Longitudinal tracking of 97 esophageal adenocarcinomas using liquid biopsy sampling

Abstract

Background: The incidence of esophageal adenocarcinoma (EAC) is rapidly rising and has a 5-year survival rate of <20%. Beyond TNM (tumorenodeemetastasis) staging, no reliable risk stratification tools exist and no large-scale studies have profiled circulating tumor DNA (ctDNA) at relapse in EAC. Here we analyze the prognostic potential of ctDNA dynamics in EAC, taking into account clonal hematopoiesis with indeterminate potential (CHIP). Patients and methods: A total of 245 samples from 97 patients treated with neoadjuvant chemotherapy and surgery were identified from the prospective national UK Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium data set. A pan-cancer ctDNA panel comprising 77 genes was used. Plasma and peripheral blood cell samples were sequenced to a mean depth of 7082Â (range 2196-28 524) and ctDNA results correlated with survival. Results: Characteristics of the 97 patients identified were as follows: 83/97 (86%) male, median age 68 years (SD 9.5 years), 100% cT3/T4, 75% cNþ. EAC-specific drivers had higher variant allele fractions than passenger mutations. Using stringent quality criteria 16/79 (20%) were ctDNA positive following resection; recurrence was observed in 12/16 (75%) of these. As much as 78/97 (80%) had CHIP analyses that enabled filtering for CHIP variants, which were found in 18/78 (23%) of cases. When CHIP was excluded, 10/63 (16%) patients were ctDNA positive and 9/10 of these (90%) recurred. With correction for CHIP, median cancer-specific survival for ctDNA-positive patients was 10.0 months versus 29.9 months for ctDNA-negative patients (hazard ratio 5.55, 95% confidence interval 2.42-12.71; P ¼ 0.0003). Similar outcomes were observed for disease-free survival. Conclusions: We demonstrate in a large, national, prospectively collected data set that ctDNA in plasma following surgery for EAC is prognostic for relapse. Inclusion of peripheral blood cell samples can reduce or eliminate false positives from CHIP. In future, post-operative ctDNA could be used to risk stratify patients into high-and low-risk groups for intensification or de-escalation of adjuvant chemotherapy.

Genome-wide cell-free DNA termini in patients with cancer

“…When analyzing the 31 samples collected postsurgery, we demonstrated that 70% of patients with a FrEIA score above the detection threshold (13 out of 18 patients) developed a recurrence. Our results are comparable to mutation-based detection of tumor-derived cfDNA in resectable EAC (7,8). In a recent publication a ctDNA panel consisting of 77 genes was tested in 97 EAC patients.…”

“…In a recent publication a ctDNA panel consisting of 77 genes was tested in 97 EAC patients. After filtering of CHIP variants, the panel showed high prognostic potential for disease-free survival (HR 5.35, 95% CI 2.10-13.63; P ≤ 0.0001) based on the post-surgery samples (7). Another paper used an EAC tumor guided sequencing approach and found ctDNA status (positive vs. negative) to be prognostic at baseline for disease-free survival (p=0.042) (8).…”

“…To evaluate the prognostic value of FrEIA in a clinical setting, we tested cfDNA from resectable EAC patients, where serial ctDNA detection has been shown to predict adverse outcome (7). Here we assessed the potential of the FrEIA score in 293 resectable EAC samples from 2 clinical cohorts: a neoadjuvant chemoradiotherapy (nCRT) cohort (n=70 patients, n = 149 plasma samples) receiving standard of care carboplatin combined with paclitaxel based nCRT and a cohort of patients who participated in the phase II PERFECT trial (n=40 patients, n = 144 samples, see Methods) received nCRT in combination with a PD-L1 inhibitor (27).…”

“…Mutation-based detection of tumor-derived cfDNA is often hampered by technical and biological noise (the latter linked to the accumulation of mutations in normal cells) (5,6). For example, in elderly patients with TP53 mutant tumors, such as in esophageal adenocarcinoma (EAC), clonal hematopoiesis of indeterminate potential (CHIP) hampers the determination of the origin of cfDNA variants (6,7). In stage I-III patients with a low tumor fraction of cfDNA this requires a high sequencing depth for cfDNA, availability of buffy coat samples, tumor-informed sequencing or computational strategies to filter CHIP-derived variants (8,9).…”

Therapeutic cancer vaccines revamping: technology advancements and pitfalls

“…Of note, growing evidence suggests a higher benefit of ICB-therapies in circulating tumor DNA (ctDNA)-positive patients in several malignancies, with a favorable prognostic role of ctDNA seroconversion rates ( 177 ) ( 178 ). Consolidated data concerning eventual prognostic/predictive roles of this biomarker could possibly instruct for the use of ctDNA seroconversion rate as a primary endpoint of (neo)adjuvant CV clinical trials, alongside long-term survival data (i.e.…”