1
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Ge Y, Weng H, Sun Y, Wu M. Integrated single-cell and spatial transcriptomic analysis reveals YBX1 drives immune regulation in GBM progression. Heliyon 2024; 10:e29451. [PMID: 38628755 PMCID: PMC11019236 DOI: 10.1016/j.heliyon.2024.e29451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The RNA modification 5-methylcytosine (m5C) is widespread across various RNA types, significantly impacting RNA stability and translational efficiency. Accumulating evidence highlights its significant role within the tumorigenesis and progression of multiple malignancies. Nevertheless, the specific process through m5C is implicated in Glioblastoma (GBM) remains unclear. We conducted acomprehensive analysis of m5C expression distribution in single-cell GBM data. Our findings revealed elevated m5C scores in GBM single-cell data compared to the normal group. Additionally, multiple tumors exhibited significantly higher m5C scores than the normal group. Moreover, there was a positive correlation observed between the m5C score and inflammation score. m5C regulatory factor YBX1 exhibited a heightened expression in GBM, correlating closely with metastatic tendencies and an unfavorable prognosis across various cancer types. YBX1 has different biological functions in myeloid cells 1 and myeloid cells 2. YBX1 may act as immunosuppressive regulator by inhibiting the NF-κB pathway and inflammatory response in myeloid cells 1. YBX1 is essential for immune infiltrates, which creates a highly immunosuppressive tumor microenvironment by TNF signaling pathway in myeloid cells 2. YBX1+ neoplastic cells promote cell proliferation by NF-κB pathway. APOE mediates the interaction of YBX1+ myeloid cells and neoplastic cells by NF-κB.
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Affiliation(s)
- Yanshan Ge
- Hunan Provincial Tumor Hospital / the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Huiting Weng
- Department of Clinical Nursing, The Second Xiangya Hospital of Central South University, Changsha, 410008, Hunan, China
| | - Yingnan Sun
- Hunan Provincial Tumor Hospital / the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital / the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, 410008, Hunan, China
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2
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Maciak P, Suder A, Wadas J, Aronimo F, Maiuri P, Bochenek M, Pyrc K, Kula-Pacurar A, Pabis M. Dynamic changes in LINC00458/HBL1 lncRNA expression during hiPSC differentiation to cardiomyocytes. Sci Rep 2024; 14:109. [PMID: 38167488 PMCID: PMC10761834 DOI: 10.1038/s41598-023-49753-3] [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: 10/18/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute the largest and most diverse class of non-coding RNAs. They localize to the nucleus, cytoplasm, or both compartments, and regulate gene expression through various mechanisms at multiple levels. LncRNAs tend to evolve faster and present higher tissue- and developmental stage-specific expression than protein-coding genes. Initially considered byproducts of erroneous transcription without biological function, lncRNAs are now recognized for their involvement in numerous biological processes, such as immune response, apoptosis, pluripotency, reprogramming, and differentiation. In this study, we focused on Heart Brake lncRNA 1 (HBL1), a lncRNA recently reported to modulate the process of pluripotent stem cell differentiation toward cardiomyocytes. We employed RT-qPCR and high-resolution RNA FISH to monitor the expression and localization of HBL1 during the differentiation progression. Our findings indicate a significant increase in HBL1 expression during mesodermal and cardiac mesodermal stages, preceding an anticipated decrease in differentiated cells. We detected the RNA in discrete foci in both the nucleus and in the cytoplasm. In the latter compartment, we observed colocalization of HBL1 with Y-box binding protein 1 (YB-1), which likely results from an interaction between the RNA and the protein, as the two were found to be coimmunoprecipitated in RNP-IP experiments. Finally, we provide evidence that HBL1, initially reported as an independent lncRNA gene, is part of the LINC00458 (also known as lncRNA-ES3 or ES3) gene, forming the last exon of some LINC00458 splice isoforms.
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Affiliation(s)
- Patrycja Maciak
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Agnieszka Suder
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Jakub Wadas
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Faith Aronimo
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Paolo Maiuri
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Michał Bochenek
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Anna Kula-Pacurar
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland.
| | - Marta Pabis
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland.
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3
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Heger J, Partsch S, Harjung C, Varga ZV, Baranyai T, Weiß J, Kremer L, Locquet F, Leszek P, Ágg B, Benczik B, Ferdinandy P, Schulz R, Euler G. YB-1 Is a Novel Target for the Inhibition of α-Adrenergic-Induced Hypertrophy. Int J Mol Sci 2023; 25:401. [PMID: 38203580 PMCID: PMC10778708 DOI: 10.3390/ijms25010401] [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: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Cardiac hypertrophy resulting from sympathetic nervous system activation triggers the development of heart failure. The transcription factor Y-box binding protein 1 (YB-1) can interact with transcription factors involved in cardiac hypertrophy and may thereby interfere with the hypertrophy growth process. Therefore, the question arises as to whether YB-1 influences cardiomyocyte hypertrophy and might thereby influence the development of heart failure. YB-1 expression is downregulated in human heart biopsies of patients with ischemic cardiomyopathy (n = 8), leading to heart failure. To study the impact of reduced YB-1 in cardiac cells, we performed small interfering RNA (siRNA) experiments in H9C2 cells as well as in adult cardiomyocytes (CMs) of rats. The specificity of YB-1 siRNA was analyzed by a miRNA-like off-target prediction assay identifying potential genes. Testing three high-scoring genes by transfecting cardiac cells with YB-1 siRNA did not result in downregulation of these genes in contrast to YB-1, whose downregulation increased hypertrophic growth. Hypertrophic growth was mediated by PI3K under PE stimulation, as well by downregulation with YB-1 siRNA. On the other hand, overexpression of YB-1 in CMs, caused by infection with an adenovirus encoding YB-1 (AdYB-1), prevented hypertrophic growth under α-adrenergic stimulation with phenylephrine (PE), but not under stimulation with growth differentiation factor 15 (GDF15; n = 10-16). An adenovirus encoding the green fluorescent protein (AdGFP) served as the control. YB-1 overexpression enhanced the mRNA expression of the Gq inhibitor regulator of G-protein signaling 2 (RGS2) under PE stimulation (n = 6), potentially explaining its inhibitory effect on PE-induced hypertrophic growth. This study shows that YB-1 protects cardiomyocytes against PE-induced hypertrophic growth. Like in human end-stage heart failure, YB-1 downregulation may cause the heart to lose its protection against hypertrophic stimuli and progress to heart failure. Therefore, the transcription factor YB-1 is a pivotal signaling molecule, providing perspectives for therapeutic approaches.
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Affiliation(s)
- Jacqueline Heger
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
| | - Stefan Partsch
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
| | - Claudia Harjung
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
| | - Zoltán V. Varga
- HCEMM-SU Cardiometabolic Immunology Research Group, 1094 Budapest, Hungary;
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1094 Budapest, Hungary; (T.B.); (B.Á.); (B.B.); (P.F.)
| | - Tamás Baranyai
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1094 Budapest, Hungary; (T.B.); (B.Á.); (B.B.); (P.F.)
| | - Johannes Weiß
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
| | - Lea Kremer
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
| | - Fabian Locquet
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
| | - Przemyslaw Leszek
- Department of Heart Failure and Transplantology, Cardinal Stefan Wyszyński Institute of Cardiology, 04-628 Warszawa, Poland;
| | - Bence Ágg
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1094 Budapest, Hungary; (T.B.); (B.Á.); (B.B.); (P.F.)
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Bettina Benczik
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1094 Budapest, Hungary; (T.B.); (B.Á.); (B.B.); (P.F.)
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Péter Ferdinandy
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1094 Budapest, Hungary; (T.B.); (B.Á.); (B.B.); (P.F.)
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Rainer Schulz
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
| | - Gerhild Euler
- Institute of Physiology, Justus Liebig University, 35392 Giessen, Germany; (S.P.); (C.H.); (J.W.); (L.K.); (F.L.); (R.S.); (G.E.)
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4
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Maltseva D, Tonevitsky A. RNA-binding proteins regulating the CD44 alternative splicing. Front Mol Biosci 2023; 10:1326148. [PMID: 38106992 PMCID: PMC10722200 DOI: 10.3389/fmolb.2023.1326148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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5
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Li H, Zhang D, Fu Q, Wang S, Wang Z, Zhang X, Chen X, Zhu X, An N, Chen Y, Zhou L, Lu D, Zhao N. YBX1 as an oncogenic factor in T-cell acute lymphoblastic leukemia. Blood Adv 2023; 7:4874-4885. [PMID: 37339496 PMCID: PMC10469076 DOI: 10.1182/bloodadvances.2022009648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/28/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Y-box-binding protein 1 (YBX1), a member of the RNA-binding protein family, is a critical regulator of cell survival in various solid tumors and acute myeloid leukemia. However, the function of YBX1 in T-cell acute lymphoblastic leukemia (T-ALL) remains elusive. Here, we found that YBX1 was upregulated in patients with T-ALL, T-ALL cell lines, and NOTCH1-induced T-ALL mice. Furthermore, depletion of YBX1 dramatically reduced cell proliferation, induced cell apoptosis, and induced G0/G1 phase arrest in vitro. Moreover, YBX1 depletion significantly decreased the leukemia burden in the human T-ALL xenograft and NOTCH1-induced T-ALL mice model in vivo. Mechanistically, downregulation of YBX1 markedly inhibited the expression of total AKT serine/threonine kinase (AKT), p-AKT, total extracellular signal-regulated kinase (ERK), and p-ERK in T-ALL cells. Taken together, our results uncovered a critical role of YBX1 in the leukemogenesis of T-ALL, which may have great potential as a biomarker and therapeutic target in T-ALL.
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Affiliation(s)
- Huan Li
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, China
| | - Danlan Zhang
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Qiuxia Fu
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Shang Wang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Zhongyuan Wang
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xin Zhang
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xin Chen
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xiaoyu Zhu
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Na An
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Yun Chen
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, China
| | - Liang Zhou
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Desheng Lu
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Na Zhao
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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6
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Zheng C, Wei Y, Zhang Q, Sun M, Wang Y, Hou J, Zhang P, Lv X, Su D, Jiang Y, Gumin J, Sahni N, Hu B, Wang W, Chen X, McGrail DJ, Zhang C, Huang S, Xu H, Chen J, Lang FF, Hu J, Chen Y. Multiomics analyses reveal DARS1-AS1/YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. SCIENCE ADVANCES 2023; 9:eadf3984. [PMID: 37540752 PMCID: PMC10403220 DOI: 10.1126/sciadv.adf3984] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The glioblastoma (GBM) stem cell-like cells (GSCs) are critical for tumorigenesis/therapeutic resistance of GBM. Mounting evidence supports tumor-promoting function of long noncoding RNAs (lncRNAs), but their role in GSCs remains poorly understood. By combining CRISPRi screen with orthogonal multiomics approaches, we identified a lncRNA DARS1-AS1-controlled posttranscriptional circuitry that promoted the malignant properties of GBM cells/GSCs. Depleting DARS1-AS1 inhibited the proliferation of GBM cells/GSCs and self-renewal of GSCs, prolonging survival in orthotopic GBM models. DARS1-AS1 depletion also impaired the homologous recombination (HR)-mediated double-strand break (DSB) repair and enhanced the radiosensitivity of GBM cells/GSCs. Mechanistically, DARS1-AS1 interacted with YBX1 to promote target mRNA binding and stabilization, forming a mixed transcriptional/posttranscriptional feed-forward loop to up-regulate expression of the key regulators of G1-S transition, including E2F1 and CCND1. DARS1-AS1/YBX1 also stabilized the mRNA of FOXM1, a master transcription factor regulating GSC self-renewal and DSB repair. Our findings suggest DARS1-AS1/YBX1 axis as a potential therapeutic target for sensitizing GBM to radiation/HR deficiency-targeted therapy.
