Chromothripsis and ecDNA initiated by N4BP2 nuclease fragmentation of cytoplasm-exposed chromosomes

Abstract

Genome instability, including chromothripsis, is a hallmark of cancer. cancer cells frequently contain micronuclei—small, nucleus-like structures formed by chromosome missegregation—that are susceptible to rupture, exposing chromatin to cytoplasmic nucleases. Through an unbiased, imaging-based small interfering rNA screen that targeted all 204 known and putative human nucleases, we identified a previously uncharacterized cytoplasmic endonuclease, NeDD4-binding protein 2 (N4bP2), that enters ruptured micronuclei and initiates DNA damage, leading to chromosome fragmentation. N4bP2 promoted genome rearrangements (including chromothripsis), formation of extrachromosomal DNA (ecDNA) in drug-induced gene amplification, tumorigenesis, and tumor cell proliferation in an induced model of human high-grade glioma. Analysis of more than 10,000 human cancer genomes revealed elevated N4bP2 expression to be predictive of chromothripsis and copy number amplifications, including ecDNA.