Researchers have used whole-genome sequencing (WGS) to show that chromothripsis is a major driver of circular extrachromosomal DNA amplification.
Gene amplification
Gene amplification was first identified in cells that developed resistance to methotrexate. Amplified DNA is often found in small, circularised DNAs known as double minutes (DMs) – a sub-type of extrachromosomal DNA (ecDNA). It can also be found within intrachromosomal homogenously staining regions (HSRs). Previous studies have suggested that DMs can integrate into host chromosomes and that HSRs are a potential source of DMs. The development of WGS has provided high-resolution views of genome rearrangements in human cancers. These rearrangements include gene amplification and chromothripsis (shattering of a chromosome). Experts have proposed various mechanisms that drive the formation of DMs. In addition, the formation of HSRs can result from multiple different mechanisms.
Chromothripsis drives amplification of ecDNA
In a study, published in Nature, researchers applied selection pressure using different concentrations of methotrexate to identify the mechanisms that underly the early acquisition of drug resistance. They found that continuous, stronger selection pressure promoted DM formation. They also examined the evolution of DMs during adaptation to an increased methotrexate concentration. Stepwise increases in dose resulted in increases in DM copy number and major structural changes. In situ Hi-C sequencing also showed that ecDNAs preferentially tethered near chromosome ends.
Most importantly, they identified non-homologous end joining and PARP-dependent repair after chromothriptic shattering as mechanisms of initial oncogene amplification or anti-cancer resistance, and as drivers of subsequent rearrangements. As a result, the authors proposed that chromothripsis is a primary mechanism that accelerates genomic DNA rearrangement and amplification into ecDNA, and enables rapid acquisition of tolerance to altered growth conditions. They also noted that given chemotherapeutic drugs can result in chromothriptically initiated rearrangements, the combination of a targeted therapy with DNA repair inhibitors may represent an effective approach to prevent initial cancer becoming more aggressive or drug resistant.
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