Developmental signals control chromosome segregation fidelity during early lineage specification and neurogenesis by modulating replicative stress
Human development and homeostasis rely on the correct replication, maintenance and segregation of our genetic blueprints. How these intracellular processes are monitored across different human cellular lineages, and why the spatio-temporal distribution of mosaicism varies during development  remain unknown. Using human and mouse pluripotent stem cells, we identify that several lineage specification signals –including WNT, BMP and FGF– converge into the modulation of DNA  replication stress and damage during S-phase, which in turn controls spindle dynamics and  chromosome segregation fidelity in mitosis. We show that patterning signals associated with  anteriorisation during mammalian gastrulation increase chromosome missegregation, while the  posteriorising signals WNT and BMP protect pluripotent stem cells from excessive origin firing,  DNA damage and chromosome missegregation derived from stalled forks. Through epistasis  experiments, we find that WNT, BMP and FGF have distinct roles during DNA replication, and  demonstrate that WNT/GSK3 signalling sits at the helm of this regulatory cascade. Cell signalling  control of chromosome segregation declines after pluripotency exit and specification into the three human germ layers, but re-emerges in differentiating neural progenitors. Through ex vivo and in vivo analyses, we also show that FGF and WNT signalling display opposite roles in chromosome segregation fidelity in mouse neural progenitors during the onset of neurogenesis (E14.5), but not during their expansion (E12.5). In particular, we find that the neurogenic factor FGF2 induces DNA replication stress-mediated chromosome missegregation, which could provide a rationale for the elevated chromosomal mosaicism of the developing brain. Our results highlight a role for patterning signals and cellular identity in genome maintenance that contributes to somatic mosaicism during mouse and human early lineage specification and neurogenesis. Overall design: hiPSC were treated with DMSO, Aphidicolin (200nM) or DKK1 (250ng/ml) for 3hrs prior to double pulse EdU labeling, single cells were sorted and subjected to scEdU-seq (van den Berg, et al., Nature Methods,2024