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King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
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Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
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2
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Wen JY, Fang YY, Li DM, Tang YL, Huang HQ, Liu LM, Zeng JH, Dang YW, Pan YF, Zeng DT, Huang WJ, Chen G, Li H. A Comprehensive Analysis of LYAR in Colorectal Cancer: Prognostic Marker and Therapeutic Target. Cancer Biother Radiopharm 2024. [PMID: 39159060 DOI: 10.1089/cbr.2023.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024] Open
Abstract
Background: Colorectal cancer (CRC) is a major global health challenge with a need for new biomarkers and therapeutic targets. This work aimed to investigate the biological mechanisms and clinical value of Ly1 antibody reactive (LYAR) in CRC. Methods: We analyzed LYAR mRNA expression across multiple public databases, including genotype-tissue expression, gene expression omnibus, Oncomine, and the cancer genome atlas, alongside in-house immunohistochemical data to evaluate LYAR protein expression in CRC and non-CRC colorectal tissues. Gene set enrichment analysis (GSEA) was used to elucidate LYAR's biological functions, and its impact on the tumor immune microenvironment was assessed using CIBERSORT, ESTIMATE, and single-cell RNA sequencing techniques. In addition, LYAR's association with clinicopathological features and patient prognosis was explored, and its influence on drug sensitivity was investigated using the Connectivity Map database. Results: LYAR was significantly upregulated in CRC tissues compared with non-CRC colorectal counterparts, associated with altered immune cell composition and enhanced RNA processing, splicing, and cell cycle regulation. High LYAR expression correlated with poor disease-free and overall survival, underscoring its prognostic value. GSEA revealed LYAR's involvement in critical cellular processes and pathways, including DNA repair, cell cycle, and mTORC1 signaling. Correlation analysis identified genes positively and negatively associated with LYAR, leading to the discovery of temsirolimus and WYE-354, mTOR inhibitors, as potential therapeutic agents for CRC. Furthermore, LYAR expression predicted increased sensitivity to cetuximab in RAS wild-type metastatic CRC, indicating its utility as a biomarker for treatment responsiveness. Conclusions: LYAR's upregulation in CRC highlights its potential as a biomarker for prognosis and therapeutic targeting, offering insights into CRC pathology and suggesting new avenues for treatment optimization.
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Affiliation(s)
- Jia-Ying Wen
- Department of Radiotherapy, The Second Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Ye-Ying Fang
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Dong-Ming Li
- Department of Pathology, Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Yu-Lu Tang
- Department of Pathology, Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - He-Qing Huang
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Li-Min Liu
- Department of Toxicology, College of Pharmacy, Guangxi Medical University, Nanning, P.R. China
| | - Jiang-Hui Zeng
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People's Hospital, Nanning, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Yan-Fang Pan
- Department of Pathology, Hospital of Guangxi Liugang Medical Co., LTD./Guangxi Liuzhou Dingshun Forensic Expert Institute, Liuzhou, P.R. China
| | - Da-Tong Zeng
- Department of Pathology, Redcross Hospital of Yulin city, Yulin, P.R. China
| | - Wei-Jian Huang
- Department of Pathology, Redcross Hospital of Yulin city, Yulin, P.R. China
| | - Gang Chen
- Department of Pathology, Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Hui Li
- Department of Colorectal & Anal Surgery, Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
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King MR, Ruff KM, Lin AZ, Pant A, Farag M, Lalmansingh JM, Wu T, Fossat MJ, Ouyang W, Lew MD, Lundberg E, Vahey MD, Pappu RV. Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient. Cell 2024; 187:1889-1906.e24. [PMID: 38503281 DOI: 10.1016/j.cell.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/02/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
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Affiliation(s)
- Matthew R King
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew Z Lin
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Avnika Pant
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Mina Farag
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jared M Lalmansingh
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tingting Wu
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Martin J Fossat
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Wei Ouyang
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Matthew D Lew
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Emma Lundberg
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael D Vahey
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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Ishioka M, Nihashi Y, Sunagawa Y, Umezawa K, Shimosato T, Kagami H, Morimoto T, Takaya T. Myogenetic Oligodeoxynucleotide Induces Myocardial Differentiation of Murine Pluripotent Stem Cells. Int J Mol Sci 2023; 24:14380. [PMID: 37762684 PMCID: PMC10532123 DOI: 10.3390/ijms241814380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
An 18-base myogenetic oligodeoxynucleotide (myoDN), iSN04, acts as an anti-nucleolin aptamer and induces myogenic differentiation of skeletal muscle myoblasts. This study investigated the effect of iSN04 on murine embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). In the undifferentiated state, iSN04 inhibited the proliferation of ESCs and iPSCs but did not affect the expression of pluripotent markers. In the differentiating condition, iSN04 treatment of ESCs/iPSCs from day 5 onward dramatically induced differentiation into Nkx2-5+ beating cardiomyocytes with upregulation of Gata4, Isl1, and Nkx2-5, whereas iSN04 treatment from earlier stages completely inhibited cardiomyogenesis. RNA sequencing revealed that iSN04 treatment from day 5 onward contributes to the generation of cardiac progenitors by modulating the Wnt signaling pathway. Immunostaining showed that iSN04 suppressed the cytoplasmic translocation of nucleolin and restricted it to the nucleoli. These results demonstrate that nucleolin inhibition by iSN04 facilitates the terminal differentiation of cardiac mesoderm into cardiomyocytes but interferes with the differentiation of early mesoderm into the cardiac lineage. This is the first report on the generation of cardiomyocytes from pluripotent stem cells using a DNA aptamer. Since iSN04 did not induce hypertrophic responses in primary-cultured cardiomyocytes, iSN04 would be useful and safe for the regenerative therapy of heart failure using stem cell-derived cardiomyocytes.
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Affiliation(s)
- Mina Ishioka
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (M.I.); (T.S.)
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan;
| | - Yoichi Sunagawa
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (Y.S.); (T.M.)
| | - Koji Umezawa
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (M.I.); (T.S.)
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Hiroshi Kagami
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
| | - Tatsuya Morimoto
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (Y.S.); (T.M.)
| | - Tomohide Takaya
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (M.I.); (T.S.)
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
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5
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Hao X, Shen Y, Chen N, Zhang W, Valverde E, Wu L, Chan HL, Xu Z, Yu L, Gao Y, Bado I, Michie LN, Rivas CH, Dominguez LB, Aguirre S, Pingel BC, Wu YH, Liu F, Ding Y, Edwards DG, Liu J, Alexander A, Ueno NT, Hsueh PR, Tu CY, Liu LC, Chen SH, Hung MC, Lim B, Zhang XHF. Osteoprogenitor-GMP crosstalk underpins solid tumor-induced systemic immunosuppression and persists after tumor removal. Cell Stem Cell 2023; 30:648-664.e8. [PMID: 37146584 PMCID: PMC10165729 DOI: 10.1016/j.stem.2023.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/09/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Remote tumors disrupt the bone marrow (BM) ecosystem (BME), eliciting the overproduction of BM-derived immunosuppressive cells. However, the underlying mechanisms remain poorly understood. Herein, we characterized breast and lung cancer-induced BME shifts pre- and post-tumor removal. Remote tumors progressively lead to osteoprogenitor (OP) expansion, hematopoietic stem cell dislocation, and CD41- granulocyte-monocyte progenitor (GMP) aggregation. The tumor-entrained BME is characterized by co-localization between CD41- GMPs and OPs. OP ablation abolishes this effect and diminishes abnormal myeloid overproduction. Mechanistically, HTRA1 carried by tumor-derived small extracellular vesicles upregulates MMP-13 in OPs, which in turn induces the alterations in the hematopoietic program. Importantly, these effects persist post-surgery and continue to impair anti-tumor immunity. Conditional knockout or inhibition of MMP-13 accelerates immune reinstatement and restores the efficacies of immunotherapies. Therefore, tumor-induced systemic effects are initiated by OP-GMP crosstalk that outlasts tumor burden, and additional treatment is required to reverse these effects for optimal therapeutic efficacy.
