Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation

Jingi Bae, Su Jin Kim, Seung Eun Lee, Wooil Kwon, Hongbeom Kim, Youngmin Han, Jin Young Jang, Min Sik Kim, Sang-Won Lee

Research output: Contribution to journalArticle

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Abstract

Certain tumors such as pancreatic ductal adenocarcinoma (PDAC) are known to contain a variety of hydrolytic enzymes including RNases and proteases that may lead to degradation of RNA and proteins during sample processing. For such tumor tissues with RNA instability, RNAlater containing a high concentration of quaternary ammonium sulfates that denature RNA-hydrolyzing enzymes is often used to protect RNAs from hydrolysis. Although a few studies have been carried out to determine the effect of RNAlater on DNA and RNA, whether RNAlater influences the proteome and phosphoproteome is largely unknown. In this study we carried out a systematic and comprehensive analysis of the effect of RNAlater on the proteome and phosphoproteome using high-resolution mass spectrometry. PDAC tissues from three patients were individually pulverized and the tissue powders of each patient were divided into two portions, one of which was incubated in RNAlater at 4 °C for 24 h (RNAlater tissue) while the other was kept at - 80 °C (frozen tissue). Comprehensive quantitative profiling experiments on the RNAlater tissues and the frozen tissues resulted in the identification of 99,136 distinct peptides of 8803 protein groups and 17,345 phosphopeptides of 16,436 phosphosites. The data exhibited no significant quantitative changes in both proteins and phosphorylation between the RNAlater tissues and the frozen tissue. In addition, the phosphoproteome data showed heterogeneously activated pathways among the three patients that were not altered by RNAlater. These results indicate that the tissue preservation method using RNAlater can be effectively used on PDAC tissues for proteogenomic studies where preservation of intact DNA, RNA and proteins is prerequisite. Data from this study are available via ProteomeXchange with the identifier PXD010710.

Original languageEnglish
Article number18
JournalClinical Proteomics
Volume16
Issue number1
DOIs
Publication statusPublished - 2019 Apr 25

Fingerprint

Phosphorylation
Proteome
Tissue
Proteins
RNA
Adenocarcinoma
RNA Stability
Tumors
Tissue Preservation
Phosphopeptides
DNA
Ammonium Sulfate
Enzymes
Ribonucleases
Powders
Proteolysis
Mass Spectrometry
Neoplasms
Mass spectrometry
Hydrolysis

ASJC Scopus subject areas

  • Molecular Medicine
  • Molecular Biology
  • Clinical Biochemistry

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Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation. / Bae, Jingi; Kim, Su Jin; Lee, Seung Eun; Kwon, Wooil; Kim, Hongbeom; Han, Youngmin; Jang, Jin Young; Kim, Min Sik; Lee, Sang-Won.

In: Clinical Proteomics, Vol. 16, No. 1, 18, 25.04.2019.

Research output: Contribution to journalArticle

Bae, Jingi ; Kim, Su Jin ; Lee, Seung Eun ; Kwon, Wooil ; Kim, Hongbeom ; Han, Youngmin ; Jang, Jin Young ; Kim, Min Sik ; Lee, Sang-Won. / Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation. In: Clinical Proteomics. 2019 ; Vol. 16, No. 1.
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