Network-Based Analysis on Orthogonal Separation of Human Plasma Uncovers Distinct High Density Lipoprotein Complexes

Abstract

High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, we present the first report that employs a network-based approach to systematically infer HDL subspecies. Healthy human plasma was separated into 58 fractions using our previously published three orthogonal chromatography techniques. Similar local migration patterns among HDL proteins were captured with a novel similarity score, and individual comigration networks were constructed for each fraction. By employing a graph mining algorithm, we identified 183 overlapped cliques, among which 38 were further selected as candidate HDL subparticles. Each of these 38 subparticles had at least two literature supports. In addition, GO function enrichment analysis showed that they were enriched with fundamental biological and CVD protective functions. Furthermore, gene knockout experiments in mouse model supported the validity of these subparticles related to three apolipoproteins. Finally, analysis of an apoA-I deficient human patient's plasma provided additional support for apoA-I related complexes. Further biochemical characterization of these putative subspecies may facilitate the mechanistic research of CVD and guide targeted therapeutics aimed at its mitigation.

Mapping Atheroprotective Functions and Related Proteins/Lipoproteins in Size Fractionated Human Plasma

“…HDL's ability to carry out multiple atheroprotective functions may be explained by its compositional heterogeneity. Recent proteomic studies show HDL is highly compositionally heterogeneous, composed of particles, most all of which contain apoA-I, with related physico-chemical properties, but differ widely in their compositions and functions (12)(13)(14)(15)(16)(17). Additionally, correlational network analysis identified distinct protein clusters, which may represent specific HDL subspecies (15).…”

Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction

“…Although facilitation of reverse cholesterol transport through cholesterol acceptor activity is considered a major function of HDL particles, ample evidence shows additional functions exist, such as antioxidant, anti-inflammatory, and anti-tumorigenic activities, and the shuttling of microRNAs or lipid-signaling molecules (10 -16). HDL is a highly heterogeneous array of distinct particles, with differing associated proteome and peptidome (17)(18)(19)(20)(21)(22). In addition to exchangeable apolipoproteins, early proteomics studies revealed the HDL-associated proteome includes known participants critical to hemostasis and thrombosis, innate and adaptive immune function, growth factors and various receptors, and hormone-associated proteins (17,20).…”

Unbiased and targeted mass spectrometry for the HDL proteome

“…The health status and lipid profile of the study subjects also impact the composition of the HDL proteome, biological variables that are often evaluated in HDL proteomics studies. Nonetheless, despite all of the sources of variability listed above, approximately 90 proteins have persisted, and are thought to comprise the consensus HDL proteome [4]. We analyzed the consensus proteome using the Markov cluster algorithm (MCL) provided by the String data base (http://string-db.org/) that sorted HDL’s proteins into two major functional networks, one pertaining to lipid metabolism, and the other grouping several biological processes including protein activation cascades, regulation of wound response and regulation of protease activities (Fig.…”

“…1a). Some of these studies have specifically addressed whether proteins are differentially localized across HDL size or density fractions [2, 4, 11, 12]. …”