Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells

The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10–18 M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (r = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru).