Meta-analysis refinement of plasma extracellular vesicle composition identifies proplatelet basic protein as a signaling messenger in type 1 diabetes

Abstract

Extracellular vesicles (EVs) play important roles in cell-to-cell communication and are potential biomarkers as they carry markers of their derived tissues and disease signatures. However, obtaining pure EV preparations from biofluids is challenging due to contaminants with similar physicochemical properties. Here, we performed a meta-analysis of plasma EV proteomics data deposited in public repositories to refine the protein composition of EVs and investigate potential roles in type 1 diabetes development. With the concept that each purification method yields different proportions of distinct contaminants, we grouped proteins into clusters based on their abundance profiles. This allowed us to separate clusters with classical EV markers, such as CD9, CD40, C63 and CD81, from clusters of well-known contaminants, such as serum albumin, apolipoproteins and components of the complement and coagulation pathways. Two clusters containing a total of 1720 proteins combined were enriched with EV markers and depleted in common contaminants; therefore, they were considered to contain bona fide EV components. As possible origins of plasma EVs, these clusters had markers of tissues such as spleen, liver, brain, lungs, pancreas, and blood/immune cells. These clusters were also enriched in cell surface markers CD antigens, and proteins from cell-to-cell communication and signaling pathways, such as chemokine signaling and antigen presentation. We also show that the EV component and type 1 diabetes biomarker, platelet basic protein (PPBP/CXCL7) regulates apoptosis in both beta and macrophage cell lines. Overall, our meta-analysis refined the composition of plasma EVs, reinforcing a primary function as messengers for cell-to-cell communication and signaling. Furthermore, this analysis identifies optimal avenues to target EVs for development of disease biomarkers.

Multi-omics characterization of highly enriched human plasma extracellular vesicles

“…Our plasma sEV preparations had minute abundances of albumin (0.9941% total protein abundance) and apolipoprotein (ApoA-I, ApoA-II and ApoB100 combined, 0.0776% total protein abundance). These values are dramatically lower compared to what was reported in a recent meta-analysis investigating the protein profile of plasma EVs (note that our study used data independent acquisition (DIA) where the meta-analysis was from data acquired using data dependent acquisition MS methods) where the albumin level ranged from approximately 10-40% of the total protein abundance in the eight studies included in the meta analysis [51].…”

“…Multiple studies have previously reported the proteomes [27,36,[40][41][42][43][44][45][46][47] and lipidomes of blood EV preparations [48][49][50] However, the large majority of isolation methods used in these studies would have co-isolated contaminates. It is well known that separation of abundant plasma proteins and lipoproteins from EVs is not fully achieved by common EV isolation protocols or commercial kits [51,52]. For molecular characterization therefore, albeit not suitable for use in high-throughput or clinical applications, combining DGUC with SEC is considered one of the most effective methods for obtaining highly enriched EVs [27,43,53].…”

Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism, and immune response

“…Our systematic review also opens opportunities to study the functions of the biomarker candidates in T1D development and pathology. For instance, our group has found that PPBP/CXCL7 can reduce pro-inflammatory cytokine-mediated apoptosis in macrophage cell cultures while it enhances it in cultured β cells [67]. This may have a role in T1D development by potentiating macrophages and killing β cells in insulitis.…”

Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism, and immune response

“…Our systematic review also opens opportunities to study the functions of the biomarker candidates in T1D development and pathology. For instance, our group has found that PPBP/CXCL7 can reduce pro-inflammatory cytokine-mediated apoptosis in macrophage cell cultures while it enhances it in cultured β cells [ 73 ]. This may have a role in T1D development by potentiating macrophages and killing β cells in insulitis.…”