Year: 2019
Type: conference-paper
Abstract: Background As functional executors, protein signatures will be more sensitive than gene signatures in characterizing biological systems. The direct study of the functional proteome is capable to complement and extend omics analysis. Especially, combining cancer research with proteome analysis can identify protein biomarkers to distinguish disease types or subtypes. Methods The progressive signatures during dynamical biological processes are attracting more and more attention. As an intuitive and interpretable signature, the trend test would disclose the continuous change during the dynamical process. Thus, the linear trend of protein expression during disease development and progression (e.g. across consecutive disease stages) would indicate the important behavior of disease-relevant proteins corresponding to worsening diseases, particularly in the pan-cancer context. Results We re-analyzed the TCGA pan-cancer proteomics data on multiple digestive cancer sites, i.e. COAD, COADREAD, LIHC, READ, STAD and STES. The proteins with significant expression trend along cancer stages can be obtained as (figure 1A.) shown. The COAD, COADREAD tend to be similar on protein signatures, and READ, STAD and STES would be grouped together, and LIHC is an outlier due to its more observed progressive protein signatures. Then, by statistics of observation frequency of protein signatures in each cancer (figure 1B), and those of cancer sites for each protein (figure 1C), we found: (i) LIHC indeed have many protein signatures than others;(ii) some protein signatures of LIHC are same in COAD, COADREAD, meanwhile many protein signatures are exclusive for LIHC, i.e. specific protein signatures for liver cancer; (iii) protein signatures would have great differences in their expression trends in different digestive cancer sites, e.g. 4E-BP1 seems to be suppressor-protein except in LIHC (figure 1D), while YB-1 tends to be onco-protein. Conclusions Totally, this work revisited the progressive markers of digestive cancers on the proteome and pan-cancer manner, and revealed new insights on understanding dynamic heterogeneity of digestive disease progression by digestive disease signatures.
Source: Gut
Authors: Tao Zeng, Xiangtian Yu, Chengming Zhang
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Open Access status: bronze
OpenAlex ID: W2948062896