Integrated genomic analysis and application of single cell and circulating free DNA sequencing in NET management


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Chrissie Thirlwell1
1University College London Cancer Institute and Royal Free Hospital NET Unit, London, UK

Abstract

Neuroendocrine tumours (NETs) are a clinically and genetically heterogeneous group of cancers with markedly different clinical outcome depending on the primary site and grade of tumour. Due to the rarity of NETs, previous genomic studies have included small sample sizes, often originating from mixed primary sites.

My group has undertaken the first large scale integrated genomic analysis of pancreatic and intestinal NETs including exome sequencing, genome-wide DNA methylation analysis, RNA expression and copy number analysis.

This analysis has identified disruption of the Wnt signalling and neurodevelopmental pathways in NET development. DNA methylation biomarkers (tissue based and circulating) have been identified which differentiate between normal tissue and NETs and also between grade of NET. This includes the identification of promoter methylation of RASSF1 as a candidate pathogenic driver; whilst analysis of circulating free DNA has identified RASSF1 hypermethyhlation in gastrointestinal GI NET patients relative to normal controls.

Gene ontology analysis has identified genes in pathways associated with everolimus resistance to be differentially methylated in tumour tissue. This is of particular significance following the introduction of everolimus therapy in pancreatic NETS with on-going phase III trials in intestinal and bronchial NETs.

Co-workers at UCL recently identified and validated circulating tumour cells (CTCs) as a prognostic biomarker in NET patients with metastatic disease. We have since isolated and sequenced DNA from single NET CTCs. Analysis of CTCs can teach us about mechanisms of metastatic spread and also determine the how resistance to systemic therapy develops. Alongside this we have also quantified and sequenced circulating free DNA in NET patients. In future, analysis of this ‘liquid biopsy' will enable us to truly personalise cancer therapy for NET patients.