Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism

Abstract

Reciprocal deletion and duplication of the 16p11.2 region is the most common copy number variation (CNV) associated with autism spectrum disorders. We generated cortical organoids from skin fibroblasts of patients with 16p11.2 CNV to investigate impacted neurodevelopmental processes. We show that organoid size recapitulates macrocephaly and microcephaly phenotypes observed in the patients with 16p11.2 deletions and duplications. The CNV dosage affects neuronal maturation, proliferation, and synapse number, in addition to its effect on organoid size. We demonstrate that 16p11.2 CNV alters the ratio of neurons to neural progenitors in organoids during early neurogenesis, with a significant excess of neurons and depletion of neural progenitors observed in deletions. Transcriptomic and proteomic profiling revealed multiple pathways dysregulated by the 16p11.2 CNV, including neuron migration, actin cytoskeleton, ion channel activity, synaptic-related functions, and Wnt signaling. The level of the active form of small GTPase RhoA was increased in both, deletions and duplications. Inhibition of RhoA activity rescued migration deficits, but not neurite outgrowth. This study provides insights into potential neurobiological mechanisms behind the 16p11.2 CNV during neocortical development.

Patient brain organoids identify a link between the 16p11.2 copy number variant and the RBFOX1 gene

“…Downregulated genes were implicated in neuron projection morphogenesis, neuron cell-cell adhesion, axon development and other terms implicating neurite process assembly and neuron-to-neuron interaction (Figure 6B). This result is consistent with a recent study which identified defects in neuronal migration in 16p11.2 hemideletion hCOs 82 . Furthermore, upregulated genes were implicated in synaptic-relevant processes such as signal transmission and neurotransmitter biosynthesis and transport (Figure 6B, Table S4).…”

“…Most of the transcriptional changes we found in hemideletion lines were specific to neuronal cell types, and gene enrichment analysis showed neuronal maturation and synaptic function relevant signatures in hemideletion patients. Despite the apparent methodological differences, the overall finding of increased neuronal maturation in hemideletions was similar to a recent study using 3D brain organoids 82 . We observed minimal changes in hemiduplication lines.…”

In Vitro Recapitulation of Neuropsychiatric Disorders with Pluripotent Stem Cells-Derived Brain Organoids

“…So far, the pathological characteristics of neuropsychiatric disorders have been extensively recapitulated in vitro in the research of human brain organoids ( Figure 2 , right panel). The consistency of in vivo and in vitro cellular results demonstrated the feasibility of the in vitro brain organoids as an experimental model of neuropsychiatric disorders [ 62 , 63 ]. Multi-omics analysis demonstrated that cerebral organoids derived from human PSCs in vitro could recapitulate cerebral cortical development corresponding to the molecular level of before 16 weeks post-conception in vivo [ 64 ].…”

Impaired OTUD7A-dependent Ankyrin regulation mediates neuronal dysfunction in mouse and human models of the 15q13.3 microdeletion syndrome

“…Due to a lack of understanding of disease mechanisms, there are no specific treatments for NDDs caused by CNVs. Evidence indicates that the loss/gain of certain genes within a CNV, known as 'genetic drivers', are the major cause of neurological deficits [3][4][5][6][7][8][9] ; however, genetic mechanisms outside of the CNV region, as well as pleiotropic and polygenic contributions, also play a role [10][11][12] . Given that multiple genes are located within a CNV, studies have focused on genetic drivers to identify relevant disease mechanisms and molecular targets for potential intervention.…”