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

Abstract

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 (R ≈ 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 .

Dataset of target mass spectromic proteome profiling for human chromosome 18

“…Proteome profiling was performed using stable isotope-labeled standards (SRM/SIS) for plasma, liver tissue and HepG2 cells. Dataset includes both positive and negative results of protein detection.These data were partly discussed in recent publications, “Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells” [1] and “Chromosome 18 transcriptoproteome of liver tissue and HepG2 Cells and targeted proteome mapping in depleted plasma: Update 2013” [2], supporting the accompanying publication “State of the Chromosome 18-centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells” [3], and are deposited at the ProteomeXchange via the PASSEL repository with the dataset identifier PASSEL: PASS00697 for liver and HepG2 cell line.…”

The Gene-Centric Content Management System and Its Application for Cognitive Proteomics

“…The third domain was supported by manual inspection of the supplementary materials of the articles reporting sufficient coverage of the proteome by bottom-up MS. Finally, the fourth domain was created using the results of the proprietary experiments, which were performed by the Russian part of the C-HPP [ 17 , 18 , 19 ].…”

Multiomics study of HepG2 cell line proteome

“…Наличие ПТМ в канонической последовательности 5 11 Представлены альтернативной последовательностью (сплайс-форма) 3…”

“…до 6 млн протеоформ [2]. Однако, несовершенство протеомных подходов зачастую позволяет констатировать лишь детекцию мастерного белка* [3]: в силу малого покрытия аминокислотной последовательности детектируемым протеотипическим пептидом идентификация конкретной протеоформы представляет собой нетривиальную задачу. Ещё одним узким местом протеомики является задача отличить белки, гены которых, в принципе, не экспрессируются в конкретном типе биологического материала при заданных условиях, от белков, которые экспрессируются в количестве, недостаточном для детекции [4].…”