Table 2 Overview of hPSC-derived ASD genetic modeling.
From: Human pluripotent stem cell (hPSC) and organoid models of autism: opportunities and limitations
Genetic variant type | Model system (guided vs unguided, 2D vs 3D) | Genetic variant | References | Phenotyping | Unique phenotypes/findings | Summary |
|---|---|---|---|---|---|---|
CNV | Guided forebrain and dissociated cultures | 22q11.2 DEL | Khan et al. [148] | Bulk/single-cell transcriptomics, calcium imaging, CRISPR/Cas9-mediated gene editing, ICC | Rescue of abnormal calcium phenotype with antipsychotic | Transcriptional profiling and phenotyping across 100 days showed disruptions in neuronal excitability genes and calcium imaging |
| Â | Guided corticostriatal assembloids | 22q13.3 DEL | Miura et al. [62] | Single-cell transcriptomics, optogenetics, calcium imaging | Hyperactivity of medium spiny neurons was only apparent in assembloid model | Defects in corticostriatal connectivity and abnormal calcium signaling |
| Â | Guided cortical organoids | 15q13.3 DUP | Meganathan et al. [209] | Bulk transcriptomics, neurite outgrowth assays, ICC | Pharmacological rescue of neuron migration and ER stress | Elevated endoplasmic reticulum stress, increased NPC proliferation, disrupted Wnt and axon guidance signaling |
| Â | Guided cortical organoids | 16p11.2 DEL & DUP | Urresti et al. [111] | Bulk transcriptomics, proteomics, cellular and molecular studies | Gene-dosage-dependent changes in organoid size in 16p11.2 duplication and deletion lines | Micro- and macrocephaly associated with duplication and deletion, respectively, dysregulated neuronal maturation, migration, and synaptic processes |
| Â | Guided cortical organoids and dissociated cultures | 7q11.23 DEL & DUP | Mihailovich et al. [210] | Ribosomal profiling, transcriptomics, proteomics, | Identified the REST pathway as a key mediator to 7q11.23 duplication | Gene-dosage effects on neuron excitability and differentiation in 7q11.23 DEL and DUP patients |
| Â | Guided forebrain organoids | 17p13.3 DEL | Iefremova et al. [211] | Molecular assays, gene rescue, drug rescue, ICC | Rescue of abnormal morphology through Wnt signaling | Disruptions in ventricular zone architecture and premature neuronal differentiation |
| Â | NPCs and cortical neurons | 7q11.23 DEL | Chailangkarn et al. [19] | Bulk transcriptomics, calcium imaging, MEA, electrophysiology, neuronal morphology studies | Established the role of a single gene within the CNV that drives cellular phenotypes and viability in NPCs | Reduced viability in 7q11.23 DEL NPCs, and excessive dendritic growth in both iPSC- and postmortem- derived neurons |
| Â | NGN2-induced neurons | 7q11.23 DUP | Cavallo et al. [212] | Drug screening, molecular studies | Performed a high-throughput drug screen from a library of 1000 compounds on patient-derived 2D glutamatergic neurons | Identified multiple HDAC-inhibitor compounds that were capable of rescuing expression of a prominent 17q11.2 driver gene |
| Â | NGN2-induced neurons | 15q13.3 DEL | Unda et al. [18] | MEA, Electrophysiology, cellular morphology | Characterizing the proteomic network of CNV driver genes in a model of ASD | 15q13.3 DEL NGN2 neurons display reduced synaptic maturation and altered AIS phenotypes in an OTUD7A-dependent manner |
| Â | NPC and cortical neurons cultures | Xp11.2 DEL | Ross et al. [213] | Electrophysiology, molecular studies, CRISPR editing | Examined the effects of locus deletions on neural circuitry | Reduced miniature excitatory postsynaptic current frequency and NMDA receptor function |
| Â | Unguided neural organoids | 7q11.2 DEL | Wegscheid et al. [214] | Bulk transcriptomics, ICC, molecular assays | Identified Ras-depending increases in NPC proliferation | 7q11.2 DEL patient-derived organoids show increased NPC proliferation, disrupted neural differentiation, and increased neural death |
| Â | Unguided neural organoids | 17p13.3 DEL | Bershteyn et al. [215] | Single-cell transcriptomics, time-lapse imaging, ICC | Identified mitotic defects in human-specific outer radial glia populations | Reduced migration of cells during neurite outgrowth, increased apoptosis of cells lining VZ-like rosettes |
Single gene KO or SNP | Guided forebrain organoids | CNTNAP2 | de Jong et al. [216] | Single-cell and bulk transcriptomics, CRISPR Correction, light sheet microscopy, ICC | CRISPR Correction was capable of rescuing both morphological and transcriptomic alterations in patient-derived lines | CNTNAP2 is predominantly expressed in several excitatory neuron subpopulations, and leads to cortical overgrowth |
| Â | Guided cortical organoids | DISC1 | Qian et al. [217] | ICC, cellular assays | Study improved nutrient flow and lamination by cutting cortical organoids into thick organotypic organoid slices | Laminar disruptions and deficits in cortical neuron fate |
| Â | Guided forebrain organoids | FMRP | Raj et al. [218] | Bulk transcriptomics, protein translation assays, flow cytometry, ICC | PI3K pathway was identified as a key regulator to the abnormal protein translation | Fragile X-Derived NPCs show global increases in protein translation |
| Â | Guided cortical organoids | MECP2 | Trujillo et al. [219] | MEA, drug screening, CRISPR/Cas9-mediated gene editing | Drug screen in cortical organoids showed increased gene expression in neurotransmitter markers | Partial, but not the complete rescue of network activity was achieved with the use of two pharmacological compounds |
