Developing a CLIA compliant LDT for detecting plasma piR-Ls/pfeRNAs to distinguish benign and malignant lung nodules

Lung cancer is the leading cause of cancer-related death in the U.S., in large part, because the diagnosis tends to be made after the cancer has progressed to its most advanced stages. However, current diagnostic techniques for detecting early-stage non-small cell lung cancer (NSCLC) are either invasive or have poor accuracy. We recently reported that piRNA-like sncRNAs (piR-Ls) and protein function effector sncRNAs (pfeRNAs) play critical roles in the tumorigenesis and differentiation of lung cancer. We have developed a novel technology for accurately and robustly measuring piR-Ls and pfeRNAs in plasma. We also have identified 2 piR-Ls and 6 pfeRNAs as promising non-invasive biomarkers using next generation sncRNAs deep sequencing of 119 biospecimens, including (i) plasma from healthy controls (ii) patient plasma with the matched, corresponding histologically proven NSCLC tissue as well as histologically normal adjacent lung tissue from patients with Stage I/II NSCLC (iii) plasma from patients with both biopsy proven benign and malignant lung nodules. Furthermore, we validated these biomarkers in 352 clinical plasma specimens, including 77 healthy controls, 44 patients with benign disease as well as 231 patients with malignant lung nodules. Moreover, we formulated prediction rules for our assay in detecting early-stage NSCLC. Using only plasma, we were able to: (1) differentiate patients with and without lung nodules, with a sensitivity and specificity of 98.5% and 98.7%, respectively (an important clinical assay needed in remote, impoverished areas of the world with a high prevalence of smokers but no access to CT scanning); (2) differentiate patients who had malignant versus benign lung nodules, with a sensitivity and specificity of 96.5% and 72.7%, respectively (important for economically advanced countries enrolling smokers to CT lung cancer screening programs). These data strongly suggest that our panel of 2 piR-Ls and 6 pfeRNAs are non-invasive putative biomarkers for detecting early-stage lung cancers. Our multi-disciplinary collaborative team consists of a physician-scientist, basic researchers, a physician-scientist in the CLIA-certified laboratory, statisticians, and a commercial developer. This team will develop a CLIA compliant LDT for validating our nucleicacid-based existing assay which now has been tested as valid in over 460 clinical specimens. The technologies that we will utilize for our testing are currently FDA-cleared for use in clinical laboratories, and the equipment as well as all reagents for our assays already are used in in-vitro-diagnostic testing. Our collaborative team aims to develop a molecular diagnostic assay that can be integrated into future clinical trials for the early detection of NSCLC, and ultimately, improve the dismal survival rates of that disease.