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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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Gao X, Lin B, Chen C, Fang Z, Yang J, Wu S, Chen Q, Zheng K, Yu Z, Li Y, Gao X, Lin G, Chen L. Lycopene from tomatoes and tomato products exerts renoprotective effects by ameliorating oxidative stress, apoptosis, pyroptosis, fibrosis, and inflammatory injury in calcium oxalate nephrolithiasis: the underlying mechanisms. Food Funct 2024; 15:4021-4036. [PMID: 38584465 DOI: 10.1039/d4fo00042k] [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: 04/09/2024]
Abstract
Several mechanisms underlying nephrolithiasis, one of the most common urological diseases, involve calcium oxalate formation, including oxidative stress, inflammatory reactions, fibrosis, pyroptosis, and apoptosis. Although lycopene has strong antioxidant activity, its protective effects against CaOx-induced injury have not yet been reported. This study aimed to systematically investigate the protective effects of lycopene and explore its mechanisms and molecular targets. Crystal deposition, renal function, oxidative stress, inflammatory response, fibrosis, pyroptosis, and apoptosis were assessed to evaluate the renoprotective effects of lycopene against crystal formation in a CaOx rat model and oxalate-stimulated NRK-52E and HK-2 cells. Lycopene markedly ameliorated crystal deposition, restored renal function, and suppressed kidney injury by reducing oxidative stress, apoptosis, inflammation, fibrosis, and pyroptosis in the rats. In cell models, lycopene pretreatment reversed reactive oxygen species increase, apoptotic damage, intracellular lactate dehydrogenase release, cytotoxicity, pyroptosis, and extracellular matrix deposition. Network pharmacology and proteomic analyses were performed to identify lycopene target proteins under CaOx-exposed conditions, and the results showed that Trappc4 might be a pivotal target gene for lycopene, as identified by cellular thermal shift assay and surface plasmon resonance analyses. Based on molecular docking, molecular dynamics simulations, alanine scanning mutagenesis, and saturation mutagenesis, we observed that lycopene directly interacts with Trappc4 via hydrophobic bonds, which may be attributed to the PHE4 and PHE142 residues, preventing ERK1/2 or elevating AMPK signaling pathway phosphorylation events. In conclusion, lycopene might ameliorate oxalate-induced renal tubular epithelial cell injury via the Trappc4/ERK1/2/AMPK pathway, indicating its potential for the treatment of nephrolithiasis.
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Affiliation(s)
- Xiaomin Gao
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Southern Baixiang, OuHai District, Wenzhou, Zhejiang, 325006, P.R. China.
| | - Binwei Lin
- Department of Urology, Rui'an People's Hospital, The Third Affiliated Hospital of the Wenzhou Medical University, Wenzhou, Zhejiang province, 325200, P.R. China
| | - Chen Chen
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China.
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China
| | - Ziyu Fang
- Department of Urology, Changhai Hospital, Navy Medical University, Changhai Road, YangPu District, Shanghai, 200433, P.R. China.
| | - Jinzhao Yang
- The Department of Pharmacy, The Third Clinical Institute Affiliated to Wenzhou Medical University (Wenzhou People's Hospital), Wenzhou, Zhejiang, 325006, P.R. China
| | - Shuzhi Wu
- The Department of Neurology, The Third Clinical Institute Affiliated to Wenzhou Medical University (Wenzhou People's Hospital), Wenzhou, Zhejiang, 325006, P.R. China
| | - Qing Chen
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China.
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China
| | - Kewen Zheng
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Southern Baixiang, OuHai District, Wenzhou, Zhejiang, 325006, P.R. China.
| | - Zhixian Yu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Southern Baixiang, OuHai District, Wenzhou, Zhejiang, 325006, P.R. China.
| | - Yeping Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Southern Baixiang, OuHai District, Wenzhou, Zhejiang, 325006, P.R. China.
| | - Xiaofeng Gao
- Department of Urology, Changhai Hospital, Navy Medical University, Changhai Road, YangPu District, Shanghai, 200433, P.R. China.
| | - Guanyang Lin
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China.
