State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells

• DOI: 10.1021/acs.jproteome.6b00380
• Publication Date: 2016-08-16T09:13:25Z
• Authors: Ekaterina V. Pove...; Arthur T. Kopylov; Elena A. Ponomarenko; Ekaterina V. Ilgi...; Victor G. Zgoda; Olga V. Tikhonova; Svetlana E. Novikova; Tatyana E. Farafo...; Yana Yu. Kiseleva; Sergey P. Radko; Igor V. Vakhrushev; Konstantin N. Yar...; Sergei A. Moshkov...; Olga I. Kiseleva; Andrey V. Lisitsa; Alexey S. Sokolov; Alexander M. Mazur; Egor B. Prokhortc...; Konstantin G. Skr...; Elena S. Kostrjukova; Alexander V. Tyakht; Alexey Yu. Gorbachev; Elena N. Ilina; Vadim M. Govorun; Alexander I. Arch...
• Keywords: Proteomics; 0303 health sciences; 03 medical and health sciences; Liver; Proteome; Gene Expression Profiling; Humans; Proteins; Hep G2 Cells; RNA, Messenger; Chromosomes, Human, Pair 18; Databases, Protein

A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line and liver tissue proteomes was ∼66%. In total, there were 16 proteins specifically observed in HepG2 cell line, while 15 proteins were found solely in the liver tissue. Comparison between proteome and transcriptome revealed a poor correlation (R2 ≈ 0.1) between corresponding mRNA and protein expression levels. The SRM and shotgun data sets (obtained during 2015-2016) are available in PASSEL (PASS00697) and ProteomeExchange/PRIDE (PXD004407). All measurements were also uploaded into the in-house Chr 18 Knowledgebase at http://kb18.ru/protein/matrix/416126 .