1
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Falini B, Sorcini D, Perriello VM, Sportoletti P. Functions of the native NPM1 protein and its leukemic mutant. Leukemia 2025; 39:276-290. [PMID: 39690184 DOI: 10.1038/s41375-024-02476-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 11/11/2024] [Accepted: 11/14/2024] [Indexed: 12/19/2024]
Abstract
The nucleophosmin (NPM1) gene encodes for the most abundant nucleolar protein. Thanks to its property to act as histone chaperone and to shuttle between the nucleus and cytoplasm, the NPM1 protein is involved in multiple cellular function that are here extensively reviewed and include the formation of the nucleolus through liquid-liquid phase separation, regulation of ribosome biogenesis and transport, control of DNA repair and centrosome duplication as well as response to nucleolar stress. NPM1 is mutated in about 30-35% of adult acute myeloid leukemia (AML). Due to its unique biological and clinical features, NPM1-mutated AML is regarded as a distinct leukemia entity in the WHO 5th edition and ICC classifications of myeloid malignancies. The NPM1 mutant undergoes changes at the C-terminus of the protein that leads to its delocalization in the cytoplasm of the leukemic cells. Here, we focus also on its biological functions discussing the murine models of NPM1 mutations and the various mechanisms that occur at cytoplasmic and nuclear levels to promote and maintain NPM1-mutated AML.
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Affiliation(s)
- Brunangelo Falini
- Institute of Hematology and Center for Hemato-Oncological research (CREO), University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy.
| | - Daniele Sorcini
- Institute of Hematology and Center for Hemato-Oncological research (CREO), University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Vincenzo Maria Perriello
- Institute of Hematology and Center for Hemato-Oncological research (CREO), University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Paolo Sportoletti
- Institute of Hematology and Center for Hemato-Oncological research (CREO), University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy
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2
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Wolfová K, Otevřelová P, Holoubek A, Brodská B. Nucleolar phosphoprotein modifications as a marker of apoptosis induced by RITA treatment. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119501. [PMID: 37276927 DOI: 10.1016/j.bbamcr.2023.119501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023]
Abstract
Reactivating p53 and Inducing Tumor Apoptosis (RITA) has been reported to increase the p53 activity and to trigger p53-dependent apoptosis in cancer cells with wild-type p53. Tumor suppressor p53 interacts with nucleolar phosphoproteins nucleophosmin (NPM) and nucleolin (NCL), which have crucial role in many cellular processes. Specific NPM mutations associated with acute myeloid leukemia (AML) cause aberrant localization of NPM and p53 in the cytoplasm with possible impact on the p53 function. We tested an effect of RITA on primary cells, and we found significant RITA-induced changes in NPM and NCL phosphorylation associated with apoptosis in cells of AML patients, but not that of healthy donors. Subsequent screening of several AML cell lines revealed heterogeneous response to RITA, and confirmed an association of the specific phosphorylation with apoptosis. While decreased NCL phosphorylation at Threonines T76 and T84 could be attributed to RITA-induced cell cycle arrest, enhanced NPM phosphorylation at Threonine T199 was not accompanied by the cell cycle changes and it correlated with sensitivity to RITA. Simultaneously, inverse changes occurred at Serine S4 of the NPM. These new findings of RITA mechanism of action could establish the NPM pT199/pS4 ratio as a marker for suitability of RITA treatment of AML cells.
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Affiliation(s)
- Kateřina Wolfová
- Department of Proteomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820 Prague 2, Czech Republic
| | - Petra Otevřelová
- Department of Proteomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820 Prague 2, Czech Republic
| | - Aleš Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820 Prague 2, Czech Republic
| | - Barbora Brodská
- Department of Proteomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820 Prague 2, Czech Republic.
