MAGIC aids the identification of chromosomal rearrangements triggered by ALT introduction

Telomeric DNA damage is an established cause of chromosomal rearrangements, drivers of
genome evolution. To achieve unlimited replicative potential, cancer cells must therefore acquire
a telomere maintenance mechanism; ALTernative lengthening of telomeres employs error-prone
DNA repair mechanisms to allow for recombination and synthesis on telomere repeat-containing
sites in the absence of telomerase.
This work investigated the effect of the different telomere maintenance modalities employed by
cancer cells on the formation of structural variants: ALT, elevating recombination rates, could
exacerbate genome instability and promote the accumulation of specific patterns of
rearrangements.
Analyses on the Pan Cancer Analysis of Whole Genomes (PCAWG) dataset highlighted
correlations between ALT(-related) features and complex rearrangements in cancer samples,
hence models of ALT-characteristic mutations and ALT induction were generated.
As the presence of aberrant nuclear structures is a known marker of ongoing genetic instability,
type and frequency of nuclear atypia across models were scored. To maximise the chance of
observing chromosomal alterations, micronuclei-bearing cells were identified, labelled and
isolated through the MAGIC (Machine learning-Assisted Genomics and Imaging Convergence)
platform; Strand-seq allowed the assessment of the spectrum of rearrangements.
While ALT-characteristic truncating mutations of ATRX only increased the number of de novo
variants identified in the cells, ALT induction alone resulted in the accumulation of mitotic errors
and in the formation of specific classes of complex rearrangements, the breakpoints of which
were enriched in G-quadruplex forming, late- and early-replicating regions. The detected
structural variants often affected simultaneously both chromosome arms, and telomere length
inversely correlated with the amount of alterations affecting each arm. Characterising
rearrangements in cells with different telomere maintenance backgrounds, the mutagenic
potential of ALT was confirmed, demonstrating its ability to cause the emergence of distinct
patterns of structural variants.