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China
| | - Lianguo Chen
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China.
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325006, P.R. China
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Nong JS, Zhou X, Liu JQ, Luo JZ, Huang JM, Xie HX, Yang KJ, Wang J, Ye XP, Peng T. Nucleoporin 107 is a prognostic biomarker in hepatocellular carcinoma associated with immune infiltration. Cancer Med 2023; 12:10990-11009. [PMID: 36952458 DOI: 10.1002/cam4.5807] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
OBJECTIVE To assess the diagnostic value and clinical significance of nucleoporin 107 (NUP107) in hepatocellular carcinoma (HCC), and explore the possible mechanisms. METHODS The transcriptomic and clinical data of HCC patients were retrieved from The Cancer Genome Atlas (TCGA) and GEO databases. Tissue specimens were collected from HCC patients in the Guangxi area. According to the expression levels and prognostic characteristics of NUP107, ROC curves and nomogram models were constructed using the R package. RESULTS NUP107 was highly expressed in 26 human cancers including HCC, and was associated with advanced HCC staging and worse prognosis. NUP107 showed satisfactory ability to predict the prognosis of HCC patients (AUC >0.8). Results of gene set enrichment analysis (GSEA) further showed that NUP107 was mainly associated with cell cycle-related pathways such as the cell cycle, DNA replication, G2M checkpoint, E2F target, and mitotic spindle. In addition, NUP107 was also associated with immune infiltration in HCC and showed significant positive correlation with immune checkpoints (PD-L1 and TIM-3).
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Affiliation(s)
- Ju-Sen Nong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Jun-Qi Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Jian-Zhu Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Jia-Mi Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Hai-Xiang Xie
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Ke-Jian Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Jing Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Xin-Ping Ye
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, Guangxi Medical University, Nanning, People's Republic of China
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Mehta SJK, Kumar V, Mishra RK. Drosophila ELYS regulates Dorsal dynamics during development. J Biol Chem 2020; 295:2421-2437. [PMID: 31941789 DOI: 10.1074/jbc.ra119.009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 01/13/2020] [Indexed: 11/06/2022] Open
Abstract
Embryonic large molecule derived from yolk sac (ELYS) is a constituent protein of nuclear pores. It initiates assembly of nuclear pore complexes into functional nuclear pores toward the end of mitosis. Using cellular, molecular, and genetic tools, including fluorescence and Electron microscopy, quantitative PCR, and RNAi-mediated depletion, we report here that the ELYS ortholog (dElys) plays critical roles during Drosophila development. dElys localized to the nuclear rim in interphase cells, but during mitosis it was absent from kinetochores and enveloped chromatin. We observed that RNAi-mediated dElys depletion leads to aberrant development and, at the cellular level, to defects in the nuclear pore and nuclear lamina assembly. Further genetic analyses indicated that dElys depletion re-activates the Dorsal (NF-κB) pathway during late larval stages. Re-activated Dorsal caused untimely expression of the Dorsal target genes in the post-embryonic stages. We also demonstrate that activated Dorsal triggers apoptosis during later developmental stages by up-regulating the pro-apoptotic genes reaper and hid The apoptosis induced by Reaper and Hid was probably the underlying cause for developmental abnormalities observed upon dElys depletion. Moreover, we noted that dElys has conserved structural features, but contains a noncanonical AT-hook-like motif through which it strongly binds to DNA. Together, our results uncover a novel epistatic interaction that regulates Dorsal dynamics by dElys during development.
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Affiliation(s)
- Saurabh Jayesh Kumar Mehta
- Nups and SUMO Biology Group, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India
| | - Vimlesh Kumar
- Laboratory of Neurogenetics, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India
| | - Ram Kumar Mishra
- Nups and SUMO Biology Group, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India.
