Automation of PRM-dependent D3-Leu tracer enrichment in HDL to study the metabolism of apoA-I, LCAT and other apolipoproteins.

We developed an automated quantification workflow for PRM-enabled detection of D3-Leu labeled apoA-I in high-density lipoprotein (HDL) isolated from humans. Subjects received a bolus injection of D3-Leu and blood was drawn at eight time points over three days. HDL was isolated and separated into six size fractions for subsequent proteolysis and PRM analysis for the detection of D3-Leu signal from ∼0.03 to 0.6% enrichment. We implemented an intensity-based quantification approach that takes advantage of high-resolution/accurate mass PRM scans to identify the D3-Leu 2HM3 ion from non-specific peaks. Our workflow includes five modules for extracting the targeted PRM peak intensities (XPIs): Peak centroiding, noise removal, fragment ion matching using Δm/z windows, nine intensity quantification options, and validation and visualization outputs. We optimized the XPI workflow using in vitro synthesized and clinical samples of D0/D3-Leu labeled apoA-I. Three subjects' apoA-I enrichment curves in six HDL size fractions, and LCAT, apoA-II and apoE from two size fractions were generated within a few hours. Our PRM strategy and automated quantification workflow will expedite the turnaround of HDL apoA-I metabolism data in clinical studies that aim to understand and treat the mechanisms behind dyslipidemia.

Multiple apolipoprotein kinetics measured in human HDL by high-resolution/accurate mass parallel reaction monitoring.

Endogenous labeling with stable isotopes is used to study the metabolism of proteins in vivo. However, traditional detection methods such as GC/MS cannot measure tracer enrichment in multiple proteins simultaneously, and multiple reaction monitoring MS cannot measure precisely the low tracer enrichment in slowly turning-over proteins as in HDL. We exploited the versatility of the high-resolution/accurate mass (HR/AM) quadrupole Orbitrap for proteomic analysis of five HDL sizes. We identified 58 proteins in HDL that were shared among three humans and that were organized into five subproteomes according to HDL size. For seven of these proteins, apoA-I, apoA-II, apoA-IV, apoC-III, apoD, apoE, and apoM, we performed parallel reaction monitoring (PRM) to measure trideuterated leucine tracer enrichment between 0.03 to 1.0% in vivo, as required to study their metabolism. The results were suitable for multicompartmental modeling in all except apoD. These apolipoproteins in each HDL size mainly originated directly from the source compartment, presumably the liver and intestine. Flux of apolipoproteins from smaller to larger HDL or the reverse contributed only slightly to apolipoprotein metabolism. These novel findings on HDL apolipoprotein metabolism demonstrate the analytical breadth and scope of the HR/AM-PRM technology to perform metabolic research.

A disease-driver population within interstitial cells of human calcific aortic valves identified via single-cell and proteomic profiling.

Cellular heterogeneity of aortic valves complicates the mechanistic evaluation of the calcification processes in calcific aortic valve disease (CAVD), and animal disease models are lacking. In this study, we identify a disease-driver population (DDP) within valvular interstitial cells (VICs). Through stepwise single-cell analysis, phenotype-guided omic profiling, and network-based analysis, we characterize the DDP fingerprint as CD44highCD29+CD59+CD73+CD45low and discover potential key regulators of human CAVD. These DDP-VICs demonstrate multi-lineage differentiation and osteogenic properties. Temporal proteomic profiling of DDP-VICs identifies potential targets for therapy, including MAOA and CTHRC1. In vitro loss-of-function experiments confirm our targets. Such a stepwise strategy may be advantageous for therapeutic target discovery in other disease contexts.

A single injection of gain-of-function mutant PCSK9 adeno-associated virus vector induces cardiovascular calcification in mice with no genetic modification.

BACKGROUND AND AIMS: Studying atherosclerotic calcification in vivo requires mouse models with genetic modifications. Previous studies showed that injection of recombinant adeno-associated virus vector (AAV) encoding a gain-of-function mutant PCSK9 into mice promotes atherosclerosis. We aimed to study cardiovascular calcification induced by PCSK9 AAV in C57BL/6J mice. METHODS: 10 week-old C57BL/6J mice received a single injection of AAV encoding mutant mPCSK9 (rAAV8/D377Y-mPCSK9). Ldlr(-/-) mice served as positive controls. Mice consumed a high-fat, high-cholesterol diet for 15 or 20 weeks. Aortic calcification was assessed by fluorescence reflectance imaging (FRI) of a near-infrared calcium tracer. RESULTS: Serum levels of PCSK9 (0.14 µg/mL to 20 µg/mL, p < 0.01) and total cholesterol (82 mg/dL to 820 mg/dL, p < 0.01) increased within one week after injection and remained elevated for 20 weeks. Atherosclerotic lesion size was similar between PCSK9 AAV and Ldlr(-/-) mice. Aortic calcification was 0.01% ± 0.01 in PCSK9 AAV mice and 15.3% ± 6.1 in Ldlr(-/-) mice at 15 weeks (p < 0.01); by 20 weeks, the PCSK9 AAV mice aortic calcification grew to 12.4% ± 4.9. Tissue non-specific alkaline phosphatase activity was similar in PCSK9 AAV mice and Ldlr(-/-) mice at 15 and 20 weeks, respectively. As example of the utility of this model in testing modulators of calcification in vivo, PCSK9 AAV injection to sortilin-deficient mice demonstrated reduced aortic calcification by 46.3% (p < 0.05) compared to littermate controls. CONCLUSIONS: A single injection of gain-of-function PCSK9 AAV into C57BL/6J mice is a useful tool to study cardiovascular calcification in mice with no genetic manipulation.

