A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation

Abstract

RNA binding proteins (RBPs) are involved in several post-transcriptional stages of gene expression and dictate the quality and quantity of the cellular proteome. When aberrantly expressed, they can lead to disease states as well as cancers. A basic requirement to understand their role in normal tissue development and cancer is the build of comprehensive gene expression maps. In this direction, we generated a list with 383 human RBPs based on the NCBI and EMSEMBL databases. SAGE and MPSS were then used to verify their levels of expression in normal tissues while SAGE and microarray datasets were used to perform comparisons between normal and tumor tissues. As main outcomes of our studies, we identified clusters of co-expressed or co-regulated genes that could act together in the development and maintenance of specific tissues; we also obtained a high confidence list of RBPs aberrantly expressed in several tumor types. This later list contains potential candidates to be explored as diagnostic and prognostic markers as well as putative targets for cancer therapy approaches.

Figure 1

RBP expression in normal tissue. The graph represents the number of RBPs expressed in each of the 33 different normal tissues analyzed either by SAGE or MPSS. The levels of expression of each individual RBP in each individual tissue were not taken into consideration to prepare the graph. Proteins are listed as long as their expression was detected.

Figure 2

RBP distribution in tissues. The graph represents the distribution of the RBPs present in our list according to the number of tissues in which they are expressed. The expression levels were not taken into consideration when preparing the graph. As can be observed, the great majority of the RBPs are ubiquitously expressed, while only a small subset can be considered tissue specific.