1
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
2
|
Liu Z, Qin Z, Liu Y, Xia X, He L, Chen N, Hu X, Peng X. Liquid‒liquid phase separation: roles and implications in future cancer treatment. Int J Biol Sci 2023; 19:4139-4156. [PMID: 37705755 PMCID: PMC10496506 DOI: 10.7150/ijbs.81521] [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: 12/04/2022] [Accepted: 07/23/2023] [Indexed: 09/15/2023] Open
Abstract
Liquid‒liquid phase separation (LLPS) is a phenomenon driven by weak interactions between biomolecules, such as proteins and nucleic acids, that leads to the formation of distinct liquid-like condensates. Through LLPS, membraneless condensates are formed, selectively concentrating specific proteins while excluding other molecules to maintain normal cellular functions. Emerging evidence shows that cancer-related mutations cause aberrant condensate assembly, resulting in disrupted signal transduction, impaired DNA repair, and abnormal chromatin organization and eventually contributing to tumorigenesis. The objective of this review is to summarize recent advancements in understanding the potential implications of LLPS in the contexts of cancer progression and therapeutic interventions. By interfering with LLPS, it may be possible to restore normal cellular processes and inhibit tumor progression. The underlying mechanisms and potential drug targets associated with LLPS in cancer are discussed, shedding light on promising opportunities for novel therapeutic interventions.
Collapse
Affiliation(s)
- Zheran Liu
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zijian Qin
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yingtong Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu 610041, Sichuan, China
| | - Xi Xia
- Shanghai ETERN Biopharma Co., Ltd., Shanghai, China
| | - Ling He
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Na Chen
- School of Pharmacy, Chengdu Medical College, Xindu Avenue No 783, Chengdu, 610500, Sichuan Province, China
| | - Xiaolin Hu
- West China School of Nursing, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xingchen Peng
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| |
Collapse
|
3
|
Tuning between Nuclear Organization and Functionality in Health and Disease. Cells 2023; 12:cells12050706. [PMID: 36899842 PMCID: PMC10000962 DOI: 10.3390/cells12050706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The organization of eukaryotic genome in the nucleus, a double-membraned organelle separated from the cytoplasm, is highly complex and dynamic. The functional architecture of the nucleus is confined by the layers of internal and cytoplasmic elements, including chromatin organization, nuclear envelope associated proteome and transport, nuclear-cytoskeletal contacts, and the mechano-regulatory signaling cascades. The size and morphology of the nucleus could impose a significant impact on nuclear mechanics, chromatin organization, gene expression, cell functionality and disease development. The maintenance of nuclear organization during genetic or physical perturbation is crucial for the viability and lifespan of the cell. Abnormal nuclear envelope morphologies, such as invagination and blebbing, have functional implications in several human disorders, including cancer, accelerated aging, thyroid disorders, and different types of neuro-muscular diseases. Despite the evident interplay between nuclear structure and nuclear function, our knowledge about the underlying molecular mechanisms for regulation of nuclear morphology and cell functionality during health and illness is rather poor. This review highlights the essential nuclear, cellular, and extracellular components that govern the organization of nuclei and functional consequences associated with nuclear morphometric aberrations. Finally, we discuss the recent developments with diagnostic and therapeutic implications targeting nuclear morphology in health and disease.
