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Guo Y, Tao T, Wu T, Hou J, Lin W. Nucleoporin Nup98 is an essential factor for ipo4 dependent protein import. J Cell Biochem 2024; 125:e30573. [PMID: 38780165 DOI: 10.1002/jcb.30573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Nucleocytoplasmic transport of macromolecules is essential in eukaryotic cells. In this process, the karyopherins play a central role when they transport cargoes across the nuclear pore complex. Importin 4 belongs to the karyopherin β family. Many studies have focused on finding substrates for importin 4, but no direct mechanism studies of its precise transport function have been reported. Therefore, this paper mainly aimed to study the mechanism of nucleoporins in mediating nuclear import and export of importin 4. To address this question, we constructed shRNAs targeting Nup358, Nup153, Nup98, and Nup50. We found that depletion of Nup98 resulted in a shift in the subcellular localization of importin 4 from the cytoplasm to the nucleus. Mutational analysis demonstrated that Nup98 physically and functionally interacts with importin 4 through its N-terminal phenylalanine-glycine (FG) repeat region. Mutation of nine of these FG motifs to SG motifs significantly attenuated the binding of Nup98 to importin 4, and we further confirmed the essential role of the six FG motifs in amino acids 121-360 of Nup98 in binding with importin 4. In vitro transport assay also confirmed that VDR, the substrate of importin 4, could not be transported into the nucleus after Nup98 knockdown. Overall, our results showed that Nup98 is required for efficient importin 4-mediated transport. This is the first study to reveal the mechanism of importin 4 in transporting substrates into the nucleus.
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Affiliation(s)
- Yingying Guo
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
| | - Tao Tao
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
| | - Ting Wu
- Department of Basic Medicine, School of Medicine, Cancer Research Center, Xiamen University, Xiamen, Fujian, China
| | - Jingjing Hou
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
- Department of Gastrointestinal Surgery, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, Xiamen, Fujian, China
| | - Wenbo Lin
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
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2
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Li Y, Bertozzi A, Mann MRW, Kühn B. Interdependent changes of nuclear lamins, nuclear pore complexes, and ploidy regulate cellular regeneration and stress response in the heart. Nucleus 2023; 14:2246310. [PMID: 37606283 PMCID: PMC10446781 DOI: 10.1080/19491034.2023.2246310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
In adult mammals, many heart muscle cells (cardiomyocytes) are polyploid, do not proliferate (post-mitotic), and, consequently, cannot contribute to heart regeneration. In contrast, fetal and neonatal heart muscle cells are diploid, proliferate, and contribute to heart regeneration. We have identified interdependent changes of the nuclear lamina, nuclear pore complexes, and DNA-content (ploidy) in heart muscle cell maturation. These results offer new perspectives on how cells alter their nuclear transport and, with that, their gene regulation in response to extracellular signals. We present how changes of the nuclear lamina alter nuclear pore complexes in heart muscle cells. The consequences of these changes for cellular regeneration and stress response in the heart are discussed.
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Affiliation(s)
- Yao Li
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alberto Bertozzi
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mellissa RW Mann
- Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Bernhard Kühn
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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3
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [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: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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4
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Juul-Dam KL, Shukla NN, Cooper TM, Cuglievan B, Heidenreich O, Kolb EA, Rasouli M, Hasle H, Zwaan CM. Therapeutic targeting in pediatric acute myeloid leukemia with aberrant HOX/MEIS1 expression. Eur J Med Genet 2023; 66:104869. [PMID: 38174649 PMCID: PMC11195042 DOI: 10.1016/j.ejmg.2023.104869] [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: 08/31/2022] [Revised: 05/21/2023] [Accepted: 10/22/2023] [Indexed: 01/05/2024]
Abstract
Despite advances in the clinical management of childhood acute myeloid leukemia (AML) during the last decades, outcome remains fatal in approximately one third of patients. Primary chemoresistance, relapse and acute and long-term toxicities to conventional myelosuppressive therapies still constitute significant challenges and emphasize the unmet need for effective targeted therapies. Years of scientific efforts have translated into extensive insights on the heterogeneous spectrum of genetics and oncogenic signaling pathways of AML and identified a subset of patients characterized by upregulation of HOXA and HOXB homeobox genes and myeloid ecotropic virus insertion site 1 (MEIS1). Aberrant HOXA/MEIS1 expression is associated with genotypes such as rearrangements in Histone-lysine N-methyltransferase 2A (KMT2A-r), nucleoporin 98 (NUP98-r) and mutated nucleophosmin (NPM1c) that are found in approximately one third of children with AML. AML with upregulated HOXA/MEIS1 shares a number of molecular vulnerabilities amenable to recently developed molecules targeting the assembly of protein complexes or transcriptional regulators. The interaction between the nuclear scaffold protein menin and KMT2A has gained particular interest and constitutes a molecular dependency for maintenance of the HOXA/MEIS1 transcription program. Menin inhibitors disrupt the menin-KMT2A complex in preclinical models of KMT2A-r, NUP98-r and NPM1c acute leukemias and its occupancy at target genes leading to leukemic cell differentiation and apoptosis. Early-phase clinical trials are either ongoing or in development and preliminary data suggests tolerable toxicities and encouraging efficacy of menin inhibitors in adults with relapsed or refractory KMT2A-r and NPM1c AML. The Pediatric Acute Leukemia/European Pediatric Acute Leukemia (PedAL/EUPAL) project is focused to advance and coordinate informative clinical trials with new agents and constitute an ideal framework for testing of menin inhibitors in pediatric study populations. Menin inhibitors in combination with standard chemotherapy or other targeting agents may enhance anti-leukemic effects and constitute rational treatment strategies for select genotypes of childhood AML, and provide enhanced safety to avoid differentiation syndrome. In this review, we discuss the pathophysiological mechanisms in KMT2A-r, NUP98-r and NPM1c AML, emerging molecules targeting the HOXA/MEIS1 transcription program with menin inhibitors as the most prominent examples and future therapeutic implications of these agents in childhood AML.
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Affiliation(s)
- Kristian L Juul-Dam
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark.
| | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Todd M Cooper
- Division of Hematology/Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Branko Cuglievan
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Olaf Heidenreich
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - E Anders Kolb
- Division of Oncology, Nemours/Alfred I. Dupont Hospital for Children, Wilmington, DE, USA
| | - Milad Rasouli
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Henrik Hasle
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - C Michel Zwaan
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
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Capelson M. You are who your friends are-nuclear pore proteins as components of chromatin-binding complexes. FEBS Lett 2023; 597:2769-2781. [PMID: 37652464 PMCID: PMC11081553 DOI: 10.1002/1873-3468.14728] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023]
Abstract
Nuclear pore complexes are large multicomponent protein complexes that are embedded in the nuclear envelope, where they mediate nucleocytoplasmic transport. In addition to supporting transport, nuclear pore components, termed nucleoporins (Nups), can interact with chromatin and influence genome function. A subset of Nups can also localize to the nuclear interior and bind chromatin intranuclearly, providing an opportunity to investigate chromatin-associated functions of Nups outside of the transport context. This review focuses on the gene regulatory functions of such intranuclear Nups, with a particular emphasis on their identity as components of several chromatin regulatory complexes. Recent proteomic screens have identified Nups as interacting partners of active and repressive epigenetic machinery, architectural proteins, and DNA replication complexes, providing insight into molecular mechanisms via which Nups regulate gene expression programs. This review summarizes these interactions and discusses their potential functions in the broader framework of nuclear genome organization.
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Affiliation(s)
- Maya Capelson
- Cell and Molecular Biology Program, Department of Biology, San Diego State University, CA, USA
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Oka M, Otani M, Miyamoto Y, Oshima R, Adachi J, Tomonaga T, Asally M, Nagaoka Y, Tanaka K, Toyoda A, Ichikawa K, Morishita S, Isono K, Koseki H, Nakato R, Ohkawa Y, Yoneda Y. Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure. Cell Rep 2023; 42:112884. [PMID: 37516964 DOI: 10.1016/j.celrep.2023.112884] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/29/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies containing CRM1, a nuclear export receptor. However, these nuclear bodies' function in controlling gene expression remains elusive. Here, we demonstrate that the nuclear bodies of NUP98::HOXA9 and SET::NUP214 promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase essential for the maintenance of HOX gene expression. These nuclear bodies are robustly associated with MLL1/CRM1 and co-localized on chromatin. Furthermore, whole-genome chromatin-conformation capture analysis reveals that NUP98::HOXA9 induces a drastic alteration in high-order genome structure at target regions concomitant with the generation of chromatin loops and/or rearrangement of topologically associating domains in a phase-separation-dependent manner. Collectively, these results show that the phase-separated nuclear bodies of nucleoporin fusion proteins can enhance the activation of target genes by promoting the condensation of MLL1/CRM1 and rearrangement of the 3D genome structure.
