A single-cell transcriptomic map of the human developing cortex in Down syndrome

Lead Research Organisation: Imperial College London
Department Name: Institute of Clinical Sciences


The human brain is a highly complex system comprised of billions of neurons interconnected to each other to form functional neural circuits. Normal brain function is dependent on effective communication between neurons, a process that requires the establishment of normal patterns of neural network activity. Several diseases that affect the brain result from impairments in the communication between neurons, which is why it is essential to understand how neural circuits are initially established and the mechanisms involved.
We are particularly interested in understanding how the emergence of neural network activity can be controlled by the precise composition of various cell types in the immature foetal human brain and in Down syndrome (DS). DS is a common neurodevelopmental disorder and a major cause of congenital intellectual disability caused by a trisomy of Chromosome 21 (Ts21). Advances in our understanding of the underlying cellular and molecular mechanisms have been hampered by the limited availability of model systems that recapitulate this complex chromosomal condition.

Cellular analyses in the immature human brain though focus on post-mortem fixed tissue samples, which cannot provide direct observation of dynamic events such the formation of electrical activity patterns. This limitation raises the question of how to study the cellular and molecular mechanisms of human neural circuit assembly and their dysfunction in DS.

My team has recently developed a new approach to study in real-time the establishment of human neuronal networks using transplanted donor-derived induced pluripotent stem cells (iPSC) and longitudinal in vivo imaging. This experimental design allows the study of human neural network activity in a vascularized human graft over several weeks, overcoming several limitations of current in vitro approaches (e.g. the lack of blood vessels). We showed that neuronal activity is less synchronous in DS, which could contribute to cognitive deficits in DS. We also found a reduction in cortical volume and identified a potential molecular mechanism. With the prospect of developing strategies to correct defects in the wiring of the fetal brain in DS, we will obtain a map of all the cell types, which populate the developing DS cortex. This map will identify cortical cell populations which are either missing/reduced or whose maturation is delayed, which could explain the reduced size of the DS brain and its altered activity patterns. We will take advantage of powerful genetic tools that allow to probe the content of individual cells in the DS brain and in human cells transplanted in the brain of laboratory animals.

The ultimate aim of this research proposal is therefore to gain new and fundamental insights into the cellular and molecular mechanisms that regulate the establishment of human cortical circuits, in the hope that this knowledge will, in the future, translate into new ways to rescue the network activity deficits in DS and guide the development of therapeutic strategies.

Technical Summary

Proper wiring of cortical circuits is a critical step in human brain development and maturation of high-order cognitive abilities. Despite their pivotal role, we do not yet clearly understand how human cortical circuits assemble in vivo, nor why this process can fail, leading to cognitive disturbances in neurodevelopmental conditions such as Down syndrome (DS), a major cause of congenital intellectual disability triggered by a trisomy of chromosome 21. My team recently discovered reduced synchronized excitatory network activity in the immature DS cortex, which could contribute to the progression of cognitive symptoms.
The overall goal of this proposal is to capture the mechanisms of cortical circuit dysfunction in DS. I will achieve this by revealing the molecular and cell type-specific landscape of the DS cortex from both human post-mortem fetal brain samples and induced pluripotent stem cell (iPSC)-derived cortical tissue grafts by single-nucleus RNA sequencing.
This atlas of human neocortical cell types, their relative proportions and the differentially regulated genes will constitute an important resource for the scientific community that will be made publicly available.
This proposal will thus deliver new fundamental insights into how the generation of cells and circuitry of the human neocortex are perturbed in DS.
Since cortical excitatory circuit activity dysfunction was detected at early stages of fetal brain development, and is likely associated with early signs of cognitive impairment in DS, clarifying the underlying mechanisms could lead to the identification of new intervention targets and the design of more effective cell type specific therapies for DS.


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Description DS organoid reanalysis
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Description Brain wiring and dysfunction
Amount $2,700,000 (SGD)
Organisation Duke-NUS Graduate Medical School 
Sector Academic/University
Country Singapore
Start 08/2021 
End 09/2026
Title DS organoids 
Description My team reanalysed scRNAseq data from Tang et al 2021 (JCI) 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? No  
Impact We found accelerated maturation of progenitors towards interneuron fate.