Collapse
|
4
|
Hussein D, Alsereihi R, Salwati AAA, Algehani R, Alhowity A, Al-Hejin AM, Schulten HJ, Baeesa S, Bangash M, Alghamdi F, Cross R, Al Zughaibi T, Saka M, Chaudhary A, Abuzenadah A. The anterior gradient homologue 2 (AGR2) co-localises with the glucose-regulated protein 78 (GRP78) in cancer stem cells, and is critical for the survival and drug resistance of recurrent glioblastoma: in situ and in vitro analyses. Cancer Cell Int 2022; 22:387. [PMID: 36482387 PMCID: PMC9730595 DOI: 10.1186/s12935-022-02814-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glioblastomas (GBs) are characterised as one of the most aggressive primary central nervous system tumours (CNSTs). Single-cell sequencing analysis identified the presence of a highly heterogeneous population of cancer stem cells (CSCs). The proteins anterior gradient homologue 2 (AGR2) and glucose-regulated protein 78 (GRP78) are known to play critical roles in regulating unfolded protein response (UPR) machinery. The UPR machinery influences cell survival, migration, invasion and drug resistance. Hence, we investigated the role of AGR2 in drug-resistant recurrent glioblastoma cells. METHODS Immunofluorescence, biological assessments and whole exome sequencing analyses were completed under in situ and in vitro conditions. Cells were treated with CNSTs clinical/preclinical drugs taxol, cisplatin, irinotecan, MCK8866, etoposide, and temozolomide, then resistant cells were analysed for the expression of AGR2. AGR2 was repressed using single and double siRNA transfections and combined with either temozolomide or irinotecan. RESULTS Genomic and biological characterisations of the AGR2-expressed Jed66_GB and Jed41_GB recurrent glioblastoma tissues and cell lines showed features consistent with glioblastoma. Immunofluorescence data indicated that AGR2 co-localised with the UPR marker GRP78 in both the tissue and their corresponding primary cell lines. AGR2 and GRP78 were highly expressed in glioblastoma CSCs. Following treatment with the aforementioned drugs, all drug-surviving cells showed high expression of AGR2. Prolonged siRNA repression of a particular region in AGR2 exon 2 reduced AGR2 protein expression and led to lower cell densities in both cell lines. Co-treatments using AGR2 exon 2B siRNA in conjunction with temozolomide or irinotecan had partially synergistic effects. The slight reduction of AGR2 expression increased nuclear Caspase-3 activation in both cell lines and caused multinucleation in the Jed66_GB cell line. CONCLUSIONS AGR2 is highly expressed in UPR-active CSCs and drug-resistant GB cells, and its repression leads to apoptosis, via multiple pathways.
Collapse
Affiliation(s)
- Deema Hussein
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Reem Alsereihi
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 80203, Jeddah, 21589 Saudi Arabia ,College of Health Sciences, Al-Rayan Colleges, 41411, Madinah AL-Munawarah, Saudi Arabia
| | - Abdulla Ahmed A. Salwati
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia
| | - Rinad Algehani
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia
| | - Alazouf Alhowity
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia
| | - Ahmed M. Al-Hejin
- grid.412125.10000 0001 0619 1117Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 80203, Jeddah, 21589 Saudi Arabia
| | - Hans-Juergen Schulten
- grid.412125.10000 0001 0619 1117Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Saleh Baeesa
- grid.412125.10000 0001 0619 1117Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Mohammed Bangash
- grid.412125.10000 0001 0619 1117Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Fahad Alghamdi
- grid.412125.10000 0001 0619 1117Pathology Department, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Richard Cross
- grid.48815.300000 0001 2153 2936School of Engineering and Sustainable Development, Emerging Technologies Research Centre (EMTERC), De Montfort University, The Gateway, Leicester, LE1 9BH UK
| | - Torki Al Zughaibi
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Mohamad Saka
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Adeel Chaudhary
- grid.412125.10000 0001 0619 1117Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Adel Abuzenadah
- grid.412125.10000 0001 0619 1117King Fahd Medical Research Center, King Abdulaziz University, 80216, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ,grid.412125.10000 0001 0619 1117Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| |
Collapse
|
5
|
Quiroga IY, Ahn JH, Wang GG, Phanstiel D. Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer. Curr Opin Genet Dev 2022; 74:101901. [PMID: 35427897 PMCID: PMC9156545 DOI: 10.1016/j.gde.2022.101901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 03/05/2022] [Indexed: 11/27/2022]
Abstract
Three-dimensional (3D) chromatin structure plays a critical role in development, gene regulation, and cellular identity. Alterations to this structure can have profound effects on cellular phenotypes and have been associated with a variety of diseases including multiple types of cancer. One of several forces that help shape 3D chromatin structure is liquid-liquid phase separation, a form of self-association between biomolecules that can sequester regions of chromatin into subnuclear droplets or even membraneless organelles like nucleoli. This review focuses on a class of oncogenic fusion proteins that appear to exert their oncogenic function via phase-separation-driven alterations to 3D chromatin structure. Here, we review what is known about the mechanisms by which these oncogenic fusion proteins phase separate in the nucleus and their role in shaping the 3D chromatin structure. We discuss the potential for this phenomenon to be a more widespread mechanism of oncogenesis.