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Affiliation(s)
- Masahiro Oka
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Laboratory of Biomedical Innovation, Graduate School of Pharmaceutical Sciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Mayumi Otani
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Rieko Oshima
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteomics for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Munehiro Asally
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - Yuya Nagaoka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan
| | - Kyoichi Isono
- Laboratory Animal Center, Wakayama Medical University, 811-1 Kimi-idera, Wakayama 641-8509, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.
| | - Yoshihiro Yoneda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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7
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Brickner JH. Inheritance of epigenetic transcriptional memory through read-write replication of a histone modification. Ann N Y Acad Sci 2023; 1526:50-58. [PMID: 37391188 PMCID: PMC11216120 DOI: 10.1111/nyas.15033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Epigenetic transcriptional regulation frequently requires histone modifications. Some, but not all, of these modifications are able to template their own inheritance. Here, I discuss the molecular mechanisms by which histone modifications can be inherited and relate these ideas to new results about epigenetic transcriptional memory, a phenomenon that poises recently repressed genes for faster reactivation and has been observed in diverse organisms. Recently, we found that the histone H3 lysine 4 dimethylation that is associated with this phenomenon plays a critical role in sustaining memory and, when factors critical for the establishment of memory are inactivated, can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism may involve a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1- COMPASS. This is the first example of a chromatin-mediated inheritance of a mark that promotes transcription.
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Affiliation(s)
- Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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Wadhwani N, Nayak S, Wang Y, Hashizume R, Jie C, Mania-Farnell B, James CD, Xi G, Tomita T. WDR82-Mediated H3K4me3 Is Associated with Tumor Proliferation and Therapeutic Efficacy in Pediatric High-Grade Gliomas. Cancers (Basel) 2023; 15:3429. [PMID: 37444539 PMCID: PMC10340597 DOI: 10.3390/cancers15133429] [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: 04/10/2023] [Revised: 05/29/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are common malignant brain tumors without effective treatment and poor patient survival. Abnormal posttranslational modification at the histone H3 tail plays critical roles in tumor cell malignancy. We have previously shown that the trimethylation of lysine 4 at histone H3 (H3K4me3) plays a significant role in pediatric ependymoma malignancy and is associated with tumor therapeutic sensitivity. Here, we show that H3K4me3 and its methyltransferase WDR82 are elevated in pHGGs. A reduction in H3K4me3 by downregulating WDR82 decreases H3K4me3 promoter occupancy and the expression of genes associated with stem cell features, cell proliferation, the cell cycle, and DNA damage repair. A reduction in WDR82-mediated H3K4me3 increases the response of pediatric glioma cells to chemotherapy. These findings suggest that WDR82-mediated H3K4me3 is an important determinant of pediatric glioma malignancy and therapeutic response. This highlights the need for a more thorough understanding of the potential of WDR82 as an epigenetic target to increase therapeutic efficacy and improve the prognosis for children with malignant gliomas.
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Affiliation(s)
- Nitin Wadhwani
- Department of Pathology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sonali Nayak
- Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yufen Wang
- Department of Radio-oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chunfa Jie
- Department of Biochemistry and Nutrition, Des Moines University Medicine and Health Sciences, Des Moines, IA 50312, USA
| | - Barbara Mania-Farnell
- Department of Biological Sciences, Purdue University Northwest, Hammond, IN 46323, USA
| | - Charles David James
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Guifa Xi
- Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tadanori Tomita
- Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Neely AE, Blumensaadt LA, Ho PJ, Lloyd SM, Kweon J, Ren Z, Bao X. NUP98 and RAE1 sustain progenitor function through HDAC-dependent chromatin targeting to escape from nucleolar localization. Commun Biol 2023; 6:664. [PMID: 37353594 PMCID: PMC10290086 DOI: 10.1038/s42003-023-05043-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
Self-renewing somatic tissues rely on progenitors to support the continuous tissue regeneration. The gene regulatory network maintaining progenitor function remains incompletely understood. Here we show that NUP98 and RAE1 are highly expressed in epidermal progenitors, forming a separate complex in the nucleoplasm. Reduction of NUP98 or RAE1 abolishes progenitors' regenerative capacity, inhibiting proliferation and inducing premature terminal differentiation. Mechanistically, NUP98 binds on chromatin near the transcription start sites of key epigenetic regulators (such as DNMT1, UHRF1 and EZH2) and sustains their expression in progenitors. NUP98's chromatin binding sites are co-occupied by HDAC1. HDAC inhibition diminishes NUP98's chromatin binding and dysregulates NUP98 and RAE1's target gene expression. Interestingly, HDAC inhibition further induces NUP98 and RAE1 to localize interdependently to the nucleolus. These findings identified a pathway in progenitor maintenance, where HDAC activity directs the high levels of NUP98 and RAE1 to directly control key epigenetic regulators, escaping from nucleolar aggregation.
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Affiliation(s)
- Amy E Neely
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Laura A Blumensaadt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Junghun Kweon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ziyou Ren
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Department of Dermatology, Northwestern University, Chicago, IL, USA.
- Simpson Querrey Institute for Epigenetics, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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10
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Li J, Kalev‐Zylinska ML. Advances in molecular characterization of pediatric acute megakaryoblastic leukemia not associated with Down syndrome; impact on therapy development. Front Cell Dev Biol 2023; 11:1170622. [PMID: 37325571 PMCID: PMC10267407 DOI: 10.3389/fcell.2023.1170622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023] Open
Abstract
Acute megakaryoblastic leukemia (AMKL) is a rare subtype of acute myeloid leukemia (AML) in which leukemic blasts have megakaryocytic features. AMKL makes up 4%-15% of newly diagnosed pediatric AML, typically affecting young children (less than 2 years old). AMKL associated with Down syndrome (DS) shows GATA1 mutations and has a favorable prognosis. In contrast, AMKL in children without DS is often associated with recurrent and mutually exclusive chimeric fusion genes and has an unfavorable prognosis. This review mainly summarizes the unique features of pediatric non-DS AMKL and highlights the development of novel therapies for high-risk patients. Due to the rarity of pediatric AMKL, large-scale multi-center studies are needed to progress molecular characterization of this disease. Better disease models are also required to test leukemogenic mechanisms and emerging therapies.
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Affiliation(s)
- Jixia Li
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Department of Laboratory Medicine, School of Medicine, Foshan University, Foshan, China
| | - Maggie L. Kalev‐Zylinska
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Haematology Laboratory, Department of Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
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11
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Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. A CpG island-encoded mechanism protects genes from premature transcription termination. Nat Commun 2023; 14:726. [PMID: 36759609 PMCID: PMC9911701 DOI: 10.1038/s41467-023-36236-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
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Affiliation(s)
- Amy L Hughes
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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12
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Schneider MF, Müller V, Müller SA, Lichtenthaler SF, Becker PB, Scheuermann JC. LncRNA RUS shapes the gene expression program towards neurogenesis. Life Sci Alliance 2022; 5:5/10/e202201504. [PMID: 35688487 PMCID: PMC9187872 DOI: 10.26508/lsa.202201504] [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: 04/25/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022] Open
Abstract
The chromatin-associated lncRNA RUS binds in the vicinity to neural differentiation-associated genes and regulates them in a context-dependent manner to enable proper neuron development. The evolution of brain complexity correlates with an increased expression of long, noncoding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for “RNA upstream of Slitrk3.” The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.
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Affiliation(s)
- Marius F Schneider
- Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany.,Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Veronika Müller
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan A Müller
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE) Munich and Neuroproteomics Unit, Technical University, Munich, Germany
| | - Stefan F Lichtenthaler
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE) Munich and Neuroproteomics Unit, Technical University, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Peter B Becker
- Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Johanna C Scheuermann
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
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13
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Sump B, Brickner DG, D'Urso A, Kim SH, Brickner JH. Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory. eLife 2022; 11:e77646. [PMID: 35579426 PMCID: PMC9129879 DOI: 10.7554/elife.77646] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/15/2022] [Indexed: 11/13/2022] Open
Abstract
For some inducible genes, the rate and molecular mechanism of transcriptional activation depend on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation, and requires both changes in chromatin structure and recruitment of poised RNA polymerase II (RNAPII) to the promoter. Memory of inositol starvation in budding yeast involves a positive feedback loop between transcription factor-dependent interaction with the nuclear pore complex and histone H3 lysine 4 dimethylation (H3K4me2). While H3K4me2 is essential for recruitment of RNAPII and faster reactivation, RNAPII is not required for H3K4me2. Unlike RNAPII-dependent H3K4me2 associated with transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and, upon degradation of an essential transcription factor, is inherited through multiple cell cycles. The writer of this mark (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication.
