Abstract A21: Longitudinal analysis of cell-free DNA for therapy monitoring of ALK-positive non-small cell lung cancer
Authors: Dietz Steffen , Christopoulos Petros , Gu Lisa , Endris Volker , Yuan Zhao , Ogrodnik Simon J. , Zemojtel Tomasz , Schneider Marc A. , Volckmar Anna-Lena , Meister Michael , Muley Thomas , Reck Martin , Schlesner Matthias , Thomas Michael , Stenzinger Albrecht , Sültmann Holger 
Published: June 2020

Abstract
Non-small cell lung cancer (NSCLC) patients with ALK rearrangements are routinely treated with tyrosine kinase inhibitors (TKIs), leading to improved survival. However, clinical courses vary widely and the disease remains incurable. Therefore, early detection and molecular characterization of treatment failure is important for therapy guidance. To identify indicators of therapy response and resistance, we performed genotyping of circulating cell-free DNA (cfDNA), including panel-based deep sequencing (&gt;4,200x coverage) and shallow whole-genome sequencing (sWGS; 0.5x coverage) from serial plasma samples (n=282) of 73 patients with ALK rearrangements. Variable mutation levels were marked in all patients and correlated with clinical features. At progression, individual dynamics of resistance mutations were seen: while some mutations became undetectable upon therapy switch, variant fractions of other alterations further increased. We also found mutated TP53 at the time of progression in patients with initially TP53 wild-type tumors. The progression-free survival of patients with acquired TP53 mutations was comparable to that of primarily TP53 mutated and shorter than that of persistently TP53 wild-type cases. Shallow WGS of cfDNA identified copy number variations (CNVs), some of which might contribute to disease progression. To quantitatively assess CNVs, trimmed median absolute deviation from copy number neutrality (t-MAD) scores were calculated from sWGS data. Longitudinal t-MAD assessment reflected the kinetics of mutant allele frequencies in cfDNA and allowed disease monitoring with increasing t-MAD and mutation levels at tumor progression. Moreover, EML4-ALK fusion variant 3 (V3) and TP53 mutations define molecular determinants of adverse outcome in ALK+ NSCLC. Shallow WGS of cfDNA identified increased t-MAD levels in patients with EML4-ALK V3 compared to those with fusion V1. Similarly, patients with TP53 mutations showed a higher t-MAD than TP53 wild-type cases. In summary, overall survival of patients with detectable mutations in plasma DNA at any time point during clinical follow-up was shorter than that of patients without detectable mutations in cfDNA. Similarly, overall survival time from the first detection of mutations cfDNA until death/end of follow-up was shorter than in cases without detectable mutations. Our data suggest that liquid biopsies could help to improve the care of ALK+ NSCLC patients through early detection of disease progression and tailored treatment of resistant tumors. Although individual courses were seen, rising mutation levels could indicate the need of radiologic reassessment earlier than scheduled. Detection of CNVs as surrogate for genomic instability and acquired TP53 mutations in liquid identified high-risk cases and suggests the potential clinical utility of cfDNA monitoring for this disease beyond profiling of ALK resistance mutations.
Citation Format: Steffen Dietz, Petros Christopoulos, Lisa Gu, Volker Endris, Zhao Yuan, Simon J. Ogrodnik, Tomasz Zemojtel, Marc A. Schneider, Anna-Lena Volckmar, Michael Meister, Thomas Muley, Martin Reck, Matthias Schlesner, Michael Thomas, Albrecht Stenzinger, Holger Sültmann. Longitudinal analysis of cell-free DNA for therapy monitoring of ALK-positive non-small cell lung cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A21.