title: The Landscape of Viral Expression Reveals Clinically Relevant Viruses with Potential Capability of Promoting Malignancy in Lower-Grade Glioma.
abstract: Purpose:RNA sequencing (RNA-seq) has recently proved to be effective for revealing novel virus-tumor associations. To get a thorough investigation of virus-glioma associations, we screened viruses in gliomas with RNA-seq data from the Chinese Glioma Genome Atlas project.Experimental Design:In total, 325 samples were enrolled into this study. Reads that failed to map to the human genome were aligned to viral genomes and screened for potential virus-derived transcripts. For quantification, VPKM was calculated according to mapped reads weighted by genome sizes and sequencing depth.Results:We observed that viruses tended to concertedly express in a certain subgroup of patients. Survival analysis revealed that individuals who were infected with Simian virus 40 (SV40) or woolly monkey sarcoma virus (WMSV) had a significantly shorter overall survival than those uninfected. A multivariate Cox proportional hazards model, taking clinical and molecular factors into account, was applied to assess the prognostic value of SV40 and WMSV. Both SV40 and WMSV were independent prognostic factors for predicting patient's survival in lower-grade gliomas. Subsequent gene analysis demonstrated that SV40 was correlated with regulation of transcription, whereas WMSV was correlated with cell-cycle phase, which indicated frequent proliferation of tumor cells.Conclusions:RNA-seq was sufficient to identify virus infection in glioma samples. SV40 and WMSV were identified to be prognostic markers for patients with lower-grade gliomas and showed potential values for targeting therapy.Clin Cancer Res; 23(9); 2177-85. ©2016 AACR.
authors.affiliation: Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.|Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.|University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Yajing
authors.initials: Y
authors.lastname: Hao
authors.affiliation: Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.|Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.
authors.forename: Chuanbao
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.
authors.forename: Zhiliang
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.|Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.
authors.forename: Guanzhang
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.|Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Sun
authors.affiliation: Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.|Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.
authors.forename: Jingshan
authors.initials: J
authors.lastname: Liang
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.|University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Luo
authors.affiliation: Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China. taojiang1964@163.com dabiao@yeah.net rschen@ibp.ac.cn.
authors.forename: Dabiao
authors.initials: D
authors.lastname: Zhou
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. taojiang1964@163.com dabiao@yeah.net rschen@ibp.ac.cn.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.affiliation: Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China. taojiang1964@163.com dabiao@yeah.net rschen@ibp.ac.cn.|Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.|Chinese Glioma Genome Atlas Network, Beijing, China.|Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.|China National Clinical Research Center for Neurological Diseases, Beijing, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D049109:Cell Proliferation / Q000235:genetics; D020077:Endogenous Retroviruses / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D005260:Female; D015894:Genome, Human; D005910:Glioma / Q000235:genetics / Q000473:pathology / Q000821:virology*; D006801:Humans; D008297:Male; D060787:Neoplasm Grading; D016016:Proportional Hazards Models; D012842:Sarcoma Virus, Woolly Monkey / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D017423:Sequence Analysis, RNA; D013539:Simian virus 40 / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D016019:Survival Analysis; D014158:Transcription, Genetic