Characterising DNA methylation patterns in tissue and circulating tumour DNA of patients with renal cancer - 11th International Symposium on Circulating Nucleic Acids in Plasma and Serum (CNAPS)

Rossi Sabrina Helena ¹ Sara Pita ^1,2 Gahee Park ^1,2 Radoslaw Lach ^1,2 Chris Smith ^1,2 Kevin Brennan ³ Tom Mitchell ² Anne Warren ² Vincent Gnanapragasam ² Olivier Gavaert Olivier Gevaert ³ Grant Duncan Stewart ² Grant Duncan Stewart Charlie Massie Charlie Massie Charlie Massie ^1,2

¹Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
²CRUK Cambridge Cancer Centre, University of Cambridge, Cambridge, UK
³Gevaert Lab, Stanford University, USA

Circulating tumour DNA (ctDNA) is a promising tool for early detection and monitoring of minimal residual disease. In particular, renal cell carcinoma (RCC) is characterised by genetic heterogeneity and liquid biopsies have the potential to overcome limited tumour sampling which occurs with renal biopsy. However, ctDNA detection is challenging in patients with early stage cancer and levels in RCC are lower compared to other malignancies.

To test whether epigenetic analysis can improve ctDNA detection rates in RCC we aim to (a) analyse multi-region samples from patients with renal tumours to map the landscape of DNA methylation heterogeneity and (b) determine whether assessing early ‘stem’ methylation markers can increase ctDNA detection rates compared to mutational analysis alone.

We have integrated data from The Cancer Genome Atlas (TCGA) and recruited a cohort of patients (n=21) across the RCC disease spectrum, from small renal masses to metastatic disease, including both clear cell (N=18) and chromophobe (N=3) pathology. Two patients with benign oncocytomas were also included. Multi-region kidney tumour samples were collected from the nephrectomy specimen, including adjacent normal tissue, as well as urine and plasma samples from the same patients. Methylation analysis was performed in tissue using the Illumina EPIC Methyl Capture library preparation kit, with post capture bisulfite conversion. We identified sets of differentially methylated regions (DMRs) in tumour tissue that (a) classify pathological subtypes of RCC and oncocytomas and (b) represent early ‘stem’ markers for ctDNA analysis, leveraging our in-house methylation sequencing data and TCGA methylation array data. We present a summary of epigenetic targets for RCC and methods for high-sensitivity targeted DNA methylation analysis in ctDNA. We will explore the detection rates of methylation markers and somatic mutations in ctDNA analysis to assess the feasibility of combined analysis to increase detection of ctDNA in low burden disease.