Figure 8.

Integration of rat differentially expressed genes (DEGs) with Connectivity Map identifies potential candidate drugs for repositioning. (A) Schematic of analytical approach whereby signatures of rat DEGs (P < 0.01 to include DEGs from rare cell types with low statistical power) for each cell type for both Sugen-hypoxia (SuHx) and monocrotaline (MCT) models against the control model were queried against the full Connectivity Map database of compound and genetic perturbational expression signatures induced in human cell lines. The pattern-matching algorithms scored each reference perturbagen profile for the direction and strength of enrichment with the query single-cell RNA sequencing (scRNA-seq) DEG signature. Perturbagens with strongly positive connectivity scores have highly similar signatures to that of the query, whereas those perturbagens with strongly negative scores have signatures that strongly oppose that of the query (i.e., genes that are upregulated in the scRNA-seq DEG query are downregulated by treatment with the perturbagen or vice versa). (B) Heatmap showing connectivity scores of rat scRNA-seq DEGs to drugs approved for use in patients with pulmonary arterial hypertension (PAH) (black), drugs currently or previously in PAH clinical trials (blue), and preclinical drugs with demonstrated efficacy in PAH animal models (green). The size of dots corresponds to absolute values of the connectivity score. The PAH-related drugs showed distinct matching patterns to cell type–specific PAH rat signatures. For example, bosentan and tacrolimus had very similar connectivity profiles across cell types and disease models, although they come from different classes of drugs. (C) The top 10 drugs with the most negative connectivity scores, which are thus predicted to most strongly reverse the transcriptional signature of SuHx nonclassical monocytes (ncMonos), are shown (out of 2,429 compounds screened). The drugs predicted against SuHx ncMonos were of particular interest, given the strong upregulation of both NF-κB signaling and human PAH genes. The drug with the most negative connectivity score was treprostinil, one of the most effective PAH-targeted therapies currently in use in patients with advanced PAH.