51
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Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J. In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Res 2018; 28:699-713. [PMID: 29643205 PMCID: PMC5932610 DOI: 10.1101/gr.229757.117] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/09/2018] [Indexed: 01/26/2023]
Abstract
Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF2 is central to splicing decisions, as it recognizes 3′ splice sites and recruits the spliceosome. We establish “in vitro iCLIP” experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF2 recognizes RNA sequences and how this is modulated by trans-acting RBPs. We measure U2AF2 affinities at hundreds of binding sites and compare in vitro and in vivo binding landscapes by mathematical modeling. We find that trans-acting RBPs extensively regulate U2AF2 binding in vivo, including enhanced recruitment to 3′ splice sites and clearance of introns. Using machine learning, we identify and experimentally validate novel trans-acting RBPs (including FUBP1, CELF6, and PCBP1) that modulate U2AF2 binding and affect splicing outcomes. Our study offers a blueprint for the high-throughput characterization of in vitro mRNP assembly and in vivo splicing regulation.
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Affiliation(s)
| | | | - Lu Huang
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Maximilian Bach
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Daniel Maticzka
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt a.M., Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Stefan Legewie
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
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52
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Hwang I, Cao D, Na Y, Kim DY, Zhang T, Yao J, Oh H, Hu J, Zheng H, Yao Y, Paik J. Far Upstream Element-Binding Protein 1 Regulates LSD1 Alternative Splicing to Promote Terminal Differentiation of Neural Progenitors. Stem Cell Reports 2018; 10:1208-1221. [PMID: 29606613 PMCID: PMC5998560 DOI: 10.1016/j.stemcr.2018.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 01/08/2023] Open
Abstract
Loss of a cell's ability to terminally differentiate because of mutations is a selected genetic event in tumorigenesis. Genomic analyses of low-grade glioma have reported recurrent mutations of far upstream element-binding protein 1 (FUBP1). Here, we show that FUBP1 expression is dynamically regulated during neurogenesis and that its downregulation in neural progenitors impairs terminal differentiation and promotes tumorigenesis collaboratively with expression of IDH1R132H. Mechanistically, collaborative action between SRRM4 and FUBP1 is necessary for mini-exon splicing of the neurospecific LSD1+8a isoform. LSD1+8a was downregulated upon loss of FUBP1 in neural progenitors, thereby impairing terminal neuronal differentiation and maturation. Reinforcing LSD1+8a expression in FUBP1-downregulated neural progenitors restored terminal differentiation and suppressed tumorigenesis; hence, LSD1+8a is an obligatory effector of FUBP1-dependent neuronal differentiation. These findings establish a direct role for FUBP1 in neuronal differentiation and also explain its tumor-suppressor function in the nervous system.
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Affiliation(s)
- Inah Hwang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dongqing Cao
- Neurosurgical Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
| | - Yoonmi Na
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Hwanhee Oh
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jian Hu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Hongwu Zheng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yu Yao
- Neurosurgical Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China; Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
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53
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Tsukamoto T, Nakano M, Sato R, Adachi H, Kiyota M, Kawata E, Uoshima N, Yasukawa S, Chinen Y, Mizutani S, Shimura Y, Kobayashi T, Horiike S, Yanagisawa A, Taniwaki M, Tashiro K, Kuroda J. High-risk follicular lymphomas harbour more somatic mutations including those in the AID-motif. Sci Rep 2017; 7:14039. [PMID: 29070849 PMCID: PMC5656578 DOI: 10.1038/s41598-017-14150-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/05/2017] [Indexed: 01/11/2023] Open
Abstract
We investigated clinical and genetic characteristics of high-risk follicular lymphoma (FL), that lacked evidence of large cell transformation at diagnosis, in the rituximab era. First, we retrospectively analysed the clinical features of 100 patients with non-transformed FL that were consecutively treated with rituximab-containing therapies in a discovery cohort. The presence of either peripheral blood and/or bone involvement was associated with short progression-free survival. This was confirmed in a validation cohort of 66 FL patients. Then, whole exome sequencing was performed on randomly selected 5 high- and 9 standard-risk FL tumours. The most common mutational signature was a CG > TG substitution-enriched signature associated with spontaneous deamination of 5-methylcytosine at CpG, but mutations in WA and WRC(Y) motifs (so-called activation-induced cytidine deaminase (AID) motifs) were also enriched throughout the whole exome. We found clustered mutations in target sequences of AID in the IG and BCL2 loci. Importantly, high-risk FLs harboured more somatic mutations (mean 190 vs. 138, P = 0.04), including mutations in WA (33 vs. 22, P = 0.038), WRC (34 vs. 22, P = 0.016) and WRCY motifs (17 vs. 11, P = 0.004). These results suggest that genomic instability that allows for emergence of distinct mutations through AID activity underlies development of the high-risk FL phenotype.
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Affiliation(s)
- Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuichi Sato
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroko Adachi
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Miki Kiyota
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Hematology, Matsushita Memorial Hospital, Osaka, Japan
| | - Eri Kawata
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Nobuhiko Uoshima
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Satoru Yasukawa
- Department of Surgical Pathology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shinsuke Mizutani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akio Yanagisawa
- Department of Surgical Pathology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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54
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Zhang J, Xiong X, Hua X, Cao W, Qin S, Dai L, Liang P, Zhang H, Liu Z. Knockdown of FUSE binding protein 1 enhances the sensitivity of epithelial ovarian cancer cells to carboplatin. Oncol Lett 2017; 14:5819-5824. [PMID: 29113212 PMCID: PMC5661610 DOI: 10.3892/ol.2017.6978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/11/2017] [Indexed: 12/20/2022] Open
Abstract
Epithelial ovarian cancer (EOC) affects almost 25,000 women annually and is the fifth most common malignancy in women in North America. A combination of surgery and cytotoxic chemotherapy may produce a favorable clinical response. The platinum-paclitaxel combination regimen is the chemotherapy gold-standard for advanced ovarian cancer, and carboplatin is one of the agents in this combination therapy. However, the majority of patients eventually experience a relapse due to the development of platinum resistance. FUSE binding protein 1 (FBP1) has been identified as an anti-apoptotic and pro-proliferative oncoprotein that is overexpressed in hepatocellular carcinoma. Its high expression is also associated with carboplatin resistance. In the present study, it was identified that the expression of FBP1 was significantly higher in EOC tissues than in normal epithelial ovarian or in epithelial ovarian adenoma tissue. FBP1 expression was significantly correlated with the grade of epithelial ovarian cancer. Carboplatin inhibited the expression of FBP1 in epithelial ovarian cancer cells and the knockdown of FBP1 enhanced the inhibition of cell viability and migration by carboplatin. In addition to FBP1, carboplatin also inhibited the expression of β-catenin and matrix metalloproteinase (MMP)-9. Furthermore, the expression of β-catenin and MMP-9 were lower in FBP1 knockdown cells compared with control EOC cells. FBP1 may thus serve a role in the regulation of the expression of β-catenin and MMP-9; the inhibition of β-catenin and MMP-9 by carboplatin may be mediated through the inhibition of FBP1. The inhibition of FBP1 expression by carboplatin may be a mechanism in the treatment of EOC by carboplatin.
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Affiliation(s)
- Jinli Zhang
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Xifeng Xiong
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Xing Hua
- Department of Pathology, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Wenjuan Cao
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Shengnan Qin
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Libing Dai
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Peihong Liang
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Huiling Zhang
- Department of Pharmacology, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Zhihe Liu
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
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55
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A proteomic portrait of dinoflagellate chromatin reveals abundant RNA-binding proteins. Chromosoma 2017; 127:29-43. [PMID: 28852823 DOI: 10.1007/s00412-017-0643-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 12/20/2022]
Abstract
Dinoflagellate chromatin is unique among eukaryotes, as the chromosomes are permanently condensed in a liquid crystal state instead of being packed in nucleosomes. However, how it is organized is still an unsolved mystery, in part due to the lack of a comprehensive catalog of dinoflagellate nuclear proteins. Here, we report the results of CHromatin Enrichment for Proteomics (CHEP) followed by shotgun mass spectrometry sequencing of the chromatin-associated proteins from the dinoflagellate Lingulodinum polyedra. Our analysis identified proteins involved in DNA replication and repair, transcription, and mRNA splicing, and showed a low level of contamination by proteins from other organelles. A limited number of proteins containing DNA-binding domains were found, consistent with the lack of diversity of these proteins in dinoflagellate transcriptomes. However, the number of proteins containing RNA-binding domains was unexpectedly high supporting a potential role for this type of protein in mediating gene expression and chromatin organization. We also identified a number of proteins involved in chromosome condensation and cell cycle progression as well as a single histone protein (H4). Our results provide the first detailed look at the nuclear proteins associated with the unusual chromatin structure of dinoflagellate nuclei and provide important insights into the biochemical basis of its structure and function.
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56
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The long noncoding RNA SNHG1 promotes tumor growth through regulating transcription of both local and distal genes. Oncogene 2017; 36:6774-6783. [PMID: 28825722 DOI: 10.1038/onc.2017.286] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 07/05/2017] [Accepted: 07/08/2017] [Indexed: 12/12/2022]
Abstract
Increasing evidence indicates that long noncoding RNAs (lncRNAs) have important roles in various physiological processes and dysfunction of lncRNAs could be a prevalent cause in human diseases. Here we functionally characterized the nuclear-enriched lncRNA SNHG1, which is highly expressed in multiple types of cancer. We also provide evidence that SNHG1 promotes cancer cell growth by regulating gene expression both in cis and in trans. SNHG1 was involved in the AKT signaling pathway as it promotes the neighboring transcription of the protein-coding gene SLC3A2 in cis by binding the Mediator complex to facilitate the establishment of enhancer-promoter interaction. In trans, SNHG1 directly interacted with central domain of FUBP1 and antagonize the binding of FBP-interacting repressor to FUBP1, thereby coordinating the expression of the oncogene MYC. Collectively, our findings demonstrate that lncRNA SNHG1 can function both in cis and in trans with distinct mechanisms to regulate transcription, promoting tumorigenesis and cancer progression.
