Exploring the Proteomic Landscape of a Gastric Cancer Biopsy with the Shotgun Imaging Analyzer

Accessing
localized proteomic profiles has emerged as a fundamental strategy
to understand the biology of diseases, as recently demonstrated, for
example, in the context of determining cancer resection margins with
improved precision. Here, we analyze a gastric cancer biopsy sectioned
into 10 parts, each one subjected to MudPIT analysis. We introduce
a software tool, named Shotgun Imaging Analyzer and inspired in MALDI
imaging, to enable the overlaying of a protein’s expression
heat map on a tissue picture. The software is tightly integrated with
the NeXtProt database, so it enables the browsing of identified proteins
according to chromosomes, quickly listing human proteins never identified
by mass spectrometry (i.e., the so-called missing proteins), and the
automatic search for proteins that are more expressed over a specific
region of interest on the biopsy, all of which constitute goals that
are clearly well-aligned with those of the C-HPP. Our software has
been able to highlight an intense expression of proteins previously
known to be correlated with cancers (e.g., glutathione S-transferase
Mu 3), and in particular, we draw attention to Gastrokine-2, a “missing
protein” identified in this work of which we were able to clearly
delineate the tumoral region from the “healthy” with
our approach. Data are available via ProteomeXchange with identifier
PXD000584.