Abstract 107: Protein Comigration Pattern Analysis to Identify High-Density Lipoprotein Subspecies
High density lipoproteins (HDL) are micromolecular complexes composed of lipids and proteins that play critical roles in the prevention of cardiovascular disease (CVD), the major cause of mortality in the United States. Recent proteomics studies have identified about 75 distinct HDL-associated proteins. Many of the newly identified proteins mediate functions that are surprisingly outside the realm of lipid transport. Recently there is strong evidence suggesting that diverse HDL functions are mediated by distinct HDL subspecies. To study the HDL subspecies and their associated functions in CVD, we have applied three orthogonal separation chromatography techniques (gel filtration, anion exchange and isoelectric focusing) to fractionate normal human plasma to phospholipid-containing subfractions. We then isolated lipid associated proteins and determined their identities and relative distribution across subfractions using mass spectrometery. The distribution patterns of 159 proteins were determined for each separation technique. Lipid associated proteins which have similar co-migration patterns when separated by different techniques are likely to form distinct lipoprotein subspecies. Two novel correlation based score systems were developed in order to identify these subspecies: the C-Score and S-Score systems. C-Score system is based on the number of fractions that contain both proteins. S-Score system is based on the variation of two proteins’ normalized patterns, which does not require the independence assumption required by regular correlation coefficient. We built two similarity networks based on these two score systems and identified 31 overlapped cliques. These 31 identified cliques may represent consistent HDL subspecies across different human plasma samples and analysis methods. To assess the significance of these cliques, we performed random permutation test. We further did functional enrichment analysis using GO annotations. All of these analyses suggest that these candidate cliques/biomarker may reveal novel interactions among HDL proteins and provide models of the underlying molecular mechanisms of CVD. The experimental validations of the identified HDL subspecies using immunoprecipitation are under way.
- © 2012 by American Heart Association, Inc.