SBIR-STTR Award

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. PROPOSED COMMERCIAL APPLICATION: 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

The overall goal of the Phase II project is to increase the information yield and reduce the labor of gene expression analysis by means of Multiplex Profiling (MP). MP is a third generation gene expression technology. To increase information, MP capitalizes on sequence signatures of protein coding DNA ("CodeSigs") to synthesize and identify transcripts differentially expressed in biological systems. To increase throughput, MP processes these samples by electrophoretic multiplexing and blotting onto nylon membranes. MP blots can then be queried by hybridization with a wide variety of probe configurations to profile gene expression. The multiplexing introduces tremendous latitude for gene transcript syntheses, while at the same time maintaining the capabilities for detection of individual transcripts in this set. We will generate a collection of 100 CodeSigs using modem informatics tools including computational analysis of sequence motifs in genes and from structural conservation of DNA sequences in critical protein domains. We will derive standard conditions for cDNA synthesis, amplification, probing and retrieval of differentially expressed transcripts with CodeSigs. PROPOSED COMMERCIAL APPLICATION: Multiplex profiling as designed in the Phase II plan represents a third generation system for profiling gene expression. The modular kit design will provide complete reagents for profiling gene expression by either domain or motif-directed cDNA synthesis, or random cDNA synthesis, allowing tremendous impact on gene discovery programs within both research and pharmaceutical platforms.