Longitudinal Cell-Free DNA Analysis in Patients with Small Cell Lung Cancer Reveals Dynamic Insights into Treatment Efficacy and Disease Relapse

Abstract

Introduction Patients with small cell lung cancer (SCLC) have a poor prognosis and limited treatment options. Since access to longitudinal tumor samples is very limited in patients with this disease, we chose to focus our studies on the characterization of plasma cell-free DNA (cfDNA) for rapid, noninvasive monitoring of disease burden. Methods We developed a liquid biopsy assay that quantifies somatic variants in cfDNA. The assay detects single nucleotide variants, copy number alterations, and insertions or deletions in 14 genes that are frequently mutated in SCLC, including TP53, RB1, BRAF, KIT, NOTCH1–4, PIK3CA, PTEN, FGFR1, MYC, MYCL1, and MYCN. Results Over 26 months of peripheral blood collection, we examined 140 plasma samples from 27 patients. We detected disease-associated mutations in 85% of patient samples with mutant allele frequencies (AFs) ranging from ≤0.1% to 84%. In our cohort, 59% of the patients had extensive stage disease, and the most common mutations occurred in TP53 (70%) and RB1 (52%). In addition to mutations in TP53 and RB1, we detected alterations in 10 additional genes in our patient population (PTEN, NOTCH1–4, MYC, MYCL1, PIK3CA, KIT, and BRAF). Observed AFs and CNAs tracked closely with treatment responses. Notably, in several cases analysis of cfDNA provided evidence of disease relapse before conventional imaging. Conclusions These results suggest that liquid biopsies are readily applicable in patients with SCLC and can potentially provide improved monitoring of disease burden, depth of responses to treatment, and timely warning of disease relapse in patients with this disease.

Targeted deep sequencing from multiple sources demonstrates increased NOTCH1 alterations in lung cancer patient plasma

“…This frequency is much higher than the frequency of 20% observed in our tumor samples and the 8% reported in the Cancer Genome Atlas . However, the NOTCH1 mutation frequency reported here is consistent with other cancer cohort studies, in terms of both lower mutation frequency in tumor tissues and higher mutation frequency in cfDNAs …”

“…16 However, the NOTCH1 mutation frequency reported here is consistent with other cancer cohort studies, in terms of both lower mutation frequency in tumor tissues 14,16 and higher mutation frequency in cfDNAs. 21,35 F I G U R E 1 Landscape of lung cancer patient mutations. The column and row represent patients and genes, respectively, and are sorted decreasingly by the number of mutated genes carried by each patient carries (barplot at the top) or the number of patients in which a gene is mutated (barplot at the right).…”

Dynamics of tumor‐specific cfDNA in response to therapy in multiple myeloma patients

“…On the other hand, a change from negative to positive cfDNA levels observed in some cases might indicate a possible non-responder to therapy. 31,34 Considering abovementioned results, we hypothesized that even CR will be reflected in tumor-specific cfDNA levels, but this was not confirmed. Since there is a trend of increasing negative cfDNA in time and P-value is almost significant, this result might be affected by low number of patients who reached CR (N = 18) and nature of used method.…”

“…Since we observed a significant increase of negative cfDNA samples in time (Table ), slower response to therapy, rather than resistance to therapy, is probably the reason why cfDNA levels remained stable in majority of patients at the time of assessment. On the other hand, a change from negative to positive cfDNA levels observed in some cases might indicate a possible non‐responder to therapy …”

Established, emerging and elusive molecular targets in the treatment of lung cancer

“…As the field moves forwards with immune checkpoint inhibitors, it will be paramount to focus on the identification of biomarkers that are predictive of response. At the same time, it will be important to develop new and dynamic ways to monitor response, such as evaluation of cell-free DNA in the plasma (so-called 'liquid biopsies') [165][166][167][168][169][170].…”