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Affiliation(s)
- Bethany Sump
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Donna G Brickner
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Agustina D'Urso
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Seo Hyun Kim
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
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14
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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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15
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Chandra B, Michmerhuizen NL, Shirnekhi HK, Tripathi S, Pioso BJ, Baggett DW, Mitrea DM, Iacobucci I, White MR, Chen J, Park CG, Wu H, Pounds S, Medyukhina A, Khairy K, Gao Q, Qu C, Abdelhamed S, Gorman SD, Bawa S, Maslanka C, Kinger S, Dogra P, Ferrolino MC, Di Giacomo D, Mecucci C, Klco JM, Mullighan CG, Kriwacki RW. Phase Separation Mediates NUP98 Fusion Oncoprotein Leukemic Transformation. Cancer Discov 2022; 12:1152-1169. [PMID: 34903620 PMCID: PMC8983581 DOI: 10.1158/2159-8290.cd-21-0674] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/08/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023]
Abstract
NUP98 fusion oncoproteins (FO) are drivers in pediatric leukemias and many transform hematopoietic cells. Most NUP98 FOs harbor an intrinsically disordered region from NUP98 that is prone to liquid-liquid phase separation (LLPS) in vitro. A predominant class of NUP98 FOs, including NUP98-HOXA9 (NHA9), retains a DNA-binding homeodomain, whereas others harbor other types of DNA- or chromatin-binding domains. NUP98 FOs have long been known to form puncta, but long-standing questions are how nuclear puncta form and how they drive leukemogenesis. Here we studied NHA9 condensates and show that homotypic interactions and different types of heterotypic interactions are required to form nuclear puncta, which are associated with aberrant transcriptional activity and transformation of hematopoietic stem and progenitor cells. We also show that three additional leukemia-associated NUP98 FOs (NUP98-PRRX1, NUP98-KDM5A, and NUP98-LNP1) form nuclear puncta and transform hematopoietic cells. These findings indicate that LLPS is critical for leukemogenesis by NUP98 FOs. SIGNIFICANCE We show that homotypic and heterotypic mechanisms of LLPS control NUP98-HOXA9 puncta formation, modulating transcriptional activity and transforming hematopoietic cells. Importantly, these mechanisms are generalizable to other NUP98 FOs that share similar domain structures. These findings address long-standing questions on how nuclear puncta form and their link to leukemogenesis. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Hazheen K. Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brittany J. Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David W. Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Diana M. Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael R. White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jingjing Chen
- Integrated Biomedical Sciences Program, the University of Tennessee Health Science Center, Memphis, Tennessee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anna Medyukhina
- Center for Bioimage Informatics, St. Jude Children's Research Hospital Memphis, Tennessee
| | - Khaled Khairy
- Center for Bioimage Informatics, St. Jude Children's Research Hospital Memphis, Tennessee
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott D. Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Simranjot Bawa
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carolyn Maslanka
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Rhodes College, Memphis, Tennessee
| | - Swati Kinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Rhodes College, Memphis, Tennessee
| | - Priyanka Dogra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mylene C. Ferrolino
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Danika Di Giacomo
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Cristina Mecucci
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Corresponding Authors: Richard W. Kriwacki, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105. Phone: 901-595-3290; Fax: 901-595-3032; E-mail: ; and Charles G. Mullighan,
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, Tennessee
- Corresponding Authors: Richard W. Kriwacki, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105. Phone: 901-595-3290; Fax: 901-595-3032; E-mail: ; and Charles G. Mullighan,
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16
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Abstract
The nuclear pore complex (NPC) is a highly conserved channel in the nuclear envelope that mediates mRNA export to the cytosol and bidirectional protein transport. Many chromosomal loci physically interact with nuclear pore proteins (Nups), and interactions with Nups can promote transcriptional repression, transcriptional activation, and transcriptional poising. Interaction with the NPC also affects the spatial arrangement of genes, interchromosomal clustering, and folding of topologically associated domains. Thus, the NPC is a spatial organizer of the genome and regulator of genome function.
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Affiliation(s)
- Michael Chas Sumner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Jason Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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17
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The Retinoblastoma Tumor Suppressor Is Required for the NUP98-HOXA9-Induced Aberrant Nuclear Envelope Phenotype. Cells 2021; 10:cells10112851. [PMID: 34831074 PMCID: PMC8616146 DOI: 10.3390/cells10112851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
Chromosomal translocations involving the nucleoporin NUP98 gene are recurrently identified in leukemia; yet, the cellular defects accompanying NUP98 fusion proteins are poorly characterized. NUP98 fusions cause changes in nuclear and nuclear envelope (NE) organization, in particular, in the nuclear lamina and the lamina associated polypeptide 2α (LAP2α), a regulator of the tumor suppressor retinoblastoma protein (RB). We demonstrate that, for NUP98-HOXA9 (NHA9), the best-studied NUP98 fusion protein, its effect(s) on nuclear architecture largely depend(s) on RB. Morphological alterations caused by the expression of NHA9 are largely diminished in the absence of RB, both in human cells expressing the human papillomavirus 16 E7 protein and in mouse embryonic fibroblasts lacking RB. We further show that NHA9 expression associates with distinct histone modification. Moreover, the pattern of trimethylation of histone H3 lysine-27 is affected by NHA9, again in an RB-dependent manner. Our results pinpoint to an unexpected interplay between NUP98 fusion proteins and RB, which may contribute to leukemogenesis.
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18
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The Menin-MLL1 interaction is a molecular dependency in NUP98-rearranged AML. Blood 2021; 139:894-906. [PMID: 34582559 PMCID: PMC8832476 DOI: 10.1182/blood.2021012806] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
A menin-MLL1 inhibitor halts leukemogenesis in models of NUP98-rearranged leukemias. Inhibition of menin-MLL1 impairs leukemogenic gene expression and disrupts chromatin binding of menin, MLL1 and NUP98 fusion proteins.
Translocations involving the NUP98 gene produce NUP98-fusion proteins and are associated with a poor prognosis in acute myeloid leukemia (AML). MLL1 is a molecular dependency in NUP98-fusion leukemia, and therefore we investigated the efficacy of therapeutic blockade of the menin-MLL1 interaction in NUP98-fusion leukemia models. Using mouse leukemia cell lines driven by NUP98-HOXA9 and NUP98-JARID1A fusion oncoproteins, we demonstrate that NUP98-fusion-driven leukemia is sensitive to the menin-MLL1 inhibitor VTP50469, with an IC50 similar to what we have previously reported for MLL-rearranged and NPM1c leukemia cells. Menin-MLL1 inhibition upregulates markers of differentiation such as CD11b and downregulates expression of proleukemogenic transcription factors such as Meis1 in NUP98-fusion-transformed leukemia cells. We demonstrate that MLL1 and the NUP98 fusion protein itself are evicted from chromatin at a critical set of genes that are essential for the maintenance of the malignant phenotype. In addition to these in vitro studies, we established patient-derived xenograft (PDX) models of NUP98-fusion-driven AML to test the in vivo efficacy of menin-MLL1 inhibition. Treatment with VTP50469 significantly prolongs survival of mice engrafted with NUP98-NSD1 and NUP98-JARID1A leukemias. Gene expression analysis revealed that menin-MLL1 inhibition simultaneously suppresses a proleukemogenic gene expression program, including downregulation of the HOXa cluster, and upregulates tissue-specific markers of differentiation. These preclinical results suggest that menin-MLL1 inhibition may represent a rational, targeted therapy for patients with NUP98-rearranged leukemias.