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Affiliation(s)
- Caishang Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yunfei Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiakai Hou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiangdong Lv
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yujie Jiang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Statistics, Rice University, Houston, TX 77005, USA
| | - Joy Gumin
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nidhi Sahni
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA
| | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Pediatric Neurosurgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Molecular and Cellular Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel J. McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
- Lerner Research Institute, Cleveland, OH 44195, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, and Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Suyun Huang
- Department of Human and Molecular Genetics, Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Han Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Frederick F. Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Hu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Cancer Biology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Neuroscience Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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7
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Chograni M, Alahdal HM, Rejili M. Autosomal recessive congenital cataract is associated with a novel 4-bp splicing deletion mutation in a novel C10orf71 human gene. Hum Genomics 2023; 17:41. [PMID: 37179318 PMCID: PMC10182639 DOI: 10.1186/s40246-023-00492-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023] Open
Abstract
Congenital cataract is one of the most genetically heterogeneous ocular conditions with different genes involved in its etiology. Here, we describe the analysis of a new candidate gene of a congenital bilateral cataract associated with polymalformative syndrome, moderate global developmental delay, microcephaly, axial hypotonia, intrauterine growth restriction and facial dysmorphism for two affected siblings. Molecular analysis included exome sequencing and genome wide homozygosity mapping revealed a region of homozygosity shared by the two affected siblings at 10q11.23. The new C10orf71 gene was included in this interval and direct sequencing of this gene revealed an already described homozygous c. 2123T > G mutation (p. L708R) for the two affected subjects. Interestingly, we revealed in contrast a 4-bp deletion on the 3'-splicing acceptor site of intron 3-exon 4, namely defined as IVS3-5delGCAA. The C10Orf71 gene expression analysis using RT-PCR showed an expression pattern in different fetal organs and tissues as well as in leukocytes and confirmed that the IVS3-5delGCAA deletion of the C10orf71 gene is a splicing mutation responsible for the shortening of the C10orf71 protein in the two related patients. The C10orf71 gene has not been described to date as associated to the autosomal recessive phenotype.
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Affiliation(s)
- M Chograni
- Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El Manar, Tunis, Tunisia
| | - H M Alahdal
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia.
| | - M Rejili
- Department of Life Sciences, College of Sciences, Al Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
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8
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Braems E, Bercier V, Van Schoor E, Heeren K, Beckers J, Fumagalli L, Dedeene L, Moisse M, Geudens I, Hersmus N, Mehta AR, Selvaraj BT, Chandran S, Ho R, Thal DR, Van Damme P, Swinnen B, Van Den Bosch L. HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS. Acta Neuropathol 2022; 144:465-488. [PMID: 35895140 PMCID: PMC9381635 DOI: 10.1007/s00401-022-02471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/24/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022]
Abstract
A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The exact mechanism resulting in these neurodegenerative diseases remains elusive, but C9 repeat RNA toxicity has been implicated as a gain-of-function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS-linked phenotype. We discovered that the RNA-binding protein heterogeneous nuclear ribonucleoprotein K (HNRNPK) reverses the toxicity of both sense and antisense repeat RNA, which is dependent on its subcellular localization and RNA recognition, and not on C9orf72 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts, induced pluripotent stem cell (iPSC)-derived motor neurons and post-mortem motor cortex and spinal cord, in line with a disrupted HNRNPK function in C9orf72 ALS. In C9orf72 ALS/FTD patient tissue, we discovered an increased nuclear translocation, but reduced expression of ribonucleotide reductase regulatory subunit M2 (RRM2), a downstream target of HNRNPK involved in the DNA damage response. Last but not least, we showed that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9orf72 RNA toxicity zebrafish model. Overall, our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9orf72 ALS and demonstrates its link with an aberrant DNA damage response, opening novel therapeutic avenues for C9orf72 ALS/FTD.
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Affiliation(s)
- Elke Braems
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Valérie Bercier
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium.
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium.
| | - Evelien Van Schoor
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
- Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
| | - Kara Heeren
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Jimmy Beckers
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Laura Fumagalli
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Lieselot Dedeene
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
- Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Department of Neurosciences, Laboratory for Molecular Neurobiomarker Research and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Ilse Geudens
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Nicole Hersmus
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Arpan R Mehta
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Bhuvaneish T Selvaraj
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Ritchie Ho
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - Dietmar R Thal
- Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Bart Swinnen
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium.
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium.
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9
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Wang JZ, Zhu H, You P, Liu H, Wang WK, Fan X, Yang Y, Xu K, Zhu Y, Li Q, Wu P, Peng C, Wong CC, Li K, Shi Y, Zhang N, Wang X, Zeng R, Huang Y, Yang L, Wang Z, Hui J. Up-regulated YB-1 protein promotes glioblastoma growth through an YB-1/CCT4/mLST8/mTOR pathway. J Clin Invest 2022; 132:146536. [PMID: 35239512 PMCID: PMC9012288 DOI: 10.1172/jci146536] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/01/2022] [Indexed: 11/17/2022] Open
Abstract
The Y-box binding protein 1 (YB-1) is a multi-functional RNA binding protein involved in virtually each step of RNA metabolism. However, the functions and mechanisms of YB-1 in one of the most aggressive cancers, glioblastoma, are not well understood. In this study, we identified that YB-1 protein was markedly overexpressed in glioblastoma and acted as a critical activator of both mTORC1 and mTORC2 signaling. Mechanistically, YB-1 bound the 5' untranslated region (UTR) of the CCT4 mRNA to promote the translation of CCT4, a component of CCT chaperone complex, that in turn activated the mTOR signal pathway by promoting mLST8 folding. In addition, YB-1 autoregulated its own translation by binding to its 5' UTR, leading to sustained activation of mTOR signaling. In glioblastoma patients, the protein level of YB-1 positively correlated with CCT4 and mLST8 expression as well as activated mTOR signaling. Importantly, the administration of RNA decoys specifically targeting YB-1 in a mouse xenograft model resulted in slower tumor growth and better survival. Taken together, these findings uncover a disrupted proteostasis pathway involving YB-1/CCT4/mLST8/mTOR axis in promoting glioblastoma growth, suggesting that YB-1 is a potential therapeutic target for the treatment of glioblastoma.
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Affiliation(s)
- Jin-Zhu Wang
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Hong Zhu
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Pu You
- Institute of Brain-Intelligence Technology, Zhangjiang Laboratory, Shanghai, China
| | - Hui Liu
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Wei-Kang Wang
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojuan Fan
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yun Yang
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Keren Xu
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yingfeng Zhu
- Department of Pathology, Fudan University, Shanghai, China
| | - Qunyi Li
- Department of Pharmacy, Fudan University, Shanghai, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Catherine Cl Wong
- Center for Precision Medicine Multi-Omics Research, Peking University, Beijing, China
| | - Kaicheng Li
- Institute of Brain-Intelligence Technology, Zhangjiang Laboratory, Shanghai, China
| | - Yufeng Shi
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Nu Zhang
- Department of Neurosurgery, The 1st Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiuxing Wang
- School of Basic Medical Science, Nanjing Medical University, Nanjing, China
| | - Rong Zeng
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ying Huang
- Department of General Surgery, Shanghai Jiao Tong University, Shanghai, China
| | - Liusong Yang
- Department of Neurosurgery, Fudan University, Shanghai, China
| | - Zefeng Wang
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jingyi Hui
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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10
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Abstract
Infection with dengue virus (DENV) induces vast rearrangements of the endoplasmic reticulum, which allows the compartmentalization of viral RNA replication and particle assembly. Both processes occur in concert with viral and cellular proteins. Prior studies from our group suggest that the host RNA-binding protein (RBP) Y-box binding protein 1 (YBX1) is required for a late step in the DENV replication cycle. Here we report that YBX1 interacts with the viral nucleocapsid, distributes to DENV assembly sites and is required for efficient assembly of intracellular infectious virions and their secretion. Genetic ablation of YBX1 decreased the spatial proximity between capsid and envelope, increased the susceptibility of envelope to proteinase K mediated degradation, resulted in the formation of rough empty-looking particles, and decreased the secretion of viral particles. We propose a model wherein YBX1 enables the interaction between the viral nucleocapsid with the structural protein E, which is required for proper assembly of intracellular virus particles and their secretion. IMPORTANCE The global incidence of dengue virus (DENV) infections has steadily increased over the past decades representing an enormous challenge for public health. During infection, DENV viral RNA interacts with numerous host RNA binding proteins (RBPs) that aid viral replication and thus constitute potential molecular targets to curb infection. We recently reported that Y-box-binding protein 1 (YBX1) interacts with DENV RNA and is required at a late step of the replication cycle. Here we describe the molecular mechanism by which YBX1 mediates DENV infection. We show that YBX1 interacts with the viral nucleocapsid, distributes to DENV assembly sites and is required for efficient assembly of intracellular infectious virions. These results provide important insights into DENV assembly, revealing novel functions of host RBPs during viral infection and opening new avenues for antiviral intervention.
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11
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Gao Y, Lin KT, Jiang T, Yang Y, Rahman MA, Gong S, Bai J, Wang L, Sun J, Sheng L, Krainer AR, Hua Y. Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA. Nucleic Acids Res 2022; 50:731-749. [PMID: 35018432 PMCID: PMC8789036 DOI: 10.1093/nar/gkab1280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Intronic splicing enhancers and silencers (ISEs and ISSs) are two groups of splicing-regulatory elements (SREs) that play critical roles in determining splice-site selection, particularly for alternatively spliced introns or exons. SREs are often short motifs; their mutation or dysregulation of their cognate proteins frequently causes aberrant splicing and results in disease. To date, however, knowledge about SRE sequences and how they regulate splicing remains limited. Here, using an SMN2 minigene, we generated a complete pentamer-sequence library that comprises all possible combinations of 5 nucleotides in intron 7, at a fixed site downstream of the 5′ splice site. We systematically analyzed the effects of all 1023 mutant pentamers on exon 7 splicing, in comparison to the wild-type minigene, in HEK293 cells. Our data show that the majority of pentamers significantly affect exon 7 splicing: 584 of them are stimulatory and 230 are inhibitory. To identify actual SREs, we utilized a motif set enrichment analysis (MSEA), from which we identified groups of stimulatory and inhibitory SRE motifs. We experimentally validated several strong SREs in SMN1/2 and other minigene settings. Our results provide a valuable resource for understanding how short RNA sequences regulate splicing. Many novel SREs can be explored further to elucidate their mechanism of action.
