Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome

Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer's disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson's disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.

Unveiling Resilience to Alzheimer's Disease: Insights From Brain Regional Proteomic Markers

Studying proteomics data of the human brain could offer numerous insights into unraveling the signature of resilience to Alzheimer's disease. In our previous study with rigorous cohort selection criteria that excluded 4 common comorbidities, we harnessed multiple brain regions from 43 research participants with 12 of them displaying cognitive resilience to Alzheimer's disease. Based on the previous findings, this work focuses on 6 proteins out of the 33 differentially expressed proteins associated with resilience to Alzheimer's disease. These proteins are used to construct a decision tree classifier, enabling the differentiation of 3 groups: (i) healthy control, (ii) resilience to Alzheimer's disease, and (iii) Alzheimer's disease with dementia. Our analysis unveiled 2 important regional proteomic markers: Aβ peptides in the hippocampus and PA1B3 in the inferior parietal lobule. These findings underscore the potential of using distinct regional proteomic markers as signatures in characterizing the resilience to Alzheimer's disease.

Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer's disease

Resilience to Alzheimer's disease is an uncommon combination of high disease burden without dementia that offers valuable insights into limiting clinical impact. Here we assessed 43 research participants meeting stringent criteria, 11 healthy controls, 12 resilience to Alzheimer's disease and 20 Alzheimer's disease with dementia and analyzed matched isocortical regions, hippocampus, and caudate nucleus by mass spectrometry-based proteomics. Of 7115 differentially expressed soluble proteins, lower isocortical and hippocampal soluble Aβ levels is a significant feature of resilience when compared to healthy control and Alzheimer's disease dementia groups. Protein co-expression analysis reveals 181 densely-interacting proteins significantly associated with resilience that were enriched for actin filament-based processes, cellular detoxification, and wound healing in isocortex and hippocampus, further supported by four validation cohorts. Our results suggest that lowering soluble Aβ concentration may suppress severe cognitive impairment along the Alzheimer's disease continuum. The molecular basis of resilience likely holds important therapeutic insights.

A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer's disease

Alzheimer's disease (AD) is a looming public health disaster with limited interventions. Alzheimer's is a complex disease that can present with or without causative mutations and can be accompanied by a range of age-related comorbidities. This diverse presentation makes it difficult to study molecular changes specific to AD. To better understand the molecular signatures of disease we constructed a unique human brain sample cohort inclusive of autosomal dominant AD dementia (ADD), sporadic ADD, and those without dementia but with high AD histopathologic burden, and cognitively normal individuals with no/minimal AD histopathologic burden. All samples are clinically well characterized, and brain tissue was preserved postmortem by rapid autopsy. Samples from four brain regions were processed and analyzed by data-independent acquisition LC-MS/MS. Here we present a high-quality quantitative dataset at the peptide and protein level for each brain region. Multiple internal and external control strategies were included in this experiment to ensure data quality. All data are deposited in the ProteomeXchange repositories and available from each step of our processing.

Abstract 180: Missense Mutations in ABCA1 and CETP Associate with Changes in the HDL Proteome in Primate Half-Sibs Discordant for HDL Cholesterol Levels

HDL protein composition and corresponding function may impact cardiovascular disease risk. Identifying genetic variation that influences the HDL proteome may reveal modifiable HDL functions that impact this risk. We studied genetic determinants of the HDL proteome in a cohort of rhesus macaques enriched for extreme HDL cholesterol levels (HDL-c). We selected macaques from 2 distinct paternal half-sibships, each comprising 8 half-sib pairs matched for age-class and sex, but with large differences in HDL-c (N=22 genomes). HDL was isolated by ultracentrifugation and the protein cargo analyzed by mass spectrometry. Identified peptide sequences were compared to a Swiss-Prot canonical human protein database using BLAST to determine ortholog matches. Among the proteins identified, 64 are among the 229 reported in similar human studies, and 45 of these 64 are among the 95 highest-confidence HDL proteins tracked by the HDL Proteome Watch. We performed deep exome sequencing, and assessed predicted function for all genetic variants in macaques, among 23 genes associated with HDL disorders or variation in HDL-c in humans. We focused on the higher-impact variants most likely to have conserved effects between macaques and humans by proximity (i.e., <10 bp) to known human mutations. This produced a set of 3 missense variants in ABCA1 associated with Tangier disease and HDL deficiency, and 4 missense variants in CETP associated with CETP deficiency, reduced CETP activity, and hyper- and hypoalphalipoproteinemias. Using a measured genotype approach, we tested for association of all 7 variants with adjusted spectral counts, while accounting for age and sex, and applied a false discovery rate (FDR) of 20% to all nominally significant results. After controlling for FDR, 3 missense variants in ABCA1 were significantly associated with spectral counts for VCAM1 , ITGA2 , and ITGB1 (nominal P-values 0.0005-0.0026), and 4 missense variants in CETP were significantly associated with spectral counts for APOA2 , APOC3 , C4BPA , and PLTP (nominal P-values 0.0002-0.0038). While our results require replication, these proteins suggest that changes in HDL-c in macaques are associated with changes in HDL that modulate vascular inflammation, immune response, and particle remodeling.