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57
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Delayed Mesoderm and Erythroid Differentiation of Murine Embryonic Stem Cells in the Absence of the Transcriptional Regulator FUBP1. Stem Cells Int 2017; 2017:5762301. [PMID: 28588622 PMCID: PMC5447289 DOI: 10.1155/2017/5762301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/02/2017] [Accepted: 03/19/2017] [Indexed: 11/18/2022] Open
Abstract
The transcriptional regulator far upstream binding protein 1 (FUBP1) is essential for fetal and adult hematopoietic stem cell (HSC) self-renewal, and the constitutive absence of FUBP1 activity during early development leads to embryonic lethality in homozygous mutant mice. To investigate the role of FUBP1 in murine embryonic stem cells (ESCs) and in particular during differentiation into hematopoietic lineages, we generated Fubp1 knockout (KO) ESC clones using CRISPR/Cas9 technology. Although FUBP1 is expressed in undifferentiated ESCs and during spontaneous differentiation following aggregation into embryoid bodies (EBs), absence of FUBP1 did not affect ESC maintenance. Interestingly, we observed a delayed differentiation of FUBP1-deficient ESCs into the mesoderm germ layer, as indicated by impaired expression of several mesoderm markers including Brachyury at an early time point of ESC differentiation upon aggregation to EBs. Coculture experiments with OP9 cells in the presence of erythropoietin revealed a diminished differentiation capacity of Fubp1 KO ESCs into the erythroid lineage. Our data showed that FUBP1 is important for the onset of mesoderm differentiation and maturation of hematopoietic progenitor cells into the erythroid lineage, a finding that is supported by the phenotype of FUBP1-deficient mice.
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58
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Abstract
Drosophila genetic studies demonstrate that cell and tissue growth regulation is a primary developmental function of P-element somatic inhibitor (Psi), the sole ortholog of FUBP family RNA/DNA-binding proteins. Psi achieves growth control through interaction with Mediator, observations that should put to rest controversy surrounding Pol II transcriptional functions for these KH domain proteins.
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Affiliation(s)
- Leonie M Quinn
- a Department of Cancer Biology and Therapeutics , The John Curtin School of Medical Research, The Australian National University , Canberra , ACT , Australia
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59
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Duan J, Bao X, Ma X, Zhang Y, Ni D, Wang H, Zhang F, Du Q, Fan Y, Chen J, Wu S, Li X, Gao Y, Zhang X. Upregulation of Far Upstream Element-Binding Protein 1 (FUBP1) Promotes Tumor Proliferation and Tumorigenesis of Clear Cell Renal Cell Carcinoma. PLoS One 2017; 12:e0169852. [PMID: 28076379 PMCID: PMC5226774 DOI: 10.1371/journal.pone.0169852] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/22/2016] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE The far upstream element (FUSE)-binding protein 1 (FUBP1) is a transactivator of human c-myc proto-oncogene transcription, with important roles in carcinogenesis. However, the expression pattern and potential biological function of FUBP1 in clear cell renal cell carcinoma (ccRCC) is yet to be established. METHODS FUBP1 expression was detected in ccRCC tissues and cell lines by real-time RT-PCR, Western blot analysis, and immunohistochemistry. The correlations of FUBP1 mRNA expression levels with clinicopathological factors were evaluated. The biological function of FUBP1 during tumor cell proliferation was studied by MTS, colony formation, and soft-agar colony formation. The effects of FUBP1 on cell cycle distribution and apoptosis were analyzed by flow cytometry. Western blot analysis was used to identify the potential mechanism of FUBP1 regulating cell cycle and apoptosis. RESULTS The levels of FUBP1 mRNA and protein expression were upregulated in human ccRCC tissues compared with adjacent noncancerous tissues. High levels of FUBP1 mRNA expression were associated with higher tumor stage and tumor size. FUBP1 knockdown inhibited cell proliferation and induced cell cycle arrest and apoptosis. Meanwhile, the expression levels of c-myc and p21 mRNA were correlated with that of FUBP1 mRNA. CONCLUSIONS FUBP1 acts as a potential oncogene in ccRCC and may be considered as a novel biomarker or an attractive treatment target of ccRCC.
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Affiliation(s)
- Junyao Duan
- School of Medicine, Nankai University, Tianjin, China
| | - Xu Bao
- School of Medicine, Nankai University, Tianjin, China
| | - Xin Ma
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Yu Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Dong Ni
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Hanfeng Wang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Fan Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Qingshan Du
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Yang Fan
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Jianwen Chen
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Shengpan Wu
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Xintao Li
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Yu Gao
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
| | - Xu Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People’s Liberation Army General Hospital, PLA Medical School, Beijing, China
- * E-mail:
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60
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Venturutti L, Russo RIC, Rivas MA, Mercogliano MF, Izzo F, Oakley RH, Pereyra MG, De Martino M, Proietti CJ, Yankilevich P, Roa JC, Guzmán P, Cortese E, Allemand DH, Huang TH, Charreau EH, Cidlowski JA, Schillaci R, Elizalde PV. MiR-16 mediates trastuzumab and lapatinib response in ErbB-2-positive breast and gastric cancer via its novel targets CCNJ and FUBP1. Oncogene 2016; 35:6189-6202. [PMID: 27157613 PMCID: PMC5832962 DOI: 10.1038/onc.2016.151] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/26/2016] [Accepted: 03/24/2016] [Indexed: 12/11/2022]
Abstract
ErbB-2 amplification/overexpression accounts for an aggressive breast cancer (BC) subtype (ErbB-2-positive). Enhanced ErbB-2 expression was also found in gastric cancer (GC) and has been correlated with poor clinical outcome. The ErbB-2-targeted therapies trastuzumab (TZ), a monoclonal antibody, and lapatinib, a tyrosine kinase inhibitor, have proved highly beneficial. However, resistance to such therapies remains a major clinical challenge. We here revealed a novel mechanism underlying the antiproliferative effects of both agents in ErbB-2-positive BC and GC. TZ and lapatinib ability to block extracellular signal-regulated kinases 1/2 and phosphatidylinositol-3 kinase (PI3K)/AKT in sensitive cells inhibits c-Myc activation, which results in upregulation of miR-16. Forced expression of miR-16 inhibited in vitro proliferation in BC and GC cells, both sensitive and resistant to TZ and lapatinib, as well as in a preclinical BC model resistant to these agents. This reveals miR-16 role as tumor suppressor in ErbB-2-positive BC and GC. Using genome-wide expression studies and miRNA target prediction algorithms, we identified cyclin J and far upstream element-binding protein 1 (FUBP1) as novel miR-16 targets, which mediate miR-16 antiproliferative effects. Supporting the clinical relevance of our results, we found that high levels of miR-16 and low or null FUBP1 expression correlate with TZ response in ErbB-2-positive primary BCs. These findings highlight a potential role of miR-16 and FUBP1 as biomarkers of sensitivity to TZ therapy. Furthermore, we revealed miR-16 as an innovative therapeutic agent for TZ- and lapatinib-resistant ErbB-2-positive BC and GC.
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Affiliation(s)
- L Venturutti
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - RI Cordo Russo
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - MA Rivas
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - MF Mercogliano
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - F Izzo
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - RH Oakley
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - MG Pereyra
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
- Servicio de Anatomía Patológica, Hospital General de Agudos ‘Juan A Fernández’, Buenos Aires, Argentina
| | - M De Martino
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - CJ Proietti
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - P Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires, CONICET—Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - JC Roa
- Departamento de Anatomía Patológica (BIOREN), Universidad de La Frontera, Temuco, Chile
- Departamento de Anatomía Patológica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago de Chile, Chile
- Advanced Center for Chronic Diseases (ACCDIS), Pontificia Universidad Católica de Chile, Santiago de Chile, Santiago, Chile
| | - P Guzmán
- Departamento de Anatomía Patológica (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - E Cortese
- Servicio de Ginecología, Hospital Aeronáutico Central, Buenos Aires, Argentina
| | - DH Allemand
- Unidad de Patología Mamaria, Hospital General de Agudos ‘Juan A Fernández’, Buenos Aires, Argentina
| | - TH Huang
- Department of Molecular Medicine/Institute of Biotechnology, Cancer Therapy and Research Center, University of Texas, San Antonio, TX, USA
| | - EH Charreau
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - JA Cidlowski
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - R Schillaci
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - PV Elizalde
- Laboratory of Molecular Mechanisms of Carcinogenesis, Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
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61
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Pyrazolo[1,5 a ]pyrimidines as a new class of FUSE binding protein 1 (FUBP1) inhibitors. Bioorg Med Chem 2016; 24:5717-5729. [DOI: 10.1016/j.bmc.2016.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/13/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022]
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Tanboon J, Williams EA, Louis DN. The Diagnostic Use of Immunohistochemical Surrogates for Signature Molecular Genetic Alterations in Gliomas. J Neuropathol Exp Neurol 2016; 75:4-18. [PMID: 26671986 DOI: 10.1093/jnen/nlv009] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A number of key mutations that affect treatment and prognosis have been identified in human gliomas. Two major ways to identify these mutations in a tumor sample are direct interrogation of the mutated DNA itself and immunohistochemistry to assess the effects of the mutated genes on proteins. Immunohistochemistry is an affordable, robust, and widely available technology that has been in place for decades. For this reason, the use of immunohistochemical approaches to assess molecular genetic changes has become an essential component of state-of-the-art practice. In contrast, even though DNA sequencing technologies are undergoing rapid development, many medical centers do not have access to such methodologies and may be thwarted by the relatively high costs of sending out such tests to reference laboratories. This review summarizes the current experience using immunohistochemistry of glioma samples to identify mutations in IDH1, TP53, ATRX, histone H3 genes, BRAF, EGFR, MGMT, CIC, and FUBP1 as well as guidelines for prudent use of DNA sequencing as a supplemental method.
