Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes

Abstract

SummaryInduced pluripotent stem cell (iPSC)-derived dopamine neurons provide an opportunity to model Parkinson’s disease (PD), but neuronal cultures are confounded by asynchronous and heterogeneous appearance of disease phenotypes in vitro. Using high-resolution, single-cell transcriptomic analyses of iPSC-derived dopamine neurons carrying the GBA-N370S PD risk variant, we identified a progressive axis of gene expression variation leading to endoplasmic reticulum stress. Pseudotime analysis of genes differentially expressed (DE) along this axis identified the transcriptional repressor histone deacetylase 4 (HDAC4) as an upstream regulator of disease progression. HDAC4 was mislocalized to the nucleus in PD iPSC-derived dopamine neurons and repressed genes early in the disease axis, leading to late deficits in protein homeostasis. Treatment of iPSC-derived dopamine neurons with HDAC4-modulating compounds upregulated genes early in the DE axis and corrected PD-related cellular phenotypes. Our study demonstrates how single-cell transcriptomics can exploit cellular heterogeneity to reveal disease mechanisms and identify therapeutic targets.

Class IIa HDACs regulate learning and memory through dynamic experience-dependent repression of transcription

“…Taken together, these results suggest that HDACs 4 and 5 redundantly act in the same pathway that restricts the induction of activitydependent transcriptional programs, thereby limiting the numbers of neurons that undergo structural and/or functional plasticity in response to sensory input. In conjunction with reports that documented aberrant nuclear retention of HDAC4 in cellular and animal models of Parkinson's disease and Ataxia telangiectasia 32,33 , our results also imply that class IIa HDACs may exert their effects via different mechanisms under the physiological and pathological conditions depending on kinetics of nuclear import/export. In other words, HDACs 4 and 5 are intrinsically capable of repressing a broad spectrum of targets and they evidently do so upon irreversible nuclear entry (Fig.…”

“…Over the past few years, HDACs have attracted considerable interest as potential therapeutic targets, prompting the design and clinical implementation of small molecule inhibitors 21,[51][52][53] . However, the precise roles of class IIa HDACs in the nervous system have remained unclear, despite the evidence that loss or mis-localization of these proteins may lead to neurological abnormalities in model organisms and humans [25][26][27][28]30,32,33,35 . Unlike constitutively nuclear class I HDACs, vertebrate class IIa HDACs are unable to deacetylate histones due to evolutionarily acquired Tyrosine to Histidine substitution in the active site of the C-terminal enzymatic domain 20,24 .…”

“…Puzzlingly, the majority of central neurons retain HDAC4 in cytoplasm 23,25,30 and Hdac4-deficient mice have been reported to have no detectable abnormalities in mRNA levels in the brain 26,31 . Despite recent reports that HDAC4 irreversibly enters neuronal nuclei under the pathological conditions, such as Ataxia telangiectasia and Parkinson's disease 32,33 , the physiological significance of the nuclear import of this protein in normal circuits is unclear.…”

Variation of human neural stem cells generating organizer statesin vitrobefore committing to cortical excitatory or inhibitory neuronal fates

“…The early developmental mechanisms operating in the telencephalon are proximal to genetic risk for neurodevelopmental disorders including autism spectrum disorder (ASD) (Marchetto et al, 2016;Mariani et al, 2015), bipolar disorder (Madison et al, 2015), fragile X syndrome (Kwan et al, 2012a), Huntington's disease (Consortium, 2017) and brain cancers (Crawley et al, 2016;Ernst, 2016). In the context of an unprecedented transcriptomic and epigenetic mapping of the human central nervous system (Amiri et al, 2018;de la Torre-Ubieta et al, 2018;Wang et al, 2018;Zhu et al, 2018), progress continues in defining disease relevant in vitro phenotypes as a central tool in the development of novel therapeutic interventions (Fujimori et al, 2018;Hubler et al, 2018;Lang et al, 2018). To achieve accurate models of risk for neuropsychiatric disease, it will be valuable to assess how patient-specific iPSCs vary as they progress through the non-linear developmental transitions described here.…”

“…Evidence of genetic risk for neuropsychiatric disorders has been found in the patterns of genes expressed in the midfetal neurogenic cortex (Gulsuner et al, 2013;Parikshak et al, 2013;State and Sestan, 2012;Willsey et al, 2013;Xu et al, 2014). Moreover, risk associated genes have been identified in the in vitro functional phenotypes of NSCs derived from patient-specific induced pluripotent stem cells (iPSCs) (Brennand et al, 2015;Consortium, 2017;Fujimori et al, 2018;Lang et al, 2018;Madison et al, 2015;Marchetto et al, 2016;Mariani et al, 2015). Thus, understanding the signaling specifying cortical NSCs in vitro is required to define pathogenic mechanisms and develop new therapies for brain disorders.…”