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Affiliation(s)
- Xiaoxin Hao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yichao Shen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Nan Chen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Weijie Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Elizabeth Valverde
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ling Wu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Hilda L Chan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhan Xu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Liqun Yu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yang Gao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Igor Bado
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Laura Natalee Michie
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Charlotte Helena Rivas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Luis Becerra Dominguez
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Graduate Program in Immunology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Sergio Aguirre
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Bradley C Pingel
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Graduate Program in Immunology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yi-Hsuan Wu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Fengshuo Liu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yunfeng Ding
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - David G Edwards
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jun Liu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Angela Alexander
- Department of Breast Medical Oncology and Morgan Welch IBC Research Program and Clinic, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology and Morgan Welch IBC Research Program and Clinic, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of Hawai'i Cancer Center (UHCC), 701 Ilalo Street, Honolulu, HI 96813, USA
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, Taichung 40402, Taiwan
| | - Chih-Yen Tu
- School of Medicine, College of Medicine, China Medical University, Taichung 406, Taiwan; Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, Taichung 40402, Taiwan
| | - Liang-Chih Liu
- School of Medicine, College of Medicine, China Medical University, Taichung 406, Taiwan; Division of Breast Surgery, Department of Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Shu-Hsia Chen
- Immunomonitoring Core, Center for Immunotherapy Research, Houston Methodist Research Institute (HMRI), Houston, TX, USA
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung 40402, Taiwan
| | - Bora Lim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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6
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Zhou F, Aroua N, Liu Y, Rohde C, Cheng J, Wirth AK, Fijalkowska D, Göllner S, Lotze M, Yun H, Yu X, Pabst C, Sauer T, Oellerich T, Serve H, Röllig C, Bornhäuser M, Thiede C, Baldus C, Frye M, Raffel S, Krijgsveld J, Jeremias I, Beckmann R, Trumpp A, Müller-Tidow C. A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia. Cancer Discov 2023; 13:332-347. [PMID: 36259929 PMCID: PMC9900322 DOI: 10.1158/2159-8290.cd-22-0210] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/12/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O-methylation regulate leukemia stem cell (LSC) activity in vivo. A comprehensive analysis of the rRNA 2'-O-methylation landscape of 94 patients with acute myeloid leukemia (AML) revealed dynamic 2'-O-methylation specifically at exterior sites of ribosomes. The rRNA 2'-O-methylation pattern is closely associated with AML development stage and LSC gene expression signature. Forced expression of the 2'-O-methyltransferase fibrillarin (FBL) induced an AML stem cell phenotype and enabled engraftment of non-LSC leukemia cells in NSG mice. Enhanced 2'-O-methylation redirected the ribosome translation program toward amino acid transporter mRNAs enriched in optimal codons and subsequently increased intracellular amino acid levels. Methylation at the single site 18S-guanosine 1447 was instrumental for LSC activity. Collectively, our work demonstrates that dynamic 2'-O-methylation at specific sites on rRNAs shifts translational preferences and controls AML LSC self-renewal. SIGNIFICANCE We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process constitutes a novel concept of how cancers reprogram cell fate and function. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Fengbiao Zhou
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
| | - Nesrine Aroua
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Yi Liu
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
| | - Christian Rohde
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Anna-Katharina Wirth
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Center Munich, German Center for Environmental Health, Munich, Germany
| | - Daria Fijalkowska
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Göllner
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Michelle Lotze
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Haiyang Yun
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Xiaobing Yu
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Caroline Pabst
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Tim Sauer
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt Am Main, Germany
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt Am Main, Germany
| | - Christoph Röllig
- Medical Department 1, University Hospital Dresden, Dresden, Germany
| | | | - Christian Thiede
- Medical Department 1, University Hospital Dresden, Dresden, Germany
| | - Claudia Baldus
- Department of Medicine II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michaela Frye
- Division of Mechanisms Regulating Gene Expression, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Raffel
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Center Munich, German Center for Environmental Health, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- National Center for Tumor Diseases, NCT Heidelberg, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
- National Center for Tumor Diseases, NCT Heidelberg, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
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7
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Sun Y, Hu X, Qiu D, Zhang Z, Lei L. rDNA Transcription in Developmental Diseases and Stem Cells. Stem Cell Rev Rep 2023; 19:839-852. [PMID: 36633782 DOI: 10.1007/s12015-023-10504-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2023] [Indexed: 01/13/2023]
Abstract
As the first and rate-limiting step in ribosome biogenesis, rDNA transcription undergoes significant dynamic changes during cell pluripotency alteration. Over the past decades, rDNA activity has demonstrated dynamic changes, but most people view it as passive compliance with cellular needs. The evidence for rDNA transcriptional activity determining stem cell pluripotency is growing as research advances, resulting in the arrest of embryonic development and impairment of stem cell lines stemness by rDNA transcription inhibition. The exact mechanism by which rDNA activation influences pluripotency remains unknown. The first objective of this opinion article is to describe rDNA changes in the pathological and physiological course of life, including developmental diseases, tumor genesis, and stem cell differentiation. After that, we propose three hypotheses regarding rDNA regulation of pluripotency: 1) Specialized ribosomes synthesized from rDNA variant, 2) Nucleolar stress induced by the drop of rDNA transcription, 3) Interchromosomal interactions between rDNA and other genes. The pluripotency regulatory center is expected to focus strongly on rDNA. A small molecule inhibitor of rDNA is used to treat tumors caused by abnormal pluripotency activation. By understanding how rDNA regulates pluripotency, we hope to treat developmental diseases and safely apply somatic cell reprogramming in clinical settings.
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Affiliation(s)
- Yuchen Sun
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Dan Qiu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Zhijing Zhang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081.
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8
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LYAR Promotes Colorectal Cancer Progression by Upregulating FSCN1 Expression and Fatty Acid Metabolism. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2021:9979707. [PMID: 35069968 PMCID: PMC8769847 DOI: 10.1155/2021/9979707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is a highly malignant tumor associated with poor prognosis, yet the molecular mechanisms are not fully understood. In this study, we showed that LYAR, a nucleolar protein, is expressed at a higher level in CRC tissue than in adjacent normal tissue and that LYAR expression is closely associated with distant CRC metastasis. LYAR not only significantly promotes the migration and invasion of CRC cells in vitro, but knockdown (KD) of LYAR in CRC cells also inhibits xenograft tumor metastasis in vivo. Microarray analysis of LYAR KD cells combined with a chromatin immunoprecipitation (ChIP) assay, gene reporter assay, and rescue experiment indicated that FSCN1 (encoding fascin actin-bundling protein 1 (Fascin-1)) serves as a novel key regulator of LYAR-promoted migration and invasion of CRC cells. Knockdown of FSCN1 significantly inhibits subcutaneous tumorigenesis of CRC cells and leads to the downregulation of FASN and SCD, genes encoding key enzymes in fatty acid synthesis. In summary, this study reveals a novel mechanism by which LYAR promotes tumor cell migration and invasion by upregulating FSCN1 expression and affecting fatty acid metabolism in CRC.
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9
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Le Clec’h W, Chevalier FD, McDew-White M, Menon V, Arya GA, Anderson TJ. Genetic architecture of transmission stage production and virulence in schistosome parasites. Virulence 2021; 12:1508-1526. [PMID: 34167443 PMCID: PMC8237990 DOI: 10.1080/21505594.2021.1932183] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/06/2021] [Accepted: 05/14/2021] [Indexed: 12/30/2022] Open
Abstract
Both theory and experimental data from pathogens suggest that the production of transmission stages should be strongly associated with virulence, but the genetic bases of parasite transmission/virulence traits are poorly understood. The blood fluke Schistosoma mansoni shows extensive variation in numbers of cercariae larvae shed and in their virulence to infected snail hosts, consistent with expected trade-offs between parasite transmission and virulence. We crossed schistosomes from two populations that differ 8-fold in cercarial shedding and in their virulence to Biomphalaria glabrata snail hosts, and determined four-week cercarial shedding profiles in F0 parents, F1 parents and 376 F2 progeny from two independent crosses in inbred snails. Sequencing and linkage analysis revealed that cercarial production is polygenic and controlled by five QTLs (i.e. Quantitative Trait Loci). These QTLs act additively, explaining 28.56% of the phenotypic variation. These results demonstrate that the genetic architecture of key traits relevant to schistosome ecology can be dissected using classical linkage mapping approaches.