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Comparative Proteomic Profiling of Tumor-Associated Proteins in Human Gastric Cancer Cells Treated with Pectolinarigenin. Nutrients 2018; 10:nu10111596. [PMID: 30380781 PMCID: PMC6265996 DOI: 10.3390/nu10111596] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 12/13/2022] Open
Abstract
Pectolinarigenin (PEC), a natural flavonoid that is present in citrus fruits, has been reported to exhibit antitumor effects in several cancers. Though the mechanism of PEC-induced cytotoxicity effects has been documented, the proteomic changes that are associated with the cellular response to this flavonoid are poorly understood in gastric cancer cells. In this study, a comparative proteomic analysis was performed to identify proteins associated with PEC-induced cell death in two human gastric cancer cell lines: AGS and MKN-28. Two-dimensional gel electrophoresis (2-DE) revealed a total of 29 and 56 protein spots with significant alteration were screened in AGS and MKN-28 cells respectively. In total, 13 (AGS) and 39 (MKN28) proteins were successfully identified by mass spectrometry from the differential spots and they are known to be involved in signal transduction, apoptosis, transcription and translation, cell structural organization, and metabolism, as is consistent with multiple effects of PEC on tumor cells. Notably, novel target proteins like Probable ATP-dependent RNA helicase DDX4 (DDX4) and E3 ubiquitin-protein ligase LRSAM1 (LRSAM1) along with the commonly differential expressed proteins on both the cell lines that are treated with PEC were confirmed by immunoblotting. The DDX4 accelerates cell cycle progression by abrogating the G2 checkpoint when overexpressed in cancer cells, while the aberrant expression of LRSAM1 may be involved in the cancer pathology. Thus, proteomic analysis provides vital information about target proteins that are important for PEC-induced cell death in gastric cancer cells.
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Dynamic mislocalizations of nuclear pore complex proteins after focal cerebral ischemia in rat. J Neurosci Res 2016; 95:1745-1759. [DOI: 10.1002/jnr.24005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 11/17/2016] [Accepted: 12/02/2016] [Indexed: 12/15/2022]
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7
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Regulation of CED-3 caspase localization and activation by C. elegans nuclear-membrane protein NPP-14. Nat Struct Mol Biol 2016; 23:958-964. [PMID: 27723735 DOI: 10.1038/nsmb.3308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 09/16/2016] [Indexed: 12/18/2022]
Abstract
Caspases are cysteine proteases with critical roles in apoptosis. The Caenorhabditis elegans caspase CED-3 is activated by autocatalytic cleavage, a process enhanced by CED-4. Here we report that the CED-3 zymogen localizes to the perinuclear region in C. elegans germ cells and that CED-3 autocatalytic cleavage is held in check by C. elegans nuclei and activated by CED-4. The nuclear-pore protein NPP-14 interacts with the CED-3 zymogen prodomain, colocalizes with CED-3 in vivo and inhibits CED-3 autoactivation in vitro. Several missense mutations in the CED-3 prodomain result in stronger association with NPP-14 and decreased CED-3 activation by CED-4 in the presence of nuclei or NPP-14, thus leading to cell-death defects. Those same mutations enhance autocatalytic cleavage of CED-3 in vitro and increase apoptosis in vivo in the absence of npp-14. Our results reveal a critical role of nuclei and nuclear-membrane proteins in regulating the activation and localization of CED-3.
