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Induced Pluripotent Stem Cells & Developmental Disorders

Over the last several years we derived more than 500 iPSC lines from patients with developmental disorders as a window into normal and abnormal neuronal development. We established protocols for converting iPSCs into brain organoids that reflect the human cerebral cortex, basal ganglia and other brain regions at prenatal stages of development. Using this model, our group has discovered neurodevelopmental alterations in autism spectrum disorders (Mariani et al, Cell, 2015) and Tourette syndrome (ongoing). As part of the PsychENCODE collaborative multi-site project, we generated a genome-scale catalog of enhancers and their associated gene targets active in early brain development (Amiri et al, Science, 2018). These data establish links between genes and enhancers active at embryonic and fetal stages of human development, and allow the study of risk alleles for human developmental disorders.

Gene regulatory element discovery in organoids and human fetal brain

Human iPSC-derived cortical organoids and their isogenic fetal brain cortex specimens were analyzed by RNA-seq, single nuclei RNA-seq, ChIP-seq and ATAC-seq to derive gene expression profiles and regulatory element datasets of early telencephalic brain development. See (Amiri et al, 2018).

Cellular composition of organoids by single cell RNAseq analysis

Organoids contain a large repertoire of neural cell types. Single-nucleus RNA sequencing time course (TD0, 11, 30) on more than 17000 nuclei revealed that forebrain organoids are composed of different types of progenitor cells, which differentiate into excitatory and inhibitory neuron lineages.

Inhibitory neuron lineages in organoids

Brain organoid showing GABAergic neuron progenitors stained by DLX1/2 (red) and GABA neurons stained by GAD1 antibodies (green).

Cortical organoid organization in layers

Layered organization of organoids revealed by canonical marker immunostainings. (VZ: ventricular zone, SVZ: subventricular zone, MZ: mantle zone).

Cortical excitatory neuron progenitors

Organoid neurons marked by GFP (green) following lentiviral infection (Synapsin-GFP) are located outside neural progenitors (PAX6+) and intermediate progenitors cells (TBR2+) zones.

Generation of cortico-basal ganglia assembloids