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Affiliation(s)
- Winka Le Clec’h
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | | | | | - Vinay Menon
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Grace-Ann Arya
- Texas Biomedical Research Institute, San Antonio, Texas, USA
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10
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Chen L, Jin C, Liu H, Feng R, Li Z, Zhang J. Analysis of the role of Ly-1 antibody reactive in different cancer types. Bioengineered 2021; 12:9452-9462. [PMID: 34696677 PMCID: PMC8809990 DOI: 10.1080/21655979.2021.1995100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
LYAR (Ly-1 antibody reactive) is a transcription factor with a specific DNA-binding domain, which plays a key role in the regulation of embryonic stem cell self-renewal and differentiation. However, the role of LYAR in human cancers remains unclear. This study aimed to analyze the prognostic value of LYAR in cancer. In this study, we evaluated the prognostic value of LYAR in various tumors. We research found that, compared with normal tissues, LYAR levels werehigher in a variety of tumors. LYAR expression level was associated with poor overall survival, progression-free interval, and disease-specific survival. LYAR expression was also related to tumor grade, stage, age, and tumor status. Cell counting kit-8, Transwell, and wound healing assay showed that knocking out LYAR significantly inhibited the proliferation, migration, and invasion of hepatocellular carcinoma cells. In addition, this study found that LYARexpression was significantly positively correlated with MKI67IP, BZW2, and CCT2. Gene set enrichment analysis results showed that samples with high LYAR expression levels were rich in spliceosomes, RNA degradation, pyrimidine metabolism, cell cycle, nucleotide excision repair, and base excision repair.
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Affiliation(s)
- Linlin Chen
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Congwen Jin
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Hao Liu
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Rongmei Feng
- Critical Care Medicine, The Lu'an Hospital Affiliated to Anhui Medical University, Luan,237000, China.,Critical Care Medicine, The Lu'an People's Hospital, Luan,237000, China
| | - Zhengdong Li
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Jiasheng Zhang
- Emergency surgery, The Lu'an Hospital Affiliated to Anhui Medical University, Luan,237000, China.,Emergency surgery, The Lu'an People's Hospital, Luan,237000, China
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11
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Characterization of Odontogenic Differentiation from Human Dental Pulp Stem Cells Using TMT-Based Proteomic Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3871496. [PMID: 33490242 PMCID: PMC7789479 DOI: 10.1155/2020/3871496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/09/2023]
Abstract
Background The repair of dental pulp injury relies on the odontogenic differentiation of dental pulp stem cells (DPSCs). To better understand the odontogenic differentiation of DPSCs and identify proteins involved in this process, tandem mass tags (TMTs) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were applied to compare the proteomic profiles of induced and control DPSCs. Methods The proteins expressed during osteogenic differentiation of human DPSCs were profiled using the TMT method combined with LC-MS/MS analysis. The identified proteins were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Then, a protein-protein interaction (PPI) network was constructed. Two selected proteins were confirmed by western blotting (WB) analysis. Results A total of 223 proteins that were differentially expressed were identified. Among them, 152 proteins were significantly upregulated and 71 were downregulated in the odontogenic differentiation group compared with the control group. On the basis of biological processes in GO, the identified proteins were mainly involved in cellular processes, metabolic processes, and biological regulation, which are connected with the signaling pathways highlighted by KEGG pathway analysis. PPI networks showed that most of the differentially expressed proteins were implicated in physical or functional interaction. The protein expression levels of FBN1 and TGF-β2 validated by WB were consistent with the proteomic analysis. Conclusions This is the first proteomic analysis of human DPSC odontogenesis using a TMT method. We identified many new differentially expressed proteins that are potential targets for pulp-dentin complex regeneration and repair.
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12
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Hu K. Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming. Cells 2020; 9:cells9112484. [PMID: 33203179 PMCID: PMC7697288 DOI: 10.3390/cells9112484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/04/2022] Open
Abstract
Induction of pluripotent stem cells (iPSC) by OCT4 (octamer-binding transcription factor 4), SOX2 (SR box 2), KLF4 (Krüppel-Like Factor 4), and MYC (cellular Myelocytomatosis, c-MYC or MYC) (collectively OSKM) is revolutionary, but very inefficient, slow, and stochastic. It is unknown as to what underlies the potency aspect of the multi-step, multi-pathway, and inefficient iPSC reprogramming. Mesenchymal-to-epithelial (MET) transition is known as the earliest pathway reprogrammed. Using the recently established concepts of reprogramome and reprogramming legitimacy, the author first demonstrated that ribosome biogenesis (RB) is globally enriched in terms of human embryonic stem cells in comparison with fibroblasts, the popular starting cells of pluripotency reprogramming. It is then shown that the RB network was reprogrammed quickly in a coordinated fashion. Human iPSCs also demonstrated a more robust ribosome biogenesis. The quick and global reprogramming of ribosome biogenesis was also observed in an independent fibroblast line from a different donor. This study additionally demonstrated that MET did not initiate substantially at the time of proper RB reprogramming. This quick, coordinated and authentic RB reprogramming to the more robust pluripotent state by the OSKM reprogramming factors dramatically contrasts the overall low efficiency and long latency of iPSC reprogramming, and aligns well with the potency aspect of the inefficient OSKM reprogramming.
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Affiliation(s)
- Kejin Hu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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13
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Sun X, Wang G, Ding P, Li S. LINC00355 promoted the progression of lung squamous cell carcinoma through regulating the miR-466/LYAR axis. ACTA ACUST UNITED AC 2020; 53:e9317. [PMID: 33111744 PMCID: PMC7584152 DOI: 10.1590/1414-431x20209317] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 08/19/2020] [Indexed: 12/03/2022]
Abstract
LINC00355 has been reported aberrantly over-expressed and associated with poor prognosis in various types of cancer. However, reports regarding the effect of LINC00355 on lung squamous cell carcinoma (SCC) are rare. This study aimed to explore the function of LINC00355 in the development and progression of lung SCC and reveal the underlying mechanism. The expression and subcellular location of LINC00355 were determined by qRT-PCR and RNA-FISH, respectively. The lung SCC cell growth was analyzed by CCK-8 assay, transwell invasion, wound healing, colony formation, and flow cytometry assays. Reactive oxygen species level was evaluated by DCFH-DA probes. Bioinformatics online websites, luciferase reporter assay, RNA binding protein immunoprecipitation (RIP), and RNA pull-down assays were utilized to investigate the interaction among LINC00355, miR-466, and Ly-1 antibody reactive clone (LYAR). The results showed that LINC00355 was upregulated in lung SCC and was positively associated with poor overall survival in lung SCC patients. LINC00355 was mainly located in the cytoplasm of SCC cells. Additionally, LINC0035 functioned as a competing endogenous RNA (ceRNA) to target miR-466, and LYAR was identified as a direct target of miR-466. LINC00355 expression negatively correlated with miR-466 level, and positively correlated with LYAR level. Mechanistically, knockdown of LINC00355 inhibited cell proliferation, migration and invasion, promoted cell apoptosis in vitro, and suppressed tumor growth in vivo through targeting miR-466, and thus down-regulated LYAR expression. These findings provide a new sight for understanding the molecular mechanism of lung SCC and indicate that LINC00355 may serve as a potential biomarker for the diagnosis and treatment of lung SCC.
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Affiliation(s)
- XueFeng Sun
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
| | - GuangSuo Wang
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
| | - PeiKun Ding
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
| | - ShiXuan Li
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
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14
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Abstract
Human pluripotent stem cells harbor the capacity to differentiate into cells from the three embryonic germ layers, and this ability grants them a central role in modeling human disorders and in the field of regenerative medicine. Here, we review pluripotency in human cells with respect to four different aspects: (1) embryonic development, (2) transcriptomes of pluripotent cell stages, (3) genes and pathways that reprogram somatic cells into pluripotent stem cells, and finally (4) the recent identification of the human pluripotent stem cell essentialome. These four aspects of pluripotency collectively culminate in a broader understanding of what makes a cell pluripotent.
