localizations by mitotic kinase and spindle microtubules.
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Affiliation(s)
- Alessandro Berto
- a Institut Jacques Monod , UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité , Paris , France.,b Ecole Doctorale Structure et Dynamique des Systèmes Vivants (#577) , Univ Paris Sud, Université Paris-Saclay , Orsay , France
| | - Valérie Doye
- a Institut Jacques Monod , UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité , Paris , France
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