Abstract 2000: Proteomic features of histological compartments in colorectal carcinoma

Abstract Proteomic analysis of cancer tissues by mass spectrometry (MS) is complicated by the fact that histological context is lost in the analysis. Knowledge on the abundance of key proteins for the different histological compartments may allow an assessment of the contribution of each of these components to the proteomic profile obtained. We studied 18 colorectal carcinoma specimens and isolated carcinoma, necrosis, normal epithelium, stroma, smooth muscle, and lymphoid infiltrate compartments using laser capture microdissection (LCM). Proteins extracted from 60 LCM caps were subjected to short-stack, gel electrophoresis, in-gel trypsin digestion and analyzed on a Thermo-Fisher QExactive Orbitrap MS instrument. Data were searched using myrimatch and MS-GF+ on a RefSeq protein database and identified proteins were assembled using IDpicker 3. The analysis identified about 2,000 non-redundant proteins at a protein FDR&amp;lt;5%. Unsupervised cluster analysis of the most abundant proteins clustered each of the compartments together with few exceptions. Surprisingly, the necrotic compartment was almost identical from the carcinoma compartment, indicating the stability of the small peptides used for MS sequence identifications. Comparisons of spectral count data between each of the compartments and the remainder of the dataset by protein enrichment analyses was performed using the online tool www.webgestalt.org. The carcinoma compartment was enriched for proteins involved in nucleic acid and general metabolism processes. Smooth muscle was enriched for proteins involved in muscle contraction and cell adhesion. The lymphoid infiltrates were enriched for chromatin and nucleosome proteins, possibly indicating the relative contribution of nuclear proteins from these small cells. The stromal component was enriched for extracellular matrix proteins and proteins involved in glycosylation processes. Using data from ProteinAtlas.org, we confirmed histological associations of the most prominent protein markers with their respective histological component. For instance, COL12A1 was highly expressed in the stromal compartment, while SMTN was highly specific for smooth muscle. Expression levels characterizing each of the histological components can thus be described in protein signatures that can serve as a measure of the relative contribution of each of the components in the complex composition of a colorectal carcinoma sample. Supported by NIH/NCI grant U24CA159988. Citation Format: Robbert JC Slebos, Lisa J. Zimmerman, Suzanne Manning, Melinda E. Sanders, Chanjuan Shi, M Kay Washington, Daniel C. Liebler. Proteomic features of histological compartments in colorectal carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2000. doi:10.1158/1538-7445.AM2015-2000</jats:p