Alcohol-responsive genes identified in human iPSC-derived neural cultures

Abstract

Alcohol use contributes to numerous diseases and injuries. The nervous system is affected by alcohol in diverse ways, though the molecular mechanisms of these effects are not clearly understood. Using human-induced pluripotent stem cells (iPSCs), we developed a neural cell culture model to identify the mechanisms of alcohol's effects. iPSCs were generated from fibroblasts and differentiated into forebrain neural cells cultures that were treated with 50 mM alcohol or sham conditions (same media lacking alcohol) for 7 days. We analyzed gene expression using total RNA sequencing (RNA-seq) for 34 samples derived from 10 subjects and for 10 samples from 5 subjects in an independent experiment that had intermittent exposure to the same dose of alcohol. We also analyzed genetic effects on gene expression and conducted a weighted correlation network analysis. We found that differentiated neural cell cultures have the capacity to recapitulate gene regulatory effects previously observed in specific primary neural tissues and identified 226 genes that were differentially expressed (FDR < 0.1) after alcohol treatment. The effects on expression included decreases in INSIG1 and LDLR, two genes involved in cholesterol homeostasis. We also identified a module of 58 co-expressed genes that were uniformly decreased following alcohol exposure. The majority of these effects were supported in independent alcohol exposure experiments. Enrichment analysis linked the alcohol responsive genes to cell cycle, notch signaling, and cholesterol biosynthesis pathways, which are disrupted in several neurological disorders. Our findings suggest that there is convergence between these disorders and the effects of alcohol exposure.

Activated microglia cause metabolic disruptions in developmental cortical interneurons that persist in interneurons from individuals with schizophrenia

“…No statistical method was used to pre-determine the sample sizes. However, the sample sizes we used in this study are similar to the largest one among previous publications 55 . This sample size was adequate to observe cIN intrinsic transcriptome abnormalities in metabolic gene expression by activated microglia co-culture.…”

Molecular Correlates of Topiramate and GRIK1 rs2832407 Genotype in Pluripotent Stem Cell–Derived Neural Cultures

“…Because the expression of kainate receptors varies by brain region (Contractor et al, 2011) and the effects of topiramate differ between excitatory and inhibitory neurons (Braga et al, 2009), future work should consider use of additional neural differentiation protocols to generate cultures enriched for inhibitory, excitatory, or dopaminergic neurons, among others (Mertens et al, 2016), to explore the effects of topiramate treatment on other neuronal cell types. The potential value of examining neurons from additional differentiation protocols is highlighted by our prior work (using the same forebrain lineage cell differentiation protocol) (Jensen et al, 2019) in which we observed that previously identified eQTLs from human cortical tissue had greater eQTL effects within the neural cultures than previously identified eQTLs from other subcortical brain regions and peripheral tissue. Finally, it remains to be determined how the effects of topiramate observed in our culture system in A/A and C/C donors relate to the differential efficacy by genotype in reducing heavy drinking.…”

“…CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted July 22, 2019. ; https://doi.org/10.1101/710343 doi: bioRxiv preprint alcohol use disorder (Lieberman et al, 2012;Lieberman et al, 2015;Lieberman et al, 2017;Jensen et al, 2019) and others have utilized this technology to examine opioid (Sheng et al, 2016) and nicotine (Oni et al, 2016) addiction. However, to our knowledge, no study has utilized iPSCs to advance our understanding of the pharmacogenetic treatment of an addictive disorder.…”

Early Actions of Neurotransmitters During Cortex Development and Maturation of Reprogrammed Neurons

“…In this context, ethanol research has also been facilitated by the use of hiPSCs-derived neurons. In these cells, transcriptome studies have shown that several notch signaling pathway genes that regulate cell fate and synaptic plasticity are affected by alcohol exposure (Jensen et al, 2019). Furthermore, genes for NMDA and GABA A subunits show significantly elevated expression on human iPSCs-derived forebrain neurons after chronic treatment with 50 mM alcohol for 7 and 21 days, respectively with daily changes (Lieberman et al, 2012, 2018).…”