Rebuilding Chromosomes After Catastrophe: Emerging Mechanisms of Chromothripsis

Abstract

Cancer genome sequencing has identified chromothripsis, a complex class of structural genomic rearrangements involving the apparent shattering of an individual chromosome into tens to hundreds of fragments. An initial error during mitosis, producing either chromosome mis-segregation into a micronucleus or chromatin bridge interconnecting two daughter cells, can trigger the catastrophic pulverization of the spatially isolated chromosome. The resultant chromosomal fragments are religated in random order by DNA double-strand break repair during the subsequent interphase. Chromothripsis scars the cancer genome with localized DNA rearrangements that frequently generate extensive copy number alterations, oncogenic gene fusion products, and/or tumor suppressor gene inactivation. Here we review emerging mechanisms underlying chromothripsis with a focus on the contribution of cell division errors caused by centromere dysfunction.

Keywords: DNA repair; chromosome rearrangements; chromothripsis; genomic instability; micronuclei; mitosis.

Figure 1. Genomic and tumorigenic consequences of chromothripsis

(A) The shattering of an individual chromosome can produce tens to hundreds of acentric DNA fragments that persist as intermediates until they are re-ligated and stabilized by intrinsic DNA repair mechanisms. These fragments reassemble to form a scrambled, derivative chromosome containing multiple rearrangements (chromothripsis), become lost, and/or self-ligate into circular DNA structures called double minutes. (B) Chromothriptic events can give rise to a characteristic mutation signature that has been detected in a broad range of cancer genomes, including oscillating copy number states and complex patterns of intrachromosomal rearrangements in apparently random fashion.

Figure 2. Chromosome segregation errors during mitotic cell division can entrap DNA within a micronucleus

During mitosis, a chromosome that fails to congress, align, and/or form proper bipolar spindle microtubule–kinetochore attachments prior to anaphase onset can be left behind during the physical separation of the duplicated genome. A nuclear envelope assembles around the missegregated chromosome, subsequently forming a micronucleus at the exit of mitosis.

Figure 3. DNA damage in micronuclei triggers in the catastrophic shattering of individual chromosomes

(A) Chromosomes isolated in micronuclei are sequestered by a highly unstable nuclear envelope, which are susceptible to disruption throughout interphase that interferes with normal nucleocytoplasmic transport and compartmentalization (i) [41]. Disruption can cause DNA replication asynchrony between the main nucleus and micronucleus (ii) [24], as well as permit exposure of micronuclear DNAs to damaging cytoplasmic components such as nucleases. In turn, DNA damage restricted to the micronucleated chromosome (iii) [26] persists throughout the cell cycle and into mitosis. Nuclear envelope breakdown and chromatin condensation initiated by mitotic entry subsequently causes the micronuclear chromosome harboring multiple double-stranded DNA breaks to undergo shattering that is accompanied by the spatial separation of chromosomal fragments (iv) [26]. Data images were modified and reproduced with permission from Elsevier (i) and Nature Publishing Group (ii–vi). NLS, nuclear localization signal.

Figure 4. DNA damage repair mechanisms contributing to the reassembly of fragmented chromosomes

(A) Chromosome fragments produced by chromothripsis spill into the mitotic cytoplasm and are subsequently incorporated into newly formed daughter cell nuclei at the exit of mitosis, possibly through the physical tethering between fragments and/or onto intact, centromere-containing chromosomes. (B) In the next interphase, reintegrated fragments activate the DNA damage response. In the absence of functional p53, DNA double-strand break repair ensues through error-prone non-homologous end joining, which directly links multiple fragments together in a haphazard manner by ligation. The reassembled chromosome is characterized by extensive DNA rearrangements harboring de novo breakpoint junctions that carry the signatures of the underlying DNA repair mechanism.

Figure 5. Chromatin bridges act as a source of focal chromothripsis

(A) Telomere fusion events can create dicentric chromosomes that harbor two active centromeres, both of which are capable of forming kinetochore–microtubule attachments during mitosis and segregation toward opposite spindle poles. Nuclear envelope reassembly at the exit of mitosis produces a chromatin bridge (dotted box, magnified in B) that persists into interphase connecting two nascent daughter cells. (B) Rupture of the nuclear envelope surrounding the chromatin bridge enables access of the normally cytoplasmic-localized TREX1 exonuclease to the underlying DNA, causing chromosome breaks restricted to the bridge that are likely repaired during the same or subsequent interphase. (C) Clustered rearrangements and hypermutation localized to a specific chromosome arm or region are common outcomes for fragmented bridges. Subsequent fusion events between telomere-free ends can facilitate further genomic instability through repeated cycles of breakage-fusion-bridge