In the US, lung cancer will add 224,210 new cases and cause 159,260 deaths in 2014. Non- small cell lung cancer (NSCLC) accounts for 80% of lung cancer. The availability of targeted therapies directed to driver oncogenes such as EGFR mutations and gene fusions (e.g., EML4- ALK) in recent years has transformed the management of NSCLC. These advances have also created an unprecedented challenge to conduct multiple molecular testing using limited diagnostic materials. In many settings, 40-50% of NSCLC patients present with advanced disease and are simultaneously diagnosed, staged and their tumors molecularly tested for targeted therapy using fine needle aspiration (FNA)-derived cytology specimen obtained during endobronchial ultrasound (EBUS). Liquid-based cytology slides, especially ThinPrep slides, have proven superior to formalin-fixed paraffin-embedded (FFPE) cell blocks for assessing ALK gene status by DNA fluorescent in situ hybridization (FISH). However, the number of ThinPrep slides that can be prepared from a typical EBUS-FNA specimen is limited (usually 2-3). In order to perform multiple testing, an in situ method with multiplexing capability beyond conventional FISH and immunohistochemistry (IHC) is needed. In this Phase I study, we propose to leverage the high sensitivity and multiplexing capability of a recently developed RNA in situ hybridization technology (RNAscope(R)) to develop a novel companion diagnostic algorithm that can efficiently and accurately detect multiple rare but "actionable" oncogenic gene fusions (ALK, ROS1, RET, NTRK1 and others) in NSCLC patients using FNA-derived ThinPrep slides.
Public Health Relevance Statement: Public Health Relevance: The current increasing use of minimally invasive diagnostic procedures in oncology poses a number of challenges to companion diagnostic testing. First, while the number of molecular targets to be tested is increasing on a regular basis, the amount of diagnostic specimen is decreasing. Second, most of the molecular changes of interest are present only in small subsets (~1%) of patients. Therefore, there is an urgent need to develop molecular diagnostic methods that have multiplexing capability beyond conventional fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) yet maintain the benefits of in situ biomarker detection. In this Phase I study, we propose to leverage the high sensitivity and multiplexing capability of the RNAscope RNA ISH technology to develop a novel companion diagnostic algorithm that can efficiently and accurately detect multiple rare but "actionable" oncogenic fusions in non-small cell lung cancer (NSCLC) using limited fine needle aspiration (FNA)-derived cytology samples.
Project Terms: Accounting; Acetone; Address; Adoption; advanced disease; Algorithms; ALK gene; Antibodies; Automation; base; Binding (Molecular Function); Biological Assay; Biological Markers; Cancer Patient; Cell Line; Cells; Cessation of life; Clinical; cohort; Companions; Computer software; Cytology; Cytopathology; Detection; Detergents; Development; Diagnosis; Diagnostic; Diagnostic Procedure; Diagnostic tests; DNA; Epidermal Growth Factor Receptor; Epitopes; Ethanol; Fine needle aspiration biopsy; Fixatives; Fluorescent in Situ Hybridization; Formalin; Gene Fusion; Genes; Image Analysis; immunocytochemistry; Immunohistochemistry; In Situ; In Situ Hybridization; instrument; interest; Liquid substance; Malignant neoplasm of lung; Malignant Neoplasms; Marketing; Masks; Methanol; Methods; minimally invasive; Molecular; Molecular Diagnostic Techniques; Molecular Target; Mutation; Non-Small-Cell Lung Carcinoma; novel; NTRK1 gene; Oncogenes; Oncogenic; oncology; Organic solvent product; Paraffin Embedding; patient population; Patients; Peptide Hydrolases; Phase; phase 1 study; Precipitation; prospective; protein aggregation; Proteins; public health relevance; RNA; RNA Stability; ROS1 gene; Sampling; screening; Sensitivity and Specificity; Slide; Specimen; Staging; Staining method; Stains; success; Technology; Testing; Tissues; Transcript; tumor; Ultrasonography; Validation; Work