Collapse
Affiliation(s)
- Ivana Y Quiroga
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Douglas Phanstiel
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| |
Collapse
|
6
|
Pulianmackal AJ, Kanakousaki K, Flegel KA, Grushko OG, Gourley E, Rozich E, Buttitta LA. Misregulation of the Nucleoporins 98 and 96 lead to defects in protein synthesis that promote hallmarks of tumorigenesis. Dis Model Mech 2022; 15:274202. [PMID: 35107131 PMCID: PMC8938402 DOI: 10.1242/dmm.049234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/15/2022] [Indexed: 11/20/2022] Open
Abstract
Nucleoporin 98KD (Nup98) is a promiscuous translocation partner in hematological malignancies. Most disease models of Nup98 translocations involve ectopic expression of the fusion protein under study, leaving the endogenous Nup98 loci unperturbed. Overlooked in these approaches is the loss of one copy of normal Nup98 in addition to the loss of Nup96 – a second Nucleoporin encoded within the same mRNA and reading frame as Nup98 – in translocations. Nup98 and Nup96 are also mutated in a number of other cancers, suggesting that their disruption is not limited to blood cancers. We found that reducing Nup98-96 function in Drosophila melanogaster (in which the Nup98-96 shared mRNA and reading frame is conserved) de-regulates the cell cycle. We found evidence of overproliferation in tissues with reduced Nup98-96, counteracted by elevated apoptosis and aberrant signaling associated with chronic wounding. Reducing Nup98-96 function led to defects in protein synthesis that triggered JNK signaling and contributed to hallmarks of tumorigenesis when apoptosis was inhibited. We suggest that partial loss of Nup98-96 function in translocations could de-regulate protein synthesis, leading to signaling that cooperates with other mutations to promote tumorigenesis. Editor's choice: Compromising Nucleoporins 98 and 96 leads to defects in protein synthesis and stress signaling via JNK that triggers compensatory and apoptosis-induced proliferation.
Collapse
Affiliation(s)
- Ajai J Pulianmackal
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kiriaki Kanakousaki
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kerry A Flegel
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olga G Grushko
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ella Gourley
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily Rozich
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura A Buttitta
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
7
|
Singh I, Lele TP. Nuclear Morphological Abnormalities in Cancer: A Search for Unifying Mechanisms. Results Probl Cell Differ 2022; 70:443-467. [PMID: 36348118 PMCID: PMC9722227 DOI: 10.1007/978-3-031-06573-6_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Irregularities in nuclear shape and/or alterations to nuclear size are a hallmark of malignancy in a broad range of cancer types. Though these abnormalities are commonly used for diagnostic purposes and are often used to assess cancer progression in the clinic, the mechanisms through which they occur are not well understood. Nuclear size alterations in cancer could potentially arise from aneuploidy, changes in osmotic coupling with the cytoplasm, and perturbations to nucleocytoplasmic transport. Nuclear shape changes may occur due to alterations to cell-generated mechanical stresses and/or alterations to nuclear structural components, which balance those stresses, such as the nuclear lamina and chromatin. A better understanding of the mechanisms underlying abnormal nuclear morphology and size may allow the development of new therapeutics to target nuclear aberrations in cancer.
Collapse
Affiliation(s)
- Ishita Singh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Tanmay P. Lele
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA,Department of Chemical Engineering, University of Florida, Gainesville, FL, USA,Department of Translational Medical Sciences, Texas A&M University, Houston, TX, USA
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Nuclear Dynamics and Chromatin Structure: Implications for Pancreatic Cancer. Cells 2021; 10:cells10102624. [PMID: 34685604 PMCID: PMC8534098 DOI: 10.3390/cells10102624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the 'gold standard' for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.
Collapse
|
10
|
Cai D, Liu Z, Lippincott-Schwartz J. Biomolecular Condensates and Their Links to Cancer Progression. Trends Biochem Sci 2021; 46:535-549. [PMID: 33579564 DOI: 10.1016/j.tibs.2021.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/14/2023]
Abstract
Liquid-liquid phase separation (LLPS) has emerged in recent years as an important physicochemical process for organizing diverse processes within cells via the formation of membraneless organelles termed biomolecular condensates. Emerging evidence now suggests that the formation and regulation of biomolecular condensates are also intricately linked to cancer formation and progression. We review the most recent literature linking the existence and/or dissolution of biomolecular condensates to different hallmarks of cancer formation and progression. We then discuss the opportunities that this condensate perspective provides for cancer research and the development of novel therapeutic approaches, including the perturbation of condensates by small-molecule inhibitors.
