title: 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 (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 .
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Ekaterina V
authors.initials: EV
authors.lastname: Poverennaya
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Arthur T
authors.initials: AT
authors.lastname: Kopylov
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Elena A
authors.initials: EA
authors.lastname: Ponomarenko
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Ekaterina V
authors.initials: EV
authors.lastname: Ilgisonis
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Victor G
authors.initials: VG
authors.lastname: Zgoda
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Tikhonova
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Svetlana E
authors.initials: SE
authors.lastname: Novikova
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Tatyana E
authors.initials: TE
authors.lastname: Farafonova
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Yana Yu
authors.initials: YY
authors.lastname: Kiseleva
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Sergey P
authors.initials: SP
authors.lastname: Radko
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Vakhrushev
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Konstantin N
authors.initials: KN
authors.lastname: Yarygin
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.|Pirogov Russian National Research Medical University , Ostrovitianov Str. 1, Moscow 117997, Russia.
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Moshkovskii
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Olga I
authors.initials: OI
authors.lastname: Kiseleva
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Lisitsa
authors.affiliation: Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia.
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Sokolov
authors.affiliation: Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia.
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Mazur
authors.affiliation: Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia.
authors.forename: Egor B
authors.initials: EB
authors.lastname: Prokhortchouk
authors.affiliation: Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia.
authors.forename: Konstantin G
authors.initials: KG
authors.lastname: Skryabin
authors.affiliation: Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia.
authors.forename: Elena S
authors.initials: ES
authors.lastname: Kostrjukova
authors.affiliation: Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Tyakht
authors.affiliation: Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia.
authors.forename: Alexey Yu
authors.initials: AY
authors.lastname: Gorbachev
authors.affiliation: Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia.
authors.forename: Elena N
authors.initials: EN
authors.lastname: Ilina
authors.affiliation: Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia.
authors.forename: Vadim M
authors.initials: VM
authors.lastname: Govorun
authors.affiliation: Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Archakov
mesh_terms: D002887:Chromosomes, Human, Pair 18; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods; D056945:Hep G2 Cells; D006801:Humans; D008099:Liver / Q000737:chemistry; D011506:Proteins / Q000032:analysis; D020543:Proteome / Q000032:analysis* / Q000235:genetics; D040901:Proteomics / Q000379:methods; D012333:RNA, Messenger / Q000032:analysis
chemical_list: D011506:Proteins; D020543:Proteome; D012333:RNA, Messenger
keywords: Human Proteome Project; RNA-Seq; human chromosome 18; proteome; quantitative PCR; selected reaction monitoring; transcriptome