Abstract 391: Sterol Efflux Function and Protein Composition of HDL Associates With Recovery From Stroke

Background: Prospective cohort studies and meta-analyses examining the relationship between HDL-cholesterol (C) and stroke are discordant and question the value of HDL-C as a marker for stroke risk prediction. Other properties of HDL-C such as cholesterol efflux capacity (CEC) and proteome, are less studied.

Methods: We investigated the changes in HDL CEC and proteome to determine if they are associated with improved stroke recovery. Plasma from age- and lipid profile-matched healthy controls (N = 35) and stroke patients were collected at 24 (early, N = 35) and 96 hour (late, N = 20) post stroke, and analyzed with three independent assays to measure macrophage-mediated, ABCA1 and ABCG1-specific sterol efflux, and HDL proteome. Stroke recovery was assessed at 3 months using the Modified Rankin Scores (MRS) and the NIH Stroke Scale (NIHSS).

Results: Both macrophage- and ABCG1-mediated CEC were reduced by 50% ( P <0.0001) and 20% ( P <0.038) in early and late post stroke samples, respectively, compared to the control group. Patients who had comparable or increased CEC between the two-time points exhibited lower NIHSS and MRS indicating better recovery. Proteomic analysis of HDL indicated a distinct time-dependent remodeling post stroke. Coagulation complement cascade proteins (FGB, FGA, A2M, C3) significantly increased (FDR>0.01) early and returned to control levels later, inflammation proteins (SAA1, SAA2, PON1, C4B) increased early and continued to increase. Interestingly, platelet adhesion proteins (DSG1, JUP, ITGB1, ITGA2, TUBB, DNAH3, PF4) were abundantly present in only later samples.

Conclusion: 1) patients who maintain or improve HDL CEC post stroke exhibit better recovery scores, 2) post stroke HDL proteome remodeling is dynamic with distinct time-dependent protein signatures that may associate with stroke recovery.

Abstract 198: HDL Function and Genetic Regulation in a Nonhuman Primate Model of HDL Cholesterol Extremes

Recent data indicate that HDL function has effects independent of HDL cholesterol (HDL-C) levels that better predict cardiovascular risk. We aimed to characterize sterol efflux across a wide range of HDL-C, and to identify genetic determinants for both traits in a non-human primate model. To do this, we took advantage of rhesus macaque families that display spontaneous, extreme variation in HDL-C (range 13-106 mg/dL), but have total cholesterol, LDL-C, and triglyceride levels considered normal in humans. We hypothesized that genetic regulation of HDL metabolism is conserved between macaques and humans, and that sterol efflux is independent of HDL-C across the observed range of HDL-C values. We selected 16 macaque half-sib pairs matched for age-class and sex, based on maximum differences in HDL-C characterized in a larger sample (n=193), and conducted deep sequencing of exons and regulatory regions. We assessed predicted function for all variants in macaques found at 23 genes that regulate reverse cholesterol transport or are associated with HDL-C in humans, and that share ~93% identity with the corresponding human proteins. We assessed sterol efflux using J774 macrophages labeled with [ 3 H]cholesterol and stimulated with a cAMP analogue in 16 sequenced macaques, plus 6 macaques selected from the <5 th />95 th percentiles of HDL-C (n=22). We found 27 predicted functional variants located at regulatory or coding regions in macaques that were within 10 bp of known variants in humans associated with HDL-C levels, coded protein deficiencies, or familial alpha-dyslipoproteinemias. Further, we show that 4 of these variants in CETP , LCAT , and ABCA1 are expected to inhibit normal protein function, as indicated by in silico prediction of changes in protein folding. Within these families, correlation between HDL-C and sterol efflux was 0.78 (P=1.65 X 10 -5 ), suggesting that a significant portion of the variation in efflux capacity cannot be accounted for by HDL-C levels. We conclude that functional genetic variation in pathways of HDL metabolism is conserved between humans and macaques, and is likely to influence both HDL-C and efflux capacity. However, a significant proportion of efflux capacity operates independently of HDL-C.