Collapse
Affiliation(s)
- Danfeng Cai
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | |
Collapse
|
11
|
Ahn JH, Davis ES, Daugird TA, Zhao S, Quiroga IY, Uryu H, Li J, Storey AJ, Tsai YH, Keeley DP, Mackintosh SG, Edmondson RD, Byrum SD, Cai L, Tackett AJ, Zheng D, Legant WR, Phanstiel DH, Wang GG. Phase separation drives aberrant chromatin looping and cancer development. Nature 2021; 595:591-595. [PMID: 34163069 PMCID: PMC8647409 DOI: 10.1038/s41586-021-03662-5] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/21/2021] [Indexed: 01/05/2023]
Abstract
The development of cancer is intimately associated with genetic abnormalities that target proteins with intrinsically disordered regions (IDRs). In human haematological malignancies, recurrent chromosomal translocation of nucleoporin (NUP98 or NUP214) generates an aberrant chimera that invariably retains the nucleoporin IDR-tandemly dispersed repeats of phenylalanine and glycine residues1,2. However, how unstructured IDRs contribute to oncogenesis remains unclear. Here we show that IDRs contained within NUP98-HOXA9, a homeodomain-containing transcription factor chimera recurrently detected in leukaemias1,2, are essential for establishing liquid-liquid phase separation (LLPS) puncta of chimera and for inducing leukaemic transformation. Notably, LLPS of NUP98-HOXA9 not only promotes chromatin occupancy of chimera transcription factors, but also is required for the formation of a broad 'super-enhancer'-like binding pattern typically seen at leukaemogenic genes, which potentiates transcriptional activation. An artificial HOX chimera, created by replacing the phenylalanine and glycine repeats of NUP98 with an unrelated LLPS-forming IDR of the FUS protein3,4, had similar enhancing effects on the genome-wide binding and target gene activation of the chimera. Deeply sequenced Hi-C revealed that phase-separated NUP98-HOXA9 induces CTCF-independent chromatin loops that are enriched at proto-oncogenes. Together, this report describes a proof-of-principle example in which cancer acquires mutation to establish oncogenic transcription factor condensates via phase separation, which simultaneously enhances their genomic targeting and induces organization of aberrant three-dimensional chromatin structure during tumourous transformation. As LLPS-competent molecules are frequently implicated in diseases1,2,4-7, this mechanism can potentially be generalized to many malignant and pathological settings.
Collapse
Affiliation(s)
- Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ivana Yoseli Quiroga
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Daniel P Keeley
- UNC Neuroscience Center and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Deyou Zheng
- Departments of Genetics, Neurology, and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, NC, USA
| | - Douglas H Phanstiel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
12
|
CDK6 is an essential direct target of NUP98 fusion proteins in acute myeloid leukemia. Blood 2021; 136:387-400. [PMID: 32344427 DOI: 10.1182/blood.2019003267] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [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.
Collapse
|
13
|
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]
|
14
|
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: 25] [Impact Index Per Article: 8.3] [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.
Collapse
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.
| |
Collapse
|
15
|
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.
Collapse
Affiliation(s)
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | | |
Collapse
|
16
|
NUP98-HBO1-fusion generates phenotypically and genetically relevant chronic myelomonocytic leukemia pathogenesis. Blood Adv 2020; 3:1047-1060. [PMID: 30944097 DOI: 10.1182/bloodadvances.2018025007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 02/27/2019] [Indexed: 12/18/2022] Open
Abstract
Chronic myelomonocytic leukemia (CMML) constitutes a hematopoietic stem cell (HSC) disorder characterized by prominent monocytosis and myelodysplasia. Although genome sequencing has revealed the CMML mutation profile, the mechanism of disease development remains unclear. Here we show that aberrant histone acetylation by nucleoporin-98 (NUP98)-HBO1, a newly identified fusion in a patient with CMML, is sufficient to generate clinically relevant CMML pathogenesis. Overexpression of NUP98-HBO1 in murine HSC/progenitors (HSC/Ps) induced diverse CMML phenotypes, such as severe leukocytosis, increased CD115+ Ly6Chigh monocytes (an equivalent subpopulation to human classical CD14+ CD16- monocytes), macrocytic anemia, thrombocytopenia, megakaryocyte-lineage dysplasia, splenomegaly, and cachexia. A NUP98-HBO1-mediated transcriptional signature in human CD34+ cells was specifically activated in HSC/Ps from a CMML patient cohort. Besides critical determinants of monocytic cell fate choice in HSC/Ps, an oncogenic HOXA9 signature was significantly activated by NUP98-HBO1 fusion through aberrant histone acetylation. Increased HOXA9 gene expression level with disease progression was confirmed in our CMML cohort. Genetic disruption of NUP98-HBO1 histone acetyltransferase activity abrogated its leukemogenic potential and disease development in human cells and a mouse model. Furthermore, treatment of azacytidine was effective in our CMML mice. The recapitulation of CMML clinical phenotypes and gene expression profile by the HBO1 fusion suggests our new model as a useful platform for elucidating the central downstream mediators underlying diverse CMML-related mutations and testing multiple compounds, providing novel therapeutic potential.
