Arrayed primer extension computing with variant mRNA splice forms. Multiple isoforms of CD44 in a human breast tumor.

Abstract

The analysis of RNA splicing is important to understanding the diversity in protein sequences at specific disease loci, in the immune response, and across the proteome. The presence of each exon in a mature mRNA formed from a genomic sequence of n exons can be represented by a Boolean variable, enabling mRNA structure to be encoded by an n-bit binary number. The CD44 locus has been studied as an example of a variantly spliced RNA. Microarray methods can be used to address RNA splicing provided they exhibit high fidelity. Our previous work showed that the arrayed primer extension (APEX; single-nucleotide polymerase extension of microarrays of DNA primers) method gives high-fidelity, digital detection of nucleic acid sequences, and it has been used for the solution of Boolean computing problems. APEX was adapted to RNA analysis by the use of reverse transcriptase and arrays of primers specific to each exon in the CD44 locus. "Splicotypes" were readily assigned for a number of variant RNA templates. Because CD44 is known to be aberrantly spliced in a number of cancers, the RNA APEX method with a CD44 microarray was applied to samples from primary tumors of individual patients. Up to four different splicing forms of CD44 were detected, whereas there have been no previous reports of the presence of more than two CD44 isoforms within the same tissue.