Abstract 14797: Single Cell Multi-Modal Analyses Reveal Epigenomic and Transcriptomic Basis Underlying Cardiac Defects in Maternal Diabetes

Introduction: Birth defects can be caused by combinations of genetic and environmental influences. Large-scale DNA sequencing efforts reveal genetic influences, yet the environmental contributions have been mainly limited to association studies with little mechanistic insight. Hyperglycemia in pre-gestational diabetic (PGDM) mothers are among the most frequent environmental contributors to congenital defects, such as congenital heart defects and craniofacial anomalies. However, the cell types involved and underlying mechanisms by which PGDM affects these regions are unknown. Methods and Results: To determine how PGDM affects the epigenomic and transcriptomic state within individual cells during cardio-pharyngeal development, we utilized multi-modal single cell analyses with streptozotocin-induced mouse PGDM model. Analysis of E10.5 embryos showed that PGDM specifically affects the epigenomic state of two small subsets of cardiac and craniofacial progenitors. In PGDM derived embryos, a newly recognized subpopulation of anterior heart field progenitors expressing Alx3 acquires a more posterior-like identity in response to PGDM, based on gene expression and chromatin status. Similarly, a sub-population of neural crest-derived cells in the second pharyngeal arch, which contributes to craniofacial structures, also displayed patterning abnormalities. Analyses of differentially accessible chromatin regions revealed disrupted patterning was due to increased intrinsic retinoic acid signaling in affected cell types in PGDM. Conclusions: We showed the selective epigenomic vulnerability of a small subset of cells that help explain cardiac and craniofacial defects observed in PGDM despite all embryonic cells experiencing similar environmental exposure. We also showed that the selectivity was partly driven by a previously unrecognized dysregulation of retinoic acid signaling in PGDM. Discovery of the consequences of environmental factors on embryonic development using multi-modal single cell genomics will lead to potential gene-environment combinations that contribute to the complex and multifactorial diseases and preventive approaches to protect vulnerable cells.