Collapse
|
17
|
Mendes A, Jühlen R, Bousbata S, Fahrenkrog B. Disclosing the Interactome of Leukemogenic NUP98-HOXA9 and SET-NUP214 Fusion Proteins Using a Proteomic Approach. Cells 2020; 9:E1666. [PMID: 32664447 PMCID: PMC7407662 DOI: 10.3390/cells9071666] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
The interaction of oncogenes with cellular proteins is a major determinant of cellular transformation. The NUP98-HOXA9 and SET-NUP214 chimeras result from recurrent chromosomal translocations in acute leukemia. Functionally, the two fusion proteins inhibit nuclear export and interact with epigenetic regulators. The full interactome of NUP98-HOXA9 and SET-NUP214 is currently unknown. We used proximity-dependent biotin identification (BioID) to study the landscape of the NUP98-HOXA9 and SET-NUP214 environments. Our results suggest that both fusion proteins interact with major regulators of RNA processing, with translation-associated proteins, and that both chimeras perturb the transcriptional program of the tumor suppressor p53. Other cellular processes appear to be distinctively affected by the particular fusion protein. NUP98-HOXA9 likely perturbs Wnt, MAPK, and estrogen receptor (ER) signaling pathways, as well as the cytoskeleton, the latter likely due to its interaction with the nuclear export receptor CRM1. Conversely, mitochondrial proteins and metabolic regulators are significantly overrepresented in the SET-NUP214 proximal interactome. Our study provides new clues on the mechanistic actions of nucleoporin fusion proteins and might be of particular relevance in the search for new druggable targets for the treatment of nucleoporin-related leukemia.
Collapse
Affiliation(s)
- Adélia Mendes
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
| | - Ramona Jühlen
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
- Present address: Institute of Biochemistry and Molecular Cell Biology, RWTH Aachen University, 52074 Aachen, Germany
| | - Sabrina Bousbata
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
| |
Collapse
|
18
|
Zhang Y, Guo Y, Gough SM, Zhang J, Vann KR, Li K, Cai L, Shi X, Aplan PD, Wang GG, Kutateladze TG. Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion. Nat Commun 2020; 11:3339. [PMID: 32620764 PMCID: PMC7335091 DOI: 10.1038/s41467-020-17098-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/12/2020] [Indexed: 12/18/2022] Open
Abstract
Chromosomal NUP98-PHF23 translocation is associated with an aggressive form of acute myeloid leukemia (AML) and poor survival rate. Here, we report the molecular mechanisms by which NUP98-PHF23 recognizes the histone mark H3K4me3 and is inhibited by small molecule compounds, including disulfiram that directly targets the PHD finger of PHF23 (PHF23PHD). Our data support a critical role for the PHD fingers of NUP98-PHF23, and related NUP98-KDM5A and NUP98-BPTF fusions in driving leukemogenesis, and demonstrate that blocking this interaction in NUP98-PHF23 expressing AML cells leads to cell death through necrotic and late apoptosis pathways. An overlap of NUP98-KDM5A oncoprotein binding sites and H3K4me3-positive loci at the Hoxa/b gene clusters and Meis1 in ChIP-seq, together with NMR analysis of the H3K4me3-binding sites of the PHD fingers from PHF23, KDM5A and BPTF, suggests a common PHD finger-dependent mechanism that promotes leukemogenesis by this type of NUP98 fusions. Our findings highlight the direct correlation between the abilities of NUP98-PHD finger fusion chimeras to associate with H3K4me3-enriched chromatin and leukemic transformation.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Yiran Guo
- Department of Biochemistry and Biophysics, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Sheryl M Gough
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jinyong Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kendra R Vann
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kuai Li
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Ling Cai
- Department of Biochemistry and Biophysics, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Peter D Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Gang Greg Wang
- Department of Biochemistry and Biophysics, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| |
Collapse
|
19
|
