Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - iPSC-derived Neural Xenografts Multiome Dataset

Down syndrome, caused by an extra copy of chromosome 21, is the most common genetic form of intellectual disability affecting up to 1 in 700 live births1-3. Yet, it remains unclear how the increased dosage of ~200 protein-coding genes on chromosome 21 affects brain development, particularly in the cerebral cortex—the area central to higher-level cognitive functions4-7. Here we generated a single-cell transcriptome and chromatin accessibility atlas from 30 human fetal cortical samples at mid gestation (10-20 weeks after conception), a critical period of cortical development8. We discovered an early global transcriptional network disruption, subtly altering ~600 genes involved in neural development and function, mostly in excitatory neurons accompanied by a significant reduction in RORB/FOXP1 expressing excitatory neurons. Multimodal network analyses predicted the chromosome 21 transcription factors BACH1, PKNOX1, and GABPA as key regulatory hubs controlling dozens of genes genetically linked to intellectual disability. Antisense-mediated normalization of the increased activity of these transcription factors in stem-cell-derived neural cells in vitro, which partially recapitulated molecular changes in the Down syndrome cortex, rescued expression of several of these predicted intellectual disability-associated targets. Finally, a humanized in vivo model replicates key molecular features of Down syndrome not recapitulated in neural cells in vitro. This resource defines the gene-regulatory landscape of the developing human cortex in Down syndrome, revealing early molecular and cellular signatures and candidate therapeutic targets, along with a human in vivo experimental platform for their preclinical testing. Overall design: We performed combined single-cell transcriptional and chromatin accessibility profiling (10X Genomics Multiome technology) of iPSC-derived neural grafts (generated with approach from Real et al., 2018) from an individual with DS and from isogenic control iPSCs (CON, normal diploid karyotype; iPSC lines DS and DS2U from Weick et al., 2013, aquired from WiCell, UWWC1-DS1 and UWWC1-DS2U). We combined graft libraries with snRNA-seq libraries generated by Singleron and compared grafts to fetal tissue and neural cells in vitro, derived from the same iPSC line.