Protein Array-based Approaches for Biomarker Discovery in Cancer

Abstract

Biomarkers are deemed to be potential tools in early diagnosis, therapeutic monitoring, and prognosis evaluation for cancer, with simplicity as well as economic advantages compared with computed tomography and biopsy. However, most of the current cancer biomarkers present insufficient sensitivity as well as specificity. Therefore, there is urgent requirement for the discovery of biomarkers for cancer. As one of the most exciting emerging technologies, protein array provides a versatile and robust platform in cancer proteomics research because it shows tremendous advantages of miniaturized features, high throughput, and sensitive detections in last decades. Here, we will present a relatively complete picture on the characteristics and advance of different types of protein arrays in application for biomarker discovery in cancer, and give the future perspectives in this area of research.

Keywords: Biomarker; Cancer; Early diagnosis; Protein array; Proteomics.

Figure 1

Classification of three types of protein arrays A. Analytical protein array is usually composed of well-characterized affinity reagents as immobilized probes, such as antibodies and lectins, to detect and/or quantify a large number of proteins present in a complex biological sample. In this class of arrays, targeted proteins can be detected either by direct labeling or using a reporter antibody in sandwich assay format. B. Functional protein arrays have broad applications in studying the biochemistry properties of proteins, such as protein binding activities and enzyme–substrate relationships. C. Reverse-phase protein arrays, comprised of many lysate samples, offer a platform to analyze signaling pathways.

Figure 2

Scheme of the two-phase strategy for biomarker identification using functional protein arrays In Phase I, a small cohort is used to rapidly identify a group of candidate biomarkers via serum profiling assays on a HuProt array of high cost. Because a small number of arrays are needed, cost of the experiments is relatively low. In Phase II, a focused protein array of low cost is fabricated by spotting down candidate proteins identified in Phase I. A much larger cohort is assayed on the focused arrays in a double-blind fashion to validate the candidates identified in Phase I. Finally, the validated biomarkers are transformed into a clinically-friendly assay platform, such as ELISA. HuProt, Human Proteome Microarray; ELISA, enzyme-linked immunosorbent assay.