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Clinical Proteomics, 2019. 16, 27-, DOI: https://doi.org/10.1186/s12014-019-9239-z
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
Certain tumors such as pancreatic ductal adenocarcinoma (PDAC) are known to contain a variety of hydrolyticenzymes 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 ammoniumsulfates that denature RNA-hydrolyzing enzymes is often used to protect RNAs from hydrolysis. Although a fewstudies have been carried out to determine the effect of RNAlater on DNA and RNA, whether RNAlater influences theproteome and phosphoproteome is largely unknown. In this study we carried out a systematic and comprehensiveanalysis 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 dividedinto two portions, one of which was incubated in RNAlater at 4 °C for 24 h (RNAlater tissue) while the other was keptat – 80 °C (frozen tissue). Comprehensive quantitative profiling experiments on the RNAlater tissues and the frozentissues resulted in the identification of 99,136 distinct peptides of 8803 protein groups and 17,345 phosphopeptidesof 16,436 phosphosites. The data exhibited no significant quantitative changes in both proteins and phosphorylationbetween the RNAlater tissues and the frozen tissue. In addition, the phosphoproteome data showed heterogeneouslyactivated pathways among the three patients that were not altered by RNAlater. These results indicate that thetissue preservation method using RNAlater can be effectively used on PDAC tissues for proteogenomic studies wherepreservation of intact DNA, RNA and proteins is prerequisite. Data from this study are available via ProteomeXchangewith the identifier PXD010710.
- DOI: https://doi.org/10.1186/s12014-019-9239-z
- ISBN or ISSN: 1542-6416
- 본 연구는 질병관리본부 연구개발과제연구비를 지원받아 수행되었습니다.
- This research was supported by a fund by Research of Korea Centers for Disease Control and Prevention.