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19
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Yang C, Wang K, Liang Q, Tian TT, Zhong Z. Role of NSD1 as potential therapeutic target in tumor. Pharmacol Res 2021; 173:105888. [PMID: 34536546 DOI: 10.1016/j.phrs.2021.105888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/29/2022]
Abstract
Nuclear receptor binding SET Domain Protein 1 (NSD1) is a bifunctional transcriptional regulatory protein that encodes histone methyltransferase. Mono- and di-methylation of H3K36 by NSD1 is mainly primarily involved in the regulation of gene expression, DNA repair, alternative splicing, and other important biological processes. Many types of cancers, including acute myelogenous leukemia (AML), liver cancer, lung cancer, endometrial carcinoma, colorectal cancer, and pancreatic cancer, are associated with NSD1 fusion, missense mutation, nonsense mutation, silent mutation, deletion, and insertion of frameshift, and deletion in a frame. Therefore, targeting NSD1 may be a potential strategy for tumor therapy. An in-depth study of the structure and biological activities of NSD1 sets the groundwork for improving tumor therapy and creating NSD1 inhibitors. This article emphasizes the role of NSD1 in tumorigenesis and the development of NSD1 targeted small-molecule inhibitors.
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Affiliation(s)
- Chao Yang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, Zhejiang Province 316022, China
| | - Kai Wang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Qilian Liang
- Oncology Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province 524001, China
| | - Tian-Tian Tian
- Center for Biological Science and Technology, Beijing Normal University, Zhuhai, Guangdong Province 519087, China.
| | - Zhangfeng Zhong
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China.
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20
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Zeisig BB, So CWE. Therapeutic Opportunities of Targeting Canonical and Noncanonical PcG/TrxG Functions in Acute Myeloid Leukemia. Annu Rev Genomics Hum Genet 2021; 22:103-125. [PMID: 33929894 DOI: 10.1146/annurev-genom-111120-102443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcriptional deregulation is a key driver of acute myeloid leukemia (AML), a heterogeneous blood cancer with poor survival rates. Polycomb group (PcG) and Trithorax group (TrxG) genes, originally identified in Drosophila melanogaster several decades ago as master regulators of cellular identity and epigenetic memory, not only are important in mammalian development but also play a key role in AML disease biology. In addition to their classical canonical antagonistic transcriptional functions, noncanonical synergistic and nontranscriptional functions of PcG and TrxG are emerging. Here, we review the biochemical properties of major mammalian PcG and TrxG complexes and their roles in AML disease biology, including disease maintenance as well as drug resistance. We summarize current efforts on targeting PcG and TrxG for treatment of AML and propose rational synthetic lethality and drug-induced antagonistic pleiotropy options involving PcG and TrxG as potential new therapeutic avenues for treatment of AML.
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Affiliation(s)
- Bernd B Zeisig
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London SE5 9NU, United Kingdom;
- Department of Haematological Medicine, King's College Hospital, London SE5 9RS, United Kingdom
| | - Chi Wai Eric So
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London SE5 9NU, United Kingdom;
- Department of Haematological Medicine, King's College Hospital, London SE5 9RS, United Kingdom
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21
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Tauchmann S, Schwaller J. NSD1: A Lysine Methyltransferase between Developmental Disorders and Cancer. Life (Basel) 2021; 11:life11090877. [PMID: 34575025 PMCID: PMC8465848 DOI: 10.3390/life11090877] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 01/25/2023] Open
Abstract
Recurrent epigenomic alterations associated with multiple human pathologies have increased the interest in the nuclear receptor binding SET domain protein 1 (NSD1) lysine methyltransferase. Here, we review the current knowledge about the biochemistry, cellular function and role of NSD1 in human diseases. Several studies have shown that NSD1 controls gene expression by methylation of lysine 36 of histone 3 (H3K36me1/2) in a complex crosstalk with de novo DNA methylation. Inactivation in flies and mice revealed that NSD1 is essential for normal development and that it regulates multiple cell type-specific functions by interfering with transcriptional master regulators. In humans, putative loss of function NSD1 mutations characterize developmental syndromes, such as SOTOS, as well as cancer from different organs. In pediatric hematological malignancies, a recurrent chromosomal translocation forms a NUP98-NSD1 fusion with SET-dependent leukemogenic activity, which seems targetable by small molecule inhibitors. To treat or prevent diseases driven by aberrant NSD1 activity, future research will need to pinpoint the mechanistic correlation between the NSD1 gene dosage and/or mutational status with development, homeostasis, and malignant transformation.
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22
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Li K, Liu T. Evaluation of Oncogene NUP37 as a Potential Novel Biomarker in Breast Cancer. Front Oncol 2021; 11:669655. [PMID: 34386417 PMCID: PMC8353244 DOI: 10.3389/fonc.2021.669655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/12/2021] [Indexed: 11/26/2022] Open
Abstract
Purpose There is an urgent need to identify oncogenes that may be beneficial to diagnose and develop target therapy for breast cancer. Methods Based on the GEO database, DECenter was used to screen the differentially overexpressed genes in breast cancer samples. Search Tool for the Retrieval of Interacting Genes and Cytoscape were performed to construct the PPI network to predict the hub gene. Functional and pathway enrichment were performed based on GO analysis. GEO2R, Oncomine, human tissue microarray staining, and western blot were applied to confirm the expression of NUP37. The association between NUP37 expression and prognosis in patients with breast cancer were assessed using the Kaplan–Meier plotter online tool and OncoLnc. siRNAs were used to knock down NUP37 and evaluate proliferation, migration, and stemness in breast cancer cells. Results We found that 138 genes were differentially upregulated in breast cancer samples, mainly comprising components of the nucleus and involved in the cell cycle process. NUP37 was identified as a hub gene that is upregulated in breast cancer patients related to a significantly worse survival rate. Furthermore, we confirmed that the downregulation of NUP37 in breast cancer cells results in the inhibition of cell growth, migration, and stemness. Conclusions High expression of NUP37 in breast cancer patients is associated with a poorer prognosis and promotion of cell growth, migration, and stemness. The multiple bioinformatics and experimental analysis help provide a comprehensive understanding of the roles of NUP37 as a potential marker for diagnosis and prognosis and as a novel therapeutic target in breast cancer.
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Affiliation(s)
- Kangdi Li
- GI Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Liu
- The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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23
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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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24
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Abstract
The genetic basis for pediatric acute myeloid leukemia (AML) is highly heterogeneous, often involving the cooperative action of characteristic chromosomal rearrangements and somatic mutations in progrowth and antidifferentiation pathways that drive oncogenesis. Although some driver mutations are shared with adult AML, many genetic lesions are unique to pediatric patients, and their appropriate identification is essential for patient care. The increased understanding of these malignancies through broad genomic studies has begun to risk-stratify patients based on their combinations of genomic alterations, a trend that will enable precision medicine in this population.
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Affiliation(s)
- Bryan Krock
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ, USA
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25
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Lim HJ, Lee JH, Lee YE, Baek HJ, Kook H, Park JH, Lee SY, Choi HW, Choi HJ, Kee SJ, Shin JH, Shin MG. The First Korean Case of NUP98-NSD1 and a Novel SNRK-ETV6 Fusion in a Pediatric Therapy-related Acute Myeloid Leukemia Patient Detected by Targeted RNA Sequencing. Ann Lab Med 2021; 41:443-446. [PMID: 33536367 PMCID: PMC7884187 DOI: 10.3343/alm.2021.41.4.443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ha Jin Lim
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Jun Hyung Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Young Eun Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Hee-Jo Baek
- Department of Pediatrics, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Hoon Kook
- Department of Pediatrics, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Ju Heon Park
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Seung Yeob Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Hyun-Woo Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Hyun-Jung Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Seung-Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Myung Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
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26
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Ganapathi SS, Raikar SS, Yatsenko SA, Djokic M, Bukowinski A. Mixed phenotype acute leukemia in a child associated with a NUP98-NSD1 fusion and NRAS p.Gly61Arg mutation. Cancer Rep (Hoboken) 2021; 4:e1372. [PMID: 33784031 PMCID: PMC8388158 DOI: 10.1002/cnr2.1372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 12/27/2022] Open
Abstract
Background Mixed phenotype acute leukemia (MPAL) is a rare subset of acute leukemia in the pediatric population associated with genetic alterations seen in both acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). Case We describe a patient with MPAL with a NUP98 (nucleoporin 98)‐NSD1 gene fusion (nuclear receptor binding SET domain protein1) and NRAS (neuroblastoma RAS viral oncogene homolog mutation) p.Gly61Arg mutation who was treated with upfront AML‐based chemotherapy, received hematopoietic stem cell transplant (HSCT), but unfortunately died from relapsed disease. Conclusion This case highlights the challenges faced in choosing treatment options in MPAL patients with complex genomics, with predominant myeloid features.