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Miyake N, Tsukaguchi H, Koshimizu E, Shono A, Matsunaga S, Shiina M, Mimura Y, Imamura S, Hirose T, Okudela K, Nozu K, Akioka Y, Hattori M, Yoshikawa N, Kitamura A, Cheong HI, Kagami S, Yamashita M, Fujita A, Miyatake S, Tsurusaki Y, Nakashima M, Saitsu H, Ohashi K, Imamoto N, Ryo A, Ogata K, Iijima K, Matsumoto N. Biallelic Mutations in Nuclear Pore Complex Subunit NUP107 Cause Early-Childhood-Onset Steroid-Resistant Nephrotic Syndrome. Am J Hum Genet 2015; 97:555-66. [PMID: 26411495 DOI: 10.1016/j.ajhg.2015.08.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 08/28/2015] [Indexed: 12/19/2022] Open
Abstract
The nuclear pore complex (NPC) is a huge protein complex embedded in the nuclear envelope. It has central functions in nucleocytoplasmic transport, nuclear framework, and gene regulation. Nucleoporin 107 kDa (NUP107) is a component of the NPC central scaffold and is an essential protein in all eukaryotic cells. Here, we report on biallelic NUP107 mutations in nine affected individuals who are from five unrelated families and show early-onset steroid-resistant nephrotic syndrome (SRNS). These individuals have pathologically focal segmental glomerulosclerosis, a condition that leads to end-stage renal disease with high frequency. NUP107 is ubiquitously expressed, including in glomerular podocytes. Three of four NUP107 mutations detected in the affected individuals hamper NUP107 binding to NUP133 (nucleoporin 133 kDa) and NUP107 incorporation into NPCs in vitro. Zebrafish with nup107 knockdown generated by morpholino oligonucleotides displayed hypoplastic glomerulus structures and abnormal podocyte foot processes, thereby mimicking the pathological changes seen in the kidneys of the SRNS individuals with NUP107 mutations. Considering the unique properties of the podocyte (highly differentiated foot-process architecture and slit membrane and the inability to regenerate), we propose a "podocyte-injury model" as the pathomechanism for SRNS due to biallelic NUP107 mutations.
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Affiliation(s)
- Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hiroyasu Tsukaguchi
- Second Department of Internal Medicine, Kansai Medical University, Osaka 570-8507, Japan.
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Akemi Shono
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Satoko Matsunaga
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Masaaki Shiina
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | | | - Shintaro Imamura
- National Research Institute of Fisheries Science, Yokohama 236-8648, Japan
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Koji Okudela
- Department of Pathology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Yuko Akioka
- Department of Pediatric Nephrology, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Motoshi Hattori
- Department of Pediatric Nephrology, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Norishige Yoshikawa
- Center for Clinical Research and Development, National Center for Child Health and Development, Tokyo 157-8535, Japan
| | - Akiko Kitamura
- Department of Immunology & Parasitology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul 03080, Korea; Research Coordination Center for Rare Diseases, Seoul National University Hospital, Seoul 03080, Korea; Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Shoji Kagami
- Department of Pediatrics, University of Tokushima Graduate School, Tokushima 770-8503, Japan
| | - Michiaki Yamashita
- National Research Institute of Fisheries Science, Yokohama 236-8648, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kenichi Ohashi
- Department of Pathology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN, Wako 351-0198, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
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9
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Garsed DW, Marshall OJ, Corbin VDA, Hsu A, Di Stefano L, Schröder J, Li J, Feng ZP, Kim BW, Kowarsky M, Lansdell B, Brookwell R, Myklebost O, Meza-Zepeda L, Holloway AJ, Pedeutour F, Choo KHA, Damore MA, Deans AJ, Papenfuss AT, Thomas DM. The architecture and evolution of cancer neochromosomes. Cancer Cell 2014; 26:653-67. [PMID: 25517748 DOI: 10.1016/j.ccell.2014.09.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 05/15/2014] [Accepted: 09/19/2014] [Indexed: 01/21/2023]
Abstract
We isolated and analyzed, at single-nucleotide resolution, cancer-associated neochromosomes from well- and/or dedifferentiated liposarcomas. Neochromosomes, which can exceed 600 Mb in size, initially arise as circular structures following chromothripsis involving chromosome 12. The core of the neochromosome is amplified, rearranged, and corroded through hundreds of breakage-fusion-bridge cycles. Under selective pressure, amplified oncogenes are overexpressed, while coamplified passenger genes may be silenced epigenetically. New material may be captured during punctuated chromothriptic events. Centromeric corrosion leads to crisis, which is resolved through neocentromere formation or native centromere capture. Finally, amplification terminates, and the neochromosome core is stabilized in linear form by telomere capture. This study investigates the dynamic mutational processes underlying the life history of a special form of cancer mutation.