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15
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Ribosome and Translational Control in Stem Cells. Cells 2020; 9:cells9020497. [PMID: 32098201 PMCID: PMC7072746 DOI: 10.3390/cells9020497] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
Embryonic stem cells (ESCs) and adult stem cells (ASCs) possess the remarkable capacity to self-renew while remaining poised to differentiate into multiple progenies in the context of a rapidly developing embryo or in steady-state tissues, respectively. This ability is controlled by complex genetic programs, which are dynamically orchestrated at different steps of gene expression, including chromatin remodeling, mRNA transcription, processing, and stability. In addition to maintaining stem cell homeostasis, these molecular processes need to be rapidly rewired to coordinate complex physiological modifications required to redirect cell fate in response to environmental clues, such as differentiation signals or tissue injuries. Although chromatin remodeling and mRNA expression have been extensively studied in stem cells, accumulating evidence suggests that stem cell transcriptomes and proteomes are poorly correlated and that stem cell properties require finely tuned protein synthesis. In addition, many studies have shown that the biogenesis of the translation machinery, the ribosome, is decisive for sustaining ESC and ASC properties. Therefore, these observations emphasize the importance of translational control in stem cell homeostasis and fate decisions. In this review, we will provide the most recent literature describing how ribosome biogenesis and translational control regulate stem cell functions and are crucial for accommodating proteome remodeling in response to changes in stem cell fate.
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16
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Izumikawa K, Ishikawa H, Yoshikawa H, Fujiyama S, Watanabe A, Aburatani H, Tachikawa H, Hayano T, Miura Y, Isobe T, Simpson RJ, Li L, Min J, Takahashi N. LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA. Nucleic Acids Res 2019; 47:10357-10372. [PMID: 31504794 PMCID: PMC6821171 DOI: 10.1093/nar/gkz747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/22/2019] [Accepted: 08/20/2018] [Indexed: 02/06/2023] Open
Abstract
Activation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine-binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.
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Affiliation(s)
- Keiichi Izumikawa
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hideaki Ishikawa
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Harunori Yoshikawa
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sally Fujiyama
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Akira Watanabe
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University 53, Shogoin-kawahara-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8507, Japan
| | - Hiroyuki Aburatani
- Laboratory for System Biology and Medicine, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroyuki Tachikawa
- Department of Applied Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Hayano
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Japan
| | - Yutaka Miura
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Richard J Simpson
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,La Trobe Institute for Molecular Science (LIMS) LIMS Building 1, Room 412 La Trobe University, Bundoora Victoria 3086, Australia
| | - Li Li
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jinrong Min
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nobuhiro Takahashi
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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17
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Chasing Intracellular Zika Virus Using Proteomics. Viruses 2019; 11:v11090878. [PMID: 31546825 PMCID: PMC6783930 DOI: 10.3390/v11090878] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 12/11/2022] Open
Abstract
Flaviviruses are the most medically relevant group of arboviruses causing a wide range of diseases in humans and are associated with high mortality and morbidity, as such posing a major health concern. Viruses belonging to this family can be endemic (e.g., dengue virus), but can also cause fulminant outbreaks (e.g., West Nile virus, Japanese encephalitis virus and Zika virus). Intense research efforts in the past decades uncovered shared fundamental strategies used by flaviviruses to successfully replicate in their respective hosts. However, the distinct features contributing to the specific host and tissue tropism as well as the pathological outcomes unique to each individual flavivirus are still largely elusive. The profound footprint of individual viruses on their respective hosts can be investigated using novel technologies in the field of proteomics that have rapidly developed over the last decade. An unprecedented sensitivity and throughput of mass spectrometers, combined with the development of new sample preparation and bioinformatics analysis methods, have made the systematic investigation of virus-host interactions possible. Furthermore, the ability to assess dynamic alterations in protein abundances, protein turnover rates and post-translational modifications occurring in infected cells now offer the unique possibility to unravel complex viral perturbations induced in the infected host. In this review, we discuss the most recent contributions of mass spectrometry-based proteomic approaches in flavivirus biology with a special focus on Zika virus, and their basic and translational potential and implications in understanding and characterizing host responses to arboviral infections.
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18
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Lu W, Yu J, Shi F, Zhang J, Huang R, Yin S, Songyang Z, Huang J. The long non-coding RNA Snhg3 is essential for mouse embryonic stem cell self-renewal and pluripotency. Stem Cell Res Ther 2019; 10:157. [PMID: 31151411 PMCID: PMC6545032 DOI: 10.1186/s13287-019-1270-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/08/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023] Open
Abstract
Background Small nucleolar RNA host gene 3 (Snhg3) is a long non-coding RNA (lncRNA) that was shown to participate in the tumorigenesis of certain cancers. However, little is known about its role in embryonic stem cells (ESCs). Methods Here, we investigated the role of Snhg3 in mouse ESCs (mESCs) through both loss-of-function (knockdown) and gain-of-function (overexpression) approaches. Alkaline phosphatase staining, secondary colony formation, propidium iodide staining, western blotting, and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to access self-renewal capacity, whereas immunofluorescence, qRT-PCR, and embryoid body formation were performed to examine pluripotency. In addition, the effect of Snhg3 on mouse embryonic development was determined based on the morphological changes, blastocyst rate, and altered pluripotency marker (Nanog, Oct4) expression. Moreover, the relationship between Snhg3 and key pluripotency factors was evaluated by chromatin immunoprecipitation qPCR, qRT-PCR, subcellular fractionation, and RNA immunoprecipitation. Finally, RNA pull-down and mass spectrometry were applied to explore the potential interacting proteins of Snhg3 in mESCs. Results We demonstrated that Snhg3 is essential for self-renewal and pluripotency maintenance in mESCs. In addition, Snhg3 knockdown disrupted mouse early embryo development. Mechanistically, Snhg3 formed a positive feedback network with Nanog and Oct4, and 126 Snhg3-interacting proteins were identified in mESCs. Conclusions Snhg3 is essential for mESC self-renewal and pluripotency, as well as mouse early embryo development. Electronic supplementary material The online version of this article (10.1186/s13287-019-1270-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weisi Lu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Jianping Yu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fengtao Shi
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, V5Z 4E8, Canada
| | - Jianing Zhang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Rui Huang
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shanshan Yin
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhou Songyang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China. .,MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Junjiu Huang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China. .,MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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19
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Jariyapong P, Pudgerd A, Cheloh N, Hirono I, Kondo H, Vanichviriyakit R, Weerachatyanukul W, Chotwiwatthanakun C. Hematopoietic tissue of Macrobrachium rosenbergii plays dual roles as a source of hemocyte hematopoiesis and as a defensive mechanism against Macrobrachium rosenbergii nodavirus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 86:756-763. [PMID: 30553890 DOI: 10.1016/j.fsi.2018.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/03/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
White tail disease caused by Macrobrachium rosenbergii nodavirus (MrNV) infection takes place only in nauplii, not adults, of M. rosenbergii prawn. Hemocyte homeostasis and immune-related functions derived from the hematopoietic tissue (Hpt) in adult prawn are presumed to play roles in resisting viral infection. To elucidate the role of the Hpt cell response to MrNV, a comparative transcriptome analysis was performed with MrNV-infected prawn at various time intervals. The results showed that there were 462 unigenes that were differentially expressed between mock and infected samples. BlastX sequence analysis revealed that two proteins, crustacean hematopoietic factor (CHF) and cell growth-regulating zinc finger protein (Lyar), are involved in hemocyte hematopoiesis and are up-regulated during MrNV infection. In fact, genes involved in cell growth regulation and immunity were highly expressed at 6 h and decreased within 24 h post-infection. Localization studies in the Hpt tissue revealed the presence of anti-lipopolysaccharide factor (ALF) and CHF mRNAs in Hpt cells. Considering these findings, we concluded that resistance to MrNV infection in adult prawn is due to an increase in humoral immune factors and the acceleration of hemocyte homeostasis by the dual roles of the Hpt organ in M. rosenbergii.