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Yum MK, Kang JS, Lee AE, Jo YW, Seo JY, Kim HA, Kim YY, Seong J, Lee EB, Kim JH, Han JM, Kim S, Kong YY. AIMP2 Controls Intestinal Stem Cell Compartments and Tumorigenesis by Modulating Wnt/β-Catenin Signaling. Cancer Res 2016; 76:4559-68. [PMID: 27262173 DOI: 10.1158/0008-5472.can-15-3357] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/03/2016] [Indexed: 11/16/2022]
Abstract
Wnt/β-catenin (CTNNB1) signaling is crucial for the proliferation and maintenance of intestinal stem cells (ISC), but excessive activation leads to ISC expansion and eventually colorectal cancer. Thus, negative regulators are required to maintain optimal levels of Wnt/β-catenin signaling. Aminoacyl-tRNA synthetase-interacting multifunctional proteins (AIMP) function in protein synthesis, but have also been implicated in signaling cascades affecting angiogenesis, immunity, and apoptosis. In this study, we investigated the relationship between AIMP2 and Wnt/β-catenin signaling in a murine model of intestinal homeostasis and tumorigenesis. Hemizygous deletion of Aimp2 resulted in enhanced Wnt/β-catenin signaling, increased proliferation of cryptic epithelial cells, and expansion of ISC compartments. In an Apc(Min/+) background, Aimp2 hemizygosity increased adenoma formation. Mechanistically, AIMP2 disrupted the interaction between AXIN and Dishevelled-1 (DVL1) to inhibit Wnt/β-catenin signaling by competing with AXIN. Furthermore, AIMP2 inhibited intestinal organoid formation and growth by suppressing Wnt/β-catenin signaling in an Aimp2 gene dosage-dependent manner. Collectively, our results showed that AIMP2 acts as a haploinsufficient tumor suppressor that fine-tunes Wnt/β-catenin signaling in the intestine, illuminating the regulation of ISC abundance and activity. Cancer Res; 76(15); 4559-68. ©2016 AACR.
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Affiliation(s)
- Min Kyu Yum
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jong-Seol Kang
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Al-Eum Lee
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Young-Woo Jo
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ji-Yun Seo
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Hyun-A Kim
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Yoon-Young Kim
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jinwoo Seong
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Eun Byul Lee
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ji-Hoon Kim
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jung Min Han
- Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, South Korea. College of Pharmacy, Yonsei University, Incheon, South Korea
| | - Sunghoon Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea. Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Republic of Korea. Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul, South Korea
| | - Young-Yun Kong
- Department of Biological Sciences, Seoul National University, Seoul, South Korea.
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Xiong X, Zhang J, Liang W, Cao W, Qin S, Dai L, Ye D, Liu Z. Fuse-binding protein 1 is a target of the EZH2 inhibitor GSK343, in osteosarcoma cells. Int J Oncol 2016; 49:623-8. [PMID: 27278257 DOI: 10.3892/ijo.2016.3541] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/17/2016] [Indexed: 11/05/2022] Open
Abstract
Osteosarcoma is the primary cancer of leaf tissue and is regarded as a differentiation disease caused by genetic and epigenetic changes which interrupt the osteoblast differentiation from mesenchymal stem cells. Because of its high malignancy degree and rapid development, the morbidity and mortality are high. The enhancer of zeste homolog 2 (EZH2) is a catalytic subunit of polycomb repressive complex 2 (PRC2) and has been demonstrated to be involved in a variety of biological processes, such as cell proliferation and program cell death. EZH2 impairs gene expression by catalyzing the tri-methylation of histone H3 lysine 27 (H3K27me3) which controls gene transcription epigenetically. It is reported that EZH2 expression is higher in osteosarcoma than in osteoblastoma and the highest expression of EZH2 is found in osteosarcoma with metastasis. In the past few years, several potent inhibitors of EZH2 have been discovered, and GSK343 is one of them. In this study, we found that GSK343 inhibited osteosarcoma cell viability, restrained cell cycle transition and promoted programmed cell death. GSK343 not only inhibited the expression of EZH2 and its target, c-Myc and H3K27me3, but it also inhibited fuse binding protein 1 (FBP1) expression, another c-Myc regulator. Furthermore, we found that FBP1 physically interacts with EZH2. Based on these results, we believe that GSK343 is a potential molecule for osteosarcoma clinical treatment. Other than the inhibition on EZH2-c-Myc signal pathway, we postulate that the inhibition on FBP1-c-Myc signal pathway is another potential underlying mechanism with which GSK343 inhibits osteosarcoma cell viability.
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Affiliation(s)
- Xifeng Xiong
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Jinli Zhang
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Weiguo Liang
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Wenjuan Cao
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Shengnan Qin
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Libing Dai
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Dongping Ye
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Zhihe Liu
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
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Guo L, Zaysteva O, Nie Z, Mitchell NC, Amanda Lee JE, Ware T, Parsons L, Luwor R, Poortinga G, Hannan RD, Levens DL, Quinn LM. Defining the essential function of FBP/KSRP proteins: Drosophila Psi interacts with the mediator complex to modulate MYC transcription and tissue growth. Nucleic Acids Res 2016; 44:7646-58. [PMID: 27207882 PMCID: PMC5027480 DOI: 10.1093/nar/gkw461] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/17/2016] [Indexed: 12/21/2022] Open
Abstract
Despite two decades of research, the major function of FBP-family KH domain proteins during animal development remains controversial. The literature is divided between RNA processing and transcriptional functions for these single stranded nucleic acid binding proteins. Using Drosophila, where the three mammalian FBP proteins (FBP1-3) are represented by one ortholog, Psi, we demonstrate the primary developmental role is control of cell and tissue growth. Co-IP-mass spectrometry positioned Psi in an interactome predominantly comprised of RNA Polymerase II (RNA Pol II) transcriptional machinery and we demonstrate Psi is a potent transcriptional activator. The most striking interaction was between Psi and the transcriptional mediator (MED) complex, a known sensor of signaling inputs. Moreover, genetic manipulation of MED activity modified Psi-dependent growth, which suggests Psi interacts with MED to integrate developmental growth signals. Our data suggest the key target of the Psi/MED network in controlling developmentally regulated tissue growth is the transcription factor MYC. As FBP1 has been implicated in controlling expression of the MYC oncogene, we predict interaction between MED and FBP1 might also have implications for cancer initiation and progression.
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Affiliation(s)
- Linna Guo
- School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Olga Zaysteva
- School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Zuqin Nie
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Naomi C Mitchell
- School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jue Er Amanda Lee
- School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Thomas Ware
- Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Linda Parsons
- School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Rodney Luwor
- Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Gretchen Poortinga
- Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, VIC 3002, Australia
| | - Ross D Hannan
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Parkville, VIC 3010, Australia Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra City, ACT 2600, Australia
| | - David L Levens
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Leonie M Quinn
- School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
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Samarin J, Laketa V, Malz M, Roessler S, Stein I, Horwitz E, Singer S, Dimou E, Cigliano A, Bissinger M, Falk CS, Chen X, Dooley S, Pikarsky E, Calvisi DF, Schultz C, Schirmacher P, Breuhahn K. PI3K/AKT/mTOR-dependent stabilization of oncogenic far-upstream element binding proteins in hepatocellular carcinoma cells. Hepatology 2016; 63:813-26. [PMID: 26901106 PMCID: PMC5262441 DOI: 10.1002/hep.28357] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/20/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Transcription factors of the far-upstream element-binding protein (FBP) family represent cellular pathway hubs, and their overexpression in liver cancer (hepatocellular carcinoma [HCC]) stimulates tumor cell proliferation and correlates with poor prognosis. Here we determine the mode of oncogenic FBP overexpression in HCC cells. Using perturbation approaches (kinase inhibitors, small interfering RNAs) and a novel system for rapalog-dependent activation of AKT isoforms, we demonstrate that activity of the phosphatidylinositol-4,5-biphosphate 3-kinase/AKT pathway is involved in the enrichment of nuclear FBP1 and FBP2 in liver cancer cells. In human HCC tissues, phospho-AKT significantly correlates with nuclear FBP1/2 accumulation and expression of the proliferation marker KI67. Mechanistic target of rapamycin (mTOR) inhibition or blockade of its downstream effector eukaryotic translation initiation factor 4E activity equally reduced FBP1/2 concentrations. The mTORC1 inhibitor rapamycin diminishes FBP enrichment in liver tumors after hydrodynamic gene delivery of AKT plasmids. In addition, the multikinase inhibitor sorafenib significantly reduces FBP levels in HCC cells and in multidrug resistance 2-deficient mice that develop HCC due to severe inflammation. Both FBP1/2 messenger RNAs are highly stable, with FBP2 being more stable than FBP1. Importantly, inhibition of phosphatidylinositol-4,5-biphosphate 3-kinase/AKT/mTOR signaling significantly diminishes FBP1/2 protein stability in a caspase-3/-7-dependent manner. CONCLUSION These data provide insight into a transcription-independent mechanism of FBP protein enrichment in liver cancer; further studies will have to show whether this previously unknown interaction between phosphatidylinositol-4,5-biphosphate 3-kinase/AKT/mTOR pathway activity and caspase-mediated FBP stabilization allows the establishment of interventional strategies in FBP-positive HCCs.
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Affiliation(s)
- Jana Samarin
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mona Malz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ilan Stein
- Department of Pathology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Elad Horwitz
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Stephan Singer
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Eleni Dimou
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Cigliano
- Institute of Pathology, University Medicine Greifswald, Greifswald, Germany
| | - Michaela Bissinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA
| | - Steven Dooley
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Eli Pikarsky
- Department of Pathology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Carsten Schultz
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
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Zheng W, Shen F, Hu R, Roy B, Yang J, Wang Q, Zhang F, King JC, Sergi C, Liu SM, Cordat E, Tang J, Cao Y, Ali D, Chen XZ. Far Upstream Element-Binding Protein 1 Binds the 3' Untranslated Region of PKD2 and Suppresses Its Translation. J Am Soc Nephrol 2016; 27:2645-57. [PMID: 26839368 DOI: 10.1681/asn.2015070836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/24/2015] [Indexed: 01/02/2023] Open
Abstract
Autosomal dominant polycystic kidney disease pathogenesis can be recapitulated in animal models by gene mutations in or dosage alterations of polycystic kidney disease 1 (PKD1) or PKD2, demonstrating that too much and too little PKD1/PKD2 are both pathogenic. Gene dosage manipulation has become an appealing approach by which to compensate for loss or gain of gene function, but the mechanisms controlling PKD2 expression remain incompletely characterized. In this study, using cultured mammalian cells and dual-luciferase assays, we found that the 3' untranslated region (3'UTR) of PKD2 mRNA inhibits luciferase protein expression. We then identified nucleotides 691-1044, which we called 3FI, as the 3'UTR fragment necessary for repressing the expression of luciferase or PKD2 in this system. Using a pull-down assay and mass spectrometry we identified far upstream element-binding protein 1 (FUBP1) as a 3FI-binding protein. In vitro overexpression of FUBP1 inhibited the expression of PKD2 protein but not mRNA. In embryonic zebrafish, FUBP1 knockdown (KD) by morpholino injection increased PKD2 expression and alleviated fish tail curling caused by morpholino-mediated KD of PKD2. Conversely, FUBP1 overexpression by mRNA injection significantly increased pronephric cyst occurrence and tail curling in zebrafish embryos. Furthermore, FUBP1 binds directly to eukaryotic translation initiation factor 4E-binding protein 1, indicating a link to the translation initiation complex. These results show that FUBP1 binds 3FI in the PKD2 3'UTR to inhibit PKD2 translation, regulating zebrafish disease phenotypes associated with PKD2 KD.
