Global analysis of the heparin-enriched plasma proteome captures matrisome-associated proteins in Alzheimer's disease

Matrisome-associated heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to {beta}-amyloid (A{beta}) and tau pathology in Alzheimers disease (AD) brain and cerebrospinal fluid (CSF). However, it remains challenging to detect these proteins in plasma using standard mass spectrometry (MS)-based proteomic approaches. Here we utilized heparin affinity chromatography for the capture and enrichment of HBPs in plasma from healthy control and individuals with AD. This method was highly reproducible and effectively enriched well-known HBPs like APOE and thrombin, while also efficiently depleting high-abundance proteins such as albumin. To increase the depth of our analysis of the heparin-enriched plasma proteome and compare differences in disease we applied off-line fractionation and tandem mass tag mass spectrometry (TMT-MS) to compare the proteomic profiles between AD and control individuals across two datasets (n = 121 total samples). This led to the identification of 2865 proteins, spanning 10 orders of magnitude in protein abundance within the plasma. Notably, HBPs were some of the most increased proteins in AD plasma compared to controls. This included members of the matrisome-associated module in brain, SMOC1, SMOC2, SPON1, MDK, OLFML3, FRZB, GPNMB and the {varepsilon}4 isoform of APOE. Heparin-enriched plasma proteins also exhibited strong correlations to conventional AD biomarkers including CSF A{beta}, total tau (tTau), and phosphorylated tau (pTau) as well as plasma pTau supporting their role as potential surrogate markers of underlying brain pathology. Utilizing a consensus AD brain protein co-expression network, we assessed relationship between the plasma and brain proteomes and observed that specific plasma proteins exhibited consistent direction of change in both brain and plasma, whereas others displayed divergent changes, further highlighting the complex interplay between the two compartments. In summary, these findings provide support for the integration of a heparin enrichment method with MS-based proteomics for identifying a wide spectrum of plasma biomarkers that mirror pathological changes in the AD brain.