Super-sensitive detection of BCR-ABL mutants driving CML recurrence

Chronic myeloid leukemiaCMLis caused by a translocation between chromosomesandwhere the BCR gene promoter drives overexpression of ABL kinaseThis rearrangement causes transformation of bloodforming cells of the bone marrow and accounts forof all new leukemia cases in adultsThree generations of tyrosine kinase inhibitorsTKIshave been developed that are used clinically to inhibit the ABL kinase in CMLThe first generation TKIimatinibcan be highly effective against CML patientsalthough many patients do not respond to the drug or acquire one or more of andgtdifferent mutations that confer resistanceSome of these mutations also confer resistance to the second generation TKIsbosutinibdasatiniband nilotinibHoweverthe second generation TKIs have slightly different drug resistance profileswhich enables appropriate targeted therapy in many casesprovided that the mutation status is knownThe BCR ABL TI mutation renders second generation TKIs inactiveThe third generation inhibitorponatinibis active against all clinically relevant BCR ABLmutants and is the only approved TKI capable of inhibiting BCR ABL TIHoweverponatinib is only approved for patients with a TI mutation or that have failed on two or more second generation inhibitorsThe overall goal of this research is to develop a quantitative real time PCR test to detect emerging drugresistance mutations in BCR ABL to help physicians determine if when treatment should be changedGeneTAG Technology develops molecular diagnostic assays for cancer and infectious diseasesOur primary systemthe internal DNA Detection SwitchiDDSprobe systemcomprises two interacting componentsa fluor labeled probeand a quencher labeled antiprobe that is nearly complementary to the probeIn the absence of the intended targetthe paired probes and antiprobes bind togetherquenching fluorescence and preventing offtarget detectionThis unique probe system shows superior single base discrimination over a much wider annealing temperature rangeCthan common methodsRecentlywe merged our iDDS probe technology with our Wild TerminatorWTxmethods that enable detection of rare mutantsfrequencyby blocking amplification of the wild type sequenceThe combined method showed greater sensitivity in detecting circulating EGFR variants from lung cancer patients than the FDA approved cobasEGFR Mutation TestvThis enhanced qPCR sensitivity meets or exceeds the sensitivity of specialized platforms without the high instrumentation costOur higher sensitivity and specificity will enable development of a platformindependentliquid biopsy assayOur Specific Aims areto develop XNA enhanced WTx assays to detect BCR ABL drug resistance mutationsandto demonstrate the feasibility of detecting drug resistant BCR ABL mutations in plasma from CML patientsSuccess in Phase I will justify expanded Phase II assay validation studies in preparation for filing for FDA approvalCurrentlyno FDA approved NAAT is available for detecting drug resistance mutations in ABLSuccess in this project will help address an unmet need in patient care Cancer is the leading cause of death worldwideand point mutations in the BCR ABL fusion gene are known to drive drug resistance against targeted therapeutics for chronic myeloid leukemiaCMLWe have invented highly precise probe systems for detecting small DNA mutations and we have developed companion methods that greatly enhance probe sensitivityWe expect to further develop and apply these methods to detect drugresistance mutationsassociated with recurrencein blood samples from CML patientsThese advances will be particularly valuable for CML diagnostics since they offer the potential to detect emerging drug resistance mutations at an early stage and to expedite appropriate therapy