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Affiliation(s)
- Wang Zheng
- Membrane Protein Disease and Cancer Research Centre, Provincial Innovation Center, Hubei University of Technology, Wuhan, China; Membrane Protein Disease Research Group, Department of Physiology
| | - Fan Shen
- Membrane Protein Disease Research Group, Department of Physiology, Medical Research Center, Zhongnan Hospital, Wuhan University, Wuhan, China; and
| | - Ruikun Hu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - JungWoo Yang
- Membrane Protein Disease Research Group, Department of Physiology
| | - Qian Wang
- Membrane Protein Disease Research Group, Department of Physiology
| | - Fan Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jennifer C King
- Membrane Protein Disease Research Group, Department of Physiology
| | - Consolato Sergi
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Song-Mei Liu
- Medical Research Center, Zhongnan Hospital, Wuhan University, Wuhan, China; and
| | | | - Jingfeng Tang
- Membrane Protein Disease and Cancer Research Centre, Provincial Innovation Center, Hubei University of Technology, Wuhan, China
| | - Ying Cao
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Xing-Zhen Chen
- Membrane Protein Disease and Cancer Research Centre, Provincial Innovation Center, Hubei University of Technology, Wuhan, China; Membrane Protein Disease Research Group, Department of Physiology,
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Hong Y, Shi Y, Shang C, Xue Y, Liu Y. Influence of far upstream element binding protein 1 gene on chemotherapy sensitivity in human U251 glioblastoma cells. Arch Med Sci 2016; 12:156-62. [PMID: 26925132 PMCID: PMC4754377 DOI: 10.5114/aoms.2016.57592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 04/02/2014] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION The aim of this study was to determine the influence of the far upstream element binding protein 1 gene (FUBP1) on chemotherapy sensitivity in human U251 glioblastoma cells. MATERIAL AND METHODS Real-time polymerase chain reaction (PCR) was used to determine the expression of the FUBP1 gene in 43 cases of human brain gliomas. Western blot analysis was used to determine the inhibitory effect of RNA interference on FUBP1 gene expression. Methyl thiazolyl tetrazolium assay (MTT) and flow cytometry methods were used to determine the growth inhibitory rate and apoptosis rate of the U251 cells with FUBP1 silencing. The growth inhibitory rate and apoptosis rate were further determined after treatment of those U251 cells with cisplatin (DDP). RESULTS The expression of FUBP1 mRNA was up-regulated significantly in gliomas, 177.65% as much as in peri-cancerous tissues (p < 0.05). The expression of FUBP1 protein was inhibited significantly with siRNA-FUBP1 (p < 0.05). In FUBP1-silenced cells, the growth inhibitory rate increased from 1.4% to 29.5%, and the apoptosis rate increased from 2.68% to 5.84% (p < 0.05 for both). After treating with DDP at various concentrations (1, 3, 5 µg/ml), the growth inhibitory rate of FUBP1-silenced cells increased from 14.42%, 17.46% and 23.55% to 21.69%, 27.51% and 37.57%; the apoptosis rate increased from 8.85%, 14.37% and 18.21% to 13.25%, 18.46% and 26.52%. CONCLUSIONS The up-regulation of FUBP1 relates to the carcinogenesis of gliomas. FUBP1 silencing increases the growth inhibitory rate and apoptosis rate of the U251 cells, and enhances the chemotherapy sensitivity of U251 cells to DDP.
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Affiliation(s)
- Yang Hong
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Yu Shi
- Department of Radiology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Chao Shang
- Department of Neurobiology, China Medical University, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, China Medical University, Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
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Zhou W, Chung YJ, Parrilla Castellar ER, Zheng Y, Chung HJ, Bandle R, Liu J, Tessarollo L, Batchelor E, Aplan PD, Levens D. Far Upstream Element Binding Protein Plays a Crucial Role in Embryonic Development, Hematopoiesis, and Stabilizing Myc Expression Levels. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:701-15. [PMID: 26774856 DOI: 10.1016/j.ajpath.2015.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/29/2015] [Accepted: 10/27/2015] [Indexed: 11/27/2022]
Abstract
The transcription factor far upstream element binding protein (FBP) binds and activates the MYC promoter when far upstream element is via TFIIH helicase activity early in the transcription cycle. The fundamental biology and pathology of FBP are complex. In some tumors FBP seems pro-oncogenic, whereas in others it is a tumor suppressor. We generated an FBP knockout (Fubp1(-/-)) mouse to study FBP deficiency. FBP is embryo lethal from embryonic day 10.5 to birth. A spectrum of pathology is associated with FBP loss; besides cerebral hyperplasia and pulmonary hypoplasia, pale livers, hypoplastic spleen, thymus, and bone marrow, cardiac hypertrophy, placental distress, and small size were all indicative of anemia. Immunophenotyping of hematopoietic cells in wild-type versus knockout livers revealed irregular trilineage anemia, with deficits in colony formation. Despite normal numbers of hematopoietic stem cells, transplantation of Fubp1(-/-) hematopoietic stem cells into irradiated mice entirely failed to reconstitute hematopoiesis. In competitive transplantation assays against wild-type donor bone marrow, Fubp1(-/-) hematopoietic stem cells functioned only sporadically at a low level. Although cultures of wild-type mouse embryo fibroblasts set Myc levels precisely, Myc levels of mouse varied wildly between fibroblasts harvested from different Fubp1(-/-) embryos, suggesting that FBP contributes to Myc set point fixation. FBP helps to hold multiple physiologic processes to close tolerances, at least in part by constraining Myc expression.
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Affiliation(s)
- Weixin Zhou
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Yang Jo Chung
- Laboratory of Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | - Ying Zheng
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Hye-Jung Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Russell Bandle
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Juhong Liu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Lino Tessarollo
- Mouse Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Eric Batchelor
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Peter D Aplan
- Laboratory of Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - David Levens
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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Papandonatos GD, Pan Q, Pajewski NM, Delahanty LM, Peter I, Erar B, Ahmad S, Harden M, Chen L, Fontanillas P, Wagenknecht LE, Kahn SE, Wing RR, Jablonski KA, Huggins GS, Knowler WC, Florez JC, McCaffery JM, Franks PW. Genetic Predisposition to Weight Loss and Regain With Lifestyle Intervention: Analyses From the Diabetes Prevention Program and the Look AHEAD Randomized Controlled Trials. Diabetes 2015; 64:4312-21. [PMID: 26253612 PMCID: PMC4657576 DOI: 10.2337/db15-0441] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/04/2015] [Indexed: 12/22/2022]
Abstract
Clinically relevant weight loss is achievable through lifestyle modification, but unintentional weight regain is common. We investigated whether recently discovered genetic variants affect weight loss and/or weight regain during behavioral intervention. Participants at high-risk of type 2 diabetes (Diabetes Prevention Program [DPP]; N = 917/907 intervention/comparison) or with type 2 diabetes (Look AHEAD [Action for Health in Diabetes]; N = 2,014/1,892 intervention/comparison) were from two parallel arm (lifestyle vs. comparison) randomized controlled trials. The associations of 91 established obesity-predisposing loci with weight loss across 4 years and with weight regain across years 2-4 after a minimum of 3% weight loss were tested. Each copy of the minor G allele of MTIF3 rs1885988 was consistently associated with greater weight loss following lifestyle intervention over 4 years across the DPP and Look AHEAD. No such effect was observed across comparison arms, leading to a nominally significant single nucleotide polymorphism×treatment interaction (P = 4.3 × 10(-3)). However, this effect was not significant at a study-wise significance level (Bonferroni threshold P < 5.8 × 10(-4)). Most obesity-predisposing gene variants were not associated with weight loss or regain within the DPP and Look AHEAD trials, directly or via interactions with lifestyle.
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Affiliation(s)
| | - Qing Pan
- The Biostatistics Center, George Washington University, Rockville, MD
| | - Nicholas M Pajewski
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Linda M Delahanty
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA Department of Medicine, Harvard Medical School, Boston, MA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bahar Erar
- Center for Statistical Sciences, Brown University, Providence, RI
| | - Shafqat Ahmad
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | | | - Ling Chen
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Pierre Fontanillas
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | | | - Lynne E Wagenknecht
- Look AHEAD Coordinating Center, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Steven E Kahn
- Division of Metabolism, Endocrinology & Nutrition, Department of Medicine, VA Puget Sound Health Care System and University of Washington, Seattle, WA
| | - Rena R Wing
- Weight Control and Diabetes Research Center, The Miriam Hospital and The Warren Alpert Medical School of Brown University, Providence, RI
| | | | - Gordon S Huggins
- Center for Translational Genomics, Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA
| | - William C Knowler
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
| | - Jose C Florez
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA Department of Medicine, Harvard Medical School, Boston, MA Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Jeanne M McCaffery
- Weight Control and Diabetes Research Center, The Miriam Hospital and The Warren Alpert Medical School of Brown University, Providence, RI
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital Malmö, Malmö, Sweden Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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71
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Weber S, Haferlach C, Jeromin S, Nadarajah N, Dicker F, Noël L, Zenger M, Alpermann T, Kern W, Haferlach T, Schnittger S. Gain of chromosome 21 or amplification of chromosome arm 21q is one mechanism for increased ERG expression in acute myeloid leukemia. Genes Chromosomes Cancer 2015; 55:148-57. [PMID: 26542308 DOI: 10.1002/gcc.22321] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/19/2023] Open
Abstract
In acute myeloid leukemia (AML), acquired genomic gains and losses are common and lead to altered expression of genes located within or nearby the affected regions. Increased expression of the ETS-related transcription factor gene ERG has been described in myeloid malignancies with chromosomal rearrangements involving chromosome band 21q22, but also in cytogenetically normal AML, where it is associated with adverse prognosis. In this study, fluorescence in situ hybridization on interphase nuclei disclosed an amplification of the ERG gene (more than six copies) in 33 AML patients with structural rearrangements of 21q22. Array comparative genomic hybridization of these cases disclosed a minimal amplified region at the position 39.6-40.0 Mbp from pter that harbors ERG as the only gene. Analysis by quantitative real-time reverse transcription polymerase chain reaction revealed significantly higher ERG mRNA expression in these patients and in a group of 95 AML patients with complete or partial gain of chromosome 21 (three to six copies) compared with 351 AML patients without gain of chromosome 21. Quantification of ERG DNA copy numbers revealed a strong correlation with ERG mRNA expression. Furthermore, in patients with gain of chromosome 21, higher ERG expression was found to be associated with RUNX1 mutations. Our results suggest that acquired gain of chromosome 21 or amplification of chromosome arm 21q is one mechanism contributing to increased ERG expression in AML.
