Mechanisms Driving the Rapid Evolution of Cancer Genomes

PROJECT SUMMARY/ABSTRACT The goal of this proposal is to identify the mechanism of catastrophic mutational processes that drive very rapid evolution of cancer genomes. One of these processes is chromothripsis, which involves massive chromosome rearrangement of only one or a few chromosomes and occurs within a single cell division. My group

identified a general mechanism that explains chromothripsis. Using single cell genomics technology developed in my laboratory (Look-Seq), we discovered that chromothripsis originates from cancer-associated aberrations of the nucleus called micronuclei or chromosome bridges (Fig. 1, Research Strategy). These structures have

fragile nuclear envelopes that undergo spontaneous rupture, which exposes the enclosed chromosome to the interphase cytoplasm where it undergoes a first wave of extensive DNA breakage. When the cell with the damaged chromosome enters mitosis, this chromosome undergoes a second wave of DNA fragmentation,

coincident with a burst of mitotic DNA replication on the damaged chromosome. After the cell exits mitosis and divides, the chromosome fragments can be segregated to one daughter cell, or the fragments can be distributed between both daughters. Reincorporation of these fragments into daughter cell nuclei results in the formation

nuclear bodies similar, if not identical to, previously described, but poorly understood, nuclear bodies called 53BP1 bodies. Chromosome fragments in these nuclear bodies are ligated to generate chromothripsis. In addition to generating chromothripsis, we recently discovered that chromosomes in these nuclear bodies are

subjected to chromatin and transcriptional alterations that can be heritable over many generations, suggesting that chromosomal instability is inherently linked to instability of transcriptional states. Despite this recent progress, many fundamental questions about the mechanism of chromothripsis remain unclear and will be addressed in this proposal. The mechanism of chromosome fragmentation, both in

interphase and in mitosis, remains poorly understood. The 53BP1 body response is one of the least well understood aspects of the DNA damage response in human cells. 53BP1 bodies are proposed to protect the genome, but this has never been directly demonstrated. 53BP1 bodies accumulate DNA end joining factors,

undergo delayed DNA replication and undergo transcriptional suppression—all by unclear mechanisms and with unclear consequences for the genome. Because of approaches we developed, including our single cell genomics methods, we are in a unique position to attack these fundamental problems. In addition to our work on

chromothripsis, we will also exploit the technologies we developed to address the mechanism of another poorly understood, catastrophic mutational process, common in cancer, called chromoplexy. A comprehensive understanding of both these mutational processes is essential to understand cancer initiation and pathogenesis

and how these events vary in different cell and tumor types.