PhD Project - Investigating cell and molecular interneuron phenotypes caused by the 16p11.2 autism genetic risk factor during forebrain development.

Vacancy Reference Number
Closing Date
16 Jan 2022
University of Edinburgh


Autism spectrum condition or ‘autism’ is associated with numerous genetic risk factors including the polygenic 16p11.2 microdeletion. Patients heterozygous for the 16p11.2 microdeletion (16p11.2+/-) account for about 1% of autism cases making it one of the most common genetic causes of autism. A central question is what neural cells are affected and how their cell and molecular biology is perturbed to predispose the brain to developing autism.

The proper functioning of the mature cerebral cortex depends on the balance between excitatory neurons (ExNs - originating from progenitors located in the ventricular zone of the cerebral cortex in the dorsal forebrain) and inhibitory interneurons (INs - originating from progenitors located in the ganglionic eminences in the ventral forebrain that migrate into the cortex). This Excitatory/Inhibitory (E/I) balance is important for normal brain function and disruption to the E/I balance is hypothesised to underpin autism.

Rationale & hypothesis:

The onset of autism in infancy suggests the hypothesis that genetic risk factors act during pre-natal brain development and we have used bioinformatic analysis to identify cells in developing human forebrain, particularly developing INs, that are vulnerable to the 16p11.2 microdeletion (Morson et al., 2021, Yang et al BioRxiv) and have pilot data from single cell RNA sequencing and ventral organoid experiments using human IPSC derived 16p11.2+/- INs supporting this hypothesis and showing cell and molecular phenotypes starting from when INs are progenitors and continuing as they differentiate.

The hypothesis is that the cell and molecular developmental trajectory of human 16p11.2+/- INs is perturbed.


The overarching aim of this project is to use human IPSC derived ventral organoids (Sloan et al., 2018) to investigate the cell and molecular phenotypes of 16p11.2+/- INs along their developmental trajectory. More specifically 16p11.2+/- and 16p11.2+/- isogenic control ventral forebrain organoids will be grown to a range of developmental stages ranging from when IN progenitors predominate (30 days in culture) to later stages when INs are more differentiated and particular IN subtypes such as SST INs have appeared (90 days in culture). Ventral organoids of the two genotypes will be compared at these different stages to investigate cell-cycle kinetics of IN progenitors, differential, gene expression as INs differentiate, and composition of cell-types. This will allow us to gain a better understanding of how the 16p11.2 microdeletion impacts on the IN developmental trajectory and the mechanism.

Training outcomes:

This project will give training in human organoid cell culture, cell and molecular biology techniques, and bioinformatic analysis of gene expression data.