title: RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings.
abstract: There are remarkable disparities among patients of different races with prostate cancer; however, the mechanism underlying this difference remains unclear. Here, we present a comprehensive landscape of the transcriptome profiles of 14 primary prostate cancers and their paired normal counterparts from the Chinese population using RNA-seq, revealing tremendous diversity across prostate cancer transcriptomes with respect to gene fusions, long noncoding RNAs (long ncRNA), alternative splicing and somatic mutations. Three of the 14 tumors (21.4%) harbored a TMPRSS2-ERG fusion, and the low prevalence of this fusion in Chinese patients was further confirmed in an additional tumor set (10/54=18.5%). Notably, two novel gene fusions, CTAGE5-KHDRBS3 (20/54=37%) and USP9Y-TTTY15 (19/54=35.2%), occurred frequently in our patient cohort. Further systematic transcriptional profiling identified numerous long ncRNAs that were differentially expressed in the tumors. An analysis of the correlation between expression of long ncRNA and genes suggested that long ncRNAs may have functions beyond transcriptional regulation. This study yielded new insights into the pathogenesis of prostate cancer in the Chinese population.
authors.affiliation: Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
authors.forename: Shancheng
authors.initials: S
authors.lastname: Ren
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Peng
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Mao
authors.forename: Yongwei
authors.initials: Y
authors.lastname: Yu
authors.forename: Changjun
authors.initials: C
authors.lastname: Yin
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
authors.forename: Zilian
authors.initials: Z
authors.lastname: Cui
authors.forename: Jibin
authors.initials: J
authors.lastname: Zhang
authors.forename: Kang
authors.initials: K
authors.lastname: Yi
authors.forename: Weidong
authors.initials: W
authors.lastname: Xu
authors.forename: Chao
authors.initials: C
authors.lastname: Chen
authors.forename: Fubo
authors.initials: F
authors.lastname: Wang
authors.forename: Xinwu
authors.initials: X
authors.lastname: Guo
authors.forename: Ji
authors.initials: J
authors.lastname: Lu
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.forename: Min
authors.initials: M
authors.lastname: Wei
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Tian
authors.forename: Yinghui
authors.initials: Y
authors.lastname: Guan
authors.forename: Liang
authors.initials: L
authors.lastname: Tang
authors.forename: Chuanliang
authors.initials: C
authors.lastname: Xu
authors.forename: Linhui
authors.initials: L
authors.lastname: Wang
authors.forename: Xu
authors.initials: X
authors.lastname: Gao
authors.forename: Wei
authors.initials: W
authors.lastname: Tian
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Yinghao
authors.initials: Y
authors.lastname: Sun
mesh_terms: D017398:Alternative Splicing; D000951:Antigens, Neoplasm / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D002681:China; D002891:Chromosomes, Human, Pair 21; D015331:Cohort Studies; D050939:Gene Fusion; D015894:Genome, Human; D006801:Humans; D008297:Male; D015778:Minor Histocompatibility Antigens; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D051059:PTEN Phosphohydrolase / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000378:metabolism* / Q000473:pathology; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012008:Recurrence; D017423:Sequence Analysis, RNA; D012697:Serine Endopeptidases / Q000235:genetics / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D000071230:Transcriptional Regulator ERG; D059467:Transcriptome; D043222:Ubiquitin Thiolesterase / Q000235:genetics / Q000378:metabolism
chemical_list: D000951:Antigens, Neoplasm; C072312:ERG protein, human; C118777:KHDRBS3 protein, human; C109278:MIA2 protein, human; D015778:Minor Histocompatibility Antigens; D009363:Neoplasm Proteins; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D015534:Trans-Activators; D000071230:Transcriptional Regulator ERG; C481724:USP9Y protein, human; D051059:PTEN Phosphohydrolase; D043222:Ubiquitin Thiolesterase; D012697:Serine Endopeptidases; C421305:TMPRSS2 protein, human