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대한화학회 제124회 학술발표회 및 총회 Comprehensive proteome profiling to investigate RNAlater effect on the human Pancreatic ductal adenocarcinoma (PDAC) tissues

등록일
2019년 8월 29일 16시 56분 52초
접수번호
1898
발표코드
ANAL.P-173 이곳을 클릭하시면 발표코드에 대한 설명을 보실 수 있습니다.
발표시간
10월 18일 (금요일) 11:00~12:30
발표형식
포스터
발표분야
Analytical Chemistry
저자 및
공동저자
Jingi Bae, Su-Jin Kim, Min-Sik Kim1, Sang-Won Lee*
Department of Chemistry, Korea University, Korea
1Department of New Biology, 대구경북과학기술원, Korea
Proteogenomic study of PDAC is particularly challenging because the tissues contain a variety of enzymes including DNases, RNases and proteases that can lead to degradation of RNA and proteins. For this reason, RNAlater is often used to protect RNAs of PDAC tissues. High concentration of quaternary ammonium sulfates of RNAlater is known to protect RNA from degradation for long time storage. However, it is still unknown whether RNAlater affects the qualitative and quantitative information of proteome and phosphoproteome. In this study, we carried out comprehensive global proteome and phosphoproteome analysis to investigate the RNAlater effect on the PDAC tissue. Tissues from three patients were individually pulverized and the tissue powders of each patient were divided into two groups. One group was kept in RNAlater at 4°C and the other group was stored at −80°C both for 24 hours. Tissue powders were digested using FASP method then labeled with 6-plex TMT. Labeled samples were separated into 24 fractions by mid pH RPLC. A portion (~8%) of each mRP fraction was subjected to LC-MS/MS to profile the global proteome and the remaining samples (~92%) were concatenated into 12 fractions, which were each performed IMAC phosphopeptide enrichment. As a result, the global proteomic profiling identified 99,163 unmodified peptides of 8,803 protein groups, and phosphoproteomic analysis resulted in the identification 17,345 phosphopeptides of 16,436 phosphosites. Our data showed that RNAlater has negligible effects on both global proteome and phosphoproteome of PDAC tissue. Thereby the use of RNAlater to protect both RNAs and proteins of PDAC tissues is a viable method for proteogenomic studies on PDAC.

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