Drucker E, Holzer K, Pusch S, Winkler J, Calvisi DF, Eiteneuer E, Herpel E, Goeppert B, Roessler S, Ori A, Schirmacher P, Breuhahn K, Singer S. Karyopherin α2-dependent import of E2F1 and TFDP1 maintains protumorigenic stathmin expression in liver cancer. Cell Commun Signal 2019; 17:159. [PMID: 31783876 PMCID: PMC6883611 DOI: 10.1186/s12964-019-0456-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Background Members of the karyopherin superfamily serve as nuclear transport receptors/adaptor proteins and provide exchange of macromolecules between the nucleo- and cytoplasm. Emerging evidence suggests a subset of karyopherins to be dysregulated in hepatocarcinogenesis including karyopherin-α2 (KPNA2). However, the functional and regulatory role of KPNA2 in liver cancer remains incompletely understood. Methods Quantitative proteomics (LC-MS/MS, ~ 1750 proteins in total) was used to study changes in global protein abundance upon siRNA-mediated KPNA2 knockdown in HCC cells. Functional and mechanistic analyses included colony formation and 2D migration assays, co-immunoprecipitation (CoIP), chromatin immunoprecipitation (ChIP), qRT-PCR, immmunblotting, and subcellular fractionation. In vitro results were correlated with data derived from a murine HCC model and HCC patient samples (3 cohorts, n > 600 in total). Results The proteomic approach revealed the pro-tumorigenic, microtubule (MT) interacting protein stathmin (STMN1) among the most downregulated proteins upon KPNA2 depletion in HCC cells. We further observed that KPNA2 knockdown leads to reduced tumor cell migration and colony formation of HCC cells, which could be phenocopied by direct knockdown of stathmin. As the underlying regulatory mechanism, we uncovered E2F1 and TFDP1 as transport substrates of KPNA2 being retained in the cytoplasm upon KPNA2 ablation, thereby resulting in reduced STMN1 expression. Finally, murine and human HCC data indicate significant correlations of STMN1 expression with E2F1/TFPD1 and with KPNA2 expression and their association with poor prognosis in HCC patients. Conclusion Our data suggest that KPNA2 regulates STMN1 by import of E2F1/TFDP1 and thereby provide a novel link between nuclear transport and MT-interacting proteins in HCC with functional and prognostic significance.
Collapse
Affiliation(s)
- Elisabeth Drucker
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Greifswald, Friedrich-Loeffler-Straße 23e, 17475, Greifswald, Germany
| | - Kerstin Holzer
- Institute of Pathology, University Medicine Greifswald, Friedrich-Loeffler-Straße 23e, 17475, Greifswald, Germany
| | - Stefan Pusch
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.,German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juliane Winkler
- Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Diego F Calvisi
- Institute of Pathology, University Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Eva Eiteneuer
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.,Leibniz-Institute on Aging, Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Stephan Singer
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany. .,Institute of Pathology, University Medicine Greifswald, Friedrich-Loeffler-Straße 23e, 17475, Greifswald, Germany.
| |
Collapse
|
20
|
Ha M, Kim JY, Han ME, Kim GH, Park SY, Jeong DC, Oh SO, Kim YH. TMEM18: A Novel Prognostic Marker in Acute Myeloid Leukemia. Acta Haematol 2018; 140:71-76. [PMID: 30199869 DOI: 10.1159/000492742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/04/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Certain nuclear envelope proteins are associated with important cancer cell characteristics, including migration and proliferation. Abnormal expression of and genetic changes in nuclear envelope proteins have been reported in acute myeloid leukemia (AML) patients. Transmembrane protein 18 (TMEM18), a nuclear envelope protein, is involved in neural stem cell migration and tumorigenicity. METHODS To examine the prognostic significance of TMEM18 in AML patients, we analyzed an AML cohort from The Cancer Genome Atlas (TCGA, n = 142). RESULTS Kaplan-Meier survival analysis revealed that TMEM18 overexpression was associated with a better AML prognosis with good discrimination (p = 0.019). Interestingly, this ability to predict the prognosis was significant in male AML patients, but not in female ones. C-index and area-under-the-curve analyses further supported this discriminative ability and multivariate analysis confirmed its prognostic significance (p = 0.00347). Correlation analysis revealed that TMEM18 had a statistically significant positive correlation with nuclear envelop protein 133 (NUP133), NUP35, NUP54, NUP62, and NUP88. CONCLUSION Because the current AML prognostic factors do not take mRNA expression into consideration unlike other cancers, the development of mRNA-based prognostic factors would be beneficial for accurate prediction of the survival of AML patients. Therefore, TMEM18 gene is a potential biomarker for AML.