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Affiliation(s)
- Shireen S Ganapathi
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA
| | - Sunil S Raikar
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA
| | - Svetlana A Yatsenko
- Department of Pathology, UPMC Cytogenetics Laboratory, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Miroslav Djokic
- Division of Hematopathology, Department of Pathology, University of Pittsburgh School of Medicine Presbyterian/Shadyside, Pittsburgh, Pennsylvania, USA
| | - Andrew Bukowinski
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
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27
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Kimura I, Konno Y, Uriu K, Hopfensperger K, Sauter D, Nakagawa S, Sato K. Sarbecovirus ORF6 proteins hamper induction of interferon signaling. Cell Rep 2021; 34:108916. [PMID: 33765414 PMCID: PMC7953434 DOI: 10.1016/j.celrep.2021.108916] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/24/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
The presence of an ORF6 gene distinguishes sarbecoviruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 from other betacoronaviruses. Here we show that ORF6 inhibits induction of innate immune signaling, including upregulation of type I interferon (IFN) upon viral infection as well as type I and III IFN signaling. Intriguingly, ORF6 proteins from SARS-CoV-2 lineages are more efficient antagonists of innate immunity than their orthologs from SARS-CoV lineages. Mutational analyses identified residues E46 and Q56 as important determinants of the antagonistic activity of SARS-CoV-2 ORF6. Moreover, we show that the anti-innate immune activity of ORF6 depends on its C-terminal region and that ORF6 inhibits nuclear translocation of IRF3. Finally, we identify naturally occurring frameshift/nonsense mutations that result in an inactivating truncation of ORF6 in approximately 0.2% of SARS-CoV-2 isolates. Our findings suggest that ORF6 contributes to the poor IFN activation observed in individuals with coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yoriyuki Konno
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan
| | - Kristina Hopfensperger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
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28
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Erez N, Israitel L, Bitman-Lotan E, Wong WH, Raz G, Cornelio-Parra DV, Danial S, Flint Brodsly N, Belova E, Maksimenko O, Georgiev P, Druley T, Mohan RD, Orian A. A Non-stop identity complex (NIC) supervises enterocyte identity and protects from premature aging. eLife 2021; 10:62312. [PMID: 33629655 PMCID: PMC7936876 DOI: 10.7554/elife.62312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
A hallmark of aging is loss of differentiated cell identity. Aged Drosophila midgut differentiated enterocytes (ECs) lose their identity, impairing tissue homeostasis. To discover identity regulators, we performed an RNAi screen targeting ubiquitin-related genes in ECs. Seventeen genes were identified, including the deubiquitinase Non-stop (CG4166). Lineage tracing established that acute loss of Non-stop in young ECs phenocopies aged ECs at cellular and tissue levels. Proteomic analysis unveiled that Non-stop maintains identity as part of a Non-stop identity complex (NIC) containing E(y)2, Sgf11, Cp190, (Mod) mdg4, and Nup98. Non-stop ensured chromatin accessibility, maintaining the EC-gene signature, and protected NIC subunit stability. Upon aging, the levels of Non-stop and NIC subunits declined, distorting the unique organization of the EC nucleus. Maintaining youthful levels of Non-stop in wildtype aged ECs safeguards NIC subunits, nuclear organization, and suppressed aging phenotypes. Thus, Non-stop and NIC, supervise EC identity and protects from premature aging.
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Affiliation(s)
- Neta Erez
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lena Israitel
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Wing H Wong
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Gal Raz
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dayanne V Cornelio-Parra
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Salwa Danial
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Na'ama Flint Brodsly
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Todd Druley
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Ryan D Mohan
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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29
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The nuclear pore complex and the genome: organizing and regulatory principles. Curr Opin Genet Dev 2021; 67:142-150. [PMID: 33556822 DOI: 10.1016/j.gde.2021.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/29/2022]
Abstract
The nuclear pore complex (NPC) is a massive nuclear envelope-embedded protein complex, the canonical function of which is to mediate selective nucleocytoplasmic transport. In addition to its transport function, the NPC has been shown to interact with the underlying chromatin and to influence both activating and repressive gene regulatory processes, contributing to the establishment and the epigenetic maintenance of cell identity. In this review, we discuss diverse gene regulatory functions of NPC components and emerging mechanisms underlying these functions, including roles in genome architecture, transcription complex assembly, chromatin remodeling, and coordination of transcription and mRNA export. These functional roles highlight the importance of the NPC as a nuclear scaffold directing genome organization and function.
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30
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One Ring to Rule them All? Structural and Functional Diversity in the Nuclear Pore Complex. Trends Biochem Sci 2021; 46:595-607. [PMID: 33563541 DOI: 10.1016/j.tibs.2021.01.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
The nuclear pore complex (NPC) is the massive protein assembly that regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent breakthroughs have provided major insights into the structure of the NPC in different eukaryotes, revealing a previously unsuspected diversity of NPC architectures. In parallel, the NPC has been shown to be a key player in regulating essential nuclear processes such as chromatin organization, gene expression, and DNA repair. However, our knowledge of the NPC structure has not been able to address the molecular mechanisms underlying its regulatory roles. We discuss potential explanations, including the coexistence of alternative NPC architectures with specific functional roles.
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31
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Seeking commonalities in fusion proteins of NUP98. Nat Struct Mol Biol 2021; 28:123-124. [PMID: 33479543 DOI: 10.1038/s41594-021-00558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Terlecki-Zaniewicz S, Humer T, Eder T, Schmoellerl J, Heyes E, Manhart G, Kuchynka N, Parapatics K, Liberante FG, Müller AC, Tomazou EM, Grebien F. Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression. Nat Struct Mol Biol 2021; 28:190-201. [PMID: 33479542 DOI: 10.1038/s41594-020-00550-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/14/2020] [Indexed: 01/15/2023]
Abstract
NUP98 fusion proteins cause leukemia via unknown molecular mechanisms. All NUP98 fusion proteins share an intrinsically disordered region (IDR) in the NUP98 N terminus, featuring repeats of phenylalanine-glycine (FG), and C-terminal fusion partners often function in gene control. We investigated whether mechanisms of oncogenic transformation by NUP98 fusion proteins are hardwired in their protein interactomes. Affinity purification coupled to mass spectrometry (MS) and confocal imaging of five NUP98 fusion proteins expressed in human leukemia cells revealed that shared interactors were enriched for proteins involved in biomolecular condensation and that they colocalized with NUP98 fusion proteins in nuclear puncta. We developed biotinylated isoxazole-mediated condensome MS (biCon-MS) to show that NUP98 fusion proteins alter the global composition of biomolecular condensates. An artificial FG-repeat-containing fusion protein phenocopied the nuclear localization patterns of NUP98 fusion proteins and their capability to drive oncogenic gene expression programs. Thus, we propose that IDR-containing fusion proteins combine biomolecular condensation with transcriptional control to induce cancer.
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Affiliation(s)
- Stefan Terlecki-Zaniewicz
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria.,Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Theresa Humer
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Johannes Schmoellerl
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Elizabeth Heyes
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | | | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabio G Liberante
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eleni M Tomazou
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria.
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33
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Michmerhuizen NL, Klco JM, Mullighan CG. Mechanistic insights and potential therapeutic approaches for NUP98-rearranged hematologic malignancies. Blood 2020; 136:2275-2289. [PMID: 32766874 PMCID: PMC7702474 DOI: 10.1182/blood.2020007093] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleoporin 98 (NUP98) fusion oncoproteins are observed in a spectrum of hematologic malignancies, particularly pediatric leukemias with poor patient outcomes. Although wild-type full-length NUP98 is a member of the nuclear pore complex, the chromosomal translocations leading to NUP98 gene fusions involve the intrinsically disordered and N-terminal region of NUP98 with over 30 partner genes. Fusion partners include several genes bearing homeodomains or having known roles in transcriptional or epigenetic regulation. Based on data in both experimental models and patient samples, NUP98 fusion oncoprotein-driven leukemogenesis is mediated by changes in chromatin structure and gene expression. Multiple cofactors associate with NUP98 fusion oncoproteins to mediate transcriptional changes possibly via phase separation, in a manner likely dependent on the fusion partner. NUP98 gene fusions co-occur with a set of additional mutations, including FLT3-internal tandem duplication and other events contributing to increased proliferation. To improve the currently dire outcomes for patients with NUP98-rearranged malignancies, therapeutic strategies have been considered that target transcriptional and epigenetic machinery, cooperating alterations, and signaling or cell-cycle pathways. With the development of more faithful experimental systems and continued study, we anticipate great strides in our understanding of the molecular mechanisms and therapeutic vulnerabilities at play in NUP98-rearranged models. Taken together, these studies should lead to improved clinical outcomes for NUP98-rearranged leukemia.
