Functional integrative genomics implicates genetically encoded dysregulation of prenatal angiogenesis in cerebral palsy

Introduction: Cerebral palsy is a neurodevelopmental disorder that is classically believed to arise from perinatal anoxia, leading to impaired motor function. Recent genomic studies of human patients have identified novel genetic causes of cerebral palsy, however, the mechanisms that link gene mutations to pathogenic manifestations of cerebral palsy remain unknown. Here, we performed unbiased functional integrative genomic analyses to identify the biological processes and cell types in which cerebral palsy gene mutations may exert their pathogenic effects.

Methods: We combined whole-exome sequencing genetic data from 250 cerebral palsy patients with bulk and single-cell RNA sequencing of the normally developing human brain to comprehensively map the expression profiles of cerebral palsy risk genes. We performed immunostaining in mouse tissue to validate the expression of cerebral palsy genes. We performed CRISPR-Cas9 gene editing in the zebrafish to characterize the functions of cerebral palsy genes in development.

Results: A heterogenous set of 439 cerebral palsy risk genes was enriched during the third trimester and first postnatal year of human brain development, corresponding with the early postnatal onset of motor dysfunction in human patients. At the cell type level, we surprisingly found that cerebral palsy risk genes were enriched in endothelial cells and mural cells of the developing human brain, consistent with immunostaining validation in mouse tissue. Knocking out Ctnnb1 and Fbxo31, mutations of which cause cerebral palsy in human patients, results in impaired angiogenesis in zebrafish embryos.

Conclusion : These findings suggest a primary impact of cerebral palsy gene mutations on the development of the brain vasculature and cerebral blood flow prenatally and during the first year of life. Thus, a genetic risk underlying the brain’s susceptibility to tissue hypoxia may provide an explanation for gene-environment interactions involved in the pathogenesis of cerebral palsy, rendering some children more vulnerable to brain injury. Our work motivates the use of whole-exome/genome sequencing as a crucial diagnostic and prognostic adjunct in the workup of children with cerebral palsy, which could help guide the development of preventative strategies.