The Hu/Mu ProtIn Chip: A Custom Dual-Species Oligonucleotide Microarray for Profiling Degradome Gene Expression in Tumors and Their Microenvironment

Abstract

Proteases and protease inhibitors of the cancer degradome derive from tumor-associated cells as well as tumor cells. Xenograft studies in which human tumor cells are implanted in mice have revealed the contribution of tumor-associated cells to progression and metastasis of the human tumors. The roles of individual host (mice) proteases or protease inhibitors can be defined by implanting the human tumors in mice deficient in the protease or protease inhibitors. Such studies are time consuming and costly. Therefore, to identify proteases and protease inhibitors of interest, we partnered with Affymetrix to develop a dual-species oliogonucleotide microarray chip, the Hu/Mu ProtIn chip, that would discriminate between human and murine proteases and protease inhibitors in the same sample. The Hu/Mu ProtIn chip can be used to determine the expression of human or murine proteases, protease inhibitors, and protease interactors in single-species specimens or in dual-species specimens. Here, we describe our rationale for the design of this chip, its characteristics and its validation. In addition, we present examples of its successful use by ourselves and others to identify host proteases that play functional roles in tumor growth, angiogenesis, and metastasis. The Hu/Mu ProtIn chip helps us to identify interactions among proteases in the tumor and its surrounding microenvironment, interactions that can then be tested for their contribution to tumor progression.