In a complex environment such as that in a diabetic foot ulcer (DFU), multiple factors, including cross talk between distinct cell types of the affected tissue, play a significant role. We identified a transcription factor (TF) cocktail that induces a transition from nonhealing to healing states across multiple cell types.
Approach:
Thirty-three skin and wound single‐cell RNA‐sequencing samples (85,928 cells) from patients with diabetes with healing or nonhealing DFU were analyzed (GSE165816). The relative activity of cell type-specific TF in healing versus nonhealing DFU was compared, and the cumulative additive effect of different TF cocktails was assessed.
Results:
We used a cumulative additive-effect approach to identify five transcription factors, FOS Like 2, AP-1 Transcription Factor Subunit (FOSL2), CAMP Responsive Element Binding Protein 3 Like 1, RELB Proto-Oncogene, NF-KB Subunit, ETS Proto-Oncogene 1 (ETS1), and X-Box Binding Protein 1, whose targets include 66.5% of pro-healing genes and only 12.5% of anti-healing genes across all cell types. In vascular endothelial cells, this TF panel accounted for 95% of vasculature-development genes; in myeloid cells, it regulated 85% of antimicrobial-response genes. In silico knockout of ETS1 or FOSL2 shifted cells toward nonhealing states, whereas Nuclear Receptor Subfamily 3 Group C Member 1 knockout shifted endothelial cells, fibroblasts, and myeloid cells toward healing-associated state.
Innovation:
This work recognizes a TF panel that is likely to have therapeutic value in promoting healing in nonhealing DFU.
Conclusion:
In this work, we identified a set of candidate TFs with the potential to induce a cell state transition favoring a switch from nonhealing to healing outcomes in patients with nonhealing DFU. Overall, our gene regulatory network-driven TF cocktail provides a rational blueprint for reprogramming DFU cell states and paves the way toward targeted regenerative therapies.
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