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3
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Sugahara S, Haga H, Ikeda C, Makino N, Matsuda A, Kakizaki Y, Hoshikawa K, Katsumi T, Ishizawa T, Kobayashi T, Maki K, Suzuki F, Murakami R, Sato H, Ueno Y. Role of Bile-Derived Extracellular Vesicles in Hepatocellular Proliferation after Partial Hepatectomy in Rats. Int J Mol Sci 2023; 24:ijms24119230. [PMID: 37298180 DOI: 10.3390/ijms24119230] [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: 04/27/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Although liver regeneration has been extensively studied, the effects of bile-derived extracellular vesicles (bile EVs) on hepatocytes has not been elucidated. We examined the influence of bile EVs, collected from a rat model of 70% partial hepatectomy (PH), on hepatocytes. We produced bile-duct-cannulated rats. Bile was collected over time through an extracorporeal bile duct cannulation tube. Bile EVs were extracted via size exclusion chromatography. The number of EVs released into the bile per liver weight 12 h after PH significantly increased. Bile EVs collected 12 and 24 h post-PH, and after sham surgery (PH12-EVs, PH24-EVs, sham-EVs) were added to the rat hepatocyte cell line, and 24 h later, RNA was extracted and transcriptome analysis performed. The analysis revealed that more upregulated/downregulated genes were observed in the group with PH24-EVs. Moreover, the gene ontology (GO) analysis focusing on the cell cycle revealed an upregulation of 28 types of genes in the PH-24 group, including genes that promote cell cycle progression, compared to the sham group. PH24-EVs induced hepatocyte proliferation in a dose-dependent manner in vitro, whereas sham-Evs showed no significant difference compared to the controls. This study revealed that post-PH bile Evs promote the proliferation of the hepatocytes, and genes promoting cell cycles are upregulated in hepatocytes.
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Affiliation(s)
- Shinpei Sugahara
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Hiroaki Haga
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Chisaki Ikeda
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Naohiko Makino
- Yamagata University Health Administration Center, 1-4-12 Kojirakawa-Machi, Yamagata 990-8560, Japan
| | - Akiko Matsuda
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Yasuharu Kakizaki
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Kyoko Hoshikawa
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Tomohiro Katsumi
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Tetsuya Ishizawa
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Toshikazu Kobayashi
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Keita Maki
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Fumiya Suzuki
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Ryoko Murakami
- Genomic Information Analysis Unit, Department of Genomic Cohort Research, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Hidenori Sato
- Genomic Information Analysis Unit, Department of Genomic Cohort Research, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
| | - Yoshiyuki Ueno
- Department of Gastroenterology, Faculty of Medicine, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-8595, Japan
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4
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Tani I, Oikawa Y, Doi S, Janairo JIB, Kamada R, Sakaguchi K. Ribosomal protein uL30 undergoes phase separation with nucleophosmin and regulates nucleolar formation in the absence of RNA. Biochem Biophys Res Commun 2023; 642:35-40. [PMID: 36543022 DOI: 10.1016/j.bbrc.2022.12.041] [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: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The nucleolus is a membrane-less structure that exists in the nucleus of cells and plays a crucial role in ribosome biogenesis. It is known to be formed through liquid-liquid phase separation (LLPS) caused by the interaction of various nucleolar proteins and nucleic acids. Recently, many studies on LLPS with nucleolar proteins in the presence of RNA showed the importance of electrostatic interactions and cation-pi interactions among RNA and intrinsically disordered regions of proteins. However, it is reported that the initiation of nucleolar formation is RNA polymerase I-independent. The mechanism of nucleolar formation in the early stage remains obscure. In this study, we showed for the first time that the ribosomal protein uL30 and a major nucleolar protein, nucleophosmin (NPM) formed liquid droplets in vitro in the absence of RNA. The liquid droplet formation with uL30 and NPM may be derived from the interaction between the basic regions of uL30 and acidic regions of the oligomeric NPM. The knockdown of uL30 in cells significantly reduced the number of nucleoli, while it did not alter the protein level of NPM. The results showed that LLPS and nucleolar formation were affected by changes in uL30 levels. Our results suggest that the protein-protein interaction between nucleolar proteins may play an important role in nucleolar formation in the early stages when the rRNA content is very low.
