This SBIR Phase I project will develop resources for large-throughput analysis of gene expression. The complement of genes that is expressed in a given cell varies during development, in disease states and in response to hormonal signals. Derangements in gene expression are the basis of cancer. This project will show the feasibility of """"""""Multiplex Profiling"""""""" (MP), an integrated large-throughput strategy for characterizing changes in gene expression and for retrieving the variable transcripts. We will perform MP on gene transcripts synthesized by two methods targeted to open reading frames and 5' regions. We will develop conditions for multiplex electrophoresis of PCR products and for hybridization and retrieval of candidate transcripts with """"""""signature"""""""" oligonucleotides derived from conserved protein motifs. MP will be applied to lung carcinoma and normal respiratory epithelium cell lines using signature oligos for G proteins. The differentially expressed transcripts could become molecular markers for these tumors.
Applications will be similar to those that historically have been based on the production and analysis of libraries and Northern blots including cDNA synthesis kits and primers, prepared blots containing the expressed sequences from specific cell lines/tissues, or signature probes for specific motifs (e.g., G. proteins, zinc fingers, homeoboxes.) One of the primary targets for MP is the pharmaceutical industry, which has embraced genome informatics as a means of drug discovery. Probes derived from advances in genome informatics can be readily used in MP. MP data can annotate the databases on gene sequences with their developmental context.
