Omics Evidence: Single Nucleotide Variants Transmissions on Chromosome 20 in Liver Cancer Cell Lines

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.