Term placenta transcriptomic atlas identifies cells with discrete transcription programs implicated in gestational diabetes subtypes

Abstract

Single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics have identified novel cell subtypes and microenvironments which compartmentalize diverse functions at the maternal-fetal interface. We aimed to combine these high-resolution technologies with a rigorous classification of transcription alterations associated with diabetes subtypes in pregnancy. We hypothesized characteristic transcriptome profiles in specific cell populations would be linked to these classifications. We clinically validated gestational diabetes mellitus type 1 (GDMA1), GDMA2, and type 2 diabetes (T2DM) classes within a cohort of placentae and compared them to healthy controls by bulk RNA-seq (N=53). We then integrated our non-diabetic term placentae spatial transcriptomics data (N=12) with 273,944 publicly available transcriptomes from term placenta scRNA-seq or single-nuclei RNA-seq (snRNA-seq) datasets (accessions phs001886, GSE173193, EGAS00001002449) with control, GDM, or SARS-CoV-2 positive subjects to create a placental transcriptomic catalog. In bulk, we identified 104 significantly differentially expressed transcripts (-2< log2fold-change >2;p< 0.05) in our GDMA1 samples, 102 with GDMA2, and 121 with T2DM (Fig. 1a). Comparisons revealed 88 transcripts uniquely marking GDMA1, 68 for GDMA2, and 85 for T2DM, while FGA and CYP1A1 perturbations were shared across diabetes classes (Fig. 1b). We then compared these bulk GDM subtype markers with the 5,211 significantly differentially expressed transcripts associated with 22 cell-type clusters in our term placenta atlas (Fig. 2), and 20 unique GDM bulk markers aligned with extravillous trophoblast, stromal, endometrial epithelia, endothelial, NK, and dendritic single-cell placental markers. Together, these results detail the gene expression profiles and the cell types in the maternal-fetal milieu of pregnancies affected by diabetes. Consistent with their distinct clinical outcomes, GDM and T2DM have unique cellular transcriptomes and would thus be targets for new therapeutics.View Large Image Figure ViewerDownload Hi-res image Download (PPT)