Origins of de novo chromosome rearrangements unveiled by coupled imaging and genomics

Abstract

Chromosomal instability results in widespread structural and numerical chromosomal abnormalities (CAs) during cancer evolution1-3. While CAs have been linked to mitotic errors resulting in the emergence of nuclear atypias4-7, the underlying processes and basal rates of spontaneous CA formation in human cells remain under-explored. Here we introduce machine learning-assisted genomics-and-imaging convergence (MAGIC), an autonomously operated platform that integrates automated live-cell imaging of micronucleated cells, machine learning in real-time, and single-cell genomics to investigate de novo CA formation at scale. Applying MAGIC to near-diploid, non-transformed cell lines, we track CA events over successive cell cycles, highlighting the common role of dicentric chromosomes as an initiating event. We determine the baseline CA rate, which approximately doubles in TP53-deficient cells, and show that chromosome losses arise more rapidly than gains. The targeted induction of DNA double-strand breaks along chromosomes triggers distinct CA processes, revealing stable isochromosomes, amplification and coordinated segregation of isoacentric segments in multiples of two, and complex CA outcomes, depending on the break location. Our data contrast de novo CA spectra from somatic mutational landscapes after selection occurred. The large-scale experimentation enabled by MAGIC provides insights into de novo CA formation, paving the way to unravel fundamental determinants of chromosome instability.