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Openshaw, M., et al. (2023) Annals of Oncology 34, pS54.
Nonacus Products: Cell3 Target: Oncology
Background
Oesophageal adenocarcinoma (OA) has a dismal survival rate and no routine blood-borne biomarker. Circulating tumour DNA (ctDNA) detection in plasma DNA is an emerging non-invasive biomarker. OA ctDNA analysis has previously been shown to track disease relapse and progression. However, little is known about how well ctDNA reflects genetic tumour evolution over time. Two patients with OA that had previously undergone tumour sampling at diagnosis and longitudinal plasma DNA collection were recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) study. Providing a unique opportunity to compare tumour- and ct-DNA from diagnosis to death.
Methods
Patients consented separately to sample storage at the University of Leicester Cancer Biobank, UHL11274 (REC: 13/EM/0196), and the PEACE study. Whole exome sequencing (WES) of primary and metastatic tumour DNA was performed. All non-synonymous predicted pathogenic variants in the primary biopsy were assigned to major and minor clones (denoted clone A & clone B variants). Variants not present in the initial primary tumour (VAF < 5%) but present in ≥1 metastatic sample (VAF ≥20%) were termed Emergent Variants (EVs). Cell3™Target Technology Patient Specific Panels (Noncaus) where designed to capture clone A, B and Emergent Variants in plasma DNA. Patient specific NGS was performed (median depth 1500X), using 20ng of plasma DNA and Cell3™Target Library Preparation.
Results
Patient 1 OA treated with curative intent. After relapse and death, metastases were sampled from liver, thoracic lymph nodes and pleural fluid. 132 non-synonymous tumour WES variants were detected. Five tier 1 variants were identified (Clone A=3, EVs=2). All timepoints (n=5) prior to relapse were ctDNA negative. Relapse and on treatment timepoints (n=3) were ctDNA positive. Only clone A variants (n=10) were identified at relapse. 61 variants (56 clone A, 5 clone B) were identified on treatment. No EVs were detected. KRAS p.G12D was the only tier 1 variant detected in ctDNA. Patient 2 Metastatic OA at diagnosis. Metastases were sampled from brain and abdominal lymph nodes after death. 287 non-synonymous tumour WES variants were detected. 13 tier 1 mutations were identified (Clone A = 8, Clone B=1, EVs=4) ctDNA was only detectable at diagnosis and disease progression, no ctDNA was detected during tumour response to chemotherapy.132-157 tumour variants were detected at timepoints 1 (diagnosis, including 21 EVs), and 3 respectively (including 26 EVs). Two tier 1 EVs (AKT1 and PTGS1) specific to the metastatic brain tumours were detectable in ctDNA at diagnosis, 90 weeks prior to clinical diagnosis. ctDNA was undetectable in samples taken prior to death in both cases, although plasma DNA levels were high.
Conclusions
As expected ctDNA was detectable at disease progression or relapse but not in prior time points. Despite high plasma DNA levels, ctDNA analysis was not useful close to death, potentially due to widespread necrosis of non-tumour cells. Interestingly, brain metastases specific ctDNA was detectable up to 90 weeks prior to clinical appearance. This preliminary study provides evidence for the utility of ctDNA monitoring in OA. This ability to confidently track metastatic specific alterations during disease progression promises new insights into OA evolution.
