Mutational Landscape of cfDNA Identifies Distinct Molecular Features Associated With Therapeutic Response to First-Line Platinum-Based Doublet Chemotherapy in Patients with Advanced NSCLC

Abstract

Rationale To investigate whether the mutational landscape of circulating cell-free DNA (cfDNA) could predict and dynamically monitor the response to first-line platinum-based chemotherapy in patients with advanced non-small-cell lung cancer (NSCLC). Methods Eligible patients were included and blood samples were collected from a phase III trial. Both cfDNA fragments and fragmented genomic DNA were extracted for enrichment in a 1.15M size panel covering exon regions of 1,086 genes. Molecular mutational burden (MMB) was calculated to investigate the relationship between molecular features of cfDNA and response to chemotherapy. Results In total, 52 eligible cases were enrolled and their blood samples were prospectively collected at baseline, every cycle of chemotherapy and time of disease progression. At baseline, alterations of 17 genes were found. Patients with partial response (PR) had significantly lower baseline MMB of these genes than those patients with either stable disease (SD) (P = 0.0006) or progression disease (PD) (P = 0.0074). Further analysis revealed that the mutational landscape of cfDNA from pretreatment blood samples were distinctly different among patients with PR vs. SD/PD. For patients with baseline TP53 mutation, those with PR experienced a significant reduction in MMB whereas patients with SD or PD experienced an increase after two, three or four cycles of chemotherapy. Furthermore, patients with low MMB had superior response rate and significantly longer progression-free survival than those with high MMB. Conclusion This study indicated that the mutational landscape of cfDNA has potential clinical value to predict the therapeutic response to first-line platinum-based doublet chemotherapy in NSCLC patients. At the single gene level, dynamic change of molecular mutational burden of TP53 is valuable to monitor efficacy (and, therefore, might aid in early recognition of resistance and relapse) in patients harboring this mutation at baseline.

Keywords: Non-small-cell lung cancer; chemotherapy; circulating cell-free DNA; molecular mutational burden.

Figure 1

The association between molecular mutational burden and treatment response. (A) alterations of 17 genes including ALK, BCL2, BRAF, CD74, CDKN2A, EML4, GSTP1, KIF5B, KRAS, MLH1, MTHFR, NRAS, RRM1, PIK3CA, SLC34A2, XPC and XRCC1 were frequently observed in 48 blood samples at baseline; (B) patients with PR had significantly lower molecular mutational burden of these genes than patients with SD. Although patients with SD appeared to have lower molecular mutational burden than those with PD, there was no statistically significant difference.

Figure 2

Low molecular mutational burden was associated with superior response rate and longer PFS. (A) The objective response rate and disease control rate in the low molecular mutational burden group was higher than in the high molecular mutational burden group; (B) patients with low molecular mutational burden had markedly longer PFS than those with high molecular mutational burden.

Figure 3

Copy number variation (CNV) ^# from cfDNA was associated with the effect of first-line chemotherapy. (A) CNV profiles from cfDNA was significantly different between patients with PR vs. SD/PD; (B) Clear segregation according to objective response was observed via hierarchical clustering of cfDNA. ^# To reduce the noise signal, the average CNV value of all patients with PR was compared to determine the relative CNV value of each patient.

Figure 4

Dynamic changes in TP53 mutational burden in cfDNA could predict the objective response. Patients with PR experienced a significant reduction in TP53 mutational burden, while patients with SD or PD experienced increased TP53 mutational burden after several cycles of chemotherapy (different colors stand for different patients).