| Â | Guided cortical organoids | PTEN | Pigoni et al. [220] | Single-cell and spatial transcriptomics, proteomics | Despite differences in early phenotypes, all lines showed consistent disruptions in the signaling of local circuits | Defects in outer radial glia progenitors and deep-layer projection neurons are influenced by the patient background |
| Â | Guided cortical organoids | SUV420H1, ARID1B and CHD8 | Paulsen et al. [221] | Single-cell transcriptomics, snATAC-Seq, MEA, Calcium imaging, proteomics | GABAergic interneurons and deep-layer projection neurons were identified as the vulnerable cell type. Divergence was mainly identified in the molecular targets of the risk genes | Identified phenotypic convergence of ASD-risk gene-derived organoids on asynchronous neuronal development |
| Â | Guided cortical organoids | TCF4 | Papes et al. [222] | MEA, scRNA Seq, CRISPR/Cas9-mediated gene editing and correction, drug rescue, ICC | TCF4-mediated Wnt signaling disruptions lead to reduced expression of SOX genes | Reduced NPC proliferation and impaired neuronal differentiation |
| Â | Guided cortical organoids | UBE3A | Sun et al. [223] | Electrophysiology, drug rescue, and molecular and mouse model studies | Treatment with potassium channel antagonist rescued seizure phenotype in both mouse and human models | Hyperexcitability phenotype in addition to increased synchronous firing |
| Â | Unguided neural organoids | UBE3A | Sen et al. [224] | Calcium imaging, drug rescue, ICC | Paternal UBE3A was shown to be silenced in early-stage cerebral organoids | Aberrant localization of UBE3A in mutant cerebral organoids that is partially rescued by topoisomerase inhibitors |
| Â | Unguided forebrain assembloids | CACNA1C | Birey et al. [57]; Birey et al. [81] | Bulk transcriptomics, live cell imaging, calcium imaging | Novel protocol for the formation of assembloids | Irregular interneuron migration saltation which was partially rescued by an L-type calcium channel blocker and GABA receptor antagonist |
| Â | Unguided neural organoids | CHD8 | Villa et al. [225] | Single-cell transcriptomics, CRISPR/Cas9-mediated gene editing, ICC | CHD8 haploinsufficiency models display impaired neurodevelopmental trajectories with accelerated inhibitory neuron development and impaired excitatory neuron development | Macrocephalic presentations and altered mRNA processing in mature neurons |
| Â | Unguided neural organoids | CHD8 | Wang et al. [226] | Bulk transcriptomics, CRISPR/Cas9-mediated gene editing | Found convergence of DEGs and pathways dysregulated in ASD, bipolar disorder, and schizophrenia | Dysregulation in genes involved in neuronal migration |
| Â | Unguided neural organoids | MECP2 | Mellios et al. [227] | Electroporation, sh-mediated knockdown, microRNA profiling, mouse in vivo studies | MECP2 regulates several miRNAs that are candidates for rescuing disease pathology | MECP2 regulates several miRNAs involved in early human neurogenesis, and KO models display alterations in AKT/ERK signaling |
| Â | Unguided neural organoids | RAB39b | Zhang et al. [228] | CRISPR/Cas9-mediated gene editing | RAB39b operates through PI3K-AKT-mTOR signaling | Mutations in RAB39b result in macrocephalic-phenotypes and hyperproliferative NPCs with defective differentiation capacities |
| Â | Unguided neural organoids | CDK5RAP2 | Lancaster et al. [49] | ICC, gene rescue, molecular studies | Proof of principal in modeling microcephalic disorders that are often ASD- associated | Disrupted symmetrical: asymmetrical division in patient-derived cerebral organoids |
| Â | Unguided neural organoids | ACTL6B | Wenderski et al. [229] | Bulk transcriptomics, ATAC-Seq, exome sequencing, molecular assays, mouse studies | Insight into chromatin regulation in a model of ASD | Alterations in activity-dependent transcription |
| Â | Unguided neural organoids | SHANK3 | Malara et al. [230] | Electron microscopy, ICC, molecular assays | Rare cell type identified in cerebral organoids shows promise to study disorders of CNS myelination in models of ASD | Alterations in myelin-producing cells |
| Â | Unguided neural organoids | SHANK3 | Wang et al. [231] | Single-cell transcriptomics, electrophysiology, CRISPR/Cas9-mediated gene editing, ICC | Protocol included formation of neural organoids from single rosettes, SHANK3 model showed impaired RhoA Signaling | Deficits in intrinsic excitability and reductions in several clustered protocadherins |
Idiopathic | Unguided neural organoids | N/A | Mariani et al. [232] | Bulk transcriptomics, electrophysiology, ICC | Recapitulated the phenotype with RNAi of FOXG1 | FOXG1 overexpression causes an increase in inhibitory neuron formation found amongst patients with idiopathic autism |
| Â | Unguided neural organoids | N/A | Ilieva et al. [164] | Proteomics, metabolic studies, ICC | Identified potential biomarkers and metabolic deficiencies in cerebral organoids derived from individuals with idiopathic autism | Reduced glutamate release and spontaneous firing rate in neurons |
| Â | Astrocyte and mature neural co-cultures | N/A | Russo et al. [106] | MEA phenotyping, molecular studies | ASD-derived astrocytes hindered the maturation of neurons derived from control lines | Reduced synaptic and glutamatergic activity in neurons. Morphologic and synaptogenesis impairments were rescued by co-culture with control astrocytes lines |