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Affiliation(s)
| | | | | | | | | | - Louisa Noël
- MLL Munich Leukemia Laboratory, Munich, Germany
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72
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Far upstream element-binding protein 1 (FUBP1) is a potential c-Myc regulator in esophageal squamous cell carcinoma (ESCC) and its expression promotes ESCC progression. Tumour Biol 2015; 37:4115-26. [PMID: 26490982 DOI: 10.1007/s13277-015-4263-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/15/2015] [Indexed: 01/12/2023] Open
Abstract
The human far upstream element (FUSE) binding protein 1 (FUBP1) belongs to an ancient family which is required for proper regulation of the c-Myc proto-oncogene. Although c-Myc plays an important role in development of various carcinomas, the relevance of FUBP1 and their contribution to esophageal squamous cell carcinoma (ESCC) development remain unclear. In this study, we aimed to investigate the relationship between FUBP1 and c-Myc as well as their contribution to ESCC development. Western blot and immunohistochemical analyses were performed to evaluate FUBP1 expression. Coimmunoprecipitation analysis was performed to explore the correlation between FUBP1 and c-Myc in ESCC. In addition, the role of FUBP1 in ESCC proliferation was studied in ESCC cells through knocking FUBP1 down. The regulation of FUBP1 on proliferation was confirmed by Cell Counting Kit-8 (CCK-8) assay, flow cytometric assays, and clone formation assays. The expressions of FUBP1 and c-Myc were both upregulated in ESCC tissues. In addition to correlation between expression of FUBP1 and tumor grade, we also confirmed the correlation of FUBP1, c-Myc, and Ki-67 expression by twos. Moreover, upregulation of FUBP1 and c-Myc in ESCC was associated with poor survival. FUBP1 was confirmed to activate c-Myc in ESCC tissues and cells. FUBP1 was demonstrated to promote proliferation of ESCC cells. Moreover, downregulation of both FUBP1 and c-Myc was confirmed to inhibit proliferation of ESCC cells. Our results indicated that FUBP1 may potentially stimulate c-Myc expression in ESCC and its expression may promote ESCC progression.
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73
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Liu ZH, Hu JL, Liang JZ, Zhou AJ, Li MZ, Yan SM, Zhang X, Gao S, Chen L, Zhong Q, Zeng MS. Far upstream element-binding protein 1 is a prognostic biomarker and promotes nasopharyngeal carcinoma progression. Cell Death Dis 2015; 6:e1920. [PMID: 26469968 PMCID: PMC4632288 DOI: 10.1038/cddis.2015.258] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/20/2015] [Accepted: 07/20/2015] [Indexed: 02/06/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor with tremendous invasion and metastasis capacities, and it has a high incidence in southeast Asia and southern China. Previous studies identified that far upstream element-binding protein 1 (FBP1), a transcriptional regulator of c-Myc that is one of the most frequently aberrantly expressed oncogenes in various human cancers, including NPC, is an important biomarker for many cancers. Our study aimed to investigate the expression and function of FBP1 in human NPC. Quantitative real-time RT-PCR (qRT-PCR), western blot and immunohistochemical staining (IHC) were performed in NPC cells and biopsies. Furthermore, the effect of FBP1 knockdown on cell proliferation, colony formation, side population tests and tumorigenesis in nude mice were measured by MTT, clonogenicity analysis, flow cytometry and a xenograft model, respectively. The results showed that the mRNA and protein levels of FBP1, which are positively correlated with c-Myc expression, were substantially higher in NPC than that in nasopharyngeal epithelial cells. IHC revealed that the patients with high FBP1 expression had a significantly poorer prognosis compared with the patients with low expression (P=0.020). In univariate analysis, high FBP1 and c-Myc expression predicted poorer overall survival (OS) and poorer progression-free survival. Multivariate analysis indicated that high FBP1 and c-Myc expression were independent prognostic markers. Knockdown of FBP1 reduced cell proliferation, clonogenicity and the ratio of side populations, as well as tumorigenesis in nude mice. These data indicate that FBP1 expression, which is closely correlated with c-Myc expression, is an independent prognostic factor and promotes NPC progression. Our results suggest that FBP1 can not only serve as a useful prognostic biomarker for NPC but also as a potential therapeutic target for NPC patients.
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Affiliation(s)
- Z-H Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China.,Collaborative Innovation Center of Cancer Medicine, National Institute of Biological Sciences, Beijing, China
| | - J-L Hu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - J-Z Liang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - A-J Zhou
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - M-Z Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - S-M Yan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - X Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - S Gao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - L Chen
- Collaborative Innovation Center of Cancer Medicine, National Institute of Biological Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Q Zhong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - M-S Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
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74
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Mutations driving CLL and their evolution in progression and relapse. Nature 2015; 526:525-30. [PMID: 26466571 PMCID: PMC4815041 DOI: 10.1038/nature15395] [Citation(s) in RCA: 758] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 08/11/2015] [Indexed: 01/05/2023]
Abstract
Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. We identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized cancer drivers (RPS15, IKZF3) and collectively identify RNA processing and export, MYC activity and MAPK signaling as central pathways involved in CLL. Clonality analysis of this large dataset further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing datasets of clinically informative samples enable the discovery of novel cancer genes and the network of relationships between the driver events and their impact on disease relapse and clinical outcome.
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75
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Störchel PH, Thümmler J, Siegel G, Aksoy-Aksel A, Zampa F, Sumer S, Schratt G. A large-scale functional screen identifies Nova1 and Ncoa3 as regulators of neuronal miRNA function. EMBO J 2015; 34:2237-54. [PMID: 26105073 DOI: 10.15252/embj.201490643] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/20/2015] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of neuronal development, network connectivity, and synaptic plasticity. While many neuronal miRNAs were previously shown to modulate neuronal morphogenesis, little is known regarding the regulation of miRNA function. In a large-scale functional screen, we identified two novel regulators of neuronal miRNA function, Nova1 and Ncoa3. Both proteins are expressed in the nucleus and the cytoplasm of developing hippocampal neurons. We found that Nova1 and Ncoa3 stimulate miRNA function by different mechanisms that converge on Argonaute (Ago) proteins, core components of the miRNA-induced silencing complex (miRISC). While Nova1 physically interacts with Ago proteins, Ncoa3 selectively promotes the expression of Ago2 at the transcriptional level. We further show that Ncoa3 regulates dendritic complexity and dendritic spine maturation of hippocampal neurons in a miRNA-dependent fashion. Importantly, both the loss of miRNA activity and increased dendrite complexity upon Ncoa3 knockdown were rescued by Ago2 overexpression. Together, we uncovered two novel factors that control neuronal miRISC function at the level of Ago proteins, with possible implications for the regulation of synapse development and plasticity.
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Affiliation(s)
- Peter H Störchel
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Juliane Thümmler
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Gabriele Siegel
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Ayla Aksoy-Aksel
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Federico Zampa
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Simon Sumer
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Gerhard Schratt
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
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76
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Idbaih A, Duran-Peña A, Bonnet C, Ducray F. Input of molecular analysis in medical management of primary brain tumor patients. Rev Neurol (Paris) 2015; 171:457-65. [PMID: 26026669 DOI: 10.1016/j.neurol.2015.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 03/22/2015] [Accepted: 04/10/2015] [Indexed: 01/04/2023]
Abstract
Primary brain tumors comprise a large group of malignant and non-malignant tumors including heterogeneous entities with various biological and clinical behaviors. Up till recently, diagnosis of brain cancers, that drives treatment decision-making, was based on integration of clinical, radiological and pathological features of patients and tumors. Over the last years, practical neuro-oncology has entered an era of molecular-based personalized medicine. Indeed, molecular features of tumors provide critical information to physicians for daily clinical management of patients and for design of relevant clinical research. Sporadic gliomas or glial tumors are the most common primary brain tumors in adults. Recently, their medical management has been revolutionized by molecular data. Indeed, optimal therapeutic management of grade III glioma patients now requires assessment of chromosome arms 1p/19q copy number and IDH mutational statuses as predictive and prognostic biomarkers. Indeed, two large phase III clinical trials have demonstrated that early chemotherapy plus radiotherapy, versus radiotherapy alone, doubles median overall survival of patients suffering from 1p/19q co-deleted and/or IDH mutated anaplastic oligodendroglial tumor. Interestingly, both biomarkers have been identified in a large proportion of WHO grade II gliomas. Their clinical value, in this population, is under investigation through multiple phase III clinical trials. In sporadic WHO grade I gliomas, and specifically in pilocytic astrocytomas, MAPK signaling pathway activation is a frequent event, mainly due to genetic alterations involving BRAF gene. This characteristic opens new therapeutic perspectives using MAPK signaling pathway inhibitors. Finally, in the most aggressive gliomas, WHO grade IV gliomas, two critical biomarkers have been identified: (i) MGMT promoter methylation associated with longer survival and better response to chemotherapy and (ii) IDH mutations predicting better prognosis. Although, further studies are needed, MGMT promoter methylation will undoubtedly be transferred soon to clinical practice. Molecular characteristics are beginning to be valuable and indispensable in neuro-oncology for better management of brain tumors patients. The near future will be marked by identification of novel molecular biomarkers and their validation for clinical practice.