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Affiliation(s)
- Pitchanee Jariyapong
- School of Medicine, Walailak University, Thasala District, Nakhonsrithammarat, 80161, Thailand; Research Center of Excellence on Shrimp, Walailak University, Thasala District, Nakhonsrithammarat, 80161, Thailand
| | - Arnon Pudgerd
- Division of Anatomy, School of Medical Science, University of Phayao, Muang, Phayao, 56000, Thailand; Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Nifareesa Cheloh
- Faculty of Agriculture, Princess of Naradhiwas University, Mueang Narathiwat District, Narathiwat, 96000, Thailand
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, 108-8477, Japan
| | - Rapeepun Vanichviriyakit
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Wattana Weerachatyanukul
- Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; Nakhonsawan Campus, Mahidol University, Nakhonsawan, 60130, Thailand.
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20
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The Nucleolar Protein LYAR Facilitates Ribonucleoprotein Assembly of Influenza A Virus. J Virol 2018; 92:JVI.01042-18. [PMID: 30209172 PMCID: PMC6232469 DOI: 10.1128/jvi.01042-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/01/2018] [Indexed: 12/13/2022] Open
Abstract
Influenza A viral ribonucleoprotein (vRNP) is responsible for transcription and replication of the viral genome in infected cells and depends on host factors for its functions. Identification of the host factors interacting with vRNP not only improves understanding of virus-host interactions but also provides insights into novel mechanisms of viral pathogenicity and the development of new antiviral strategies. Here, we have identified 80 host factors that copurified with vRNP using affinity purification followed by mass spectrometry. LYAR, a cell growth-regulating nucleolar protein, has been shown to be important for influenza A virus replication. During influenza A virus infection, LYAR expression is increased and partly translocates from the nucleolus to the nucleoplasm and cytoplasm. Furthermore, LYAR interacts with RNP subunits, resulting in enhancing viral RNP assembly, thereby facilitating viral RNA synthesis. Taken together, our studies identify a novel vRNP binding host partner important for influenza A virus replication and further reveal the mechanism of LYAR regulating influenza A viral RNA synthesis by facilitating viral RNP assembly.IMPORTANCE Influenza A virus (IAV) must utilize the host cell machinery to replicate, but many of the mechanisms of IAV-host interaction remain poorly understood. Improved understanding of interactions between host factors and vRNP not only increases our basic knowledge of the molecular mechanisms of virus replication and pathogenicity but also provides insights into possible novel antiviral targets that are necessary due to the widespread emergence of drug-resistant IAV strains. Here, we have identified LYAR, a cell growth-regulating nucleolar protein, which interacts with viral RNP components and is important for efficient replication of IAVs and whose role in the IAV life cycle has never been reported. In addition, we further reveal the role of LYAR in viral RNA synthesis. Our results extend and improve current knowledge on the mechanisms of IAV transcription and replication.
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21
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Scaturro P, Stukalov A, Haas DA, Cortese M, Draganova K, Płaszczyca A, Bartenschlager R, Götz M, Pichlmair A. An orthogonal proteomic survey uncovers novel Zika virus host factors. Nature 2018; 561:253-257. [PMID: 30177828 DOI: 10.1038/s41586-018-0484-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/20/2018] [Indexed: 11/09/2022]
Abstract
Zika virus (ZIKV) has recently emerged as a global health concern owing to its widespread diffusion and its association with severe neurological symptoms and microcephaly in newborns1. However, the molecular mechanisms that are responsible for the pathogenicity of ZIKV remain largely unknown. Here we use human neural progenitor cells and the neuronal cell line SK-N-BE2 in an integrated proteomics approach to characterize the cellular responses to viral infection at the proteome and phosphoproteome level, and use affinity proteomics to identify cellular targets of ZIKV proteins. Using this approach, we identify 386 ZIKV-interacting proteins, ZIKV-specific and pan-flaviviral activities as well as host factors with known functions in neuronal development, retinal defects and infertility. Moreover, our analysis identified 1,216 phosphorylation sites that are specifically up- or downregulated after ZIKV infection, indicating profound modulation of fundamental signalling pathways such as AKT, MAPK-ERK and ATM-ATR and thereby providing mechanistic insights into the proliferation arrest elicited by ZIKV infection. Functionally, our integrative study identifies ZIKV host-dependency factors and provides a comprehensive framework for a system-level understanding of ZIKV-induced perturbations at the levels of proteins and cellular pathways.
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Affiliation(s)
- Pietro Scaturro
- Max-Planck Institute of Biochemistry, Innate Immunity Laboratory, Martinsried, Germany. .,Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany.
| | - Alexey Stukalov
- Max-Planck Institute of Biochemistry, Innate Immunity Laboratory, Martinsried, Germany.,Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany
| | - Darya A Haas
- Max-Planck Institute of Biochemistry, Innate Immunity Laboratory, Martinsried, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Kalina Draganova
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universitaet, Munich, Germany
| | - Anna Płaszczyca
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universitaet, Munich, Germany.,Synergy, Excellence Cluster for Systems Neurology, Biomedical Center, Ludwig-Maximilians-Universitaet, Munich, Germany
| | - Andreas Pichlmair
- Max-Planck Institute of Biochemistry, Innate Immunity Laboratory, Martinsried, Germany. .,Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany. .,German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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22
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Luna-Peláez N, García-Domínguez M. Lyar-Mediated Recruitment of Brd2 to the Chromatin Attenuates Nanog Downregulation Following Induction of Differentiation. J Mol Biol 2018; 430:1084-1097. [PMID: 29505757 DOI: 10.1016/j.jmb.2018.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/08/2018] [Accepted: 02/26/2018] [Indexed: 01/24/2023]
Abstract
During development, cellular differentiation programs need tight regulation for proper display of the activity of multiple factors in time and space. Chromatin adaptors of the BET family (Brd2, Brd3, Brd4 and Brdt in vertebrates) are transcription co-regulators tightly associated with the progression of the cell cycle. A key question regarding their function is whether they work as part of the general transcription machinery or, on the contrary, they are precisely recruited to the chromatin through specific transcription factors. Here, we report the selective recruitment of Brd2 to the chromatin by the transcription factor Lyar. We show that Lyar downregulation results in Brd2 dissociation from a number of promoters studied. On the contrary, dissociation of BET proteins from the chromatin has no effect on Lyar occupancy. Under differentiation conditions, the absence of Lyar leads to impaired downregulation of the pluripotency gene Nanog, with concomitant reduction in the upregulation of differentiation markers. Interestingly, following the induction of differentiation, Brd2 depletion exhibits the same effects as expressing a truncated Lyar molecule lacking the Brd2 interacting domain. Both approaches result in stronger Nanog repression, indicating that Lyar-mediated recruitment of Brd2 moderates Nanog downregulation when differentiation is triggered. Moreover, expression of truncated Lyar leads to impaired differentiation and increased apoptosis. Thus, Lyar-mediated recruitment of Brd2 would participate in preserving a proper timing for Nanog silencing ensuring the appropriate establishment of the differentiation program.
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Affiliation(s)
- Noelia Luna-Peláez
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain
| | - Mario García-Domínguez
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
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23
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Affiliation(s)
- Shenglong Qiu
- a Department of General Surgery, Shanghai General Hospital , Shanghai Jiao Tong University , Shanghai , China
| | - Pei Y Liu
- b Children's Cancer Institute Australia for Medical Research , Randwick , Sydney , Australia.,c Centre for Childhood Cancer Research , UNSW Medicine, UNSW Australia , Sydney , Australia
| | - Tao Liu
- b Children's Cancer Institute Australia for Medical Research , Randwick , Sydney , Australia.,c Centre for Childhood Cancer Research , UNSW Medicine, UNSW Australia , Sydney , Australia
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24
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Upregulation of LYAR induces neuroblastoma cell proliferation and survival. Cell Death Differ 2017; 24:1645-1654. [PMID: 28686580 DOI: 10.1038/cdd.2017.98] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/24/2017] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
The N-Myc oncoprotein induces neuroblastoma by regulating gene transcription and consequently causing cell proliferation. Paradoxically, N-Myc is well known to induce apoptosis by upregulating pro-apoptosis genes, and it is not clear how N-Myc overexpressing neuroblastoma cells escape N-Myc-mediated apoptosis. The nuclear zinc finger protein LYAR has recently been shown to modulate gene expression by forming a protein complex with the protein arginine methyltransferase PRMT5. Here we showed that N-Myc upregulated LYAR gene expression by binding to its gene promoter. Genome-wide differential gene expression studies revealed that knocking down LYAR considerably upregulated the expression of oxidative stress genes including CHAC1, which depletes intracellular glutathione and induces oxidative stress. Although knocking down LYAR expression with siRNAs induced oxidative stress, neuroblastoma cell growth inhibition and apoptosis, co-treatment with the glutathione supplement N-acetyl-l-cysteine or co-transfection with CHAC1 siRNAs blocked the effect of LYAR siRNAs. Importantly, high levels of LYAR gene expression in human neuroblastoma tissues predicted poor event-free and overall survival in neuroblastoma patients, independent of the best current markers for poor prognosis. Taken together, our data suggest that LYAR induces proliferation and promotes survival of neuroblastoma cells by repressing the expression of oxidative stress genes such as CHAC1 and suppressing oxidative stress, and identify LYAR as a novel co-factor in N-Myc oncogenesis.
