Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines

Abstract

Under the guidance of the Chromosome-centric Human Proteome Project (C-HPP), (1, 2) we conducted a systematic survey of the expression status of genes located at human chromosome 20 (Chr.20) in three cancer tissues, gastric, colon, and liver carcinoma, and their representative cell lines. We have globally profiled proteomes in these samples with combined technology of LC-MS/MS and acquired the corresponding mRNA information upon RNA-seq and RNAchip. In total, 323 unique proteins were identified, covering 60% of the coding genes (323/547) in Chr.20. With regards to qualitative information of proteomics, we overall evaluated the correlation of the identified Chr.20 proteins with target genes of transcription factors or of microRNA, conserved genes and cancer-related genes. As for quantitative information, the expression abundances of Chr.20 genes were found to be almost consistent in both tissues and cell lines of mRNA in all individual chromosome regions, whereas those of Chr.20 proteins in cells are different from tissues, especially in the region of 20q13.33. Furthermore, the abundances of Chr.20 proteins were hierarchically evaluated according to tissue- or cancer-related distribution. The analysis revealed several cancer-related proteins in Chr.20 are tissue- or cell-type dependent. With integration of all the acquired data, for the first time we established a solid database of the Chr.20 proteome.

Differential protein expression analysis following olfactory learning in Apis cerana

“…This observation was not consistent with the reported down-regulation of coding genes after learning in A. mellifera by Wang et al (2013a) and Cristino et al (2014). The present experimental procedure was similar to that utilized by Wang et al (2013a), but different results were obtained.…”

“…Intriguingly, although the expression levels of two proteins (gi|151368183| and gi|373194840|) were in line with the results reported by Wang et al (2013a), 87 (59.15 %) differentially expressed proteins were up-regulated after learning in A. cerana. This observation was not consistent with the reported down-regulation of coding genes after learning in A. mellifera by Wang et al (2013a) and Cristino et al (2014).…”

“…The PER experimental procedure was based on the reports of Letzkus et al (2006) and Wang et al (2013a). The honeybees were briefly immobilized on ice for 3-5 min.…”

“…Using a tag-based digital gene expression (DGE) and microarray transcriptome analysis, Wang et al (2013a) and Cristino et al (2014), respectively, demonstrated a general downregulation of protein-coding genes after associative olfactory learning in Apis mellifera. Qin et al (2014) found that 88.40 % of differentially expressed mRNAs are down-regulated after maze learning, as evidenced by DGE.…”

Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development

“…The aim of this project is to confirm all of the coding genes in the genome using a proteomics approach and re-annotate the human genome. The portion implemented by CNHUPO occupied about one fifth of this international project, showing the determination and confidence of Chinese proteomists to go from following the lead of international colleagues to taking the lead in an international collaboration [76][77][78][79].…”