Development and Validation of a Novel Biomarker Assay for Cancer Diagnostics

DESCRIPTION provided by applicant In this Phase I project Blondin Bioscience LLC a start up company in Birmingham AL proposes to develop a rapid accurate and precise fluorometric assay for quantifying cell free telomeric DNA fragments cf tDNA within serum in order to monitor the effectiveness of chemotherapy treatments In our preliminary work conducted at the University of Alabama at Birmingham UAB we have detected a significant increase in cf tDNA released from cancer cells into extracellular milieu following chemotherapy induced apoptosis We also found a reproducible serum peak of cf tDNA release following initiation of chemotherapy in leukemia patients We attribute this release of cf tDNA to in vivo cancer cell apoptosis We propose that the measurement of cf tDNA would decrease the time cost and side effects of a potentially inadequate cancer treatment allowing early switching to a better treatment Blondin is negotiating an exclusive license for the use of this intellectual property from UAB Currently cf tDNA are measured with quantitative PCR qPCR which is cumbersome and imprecise due to the difficulty in amplifying repetitive telomere sequences and the very low ng ml amounts of cell free DNA obtained from clinical samples This new assay will utilize novel gamma modified peptide nucleic acid PNA miniprobes that are complimentary to the telomeric sequence PNA hybridize to complementary DNA with fold higher affinity than unmodified PNA This increase in binding affinity should allow detection of the very dilute target cf tDNA found in clinical samples The PNA miniprobes will be designed to exhibit a FRET signal only in the presence of a telomeric DNA target thus further improving the signal to noise ratio The proposed research will have three specific aims In the first aim we will characterize and adapt PNA miniprobes for use in a purified model system to detect and quantify cf tDNA Test conditions with the best precision and accuracy at the lowest target concentrations will be determined The second aim is directed toward optimizing and validating the PNA cf tDNA assay for use with complex biological samples The assay will be validated by assessing the accuracy precision specificity limit of detection and quantification linearity and range ruggedness and robustness as per current FDA method validation guidelines The final aim will assess the PNA cf tDNA assay in a clinical setting We will test the ability of the PNA cf tDNA assay to prospectively predict survival in a trial enrolling metastatic prostate cancer patients starting chemotherapy treatment The main goal of this aim is to test the performance of the PNA cf tDNA assay in a clinical situation The study is statistically powered to determine if the PNA cf tDNA assay is able to outperform the current response biomarkers prostate specific antigen and circulating tumor cells in this group of patients PUBLIC HEALTH RELEVANCE NARRATIVE We are developing a novel blood test to measure cell free telomeric DNA fragments The goal of this simple test is to allow the patient and their doctor to quickly tell ifthe chemotherapy treatment is working This test may allow doctors to quickly identify ineffective treatments and switch to a better treatment thus reducing the cancer burden which is an important part of our healthcare responsibility