Our CEVIR consortium brought together experts from different fields of academic and non-academic biomedical research aiming to improved detection of systemic cancer and study the evolutionary processes underlying systemic progression of non-small cell lung cancer (NSCLC). To achieve this goal, we recruited a cohort of advanced (n=52) and early-stage (n=250) NSCLC patients, adopted and optimized workflows for isolation of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), as well as conducted a phylogenetic analysis of collected cells.
Isolation of ctDNA was most effective, when conducted on whole plasma samples compared to plasma-derived extracellular vesicles. To this end, the automated Maxwell RSC system proved to be the most reliable providing purified ctDNA in sufficient quantities. To study the profiles of genetic alteration in the ctDNA samples we utilized a commercial targeted NGS panel (Roche Avenio assay) and a custom real-time ddPCR assay. The ddPCR workflow enabled longitudinal study of tumor progression in NSCLC providing results well reflecting dynamics of the primary tumor growth during the course of therapy. Noteworthy, analysis of Roche Avenio datasets revealed presence of a EGFR pT790M mutation (conferring resistance to tyrosine kinase inhibitors) in treatment-naïve ctDNA samples that was not identified during genetic profiling of the corresponding PT specimens. In addition, we developed a MSRE-ddPCR assays allowing for epigenetic profiling of ctDNA allowing for accurate (AUC > 0.9) detection of tumor-associated methylation patterns in ctDNA samples of NSCLC patients. An integrative approach for genetic and epigenetic analysis of ctDNA enabled to monitor tumour progression over time in individual patients. This workflow was established and validated using an independent cohort of 222 ctDNA samples obtained from 73 patients with Ewing Sarcoma enabling to monitor genetic and epigenetic tumor progression in individual patients and can now be applied to NSCLC patients.
Isolation of CTCs was limited by the ability of the utilized methods to detect tumor cells in bloods samples of NSCLC patients. This most likely results from phenotypic heterogeneity of tumor cells in NSCLC and reflect limitations of the detection systems utilized in our study focusing tumor cells exhibiting epithelial phenotype. We optimized and adopted two CTC enrichment methods (i.e. CellSearch and Parsortix) but neither of the two provided significant yields of tumor cells. Fortunately, detection of disseminated tumor cells (DCCs) in lymph nodes and bone marrow proved to be effective yielding sufficient samples for downstream analyses. Phylogenetic analysis of the collected cell collective revealed that DCCs represent an earlier stage of tumor progression than cells derived from the corresponding primary tumors. We will continue to collaborate to further resolve the origin of metastatic founder and relapse-initiating cells.
In summary, during the course of Cevir study we established a number of protocols suitable for detection and characterization of cfDNA and laid the ground for a large-longitudinal study to unravel the phylogenetic relationships of progression-driving cancer cells in NSCLC.