Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer

Abstract

Subclonal architecture and genomic evolution of small-cell lung cancer (SCLC) under treatment has not been well studied primarily due to lack of tumor specimens, particularly longitudinal samples acquired during treatment. SCLC is characterized by early hematogenous spread, which makes circulating cell-free tumor DNA (ctDNA) sequencing a promising modality for genomic profiling. Here, we perform targeted deep sequencing of 430 cancer genes on pre-treatment tumor biopsies, as well as on plasma samples collected prior to and during treatment from 22 SCLC patients. Similar subclonal architecture is observed between pre-treatment ctDNA and paired tumor DNA. Mean variant allele frequency of clonal mutations from pre-treatment ctDNA is associated with progression-free survival and overall survival. Pre- and post-treatment ctDNA mutational analysis demonstrate that mutations of DNA repair and NOTCH signaling pathways are enriched in post-treatment samples. These data suggest that ctDNA sequencing is promising to delineate genomic landscape, subclonal architecture, and genomic evolution of SCLC.

Conflict of interest statement

The authors declare the following competing interests: Y.H.G., Y.F.G., X.Y., Y.T.Y., L.P.C., L.Y., Y.X.C., and T.L. are current employees of Geneplus-Beijing. X.Y. and L.Y. hold leadership positions and stocks of Geneplus-Beijing. J.V.H. is a consultant for AstraZeneca, Abbvie, Boehringer Ingelheim, Bristol-Myers Squibb, Medivation, ARIAD, Synta, Oncomed, Novartis, Genentech, and Calithera Biosciences, holds stock in Cardinal Spine LLC and Bio-Tree, and has received funding from AstraZeneca. J.Z. is a consultant for AstraZeneca and receives honoraria from Bristol-Myers Squibb. I.I.W. receives honoraria from Roche/Genentech, Ventana, GlaxoSmithKline, Celgene, Bristol-Myers Squibb, Synta Pharmaceuticals, Boehringer Ingelheim, Medscape, Clovis, AstraZeneca, and Pfizer, and research support from Roche/Genentech, Oncoplex, and HGT. The remaining authors declare no competing interests.

Figures

Fig. 1

Somatic mutation profiles of 22 SCLC patients from pre-treatment ctDNA sequencing of 430 cancer genes. Twenty-two patients were arranged along the x-axis. Mutation per Mb region, clinical and pathological characters were shown in the upper panel. Genes with somatic mutations were shown in the middle panel. Mutation frequencies of each gene were shown on the left and mutation frequencies of these genes in previous report were shown on the right to each gene. The mutational spectrum was shown at the bottom

Fig. 2

Somatic mutations detected in paired tumor DNA and ctDNA. Genes with somatic mutations were listed on the x-axis, and samples were shown on the y-axis. Mutations detected only in tumor DNA (tDNA), only in ctDNA or in both were shown in blue, red and orange, respectively

Fig. 3

Comparison of genomic architecture derived from paired ctDNA versus tumor DNA. CCF of mutations were calculated in ctDNA and tumor DNA. Each dot represents one mutation and the color of each dot indicates the subclone that given mutation was clustered to. Correlation of CCF of all mutations in each pair of samples was shown in the table at lower-right corner. CCF_P: CCF of mutations in ctDNA; CCF_T: CCF of mutations in tumor DNA

Fig. 4

The association of PFS and OS with ctDNA level measured by the average VAF of clonal mutations. Left, Patients were divided into two groups by ctDNA level. High ctDNA level group (higher than median of 0.18, dot line) was significantly associated with shorter PFS. Three patients were excluded from PFS analysis for three different reasons, including one patient who did not receive any treatment based on the patient's choice, one patient received surgery, and one could not offer out-patient otherapeutic records. Right, Patients were divided into two groups using the median ctDNA level of 0.18. Significantly shorter OS was observed in patients with higher ctDNA level (dot line). Small-cell lung cancer (SCLC) may evolve under treatment. But tumor tissues are often not available to study evolution of SCLC. Here, the authors utilize circulating tumor DNA to investigate the genomic evolution and subclonal architecture of SCLC during therapy