We propose to develop ground-breaking molecular biomarkers discovered through the detection of DNA methylation patterns. These markers will form the basis of assays that will detect and analyze trace amounts of UPEC directly from urine. Such analysis will save valuable treatment time and provide clinicians with information of outcome-prognostic relevance. The technology to be used in the research described, trademarked as MethylScope(tm) technology, is based on the detection of DNA methylation patterns. DNA methylation patterns are an untapped source for highly sensitive diagnostic and clinically relevant biomarkers. Generally, DNA methylation is mitotically stabile layer of genetic information written on top of DNA sequence by a cell after it divides, and is more environmentally malleable (i.e., more responsive to changes in a local environment) than DNA sequence alone. Orion's product goals are to identify a minimal DNA methylation biomarker set that is capable of specifying UPEC strains, and confirming UTI's by real-time PCR directly from urine. Ideally, our biomarkers will not only be capable of discriminating cystits inducing strains from pyelonephritis inducing strains, but also providing a measure of relative virulence through the analysis of the methylation pattern of the UPEC specific sequences. These molecular clues may identify the precise strain, its propensity to cause disease, and may even reveal its potential clinical outcomes. Phase I of this proposal will leverage MethylScope(tm) technology in a feasibility study to discover a novel class of molecular markers that can specifically detect and specify the disease propensity of a small number of UPEC strains. The future Phase II will expand the number of strain specifying markers, and identify novel pathogenesis-associated patterns. Additionally, Phase II will focus upon the optimization of disease agents detection/characterization from urine. By implementing the aims of this Phase I proposal, a new class of treatment altering microbial biomarker products will be enabled for marketing to the emerging molecular diagnostic markets
