Chromosome 18 Transcriptoproteome of Liver Tissue and HepG2 Cells and Targeted Proteome Mapping in Depleted Plasma: Update 2013

We
report the results obtained in 2012–2013 by the Russian
Consortium for the Chromosome-centric Human Proteome Project (C-HPP).
The main scope of this work was the transcriptome profiling of genes
on human chromosome 18 (Chr 18), as well as their encoded proteome,
from three types of biomaterials: liver tissue, the hepatocellular
carcinoma-derived cell line HepG2, and blood plasma. The transcriptome
profiling for liver tissue was independently performed using two RNaseq
platforms (SOLiD and Illumina) and also by droplet digital PCR (ddPCR)
and quantitative RT-PCR. The proteome profiling of Chr 18 was accomplished
by quantitatively measuring protein copy numbers in the three types
of biomaterial (the lowest protein concentration measured was 10–13 M) using
selected reaction monitoring (SRM). In total, protein copy numbers
were estimated for 228 master proteins, including quantitative data
on 164 proteins in plasma, 171 in the HepG2 cell line, and 186 in
liver tissue. Most proteins were present in plasma at 108 copies/μL, while the median abundance was 104 and
105 protein copies per cell in HepG2 cells and liver tissue,
respectively. In summary, for liver tissue and HepG2 cells a “transcriptoproteome”
was produced that reflects the relationship between transcript and
protein copy numbers of the genes on Chr 18. The quantitative data
acquired by RNaseq, PCR, and SRM were uploaded into the “Update_2013”
data set of our knowledgebase (www.kb18.ru) and investigated for linear correlations.