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Affiliation(s)
- Itsumi Tani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yui Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Seiyo Doi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Jose Isagani B Janairo
- Department of Biology, College of Science, De La Salle University, Manila, 0922, Philippines
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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5
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Lipid Droplet Formation Is Regulated by Ser/Thr Phosphatase PPM1D via Dephosphorylation of Perilipin 1. Int J Mol Sci 2022; 23:ijms231912046. [PMID: 36233344 PMCID: PMC9569567 DOI: 10.3390/ijms231912046] [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: 08/25/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Hypertrophy and hyperplasia of white adipocytes induce obesity, leading to diseases such as type 2 diabetes and hypertension, and even cancer. Hypertrophy of white adipocytes is attributed to the excessive storage of the energy form of triglycerides in lipid droplets (LDs). LDs are fat storage organelles that maintain whole-body energy homeostasis. It is important to understand the mechanism of LD formation for the development of obesity therapy; however, the regulatory mechanisms of LD size and formation are not fully understood. In this study, we demonstrated that the PPM family phosphatase PPM1D regulates LD formation. PPM1D specific inhibitor, SL-176 significantly decreased LD formation via two different pathways: dependent of and independent of adipocyte-differentiation processes. In the mature white adipocytes after differentiation, LD formation was found to be controlled by PPM1D via dephosphorylation of Ser511 of perilipin 1. We found that inhibition of PPM1D in mature white adipocytes significantly reduced the size of the LDs via dephosphorylation of Ser511 of perilipin 1 but did not change the lipolysis sensitivity and the total amount of lipid in cells. Collectively, the results of this study provide evidence that PPM1D plays an important role in LD formation in mature adipocytes.
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6
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Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks. iScience 2022; 25:104892. [PMID: 36060052 PMCID: PMC9436757 DOI: 10.1016/j.isci.2022.104892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/03/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022] Open
Abstract
PPM1D is a p53-regulated protein phosphatase that modulates the DNA damage response (DDR) and is frequently altered in cancer. Here, we employed chemical inhibition of PPM1D and quantitative mass spectrometry-based phosphoproteomics to identify the substrates of PPM1D upon induction of DNA double-strand breaks (DSBs) by etoposide. We identified 73 putative PPM1D substrates that are involved in DNA repair, regulation of transcription, and RNA processing. One-third of DSB-induced S/TQ phosphorylation sites are dephosphorylated by PPM1D, demonstrating that PPM1D only partially counteracts ATM/ATR/DNA-PK signaling. PPM1D-targeted phosphorylation sites are found in a specific amino acid sequence motif that is characterized by glutamic acid residues, high intrinsic disorder, and poor evolutionary conservation. We identified a functionally uncharacterized protein Kanadaptin as ATM and PPM1D substrate upon DSB induction. We propose that PPM1D plays a role during the response to DSBs by regulating the phosphorylation of DNA- and RNA-binding proteins in intrinsically disordered regions. MS-based phosphoproteomic profiling of PPM1D substrates in U2OS and HCT116 cells PPM1D counteracts ATM in the cellular response to DNA double-strand breaks PPM1D target sites localize to glutamic acid-rich regions with high intrinsic disorder Kanadaptin is a putative DNA damage response factor regulated by ATM and PPM1D
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7
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Lin HW, Lee JY, Chou NL, Shih TW, Chang MS. Phosphorylation of PUF-A/PUM3 on Y259 modulates PUF-A stability and cell proliferation. PLoS One 2021; 16:e0256282. [PMID: 34407138 PMCID: PMC8372891 DOI: 10.1371/journal.pone.0256282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/03/2021] [Indexed: 01/24/2023] Open
Abstract
Human PUF-A/PUM3 is a RNA and DNA binding protein participating in the nucleolar processing of 7S to 5.8S rRNA. The nucleolar localization of PUF-A redistributes to the nucleoplasm upon the exposure to genotoxic agents in cells. However, little is known regarding the roles of PUF-A in tumor progression. Phosphoprotein database analysis revealed that Y259 phosphorylation of PUF-A is the most prevalent residue modified. Here, we reported the importance of PUF-A’s phosphorylation on Y259 in tumorigenesis. PUF-A gene was knocked out by the Crispr/Cas9 method in human cervix epithelial HeLa cells. Loss of PUF-A in HeLa cells resulted in reduced clonogenic and lower transwell invasion capacity. Introduction of PUF-AY259F to PUF-A deficient HeLa cells was unable to restore colony formation. In addition, the unphosphorylated mutant of PUF-A, PUF-AY259F, attenuated PUF-A protein stability. Our results suggest the important role of Y259 phosphorylation of PUF-A in cell proliferation.
