Bulk RNA-seq on isogenic PTEN panel iPSC-derived neural progenitor cells to study the effect of ASD specific PTEN mutation and the effects of autism genetic background

Alterations in cortical neurogenesis are implicated in neurodevelopmental disorders including autism spectrum disorders (ASDs). Many ASD risk genes have been identified as critical for brain development, but the contribution of genetic backgrounds, although inferred in complex genetic disorders such as ASD, remains unclear. Here, using isogenic induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs) and cortical organoid models, we report that a heterozygous PTEN p.I135L mutation found in an ASD patient with macrocephaly dysregulates cortical neurogenesis in an ASD genetic background-dependent fashion. We found that this PTEN p.I135L mutation led to overproduction of NPC subtypes as well as neuronal subtypes including both deep and upper layer neurons in its ASD background, but not when introduced into a control genetic background. ASD and control background differences in neurogenesis, neural development and synapse signaling were also observed. These findings provide experimental evidence that both a PTEN p.I135L mutation and ASD genetic background contribute to cellular features consistent with ASD associated with macrocephaly. We compared RNA-Seq libraries of neural progenitor cells Apex WT/I135L vs Apex WT/WT, Chap WT/I135L vs Chap WT/WT to study the effect of PTEN WT/I135L in either control genetic background or ASD genetic background, we then compared Apex WT/WT vs Chap WT/WT; Apex WT/I135L vs Chap WT/I135L and Apex KO/KO vs Chap KO/KO to study the effect of ASD genetic bakcground with different PTEN genotypes. Libraries for each genotype include three independent cell culture replicates and three separate passages