Chromothripsis drives the evolution of gene amplification in cancer

Abstract

Focal chromosomal amplification is an important route to generating cancer through mediating over-expression of oncogenes 1 – 3 or to developing cancer therapy resistance by increasing expression of a gene whose action diminishes efficacy of an anti-cancer drug. Here we used whole-genome sequencing of clonal isolates developing chemotherapeutic resistance to identify chromothripsis as a major driver of extrachromosomal DNA (ecDNA) amplification into circular double minutes (DMs) through PARP- and DNA-PKcs-dependent mechanisms. Longitudinal analyses revealed that DMs undergo continuing structural evolution to promote increased drug tolerance through additional chromothriptic events. In-situ Hi-C sequencing is used to demonstrate that DMs preferentially tether near chromosome ends where they re-integrate when DNA damage is present. Intrachromosomal amplifications formed initially under low-level drug selection undergo continuing breakage-fusion-bridge cycles, generating >100 megabase-long amplicons that we show become trapped within interphase bridges and then shattered, producing micronuclei that mediate DM formation. Similar genome rearrangement profiles linked to localized gene amplification are identified in human cancers with acquired drug resistance or with oncogene amplifications. We propose that chromothripsis is a primary mechanism accelerating genomic DNA amplification and which enables rapid acquisition of tolerance to altered growth conditions.

Structural variants shape driver combinations and outcomes in pediatric high-grade glioma

“…A single SV can have long-range effects on dozens to hundreds of genes. In some cases, SVs result in extrachromosomal amplifications (otherwise known as double minutes) 10 that can lead to hundreds of copies of an oncogene per cell [11][12][13][14][15] . Moreover, the effects of SVs on cellular fitness often result from changes in chromatin structure such as disruption of topologically associated domains (TADs) and gene-enhancer interactions [16][17][18][19][20][21] .…”

The Last Chance Saloon

“…The requirement for abscission delay to prevent breakage of chromatin bridges raises the question of whether there are active mechanisms of chromatin bridges resolution to avoid the severing of chromosomes, possibly coupled with the Aurora B-dependent NoCut pathway. Careful examination of chromatin bridges in mammalian cells by correlative light and electron microscopy revealed a constriction in chromatin bridges at the midbody region (Shoshani et al, 2020). In addition, the chromatin bridge DNA and Aurora B kinase which resides at midbody showed a mutually exclusive localization after chromatin bridge cleavage, suggesting that the chromatin bridge resolution takes place at the midbody (Shoshani et al, 2020).…”

“…In addition, fused chromosomes often missegregate, frequently leading to the formation of micronuclei. Micronuclei can fuse with the nucleus and circular extrachromosomal DNA (ecDNA) contained in micronuclei might serve as a source for DNA fragments, which can be randomly integrated at or close to breakpoints further enhancing chromothripsis (Zhang et al, 2015;Kneissig et al, 2019;Koltsova et al, 2019;Shoshani et al, 2020;Umbreit et al, 2020). The NoCut checkpoint delays abscission, which allows time for subsequent chromatin bridge resolution.…”

“…Careful examination of chromatin bridges in mammalian cells by correlative light and electron microscopy revealed a constriction in chromatin bridges at the midbody region (Shoshani et al, 2020). In addition, the chromatin bridge DNA and Aurora B kinase which resides at midbody showed a mutually exclusive localization after chromatin bridge cleavage, suggesting that the chromatin bridge resolution takes place at the midbody (Shoshani et al, 2020). Indeed, using C. elegans genetics and cell biological approaches we recently uncovered a novel mechanism for the chromatin bridge resolution, conferred by a midbody associated endonuclease called LEM-3 (Hong et al, 2018a).…”

Chromothripsis—Explosion in Genetic Science

“…The chromothripsis is a poor prognostic marker in such types of cancer as medulloblastoma [ 73 ], acute myeloid leukemia [ 77 ], neuroblastoma [ 92 ]. In the study by Dr. Shoshani and colleagues, it was found that having double minutes in cancer cells with chromothripsis is a poor predictor for patients [ 93 ]. In such cases, resistance to cancer therapy is often observed.…”