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Affiliation(s)
- A Idbaih
- AP-HP, Hopital Universitaire La Pitié-Salpêtrière, Service de neurologie 2-Mazarin, 47-83, boulevard de l'Hôpital, 75013 Paris, France; Sorbonne Universités, UPMC Université Paris 06, UM 75, ICM, 47, boulevard de l'Hôpital, 75013 Paris, France; Inserm, U 1127, ICM, 47, boulevard de l'Hôpital, 75013 Paris, France; CNRS, UMR 7225, ICM, 47, boulevard de l'Hôpital, 75013 Paris, France; ICM, 47, boulevard de l'Hôpital, 75013 Paris, France.
| | - A Duran-Peña
- AP-HP, Hopital Universitaire La Pitié-Salpêtrière, Service de neurologie 2-Mazarin, 47-83, boulevard de l'Hôpital, 75013 Paris, France; Sorbonne Universités, UPMC Université Paris 06, UM 75, ICM, 47, boulevard de l'Hôpital, 75013 Paris, France; Inserm, U 1127, ICM, 47, boulevard de l'Hôpital, 75013 Paris, France; CNRS, UMR 7225, ICM, 47, boulevard de l'Hôpital, 75013 Paris, France; ICM, 47, boulevard de l'Hôpital, 75013 Paris, France
| | - C Bonnet
- Service de Neuro-oncologie, Hôpital Neurologique, Hospices Civils de Lyon, 3, quai des Célestins, 69002 Lyon, France; Université Claude-Bernard Lyon 1, 43, boulevard du 11 Novembre 1918, 69100 Villeurbanne, France
| | - F Ducray
- Service de Neuro-oncologie, Hôpital Neurologique, Hospices Civils de Lyon, 3, quai des Célestins, 69002 Lyon, France; Université Claude-Bernard Lyon 1, 43, boulevard du 11 Novembre 1918, 69100 Villeurbanne, France
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77
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FUSE Binding Protein 1 Facilitates Persistent Hepatitis C Virus Replication in Hepatoma Cells by Regulating Tumor Suppressor p53. J Virol 2015; 89:7905-21. [PMID: 25995247 DOI: 10.1128/jvi.00729-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/14/2015] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) is a leading cause of chronic hepatitis C (CHC), liver cirrhosis, and hepatocellular carcinoma (HCC). Immunohistochemistry of archived HCC tumors showed abundant FBP1 expression in HCC tumors with the CHC background. Oncomine data analysis of normal versus HCC tumors with the CHC background indicated a 4-fold increase in FBP1 expression with a concomitant 2.5-fold decrease in the expression of p53. We found that FBP1 promotes HCV replication by inhibiting p53 and regulating BCCIP and TCTP, which are positive and negative regulators of p53, respectively. The severe inhibition of HCV replication in FBP1-knockdown Huh7.5 cells was restored to a normal level by downregulation of either p53 or BCCIP. Although p53 in Huh7.5 cells is transcriptionally inactive as a result of Y220C mutation, we found that the activation and DNA binding ability of Y220C p53 were strongly suppressed by FBP1 but significantly activated upon knockdown of FBP1. Transient expression of FBP1 in FBP1 knockdown cells fully restored the control phenotype in which the DNA binding ability of p53 was strongly suppressed. Using electrophoretic mobility shift assay (EMSA) and isothermal titration calorimetry (ITC), we found no significant difference in in vitro target DNA binding affinity of recombinant wild-type p53 and its Y220C mutant p53. However, in the presence of recombinant FBP1, the DNA binding ability of p53 is strongly inhibited. We confirmed that FBP1 downregulates BCCIP, p21, and p53 and upregulates TCTP under radiation-induced stress. Since FBP1 is overexpressed in most HCC tumors with an HCV background, it may have a role in promoting persistent virus infection and tumorigenesis. IMPORTANCE It is our novel finding that FUSE binding protein 1 (FBP1) strongly inhibits the function of tumor suppressor p53 and is an essential host cell factor required for HCV replication. Oncomine data analysis of a large number of samples has revealed that overexpression of FBP1 in most HCC tumors with chronic hepatitis C is significantly linked with the decreased expression level of p53. The most significant finding is that FBP1 not only physically interacts with p53 and interferes with its binding to the target DNA but also functions as a negative regulator of p53 under cellular stress. FBP1 is barely detectable in normal differentiated cells; its overexpression in HCC tumors with the CHC background suggests that FBP1 has an important role in promoting HCV infection and HCC tumors by suppressing p53.
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Abstract
Low-grade gliomas (LGG) constitute grades I and II tumors of astrocytic and grade II tumors of oligodendroglial lineage. Although these tumors are typically slow growing, they may be associated with significant morbidity and mortality because of recurrence and malignant progression, even in the setting of optimal resection. LGG in pediatric and adult age groups are currently classified by morphologic criteria. Recent years have heralded a molecular revolution in understanding brain tumors, including LGG. Next-generation sequencing has definitively demonstrated that pediatric and adult LGG fundamentally differ in their underlying molecular characteristics, despite being histologically similar. Pediatric LGG show alterations in FGFR1 and BRAF in pilocytic astrocytomas and FGFR1 alterations in diffuse astrocytomas, each converging on the mitogen-activated protein kinase signaling pathway. Adult LGG are characterized by IDH1/2 mutations and ATRX mutations in astrocytic tumors and IDH1/2 mutations and 1p/19q codeletions in oligodendroglial tumors. TERT promoter mutations are also noted in LGG and are mainly associated with oligodendrogliomas. These findings have considerably refined approaches to classifying these tumors. Moreover, many of the molecular alterations identified in LGG directly impact on prognosis, tumor biology, and the development of novel therapies.
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79
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Rahmutulla B, Matsushita K, Satoh M, Seimiya M, Tsuchida S, Kubo S, Shimada H, Ohtsuka M, Miyazaki M, Nomura F. Alternative splicing of FBP-interacting repressor coordinates c-Myc, P27Kip1/cyclinE and Ku86/XRCC5 expression as a molecular sensor for bleomycin-induced DNA damage pathway. Oncotarget 2015; 5:2404-17. [PMID: 24811221 PMCID: PMC4058014 DOI: 10.18632/oncotarget.1650] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The far-upstream element-binding protein-interacting repressor (FIR) is a c-myc transcriptional suppressor. FIR is alternatively spliced to lack the transcriptional repression domain within exon 2 (FIRΔexon2) in colorectal cancers. FIR and FIRΔexon2 form homo- or heterodimers that complex with SAP155. SAP155, a subunit of the essential splicing factor 3b subcomplex in the spliceosome, is required for proper P27Kip1 pre-mRNA splicing, and P27Kip1 arrests cells at G1. In contrast, FIR was co-immunoprecipitated with Ku86 and DNA-PKcs. siRNA against Ku86/Ku70 decreased FIR and P27Kip1 expression, whereas siRNA against FIR decreased Ku86/XRCC5 and P27Kip1 expression. Thus the mechanical interaction of FIR/FIRΔexon2/SAP155 bridges c-myc and P27Kip1 expression, potentially integrates cell-cycle progression and c-myc transcription in cell. Bleomycin (BLM) is an anticancer agent that introduces DNA breaks. Because DNA breaks generate the recruitment of Ku86/Ku70 to bind to the broken DNA ends, the possible involvement of FIR and Ku86/Ku70 interaction in the BLM-induced DNA damage repair response was investigated in this study. First, BLM treatment reduced SAP155 expression and increased FIR and FIRΔexon2 mRNA expression as well as the ratio of FIRΔexon2:FIR in hepatoblastoma cells (HLE and HLF). Second, FIR or FIRΔexon2 adenovirus vectors (Ad-FIR or Ad-FIRΔexon2) increased Ku86/Ku70 and P27Kip1 expression in vitro. Third, BLM decreased P27Kip1 protein expression, whereas increased P27Kip1 and γH2AX expression with Ad-FIRΔexon2. Together, the interaction of FIR/SAP155 modulates FIR splicing and involves in cell-cycle control or cell fate via P27Kip1 and c-myc in BLM-induced DNA damage pathway. This novel function of FIR splicing will contribute to clinical studies of cancer management through elucidating the mechanical interaction of FIR/FIRΔexon2/SAP155 as a potential target for cancer treatment.
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Affiliation(s)
- Bahityar Rahmutulla
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba City, Chiba, Japan
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Miro J, Laaref AM, Rofidal V, Lagrafeuille R, Hem S, Thorel D, Méchin D, Mamchaoui K, Mouly V, Claustres M, Tuffery-Giraud S. FUBP1: a new protagonist in splicing regulation of the DMD gene. Nucleic Acids Res 2015; 43:2378-89. [PMID: 25662218 PMCID: PMC4344520 DOI: 10.1093/nar/gkv086] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We investigated the molecular mechanisms for in-frame skipping of DMD exon 39 caused by the nonsense c.5480T>A mutation in a patient with Becker muscular dystrophy. RNase-assisted pull down assay coupled with mass spectrometry revealed that the mutant RNA probe specifically recruits hnRNPA1, hnRNPA2/B1 and DAZAP1. Functional studies in a human myoblast cell line transfected with DMD minigenes confirmed the splicing inhibitory activity of hnRNPA1 and hnRNPA2/B1, and showed that DAZAP1, also known to activate splicing, acts negatively in the context of the mutated exon 39. Furthermore, we uncovered that recognition of endogenous DMD exon 39 in muscle cells is promoted by FUSE binding protein 1 (FUBP1), a multifunctional DNA- and RNA-binding protein whose role in splicing is largely unknown. By serial deletion and mutagenesis studies in minigenes, we delineated a functional intronic splicing enhancer (ISE) in intron 38. FUBP1 recruitment to the RNA sequence containing the ISE was established by RNA pull down and RNA EMSA, and further confirmed by RNA-ChIP on endogenous DMD pre-mRNA. This study provides new insights about the splicing regulation of DMD exon 39, highlighting the emerging role of FUBP1 in splicing and describing the first ISE for constitutive exon inclusion in the mature DMD transcript.
