Identification of unannotated microproteins involved in endothelial cell homeostasis, dysfunction, and vascular disease

Microproteins (miPs) translated from small open reading frames (smORFs) are crucial regulators of cell function. However, the expression and function of miPs in endothelial cells and alterations in miP expression linked with inflammation and cardiovascular disease, remain largely unexplored.

An optimized proteogenomic approach combining RiboTag RNA-sequencing and mass spectrometry of the small molecular mass proteome was utilized to identify endothelial cell-specific miPs. Heart, lung, and blood vessels from endothelial cell-specific RiboTag mice and human endothelial cells were studied under homeostatic and inflammatory conditions. We identified 2739 murine as well as 1365 intracellular and 607 extracellular human endothelial cell miPs encoded from previously non-canonical (unannotated) smORFs. Vascular inflammation induced in vitro by interleukin-1β (IL-1β) and in vivo through PCSK9 overexpression, high-fat diet, and partial carotid artery ligation significantly altered smORF expression. An additional 347 miPs were detected in human serum, 23 decreasing and 31 increasing, after cardiac damage. The expression of an inflammation-induced miP encoded by an internal smORF within the proline-serine-threonine phosphatase interacting protein 2 (PSTPIP2) transcript, that is, miP-PSTPIP2, was assessed using a custom antibody. miP-PSTPIP2 expression was upregulated in IL-1β-treated human endothelial cells, in pre-atherosclerotic murine carotid arteries and detected in carotid arteries from patients with atherosclerosis. The relevance of 250 miPs for endothelial cell growth and viability was demonstrated using a high-throughput clustered regularly interspaced Short palindromic Repeats (CRISPR)/Cas9 screen.

Taken together, we document the existence of a large number of human and murine miPs encoded by non-canonical smORFs and their altered expression in inflammatory conditions. The identification of secreted miPs suggests that they may also exert autocrine or paracrine functions. These novel small peptides modulate cell proliferation and survival in endothelial cells and may play a significant role in human cardiovascular disease.