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Affiliation(s)
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
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34
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Abstract
Acute myeloid leukemia (AML) is a clinically, morphologically, and genetically heterogeneous disorder. Like many malignancies, the genomic landscape of pediatric AML has been mapped recently through sequencing of large cohorts of patients. Much has been learned about the biology of AML through studies of specific recurrent genetic lesions. Further, genetic lesions have been linked to specific clinical features, response to therapy, and outcome, leading to improvements in risk stratification. Lastly, targeted therapeutic approaches have been developed for the treatment of specific genetic lesions, some of which are already having a positive impact on outcomes. While the advances made based on the discoveries of sequencing studies are significant, much work is left. The biologic, clinical, and prognostic impact of a number of genetic lesions, including several seemingly unique to pediatric patients, remains undefined. While targeted approaches are being explored, for most, the efficacy and tolerability when incorporated into standard therapy is yet to be determined. Furthermore, the challenge of how to study small subpopulations with rare genetic lesions in an already rare disease will have to be considered. In all, while questions and challenges remain, precisely defining the genomic landscape of AML, holds great promise for ultimately leading to improved outcomes for affected patients.
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Affiliation(s)
- Shannon E Conneely
- Division of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, 1102 Bates Avenue, Feigin Tower, Suite 1025, Houston, TX, 77030, USA
| | - Rachel E Rau
- Division of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, 1102 Bates Avenue, Feigin Tower, Suite 1025, Houston, TX, 77030, USA.
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35
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Targeted Inhibition of the NUP98-NSD1 Fusion Oncogene in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12102766. [PMID: 32993115 PMCID: PMC7600396 DOI: 10.3390/cancers12102766] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary NUP98-NSD1-positive acute myeloid leukemia (AML) frequently shows an additional mutation in Neuroblastoma rat sarcoma (NRAS). However, the synergistic effect of NUP98-NSD1 and NRASG12D in leukemic transformation remained unclear. In addition, NUP98-NSD1 positive AML patients respond poorly to chemotherapy and lack a targeted therapeutic option. Our study aimed to identify the cooperation of NUP98-NSD1 fusion and NRASG12D mutation and to develop a novel therapeutic approach for this AML. We found that NUP98-NSD1 alone can cause leukemia with long latency, and NRASG12D contributes to the aggressiveness of this AML. Additionally, we validated a novel NUP98-NSD1-targeting siRNA/lipid nanoparticle formulation that significantly prolonged the survival of patient-derived xenograft (PDX) mice with NUP98-NSD1-positive AML. Abstract NUP98-NSD1-positive acute myeloid leukemia (AML) is a poor prognostic subgroup that is frequently diagnosed in pediatric cytogenetically normal AML. NUP98-NSD1-positive AML often carries additional mutations in genes including FLT3, NRAS, WT1, and MYC. The purpose of our study was to characterize the cooperative potential of the fusion and its associated Neuroblastoma rat sarcoma (NRAS) mutation. By constitutively expressing NUP98-NSD1 and NRASG12D in a syngeneic mouse model and using a patient-derived xenograft (PDX) model from a NUP98-NSD1-positive AML patient, we evaluated the functional role of these genes and tested a novel siRNA formulation that inhibits the oncogenic driver NUP98-NSD1. NUP98-NSD1 transformed murine bone marrow (BM) cells in vitro and induced AML in vivo. While NRASG12D expression was insufficient to transform cells alone, co-expression of NUP98-NSD1 and NRASG12D enhanced the leukemogenicity of NUP98-NSD1. We developed a NUP98-NSD1-targeting siRNA/lipid nanoparticle formulation that significantly prolonged the survival of the PDX mice. Our study demonstrates that mutated NRAS cooperates with NUP98-NSD1 and shows that direct targeting of the fusion can be exploited as a novel treatment strategy in NUP98-NSD1-positive AML patients.
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36
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Cho UH, Hetzer MW. Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging. Neuron 2020; 106:899-911. [PMID: 32553207 DOI: 10.1016/j.neuron.2020.05.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 12/27/2022]
Abstract
In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging.
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Affiliation(s)
- Ukrae H Cho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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37
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Schmoellerl J, Barbosa IAM, Eder T, Brandstoetter T, Schmidt L, Maurer B, Troester S, Pham HTT, Sagarajit M, Ebner J, Manhart G, Aslan E, Terlecki-Zaniewicz S, Van der Veen C, Hoermann G, Duployez N, Petit A, Lapillonne H, Puissant A, Itzykson R, Moriggl R, Heuser M, Meisel R, Valent P, Sexl V, Zuber J, Grebien F. CDK6 is an essential direct target of NUP98 fusion proteins in acute myeloid leukemia. Blood 2020; 136:387-400. [PMID: 32344427 PMCID: PMC7115844 DOI: 10.1182/blood.2019003267] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/08/2020] [Indexed: 01/25/2023] Open
Abstract
Fusion proteins involving Nucleoporin 98 (NUP98) are recurrently found in acute myeloid leukemia (AML) and are associated with poor prognosis. Lack of mechanistic insight into NUP98-fusion-dependent oncogenic transformation has so far precluded the development of rational targeted therapies. We reasoned that different NUP98-fusion proteins deregulate a common set of transcriptional targets that might be exploitable for therapy. To decipher transcriptional programs controlled by diverse NUP98-fusion proteins, we developed mouse models for regulatable expression of NUP98/NSD1, NUP98/JARID1A, and NUP98/DDX10. By integrating chromatin occupancy profiles of NUP98-fusion proteins with transcriptome profiling upon acute fusion protein inactivation in vivo, we defined the core set of direct transcriptional targets of NUP98-fusion proteins. Among those, CDK6 was highly expressed in murine and human AML samples. Loss of CDK6 severely attenuated NUP98-fusion-driven leukemogenesis, and NUP98-fusion AML was sensitive to pharmacologic CDK6 inhibition in vitro and in vivo. These findings identify CDK6 as a conserved, critical direct target of NUP98-fusion proteins, proposing CDK4/CDK6 inhibitors as a new rational treatment option for AML patients with NUP98-fusions.
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MESH Headings
- Animals
- Cyclin-Dependent Kinase 6/antagonists & inhibitors
- Cyclin-Dependent Kinase 6/genetics
- Cyclin-Dependent Kinase 6/metabolism
- Drug Delivery Systems
- Gene Expression Profiling
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Nuclear Pore Complex Proteins/genetics
- Nuclear Pore Complex Proteins/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
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Affiliation(s)
- Johannes Schmoellerl
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | | | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | - Tania Brandstoetter
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Austria
| | - Luisa Schmidt
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | - Barbara Maurer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Austria
| | - Selina Troester
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | - Ha Thi Thanh Pham
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Austria
| | - Mohanty Sagarajit
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Jessica Ebner
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | - Ezgi Aslan
- Team of Project Machine, Medical Faculty, Istanbul Medeniyet University, Istanbul, Turkey
| | | | | | - Gregor Hoermann
- Department of Laboratory Medicine, Medical University of Vienna, Austria
- Central Institute for Medical and Chemical Laboratory Diagnosis, University Hospital Innsbruck, Innsbruck, Austria
| | - Nicolas Duployez
- Laboratory of Hematology, INSERM UMR-S 1172, Lille University Hospital, France
| | - Arnaud Petit
- Hopital Trousseau, Assistance Publique -Hopitaux de Paris, Paris, France
| | - Helene Lapillonne
- Hopital Trousseau, Assistance Publique -Hopitaux de Paris, Paris, France
| | - Alexandre Puissant
- INSERM U944, Saint-Louis Research Institute, University of Paris, Paris, France
| | - Raphael Itzykson
- INSERM U944, Saint-Louis Research Institute, University of Paris, Paris, France
| | - Richard Moriggl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Roland Meisel
- Division of Pediatric Stem Cell Therapy, Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
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38
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Xiao L, Jiang S, Huang P, Chen F, Wang X, Cheng Z, Miao Y, Liu L, Searle I, Liu C, Wu XX, Fu YF, Chen Q, Zhang XM. Two Nucleoporin98 homologous genes jointly participate in the regulation of starch degradation to repress senescence in Arabidopsis. BMC PLANT BIOLOGY 2020; 20:292. [PMID: 32586274 PMCID: PMC7318766 DOI: 10.1186/s12870-020-02494-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/15/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Starch is synthesized during daylight for temporary storage in leaves and then degraded during the subsequent night to support plant growth and development. Impairment of starch degradation leads to stunted growth, even senescence and death. The nuclear pore complex is involved in many cellular processes, but its relationship with starch degradation has been unclear until now. We previously identified that two Nucleoporin98 genes (Nup98a and Nup98b) redundantly regulate flowering via the CONSTANS (CO)-independent pathway in Arabidopsis thaliana. The double mutant also shows severe senescence phenotypes. RESULTS We find that Nucleoporin 98 participates in the regulation of sugar metabolism in leaves and is also involved in senescence regulation in Arabidopsis. We show that Nup98a and Nup98b function redundantly at different stages of starch degradation. The nup98a-1 nup98b-1 double mutant accumulates more starch, showing a severe early senescence phenotype compared to wild type plants. The expression of marker genes related to starch degradation is impaired in the nup98a-1 nup98b-1 double mutant, and marker genes of carbon starvation and senescence express their products earlier and in higher abundance than in wild type plants, suggesting that abnormalities in energy metabolism are the main cause of senescence in the double mutant. Addition of sucrose to the growth medium rescues early senescence phenotypes of the nup98a-1 nup98b-1 mutant. CONCLUSIONS Our results provide evidence for a novel role of the nuclear pore complex in energy metabolism related to growth and development, in which Nup98 functions in starch degradation to control growth regulation in Arabidopsis.
