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Understanding Autism with Patient-Specific Stem Cell Derived Brain Organoids

Review of “FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders” from Cell by Stuart P. Atkinson.

Years of study have gone into assessing if specific mutations in autism-associated genes can contribute to the abnormal brain development observed in autism spectrum disorder (ASD) with little or no luck. Additionally, recreating and studying the developmental processes behind brain development in humans has also been a difficult task using current techniques. Seeing these problems, researchers from the laboratory of Flora M. Vaccarino (Yale University, USA) decided to combine two cutting edge techniques to try to begin to understand disease development of autism. 

In their new study, published in Cell, induced pluripotent stem cells (iPSCs) generated from ASD patients was then followed by their differentiation in a three-dimensional (3D) brain “organoid” culture. Their new findings demonstrate how their technique recapitulates normal human development and that the dysregulation of a single transcription factor, FOXG1, can cause the over-production of specific neurons, and that this may be one of the root causes of ASD [1].

The group first generated iPSCs via retroviral or viral-free episomal reprogramming of fibroblasts taken from ASD patients presenting with an abnormally large head/brain (macrocephaly). Increased head size is a common trait in ASD sufferers and is tightly correlated with clinical severity. Their analyses of these cells agreed with previous studies, in that they found no mutations in genes linked to ASD [2]. To study brain development, the group next used a modified free-floating three-dimensional (3D) culture method [3] to differentiate iPSCs into brain organoids of a few millimeters in diameter. These organoids presented with organized layers of radial glia, intermediate progenitors, and neurons, and, importantly, the researchers also saw evidence that neurons in these brain organoids formed functional synaptic connections. 

Transcriptional analyses of the organoids found that even though they found no common mutations linked to ASD in the iPSCs, organoids presented with a common pattern of gene dysregulation - the upregulation of cell proliferation, neuronal differentiation, and synaptic assembly genes. Subsequent in-depth analyses demonstrated that GABAergic neural progenitor cells (NPCs) proliferated at a higher rate than normally observed, leading to the overproduction of GABAergic neurons. This creates an overabundance of cells, and may contribute to macrocephaly while also creating an imbalance in the ratio of the inhibitory GABAergic and the excitatory glutamatergic neurons which make up most neural circuits. Excitingly, the researchers then linked high progenitor proliferation, overproduction of neurons, and disease severity to the overexpression of a single gene – the transcription factor FOXG1. In order to confirm the importance of this gene, the group finally inhibited FOXG1 expression using small interfering (si)RNA, finding that this repressed cell proliferation and the excessive GABAergic differentiation seen in the ASD organoids.

This exciting combination of cutting edge techniques may have just uncovered a key mechanism which may drive the development of ASD in some patients. FOXG1 now not only represents a molecular signature of ASD but also represents a potentially druggable target. Furthermore, the researchers note that the search is now on to discover just how FOXG1 is upregulated in these patients. However, there is a bigger picture; this type of research can be applied in the understanding of multiple diseases and disorders of unknown origin and could lead to new effective therapeutic strategies.


  1. Mariani J, Coppola G, Zhang P, et al. FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders. Cell 2015;162:375-390.
  2. Willsey AJ, Sanders SJ, Li M, et al. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 2013;155:997-1007.
  3. Mariani J, Simonini MV, Palejev D, et al. Modeling human cortical development in vitro using induced pluripotent stem cells. Proc Natl Acad Sci U S A 2012;109:12770-12775.