Collapse
Affiliation(s)
- Mihyang Ha
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Ji-Young Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Ga Hyun Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Si Young Park
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Dae Cheon Jeong
- Deloitte Analytics Group, Deloitte Consulting LLC, Seoul, Republic of Korea
| | - Sae-Ock Oh
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
- BEER, Busan Society of Evidence-Based Medicine and Research, Busan, Republic of Korea
| |
Collapse
|
21
|
CCI-007, a novel small molecule with cytotoxic activity against infant leukemia with MLL rearrangements. Oncotarget 2018; 7:46067-46087. [PMID: 27317766 PMCID: PMC5216782 DOI: 10.18632/oncotarget.10022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/28/2016] [Indexed: 12/17/2022] Open
Abstract
There is an urgent need for the development of less toxic, more selective and targeted therapies for infants with leukemia characterized by translocation of the mixed lineage leukemia (MLL) gene. In this study, we performed a cell-based small molecule library screen on an infant MLL-rearranged (MLL-r) cell line, PER-485, in order to identify selective inhibitors for MLL-r leukemia. After screening initial hits for a cytotoxic effect against a panel of 30 cell lines including MLL-r and MLL wild-type (MLL-wt) leukemia, solid tumours and control cells, small molecule CCI-007 was identified as a compound that selectively and significantly decreased the viability of a subset of MLL-r and related leukemia cell lines with CALM-AF10 and SET-NUP214 translocation. CCI-007 induced a rapid caspase-dependent apoptosis with mitochondrial depolarization within twenty-four hours of treatment. CCI-007 altered the characteristic MLL-r gene expression signature in sensitive cells with downregulation of the expression of HOXA9, MEIS1, CMYC and BCL2, important drivers in MLL-r leukemia, within a few hours of treatment. MLL-r leukemia cells that were resistant to the compound were characterised by significantly higher baseline gene expression levels of MEIS1 and BCL2 in comparison to CCI-007 sensitive MLL-r leukemia cells. In conclusion, we have identified CCI-007 as a novel small molecule that displays rapid toxicity towards a subset of MLL-r, CALM-AF10 and SET-NUP214 leukemia cell lines. Our findings suggest an important new avenue in the development of targeted therapies for these deadly diseases and indicate that different therapeutic strategies might be needed for different subtypes of MLL-r leukemia.
Collapse
|
22
|
Tosato V, West N, Zrimec J, Nikitin DV, Del Sal G, Marano R, Breitenbach M, Bruschi CV. Bridge-Induced Translocation between NUP145 and TOP2 Yeast Genes Models the Genetic Fusion between the Human Orthologs Associated With Acute Myeloid Leukemia. Front Oncol 2017; 7:231. [PMID: 29034209 PMCID: PMC5626878 DOI: 10.3389/fonc.2017.00231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/07/2017] [Indexed: 01/03/2023] Open
Abstract
In mammalian organisms liquid tumors such as acute myeloid leukemia (AML) are related to spontaneous chromosomal translocations ensuing in gene fusions. We previously developed a system named bridge-induced translocation (BIT) that allows linking together two different chromosomes exploiting the strong endogenous homologous recombination system of the yeast Saccharomyces cerevisiae. The BIT system generates a heterogeneous population of cells with different aneuploidies and severe aberrant phenotypes reminiscent of a cancerogenic transformation. In this work, thanks to a complex pop-out methodology of the marker used for the selection of translocants, we succeeded by BIT technology to precisely reproduce in yeast the peculiar chromosome translocation that has been associated with AML, characterized by the fusion between the human genes NUP98 and TOP2B. To shed light on the origin of the DNA fragility within NUP98, an extensive analysis of the curvature, bending, thermostability, and B-Z transition aptitude of the breakpoint region of NUP98 and of its yeast ortholog NUP145 has been performed. On this basis, a DNA cassette carrying homologous tails to the two genes was amplified by PCR and allowed the targeted fusion between NUP145 and TOP2, leading to reproduce the chimeric transcript in a diploid strain of S. cerevisiae. The resulting translocated yeast obtained through BIT appears characterized by abnormal spherical bodies of nearly 500 nm of diameter, absence of external membrane and defined cytoplasmic localization. Since Nup98 is a well-known regulator of the post-transcriptional modification of P53 target genes, and P53 mutations are occasionally reported in AML, this translocant yeast strain can be used as a model to test the constitutive expression of human P53. Although the abnormal phenotype of the translocant yeast was never rescued by its expression, an exogenous P53 was recognized to confer increased vitality to the translocants, in spite of its usual and well-documented toxicity to wild-type yeast strains. These results obtained in yeast could provide new grounds for the interpretation of past observations made in leukemic patients indicating a possible involvement of P53 in cell transformation toward AML.