mIMT-visHTS: A novel method for multiplexing isobaric mass tagged datasets with an accompanying visualization high throughput screening tool for protein profiling.

Isobaric mass tagging (IMT) methods enable the analysis of thousands of proteins simultaneously. We used tandem mass tagging reagents (TMT™) to monitor the relative changes in the proteome of the mouse macrophage cell line RAW264.7 at the same six time points after no stimulation (baseline phenotype), stimulation with interferon gamma (pro-inflammatory phenotype) or stimulation with interleukin-4 (anti-inflammatory phenotype). The combined TMT datasets yielded nearly 12,000 protein profiles for comparison. To facilitate this large analysis, we developed a novel method that combines or multiplexes the separate IMT (mIMT) datasets into a single super dataset for subsequent model-based clustering and co-regulation analysis. Specially designed visual High Throughput Screening (visHTS) software screened co-regulated proteins. visHTS generates an interactive and visually intuitive color-coded bullseye plot that enables users to browse the cluster outputs and identify co-regulated proteins.

Mammotomography with pinhole incomplete circular orbit SPECT.

UNLABELLED: Dedicated mammotomography with pinhole incomplete circular orbit (PICO) SPECT imaging of an uncompressed pendant breast was evaluated with small, very-high-stopping-power pinhole apertures. Comparisons were made with planar pinhole scintimammography. Enhanced 3-dimensional imaging performance with very-high-stopping-power apertures is thought to ultimately yield improved sensitivities for lesion detection and identification in breast disease. METHODS: Pinhole collimators made of high-density and high atomic number (184)W or depleted (238)U, with aperture diameters from 1 to 4 mm, were used to image 0.6- and 1.0-cm-diameter spherical lesions in a pendulous, uncompressed breast phantom in planar and PICO-SPECT modes. The breast was centered on the horizontal axis of rotation of an incomplete circular orbit. Lesion, breast and body, and myocardial activities (L:B:M) were included in the phantoms to simulate clinical imaging conditions with (99m)Tc (140 keV). Lesion contrasts and signal-to-noise ratios (SNRs) for all apertures were determined for near clinical acquisition times for L:B:M ratios of 12:1:20 and 7:1:25. A set of minidisks inserted in the breast phantom was scanned to determine sampling limitations at depth from the nipple. In an initial study, a patient with biopsy-confirmed breast carcinoma was injected with 960 MBq (99m)Tc-tetrofosmin and scanned 2 h later with planar pinhole and PICO-SPECT techniques. RESULTS: Overall, for PICO-SPECT imaging there were small differences in measured counting rate sensitivity (4.9%) and lesion contrast (8.8%) with larger SNR differences (20.8%) between tungsten and depleted uranium pinhole materials at this energy and these lesion sizes. Backgrounds from simulated myocardial uptake had minor contributions in all reconstructed image volumes because of the rapid sensitivity fall-off for pinhole apertures. An optimal aperture diameter between 2 and 3 mm was determined from peak SNR, indicating that these aperture sizes may have the best performance for lesions as small as 0.6 cm in diameter with activity concentration ratios of (99m)Tc similar to those currently seen in patients. Both lesions were visualized with PICO-SPECT better than with planar pinhole imaging, with respective contrast improvements >20 times the values obtained from planar imaging for the same pinholes. In the patient study, higher contrast (>6) visualization of the active tumor periphery was obtained with PICO-SPECT than with planar imaging. CONCLUSION: These results indicate that the enhanced spatial resolution of smaller apertures outweighs the loss in sensitivity in small lesion identification with PICO-SPECT. Although the imaging differences between investigated aperture types are small and some limitations to this imaging approach exist, dedicated PICO-SPECT of the breast appears to be an improved technique compared with conventional planar pinhole scintimammography. This technique provides enhanced contrast and SNR for imaging small lesions with the high-resolution pinhole apertures along with 3-dimensional localization of the lesions.