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25
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Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LTY, Niakan KK, Martinez-Arias A, Lilley KS. Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Stem Cells 2015; 33:2712-25. [DOI: 10.1002/stem.2067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/20/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Claire M. Mulvey
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Genetics; University of Cambridge; Cambridge United Kingdom
| | - Christian Schröter
- Department of Genetics; University of Cambridge; Cambridge United Kingdom
| | - Laurent Gatto
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Computational Proteomics Unit; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
| | - Duygu Dikicioglu
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
| | - Isik Baris Fidaner
- Department of Computer Engineering; Bogazici University; Istanbul Turkey
| | - Andy Christoforou
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
| | - Lily T. Y. Cho
- Neusentis; Pfizer Worldwide Research and Development; Granta Park Science Park, Great Abington; Cambridge United Kingdom
| | - Kathy K. Niakan
- The Francis Crick Institute, Mill Hill Laboratory; London United Kingdom
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
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26
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DeBoer J, Jagadish T, Haverland NA, Madson CJ, Ciborowski P, Belshan M. Alterations in the nuclear proteome of HIV-1 infected T-cells. Virology 2014; 468-470:409-420. [PMID: 25240327 DOI: 10.1016/j.virol.2014.08.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/17/2023]
Abstract
Virus infection of a cell involves the appropriation of host factors and the innate defensive response of the cell. The identification of proteins critical for virus replication may lead to the development of novel, cell-based inhibitors. In this study we mapped the changes in T-cell nuclei during human immunodeficiency virus type 1 (HIV-1) at 20 hpi. Using a stringent data threshold, a total of 13 and 38 unique proteins were identified in infected and uninfected cells, respectively, across all biological replicates. An additional 15 proteins were found to be differentially regulated between infected and control nuclei. STRING analysis identified four clusters of protein-protein interactions in the data set related to nuclear architecture, RNA regulation, cell division, and cell homeostasis. Immunoblot analysis confirmed the differential expression of several proteins in both C8166-45 and Jurkat E6-1 T-cells. These data provide a map of the response in host cell nuclei upon HIV-1 infection.
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Affiliation(s)
- Jason DeBoer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Teena Jagadish
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nicole A Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Christian J Madson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA.
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27
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Ju J, Wang Y, Liu R, Zhang Y, Xu Z, Wang Y, Wu Y, Liu M, Cerruti L, Zou F, Ma C, Fang M, Tan R, Jane SM, Zhao Q. Human fetal globin gene expression is regulated by LYAR. Nucleic Acids Res 2014; 42:9740-52. [PMID: 25092918 PMCID: PMC4150809 DOI: 10.1093/nar/gku718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human globin gene expression during development is modulated by transcription factors in a stage-dependent manner. However, the mechanisms controlling the process are still largely unknown. In this study, we found that a nuclear protein, LYAR (human homologue of mouse Ly-1 antibody reactive clone) directly interacted with the methyltransferase PRMT5 which triggers the histone H4 Arg3 symmetric dimethylation (H4R3me2s) mark. We found that PRMT5 binding on the proximal γ-promoter was LYAR-dependent. The LYAR DNA-binding motif (GGTTAT) was identified by performing CASTing (cyclic amplification and selection of targets) experiments. Results of EMSA and ChIP assays confirmed that LYAR bound to a DNA region corresponding to the 5′-untranslated region of the γ-globin gene. We also found that LYAR repressed human fetal globin gene expression in both K562 cells and primary human adult erythroid progenitor cells. Thus, these data indicate that LYAR acts as a novel transcription factor that binds the γ-globin gene, and is essential for silencing the γ-globin gene.
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Affiliation(s)
- Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ronghua Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yichong Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Zhen Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yadong Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yupeng Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Loretta Cerruti
- Department of Medicine, Monash University Central Clinical School, Prahran, VIC 3181, Australia
| | - Fengwei Zou
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Chi Ma
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ming Fang
- Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Renxiang Tan
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Stephen M Jane
- Department of Medicine, Monash University Central Clinical School, Prahran, VIC 3181, Australia
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
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Lyar, a cell growth-regulating zinc finger protein, was identified to be associated with cytoplasmic ribosomes in male germ and cancer cells. Mol Cell Biochem 2014; 395:221-9. [PMID: 24990247 DOI: 10.1007/s11010-014-2128-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 06/17/2014] [Indexed: 12/31/2022]
Abstract
Translational control is a basic mechanism for gene regulation in cells and important for tissue growth and development in mammals. Deregulation of the mechanism thus causes diseases such as cancer. Considering the importance of the ribosome as a factory of polypeptide synthesis, some new factors have been expected to be associated with the ribosome and involved in translational control. Our proteomic survey for these factors identified a zinc finger protein, Lyar, in cytoplasmic ribosomes of the rodent testis. Subcellular fractionation of the testis provided data supporting association of Lyar with ribosomes. Lyar was then suggested to be included in the 60S large subunit, but not in polysomes, by ultracentrifugation of testicular ribosomes. While analysis of tissue distribution of Lyar has indicated its testis-predominant expression, Lyar mRNA was expressed in the cancer cells originated from tissues other than testis, and Lyar promoted proliferation of NIH-3T3 cells. Furthermore, translation was increased by Lyar in vitro, pointing out the first experimental link between this protein and translation. Taken together, Lyar seems to be a new player in translational control and a potential target for cancer therapy.
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De Antonellis P, Carotenuto M, Vandenbussche J, De Vita G, Ferrucci V, Medaglia C, Boffa I, Galiero A, Di Somma S, Magliulo D, Aiese N, Alonzi A, Spano D, Liguori L, Chiarolla C, Verrico A, Schulte JH, Mestdagh P, Vandesompele J, Gevaert K, Zollo M. Early targets of miR-34a in neuroblastoma. Mol Cell Proteomics 2014; 13:2114-31. [PMID: 24912852 DOI: 10.1074/mcp.m113.035808] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Several genes encoding for proteins involved in proliferation, invasion, and apoptosis are known to be direct miR-34a targets. Here, we used proteomics to screen for targets of miR-34a in neuroblastoma (NBL), a childhood cancer that originates from precursor cells of the sympathetic nervous system. We examined the effect of miR-34a overexpression using a tetracycline inducible system in two NBL cell lines (SHEP and SH-SY5Y) at early time points of expression (6, 12, and 24 h). Proteome analysis using post-metabolic labeling led to the identification of 2,082 proteins, and among these 186 were regulated (112 proteins down-regulated and 74 up-regulated). Prediction of miR-34a targets via bioinformatics showed that 32 transcripts held miR-34a seed sequences in their 3'-UTR. By combining the proteomics data with Kaplan Meier gene-expression studies, we identified seven new gene products (ALG13, TIMM13, TGM2, ABCF2, CTCF, Ki67, and LYAR) that were correlated with worse clinical outcomes. These were further validated in vitro by 3'-UTR seed sequence regulation. In addition, Michigan Molecular Interactions searches indicated that together these proteins affect signaling pathways that regulate cell cycle and proliferation, focal adhesions, and other cellular properties that overall enhance tumor progression (including signaling pathways such as TGF-β, WNT, MAPK, and FAK). In conclusion, proteome analysis has here identified early targets of miR-34a with relevance to NBL tumorigenesis. Along with the results of previous studies, our data strongly suggest miR-34a as a useful tool for improving the chance of therapeutic success with NBL.
