Chromatin network markers of leukemia

Motivation The structure of chromatin impacts gene expression. Its alteration has been shown to coincide with the occurrence of cancer. A key challenge is in understanding the role of chromatin structure (CS) in cellular processes and its implications in diseases. Results We propose a comparative pipeline to analyze CSs and apply it to study chronic lymphocytic leukemia (CLL). We model the chromatin of the affected and control cells as networks and analyze the network topology by state-of-the-art methods. Our results show that CSs are a rich source of new biological and functional information about DNA elements and cells that can complement protein–protein and co-expression data. Importantly, we show the existence of structural markers of cancer-related DNA elements in the chromatin. Surprisingly, CLL driver genes are characterized by specific local wiring patterns not only in the CS network of CLL cells, but also of healthy cells. This allows us to successfully predict new CLL-related DNA elements. Importantly, this shows that we can identify cancer-related DNA elements in other cancer types by investigating the CS network of the healthy cell of origin, a key new insight paving the road to new therapeutic strategies. This gives us an opportunity to exploit chromosome conformation data in healthy cells to predict new drivers. Availability and implementation Our predicted CLL genes and RNAs are provided as a free resource to the community at https://life.bsc.es/iconbi/chromatin/index.html. Supplementary information Supplementary data are available at Bioinformatics online.This work was supported by the European Research Council (ERC) Consolidator Grant 770827, the Serbian Ministry of Education and Science Project III44006, the Slovenian Research Agency project J1-8155, The Prostate Project, and the Foundation Toulouse Cancer Santé and Pierre Fabre Research Institute as part of the Chair of Bio-Informatics in Oncology of the CRCT.Peer ReviewedPostprint (published version