Highly sensitive fusion detection using plasma cell-free RNA in non-small-cell lung cancers
Nobuhiko Hasegawa1,2, Shinji Kohsaka1, Kana Kurokawa3
1Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.
Abstract:
ALK, ROS1, and RET kinase fusions are important predictive biomarkers of tyrosine kinase inhibitors (TKIs) in non-small-cell lung cancer (NSCLC). Analysis of cell-free DNA (cfDNA) provides a noninvasive method to identify gene changes in tumor cells. The present study sought to use cfRNA and cfDNA for identifying fusion genes. A reliable protocol was established to detect fusion genes using cfRNA and assessed the analytical validity and clinical usefulness in 30 samples from 20 cases of fusion-positive NSCLC. The results of cfRNA-based assays were compared with tissue biopsy and cfDNA-based liquid biopsy (Guardant360 plasma next-generation sequencing [NGS] assay). The overall sensitivity of the cfRNA-based assay was 26.7% (8/30) and that of cfDNA-based assay was 16.7% (3/18). When analysis was limited to the samples collected at chemo-naïve or progressive disease status and available for both assays, the sensitivity of the cfRNA-based assay was 77.8% (7/9) and that of cfDNA-based assay was 33.3% (3/9). Fusion gene identification in cfRNA was correlated with treatment response. These results suggest that the proposed cfRNA assay is a useful diagnostic test for patients with insufficient tissues to facilitate effective administration of first-line treatment and is a useful tool to monitor the progression of NSCLC for consideration of second-line treatments.
Insights
Cell-free RNA (cfRNA) shows promise for detecting fusion genes in non-small-cell lung cancer (NSCLC), aiding treatment decisions. This noninvasive method is particularly useful for patients with limited tissue samples.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genomics
Background:
- ALK, ROS1, and RET kinase fusions are key biomarkers for tyrosine kinase inhibitor (TKI) therapy in non-small-cell lung cancer (NSCLC).
- Noninvasive detection of these fusions using cell-free DNA (cfDNA) is established, but alternative methods are needed.
- Cell-free RNA (cfRNA) offers a potential avenue for identifying these critical genetic alterations.
Purpose of the Study:
- To establish and validate a protocol for detecting fusion genes in NSCLC using cfRNA.
- To compare the diagnostic performance of cfRNA-based assays with cfDNA-based liquid biopsies and tissue biopsies.
- To assess the clinical utility of cfRNA for guiding NSCLC treatment decisions.
Main Methods:
- A reliable protocol was developed to detect fusion genes in cfRNA from NSCLC patient samples.
- Analytical validity and clinical usefulness were assessed in 30 samples from 20 fusion-positive NSCLC cases.
- cfRNA assay results were compared against tissue biopsy and a commercial cfDNA next-generation sequencing (NGS) assay (Guardant360).
Main Results:
- The overall sensitivity of the cfRNA assay was 26.7% (8/30), compared to 16.7% (3/18) for the cfDNA assay.
- In chemo-naïve or progressive disease samples available for both assays, cfRNA sensitivity reached 77.8% (7/9), significantly higher than cfDNA's 33.3% (3/9).
- Fusion gene detection in cfRNA correlated with patient treatment response.
Conclusions:
- The developed cfRNA assay is a valuable diagnostic tool for NSCLC patients with insufficient tissue for molecular profiling.
- cfRNA analysis can aid in timely administration of first-line treatments.
- This method serves as a useful tool for monitoring NSCLC progression and informing second-line treatment strategies.