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Affiliation(s)
- Julie Miro
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
| | - Abdelhamid Mahdi Laaref
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
| | - Valérie Rofidal
- UR1199 Laboratoire de Protéomique Fonctionnelle, INRA, 34060 Montpellier cedex, France
| | - Rosyne Lagrafeuille
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
| | - Sonia Hem
- UR1199 Laboratoire de Protéomique Fonctionnelle, INRA, 34060 Montpellier cedex, France
| | - Delphine Thorel
- CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, F-34000 Montpellier, France
| | - Déborah Méchin
- CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, F-34000 Montpellier, France
| | - Kamel Mamchaoui
- Institut de Myologie, UM76 Université Pierre et Marie Curie (UPMC), Paris, France INSERM U 974, Paris, France CNRS UMR 7215, Paris, France
| | - Vincent Mouly
- Institut de Myologie, UM76 Université Pierre et Marie Curie (UPMC), Paris, France INSERM U 974, Paris, France CNRS UMR 7215, Paris, France
| | - Mireille Claustres
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, F-34000 Montpellier, France
| | - Sylvie Tuffery-Giraud
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
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Dixit U, Liu Z, Pandey AK, Kothari R, Pandey VN. Fuse binding protein antagonizes the transcription activity of tumor suppressor protein p53. BMC Cancer 2014; 14:925. [PMID: 25487856 PMCID: PMC4295397 DOI: 10.1186/1471-2407-14-925] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/01/2014] [Indexed: 01/03/2023] Open
Abstract
Background FUSE binding protein1 (FBP1) is a transactivator of transcription of human c-myc proto-oncogene and expressed mainly in undifferentiated cells. It is also present in differentiated normal cells albeit with very low background. FBP1 is abundantly expressed in the majority of hepatocellular carcinoma tumors and has been implicated in tumor development. Although it down-regulates the expression of proapoptotic p21 protein, it is not known whether FBP1 also interacts and antagonizes the function of tumor suppressor protein p53. Methods Western blotting was carried out to detect the expression level of FBP1, p21 and p53, and also p53 regulatory factors, BCCIP and TCTP; real-time quantitative PCR was done to determine the fold change in mRNA levels of target proteins; immunoprecipitation was carried out to determine the interaction of FBP1 with p53, BCCIP and TCTP. Cells stably knockdown for either FBP1; p53 or BCCIP were examined for p53 reporter activity under normal and radiation-induced stress. Results FBP1 physically interacted with p53, impairing its transcription activity and reducing p53-mediated sensitivity to cellular stress. Knockdown of FBP1 expression activated p53-mediated response to cellular stress while transient expression of FBP1 in FBP-knockdown cells restored the inhibition of p53 activity. FBP1 not only interacted with both BCCIP and TCTP, which, respectively, function as positive and negative regulators of p53, but also regulated their expression under cellular stress. In FBP knockdown cells, TCTP expression was down-regulated under radiation-induced stress whereas expression of BCCIP and p21 were significantly up-regulated suggesting FBP1 as a potential regulator of these proteins. We hypothesize that the FBP1-mediated suppression of p53 activity may occur via preventing the interaction of p53 with BCCIP as well as by FBP1-mediated regulation of p53 regulatory proteins, TCTP and BCCIP. Since FBP1 suppresses p53 activity and is overexpressed in most HCC tumors, it may have a possible role in tumorigenesis. Conclusion FBP1 physically interacts with p53, functions as a regulator of p53-regulatory proteins (TCTP and BCCIP), and suppresses p53 transactivation activity under radiation-induced cellular stress. Since it is abundantly expressed in most HCC tumors, it may have implication in tumorigenesis and thus may be a possible target for drug development.
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Affiliation(s)
| | | | | | | | - Virendra N Pandey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Rutgers University, 185 South Orange Avenue, Newark, NJ 07103, USA.
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Malz M, Bovet M, Samarin J, Rabenhorst U, Sticht C, Bissinger M, Roessler S, Bermejo JL, Renner M, Calvisi DF, Singer S, Ganzinger M, Weber A, Gretz N, Zörnig M, Schirmacher P, Breuhahn K. Overexpression of far upstream element (FUSE) binding protein (FBP)-interacting repressor (FIR) supports growth of hepatocellular carcinoma. Hepatology 2014; 60:1241-50. [PMID: 24824848 DOI: 10.1002/hep.27218] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/09/2014] [Indexed: 12/24/2022]
Abstract
UNLABELLED The far upstream element binding protein (FBP) and the FBP-interacting repressor (FIR) represent molecular tools for transcriptional fine tuning of target genes. Strong overexpression of FBP in human hepatocellular carcinoma (HCC) supports tumor growth and correlates with poor patient prognosis. However, the role of the transcriptional repressor FIR in hepatocarcinogenesis remains poorly delineated. We show that overexpression of FIR correlates with tumor dedifferentiation and tumor cell proliferation in about 60% of primary HCCs. Elevated FIR levels are associated with genomic gains of the FIR gene locus at chromosome 8q24.3 in human HCC specimens. In vitro, nuclear enrichment of FIR supports HCC cell proliferation and migration. Expression profiling of HCC cells after small interfering RNA (siRNA)-mediated silencing of FIR identified the transcription factor DP-1 (TFDP1) as a transcriptional target of FIR. Surprisingly, FIR stimulates the expression of FBP in a TFDP1/E2F1-dependent manner. FIR splice variants lacking or containing exon 2 and/or exon 5 are expressed in the majority of HCCs but not in normal hepatocytes. Specific inhibition of FIR isoforms with and without exon 2 revealed that both groups of FIR splice variants facilitate tumor-supporting effects. This finding was confirmed in xenograft transplantation experiments with lentiviral-infected short hairpin RNA (shRNA) targeting all FIR variants as well as FIR with and without exon 2. CONCLUSION High-level nuclear FIR does not facilitate repressor properties but supports tumor growth in HCC cells. Thus, the pharmacological inhibition of FIR might represent a promising therapeutic strategy for HCC patients with elevated FIR expression.
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Affiliation(s)
- Mona Malz
- Institute of Pathology, University Hospital Heidelberg, Germany
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84
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Lu YC, Chen CN, Chu CY, Lu J, Wang BJ, Chen CH, Huang MC, Lin TH, Pan CC, Chen SSA, Hsu WM, Liao YF, Wu PY, Hsia HY, Chang CC, Lee H. Calreticulin activates β1 integrin via fucosylation by fucosyltransferase 1 in J82 human bladder cancer cells. Biochem J 2014; 460:69-78. [PMID: 24593306 DOI: 10.1042/bj20131424] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fucosylation regulates various pathological events in cells. We reported that different levels of CRT (calreticulin) affect the cell adhesion and metastasis of bladder cancer. However, the precise mechanism of tumour metastasis regulated by CRT remains unclear. Using a DNA array, we identified FUT1 (fucosyltransferase 1) as a gene regulated by CRT expression levels. CRT regulated cell adhesion through α1,2-linked fucosylation of β1 integrin and this modification was catalysed by FUT1. To clarify the roles for FUT1 in bladder cancer, we transfected the human FUT1 gene into CRT-RNAi stable cell lines. FUT1 overexpression in CRT-RNAi cells resulted in increased levels of β1 integrin fucosylation and rescued cell adhesion to type-I collagen. Treatment with UEA-1 (Ulex europaeus agglutinin-1), a lectin that recognizes FUT1-modified glycosylation structures, did not affect cell adhesion. In contrast, a FUT1-specific fucosidase diminished the activation of β1 integrin. These results indicated that α1,2-fucosylation of β1 integrin was not involved in integrin-collagen interaction, but promoted β1 integrin activation. Moreover, we demonstrated that CRT regulated FUT1 mRNA degradation at the 3'-UTR. In conclusion, the results of the present study suggest that CRT stabilized FUT1 mRNA, thereby leading to an increase in fucosylation of β1 integrin. Furthermore, increased fucosylation levels activate β1 integrin, rather than directly modifying the integrin-binding sites.
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Affiliation(s)
- Yi-Chien Lu
- *Department of Life Science, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | | | | | - Jenher Lu
- ∥Department of Pediatrics and Pediatric Cardiology, Taipei Veterans General Hospital 112, Taiwan, Republic of China
| | - Bo-Jeng Wang
- ¶Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
| | - Chia-Hua Chen
- **Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei 106, Taiwan, Republic of China
| | - Min-Chuan Huang
- **Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei 106, Taiwan, Republic of China
| | - Tsui-Hwa Lin
- *Department of Life Science, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Chin-Chen Pan
- ††Department of Pathology, Taipei Veterans General Hospital 112, Taiwan, Republic of China
| | - Swey-Shen Alex Chen
- ‡‡Department of Molecular Biology, the Scripps Research Institute, San Diego, CA 92037, U.S.A
| | - Wen-Ming Hsu
- §Department of Surgery, National Taiwan University Hospital and College of Medicine, Taipei 100, Taiwan, Republic of China
| | - Yung-Feng Liao
- ¶Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
| | - Pei-Yi Wu
- *Department of Life Science, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Hsin-Yi Hsia
- *Department of Life Science, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Cheng-Chi Chang
- §§Graduate Institute of Oral Biology, School of Dentistry, National Taiwan University, Taipei 100, Taiwan, Republic of China
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85
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Kustatscher G, Hégarat N, Wills KLH, Furlan C, Bukowski-Wills JC, Hochegger H, Rappsilber J. Proteomics of a fuzzy organelle: interphase chromatin. EMBO J 2014; 33:648-64. [PMID: 24534090 PMCID: PMC3983682 DOI: 10.1002/embj.201387614] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 12/30/2022] Open
Abstract
Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology.
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Affiliation(s)
- Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | - Nadia Hégarat
- Genome Damage and Stability Centre, University of SussexBrighton, UK
| | - Karen L H Wills
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | - Cristina Furlan
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | | | - Helfrid Hochegger
- Genome Damage and Stability Centre, University of SussexBrighton, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
- Department of Biotechnology, Technische Universität BerlinBerlin, Germany
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86
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Dickey TH, Altschuler SE, Wuttke DS. Single-stranded DNA-binding proteins: multiple domains for multiple functions. Structure 2014; 21:1074-84. [PMID: 23823326 DOI: 10.1016/j.str.2013.05.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/15/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The recognition of single-stranded DNA (ssDNA) is integral to myriad cellular functions. In eukaryotes, ssDNA is present stably at the ends of chromosomes and at some promoter elements. Furthermore, it is formed transiently by several cellular processes including telomere synthesis, transcription, and DNA replication, recombination, and repair. To coordinate these diverse activities, a variety of proteins have evolved to bind ssDNA in a manner specific to their function. Here, we review the recognition of ssDNA through the analysis of high-resolution structures of proteins in complex with ssDNA. This functionally diverse set of proteins arises from a limited set of structural motifs that can be modified and arranged to achieve distinct activities, including a range of ligand specificities. We also investigate the ways in which these domains interact in the context of large multidomain proteins/complexes. These comparisons reveal the structural features that define the range of functions exhibited by these proteins.