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Affiliation(s)
- Long Xiao
- Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Shanshan Jiang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Penghui Huang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Fulu Chen
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Xu Wang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Zhiyuan Cheng
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Yuchen Miao
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Liangyu Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Iain Searle
- School of Biological Sciences, School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Chunyan Liu
- Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiao-Xia Wu
- Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Yong-Fu Fu
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China.
| | - Qingshan Chen
- Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiao-Mei Zhang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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40
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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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41
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Abstract
Comprehensive cataloguing of the acute myeloid leukaemia (AML) genome has revealed a high frequency of mutations and deletions in epigenetic factors that are frequently linked to treatment resistance and poor patient outcome. In this review, we discuss how the epigenetic mechanisms that underpin normal haematopoiesis are subverted in AML, and in particular how these processes are altered in childhood and adolescent leukaemias. We also provide a brief summary of the burgeoning field of epigenetic-based therapies, and how AML treatment might be improved through provision of better conceptual frameworks for understanding the pleiotropic molecular effects of epigenetic disruption.
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Affiliation(s)
- Luke Jones
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Peter McCarthy
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
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42
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Cardin S, Bilodeau M, Roussy M, Aubert L, Milan T, Jouan L, Rouette A, Laramée L, Gendron P, Duchaine J, Decaluwe H, Spinella JF, Mourad S, Couture F, Sinnett D, Haddad É, Landry JR, Ma J, Humphries RK, Roux PP, Hébert J, Gruber TA, Wilhelm BT, Cellot S. Human models of NUP98-KDM5A megakaryocytic leukemia in mice contribute to uncovering new biomarkers and therapeutic vulnerabilities. Blood Adv 2019; 3:3307-3321. [PMID: 31698461 PMCID: PMC6855103 DOI: 10.1182/bloodadvances.2019030981] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 08/11/2019] [Indexed: 12/13/2022] Open
Abstract
Acute megakaryoblastic leukemia (AMKL) represents ∼10% of pediatric acute myeloid leukemia cases and typically affects young children (<3 years of age). It remains plagued with extremely poor treatment outcomes (<40% cure rates), mostly due to primary chemotherapy refractory disease and/or early relapse. Recurrent and mutually exclusive chimeric fusion oncogenes have been detected in 60% to 70% of cases and include nucleoporin 98 (NUP98) gene rearrangements, most commonly NUP98-KDM5A. Human models of NUP98-KDM5A-driven AMKL capable of faithfully recapitulating the disease have been lacking, and patient samples are rare, further limiting biomarkers and drug discovery. To overcome these impediments, we overexpressed NUP98-KDM5A in human cord blood hematopoietic stem and progenitor cells using a lentiviral-based approach to create physiopathologically relevant disease models. The NUP98-KDM5A fusion oncogene was a potent inducer of maturation arrest, sustaining long-term proliferative and progenitor capacities of engineered cells in optimized culture conditions. Adoptive transfer of NUP98-KDM5A-transformed cells into immunodeficient mice led to multiple subtypes of leukemia, including AMKL, that phenocopy human disease phenotypically and molecularly. The integrative molecular characterization of synthetic and patient NUP98-KDM5A AMKL samples revealed SELP, MPIG6B, and NEO1 as distinctive and novel disease biomarkers. Transcriptomic and proteomic analyses pointed to upregulation of the JAK-STAT signaling pathway in the model AMKL. Both synthetic models and patient-derived xenografts of NUP98-rearranged AMKL showed in vitro therapeutic vulnerability to ruxolitinib, a clinically approved JAK2 inhibitor. Overall, synthetic human AMKL models contribute to defining functional dependencies of rare genotypes of high-fatality pediatric leukemia, which lack effective and rationally designed treatments.
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MESH Headings
- Animals
- Biomarkers
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Computational Biology/methods
- Disease Models, Animal
- Disease Susceptibility
- Gene Expression
- Gene Expression Profiling
- High-Throughput Nucleotide Sequencing
- Humans
- Immunophenotyping
- Leukemia, Megakaryoblastic, Acute/etiology
- Leukemia, Megakaryoblastic, Acute/pathology
- Leukemia, Megakaryoblastic, Acute/therapy
- Mice
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Nuclear Pore Complex Proteins/genetics
- Nuclear Pore Complex Proteins/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Retinoblastoma-Binding Protein 2/genetics
- Retinoblastoma-Binding Protein 2/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Sophie Cardin
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
| | - Mélanie Bilodeau
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
| | - Mathieu Roussy
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
- Department of Biomedical Sciences
- Faculty of Medicine
| | - Léo Aubert
- Cell Signaling and Proteomics Research Unit, and
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Thomas Milan
- Laboratory for High-Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Loubna Jouan
- Integrated Centre for Pediatric Clinical Genomics, CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Alexandre Rouette
- Integrated Centre for Pediatric Clinical Genomics, CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Louise Laramée
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Bioinformatics Platform, Université de Montréal, Montréal, QC, Canada
| | - Jean Duchaine
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Hélène Decaluwe
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Jean-François Spinella
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Stéphanie Mourad
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
| | - Françoise Couture
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
| | - Daniel Sinnett
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Élie Haddad
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Microbiology, Infectiology and Immunology, CHU Sainte-Justine, Montréal, QC, Canada
| | - Josette-Renée Landry
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Streamline Genomics, Montréal, QC, Canada
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Philippe P Roux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Laboratory for High-Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Josée Hébert
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Division of Hematology, and
- Québec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada; and
| | - Tanja A Gruber
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Brian T Wilhelm
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Laboratory for High-Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Sonia Cellot
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Québec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada; and
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43
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Kuhn TM, Capelson M. Nuclear Pore Proteins in Regulation of Chromatin State. Cells 2019; 8:cells8111414. [PMID: 31717499 PMCID: PMC6912232 DOI: 10.3390/cells8111414] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/31/2022] Open
Abstract
Nuclear pore complexes (NPCs) are canonically known to regulate nucleocytoplasmic transport. However, research efforts over the last decade have demonstrated that NPCs and their constituent nucleoporins (Nups) also interact with the genome and perform important roles in regulation of gene expression. It has become increasingly clear that many Nups execute these roles specifically through regulation of chromatin state, whether through interactions with histone modifiers and downstream changes in post-translational histone modifications, or through relationships with chromatin-remodeling proteins that can result in physical changes in nucleosome occupancy and chromatin compaction. This review focuses on these findings, highlighting the functional connection between NPCs/Nups and regulation of chromatin structure, and how this connection can manifest in regulation of transcription.
