Periodic Reporting for period 2 - CancerCirculome (Circular DNA-driven cancer genome remodeling)
Periodo di rendicontazione: 2022-08-01 al 2024-01-31
Even after decades of research and the development of many new therapies, many cancers remain difficult to treat. One major problem that occurs in cancers is the acquisition of therapy resistance. Understanding the causes of this resistance may help improve treatments. Genes causing therapy resistance can be altered in cancer. One such alteration found in up to one third of all cancers is the increase of the gene’s number per cancer cell on circular DNA elements that are not part of regular chromosomes, termed extrachromosomal DNA (ecDNA). Extrachromosomal ecDNA has emerged as an important cause of therapy resistance in cancer. Our current understanding on how ecDNA are formed, how they are maintained, how they evolve under cancer therapy and how this contributes to therapy resistance is currently still limited. The project CancerCirculome was planned to address some of these open questions in pediatric tumors that recurrently harbor ecDNA. Studying how ecDNA is formed and how it contributes to resistance may reveal new principles of resistance, which may positively impact the way oncologists diagnose and treat their patients. We envision that new forms of therapies, cancer monitoring and risk stratifications will emerge from such research. As ecDNA is found in up to one third of all cancers, such new diagnostic and therapeutic approaches have the potential to improve many patient lives. The overall goal of CancerCirculome is to address the fundamental lack of knowledge about ecDNA to exploit their cancer cell-specific traits for cancer therapy, diagnosis and clinical patient monitoring. The broader aim is to better understand this, as yet under researched level of genomic adaptation, which could be one of the main driving forces in cancer development, progression and/or treatment resistance. To address these important questions in the field of ecDNA, we aim to determine mechanisms of ecDNA generation and propagation, as well as uncover the oncogenic consequences of ecDNA and their re-integration for malignant features of cancer.
In the first half of CancerCirculome we were able to i. develop new methods and preclinical models for the investigation of ecDNA, ii. successfully apply some of these methods to tumors biopsies harboring ecDNA and iii. uncover new principles of ecDNA evolution under therapy. More specifically, we developed computational algorithms that allow us to detect and characterize ecDNA from tumor sequencing data. This allowed us to create new maps of structurally very complex ecDNA elements in tumors. Such maps help us better understand how genes incorporated on ecDNA are abnormally regulated leading to their aberrant high expression. We also developed a method that allows us to purify ecDNA from single cancer cells and when combined with DNA sequencing uncovered an unexpectedly high inter-cellular structural heterogeneity of these elements in cancer. Applying our methods on tumors and cell line models enabled us to describe their evolution under therapy. This revealed that ecDNA dynamics can drive therapy resistance.
Using our single cell ecDNA sequencing method we unexpectedly observed that small circular DNA seem to follow different rules of propagation than large, oncogene-containing ecDNA. Whereas the oncogene-containing elements were shared between the majorities of cells, small circular DNAs were almost exclusively found in single cells. This raises many fascinating questions about the molecular requirements for circular DNA propagation. Furthermore, we also helped others in the field describe an unexpected clustering of ecDNA in cells, termed ecDNA hubs, which seem to contribute to the deregulation of oncogenes. We described how trans interactions of ecDNA may occur in pediatric tumor cell lines within these hubs and how such interactions contribute to the transcriptional regulation of oncogenes. We envision that some of the abovementioned observations may lead to interesting new discoveries during the last part of this project. We also expect that the application of the newly developed methods will enable us to investigate how ecDNA structurally evolve over time, which DNA sequences determine their positive selection and how the inter-cellular ecDNA heterogeneity impacts phenotypic differences between cancer cells. Lastly, we will perform proof-of-principle preclinical experiments to investigate how we can make use of these new insights to improve cancer monitoring.