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Affiliation(s)
- Thayne H Dickey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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87
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Zaman S, Sukhodolets K, Wang P, Qin J, Levens D, Agarwal SK, Marx SJ. FBP1 Is an Interacting Partner of Menin. Int J Endocrinol 2014; 2014:535401. [PMID: 25132853 PMCID: PMC4123598 DOI: 10.1155/2014/535401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 12/16/2022] Open
Abstract
Multiple endocrine neoplasia type 1 (MEN1) is a syndrome characterized by tumors in multiple endocrine tissues such as the parathyroid glands, the pituitary gland, and the enteropancreatic neuroendocrine tissues. MEN1 is usually caused by mutations in the MEN1 gene that codes for the protein menin. Menin interacts with proteins that regulate transcription, DNA repair and processing, and maintenance of cytoskeletal structure. We describe the identification of FBP1 as an interacting partner of menin in a large-scale pull-down assay that also immunoprecipitated RBBP5, ASH2, and LEDGF, which are members of complex proteins associated with SET1 (COMPASS), a protein complex that methylates histone H3. This interaction was confirmed by coimmunoprecipitation and Flag-pull-down assays. Furthermore, menin localized to the FUSE site on the MYC promoter, a site that is transactivated by FBP1. This investigation therefore places menin in a pathway that regulates MYC gene expression and has important implications for the biological function of menin.
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Affiliation(s)
- Shadia Zaman
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Building 10, Room 9C-103, 9000 Rockville, Bethesda, MD 20892, USA
| | - Karen Sukhodolets
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Building 10, Room 9C-103, 9000 Rockville, Bethesda, MD 20892, USA
| | - Patricia Wang
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Building 10, Room 9C-103, 9000 Rockville, Bethesda, MD 20892, USA
| | - Jun Qin
- Departments of Biochemistry & Molecular Biology and Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sunita K. Agarwal
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Building 10, Room 9C-103, 9000 Rockville, Bethesda, MD 20892, USA
| | - Stephen J. Marx
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Building 10, Room 9C-103, 9000 Rockville, Bethesda, MD 20892, USA
- *Stephen J. Marx:
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88
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Eisenreich S, Abou-El-Ardat K, Szafranski K, Campos Valenzuela JA, Rump A, Nigro JM, Bjerkvig R, Gerlach EM, Hackmann K, Schröck E, Krex D, Kaderali L, Schackert G, Platzer M, Klink B. Novel CIC point mutations and an exon-spanning, homozygous deletion identified in oligodendroglial tumors by a comprehensive genomic approach including transcriptome sequencing. PLoS One 2013; 8:e76623. [PMID: 24086756 PMCID: PMC3785522 DOI: 10.1371/journal.pone.0076623] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/26/2013] [Indexed: 12/26/2022] Open
Abstract
Oligodendroglial tumors form a distinct subgroup of gliomas, characterized by a better response to treatment and prolonged overall survival. Most oligodendrogliomas and also some oligoastrocytomas are characterized by a unique and typical unbalanced translocation, der(1,19), resulting in a 1p/19q co-deletion. Candidate tumor suppressor genes targeted by these losses, CIC on 19q13.2 and FUBP1 on 1p31.1, were only recently discovered. We analyzed 17 oligodendrogliomas and oligoastrocytomas by applying a comprehensive approach consisting of RNA expression analysis, DNA sequencing of CIC, FUBP1, IDH1/2, and array CGH. We confirmed three different genetic subtypes in our samples: i) the “oligodendroglial” subtype with 1p/19q co-deletion in twelve out of 17 tumors; ii) the “astrocytic” subtype in three tumors; iii) the “other” subtype in two tumors. All twelve tumors with the 1p/19q co-deletion carried the most common IDH1 R132H mutation. In seven of these tumors, we found protein-disrupting point mutations in the remaining allele of CIC, four of which are novel. One of these tumors also had a deleterious mutation in FUBP1. Only by integrating RNA expression and array CGH data, were we able to discover an exon-spanning homozygous microdeletion within the remaining allele of CIC in an additional tumor with 1p/19q co-deletion. Therefore we propose that the mutation rate might be underestimated when looking at sequence variants alone. In conclusion, the high frequency and the spectrum of CIC mutations in our 1p/19q-codeleted tumor cohort support the hypothesis that CIC acts as a tumor suppressor in these tumors, whereas FUBP1 might play only a minor role.
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Affiliation(s)
- Sophie Eisenreich
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Khalil Abou-El-Ardat
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karol Szafranski
- Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jaime A. Campos Valenzuela
- Institut für Medizinische Informatik und Biometrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Andreas Rump
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Janice M. Nigro
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Rolf Bjerkvig
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Eva-Maria Gerlach
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Hackmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Dietmar Krex
- Klinik und Poliklinik für Neurochirurgie, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Lars Kaderali
- Institut für Medizinische Informatik und Biometrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gabriele Schackert
- Klinik und Poliklinik für Neurochirurgie, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Matthias Platzer
- Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Barbara Klink
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- * E-mail:
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Matsushita K, Tamura M, Tanaka N, Tomonaga T, Matsubara H, Shimada H, Levens D, He L, Liu J, Yoshida M, Nomura F. Interactions between SAP155 and FUSE-binding protein-interacting repressor bridges c-Myc and P27Kip1 expression. Mol Cancer Res 2013; 11:689-98. [PMID: 23594796 DOI: 10.1158/1541-7786.mcr-12-0673] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Oncogenic c-Myc plays a critical role in cell proliferation, apoptosis, and tumorigenesis, but the precise mechanisms that drive this activity remain largely unknown. P27Kip1 (CDKN1B) arrests cells in G1, and SAP155 (SF3B1), a subunit of the essential splicing factor 3b (SF3b) subcomplex of the spliceosome, is required for proper P27 pre-mRNA splicing. FUSE-binding protein-interacting repressor (FIR), a splicing variant of PUF60 lacking exon5, is a c-Myc transcriptional target that suppresses the DNA helicase p89 (ERCC3) and is alternatively spliced in colorectal cancer lacking the transcriptional repression domain within exon 2 (FIRΔexon2). FIR and FIRΔexon2 form a homo- or hetero-dimer that complexes with SAP155. Our study indicates that the FIR/FIRΔexon2/SAP155 interaction bridges c-Myc and P27 expression. Knockdown of FIR/FIRΔexon2 or SAP155 reduced p27 expression, inhibited its pre-mRNA splicing, and reduced CDK2/Cyclin E expression. Moreover, spliceostatin A, a natural SF3b inhibitor, markedly inhibited P27 expression by disrupting its pre-mRNA splicing and reduced CDK2/Cyclin E expression. The expression of P89, another FIR target, was increased in excised human colorectal cancer tissues. Knockdown of FIR reduced P89; however, the effects on P27 and P89 expression are not simply or directly related to altered FIR expression levels, indicating that the mechanical or physical interaction of the SAP155/FIR/FIRΔexon2 complex is potentially essential for sustained expression of both P89 and P27. Together, the interaction between SAP155 and FIR/FIRΔexon2 not only integrates cell-cycle progression and c-Myc transcription by modifying P27 and P89 expression but also suggests that the interaction is a potential target for cancer screening and treatment.
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Affiliation(s)
- Kazuyuki Matsushita
- Department of Molecular Diagnosis (F8), Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
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90
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Protein-protein interactions and multi-component complexes of aminoacyl-tRNA synthetases. Top Curr Chem (Cham) 2013; 344:119-44. [PMID: 24072587 DOI: 10.1007/128_2013_479] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protein-protein interaction occurs transiently or stably when two or more proteins bind together to mediate a wide range of cellular processes such as protein modification, signal transduction, protein trafficking, and structural folding. The macromolecules involved in protein biosynthesis such as aminoacyl-tRNA synthetase (ARS) have a number of protein-protein interactions. The mammalian multi-tRNA synthetase complex (MSC) consists of eight different enzymes: EPRS, IRS, LRS, QRS, MRS, KRS, RRS, and DRS, and three auxiliary proteins: AIMP1/p43, AIMP2/p38, and AIMP/p18. The distinct ARS proteins are also connected to diverse protein networks to carry out biological functions. In this chapter we first show the protein networks of the entire MSC and explain how MSC components interact with or can regulate other proteins. Finally, it is pointed out that the understanding of protein-protein interaction mechanism will provide insight to potential therapeutic application for diseases related to the MSC network.
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91
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Kajiwara T, Matsushita K, Itoga S, Tamura M, Tanaka N, Tomonaga T, Matsubara H, Shimada H, Habara Y, Matsuo M, Nomura F. SAP155-mediated c-myc suppressor far-upstream element-binding protein-interacting repressor splicing variants are activated in colon cancer tissues. Cancer Sci 2012; 104:149-56. [PMID: 23113893 DOI: 10.1111/cas.12058] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/23/2012] [Accepted: 10/28/2012] [Indexed: 12/12/2022] Open
Abstract
The c-myc transcriptional suppressor, far-upstream element (FUSE)-binding protein (FBP)-interacting repressor (FIR), is alternatively spliced in colorectal cancer tissue (Matsushita et al., Cancer Res 2006). Recently, the knockdown of SAP155 pre-mRNA-splicing factor, a subunit of SF3b, was reported to disturb FIR pre-mRNA splicing and yield FIRΔexon2, an exon 2-spliced variant of FIR, which lacks c-myc repression activity. In the present study, novel splicing variants of FIR, Δ3 and Δ4, were also generated by SAP155 siRNA, and these variants were found to be activated in human colorectal cancer tissue. Furthermore, the expression levels of FIR variant mRNA were examined in the peripheral blood of colorectal cancer patients and healthy volunteers to assess its potency for tumor detection. As expected, circulating FIR variant mRNA in the peripheral blood of cancer patients were significantly overexpressed compared to that in healthy volunteers. In particular, the area under the receiving operating characteristic curve of FIR, FIRΔexon2 or FIRΔexon2/FIR, was greater than those of conventional carcinoembryonic antigen or carbohydrate antigen 19-9. In addition, FIRΔexon2 or FIR mRNA expression in the peripheral blood was significantly reduced after operative removal of colorectal tumors. Thus, circulating FIR and FIRΔexon2 mRNA are potential novel screening markers for colorectal cancer testing with conventional carcinoembryonic antigen and or carbohydrate antigen 19-9. Taken together, our results indicate that overexpression of FIR and its splicing variants in colorectal cancer directs feed-forward or addicted circuit c-myc transcriptional activation. Clinical implications for colorectal cancers of novel FIR splicing variants are also discussed in the present paper.
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Affiliation(s)
- Toshiko Kajiwara
- Department of Molecular Diagnosis, Chiba University Graduate School of Medicine, Chiba, Japan
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