Abstract LB-413: Nanopore-based assay for discovery and enrichment of tumor progression biomarkers from human serum
Authors: Hu Ye , Ferrari Mauro 
Published: August 2012

Objective Without a blood-based biomarker, the current method for diagnosing cancer diseases is mostly limited to costly imaging, such as CT or MRI. Despite recent advances in molecular biology, no clinically approved biomarker has been found due to lack of specificity and sensitivity. Furthermore, imaging is also used to determine therapeutic efficacy of tumor treatments, but sometimes imaging is not sensitive enough to show early response of tumor and development of resistance to therapy. However, studies have shown that tumor cells undergoing apoptosis immediately release cell components into cell culture media. Building upon the in vitro models, the proteome of a blood samples can be used as basis for a discovery of biomarker which is released from the tumor cells undergo apoptosis and is correlated to treatment efficacy. Previous studies have examined cancer biomarkers, but the method of fractionation of serum samples utilized in these studies involved commercially available protein profiling kits, and the identification of these biomarkers has revealed only high molecular weight, acute phase proteins and their components at high concentration. Here, we present the use of novel nanoporous silica chips to enrich low molecular weight proteins for cancer biomarker discovery. The circulating low molecular weight proteome (LMWP), composed of small proteins shed from tissues and cells or peptide fragments derived from the proteolytic degradation of larger proteins, has been associated with the pathological condition in patients. Methodology The serum from mice models with primary breast cancer, lung metastasis breast cancer and melanoma cancer were processed by our nanopore-based array to identify specific biomarkers or patterns of biomarkers that can be correlated to tumor progression. By matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI-TOF MS) and principle component analysis, we were able to identify low molecular weight protein signatures unique to different stages of cancer development. Preliminary Results We have shown that the nanopore-based technology can be used to identify subtle changes in LMW protein expression patterns using negative control and diseased serum samples collected from imaging-proven stage I-III cancer mice models. The significant protein/ peptide for various cancer diseases considered as a potential biomarker would stand out in the protein mass spectrum acquired by MALDI MS. The protein profiles were further sequenced and analyzed using liquid chromatography-mass spectrometry (LC-MS). The identified protein biomarkers allow designing new prevention, early-detection, treatment and monitoring strategies for a particular disease, as well as extended application to a host of other pathologies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-413. doi:1538-7445.AM2012-LB-413