CRISPR-Enabled Functional Genomics in hPSC-Derived Neural Models for Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) is a genetically heterogeneous neurodevelopmental condition driven by rare de novo variants, copy number variations, and polygenic risk. SFARI-curated genes show high mutational constraint and enriched expression in cortical neurons and glia. This review highlights recent advances in CRISPR-based functional genomics using human pluripotent stem cells and induced pluripotent stem cells differentiated into neural progenitors, excitatory and inhibitory neurons, astrocytes, microglia, and brain organoids. CRISPR modalities including knockouts, CRISPRi and CRISPRa, base and prime editing, and Cas13 enable pooled and arrayed screens with high coverage at low multiplicity of infection. Integration of multimodal readouts such as Perturb-seq, single-cell and spatial transcriptomics, proximity labeling proteomics, and functional assays including microelectrode arrays and calcium imaging provides system-level insights into ASD gene function. Computational frameworks like MIMOSCA and SCEPTRE facilitate network reconstruction and pseudo-time inference. Case studies reveal Wnt and BAF complex dysregulation, microglial pruning deficits, and non-cell autonomous effects. Translational approaches target haplo-insufficient genes such as CHD8 and SCN2A using AAV or antisense oligonucleotides supported by isogenic iPSC models. Remaining challenges include model immaturity and scalability, while future directions focus on spatial perturb-omics, AI-driven causal inference, and standardized biobanks for precision ASD therapeutics.