Nikos Sidiropoulos

Primary fields of research

Chromatin Architecture, Structural Variants, Cancer Genomics, Visualization, Bioinformatics

Current research

Cancer is caused by the accumulation of genomic structural variants (SVs), such as deletions and translocations, that cause uncontrolled cell growth, and accumulation of SVs are associated with aggressive cancers. SVs can affect up to hundreds of genes and can be used as robust biomarkers for earlier diagnosis and more precise prognosis. However, we have only rudimentary knowledge of why certain regions are more prone to form SVs, and how SVs affect gene regulation, such as activation of oncogenes. A better understanding of the causes and consequences of SVs has therefore important implications for improving diagnosis and treatment.

Previous work has shown that genomic proximity can be used to identify where SVs form, but this has not been done on a genome-wide scale, which is what we aim to investigate in this project. We have prepared and generated next-generation sequencing data from a phylogeny of cancer cells with acquired SVs, which provide a unique system to examine the interplay between long-range interactions and SV formation in cancer.

The current project will develop and apply novel next-generation sequencing-based methods to cancer cells to answer the question, why certain regions are more prone to form SVs such as fusion genes. We aim to identify the impact of long-range interactions on SV formation and gene regulation in cancer, with important implications for improving the understanding and utility of clinically relevant SVs.