The primary goal of this proposal is to elucidate the mechanism of a newly discovered mutational process called chromothripsis. Chromothripsis generates rapid karyotype evolution in cancer, congenital disease, and other contexts. Chromothripsis is characterized by extensive genomic rearrangements and an oscillating pattern of DNA copy number levels, all surprisingly restricted to one or a few chromosomes. We have made significant recent progress in defining a mechanism for chromothripsis. We showed that intact chromosomes missegregated into aberrant cancer-associated nuclear structures called micronuclei (MN) develop extensive DNA damage. This led us to propose that the physical isolation of chromosomes into MN could cause chromothripsis. Recently, we developed a method (Look-Seq) to combine live cell imaging and single cell genome sequencing, enabling us to recreate chromothripsis in the laboratory and directly demonstrate that it can originate from disrupted MN. We established that chromothripsis could arise by fragmentation and reassembly of MN chromosomes. These fragments can also circularize, potentially providing a mechanism for forming double minute chromosomes, major vehicles for oncogene amplification in cancer. The Look-Seq approach now positions the laboratory to attack the key mechanistic questions in the field: the timing and order of chromosome fragmentation and reassembly, the mechanism of MN chromosome fragmentation; and how it is reassembled. We also propose a series of experiments to define the contribution of DNA replication errors in generating localized chromosome rearrangements. Finally, we propose experiments to elucidate the mechanistic basis for two major sources of oncogene amplification in cancer.

Public Health Relevance

Cancer genomes are shaped by mutation and chromosome rearrangement. Understanding mutational processes has led to new understanding of how cancer develops as well as to the development of new cancer therapies. Building on preliminary work, we now propose to elucidate a newly discovered mutational process in cancer called chromothripsis.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA213404-20
Application #
9404986
Study Section
Cellular Signaling and Regulatory Systems Study Section (CSRS)
Program Officer
Witkin, Keren L
Project Start
1997-05-01
Project End
2021-11-30
Budget Start
2017-12-01
Budget End
2018-11-30
Support Year
20
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Dana-Farber Cancer Institute
Department
Type
DUNS #
076580745
City
Boston
State
MA
Country
United States
Zip Code
02215
Li, Hubo; Mar, Brenton G; Zhang, Huadi et al. (2017) The EMT regulator ZEB2 is a novel dependency of human and murine acute myeloid leukemia. Blood 129:497-508