Molecular and functional variation in iPSC-derived sensory neurons

Abstract

Induced pluripotent stem cells (iPSCs), and cells derived from them, have become key tools to model biological processes and disease mechanisms, particularly in cell types such as neurons that are difficult to access from living donors. Here, we present the first map of regulatory variants in an iPSC-derived cell type. To investigate genetic contributions to human sensory function, we performed 123 differentiations of iPSCs from 103 unique donors to a sensory neuronal fate, and measured gene expression, chromatin accessibility, and neuronal excitability. Compared with primary dorsal root ganglion, where sensory nerves collect near the spinal cord, gene expression was more variable across iPSC-derived neuronal cultures, particularly in genes related to differentiation and nervous system development. Single cell RNA-sequencing revealed that although the majority of cells are neuronal and express the expected marker genes, a substantial fraction have a fibroblast-like expression profile. By applying an allele-specific method we identify 3,778 quantitative trait loci influencing gene expression, 6,318 for chromatin accessibility, and 2,097 for RNA splicing at FDR 10%. A number of these overlap with common disease associations, and suggest candidate causal variants and target genes. These include known causal variants at SNCA for Parkinson's disease and TNFRSF1A for multiple sclerosis, as well as new candidates for migraine, Parkinson's disease, and schizophrenia.

Stem Cells, Genome Editing, and the Path to Translational Medicine

“…The subsequent analysis of eQTLs and chromatin accessibility in hiPSC-derived sensory neurons (Schwartzentruber et al, 2017), and eQTLs and metabolic alterations (mQTLs) in hiPSC-derived hepatocyte-like cells (Pashos et al, 2017; Warren et al, 2017b) showed a significant overlap between primary tissues and in vitro identified QTLs that may complement in vivo datasets with novel associations not observed in primary tissues or patients. The unique advantage of this approach is that in vitro differentiated somatic cells not only serve as discovery platform for QTLs but at the same time provide an experimental system to perform functional cellular genomic experiments.…”

“…Comparing in vitro derived sensory neurons with primary dorsal root ganglia however reveals experimental variation of in vitro derived cells as major limitation of this approach. Given that detecting effects of regulatory variants with moderately large effect sizes requires at least 20 to 80 hiPSC lines, this approach depends on simple and robust protocols to differentiate large cohorts of hPSCs (Schwartzentruber et al, 2017). It remains to be seen whether in vitro association studies can reliably detect novel associations not observed in primary tissues or patients.…”

Mapping causal pathways from genetics to neuropsychiatric disorders using genome‐wide imaging genetics: Current status and future directions

“…Mapping how genetic variation impacts multiple levels of biology requires measuring multiple relevant phenotypes (cell‐ or tissue‐specific chromatin accessibility, cell‐ or tissue‐specific gene expression, and brain structure) in large, genetically diverse populations. Such maps are being created for chromatin accessibility and gene expression in large samples of post‐mortem and stem‐cell derived brain cells . Similar maps of genetic influences on neuroimaging measures serve as another crucial tool for identifying and characterizing links on causal pathways.…”

“…Such maps are being created for chromatin accessibility and gene expression in large samples of post-mortem and stem-cell derived brain cells. [25][26][27] Similar maps of genetic influences on neuroimaging measures serve as another crucial tool for identifying and characterizing links on causal pathways. They allow interpretation of whether genetic variants associated with neuropsychiatric illness are also associated with the structure or function of the human brain within specific regions.…”

“…23 When genetic variation impacts gene expression, sometimes through alterations in chromatin accessibility, these loci are referred to as 'expression QTLs' (eQTLs). 24 Large-scale maps of genetic variation impacting molecular measures, like caQTLs and eQTLs, have been and are continuing to be developed to allow the identification of regulatory elements or genes impacted by genetic variants associated with neuropsychiatric disorders [25][26][27][28] (Fig. 1).…”