Improved EGFR mutation detection using combined exosomal RNA and circulating tumor DNA in NSCLC patient plasma

A K Krug, D Enderle, C Karlovich, T Priewasser, S Bentink, A Spiel, K Brinkmann, J Emenegger, D G Grimm, E Castellanos-Rizaldos, J W Goldman, L V Sequist, J-C Soria, D R Camidge, S M Gadgeel, H A Wakelee, M Raponi, M Noerholm, J Skog, A K Krug, D Enderle, C Karlovich, T Priewasser, S Bentink, A Spiel, K Brinkmann, J Emenegger, D G Grimm, E Castellanos-Rizaldos, J W Goldman, L V Sequist, J-C Soria, D R Camidge, S M Gadgeel, H A Wakelee, M Raponi, M Noerholm, J Skog

Abstract

Background: A major limitation of circulating tumor DNA (ctDNA) for somatic mutation detection has been the low level of ctDNA found in a subset of cancer patients. We investigated whether using a combined isolation of exosomal RNA (exoRNA) and cell-free DNA (cfDNA) could improve blood-based liquid biopsy for EGFR mutation detection in non-small-cell lung cancer (NSCLC) patients.

Patients and methods: Matched pretreatment tumor and plasma were collected from 84 patients enrolled in TIGER-X (NCT01526928), a phase 1/2 study of rociletinib in mutant EGFR NSCLC patients. The combined isolated exoRNA and cfDNA (exoNA) was analyzed blinded for mutations using a targeted next-generation sequencing panel (EXO1000) and compared with existing data from the same samples using analysis of ctDNA by BEAMing.

Results: For exoNA, the sensitivity was 98% for detection of activating EGFR mutations and 90% for EGFR T790M. The corresponding sensitivities for ctDNA by BEAMing were 82% for activating mutations and 84% for T790M. In a subgroup of patients with intrathoracic metastatic disease (M0/M1a; n = 21), the sensitivity increased from 26% to 74% for activating mutations (P = 0.003) and from 19% to 31% for T790M (P = 0.5) when using exoNA for detection.

Conclusions: Combining exoRNA and ctDNA increased the sensitivity for EGFR mutation detection in plasma, with the largest improvement seen in the subgroup of M0/M1a disease patients known to have low levels of ctDNA and poses challenges for mutation detection on ctDNA alone.

Clinical trials: NCT01526928.

Figures

Figure 1.
Figure 1.
NSCLC patient subgroups. Overview of the n = 84 patients in this study, in three partially overlapping subgroups: the TIGER-X representative subgroup A, the low copy subgroup B and the M0/M1a subgroup C.
Figure 2.
Figure 2.
Comparison between exoNA (EXO1000) and ctDNA-only (BEAMing) platforms. Combined exosomal RNA and cell-free DNA (exoNA) was analyzed using the EXO1000 liquid biopsy platform and compared with ctDNA analysis by BEAMing. (A) EGFR mutant copies found in exoNA compared with copies in ctDNA within the complete patient cohort. The triangles represent del19, hollow circles L858R, full circle L861Q (activating mutations) and squares T790M mutations; identity line shows equal copies/mL plasma. (B) Summary of EGFR detection in plasma within all tumor EGFR positives. (C) Summary of mutant copies found in exoNA and ctDNA. P-values were derived from a paired, one-tailed t-test comparing the two groups. ND, not detected; cps, copies; MUT, mutations.

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Source: PubMed

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