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Affiliation(s)
- Hung-Wei Lin
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jin-Yu Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Nai-Lin Chou
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ting-Wei Shih
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Mau-Sun Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail:
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8
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Pharmacological Inhibition of WIP1 Sensitizes Acute Myeloid Leukemia Cells to the MDM2 Inhibitor Nutlin-3a. Biomedicines 2021; 9:biomedicines9040388. [PMID: 33917342 PMCID: PMC8067413 DOI: 10.3390/biomedicines9040388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022] Open
Abstract
In acute myeloid leukemia (AML), the restoration of p53 activity through MDM2 inhibition proved efficacy in combinatorial therapies. WIP1, encoded from PPM1D, is a negative regulator of p53. We evaluated PPM1D expression and explored the therapeutic efficacy of WIP1 inhibitor (WIP1i) GSK2830371, in association with the MDM2 inhibitor Nutlin-3a (Nut-3a) in AML cell lines and primary samples. PPM1D transcript levels were higher in young patients compared with older ones and in core-binding-factor AML compared with other cytogenetic subgroups. In contrast, its expression was reduced in NPM1-mutated (mut, irrespective of FLT3-ITD status) or TP53-mut cases compared with wild-type (wt) ones. Either Nut-3a, and moderately WIP1i, as single agent decreased cell viability of TP53-wt cells (MV-4-11, MOLM-13, OCI-AML3) in a time/dosage-dependent manner, but not of TP53-mut cells (HEL, KASUMI-1, NOMO-1). The drug combination synergistically reduced viability and induced apoptosis in TP53-wt AML cell line and primary cells, but not in TP53-mut cells. Gene expression and immunoblotting analyses showed increased p53, MDM2 and p21 levels in treated TP53-wt cells and highlighted the enrichment of MYC, PI3K-AKT-mTOR and inflammation-related signatures upon WIP1i, Nut-3a and their combination, respectively, in the MV-4-11 TP53-wt model. This study demonstrated that WIP1 is a promising therapeutic target to enhance Nut-3a efficacy in TP53-wt AML.
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9
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Metal-dependent Ser/Thr protein phosphatase PPM family: Evolution, structures, diseases and inhibitors. Pharmacol Ther 2020; 215:107622. [PMID: 32650009 DOI: 10.1016/j.pharmthera.2020.107622] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
Protein phosphatases and kinases control multiple cellular events including proliferation, differentiation, and stress responses through regulating reversible protein phosphorylation, the most important post-translational modification. Members of metal-dependent protein phosphatase (PPM) family, also known as PP2C phosphatases, are Ser/Thr phosphatases that bind manganese/magnesium ions (Mn2+/Mg2+) in their active center and function as single subunit enzymes. In mammals, there are 20 isoforms of PPM phosphatases: PPM1A, PPM1B, PPM1D, PPM1E, PPM1F, PPM1G, PPM1H, PPM1J, PPM1K, PPM1L, PPM1M, PPM1N, ILKAP, PDP1, PDP2, PHLPP1, PHLPP2, PP2D1, PPTC7, and TAB1, whereas there are only 8 in yeast. Phylogenetic analysis of the DNA sequences of vertebrate PPM isoforms revealed that they can be divided into 12 different classes: PPM1A/PPM1B/PPM1N, PPM1D, PPM1E/PPM1F, PPM1G, PPM1H/PPM1J/PPM1M, PPM1K, PPM1L, ILKAP, PDP1/PDP2, PP2D1/PHLPP1/PHLPP2, TAB1, and PPTC7. PPM-family members have a conserved catalytic core region, which contains the metal-chelating residues. The different isoforms also have isoform specific regions within their catalytic core domain and terminal domains, and these regions may be involved in substrate recognition and/or functional regulation of the phosphatases. The twenty mammalian PPM phosphatases are involved in regulating diverse cellular functions, such as cell cycle control, cell differentiation, immune responses, and cell metabolism. Mutation, overexpression, or deletion of the PPM phosphatase gene results in abnormal cellular responses, which lead to various human diseases. This review focuses on the structures and biological functions of the PPM-phosphatase family and their associated diseases. The development of specific inhibitors against the PPM phosphatase family as a therapeutic strategy will also be discussed.
