Defining molecular and gene-regulatory dysregulation in Down Syndrome tissues and models - PROJECT ABSTRACT
Down syndrome (DS) is a neurodevelopmental disorder causing cognitive deficits including impaired learning
and memory, and language development, affecting 1 in 750 newborns. DS is caused by triplication of
chromosome 21 (T21), leading to altered gene dosage, and to changes in the proportion of brain cell types, and
in neuronal morphology and maturation, suggesting a neurodevelopmental etiology. However, the underlying
molecular mechanisms causing the observed neuropathology and functional deficits are still largely unknown.
Progress has been hindered by the overall complexity of brain architecture, an incomplete knowledge of the cell
types and molecular pathways dysregulated in DS during development, and limited human-relevant experimental
models. Moreover, bulk transcriptome and epigenome profiling indicates that T21 not only alters gene dosage
within the locus, but also leads to broad changes in gene expression and may lead to altered gene regulatory
dynamics. Based on these data, we hypothesize that increased chr21 gene dosage alters global gene expression
in neural progenitors, changing neural cell fate specification and differentiation. Here, we leverage novel genomic
technologies including joint single-nucleus transcriptome (snRNAseq), single-nucleus chromatin accessibility
(snATACseq) profiling, and single-cell joint chromatin interaction and methylation profiling (sc-m3C-seq), as well
as primary human neural progenitors (phNPCs), a validated model of human corticogenesis, to test this
hypothesis. We will first define cell-specific molecular and gene-regulatory dysregulation in DS by performing
joint snRNAseq, snATACseq and sc-m3C-seq in a collection of control and DS developing neocortex, at a time
period of peak neurogenesis. This comprehensive multi-omic profiling will uncover changes in cell composition
and cell-specific gene expression signatures in DS neocortex as well as reveal perturbations in cellular lineage
maps and specification. By integrating single-cell expression and epigenetic profiles we will define the proximal
and distal gene regulatory elements, as well as the transcription factors driving DS disease mechanisms. Finally,
we will leverage a unique collection of DS patient-derived and control phNPC lines to model disease in vitro in
order to characterize neural progenitor proliferation and specification in DS, as well as changes in neuronal
morphogenesis and synaptogenesis. We perform joint snRNAseq and snATACseq over a differentiation timeline
that recapitulates embryonic to mid-gestation corticogenesis in order to interrogate cellular, molecular and gene
regulatory dysregulation in DS and directly compare this model with in vivo DS mechanisms. Altogether, we
present a comprehensive project providing an in-depth cell biological and molecular characterization of DS
progression using in vivo tissues and a human-relevant model, and establishes this model for future mechanistic
interrogation. The long-term goal of this research is to provide the foundational molecular knowledge that will
ultimately contribute to the development of treatments for DS.
