Harnessing Genetic Diversity to Uncover Gene Networks Shaping Cellular States in Response to External Signals

Genetic background drives phenotypic variability in mouse embryonic stem cells (mESCs) and influences their differentiation capacity to various cell types. Specifically, mESCs from different genetic backgrounds cultured under identical conditions show variable responses to external signals. We utilize a systems genetics approach to dissect the molecular basis of this divergent response to extracellular cues using a set of genetically diverse mESCs derived from Diversity Outbred (DO) mice maintained under sensitized conditions and differentiated into neural progenitor cells (mNPCs). Through profiling chromatin accessibility, gene expression, and protein abundance, and genetic mapping in DO mESCs, we were able to identify a single causal variant that impacts the expression of Lifr, that further influences the stability of ground-state pluripotency. Using multi-omics data integration, we were able to identify additional genes that were impacted by the variation at the Lifr locus that we missed in our single molecular QTL mapping analyses. Similar to DO mESCs, we observed a strong influence of genetic variation on gene expression in DO mNPCs. Most local impacts of genetic variation on mNPC expression were similarly observed to affect mESC expression, highlighting conserved regulatory mechanisms. On the other hand, there were genes that are exclusively influenced by genetic variation, primarily through distal effects, in each cell state, highlighting the specialized regulation of pluripotency maintenance and neurodevelopment. Currently, we are expanding our systems genetics approach to single cell profiling of gene expression in DO mESCs and mNPCs to investigate how cellular heterogeneity is influenced by genetic variation.