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10
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Ogasawara S, Chuman Y, Michiba T, Kamada R, Imagawa T, Sakaguchi K. Inhibition of protein phosphatase PPM1D enhances retinoic acid-induced differentiation in human embryonic carcinoma cell line. J Biochem 2018; 165:471-477. [PMID: 30576481 DOI: 10.1093/jb/mvy119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/14/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Sari Ogasawara
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, Japan
| | - Yoshiro Chuman
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, Japan
| | - Takahiro Michiba
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, Japan
| | - Rui Kamada
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, Japan
| | - Toshiaki Imagawa
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, Japan
| | - Kazuyasu Sakaguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, Japan
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11
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Wiesmann N, Gieringer R, Grus F, Brieger J. Phosphoproteome Profiling Reveals Multifunctional Protein NPM1 as part of the Irradiation Response of Tumor Cells. Transl Oncol 2018; 12:308-319. [PMID: 30453269 PMCID: PMC6240713 DOI: 10.1016/j.tranon.2018.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 12/27/2022] Open
Abstract
To fight resistances to radiotherapy, the understanding of escape mechanisms of tumor cells is crucial. The aim of this study was to identify phosphoproteins that are regulated upon irradiation. The comparative analysis of the phosphoproteome before and after irradiation brought nucleophosmin (NPM1) into focus as a versatile phosphoprotein that has already been associated with tumorigenesis. We could show that knockdown of NPM1 significantly reduces tumor cell survival after irradiation. NPM1 is dephosphorylated stepwise within 1 hour after irradiation at two of its major phosphorylation sites: threonine-199 and threonine-234/237. This dephosphorylation is not the result of a fast cell cycle arrest, and we found a heterogenous intracellular distribution of NPM1 between the nucleoli, the nucleoplasm, and the cytoplasm after irradiation. We hypothesize that the dephosphorylation of NPM1 at threonine-199 and threonine-234/237 is part of the immediate response to irradiation and of importance for tumor cell survival. These findings could make NPM1 an attractive pharmaceutical target to radiosensitize tumor cells and improve the outcome of radiotherapy by inhibiting the pathways that help tumor cells to escape cell death after gamma irradiation.
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Affiliation(s)
- Nadine Wiesmann
- Molecular Tumor Biology, Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Centre of the Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Rita Gieringer
- Molecular Tumor Biology, Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Centre of the Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Franz Grus
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Juergen Brieger
- Molecular Tumor Biology, Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Centre of the Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany.
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12
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Bhattacharya D, Hiregange D, Rao BJ. ATR kinase regulates its attenuation via PPM1D phosphatase recruitment to chromatin during recovery from DNA replication stress signalling. J Biosci 2018; 43:25-47. [PMID: 29485113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In eukaryotes, in response to replication stress, DNA damage response kinase, ATR is activated, whose signalling abrogation leads to cell lethality due to aberrant fork remodelling and excessive origin firing. Here we report that inhibition of ATR kinase activity specifically during replication stress recovery results in persistent ATR signalling, evidenced by the presence of ATR-dependent phosphorylation marks (gamma H2AX, pChk1 and pRad17) and delayed cell cycle re-entry. Further, such disruption of ATR signalling attenuation leads to double-strand breaks, fork collapse and thereby 'replication catastrophe'. PPM1D phosphatase, a nucleolar localized protein, relocates to chromatin during replication stress and reverts back to nucleolus following stress recovery, under the control of ATR kinase action. Inhibition of ATR kinase activity, specifically during post replication stress, triggers dislodging of the chromatin-bound PPM1D from nucleus to cytoplasm followed by its degradation, thereby leading to persistence of activated ATR marks in the nuclei. Chemical inhibition of PPM1D activity or SiRNA mediated depletion of the protein during post replication stress recovery 'phenocopies' ATR kinase inhibition by failing to attenuate ATR signalling. Collectively, our observations suggest a novel role of ATR kinase in mediating its own signal attenuation via PPM1D recruitment to chromatin as an essential mechanism for restarting the stalled forks, cell-cycle re-entry and cellular recovery from replication stress.
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Affiliation(s)
- Debadrita Bhattacharya
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
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13
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Mitrea DM, Cika JA, Stanley CB, Nourse A, Onuchic PL, Banerjee PR, Phillips AH, Park CG, Deniz AA, Kriwacki RW. Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation. Nat Commun 2018; 9:842. [PMID: 29483575 PMCID: PMC5827731 DOI: 10.1038/s41467-018-03255-3] [Citation(s) in RCA: 289] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/31/2018] [Indexed: 12/20/2022] Open
Abstract
Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid-liquid phase separation (LLPS) via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes within NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process.