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Affiliation(s)
- Pasqualino De Antonellis
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Marianeve Carotenuto
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Jonathan Vandenbussche
- ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; **Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Gennaro De Vita
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Veronica Ferrucci
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Chiara Medaglia
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Iolanda Boffa
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Alessandra Galiero
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Sarah Di Somma
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Daniela Magliulo
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Nadia Aiese
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Alessandro Alonzi
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Daniela Spano
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Lucia Liguori
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Cristina Chiarolla
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Antonio Verrico
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy; ‡‡Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, 80131 Naples, Italy
| | | | - Pieter Mestdagh
- ¶¶Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Jo Vandesompele
- ¶¶Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Kris Gevaert
- ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; **Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Massimo Zollo
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy; ‖‖Centro di Medicina Trasfusionale, Azienda Ospedaliera Federico II, 80131 Naples, Italy
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Wei Z, Sun M, Liu X, Zhang J, Jin Y. Rufy3, a protein specifically expressed in neurons, interacts with actin-bundling protein Fascin to control the growth of axons. J Neurochem 2014; 130:678-92. [PMID: 24720729 DOI: 10.1111/jnc.12740] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 01/10/2023]
Abstract
For our nervous system to function properly, each neuron must generate a single axon and elongate the axon to reach its target. It is known that actin filaments and their dynamic interaction with microtubules within growth cones play important roles in inducing axon extension. However, it remains unclear how cytoskeletal dynamics is controlled in growth cones. In this study, we report that Rufy3, a RUN domain-containing protein, is a neuron-specific and actin filament-relevant protein. We find that the appropriate expression of Rufy3 in mouse hippocampal neurons is required for the development of a single axon and axon growth. Our results show that Rufy3 specifically interacts with actin filament-binding proteins, such as Fascin, and colocalizes with Fascin in growth cones. Knockdown of Rufy3 impairs the distribution of Fascin and actin filaments, accompanied by an increased proportion of neurons with multiple axons and a decrease in the axon length. Therefore, Rufy3 may be particularly important for neuronal axon elongation by interacting with Fascin to control actin filament organization in axonal growth cones. We propose that Rufy3 may control mouse neuron axon development through its specific interaction with Fascin and Drebrin. Over-expression of Rufy3 (Rufy3 OE) leads to longer axons and expands the distribution of Drebrin to almost the entire growth cone. In contrast, knockdown of Rufy3 (Rufy3 RNAi) results in shortened axons and enhanced the percentage of mutipolar neurons. Moreover, silencing of Rufy3 reduces and restricts the expression of Fascin and F-actin to the edge of the growth cone. These findings provide new insights into the molecular regulation of axonal outgrowth and cell polarization in neurons.
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Affiliation(s)
- Zhe Wei
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
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Miyazawa N, Yoshikawa H, Magae S, Ishikawa H, Izumikawa K, Terukina G, Suzuki A, Nakamura-Fujiyama S, Miura Y, Hayano T, Komatsu W, Isobe T, Takahashi N. Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA. Genes Cells 2014; 19:273-86. [DOI: 10.1111/gtc.12129] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/05/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Naoki Miyazawa
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
| | - Harunori Yoshikawa
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
| | - Satomi Magae
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Hideaki Ishikawa
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Keiichi Izumikawa
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Goro Terukina
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
| | - Ai Suzuki
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Sally Nakamura-Fujiyama
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
| | - Yutaka Miura
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Toshiya Hayano
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Wataru Komatsu
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Toshiaki Isobe
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Chemistry; Graduate School of Sciences and Engineering; Tokyo Metropolitan University; 1-1 Minamiosawa Hachiouji-shi Tokyo 192-0397 Japan
| | - Nobuhiro Takahashi
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
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Lee B, Jin S, Choi H, Kwon JT, Kim J, Jeong J, Kwon YI, Cho C. Expression and function of the testis-predominant protein LYAR in mice. Mol Cells 2013; 35:54-60. [PMID: 23212345 PMCID: PMC3887849 DOI: 10.1007/s10059-013-2271-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/13/2012] [Accepted: 11/14/2012] [Indexed: 11/28/2022] Open
Abstract
Mammalian spermatogenesis is a complex process involving an intrinsic genetic program of germ cell-specific and -predominant genes. In the present study, we analyzed the Ly-1 reactive clone (Lyar) gene in the mouse. Lyar, which is known to be expressed abundantly in the testis, encodes a nucleolar protein that contains a LYAR-type C2HC zinc finger motif and three nuclear localization signals. We herein confirmed that Lyar is expressed predominantly in the testis, and further showed that this expression is specific to germ cells. Protein analyses with an anti-LYAR antibody demonstrated that the LYAR protein is present in spermatocytes and spermatids, but not in sperm. To assess the functional role of LYAR in vivo, we used a genetrap mutagenesis approach to establish a LYAR-null mouse model. Lyar mutant mice were born live and developed normally. Male mutant mice lacking LYAR were fully fertile and showed intact spermatogenesis. Taken together, our results demonstrate that LYAR is strongly preferred in male germ cells, but has a dispensable role in spermatogenesis and fertility.
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Affiliation(s)
- Boyeon Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Sora Jin
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Heejin Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Jun Tae Kwon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Jihye Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Juri Jeong
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | | | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
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Wang G, Fulkerson CM, Malek R, Ghassemifar S, Snyder PW, Mendrysa SM. Mutations in Lyar and p53 are synergistically lethal in female mice. ACTA ACUST UNITED AC 2012; 94:729-37. [PMID: 22815056 DOI: 10.1002/bdra.23048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 05/30/2012] [Accepted: 05/31/2012] [Indexed: 11/08/2022]
Abstract
BACKGROUND Ly-1 antibody reactive clone (LYAR) is a nucleolar zinc finger protein that has been implicated in cell growth, self-renewal of embryonic stem cells, and medulloblastoma. To test whether LYAR is critical for cell growth and development, we generated Lyar mutant mice. METHODS Mice carrying the mutant Lyar(gt) allele were generated from embryonic stem cells that contained a gene-trap insertion in the Lyar gene. Phenotypic analyses were performed on Lyar mutant mice and mouse embryonic fibroblasts. Lyar(gt/gt) mice were crossed to mice lacking the p53 tumor suppressor protein and Lyar/p53 compound mutants scored for external abnormalities. RESULTS Lyar(gt/gt) homozygotes are viable, fertile, and indistinguishable from wild type littermates. However, the growth of Lyar(+/gt) and Lyar(gt/gt) mouse embryonic fibroblasts (MEFs) was impaired, coincident with an increase in the steady-state level of p53 and a key p53 effector of growth arrest, p21, suggesting that a cellular stress response is triggered in the absence of a wild type level of LYAR. Remarkably, the majority of Lyar(+/gt) and Lyar(gt/gt) female mice lacking p53 mice failed to survive. The neural tube defect (NTD) exencephaly was observed in ≈26% and ≈61% of female Lyar(+/gt;) p53(-/-) and Lyar(gt/gt;) p53(-/-) embryos, respectively. CONCLUSIONS Lyar/p53 mutant mice represent a new digenic model of NTDs. Furthermore, these studies identify Lyar as a novel candidate gene for a role in human NTDs. These results provide new data to support the idea that loss of a p53-mediated developmental checkpoint may increase the risk of NTDs owing to some germline mutations.
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Affiliation(s)
- Guan Wang
- Department of Basic Medical Sciences, School of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, USA
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Jadaliha M, Lee HJ, Pakzad M, Fathi A, Jeong SK, Cho SY, Baharvand H, Paik YK, Salekdeh GH. Quantitative proteomic analysis of human embryonic stem cell differentiation by 8-plex iTRAQ labelling. PLoS One 2012; 7:e38532. [PMID: 22723866 PMCID: PMC3377673 DOI: 10.1371/journal.pone.0038532] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 05/07/2012] [Indexed: 12/24/2022] Open
Abstract
Analysis of gene expression to define molecular mechanisms and pathways involved in human embryonic stem cells (hESCs) proliferation and differentiations has allowed for further deciphering of the self-renewal and pluripotency characteristics of hESC. Proteins associated with hESCs were discovered through isobaric tags for relative and absolute quantification (iTRAQ). Undifferentiated hESCs and hESCs in different stages of spontaneous differentiation by embryoid body (EB) formation were analyzed. Using the iTRAQ approach, we identified 156 differentially expressed proteins involved in cell proliferation, apoptosis, transcription, translation, mRNA processing, and protein synthesis. Proteins involved in nucleic acid binding, protein synthesis, and integrin signaling were downregulated during differentiation, whereas cytoskeleton proteins were upregulated. The present findings added insight to our understanding of the mechanisms involved in hESC proliferation and differentiation.
