Rapid FISH Assay for Disease-Related Nuclear RNA Transcripts

DESCRIPTION (provided by applicant): The most common diagnostic and commercial applications of FISH are in the detection of structural aberrations, such as chromosomal translocations and gene amplifications, both commonly found in a variety of cancers. This is typically accomplished using DNA probes several hundreds of kilobases (kb) in size, targeting similarly sized DNA regions. The large size of the probe constructs, primarily for increasing hybridization signal sensitivity, introduce a variety of design, labeling, and usage problems. It is also difficult to detect specific microdeletions or single-base changes using these probes. More fundamentally, these procedures target structural defects, but do not provide information on the expression status of the defect, which ultimately is involved in determining disease phenotype. To accomplish this, gene expression must be targeted, requiring detection of RNA instead of DNA. Although detection of cellular RNA using in situ hybridization has long been reported, most applications target cytoplasmic RNAs, primarily due to their increased copy number, with the intent of determining whether a specific gene is transcribed or quiescent. A novel variation of RNA detection, which greatly expands the information obtained, is detection of nuclear RNA, not cytoplasmic RNA, as the targeted molecule. Several different nuclear RNA molecules have been detected and in all cases, the nuclear RNA transcript focus is coincident with the transcribed gene. In addition, since the nuclear RNA hybridization signal was tightly restricted to a defined space, detection sensitivity was increased relative to that from the more diffuse cytoplasmic mRNA. Using a novel probe labeling method, this SBIR aims to develop a rapid, multi-color RNA FISH assay for detecting aberrant nuclear RNA transcripts, which are powerful surrogate markers for certain disease-specific genetic defects. Phase I research will use two disease models: Chronic Myelogenous Leukemia and Spinal Muscular Atrophy.