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Affiliation(s)
- Yuan Gao
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Tao Jiang
- Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Yang Yang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Mohammad A Rahman
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Shuaishuai Gong
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jialin Bai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Junjie Sun
- Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Lei Sheng
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Yimin Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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12
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Hamon L, Budkina K, Pastré D. YB-1 Structure/Function Relationship in the Packaging of mRNPs and Consequences for Translation Regulation and Stress Granule Assembly in Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S20-S93. [PMID: 35501984 DOI: 10.1134/s0006297922140036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
From their synthesis in the nucleus to their degradation in the cytoplasm, all mRNAs have the same objective, which is to translate the DNA-stored genetic information into functional proteins at the proper time and location. To this end, many proteins are generally associated with mRNAs as soon as transcription takes place in the nucleus to organize spatiotemporal regulation of the gene expression in cells. Here we reviewed how YB-1 (YBX1 gene), one of the major mRNA-binding proteins in the cytoplasm, packaged mRNAs into either compact or extended linear nucleoprotein mRNPs. Interestingly the structural plasticity of mRNPs coordinated by YB-1 could provide means for the contextual regulation of mRNA translation. Posttranslational modification of YB-1, notably in the long unstructured YB-1 C-terminal domain (CTD), and/or the protein partners of YB-1 may play a key role in activation/inactivation of mRNPs in the cells notably in response to cellular stress.
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Affiliation(s)
- Loïc Hamon
- SABNP, UnivEvry, INSERM U1204, Université Paris-Saclay, Evry, 91025, France.
| | - Karina Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - David Pastré
- SABNP, UnivEvry, INSERM U1204, Université Paris-Saclay, Evry, 91025, France.
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13
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YBX1 mediates translation of oncogenic transcripts to control cell competition in AML. Leukemia 2021; 36:426-437. [PMID: 34465866 PMCID: PMC8807392 DOI: 10.1038/s41375-021-01393-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022]
Abstract
Persistence of malignant clones is a major determinant of adverse outcome in patients with hematologic malignancies. Despite the fact that the majority of patients with acute myeloid leukemia (AML) achieve complete remission after chemotherapy, a large proportion of them relapse as a result of residual malignant cells. These persistent clones have a competitive advantage and can re-establish disease. Therefore, targeting strategies that specifically diminish cell competition of malignant cells while leaving normal cells unaffected are clearly warranted. Recently, our group identified YBX1 as a mediator of disease persistence in JAK2-mutated myeloproliferative neoplasms. The role of YBX1 in AML, however, remained so far elusive. Here, inactivation of YBX1 confirms its role as an essential driver of leukemia development and maintenance. We identify its ability to amplify the translation of oncogenic transcripts, including MYC, by recruitment to polysomal chains. Genetic inactivation of YBX1 disrupts this regulatory circuit and displaces oncogenic drivers from polysomes, with subsequent depletion of protein levels. As a consequence, leukemia cells show reduced proliferation and are out-competed in vitro and in vivo, while normal cells remain largely unaffected. Collectively, these data establish YBX1 as a specific dependency and therapeutic target in AML that is essential for oncogenic protein expression.
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14
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Alkrekshi A, Wang W, Rana PS, Markovic V, Sossey-Alaoui K. A comprehensive review of the functions of YB-1 in cancer stemness, metastasis and drug resistance. Cell Signal 2021; 85:110073. [PMID: 34224843 DOI: 10.1016/j.cellsig.2021.110073] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
The Y Box binding protein 1 (YB-1) is a member of the highly conserved Cold Shock Domain protein family with multifunctional properties both in the cytoplasm and inside the nucleus. YB-1 is also involved in various cellular functions, including regulation of transcription, mRNA stability, and splicing. Recent studies have associated YB-1 with the regulation of the malignant phenotypes in several tumor types. In this review article, we provide an in-depth and expansive review of the literature pertaining to the multiple physiological functions of YB-1. We will also review the role of YB-1 in cancer development, progression, metastasis, and drug resistance in various malignancies, with more weight on literature published in the last decade. The methodology included querying databases PubMed, Embase, and Google Scholar for Y box binding protein 1, YB-1, YBX1, and Y-box-1.
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Affiliation(s)
- Akram Alkrekshi
- Department of Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.; MetroHealth Medical Center, Rammelkamp Center for Research, R457, 2500 MetroHealth Drive, Cleveland, OH 44109, USA
| | - Wei Wang
- Department of Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.; MetroHealth Medical Center, Rammelkamp Center for Research, R457, 2500 MetroHealth Drive, Cleveland, OH 44109, USA
| | - Priyanka Shailendra Rana
- Department of Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.; MetroHealth Medical Center, Rammelkamp Center for Research, R457, 2500 MetroHealth Drive, Cleveland, OH 44109, USA
| | - Vesna Markovic
- MetroHealth Medical Center, Rammelkamp Center for Research, R457, 2500 MetroHealth Drive, Cleveland, OH 44109, USA
| | - Khalid Sossey-Alaoui
- Department of Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.; MetroHealth Medical Center, Rammelkamp Center for Research, R457, 2500 MetroHealth Drive, Cleveland, OH 44109, USA; Case Comprehensive Cancer Center, Cleveland, OH, USA.
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15
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Tailor D, Resendez A, Garcia-Marques FJ, Pandrala M, Going CC, Bermudez A, Kumar V, Rafat M, Nambiar DK, Honkala A, Le QT, Sledge GW, Graves E, Pitteri SJ, Malhotra SV. Y box binding protein 1 inhibition as a targeted therapy for ovarian cancer. Cell Chem Biol 2021; 28:1206-1220.e6. [PMID: 33713600 DOI: 10.1016/j.chembiol.2021.02.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 12/29/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022]
Abstract
Y box binding protein 1 (YB-1) is a multifunctional protein associated with tumor progression and the emergence of treatment resistance (TR). Here, we report an azopodophyllotoxin small molecule, SU056, that potently inhibits tumor growth and progression via YB-1 inhibition. This YB-1 inhibitor inhibits cell proliferation, resistance to apoptosis in ovarian cancer (OC) cells, and arrests in the G1 phase. Inhibitor treatment leads to enrichment of proteins associated with apoptosis and RNA degradation pathways while downregulating spliceosome pathway. In vivo, SU056 independently restrains OC progression and exerts a synergistic effect with paclitaxel to further reduce disease progression with no observable liver toxicity. Moreover, in vitro mechanistic studies showed delayed disease progression via inhibition of drug efflux and multidrug resistance 1, and significantly lower neurotoxicity as compared with etoposide. These data suggest that YB-1 inhibition may be an effective strategy to reduce OC progression, antagonize TR, and decrease patient mortality.
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Affiliation(s)
- Dhanir Tailor
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Cell, Development and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Angel Resendez
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Fernando Jose Garcia-Marques
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Mallesh Pandrala
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Cell, Development and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Catherine C Going
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Abel Bermudez
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Vineet Kumar
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Marjan Rafat
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37212, USA
| | - Dhanya K Nambiar
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Alexander Honkala
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - George W Sledge
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Edward Graves
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sanjay V Malhotra
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Cell, Development and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA.
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16
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Jayavelu AK, Schnöder TM, Perner F, Herzog C, Meiler A, Krishnamoorthy G, Huber N, Mohr J, Edelmann-Stephan B, Austin R, Brandt S, Palandri F, Schröder N, Isermann B, Edlich F, Sinha AU, Ungelenk M, Hübner CA, Zeiser R, Rahmig S, Waskow C, Coldham I, Ernst T, Hochhaus A, Jilg S, Jost PJ, Mullally A, Bullinger L, Mertens PR, Lane SW, Mann M, Heidel FH. Splicing factor YBX1 mediates persistence of JAK2-mutated neoplasms. Nature 2020; 588:157-163. [PMID: 33239784 DOI: 10.1038/s41586-020-2968-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 09/15/2020] [Indexed: 11/09/2022]
Abstract
Janus kinases (JAKs) mediate responses to cytokines, hormones and growth factors in haematopoietic cells1,2. The JAK gene JAK2 is frequently mutated in the ageing haematopoietic system3,4 and in haematopoietic cancers5. JAK2 mutations constitutively activate downstream signalling and are drivers of myeloproliferative neoplasm (MPN). In clinical use, JAK inhibitors have mixed effects on the overall disease burden of JAK2-mutated clones6,7, prompting us to investigate the mechanism underlying disease persistence. Here, by in-depth phosphoproteome profiling, we identify proteins involved in mRNA processing as targets of mutant JAK2. We found that inactivation of YBX1, a post-translationally modified target of JAK2, sensitizes cells that persist despite treatment with JAK inhibitors to apoptosis and results in RNA mis-splicing, enrichment for retained introns and disruption of the transcriptional control of extracellular signal-regulated kinase (ERK) signalling. In combination with pharmacological JAK inhibition, YBX1 inactivation induces apoptosis in JAK2-dependent mouse and primary human cells, causing regression of the malignant clones in vivo, and inducing molecular remission. This identifies and validates a cell-intrinsic mechanism whereby differential protein phosphorylation causes splicing-dependent alterations of JAK2-ERK signalling and the maintenance of JAK2V617F malignant clones. Therapeutic targeting of YBX1-dependent ERK signalling in combination with JAK2 inhibition could thus eradicate cells harbouring mutations in JAK2.
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Affiliation(s)
| | - Tina M Schnöder
- Innere Medizin II, Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany.,Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Florian Perner
- Innere Medizin II, Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Carolin Herzog
- Department of Haematology and Oncology, Center of Internal Medicine, Otto von Guericke University Medical Center, Magdeburg, Germany
| | - Arno Meiler
- Max Planck Institute of Biochemistry, Munich, Germany
| | | | - Nicolas Huber
- Innere Medizin II, Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Juliane Mohr
- Innere Medizin II, Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Bärbel Edelmann-Stephan
- Department of Haematology and Oncology, Center of Internal Medicine, Otto von Guericke University Medical Center, Magdeburg, Germany
| | - Rebecca Austin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Cancer Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.,University of Queensland, Brisbane, Queensland, Australia
| | - Sabine Brandt
- Department of Nephrology and Endocrinology, Center of Internal Medicine, Otto von Guericke University Medical Center, Magdeburg, Germany
| | | | | | - Berend Isermann
- Institute for Clinical Chemistry and Pathobiochemistry, Center of Internal Medicine, Otto von Guericke University Medical Center, Magdeburg, Germany
| | - Frank Edlich
- Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,BIOSS, Centre for Biological Signaling Studies, Freiburg, Germany
| | | | - Martin Ungelenk
- Institut für Humangenetik, Universitätsklinikum Jena, Jena, Germany
| | | | - Robert Zeiser
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Department of Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Susann Rahmig
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.,Immunology of Aging, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Claudia Waskow
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.,Immunology of Aging, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Iain Coldham
- Department of Chemistry, University of Sheffield, Sheffield, UK
| | - Thomas Ernst
- Innere Medizin II, Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Andreas Hochhaus
- Innere Medizin II, Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Stefanie Jilg
- Medical Department III for Haematology and Oncology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Philipp J Jost
- Medical Department III for Haematology and Oncology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lars Bullinger
- Clinic for Hematology, Oncology and Tumor Immunology, Charite University, Berlin, Germany
| | - Peter R Mertens
- Department of Nephrology and Endocrinology, Center of Internal Medicine, Otto von Guericke University Medical Center, Magdeburg, Germany
| | - Steven W Lane
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Cancer Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.,University of Queensland, Brisbane, Queensland, Australia
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Munich, Germany.
