Single-cell transcriptomic profiling and characterization of endothelial progenitor cells: new approach for finding novel markers

Abstract Background Endothelial progenitor cells (EPCs) are promising candidates for the cellular therapy of peripheral arterial and cardiovascular diseases. However, hitherto there is no specific marker(s) defining precisely EPCs. Herein, we proposing a new in silico approach finding novel EPC markers. Methods We assembled five groups chosen EPC-related genes/factors using PubMed literature Gene Ontology databases. This shortened database factors was fed into publically published transcriptome matrix to compare their expression between endothelial colony-forming (ECFCs), HUVECs, two adult cell types (ECs) from skin adipose tissue. Further, used functional enrichment on Mouse Phenotype protein-protein interaction network analyses. Moreover, built digital healthy donors’ PBMCs (33 thousand single-cell transcriptomes) analyzed these factors. Results Transcriptome analyses showed that BMP2, 4, ephrinB2 were exclusively highly expressed EPCs; neuropilin-1 VEGF-C significantly higher EPCs HUVECs compared with other ECs; Notch 1 skin-ECs; MIR21 PECAM-1 ECs. genes STRING protein has revealed significant relations vascular functions, development, morphogenesis, where ephrinB2, BMP4 connected abnormal functions. Single-cell RNA-sequencing have among EPC-regulated markers analyses, (i) ICAM1 Endoglin weekly monocyte compartment blood; (ii) CD163 CD36 CD14+ whereas CSF1R CD16+ compartment, (iii) L-selectin IL6R globally lymphoid/myeloid compartments, (iv) interestingly, PLAUR/UPAR NOTCH2 both monocytic compartments. Conclusions The current study identified could be better characterization subpopulation blood subsequent usage various regenerative medicine applications.