title: Omics evidence: single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines.
abstract: Cancer genomics unveils many cancer-related mutations, including some chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs; however, whether they could be translated to proteins still requires more evidence. Herein, we proposed a transomics strategy to profile the expression status of human Chr.20 genes (555 in Ensembl v72). The data of transcriptome and translatome (the mRNAs bound with ribosome, translating mRNAs) revealed that ∼80% of the coding genes on Chr.20 were detected with mRNA signals in three liver cancer cell lines, whereas of the proteome identified, only ∼45% of the Chr.20 coding genes were detected. The high amount of overlapping of identified genes in mRNA and RNC-mRNA (ribosome nascent-chain complex-bound mRNAs, translating mRNAs) and the consistent distribution of the abundance averages of mRNA and RNC-mRNA along the Chr.20 subregions in three liver cancer cell lines indicate that the mRNA information is efficiently transmitted from transcriptional to translational stage, qualitatively and quantitatively. Of the 457 genes identified in mRNAs and RNC-mRNA, 136 were found to contain SNVs with 213 sites, and >40% of these SNVs existed only in metastatic cell lines, suggesting them as the metastasis-related SNVs. Proteomics analysis showed that 16 genes with 20 SNV sites were detected with reliable MS/MS signals, and some SNVs were further validated by the MRM approach. With the integration of the omics data at the three expression phases, therefore, we are able to achieve the overall view of the gene expression of Chr.20, which is constructive in understanding the potential trend of encoding genes in a cell line and exploration of a new type of markers related to cancers.
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Beijing 100101, China.
authors.forename: Quanhui
authors.initials: Q
authors.lastname: Wang
authors.forename: Bo
authors.initials: B
authors.lastname: Wen
authors.forename: Tong
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authors.lastname: Wang
authors.forename: Zhongwei
authors.initials: Z
authors.lastname: Xu
authors.forename: Xuefei
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authors.forename: Shaohang
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authors.forename: Shenyan
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authors.forename: Huan
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authors.lastname: Gao
authors.forename: Xiaomin
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authors.forename: Haidan
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authors.lastname: Sun
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authors.lastname: Chang
authors.forename: Peibin
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authors.lastname: Qin
authors.forename: Chengpu
authors.initials: C
authors.lastname: Zhang
authors.forename: Ning
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authors.lastname: Li
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
authors.forename: Wei
authors.initials: W
authors.lastname: Gu
authors.forename: Jiayong
authors.initials: J
authors.lastname: Zhong
authors.forename: Gong
authors.initials: G
authors.lastname: Zhang
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Yang
authors.forename: Guoquan
authors.initials: G
authors.lastname: Yan
authors.forename: Huali
authors.initials: H
authors.lastname: Shen
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Liu
authors.forename: Haojie
authors.initials: H
authors.lastname: Lu
authors.forename: Fan
authors.initials: F
authors.lastname: Zhong
authors.forename: Qing-Yu
authors.initials: QY
authors.lastname: He
authors.forename: Ping
authors.initials: P
authors.lastname: Xu
authors.forename: Liang
authors.initials: L
authors.lastname: Lin
authors.forename: Siqi
authors.initials: S
authors.lastname: Liu
mesh_terms: D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D002890:Chromosomes, Human, Pair 20; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology; D020641:Polymorphism, Single Nucleotide; D053719:Tandem Mass Spectrometry