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44
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Developmental conservation of microRNA gene localization at the nuclear periphery. PLoS One 2019; 14:e0223759. [PMID: 31682635 PMCID: PMC6827902 DOI: 10.1371/journal.pone.0223759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/27/2019] [Indexed: 12/21/2022] Open
Abstract
microRNAs are of vital importance for the regulation of the adaptive and innate immune responses, modulating gene expression at the post transcriptional level. Although there is cumulative information regarding the steady state mature microRNA levels and their respective targets, little is known about the effect of the three-dimensional chromatin architecture on the transcriptional regulation of microRNA gene loci. Here, we sought to investigate the effect of subnuclear localization on the transcriptional activation of eight murine microRNA loci in the immune system. Our results show that microRNA genes display a preferential monoallelic gene expression profile accompanied with perinuclear localization irrespectively of their transcription status or differentiation state. The expression profile and perinuclear localization are developmentally conserved while microRNA gene loci localization outside constitutive lamin associated domains is cross-species conserved. Our findings provide support for an active nuclear periphery and its role in chromatin organization of the non-coding genome.
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45
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Fisher JN, Thanasopoulou A, Juge S, Tzankov A, Bagger FO, Mendez MA, Peters AHFM, Schwaller J. Transforming activities of the NUP98-KMT2A fusion gene associated with myelodysplasia and acute myeloid leukemia. Haematologica 2019; 105:1857-1867. [PMID: 31558671 PMCID: PMC7327646 DOI: 10.3324/haematol.2019.219188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/24/2019] [Indexed: 12/25/2022] Open
Abstract
Inv(11)(p15q23), found in myelodysplastic syndromes and acute myeloid leukemia, leads to expression of a fusion protein consisting of the N-terminal of nucleoporin 98 (NUP98) and the majority of the lysine methyltransferase 2A (KMT2A). To explore the transforming potential of this fusion we established inducible iNUP98-KMT2A transgenic mice. After a median latency of 80 weeks, over 90% of these mice developed signs of disease, with anemia and reduced bone marrow cellularity, increased white blood cell numbers, extramedullary hematopoiesis, and multilineage dysplasia. Additionally, induction of iNUP98-KMT2A led to elevated lineage marker-negative Sca-1+ c-Kit+ cell numbers in the bone marrow, which outcompeted wildtype cells in repopulation assays. Six iNUP98-KMT2A mice developed transplantable acute myeloid leukemia with leukemic blasts infiltrating multiple organs. Notably, as reported for patients, iNUP98-KMT2A leukemic blasts did not express increased levels of the HoxA-B-C gene cluster, and in contrast to KMT2A-AF9 leukemic cells, the cells were resistant to pharmacological targeting of menin and BET family proteins by MI-2-2 or JQ1, respectively. Expression of iNUP98-KMT2A in mouse embryonic fibroblasts led to an accumulation of cells in G1 phase, and abrogated replicative senescence. In bone marrow-derived hematopoietic progenitors, iNUP98-KMT2A expression similarly resulted in increased cell numbers in the G1 phase of the cell cycle, with aberrant gene expression of Sirt1, Tert, Rbl2, Twist1, Vim, and Prkcd, mimicking that seen in mouse embryonic fibroblasts. In summary, we demonstrate that iNUP98-KMT2A has in vivo transforming activity and interferes with cell cycle progression rather than primarily blocking differentiation.
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Affiliation(s)
- James N Fisher
- University Children's Hospital Basel (UKBB).,Department of Biomedicine, University of Basel
| | - Angeliki Thanasopoulou
- University Children's Hospital Basel (UKBB).,Department of Biomedicine, University of Basel
| | - Sabine Juge
- University Children's Hospital Basel (UKBB).,Department of Biomedicine, University of Basel
| | | | - Frederik O Bagger
- University Children's Hospital Basel (UKBB).,Department of Biomedicine, University of Basel
| | - Max A Mendez
- University Children's Hospital Basel (UKBB).,Department of Biomedicine, University of Basel
| | - Antoine H F M Peters
- Faculty of Sciences, University of Basel.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Juerg Schwaller
- University Children's Hospital Basel (UKBB) .,Department of Biomedicine, University of Basel
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46
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Kuhn TM, Pascual-Garcia P, Gozalo A, Little SC, Capelson M. Chromatin targeting of nuclear pore proteins induces chromatin decondensation. J Cell Biol 2019; 218:2945-2961. [PMID: 31366666 PMCID: PMC6719443 DOI: 10.1083/jcb.201807139] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 04/05/2019] [Accepted: 07/08/2019] [Indexed: 12/03/2022] Open
Abstract
Nuclear pore complexes have emerged in recent years as chromatin-binding nuclear scaffolds, able to influence target gene expression. However, how nucleoporins (Nups) exert this control remains poorly understood. Here we show that ectopically tethering Drosophila Nups, especially Sec13, to chromatin is sufficient to induce chromatin decondensation. This decondensation is mediated through chromatin-remodeling complex PBAP, as PBAP is both robustly recruited by Sec13 and required for Sec13-induced decondensation. This phenomenon is not correlated with localization of the target locus to the nuclear periphery, but is correlated with robust recruitment of Nup Elys. Furthermore, we identified a biochemical interaction between endogenous Sec13 and Elys with PBAP, and a role for endogenous Elys in global as well as gene-specific chromatin decompaction. Together, these findings reveal a functional role and mechanism for specific nuclear pore components in promoting an open chromatin state.
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Affiliation(s)
- Terra M Kuhn
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Alejandro Gozalo
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Shawn C Little
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
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47
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Abstract
During my postdoc interview in June of 1998, I asked Günter why he was moving more towards the nucleus in his latest studies. He said, "Well Joe, that's where everything starts." By the end of the interview, I accepted the postdoc. He had a way of making everything sound so cool. Günter's progression was natural, since the endoplasmic reticulum and the nucleus are the only organelles that share the same membrane. The nuclear envelope extends into a double membrane system with nuclear pore complexes embedded in the pore membrane openings. Even while writing this review, I remember Günter stressing; it is the nuclear pore complex. Just saying nuclear pore doesn't encompass the full magnitude of its significance. The nuclear pore complex is one of the largest collection of proteins that fit together for an overall function: transport. This review will cover the Blobel lab contributions in the quest for the blueprint of the nuclear pore complex from isolation of the nuclear envelope and nuclear lamin to the ring structures.
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48
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Sun J, Shi Y, Yildirim E. The Nuclear Pore Complex in Cell Type-Specific Chromatin Structure and Gene Regulation. Trends Genet 2019; 35:579-588. [PMID: 31213386 DOI: 10.1016/j.tig.2019.05.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022]
Abstract
Nuclear pore complex (NPC)-mediated nucleocytoplasmic trafficking is essential for key cellular processes, such as cell growth, cell differentiation, and gene regulation. The NPC has also been viewed as a nuclear architectural platform that impacts genome function and gene expression by mediating spatial and temporal coordination between transcription factors, chromatin regulatory proteins, and transcription machinery. Recent findings have uncovered differential and cell type-specific expression and distinct chromatin-binding patterns of individual NPC components known as nucleoporins (Nups). Here, we examine recent studies that investigate the functional roles of NPCs and Nups in transcription, chromatin organization, and epigenetic gene regulation in the context of development and disease.
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Affiliation(s)
- Jiayu Sun
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Durham, NC 27710, USA
| | - Yuming Shi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Durham, NC 27710, USA
| | - Eda Yildirim
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Durham, NC 27710, USA.
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49
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Buchwalter A, Kaneshiro JM, Hetzer MW. Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet 2019; 20:39-50. [PMID: 30356165 DOI: 10.1038/s41576-018-0063-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing.
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Affiliation(s)
- Abigail Buchwalter
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Jeanae M Kaneshiro
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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Pascual-Garcia P, Capelson M. Nuclear pores in genome architecture and enhancer function. Curr Opin Cell Biol 2019; 58:126-133. [PMID: 31063899 DOI: 10.1016/j.ceb.2019.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 01/28/2023]
Abstract
Nuclear genome architecture relies on interactions between the genome and various nuclear scaffolds. One such a nuclear scaffold is the nuclear pore complex (NPC), which in addition to its nuclear transport function, can interact with underlying chromatin. In particular, NPCs have been recently reported to associate with a number of enhancers and superenhancers in metazoan genomes, and select NPC components have been shown to promote the formation of specific genomic loops. Here, we provide a brief overview of current models of enhancer function, and discuss recent evidence that NPCs bind enhancers and contribute to topological genome organization. We also examine possible models of how gene and enhancer targeting to NPCs may contribute to tissue-specific genome architecture and expression programs, including the possibility that NPCs may promote phase separation of transcriptional compartments.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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