A novel AI toolbox based on Oxford Nanopore sequencing to study DNA replication in cancer | LC 25

Biography

Pauline Pfuderer is a PhD candidate in Computational Cancer Research at the University of Cambridge, where she previously completed an MRes in Cancer Biology. Prior to this, she received an MSc and BSc in Molecular Biotechnology at the University of Heidelberg, Germany, as a scholar of the German National Academic Foundation.

She studied abroad at Harvard University and was a visiting researcher at the German Cancer Research Centre (DKFZ), the European Bioinformatics Institute (EBI), and the Dana-Farber Cancer Institute.

Abstract

DNA replication differs between healthy cells and cancer cells and can be exploited as a therapeutic target. Recently, the role of extrachromosomal DNA (ecDNA) in cancer has gained a lot of attention because ecDNA often harbours oncogene amplifications, driving rapid tumour evolution, and occurs in ~14% of all newly diagnosed cancers. We advanced DNAscent, an AI-based method that allows us to study the DNA replication dynamics on ecDNA and identify differences between ecDNA and chromosomal DNA. DNAscent can detect two base analogues (BrdU and EdU) in single molecules of DNA sequenced on the Oxford Nanopore Technologies platform. Recently we added a new feature to DNAscent, to automatically annotate erroneously stopped or stalled forks. DNAscent has been adapted for the R10.4.1 nanopore and allows us to decipher replication fork velocity, replication stalling and the location of origins of replication. We compare replication fork velocities and stall scores on single molecules between an ecDNA+ and an ecDNA- colorectal cancer cell line derived from the same tumour. With DNAscent we can differentiate between ecDNA and chromosomal DNA within the same cell line, and find significantly slower fork velocities on ecDNA compared to chromosomal DNA alongside a significant increase in replication fork stalling. Our findings indicate that DNA replication dynamics differ between ecDNA and chromosomal DNA and the presence of ecDNA affects the replication dynamics on chromosomal DNA. Our study further suggests how ecDNA replication may be vulnerable to interference with therapeutic agents to target cells with oncogene amplifications.