| | - Florian H Heidel
- Innere Medizin II, Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany. .,Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany. .,Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
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17
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McCauley C, Anang V, Cole B, Simmons GE. Potential Links between YB-1 and Fatty Acid Synthesis in Clear Cell Renal Carcinoma. ACTA ACUST UNITED AC 2020; 8. [PMID: 33778158 DOI: 10.18103/mra.v8i10.2273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
According to the National Institutes of Health, clear cell renal cell carcinoma (ccRCC) is the most common type of Renal Cell Carcinoma (RCC), making up approximately 75% of total renal carcinoma cases. Clear cell Renal Cell Carcinoma is characterized by a significant accumulation of lipids in the cytoplasm, which allows light from microscopes to pass through giving them a "clear" phenotype. Many of these lipids are in the form of fatty acids, both free and incorporated into lipid droplets. RCC is typically associated with a poor prognosis due to the lack of specific symptoms. Some symptoms include blood in urine, fever, lump on the side, weight loss, fatigue, to name a few; all of which can be associated with non-specific, non-cancerous, health conditions that contribute to difficult diagnosis. Treatment of RCC has typically been centered around radical nephrectomy as the standard of care, but due to the potentially small size of lesions and the possibility of causing surgically induced chronic kidney disease, treatments have shifted to more cautious, less invasive approaches. These approaches include active surveillance, nephron-sparing surgery, and other minimally invasive techniques like cryotherapy and renal ablation. Although these techniques have had the desired effect of reducing the number of surgeries, there is still considerable potential for renal impairment and the chance that tumors can grow out of control without surgery. With the difficulty that surrounds the treatment of ccRCC and its considerably high mortality rate amongst urological cancers, it is important to look for novel approaches to improve patient outcomes. This review looks at available literature and our data that suggests the lipogenic enzyme stearoyl-CoA desaturase may be more beneficial to patient survival than once thought. As our understanding of the importance of lipids in cell metabolism and longevity matures, it is important to present new perspectives that present a new understanding of ccRCC and the role of lipids in survival mechanisms engaged by transformed cells during cancer progression. In this review, we provide evidence that pharmacological inhibition of lipid desaturation in renal cancer patients is not without risk, and that the presence of unsaturated fatty acids may be a beneficial factor in patient outcomes. Although more direct experimental evidence is needed to make definitive conclusions, it is clear that the work reviewed herein should challenge our current understanding of cancer biology and may inform novel approaches to the diagnosis and treatment of ccRCC.
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Affiliation(s)
- Carter McCauley
- University of Minnesota Medical School, Duluth, MN, MN 55812, USA
| | - Vasthy Anang
- Clinical and Translational Science Institute PREP Program, University of Minnesota Medical School, Minneapolis, MN, MN 55812, USA
| | - Breanna Cole
- Department of Biology, The College of St. Scholastica, Duluth, MN, 55811, USA
| | - Glenn E Simmons
- University of Minnesota Medical School, Duluth, MN, MN 55812, USA.,Clinical and Translational Science Institute PREP Program, University of Minnesota Medical School, Minneapolis, MN, MN 55812, USA.,Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, MN 55812, USA.,Carcinogenesis and Chemoprevention program, Masonic Cancer Center, Minneapolis, MN 55455, USA
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18
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Hartley AV, Wang B, Mundade R, Jiang G, Sun M, Wei H, Sun S, Liu Y, Lu T. PRMT5-mediated methylation of YBX1 regulates NF-κB activity in colorectal cancer. Sci Rep 2020; 10:15934. [PMID: 32985589 PMCID: PMC7522246 DOI: 10.1038/s41598-020-72942-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/25/2020] [Indexed: 12/25/2022] Open
Abstract
The multifunctional protein Y-box binding protein 1 (YBX1), is a critical regulator of transcription and translation, and is widely recognized as an oncogenic driver in several solid tumors, including colorectal cancer (CRC). However, very little is known about the upstream or downstream factors that underlie YBX1′s regulation and involvement in CRC. Previously, we demonstrated that YBX1 overexpression correlated with potent activation of nuclear factor κB (NF-κB), a well-known transcription factor believed to be crucial in CRC progression. Here, we report a novel interaction between NF-κB, YBX1 and protein arginine methyltransferase 5 (PRMT5). Our findings reveal for the first time that PRMT5 catalyzes methylation of YBX1 at arginine 205 (YBX1-R205me2), an event that is critical for YBX1-mediated NF-κB activation and its downstream target gene expression. Importantly, when WT-YBX1 is overexpressed, this methylation exists under basal (unstimulated) conditions and is further augmented upon interleukin-1β (IL-1β) stimulation. Mechanistically, co-immunoprecipitation studies reveal that the R205 to alanine (A) mutant of YBX1 (YBX1-R205A) interacted less well with the p65 subunit of NF-κB and attenuated the DNA binding ability of p65. Importantly, overexpression of YBX1-R205A significantly reduced cell growth, migration and anchorage-independent growth of CRC cells. Collectively, our findings shed important light on the regulation of a novel PRMT5/YBX1/NF-κB axis through PRMT5-mediated YBX1-R205 methylation. Given the fact that PRMT5, YBX1 and NF-κB are all among top crucial factors in cancer progression, pharmacological disruption of this pivotal axis could serve as the basis for new therapeutics for CRC and other PRMT5/YBX1/NF-κB-associated cancers.
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Affiliation(s)
- Antja-Voy Hartley
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, 46202, USA
| | - Benlian Wang
- Case Western Reserve University, Cleveland, OH, USA
| | - Rasika Mundade
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, 46202, USA
| | - Guanglong Jiang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mengyao Sun
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, 46202, USA
| | - Han Wei
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, 46202, USA
| | - Steven Sun
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, 46202, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tao Lu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, 46202, USA. .,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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19
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Zhang J, Fan JS, Li S, Yang Y, Sun P, Zhu Q, Wang J, Jiang B, Yang D, Liu M. Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation. Nucleic Acids Res 2020; 48:9361-9371. [PMID: 32710623 PMCID: PMC7498358 DOI: 10.1093/nar/gkaa619] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/27/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Human Y-box binding protein 1 (YB-1) is a multifunctional protein and overexpressed in many types of cancer. It specifically recognizes DNA/RNA through a cold shock domain (CSD) and regulates nucleic acid metabolism. The C-terminal extension of CSD and the phosphorylation of S102 are indispensable for YB-1 function. Until now, the roles of the C-terminal extension and phosphorylation in gene transcription and translation are still largely unknown. Here, we solved the structure of human YB-1 CSD with a C-terminal extension sequence (CSDex). The structure reveals that the extension interacts with several residues in the conventional CSD and adopts a rigid structure instead of being disordered. Either deletion of this extension or phosphorylation of S102 destabilizes the protein and results in partial unfolding. Structural characterization of CSDex in complex with a ssDNA heptamer shows that all the seven nucleotides are involved in DNA-protein interactions and the C-terminal extension provides a unique DNA binding site. Our DNA-binding study indicates that CSDex can recognize more DNA sequences than previously thought and the phosphorylation reduces its binding to ssDNA dramatically. Our results suggest that gene transcription and translation can be regulated by changing the affinity of CSDex binding to DNA and RNA through phosphorylation, respectively.
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Affiliation(s)
- Jingfeng Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Peng Sun
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Qinjun Zhu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Jiannan Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
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20
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Bates M, Boland A, McDermott N, Marignol L. YB-1: The key to personalised prostate cancer management? Cancer Lett 2020; 490:66-75. [PMID: 32681926 DOI: 10.1016/j.canlet.2020.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Y-box-binding protein 1 (YB-1) is a DNA/RNA binding protein increasingly implicated in the regulation of cancer cell biology. Normally located in the cytoplasm, nuclear localisation in prostate cancer is associated with more aggressive, potentially treatment-resistant disease. This is attributed to the ability of YB-1 to act as a transcription factor for various target genes associated with androgen receptor signalling, survival, DNA repair, proliferation, invasion, differentiation, angiogenesis and hypoxia. This review aims to examine the clinical potential of YB-1 in the detection and therapeutic management of prostate cancer.
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Affiliation(s)
- Mark Bates
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland
| | - Anna Boland
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland
| | - Niamh McDermott
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland
| | - Laure Marignol
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland.
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21
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Gopanenko AV, Malygin AA, Kossinova OA, Tupikin AE, Kabilov MR, Karpova GG. Degenerate consensus sequences in the 3'-untranslated regions of cellular mRNAs as specific motifs potentially involved in the YB-1-mediated packaging of these mRNAs. Biochimie 2020; 170:152-162. [PMID: 31935443 DOI: 10.1016/j.biochi.2020.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/09/2020] [Indexed: 02/08/2023]
Abstract
The multifunctional protein YB-1 has previously been shown to be the only protein of the cytoplasmic extract of HEK293 cells, which is able to specifically interact with imperfect RNA hairpins containing motifs that are often found in exosomal (e) RNAs. In addition, it has been revealed that similar hairpins formed by degenerate consensus sequences corresponding to three eRNA-specific motifs are responsible for the cooperative binding of YB-1 to RNA in vitro. Here, using the photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation method applied to HEK293 cells producing FLAG-labeled YB-1, we identified mRNAs cross-linked to YB-1 in vivo and then carried out a search for the aforementioned sequences in the regions of the YB-1 cross-linking sites. It turned out that many of the mRNAs found cross-linked to YB-1 encode proteins associated with various regulatory processes, including responses to stress. More than half of all cross-linked mRNAs contained degenerate consensus sequences, which were preferably located in 3'-untranslated regions (UTRs), where most of the YB-1 cross-linking sites appeared, although not close to these sequences. Furthermore, YB-1 was mainly cross-linked to those mRNAs with degenerate consensus sequences, which could be classified as packaged because their translation levels were low compared to cellular levels. This suggests that the cooperative binding of YB-1 to mRNAs through the above sequences probably triggers the well-known multimerization of YB-l, leading to the packaging of these mRNAs. Thus, our findings indicate a previously unknown link between the degenerate consensus sequences present in the 3'-UTRs of many cytoplasmic mRNAs and YB-1-mediated translational silencing.
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Affiliation(s)
- Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Olga A Kossinova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk, 630090, Russia.
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22
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Inhibition of Transcription Induces Phosphorylation of YB-1 at Ser102 and Its Accumulation in the Nucleus. Cells 2019; 9:cells9010104. [PMID: 31906126 PMCID: PMC7016903 DOI: 10.3390/cells9010104] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/26/2019] [Accepted: 12/30/2019] [Indexed: 02/04/2023] Open
Abstract
The Y-box binding protein 1 (YB-1) is an RNA/DNA-binding protein regulating gene expression in the cytoplasm and the nucleus. Although mostly cytoplasmic, YB-1 accumulates in the nucleus under stress conditions. Its nuclear localization is associated with aggressiveness and multidrug resistance of cancer cells, which makes the understanding of the regulatory mechanisms of YB-1 subcellular distribution essential. Here, we report that inhibition of RNA polymerase II (RNAPII) activity results in the nuclear accumulation of YB-1 accompanied by its phosphorylation at Ser102. The inhibition of kinase activity reduces YB-1 phosphorylation and its accumulation in the nucleus. The presence of RNA in the nucleus is shown to be required for the nuclear retention of YB-1. Thus, the subcellular localization of YB-1 depends on its post-translational modifications (PTMs) and intracellular RNA distribution.
