Autism-associated deletions of the lncRNA PTCHD1-AS result in synaptic dysfunction in human neurons

The long non-coding (lnc) RNA PTCHD1-AS is frequently disrupted in males with autism spectrum disorder (ASD), but its role in neuron function is unknown. We generated induced pluripotent stem (iPS) cells from two ASD subjects with PTCHD1 locus microdeletions, and produced neurons that exhibited reduced miniature excitatory post-synaptic current (mEPSC) frequency and NMDA receptor hypofunction. Mutation of the lncRNA PTCHD1-AS had no impact on expression of the divergently transcribed neighboring PTCHD1 gene in cis, but 14 genes were differentially expressed. Alternative splicing patterns of the nuclear lncRNA were affected by exon 3 loss, and its importance was reinforced by discovery of a novel ASD-associated exon 3 deletion. Finally, genome editing of exon 3 in iPS cells recapitulated diminished mEPSC frequency in neurons. Our findings directly implicate PTCHD1-AS in excitatory synapse function, and reveal the first association of lncRNA deletion with neuronal under-connectivity in ASD. Neural precursor cells from iPSC lines of two probands (Prb1 and Prb2) and two controls (Ctl1 and Ctl2) were differentiated into neurons. At three weeks of differentiation, neurons were purified using magnetic activated cell sorting and seeded onto plates. Following a one-week recovery, RNA was harvested. The experiment was repeated in duplicate. We compared transcriptomes of Ctl vs. PRB1 and Ctl vs. PRB2 separately.