Molecular and functional variation in iPSC-derived sensory neurons

Area of Science:

• Genomics
• Neuroscience
• Stem Cell Biology

Background:

• Induced pluripotent stem cells (iPSCs) are crucial for modeling cell types difficult to obtain from donors.
• iPSC-derived neurons are increasingly used to study nervous system development and disease.

Purpose of the Study:

• To create a regulatory variant map in iPSC-derived sensory neurons.
• To investigate gene expression variability and identify quantitative trait loci (QTLs) influencing neuronal function.

Main Methods:

• 123 differentiations of iPSCs into sensory neurons.
• Single-cell RNA-sequencing to assess cell composition.
• Allele-specific methods to detect regulatory variants and their effects on gene expression, chromatin accessibility, and RNA splicing.

Main Results:

• Gene expression in iPSC-derived neurons showed higher variability compared to primary dorsal root ganglion neurons.
• Neuronal cell yield was influenced by pre-differentiation iPSC culture conditions.
• Thousands of QTLs were detected, impacting gene expression, chromatin accessibility, and RNA splicing.

Conclusions:

• iPSC-derived neurons are a powerful model system, but variability must be considered.
• Regulatory variants significantly influence multiple molecular layers in these cells.
• Recall-by-genotype studies using iPSCs require careful consideration of sample size (20-80 individuals) for detecting variant effects.