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23
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Kretov DA, Clément MJ, Lambert G, Durand D, Lyabin DN, Bollot G, Bauvais C, Samsonova A, Budkina K, Maroun RC, Hamon L, Bouhss A, Lescop E, Toma F, Curmi PA, Maucuer A, Ovchinnikov LP, Pastré D. YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis. Nucleic Acids Res 2019; 47:3127-3141. [PMID: 30605522 PMCID: PMC6451097 DOI: 10.1093/nar/gky1303] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022] Open
Abstract
The structural rearrangements accompanying mRNA during translation in mammalian cells remain poorly understood. Here, we discovered that YB-1 (YBX1), a major partner of mRNAs in the cytoplasm, forms a linear nucleoprotein filament with mRNA, when part of the YB-1 unstructured C-terminus has been truncated. YB-1 possesses a cold-shock domain (CSD), a remnant of bacterial cold shock proteins that have the ability to stimulate translation under the low temperatures through an RNA chaperone activity. The structure of the nucleoprotein filament indicates that the CSD of YB-1 preserved its chaperone activity also in eukaryotes and shows that mRNA is channeled between consecutive CSDs. The energy benefit needed for the formation of stable nucleoprotein filament relies on an electrostatic zipper mediated by positively charged amino acid residues in the YB-1 C-terminus. Thus, YB-1 displays a structural plasticity to unfold structured mRNAs into extended linear filaments. We anticipate that our findings will shed the light on the scanning of mRNAs by ribosomes during the initiation and elongation steps of mRNA translation.
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Affiliation(s)
- Dmitry A Kretov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation.,SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Marie-Jeanne Clément
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Guillaume Lambert
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation
| | | | - Cyril Bauvais
- Synsight, a/s IncubAlliance 86 rue de Paris Orsay 91400, France
| | - Anastasiia Samsonova
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Karina Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation.,SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Rachid C Maroun
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ahmed Bouhss
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Flavio Toma
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Patrick A Curmi
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Alexandre Maucuer
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation
| | - David Pastré
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
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24
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Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y. Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. J Biol Chem 2019; 294:10998-11010. [PMID: 31160337 PMCID: PMC6635445 DOI: 10.1074/jbc.ra119.007545] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/26/2019] [Indexed: 01/07/2023] Open
Abstract
The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1-mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunoprecipitation coupled RNA-Seq (iCLIP-Seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of a CD44 variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1-RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 Å resolution. The structure revealed that CSD interacts with RNA mainly through π-π stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA-binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD-RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.
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Affiliation(s)
- Xiao-Juan Yang
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Hong Zhu
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Shi-Rong Mu
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Wen-Juan Wei
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Xun Yuan
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Meng Wang
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Yanchao Liu
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Jingyi Hui
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and , To whom correspondence may be addressed:
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. Tel.:
86-21-54921354; E-mail:
| | - Ying Huang
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China, To whom correspondence may be addressed:
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. Tel.:
86-21-20778200; E-mail:
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25
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Stavrovskaya AA, Rybalkina EY. Recent Advances in the Studies of Molecular Mechanisms Regulating Multidrug Resistance in Cancer Cells. BIOCHEMISTRY (MOSCOW) 2018; 83:779-786. [PMID: 30200862 DOI: 10.1134/s0006297918070015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we present new approaches to better understanding multidrug resistance (MDR) development in cancer cells, such as identification of components of a complex process of MDR evolution. Recent advances in the studies of MDR are discussed: 1) chemotherapy agents might be involved in the selection of cancer stem cells resulting in the elevated drug resistance and enhanced tumorigenicity; 2) cell-cell interactions have a great effect on the MDR emergence and evolution; 3) mechanotransduction is an important signaling mechanism in cell-cell interactions; 4) proteins of the ABC transporter family which are often involved in MDR might be transferred between cells via microvesicles (epigenetic MDR regulation); 5) proteins providing cell-to-cell transfer of functional P-glycoprotein (MDR1 protein) via microvesicles have been investigated; 6) P-glycoprotein may serve to regulate apoptosis, as well as transcription and translation of target genes/proteins. Although proving once again that MDR is a complex multi-faceted process, these data open new approaches to overcoming it.
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Affiliation(s)
- A A Stavrovskaya
- Blokhin Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia.
| | - E Yu Rybalkina
- Blokhin Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia
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26
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Youneszadeh-Fashalami M, Salati AP, Keyvanshokooh S. Comparison of proteomic profiles in the ovary of Sterlet sturgeon (Acipenser ruthenus) during vitellogenic stages. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 27:23-29. [PMID: 29738886 DOI: 10.1016/j.cbd.2018.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 11/29/2022]
Abstract
One of the challenges of sturgeon aquaculture is that sturgeon takes an extended amount of time to reach sexual maturity. The pattern of the protein expression in relation to the late maturity of sturgeon can help to better understand changes in sexual maturity. 17β-estradiol (E2), testosterone (T) and vitellogenin (Vtg) levels were examined at all stages of sexual maturation in Sterlet sturgeon (Acipenser ruthenus). Two-dimensional gel electrophoresis and mass spectrometry analysis were used to show the pattern of the ovarian proteins. The T levels increased from the previtellogenic to the postvitellogenic stages (P < 0.05) and Vtg showed a decremental pattern in pre- and postvitellogenic, and atresia (not significantly). The analysis showed 900 protein spots, 19 of which were successfully identified and had significant differences between the previtellogenic and the vitellogenic groups (P < 0.05). Among the identified proteins, 40% involved in cell defense (heat shock protein, Glutathione peroxidase, natural killer enhancing factor, peroxiredoxin-2), 30% in transcription and translation (constitutive photomorphogenesis 9 and Ybx2), 20% in metabolism and energy production (triose-phosphate isomerase (TPI)) and 10% in transport (glycolipid transfer protein). In the vitellogenic stage, the proteins were related to metabolism and energy production (TPI, ES1, creatin kinase, enolase, nucleoside diphosphate kinase, 50%), cell defense (thioredoxin and dislophid isomerase, 20%) and transport (fatty acid binding protein, 10%). Our findings show changes in protein expression pattern from cell defense to metabolism during egg development.
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Affiliation(s)
- Mohammad Youneszadeh-Fashalami
- Department of Fisheries, Faculty of marine Natural Resources, Khorramshahr University of Marine Science and Technology, Iran; South Iranian Aquaculture Research Center, Ahwaz, Iran
| | - Amir Parviz Salati
- Department of Fisheries, Faculty of marine Natural Resources, Khorramshahr University of Marine Science and Technology, Iran.
| | - Saeed Keyvanshokooh
- Department of Fisheries, Faculty of marine Natural Resources, Khorramshahr University of Marine Science and Technology, Iran
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27
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Kwon E, Todorova K, Wang J, Horos R, Lee KK, Neel VA, Negri GL, Sorensen PH, Lee SW, Hentze MW, Mandinova A. The RNA-binding protein YBX1 regulates epidermal progenitors at a posttranscriptional level. Nat Commun 2018; 9:1734. [PMID: 29712925 PMCID: PMC5928080 DOI: 10.1038/s41467-018-04092-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/29/2018] [Indexed: 01/10/2023] Open
Abstract
The integrity of stratified epithelia depends on the ability of progenitor cells to maintain a balance between proliferation and differentiation. While much is known about the transcriptional pathways underlying progenitor cells’ behavior in the epidermis, the role of posttranscriptional regulation by mRNA binding proteins—a rate-limiting step in sculpting the proteome—remains poorly understood. Here we report that the RNA binding protein YBX1 (Y-box binding protein-1) is a critical effector of progenitors’ function in the epidermis. YBX1 expression is restricted to the cycling keratinocyte progenitors in vivo and its genetic ablation leads to defects in the architecture of the skin. We further demonstrate that YBX1 negatively controls epidermal progenitor senescence by regulating the translation of a senescence-associated subset of cytokine mRNAs via their 3′ untranslated regions. Our study establishes YBX1 as a posttranscriptional effector required for maintenance of epidermal homeostasis. The integrity of the stratified epithelia relies on controlled cell turnover but it is unclear how mRNA binding proteins regulates this. Here, the authors show that the RNA binding protein Y-box binding protein-1 translationally represses cytokines, so preventing senescence and maintaining epidermal homeostasis.
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Affiliation(s)
- Eunjeong Kwon
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Kristina Todorova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Jun Wang
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Rastislav Horos
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Kevin K Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Victor A Neel
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Sam W Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA.,Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Anna Mandinova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA. .,Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA, 02142, USA. .,Harvard Stem Cell Institute, 7 Divinity Avenue Cambridge, Cambridge, MA, 02138, USA.
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28
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Wang Y, Wang Y, Xu L, Lu X, Fu D, Su J, Geng H, Qin G, Chen R, Quan C, Niu Y, Yue D. CD4 + T cells promote renal cell carcinoma proliferation via modulating YBX1. Exp Cell Res 2017; 363:95-101. [PMID: 29289594 DOI: 10.1016/j.yexcr.2017.12.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/14/2017] [Accepted: 12/27/2017] [Indexed: 12/25/2022]
Abstract
Renal cell carcinoma (RCC) is a common urologic tumor and the third leading cause of death among urological tumors. Recent studies demonstrate that RCC tumors are more heavily infiltrated by lymphocytes than other cancers. However, the exact roles played by CD4 + T cells in RCC proliferation remain unknown. In this study, we cocultured RCC cells with CD4 + T cells. Stable knockdown of YBX1 in RCC cells was constructed. The effects of CD4 + T cells, TGFβ1 and YBX1 on RCC cells were investigated using cell viability assays. In situ RCC nude mouse model was used to observe the tumor growth. The potential mechanisms of CD4 + T cells and YBX1 in RCC cells proliferation were explored by qRT-PCR and western blot. Expression of CD4, Foxp3 and TGFβ1 in RCC were quantified by immunohistochemical staining. The results indicated that CD4, Foxp3 and TGFβ1 were significantly up-regulated in RCC tissues. Human clinical sample and in vitro cell lines studies showed that RCC cells had better capacity than its surrounding normal kidney epithelial cells to recruit the CD4 + T cells. In vivo mouse model studies were consistent with the results by in vitro cell lines studies showing infiltrating T cells enhanced RCC cell proliferation. qRT-PCR and western blot exhibited that CD4 + T cells could enhance RCC cell proliferation via activating YBX1/HIF2α signaling pathway. Furthermore, CD4 + T cells functioned through inducing TGFβ1 expression. In a word, infiltrating CD4 + T cells promoted TGFβ1 expression in both RCC and T cells and regulated RCC cells proliferation via modulating TGFβ1/YBX1/ HIF2α signals.
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Affiliation(s)
- Yong Wang
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Yiting Wang
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Liang Xu
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Xianqi Lu
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Donghe Fu
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Jing Su
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Hua Geng
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Guoxuan Qin
- School of Microelectronics, Tianjin University, Tianjin 300072, China
| | - Ruibing Chen
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Changyi Quan
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Yuanjie Niu
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Dan Yue
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China.
