Mass Spectrometry-Based Study of the Plasma Proteome in a Mouse Intestinal Tumor Model

Early detection of cancer can greatly improve prognosis. Identification of proteins or peptides in the
circulation, at different stages of cancer, would greatly enhance treatment decisions. Mass spectrometry
(MS) is emerging as a powerful tool to identify proteins from complex mixtures such as plasma that
may help identify novel sets of markers that may be associated with the presence of tumors. To examine
this feature we have used a genetically modified mouse model, ApcMin, which develops intestinal tumors
with 100% penetrance. Utilizing liquid chromatography-tandem mass spectrometry (LC−MS/MS), we
identified total plasma proteome (TPP) and plasma glycoproteome (PGP) profiles in tumor-bearing
mice. Principal component analysis (PCA) and agglomerative hierarchial clustering analysis revealed
that these protein profiles can be used to distinguish between tumor-bearing ApcMin and wild-type
control mice. Leave-one-out cross-validation analysis established that global TPP and global PGP profiles
can be used to correctly predict tumor-bearing animals in 17/19 (89%) and 19/19 (100%) of cases,
respectively. Furthermore, leave-one-out cross-validation analysis confirmed that the significant
differentially expressed proteins from both the TPP and the PGP were able to correctly predict tumor-bearing animals in 19/19 (100%) of cases. A subset of these proteins was independently validated by
antibody microarrays using detection by two color rolling circle amplification (TC−RCA). Analysis of
the significant differentially expressed proteins indicated that some might derive from the stroma or
the host response. These studies suggest that mass spectrometry-based approaches to examine the
plasma proteome may prove to be a valuable method for determining the presence of intestinal tumors.
Keywords: colon cancer • mouse • plasma biomarker • proteomics • mass spectrometry