PCSK9 Association With Lipoprotein(a)

RATIONALE

Lipoprotein(a) [Lp(a)] is a highly atherogenic low-density lipoprotein-like particle characterized by the presence of apoprotein(a) [apo(a)] bound to apolipoprotein B. Proprotein convertase subtilisin/kexin type 9 (PCSK9) selectively binds low-density lipoprotein; we hypothesized that it can also be associated with Lp(a) in plasma.

OBJECTIVE

Characterize the association of PCSK9 and Lp(a) in 39 subjects with high Lp(a) levels (range 39-320 mg/dL) and in transgenic mice expressing either human apo(a) only or human Lp(a) (via coexpression of human apo(a) and human apolipoprotein B).

METHODS AND RESULTS

We show that PCSK9 is physically associated with Lp(a) in vivo using 3 different approaches: (1) analysis of Lp(a) fractions isolated by ultracentrifugation; (2) immunoprecipitation of plasma using antibodies to PCSK9 and immunodetection of apo(a); (3) ELISA quantification of Lp(a)-associated PCSK9. Plasma PCSK9 levels correlated with Lp(a) levels, but not with the number of kringle IV-2 repeats. PCSK9 did not bind to apo(a) only, and the association of PCSK9 with Lp(a) was not affected by the loss of the apo(a) region responsible for binding oxidized phospholipids. Preferential association of PCSK9 with Lp(a) versus low-density lipoprotein (1.7-fold increase) was seen in subjects with high Lp(a) and normal low-density lipoprotein. Finally, Lp(a)-associated PCSK9 levels directly correlated with plasma Lp(a) levels but not with total plasma PCSK9 levels.

CONCLUSIONS

Our results show, for the first time, that plasma PCSK9 is found in association with Lp(a) particles in humans with high Lp(a) levels and in mice carrying human Lp(a). Lp(a)-bound PCSK9 may be pursued as a biomarker for cardiovascular risk.

Human PCSK9 promotes hepatic lipogenesis and atherosclerosis development via apoE- and LDLR-mediated mechanisms

AIMS

Proprotein convertase subtilisin/kexin type 9 (PCSK9) promotes the degradation of hepatic low-density lipoprotein (LDL) receptors (LDLR), thereby, decreasing hepatocyte LDL-cholesterol (LDL-C) uptake. However, it is unknown whether PCSK9 has effects on atherogenesis that are independent of lipid changes. The present study investigated the effect of human (h) PCSK9 on plasma lipids, hepatic lipogenesis, and atherosclerotic lesion size and composition in transgenic mice expressing hPCSK9 (hPCSK9tg) on wild-type (WT), LDLR⁻/⁻, or apoE⁻/⁻ background.

METHODS AND RESULTS

hPCSK9 expression significantly increased plasma cholesterol (+91%), triglycerides (+18%), and apoB (+57%) levels only in WT mice. The increase in plasma lipids was a consequence of both decreased hepatic LDLR and increased hepatic lipid production, mediated transcriptionally and post-transcriptionally by PCSK9 and dependent on both LDLR and apoE. Despite the lack of changes in plasma lipids in mice expressing hPCSK9 and lacking LDLR (the main target for PCSK9) or apoE (a canonical ligand for the LDLR), hPCSK9 expression increased aortic lesion size in the absence of apoE (268 655 ± 97 972 µm² in hPCSK9tg/apoE⁻/⁻ vs. 189 423 ± 65 700 µm(2) in apoE⁻/⁻) but not in the absence of LDLR. Additionally, hPCSK9 accumulated in the atheroma and increased lesion Ly6C(hi) monocytes (by 21%) in apoE⁻/⁻ mice, but not in LDLR⁻/⁻ mice.

CONCLUSIONS

PCSK9 increases hepatic lipid and lipoprotein production via apoE- and LDLR-dependent mechanisms. However, hPCSK9 also accumulate in the artery wall and directly affects atherosclerosis lesion size and composition independently of such plasma lipid and lipoprotein changes. These effects of hPCSK9 are dependent on LDLR but are independent of apoE.