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29
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Rambout X, Dequiedt F, Maquat LE. Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing. Chem Rev 2017; 118:4339-4364. [PMID: 29251915 DOI: 10.1021/acs.chemrev.7b00470] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Whereas individual steps of protein-coding gene expression in eukaryotes can be studied in isolation in vitro, it has become clear that these steps are intimately connected within cells. Connections not only ensure quality control but also fine-tune the gene expression process, which must adapt to environmental changes while remaining robust. In this review, we systematically present proven and potential mechanisms by which sequence-specific DNA-binding transcription factors can alter gene expression beyond transcription initiation and regulate pre-mRNA splicing, and thereby mRNA isoform production, by (i) influencing transcription elongation rates, (ii) binding to pre-mRNA to recruit splicing factors, and/or (iii) blocking the association of splicing factors with pre-mRNA. We propose various mechanistic models throughout the review, in some cases without explicit supportive evidence, in hopes of providing fertile ground for future studies.
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30
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Structural features of the interaction of the 3'-untranslated region of mRNA containing exosomal RNA-specific motifs with YB-1, a potential mediator of mRNA sorting. Biochimie 2017; 144:134-143. [PMID: 29133115 DOI: 10.1016/j.biochi.2017.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/08/2017] [Indexed: 12/18/2022]
Abstract
We have previously shown that YB-1 is the only protein of the HEK293 cell cytoplasmic (S100) extract that specifically interacts with RNA hairpins each containing one of the motifs ACCAGCCU (1), CAGUGAGC (2) and UAAUCCCA (3), which had been identified as often found in exosomal RNA and proposed as potential cis-acting elements targeting RNAs into exosomes. Here we explored the interactions of YB-1 with a fragment of the 3'-untranslated region (UTR) of septin 14 mRNA (SEPT14 RNA), which contains all three motifs. We demonstrated the occurrence of YB-1 among proteins pulled down from the HEK293 S100 extract using biotinylated SEPT14 RNA. With recombinant YB-1, it was found that SEPT14 RNA can bind up to 5 moles of protein per mole of RNA in a cooperative manner, which was shown to be mainly facilitated by the presence of the above motifs. RNA hairpins with motifs 1 and 2 competed with SEPT14 RNA for binding to the protein, whereas that with motif 3 was less competitive, in accordance with the affinity of YB-1 for these RNA hairpins. With YB-1-bound RNA, nucleotides protected from attack by hydroxyl radicals were revealed in all three motifs, although hairpins with motif 2 and especially with motif 1 contained many protected nucleotides outside the motifs, suggesting that the specific environments of these motifs contribute significantly to the YB-1 binding. An analysis of the environments of motifs 1-3 in the HEK293 cell mRNA 3' UTRs gained from RNA-seq data led us to conclude that the primary binding sites of YB-1 in the 3' UTRs are hairpins containing some part of the motif along with its specific surroundings; the consensus sequences of these hairpins were derived. Thus, our findings provide a new understanding of the structural basis of the interactions between YB-1 and mRNAs carrying the aforementioned motifs.
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31
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Liu H, Zhang L, Wei Q, Shi Z, Shi X, Du J, Huang C, Zhang Y, Guo Z. Comprehensive Proteomic Analysis of PGC7-Interacting Proteins. J Proteome Res 2017; 16:3113-3123. [PMID: 28712289 DOI: 10.1021/acs.jproteome.6b00883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Primordial germ cell 7 (PGC7), a maternal factor essential for early development, plays a critical role in the regulation of DNA methylation, transcriptional repression, chromatin condensation, and cell division and the maintenance of cell pluripotentiality. Despite the fundamental roles of PGC7 in these cellular processes, only a few molecular and functional interactions of PGC7 have been reported. Here, a streptavidin-biotin affinity purification technique combined with LC-MS/MS was used to analyze potential proteins that interact with PGC7. In total, 291 potential PGC7-interacting proteins were identified. Through an in-depth bioinformatic analysis of potential interactors, we linked PGC7 to critical cellular processes including translation, RNA processing, cell cycle, and regulation of heterochromatin structure. To better understand the functional interactions of PGC7 with its potential interactors, we constructed a protein-protein interaction network using the STRING database. In addition, we discussed in detail the interactions between PGC7 and some of its newly validated partners. The identification of these potential interactors of PGC7 expands our knowledge on the PGC7 interactome and provides a valuable resource for understanding the diverse functions of this protein.
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Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Lei Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zhaopeng Shi
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Xiaoyan Shi
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medical Experiment Center of Shaanxi University of Chinese Medicine , Xianyang, Shaanxi 712000, China
| | - Juan Du
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medicine School of Yan'an University , Yan'an, Shaanxi 716000, China
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
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32
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Maurya PK, Mishra A, Yadav BS, Singh S, Kumar P, Chaudhary A, Srivastava S, Murugesan SN, Mani A. Role of Y Box Protein-1 in cancer: As potential biomarker and novel therapeutic target. J Cancer 2017; 8:1900-1907. [PMID: 28819388 PMCID: PMC5556654 DOI: 10.7150/jca.17689] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
The Y-box binding protein (YB-1) is known to be a multifunctional transcription and translation factor during expression of several proteins. It is a vital oncoprotein that regulates cancer cell progression and proliferation. YB-1 is over-expressed in various human cancers such as breast cancer, colon cancer, lung cancer, gastric cancer, oesophageal cancer and glioblastoma. Nuclear expression of YB-1 is found to be associated with multidrug resistance and cancer cell progression. YB-1 is reported to regulate many cellular signalling pathways in different types of cancer proliferation. Knowledge about nuclear localization and nuclear level expression of YB-1 in different cancers has been correlated with prospective prognosis of cancer. This review discusses the prospects of YB-1 as a potential biomarker as well as therapeutic target in lieu of their role during cancer progression and multidrug resistance.
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Affiliation(s)
| | - Alok Mishra
- Department of Biotechnology, MNNIT Allahabad-211004
| | | | - Swati Singh
- Center of Bioinformatics, University of Allahabad, Allahabad-211002
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33
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Xiping Z, Qingshan W, Shuai Z, Hongjian Y, Xiaowen D. A summary of relationships between alternative splicing and breast cancer. Oncotarget 2017; 8:51986-51993. [PMID: 28881705 PMCID: PMC5584306 DOI: 10.18632/oncotarget.17727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/05/2017] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is the process of combinatorial rearrangement of parts of exons, and/or parts of introns into mature RNA to result in a multitude of transcripts. AS is a biological process through which organisms produce as many protein variants as possible by a limited genetic resource. It plays an important role in growth and development of the organisms. Over the past few years, alternative splicing has been discovered to be critical for genesis and development of malignant tumors, including breast cancer. If the relationships between AS and breast cancer can be discussed more deeply, it will be helpful for better diagnosis, judging prognosis and intervening with breast cancer. In this paper, the relationships between AS and breast cancer are elaborated from different angles, in hope that this summary is beneficial for readers to understand the roles of AS and breast cancer.
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Affiliation(s)
- Zhang Xiping
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Wei Qingshan
- Cataloging Department, Library of Xi'an Jiaotong University, Xi'an 710049, Shaanxi Province, China
| | - Zhao Shuai
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Yang Hongjian
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Ding Xiaowen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
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34
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Wu W, Zong J, Wei N, Cheng J, Zhou X, Cheng Y, Chen D, Guo Q, Zhang B, Feng Y. CASH: a constructing comprehensive splice site method for detecting alternative splicing events. Brief Bioinform 2017; 19:905-917. [DOI: 10.1093/bib/bbx034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/03/2023] Open
Affiliation(s)
- Wenwu Wu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Hangzhou, China
| | - Jie Zong
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ning Wei
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jian Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xuexia Zhou
- Tianjin Medical University General Hospital, China
| | - Yuanming Cheng
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Dai Chen
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Qinghua Guo
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Bo Zhang
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ying Feng
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
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35
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Kossinova OA, Gopanenko AV, Tamkovich SN, Krasheninina OA, Tupikin AE, Kiseleva E, Yanshina DD, Malygin AA, Ven'yaminova AG, Kabilov MR, Karpova GG. Cytosolic YB-1 and NSUN2 are the only proteins recognizing specific motifs present in mRNAs enriched in exosomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:664-673. [PMID: 28341602 DOI: 10.1016/j.bbapap.2017.03.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/27/2022]
Abstract
Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC. RNA hairpins other than those mentioned above pull out neither YB-1 nor NSUN2. Both these proteins are found in exosomes secreted by HEK293 cells. YB-1 for all that is detected as a form having a slightly higher electrophoretic mobility than that of YB-1 associated with the above RNA hairpins, assuming changes in posttranslational modifications of the protein during its transfer from cytoplasm into exosomes. Next generation sequencing of total exosomal RNA (eRNA) reveals a large representative set of RNA species, including mRNAs containing the above-mentioned motifs. The degree of enrichment in exosomes with this kind of mRNAs strongly depends on the locations of eRNA-specific motifs within the mRNA sequences. Altogether, our findings point to YB-1 and NSUN2 as possible mediators of the process of transfer of specific mRNAs into exosomes, allowing us to speculate on an involvement of these proteins in the mRNA sorting via the recognition of the above motifs.
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Affiliation(s)
- Olga A Kossinova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Svetlana N Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Elena Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 10, Novosibirsk 630090, Russia
| | - Darya D Yanshina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alia G Ven'yaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia.
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Rajendran D, Zhang Y, Berry DM, McGlade CJ. Regulation of Numb isoform expression by activated ERK signaling. Oncogene 2016; 35:5202-13. [PMID: 27041567 DOI: 10.1038/onc.2016.69] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 12/23/2015] [Accepted: 01/25/2016] [Indexed: 12/29/2022]
Abstract
The endocytic adaptor protein Numb has a major role in development as an intrinsic regulator of cell fate determination and inhibitor of the Notch signaling pathway. In vertebrates, four protein isoforms of Numb are produced through alternative splicing (AS) of two cassette exons (exons 3 and 9). AS of coding exon 9 (E9) produces E9-included (p72/p71) and -excluded (p66/p65) protein products. Expression of Numb isoforms is developmentally regulated and E9-included products are expressed in progenitors, whereas E9-excluded isoforms are dominantly expressed in differentiated cells. Analyses of AS events in multiple cancers previously identified a switch in Numb transcript and protein expression from the E9-excluded to the E9-included isoform, suggesting that misregulation of the mechanisms that control E9 inclusion may have a role in tumorigenesis. Here we identify splicing factors ASF/SF2 and PTBP1 as regulators of E9 splicing and show that activation of the mitogen-activated protein kinase/extracellular signal-regulated kinase pathway promotes E9 inclusion in cancer cells. Our evidence supports a mechanism by which Numb AS is regulated in response to oncogenic signaling pathways, and contributes to activation of downstream pathways to promote tumorigenesis.
