The use of liquid biopsies based on ctDNA sequencing for the detection of residual disease in locally advanced rectal cancer patients after neoadjuvant chemoradiotherapy (nCRT)

Abstract

Monitoring and detection of genetic changes associated with acquired resistance to anti-EGFR therapy in ctDNA from patients with lung and colon cancerThe Epidermal Growth Factor Receptor (EGFR) was the first receptor to be proposed as a target for cancer therapy after two decades of intense research. Anti-EGFR therapies are used in the clinic to treat non-small cell lung cancer (NSCLC) and metastatic colorectal cancer (mCRC). Tyrosine kinase inhibitors (TKIs) - Gefitinib, Erlotinib, Afatinib and Osimertinib - are used to treat patients with non-small cell lung cancer (NSCLC) with activating mutations in EGFR, while anti-EGFR monoclonal antibodies - Cetuximab and Panitumumab - are used to treat KRAS wild type mCRC. Although these agents present an overall good response rate and confer important gains in progression-free survival and overall survival, patients invariably develop acquired resistance (AR), leading to progressive disease (PD). In our ongoing project, we are using serial liquid biopsies and droplet digital PCR (ddPCR) to monitor the clonal evolution of known genetic alterations associated with AR to anti-EGFR agents in NSCLC and mCRC. We also intend to characterize new genetic alterations associated with acquired resistance to anti-EGFR therapy through direct sequencing of ctDNA from patients with NSCLC and CRC experiencing disease progression during anti-EGFR therapy. A total of 36 patients NSCLC with and 15 patients with mCRC were enrolled in our study. In NSCLC patients, EGFR T790M was the main resistance mechanism associated with erlotinib, gefitinib and afatinib, while EGFR C797S and EGFR-exon19del amplification were observed in a patient progressing to osimertinib. In mCRC, KRAS mutations were observed in 2 patients presenting PD. We were unable to identify known mutations associated with acquired resistance to anti-EGFR therapy for a significant fraction of NSCLC and mCRC patients enrolled in our study and that developed PD. ctDNA sequencing using next generation sequencing (NGS) is a powerful tool to identify and characterize new molecular mechanism of acquired resistance to targeted therapy. However, its use is limited by the low concentrations of ctDNA in the plasma from cancer patients and the high sequencing error rate of current NGS platforms. To overcome these limitations, Dr. Gerlinger's group have recently developed an error suppression sequencing protocol using molecular barcodes and a bioinformatics pipeline for the identification of somatic mutations occurring at low concentrations in the ctDNA of cancer patients. The collaboration with Dr. Gerlinger's group will allow us to learn and apply this sequencing strategy to investigate new mechanisms of acquired resistance to anti-EGFR TKI in our patients.