Sensitive and reproducible determination of clinical HDL proteotypes

BackgroundHigh-density lipoprotein (HDL) is a heterogenous mixture of blood-circulating multimolecular particles containing many different proteins, lipids, and RNAs. Recent advancements in mass spectrometry-based proteotype analysis strategies enable the sensitive and reproducible quantification of proteins across large patient cohorts. MethodsHDL particles were isolated from plasma of more than 300 healthy individuals or patients with a multiplicity of physiological HDL states. From these, peptides were extracted and HDL proteome spectral libraries were generated. This is a prerequisite for using data-independent acquisition (DIA) strategies to analyze HDL particles from clinical cohorts using mass spectrometry. ResultsThe resulting HDL proteome spectral libraries consist of 296 protein groups and 341 peptidoforms of potential biological significance identified with high confidence. We used the HDL proteome libraries to evaluate HDL proteotype differences in between healthy individuals and patients suffering from diabetes mellitus type 2 (T2DM) and/or coronary heart disease (CHD). Bioinformatic interrogation of the data revealed significant quantitative differences in the HDL proteotypes including a significant depletion of phosphatidylinositol-glycan-specific phospholipase D (PHLD) from disease-derived HDL particles. ConclusionThe DIA-based HDL proteotyping strategy enabled sensitive and reproducible digitization of HDL proteotypes derived from patient cohorts and provides new insights into the composition of HDL particles as a rational basis to decode structure-function-disease relationships of HDL. List of human genes and protein names discussed in the paper- APOA1 (Apolipoprotein A-I) - APOA2 (Apolipoprotein A-II) - APOE (Apolipoprotein E) - APOC3 (Apolipoprotein C3) - CLUS (Clusterin) - PHLD (Phosphatidylinositol-glycan-specific phospholipase D) - PON1 (Serum paraoxonase/arylesterase 1) - PON3 (Serum paraoxonase/lactonase 3) - PSPB (Pulmonary surfactant-associated protein B) - RAB1B (Ras-related protein Rab-1B) - RAB6A (Ras-related protein Rab-6A) - RB11A/B (Ras-related protein Rab-11A/B) - RP1BL (Ras-related protein Rap-1b-like protein) - RAB10 (Ras-related protein Rab-10) - SAA1 (Serum amyloid A-1 protein) - SAA2 (Serum amyloid A-2 protein) - SAA4 (Serum amyloid A-4 protein) - SCRB1 (Scavenger receptor class B member 1)