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Affiliation(s)
- D Rajendran
- Program in Cell Biology, and The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Y Zhang
- Program in Cell Biology, and The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - D M Berry
- Program in Cell Biology, and The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - C J McGlade
- Program in Cell Biology, and The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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Cellular responses to HSV-1 infection are linked to specific types of alterations in the host transcriptome. Sci Rep 2016; 6:28075. [PMID: 27354008 PMCID: PMC4926211 DOI: 10.1038/srep28075] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/26/2016] [Indexed: 02/06/2023] Open
Abstract
Pathogen invasion triggers a number of cellular responses and alters the host transcriptome. Here we report that the type of changes to cellular transcriptome is related to the type of cellular functions affected by lytic infection of Herpes Simplex Virus type I in Human primary fibroblasts. Specifically, genes involved in stress responses and nuclear transport exhibited mostly changes in alternative polyadenylation (APA), cell cycle genes showed mostly alternative splicing (AS) changes, while genes in neurogenesis, rarely underwent these changes. Transcriptome wide, the infection resulted in 1,032 cases of AS, 161 incidences of APA, 1,827 events of isoform changes, and up regulation of 596 genes and down regulations of 61 genes compared to uninfected cells. Thus, these findings provided important and specific links between cellular responses to HSV-1 infection and the type of alterations to the host transcriptome, highlighting important roles of RNA processing in virus-host interactions.
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Kleene KC. Position-dependent interactions of Y-box protein 2 (YBX2) with mRNA enable mRNA storage in round spermatids by repressing mRNA translation and blocking translation-dependent mRNA decay. Mol Reprod Dev 2016; 83:190-207. [PMID: 26773323 DOI: 10.1002/mrd.22616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/08/2016] [Indexed: 12/18/2022]
Abstract
Many mRNAs encoding proteins needed for the construction of the specialized organelles of spermatozoa are stored as translationally repressed, free messenger ribonucleoproteins in round spermatids, to be actively translated in elongating and elongated spermatids. The factors that repress translation in round spermatids, however, have been elusive. Two lines of evidence implicate the highly abundant and well-known translational repressor, Y-box protein 2 (YBX2), as a critical factor: First, protamine 1 (Prm1) and sperm-mitochondria cysteine-rich protein (Smcp) mRNAs are prematurely recruited onto polysomes in Ybx2-knockout mouse round spermatids. Second, mutations in 3' untranslated region (3'UTR) cis-elements that abrogate YBX2 binding activate translation of Prm1 and Smcp mRNAs in round spermatids of transgenic mice. The abundance of YBX2 and its affinity for variable sequences, however, raise questions of how YBX2 targets specific mRNAs for repression. Mutations to the Prm1 and Smcp mRNAs in transgenic mice reveal that strong repression in round spermatids requires YBX2 binding sites located near the 3' ends of their 3'UTRs as locating the same sites in upstream positions produce negligible repression. This location-dependence implies that the assembly of repressive complexes is nucleated by adjacent cis-elements that enable cooperative interactions of YBX2 with co-factors. The available data suggest that, in vertebrates, YBX2 has the important role of coordinating the storage of translationally repressed mRNAs in round spermatids by inhibiting translational activity and the degradation of transcripts via translation-dependent deadenylation. These insights should facilitiate future experiments designed to unravel how YBX2 targets mRNAs for repression in round spermatids and how mutations in the YBX2 gene cause infertility in humans. Mol. Reprod. Dev. 83: 190-207, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kenneth C Kleene
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts
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Shiota M, Fujimoto N, Imada K, Yokomizo A, Itsumi M, Takeuchi A, Kuruma H, Inokuchi J, Tatsugami K, Uchiumi T, Oda Y, Naito S. Potential Role for YB-1 in Castration-Resistant Prostate Cancer and Resistance to Enzalutamide Through the Androgen Receptor V7. J Natl Cancer Inst 2016; 108:djw005. [DOI: 10.1093/jnci/djw005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 01/06/2016] [Indexed: 12/17/2022] Open
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Ajiro M, Jia R, Yang Y, Zhu J, Zheng ZM. A genome landscape of SRSF3-regulated splicing events and gene expression in human osteosarcoma U2OS cells. Nucleic Acids Res 2015; 44:1854-70. [PMID: 26704980 PMCID: PMC4770227 DOI: 10.1093/nar/gkv1500] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023] Open
Abstract
Alternative RNA splicing is an essential process to yield proteomic diversity in eukaryotic cells, and aberrant splicing is often associated with numerous human diseases and cancers. We recently described serine/arginine-rich splicing factor 3 (SRSF3 or SRp20) being a proto-oncogene. However, the SRSF3-regulated splicing events responsible for its oncogenic activities remain largely unknown. By global profiling of the SRSF3-regulated splicing events in human osteosarcoma U2OS cells, we found that SRSF3 regulates the expression of 60 genes including ERRFI1, ANXA1 and TGFB2, and 182 splicing events in 164 genes, including EP300, PUS3, CLINT1, PKP4, KIF23, CHK1, SMC2, CKLF, MAP4, MBNL1, MELK, DDX5, PABPC1, MAP4K4, Sp1 and SRSF1, which are primarily associated with cell proliferation or cell cycle. Two SRSF3-binding motifs, CCAGC(G)C and A(G)CAGCA, are enriched to the alternative exons. An SRSF3-binding site in the EP300 exon 14 is essential for exon 14 inclusion. We found that the expression of SRSF1 and SRSF3 are mutually dependent and coexpressed in normal and tumor tissues/cells. SRSF3 also significantly regulates the expression of at least 20 miRNAs, including a subset of oncogenic or tumor suppressive miRNAs. These data indicate that SRSF3 affects a global change of gene expression to maintain cell homeostasis.
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Affiliation(s)
- Masahiko Ajiro
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Rong Jia
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yanqin Yang
- DNA Sequencing and Genomics Core, System Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Zhu
- DNA Sequencing and Genomics Core, System Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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Paquet ÉR, Hovington H, Brisson H, Lacombe C, Larue H, Têtu B, Lacombe L, Fradet Y, Lebel M. Low level of the X-linked ribosomal protein S4 in human urothelial carcinomas is associated with a poor prognosis. Biomark Med 2015; 9:187-97. [PMID: 25731206 DOI: 10.2217/bmm.14.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM We determined whether the Y-box binding protein-1 (YB-1) and its binding partner, the X-linked ribosomal protein S4 (RPS4X), are associated with clinical outcome in bladder cancer. MATERIALS & METHODS A population of 167 patients with muscle-invasive bladder tumor without evidence of metastasis at time of cystectomy was analyzed retrospectively. YB-1 and RPS4X expressions were evaluated immunohistochemically in tumors and analyzed for association with clinical variables and survival. RESULTS Kaplan-Meier and multivariate Cox regression analyses indicated that low expression of RPS4X was associated with a higher risk of death or disease recurrence. In contrast, YB-1 was not significantly associated with either recurrence-free or overall survival. CONCLUSION Low RPS4X expression is associated with poor disease-specific and recurrence-free survival in bladder cancer.
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Affiliation(s)
- Éric R Paquet
- Centre de Recherche sur le Cancer de l'Université Laval, 9 McMahon Street, Québec City, Québec, Canada
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Kretov DA, Curmi PA, Hamon L, Abrakhi S, Desforges B, Ovchinnikov LP, Pastré D. mRNA and DNA selection via protein multimerization: YB-1 as a case study. Nucleic Acids Res 2015; 43:9457-73. [PMID: 26271991 PMCID: PMC4627072 DOI: 10.1093/nar/gkv822] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/29/2015] [Indexed: 12/16/2022] Open
Abstract
Translation is tightly regulated in cells for keeping adequate protein levels, this task being notably accomplished by dedicated mRNA-binding proteins recognizing a specific set of mRNAs to repress or facilitate their translation. To select specific mRNAs, mRNA-binding proteins can strongly bind to specific mRNA sequences/structures. However, many mRNA-binding proteins rather display a weak specificity to short and redundant sequences. Here we examined an alternative mechanism by which mRNA-binding proteins could inhibit the translation of specific mRNAs, using YB-1, a major translation regulator, as a case study. Based on a cooperative binding, YB-1 forms stable homo-multimers on some mRNAs while avoiding other mRNAs. Via such inhomogeneous distribution, YB-1 can selectively inhibit translation of mRNAs on which it has formed stable multimers. This novel mechanistic view on mRNA selection may be shared by other proteins considering the elevated occurrence of multimerization among mRNA-binding proteins. Interestingly, we also demonstrate how, by using the same mechanism, YB-1 can form multimers on specific DNA structures, which could provide novel insights into YB-1 nuclear functions in DNA repair and multi-drug resistance.
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Affiliation(s)
- Dmitry A Kretov
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Patrick A Curmi
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Loic Hamon
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Sanae Abrakhi
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Bénédicte Desforges
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - David Pastré
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
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Wu SL, Fu X, Huang J, Jia TT, Zong FY, Mu SR, Zhu H, Yan Y, Qiu S, Wu Q, Yan W, Peng Y, Chen J, Hui J. Genome-wide analysis of YB-1-RNA interactions reveals a novel role of YB-1 in miRNA processing in glioblastoma multiforme. Nucleic Acids Res 2015; 43:8516-28. [PMID: 26240386 PMCID: PMC4787835 DOI: 10.1093/nar/gkv779] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022] Open
Abstract
Altered miRNA expression is believed to play a crucial role in a variety of human cancers; however, the mechanisms leading to the dysregulation of miRNA expression remain elusive. In this study, we report that the human Y box-binding protein (YB-1), a major mRNA packaging protein, is a novel modulator of miRNA processing in glioblastoma multiforme (GBM). Using individual nucleotide-resolution crosslinking immunoprecipitation coupled to deep sequencing (iCLIP-seq), we performed the first genome-wide analysis of the in vivo YB-1-RNA interactions and found that YB-1 preferentially recognizes a UYAUC consensus motif and binds to the majority of coding gene transcripts including pre-mRNAs and mature mRNAs. Remarkably, our data show that YB-1 also binds extensively to the terminal loop region of pri-/pre-miR-29b-2 and regulates the biogenesis of miR-29b-2 by blocking the recruitment of microprocessor and Dicer to its precursors. Furthermore, we show that down-regulation of miR-29b by YB-1, which is up-regulated in GBM, is important for cell proliferation. Together, our findings reveal a novel function of YB-1 in regulating non-coding RNA expression, which has important implications in tumorigenesis.
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Affiliation(s)
- Shuai-Lai Wu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ting-Ting Jia
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Feng-Yang Zong
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shi-Rong Mu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Zhu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Yan
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Chang Zheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Shuwei Qiu
- Department of Neurology, The Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Qun Wu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Wei Yan
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Ying Peng
- Department of Neurology, The Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Juxiang Chen
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Chang Zheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Liu TT, Arango-Argoty G, Li Z, Lin Y, Kim SW, Dueck A, Ozsolak F, Monaghan AP, Meister G, DeFranco DB, John B. Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells. RNA (NEW YORK, N.Y.) 2015; 21:1159-72. [PMID: 25904138 PMCID: PMC4436668 DOI: 10.1261/rna.045559.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
The highly conserved, multifunctional YB-1 is a powerful breast cancer prognostic indicator. We report on a pervasive role for YB-1 in which it associates with thousands of nonpolyadenylated short RNAs (shyRNAs) that are further processed into small RNAs (smyRNAs). Many of these RNAs have previously been identified as functional noncoding RNAs (http://www.johnlab.org/YB1). We identified a novel, abundant, 3'-modified short RNA antisense to Dicer1 (Shad1) that colocalizes with YB-1 to P-bodies and stress granules. The expression of Shad1 was shown to correlate with that of YB-1 and whose inhibition leads to an increase in cell proliferation. Additionally, Shad1 influences the expression of additional prognostic markers of cancer progression such as DLX2 and IGFBP2. We propose that the examination of these noncoding RNAs could lead to better understanding of prostate cancer progression.