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Affiliation(s)
- Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jaclyn A Cika
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrative Biomedical Sciences Program, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY, 10016, USA
| | - Christopher B Stanley
- Biology and Biomedical Sciences Group, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Paulo L Onuchic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Physics, University of Buffalo, Buffalo, NY, 14260, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA.
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14
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Bhattacharya D, Hiregange D, Rao BJ. ATR kinase regulates its attenuation via PPM1D phosphatase recruitment to chromatin during recovery from DNA replication stress signalling. J Biosci 2018. [DOI: 10.1007/s12038-018-9736-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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15
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Sen Gupta A, Sengupta K. Lamin B2 Modulates Nucleolar Morphology, Dynamics, and Function. Mol Cell Biol 2017; 37:e00274-17. [PMID: 28993479 PMCID: PMC5705821 DOI: 10.1128/mcb.00274-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/05/2017] [Accepted: 09/29/2017] [Indexed: 01/11/2023] Open
Abstract
The nucleolus is required for ribosome biogenesis. Human cells have 2 or 3 nucleoli associated with nucleolar organizer region (NOR)-bearing chromosomes. An increase in number and altered nucleolar morphology define cancer cells. However, the mechanisms that modulate nucleolar morphology and function are unclear. Here we show that in addition to localizing at the nuclear envelope, lamin B2 localizes proximal to nucleolin at the granular component (GC) of the nucleolus and associates with the nucleolar proteins nucleolin and nucleophosmin. Lamin B2 knockdown severely disrupted the nucleolar morphology, which was rescued to intact and discrete nucleoli upon lamin B2 overexpression. Furthermore, two mutually exclusive lamin B2 deletion mutants, ΔHead and ΔSLS, rescued nuclear and nucleolar morphology defects, respectively, induced upon lamin B2 depletion, suggesting independent roles for lamin B2 at the nucleolus and nuclear envelope. Lamin B2 depletion increased nucleolin aggregation in the nucleoplasm, implicating lamin B2 in stabilizing nucleolin within the nucleolus. Lamin B2 knockdown upregulated nucleolus-specific 45S rRNA and upstream intergenic sequence (IGS) transcripts. The IGS transcripts colocalized with aggregates of nucleolin speckles, which were sustained in the nucleoplasm upon lamin B2 depletion. Taken together, these studies uncover a novel role for lamin B2 in modulating the morphology, dynamics, and function of the nucleolus.
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Affiliation(s)
- Ayantika Sen Gupta
- Biology, Indian Institute of Science Education and Research, Pune, India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research, Pune, India
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16
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Kamada R, Kudoh F, Yoshimura F, Tanino K, Sakaguchi K. Inhibition of Ser/Thr phosphatase PPM1D induces neutrophil differentiation in HL-60 cells. J Biochem 2017; 162:303-308. [PMID: 28486685 DOI: 10.1093/jb/mvx032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/18/2017] [Indexed: 12/21/2022] Open
Abstract
Protein phosphatase Magnesium-dependent 1, Delta (PPM1D) is a wild-type p53-inducible Ser/Thr phosphatase that acts as a negative regulator of the p53 tumor suppressor. Gene amplification and overexpression of PPM1D have been reported in various cancers including leukemia and neuroblastoma. Therefore, PPM1D is a promising target in cancer therapy. It has been reported that PPM1D knockout mice exhibit neutrophilia in blood and show a defective immune response. Here, we found that inhibition of PPM1D induced neutrophil differentiation of human promyelocytic leukemia cell line HL-60. The combination of a PPM1D inhibitor and all-trans retinoic acid significantly increased their differentiation efficiency. The PPM1D inhibitor also induced G1 arrest in HL-60 cells. Our results suggest that PPM1D may be a potential therapeutic target for blood cell diseases including leukemia.
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Affiliation(s)
- Rui Kamada
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North10, West8, Kita-ku, Sapporo 060-0810, Japan
| | - Fuki Kudoh
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North10, West8, Kita-ku, Sapporo 060-0810, Japan
| | - Fumihiko Yoshimura
- Laboratory of Organic Chemistry II, Department of Chemistry, Faculty of Science, Hokkaido University, North10, West8, Kita-ku, Sapporo 060-0810, Japan
| | - Keiji Tanino
- Laboratory of Organic Chemistry II, Department of Chemistry, Faculty of Science, Hokkaido University, North10, West8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, North10, West8, Kita-ku, Sapporo 060-0810, Japan
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