Mitotic clustering of pulverized chromosomes from micronuclei

Complex genome rearrangements can be generated by the catastrophic pulverization of mis-segregated chromosomes trapped within micronuclei through a process known as chromothripsis. Since each chromosome harbors a single centromere, it remains unknown how acentric fragments derived from shattered chromosomes are inherited between daughter cells during mitosis. Here we tracked micronucleated chromosomes by live-cell imaging and show that acentric fragments cluster in close spatial proximity throughout mitosis for asymmetric inheritance by a single daughter cell. Mechanistically, the CIP2A-TOPBP1 complex prematurely associates with DNA lesions within ruptured micronuclei during interphase, which poises pulverized chromosomes for clustering upon mitotic entry. Inactivation of CIP2A or TOPBP1 caused acentric fragments to disperse throughout the mitotic cytoplasm, stochastically partition into both daughter cells, and mis-accumulate as cytoplasmic DNA fragments that trigger an inflammatory response. Mitotic clustering facilitates the re-assembly of acentric fragments into rearranged chromosomes lacking the extensive DNA copy number losses characteristic of canonical chromothripsis. Comprehensive analysis of pan-cancer genomes revealed clusters of DNA copy number-neutral rearrangements – termed balanced chromothripsis – across diverse tumor types resulting in the acquisition of known cancer driver events. Thus, distinct patterns of chromothripsis can be explained by the spatial clustering of pulverized chromosomes from micronuclei.