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Affiliation(s)
- Dale W Garsed
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia; Department of Pathology, University of Melbourne, VIC 3010, Australia
| | - Owen J Marshall
- Chromosome Research, Murdoch Childrens Research Institute, and Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | - Vincent D A Corbin
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia; Bioinformatics and Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC, 3002, Australia
| | - Arthur Hsu
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Leon Di Stefano
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Jan Schröder
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia
| | - Jason Li
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Zhi-Ping Feng
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia
| | - Bo W Kim
- Chromosome Research, Murdoch Childrens Research Institute, and Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | - Mark Kowarsky
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Ben Lansdell
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Ross Brookwell
- Sullivan Nicolaides Pathology, Indooroopilly, QLD 4068, Australia
| | - Ola Myklebost
- Department of Tumor Biology, Oslo University Hospital, Norwegian Radium Hospital, Oslo 0424, Norway
| | - Leonardo Meza-Zepeda
- Department of Tumor Biology, Oslo University Hospital, Norwegian Radium Hospital, Oslo 0424, Norway
| | - Andrew J Holloway
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Florence Pedeutour
- Laboratory of Solid Tumors Genetics, Nice University Hospital, Nice 06107, France
| | - K H Andy Choo
- Chromosome Research, Murdoch Childrens Research Institute, and Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | | | | | - Anthony T Papenfuss
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia; Department of Mathematics and Statistics, University of Melbourne, VIC, 3010, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia; Bioinformatics and Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC, 3002, Australia.
| | - David M Thomas
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia; The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
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Sturrock M, Hellander A, Aldakheel S, Petzold L, Chaplain MAJ. The role of dimerisation and nuclear transport in the Hes1 gene regulatory network. Bull Math Biol 2013; 76:766-98. [PMID: 23686434 DOI: 10.1007/s11538-013-9842-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/05/2013] [Indexed: 02/06/2023]
Abstract
Hes1 is a member of the family of basic helix-loop-helix transcription factors and the Hes1 gene regulatory network (GRN) may be described as the canonical example of transcriptional control in eukaryotic cells, since it involves only the Hes1 protein and its own mRNA. Recently, the Hes1 protein has been established as an excellent target for an anti-cancer drug treatment, with the design of a small molecule Hes1 dimerisation inhibitor representing a promising if challenging approach to therapy. In this paper, we extend a previous spatial stochastic model of the Hes1 GRN to include nuclear transport and dimerisation of Hes1 monomers. Initially, we assume that dimerisation occurs only in the cytoplasm, with only dimers being imported into the nucleus. Stochastic simulations of this novel model using the URDME software show that oscillatory dynamics in agreement with experimental studies are retained. Furthermore, we find that our model is robust to changes in the nuclear transport and dimerisation parameters. However, since the precise dynamics of the nuclear import of Hes1 and the localisation of the dimerisation reaction are not known, we consider a second modelling scenario in which we allow for both Hes1 monomers and dimers to be imported into the nucleus, and we allow dimerisation of Hes1 to occur everywhere in the cell. Once again, computational solutions of this second model produce oscillatory dynamics in agreement with experimental studies. We also explore sensitivity of the numerical solutions to nuclear transport and dimerisation parameters. Finally, we compare and contrast the two different modelling scenarios using numerical experiments that simulate dimer disruption, and suggest a biological experiment that could distinguish which model more faithfully captures the Hes1 GRN.
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