"The Ch4 team integrates in silico prediction, deep membrane proteomic profiling, and MRM-MS for discovery and validation of missing proteins from stem cells, cancer cells and tissues. Based on the unique features of Asian cohort, we focus on functional characterization of missing protein in lung cancer"
PI : Yu Ju CHEN
Chromosome 4 contains approximately 191 megabases (~6.4% of the human genome) with 769 protein-coding genes (NeXtprot, May 2021). Over one-third of missing proteins are annotated as membrane proteins (MPs), owing to their relatively challenging accessibility with standard shotgun proteomics. We hypothesize that the under-explored membrane subproteome is a rich resource to find missing proteins. Thus, our team has integrated strategies of in silico prediction, deep membrane proteomic profiling, and MRM-MS for discovery and validation of missing proteins from stem cells, cancer cells and tissues. Following the initiative of the neXt-CP50 Challenge Proteins, we also started to explore the functional characterization of missing proteins in lung adenocarcinoma, which is a unique disease with unmet clinical needs for non-smoking patients.
Progress on Missing Proteins Using non-small cell lung cancer (NSCLC) as a model study, we applied high-pH reverse-phase stop-and-go extraction tip fractionation of membrane-enriched samples from 11 NSCLC cell lines and incorporated membrane samples from 20 pairs of tumor and adjacent normal lung tissue, followed by high-resolution MS analysis. The result revealed 178 missing proteins, including 74 membrane proteins and 9 proteins from chromosome 4 (J. Proteome Res. 2015). Under joint efforts from AOHUPO colleagues, the deep subcellular proteomics strategy was applied to establish, to our knowledge, the largest proteomic landscape of 11,970 unique proteins in human embryonic stem cells. Following the HPP guideline, we verified 26 gold and 87 silver MPs (J. Proteome Res. 2018). Functional annotation of the MPs revealed their potential roles in the pluripotency-related pathways and the lineage- and tissue-specific differentiation processes. Based on our recent large-scale tissue proteomics profiling on non-smoking NSCLC patients (Cell, 2020), we identified 125 MPs (115 PE2, 9 PE3 and 1 PE4) and their verification and functional study are under investigation according to guideline 3.0.