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Affiliation(s)
- Mahdieh Jadaliha
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Hyoung-Joo Lee
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Mohammad Pakzad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ali Fathi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seul-Ki Jeong
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Sang-Yun Cho
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Young-Ki Paik
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
- * E-mail: (GSH); (Y-KP)
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
- * E-mail: (GSH); (Y-KP)
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Abstract
Nucleolin is a multifunctional protein localized primarily in the nucleolus, but also found in the nucleoplasm, cytoplasm and cell membrane. It is involved in several aspects of DNA metabolism, and participates extensively in RNA regulatory mechanisms, including transcription, ribosome assembly, mRNA stability and translation, and microRNA processing. Nucleolin's implication in disease is linked to its ability to associate with target RNAs via its four RNA-binding domains and its arginine/glycin-rich domain. By modulating the post-transcriptional fate of target mRNAs, which typically bear AU-rich and/or G-rich elements, nucleolin has been linked to cellular events that influence disease, notably cell proliferation and protection against apoptotic death. Through its diverse RNA functions, nucleolin is increasingly implicated in pathological processes, particularly cancer and viral infection. Here, we review the RNA-binding activities of nucleolin, its influence on gene expression patterns, and its impact upon diseases. We also discuss the rising interest in targeting nucleolin therapeutically.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
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Yang A, Shi G, Zhou C, Lu R, Li H, Sun L, Jin Y. Nucleolin maintains embryonic stem cell self-renewal by suppression of p53 protein-dependent pathway. J Biol Chem 2011; 286:43370-82. [PMID: 22013067 PMCID: PMC3234871 DOI: 10.1074/jbc.m111.225185] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 10/18/2011] [Indexed: 11/06/2022] Open
Abstract
Embryonic stem cells (ESCs) can undergo unlimited self-renewal and retain pluripotent developmental potential. The unique characteristics of ESCs, including a distinct transcriptional network, a poised epigenetic state, and a specific cell cycle profile, distinguish them from somatic cells. However, the molecular mechanisms underlying these special properties of ESCs are not fully understood. Here, we report that nucleolin, a nucleolar protein highly expressed in undifferentiated ESCs, plays an essential role for the maintenance of ESC self-renewal. When nucleolin is knocked down by specific short hairpin RNA (shRNA), ESCs display dramatically reduced cell proliferation rate, increased cell apoptosis, and G(1) phase accumulation. Down-regulation of nucleolin also leads to evident ESC differentiation as well as decreased self-renewal ability. Interestingly, expression of pluripotency markers (Oct4 and Nanog) is unaltered in these differentiated cells. Mechanistically, depletion of nucleolin up-regulates the p53 protein level and activates the p53-dependent pathway, at least in part, via increasing p53 protein stability. Silencing of p53 rescues G(1) phase accumulation and apoptosis caused by nucleolin deficiency entirely, although it partially blocks abnormal differentiation in nucleolin-depleted ESCs. It is noteworthy that knocking down nucleolin in NIH3T3 cells affected cell survival and proliferation in a much milder way, despite the comparable silencing efficiency obtained in ESCs and NIH3T3 cells. Collectively, our data demonstrate that nucleolin is a critical regulator of ESC self-renewal and that suppression of the p53-dependent pathway is the major molecular mechanism underlying functions of nucleolin in ESCs.
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Affiliation(s)
- Acong Yang
- From the Shanghai Stem Cell Institute, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine and
- the Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guilai Shi
- the Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chenlin Zhou
- the Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Rui Lu
- the Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hui Li
- From the Shanghai Stem Cell Institute, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine and
- the Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Sun
- the Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ying Jin
- From the Shanghai Stem Cell Institute, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine and
- the Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Choi HS, Kim WT, Kim H, Kim JJ, Ko JY, Lee SW, Jang YJ, Kim SJ, Lee MJ, Jung HS, Kzhyshkowska J, Um SJ, Lee MY, Lee SH, Kim CH, Ryu CJ. Identification and characterization of adenovirus early region 1B-associated protein 5 as a surface marker on undifferentiated human embryonic stem cells. Stem Cells Dev 2011; 20:609-20. [PMID: 21083500 DOI: 10.1089/scd.2010.0265] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pluripotent human embryonic stem cells (hESCs) provide appropriate systems for developmental studies and prospective donor cell sources for regenerative medicine. Identification of surface markers specific to hESCs is a prerequisite for studying hESC biology and can be used to generate clinical-level donor cell preparations that are free from tumorigenic undifferentiated hESCs. We previously reported the generation of monoclonal antibodies that specifically recognize hESC surface antigens using a decoy immunization strategy. In this study, we show that monoclonal antibody 57-C11 recognizes a phosphorylated form of adenovirus early region 1B-associated protein 5 (E1B-AP5). E1B-AP5 is a nuclear RNA-binding protein, but we report that 57-C11-reactive E1B-AP5 is expressed on the surface of undifferentiated hESCs. In undifferentiated hESCs, 57-C11-reactive E1B-AP5 is localized to SSEA3-, SSEA4-, TRA-1-60-, TRA-1-81-, OCT4-, SOX2-, and NANOG-positive hESCs. In mixtures of undifferentiated hESCs and hESC-derived neurons, 57-C11 exclusively recognizes undifferentiated hESCs but not hESC-derived neuronal cells. Further, the expression of 57-C11-reactive E1B-AP5 decreases upon differentiation. Our results demonstrate that 57-C11-reactive E1B-AP5 is a novel surface molecule that is involved in the undifferentiated state of hESCs. As far as we know, this is the first report demonstrating that heterogeneous nuclear RNA-binding protein is expressed on the surface of undifferentiated hESCs.
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Affiliation(s)
- Hong Seo Choi
- Department of Bioscience and Biotechnology, Institute of Bioscience, Sejong University, Seoul, Korea
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Swartling FJ, Grimmer MR, Hackett CS, Northcott PA, Fan QW, Goldenberg DD, Lau J, Masic S, Nguyen K, Yakovenko S, Zhe XN, Gilmer HCF, Collins R, Nagaoka M, Phillips JJ, Jenkins RB, Tihan T, Vandenberg SR, James CD, Tanaka K, Taylor MD, Weiss WA, Chesler L. Pleiotropic role for MYCN in medulloblastoma. Genes Dev 2010; 24:1059-72. [PMID: 20478998 DOI: 10.1101/gad.1907510] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Sonic Hedgehog (SHH) signaling drives a minority of MB, correlating with desmoplastic pathology and favorable outcome. The majority, however, arises independently of SHH and displays classic or large cell anaplastic (LCA) pathology and poor prognosis. To identify common signaling abnormalities, we profiled mRNA, demonstrating misexpression of MYCN in the majority of human MB and negligible expression in normal cerebella. We clarified a role in pathogenesis by targeting MYCN (and luciferase) to cerebella of transgenic mice. MYCN-driven MB showed either classic or LCA pathologies, with Shh signaling activated in approximately 5% of tumors, demonstrating that MYCN can drive MB independently of Shh. MB arose at high penetrance, consistent with a role for MYCN in initiation. Tumor burden correlated with bioluminescence, with rare metastatic spread to the leptomeninges, suggesting roles for MYCN in both progression and metastasis. Transient pharmacological down-regulation of MYCN led to both clearance and senescence of tumor cells, and improved survival. Targeted expression of MYCN thus contributes to initiation, progression, and maintenance of MB, suggesting a central role for MYCN in pathogenesis.
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Affiliation(s)
- Fredrik J Swartling
- University of California at San Francisco, San Francisco, California 94158, USA
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