Objective

Cockayne syndrome (CS) is a rare monogenic disorder marked by neurodevelopmental defects, progressive neurodegeneration, and premature ageing. Clinical expression is highly variable, ranging from congenital microcephaly to milder adult-onset forms. Although caused by mutations in either CSA or CSB, proteins involved in DNA repair, but also transcription and chromatin remodeling, the molecular mechanisms underlying disease variability as well as the overlap with physiological ageing remain unclear. Interestingly, mutations in the same genes can cause UV-sensitive syndrome (UVSS), a condition with UV-hypersensitivity but no neurodegeneration or progeroid features, offering a unique opportunity to dissect the drivers of progeroid-related decline.

Methods

We used fibroblasts and induced pluripotent stem cell (iPSC)-derived neural organoids (NOs) from CS and UVSS patients with different clinical severities, including a case where no neurodegeneration was observed despite protein impairment. We complemented these with isogenic iPSC models generated via CRISPR/Cas9-mediated correction or insertion of CSB mutations. We performed transcriptomic and epigenomic profiling to uncover key pathways and molecular signatures involved in disease manifestation.

Results

CS-derived NOs showed defects in neural maturation and cytoarchitecture, which remarkably correlated with clinical severity, and the presence or not of congenital defects. These abnormalities were absent in UVSS NOs, despite equivalent protein impairment. Importantly, healthy NOs engineered to carry CSB mutations did not fully reproduce the observed patient-derived NOs defects, underscoring the importance of genetic background in the pathological phenotype. Combined omics data from fibroblasts and NOs suggest that transcriptional reprogramming, alongside mitochondrial dysfunction due, in some cases, to epigenomic alterations, underlies neurodegenerative and progeroid features. These defects were partially or fully rescued in functional assays.

Conclusion

CS is a mechanistically informative model of neurodevelopmental defects and their link with neurodegeneration and accelerated ageing. Our data indicate that mutation-independent modifiers and stress-driven transcriptional dysregulation, rather than CSA/CSB loss alone, shape disease severity. These insights may extend to physiological ageing, offering potential therapeutic avenues for both rare and common neurodegenerative conditions.