Collapse
Affiliation(s)
- Valentina Tosato
- Ulisse Biomed S.r.l., AREA Science Park, Trieste, Italy.,Faculty of Health Sciences, University of Primorska, Izola, Slovenia.,Yeast Molecular Genetics, ICGEB, AREA Science Park, Trieste, Italy
| | - Nicole West
- Clinical Pathology, Hospital Maggiore, Trieste, Italy
| | - Jan Zrimec
- Faculty of Health Sciences, University of Primorska, Izola, Slovenia
| | - Dmitri V Nikitin
- Biology Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Roberto Marano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Michael Breitenbach
- Genetics Division, Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Carlo V Bruschi
- Yeast Molecular Genetics, ICGEB, AREA Science Park, Trieste, Italy.,Genetics Division, Department of Cell Biology, University of Salzburg, Salzburg, Austria
| |
Collapse
|
23
|
Kivioja JL, Lopez Martí JM, Kumar A, Kontro M, Edgren H, Parsons A, Lundán T, Wolf M, Porkka K, Heckman CA. Chimeric NUP98-NSD1 transcripts from the cryptic t(5;11)(q35.2;p15.4) in adult de novo acute myeloid leukemia. Leuk Lymphoma 2017; 59:725-732. [PMID: 28776436 DOI: 10.1080/10428194.2017.1357174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The t(5;11)(q35;p15.4) is a clinically significant marker of poor prognosis in acute myeloid leukemia (AML), which is difficult to detect due to sub-telomeric localization of the breakpoints. To facilitate the detection of this rearrangement, we studied NUP98-NSD1 transcript variants in patients with the t(5;11) using paired-end RNA sequencing and standard molecular biology techniques. We discovered three NUP98-NSD1 transcripts with two fusion junctions (NUP98 exon 11-12/NSD1 exon 6), alternative 5' donor site in NUP98 exon 7, and NSD1 exon 7 skipping. Two of the transcripts were in-frame and occurred in all t(5;11) samples (N = 5). The exonic splicing events were present in all samples (N = 23) regardless of the NUP98-NSD1 suggesting that these novel splice events are unassociated with t(5;11). In conclusion, we provide evidence of two different NUP98-NSD1 fusion transcripts in adult AML, which result in functional proteins and represent suitable molecular entities for monitoring t(5;11) AML patients.
Collapse
Affiliation(s)
- Jarno L Kivioja
- a Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science , University of Helsinki , Helsinki , Finland
| | - Jesus M Lopez Martí
- a Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science , University of Helsinki , Helsinki , Finland
| | - Ashwini Kumar
- a Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science , University of Helsinki , Helsinki , Finland
| | - Mika Kontro
- b Department of Hematology , Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center , Helsinki , Finland
| | | | - Alun Parsons
- a Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science , University of Helsinki , Helsinki , Finland
| | - Tuija Lundán
- d Department of Clinical Chemistry and TYKSLAB , Turku University Central Hospital, University of Turku , Turku , Finland
| | - Maija Wolf
- a Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science , University of Helsinki , Helsinki , Finland
| | - Kimmo Porkka
- b Department of Hematology , Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center , Helsinki , Finland
| | - Caroline A Heckman
- a Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science , University of Helsinki , Helsinki , Finland
| |
Collapse
|
24
|
The functional versatility of the nuclear pore complex proteins. Semin Cell Dev Biol 2017; 68:2-9. [DOI: 10.1016/j.semcdb.2017.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/11/2017] [Indexed: 12/28/2022]
|
25
|
Sakuma S, D'Angelo MA. The roles of the nuclear pore complex in cellular dysfunction, aging and disease. Semin Cell Dev Biol 2017; 68:72-84. [PMID: 28506892 DOI: 10.1016/j.semcdb.2017.05.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/11/2017] [Indexed: 12/19/2022]
Abstract
The study of the Nuclear Pore Complex (NPC), the proteins that compose it (nucleoporins), and the nucleocytoplasmic transport that it controls have revealed an unexpected layer to pathogenic disease onset and progression. Recent advances in the study of the regulation of NPC composition and function suggest that the precise control of this structure is necessary to prevent diseases from arising or progressing. Here we discuss the role of nucleoporins in a diverse set of diseases, many of which directly or indirectly increase in occurrence and severity as we age, and often shorten the human lifespan. NPC biology has been shown to play a direct role in these diseases and therefore in the process of healthy aging.
Collapse
Affiliation(s)
- Stephen Sakuma
- Development, Aging and Regeneration Program (DARe), Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maximiliano A D'Angelo
- Development, Aging and Regeneration Program (DARe), Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
| |
Collapse
|