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Affiliation(s)
- Teresa T Liu
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Gustavo Arango-Argoty
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Zhihua Li
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Yuefeng Lin
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Sang Woo Kim
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Anne Dueck
- University of Regensburg, Biochemistry I, 93053 Regensburg, Bavaria, Germany
| | - Fatih Ozsolak
- Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA
| | - A Paula Monaghan
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Gunter Meister
- University of Regensburg, Biochemistry I, 93053 Regensburg, Bavaria, Germany
| | - Donald B DeFranco
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Bino John
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
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Innate immunity: Bacterial cell-wall muramyl peptide targets the conserved transcription factor YB-1. FEBS Lett 2015; 589:1819-24. [PMID: 26026270 DOI: 10.1016/j.febslet.2015.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 01/21/2023]
Abstract
The bacterial cell wall muramyl dipeptides MDP and glucosaminyl-MDP (GMDP) are powerful immunostimulators but their binding target remains controversial. We previously reported expression cloning of GMDP-binding polypeptides and identification of Y-box protein 1 (YB-1) as their sole target. Here we show specific binding of GMDP to recombinant YB-1 protein and subcellular colocalization of YB-1 and GMDP. GMDP binding to YB-1 upregulated gene expression levels of NF-κB2, a mediator of innate immunity. Furthermore, YB-1 knockdown abolished GMDP-induced Nfkb2 expression. GMDP/YB-1 stimulation led to NF-κB2 cleavage, transport of activated NF-κB2 p52 to the nucleus, and upregulation of NF-κB2-dependent chemokine Cxcr4 gene expression. Therefore, our findings identify YB-1 as new target for muramyl peptide signaling.
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Farrokh S, Brillen AL, Haendeler J, Altschmied J, Schaal H. Critical regulators of endothelial cell functions: for a change being alternative. Antioxid Redox Signal 2015; 22:1212-29. [PMID: 25203279 DOI: 10.1089/ars.2014.6023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
SIGNIFICANCE The endothelium regulates vessel dilation and constriction, balances hemostasis, and inhibits thrombosis. In addition, pro- and anti-angiogenic molecules orchestrate proliferation, survival, and migration of endothelial cells. Regulation of all these processes requires fine-tuning of signaling pathways, which can easily be tricked into running the opposite direction when exogenous or endogenous signals get out of hand. Surprisingly, some critical regulators of physiological endothelial functions can turn malicious by mere alternative splicing, leading to the expression of protein isoforms with opposite functions. RECENT ADVANCES While reviewing the evidence of alternative splicing on cellular physiology, it became evident that expression of splice factors and their activities are regulated by externally triggered signaling cascades. Furthermore, genome-wide identification of RNA-binding sites of splicing regulatory proteins now offer a glimpse into the splicing code responsible for alternative splicing of molecules regulating endothelial functions. CRITICAL ISSUES Due to the constantly growing number of transcript and protein isoforms, it will become more and more important to identify and characterize all transcripts and proteins regulating endothelial cell functions. One critical issue will be a non-ambiguous nomenclature to keep consistency throughout different laboratories. FUTURE DIRECTIONS RNA-deep sequencing focusing on exon-exon junction needs to more reliably identify alternative splicing events combined with functional analyses that will uncover more splice variants contributing to or inhibiting proper endothelial functions. In addition, understanding the signals mediating alternative splicing and its regulation might allow us to derive new strategies to preserve endothelial function by suppressing or upregulating specific protein isoforms. Antioxid. Redox Signal. 22, 1212-1229.
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Affiliation(s)
- Sabrina Farrokh
- 1 Heisenberg-Group-Environmentally-Induced Cardiovascular Degeneration, IUF-Leibniz Research Institute for Environmental Medicine , Düsseldorf, Germany
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Lenarcic EM, Ziehr BJ, Moorman NJ. An unbiased proteomics approach to identify human cytomegalovirus RNA-associated proteins. Virology 2015; 481:13-23. [PMID: 25765003 DOI: 10.1016/j.virol.2015.02.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/18/2014] [Accepted: 02/06/2015] [Indexed: 12/13/2022]
Abstract
Post-transcriptional events regulate herpesvirus gene expression, yet few herpesvirus RNA-binding proteins have been identified. We used an unbiased approach coupling oligo(dT) affinity capture with proteomics to identify viral RNA-associated proteins during infection. Using this approach, we identified and confirmed changes in the abundance or activity of two host RNA-associated proteins, DHX9 and DDX3, in cells infected with human cytomegalovirus (HCMV). We also identified and confirmed previously unreported activities for the HCMV US22 and pp71 proteins as RNA-associated viral proteins and confirmed that a known viral RNA-binding protein, pTRS1, associates with RNA in infected cells. Further, we found that HCMV pp71 co-sedimented with polysomes, associated with host and viral RNAs, and stimulated the overall rate of protein synthesis. These results demonstrate that oligo(dT) affinity capture coupled with proteomics provides a rapid and straightforward means to identify RNA-associated viral proteins during infection that may participate in the post-transcriptional control of gene expression.
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Affiliation(s)
- Erik M Lenarcic
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Benjamin J Ziehr
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Nathaniel J Moorman
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States.
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Ha B, Lee EB, Cui J, Kim Y, Jang HH. YB-1 overexpression promotes a TGF-β1-induced epithelial-mesenchymal transition via Akt activation. Biochem Biophys Res Commun 2015; 458:347-51. [PMID: 25645014 DOI: 10.1016/j.bbrc.2015.01.114] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 11/28/2022]
Abstract
The Y-box binding protein-1 (YB-1) is a transcription/translation regulatory protein, and the expression thereof is associated with cancer aggressiveness. In the present study, we explored the regulatory effects of YB-1 during the transforming growth factor-β1 (TGF-β1)-induced epithelial-to-mesenchymal transition (EMT) in lung adenocarcinoma cells. Downregulation of YB-1 increased E-cadherin promoter activity, and upregulation of YB-1 decreased promoter activity, suggesting that the YB-1 level may be correlated with the EMT. TGF-β1 induced YB-1 expression, and TGF-β1 translocated cytosolic YB-1 into the nucleus. YB-1 overexpression promoted TGF-β1-induced downregulation of epithelial markers, upregulation of mesenchymal markers, and cell migration. Moreover, YB-1 overexpression enhanced the expression of E-cadherin transcriptional repressors via TGF-β1-induced Akt activation. Our findings afford new insights into the role played by YB-1 in the TGF-β1 signaling pathway.
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Affiliation(s)
- Bin Ha
- Department of Molecular Medicine, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-799, Republic of Korea
| | - Eun Byul Lee
- Department of Molecular Medicine, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-799, Republic of Korea
| | - Jun Cui
- Department of Molecular Medicine, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-799, Republic of Korea
| | - Yosup Kim
- Department of Molecular Medicine, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-799, Republic of Korea
| | - Ho Hee Jang
- Department of Molecular Medicine, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-799, Republic of Korea; Gachon Medical Research Institute, Gil Medical Center, Gachon University, Incheon, Republic of Korea.
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Fong N, Kim H, Zhou Y, Ji X, Qiu J, Saldi T, Diener K, Jones K, Fu XD, Bentley DL. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev 2015; 28:2663-76. [PMID: 25452276 PMCID: PMC4248296 DOI: 10.1101/gad.252106.114] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Fong et al. examined cotranscriptional pre-mRNA splicing using RNA polymerase II mutants that change average elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing and often both increased or both decreased inclusion of a particular exon or retained intron. These results suggest that an optimal rate of transcriptional elongation is required for normal cotranscriptional pre-mRNA splicing. Alternative splicing modulates expression of most human genes. The kinetic model of cotranscriptional splicing suggests that slow elongation expands and that fast elongation compresses the “window of opportunity” for recognition of upstream splice sites, thereby increasing or decreasing inclusion of alternative exons. We tested the model using RNA polymerase II mutants that change average elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing, frequently altering exon inclusion and intron retention in ways not predicted by the model. Cassette exons included by slow and excluded by fast elongation (type I) have weaker splice sites, shorter flanking introns, and distinct sequence motifs relative to “slow-excluded” and “fast-included” exons (type II). Many rate-sensitive exons are misspliced in tumors. Unexpectedly, slow and fast elongation often both increased or both decreased inclusion of a particular exon or retained intron. These results suggest that an optimal rate of transcriptional elongation is required for normal cotranscriptional pre-mRNA splicing.
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Affiliation(s)
- Nova Fong
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Hyunmin Kim
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - Xiong Ji
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - Tassa Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Katrina Diener
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Ken Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
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50
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Marzese DM, Liu M, Huynh JL, Hirose H, Donovan NC, Huynh KT, Kiyohara E, Chong K, Cheng D, Tanaka R, Morton DL, Barkhoudarian G, Kelly DF, Hoon DS. Brain metastasis is predetermined in early stages of cutaneous melanoma by CD44v6 expression through epigenetic regulation of the spliceosome. Pigment Cell Melanoma Res 2015; 28:82-93. [PMID: 25169209 PMCID: PMC4309554 DOI: 10.1111/pcmr.12307] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/12/2014] [Accepted: 08/12/2014] [Indexed: 12/20/2022]
Abstract
Melanoma brain metastasis (MBM) is frequent and has a very poor prognosis with no current predictive factors or therapeutic molecular targets. Our study unravels the molecular alterations of cell-surface glycoprotein CD44 variants during melanoma progression to MBM. High expression of CD44 splicing variant 6 (CD44v6) in primary melanoma (PRM) and regional lymph node metastases from AJCC Stage IIIC patients significantly predicts MBM development. The expression of CD44v6 also enhances the migration of MBM cells by hyaluronic acid and hepatocyte growth factor exposure. Additionally, CD44v6-positive MBM migration is reduced by blocking with a CD44v6-specific monoclonal antibody or knocking down CD44v6 by siRNA. ESRP1 and ESRP2 splicing factors correlate with CD44v6 expression in PRM, and ESRP1 knockdown significantly decreases CD44v6 expression. However, an epigenetic silencing of ESRP1 is observed in metastatic melanoma, specifically in MBM. In advanced melanomas, CD44v6 expression correlates with PTBP1 and U2AF2 splicing factors, and PTBP1 knockdown significantly decreases CD44v6 expression. Overall, these findings open a new avenue for understanding the high affinity of melanoma to progress to MBM, suggesting CD44v6 as a potential MBM-specific factor with theranostic utility for stratifying patients.
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Affiliation(s)
- Diego M. Marzese
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Michelle Liu
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Jamie L. Huynh
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Hajime Hirose
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Nicholas C. Donovan
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Kelly T. Huynh
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Eiji Kiyohara
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Kelly Chong
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - David Cheng
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Ryo Tanaka
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Donald L. Morton
- Division of Surgical Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Garni Barkhoudarian
- Brain Tumor Center & Pituitary Disorders Program, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Daniel F. Kelly
- Brain Tumor Center & Pituitary Disorders Program, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Dave S.B. Hoon
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
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