Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington’s disease

Transcriptional dysregulation in Huntington’s disease (HD) causes functional deficits in striatal neurons. Here, we performed Patch-seq in an in vitro HD model to investigate the effects of mutant huntingtin (Htt) on synaptic transmission and gene transcription in single striatal neurons. We found that expression of mutant Htt decreased the synaptic output of striatal neurons in a cell autonomous fashion and identified a number of genes, whose dysregulation was correlated with physiological deficiencies in mutant Htt neurons. In support of a pivotal role for epigenetic mechanisms in HD pathophysiology, we found that inhibiting histone deacetylase 1/3 activities rectified several functional and morphological deficits and alleviated the aberrant transcriptional profiles in mutant Htt neurons. With this study, we demonstrate that Patch-seq technology can be applied both to better understand molecular mechanisms underlying a complex neurological disease at single-cell level and to provide a platform for screening for therapeutics for the disease. Isolated striatal neurons from newborn C57BL6 mice were infected with lentiviruses expressing human HTT exon 1 fused to GFP with normal (25Q-Htt) or expanded (97Q-Htt) number of glutamine (Q) repeats. Also, we treated cultured striatal neurons with RGFP109, a specific HDAC1/3 inhibitor (100 nM treatments at DIV 6, 9, 12). To assess phenotypic differences between the groups, we used 25Q-Htt, and 97Q-Htt neurons treated with vehicle or RGFP109. As an overall control construct, an empty vector alone (without the inserted gene cassette) was used to infect cultured striatal neurons. In total, we sequenced RNA-seq libraries from 117 single striatal GABAergic neurons and 14 astrocytes.