Routine Screening for Triple-Negative Adenocarcinoma (TNA) Lung Cancer Patients: A New Hope for a Poor-Prognosis Population

Abstract

Lung cancer is the main cause of cancer mortality worldwide, 80% of which are non-small cell lung cancer (NSCLC) in type and >50% are adenocarcinoma in histology. Lung adenocarcinomas are mainly driven by three oncogenes, KRAS, EGFR, and ALK, leaving the remaining cases placed into a triple-negative adenocarcinoma (TNA) category, driven in part by recently identified oncogenic drivers, chromosomal fusions of ROS1 and RET and overexpression of DEPDC1, in up to ~12% of all TNA cases. The utilization of FISH assays has been predominant in the market for detection of biomarker fusions such as ROS1 and RET, yet the sensitivity of these tests is low, interpretation remains subjective, and genetic anomalies can lead to false-negatives. Herein, we hypothesize that a comprehensive quantitative polymerase chain reaction (qPCR) panel could be developed and used as a broad-based TNA detection assay to classify a previously unidentified, but clinically significant, cohort of TNA patients who are readily treatable with currently available therapeutic agents. Single-plexed qPCR strategies, both conventional and proprietary, were collectively developed to fabricate a TNA diagnostic panel specific for the detection of ROS1 and RET fusions and overexpression of DEPDC1 variants. All novel assay designs were validated according to CLIA guidelines in cell line-based studies and further subjected to feasibility testing in retrospective patient specimens. Extensive validation of each qPCR TNA assay showed analytical limits of detection of 1% or better and clinical applicability in patient FFPEs, thus establishing a feasible strategy for a multiplexed TNA panel. Until now, the ability to develop a commercially available multiplex diagnostic panel to reliably identify ROS1 and RET fusions and DEPDC1 overexpression in TNA patients remained elusive. Use of the comprehensive and easily adaptable qPCR strategy described here would therefore be ideally suited for routine clinical testing of such poorly prognostic NSCLC patients.