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1

Multiplex ELISA for Proinflammatory Cytokines

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Proinflammatory cytokines (IL-1β, IL-6, INF-γ, and TNF-α) were analyzed using a multiplex sandwich ELISA (SearchLight, Pierce Biotechnology, Rockford, IL, USA) according to the manufacturer's instructions. Each sample was tested in duplicate. Results are expressed as pg/mL.
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2

Plasma Biomarkers in Cancer Treatment

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Blood was collected at baseline and following the first cycle of treatment (28 days) in heparin-coated tubes and immediately spun at 3000×g for 15 min to isolate the plasma layer. Plasma was stored at −80 °C until time of analysis. Patient plasma was assayed for: VEGF-A, VEGF-C, VEGF-R1, VEGF-R2, platelet-derived growth factor beta heterodimer, (PDGF-BB), osteopontin (OPN), angiopoietin 2 (ANG-2), interleukin-6 (Il-6), and soluble interleukin six receptor (sIL-6R) (Searchlight, Pierce Biotechnology Multiplex ELISA and IL-6 and sIL-6R using R&D Systems). Serum LDH levels were analyzed in the local commercial clinical laboratories.
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3

Monocyte-Derived Cytokine Profiling

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Monocytes (1 million) were incubated in 500 μl medium (0.1% bovine serum albumin in minimental essential medium, pH 7.2) overnight in an open BD tube at 37°/5%CO2. The next day cells were centrifuged (5 min 300×g) and the supernatant was frozen at −80°C until use. For the detection of multiple cytokines (interleukin-1 β (IL1β), monocyte chemotactic protein-1 (MCP-1), macrophage inflammatory protein 1α (MIP1α/CCL3; only humans), macrophage inflammatory protein 2 (MIP2) and tumor necrosis factor α (TNFα)) Thermo Scientific SearchLight Protein Array Technology (THP Medical Products, Vienna) was used as described by us [43 (link)]. In brief, diluted (1:2 in diluent) supernatants or calibrated standards were added to coated wells and incubated for 3 hours. Next, wells were washed and biotinylated antibodies added, again incubated for 30 min and subsequently washed. Afterwards, streptavidin-horseradish peroxidase conjugate was added, incubated, washed and the substrate was added. All incubation steps were carried out on a shaker at 20° C. Imaging was performed with a cooled CCD camera (SearchLight, Thermoscience). All sample values were calculated according to the standard curve in a linear range.
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4

Biomarker Assay Procedures for TNFα System

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Fasting blood samples were centrifuged for 10 min at 4°C, aliquoted in 0.5–1 mL volumes of EDTA plasma (serum for CRP), and stored at −80°C within 2 h of venipuncture. Frozen samples from the Jackson field center were shipped to the Mayo Clinic Immunochemical Core Laboratory (Rochester, MN) overnight on dry ice. Samples were thawed on ice, repackaged into Eppendorf tubes with bar codes and refrozen for shipping to SearchLight (ThermoScientific). CRP assays were performed using immunoturbidometric assays (Diasorin, Inc, Stillwater, MN; inter-assay imprecision 1.8–2.6%; intra-assay imprecision 1.0–9.2%) and multiplex assays (SearchLight™, Pierce, Boston, MA) were used for IL-6 and sTNFRs. sTNFR fractions show stability over time with longer half-lives than TNFα levels and have been validated as sensitive indicators of TNFα system activation34 (link). Precision of the assays performed by SearchLightTM was retrospectively determined based on data derived from a blinded, internal plasma control sample. Algorithms were developed to reduce plate-to-plate variations in protein levels and all analyses used these normalized data.35 (link)
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5

Neprilysin Quantification in Hydrogels

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Collagen hydrogels, neprilysin standards (20-50-100 ng/lane) or medium with released neprilysin (20 μl per lane) were denatured (10 min 70°C with reducing agent) and loaded onto 10% Bis-Tris polyacrylamide gel (Invitrogen) and electrophoresis was performed for 35 min at 200 V. Samples were electrotransferred onto PVDF membranes for 20 min at 25 V in a semi-dry transfer cell (Thermo Fisher Scientific). Blotting was done by using WesternBreeze Chemiluminescent immunodetection system (Invitrogen). Blots were blocked with blocking buffer for 30 min and incubated overnight on a shaker at 4°C with primary antibodies against neprilysin (abcam ab210932; 1:1000). Subsequently, blots were briefly washed and incubated with alkaline phosphatase-conjugated secondary mouse (neprilysin) for 30 min at room temperature. Afterward, the blots were briefly washed again, incubated for 15 min in CDP-Star chemiluminescent substrate solution (Roche) and visualized with a cooled CCD camera (SearchLight, Thermo Fisher Scientific).
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6

Platelet Protein Expression Analysis

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Western blot analysis was performed as previously described by us (21 (link)). Platelet samples (−80°C) were thawed and tubes dissolved in 100 μL ice-cold PBS containing a protease inhibitor cocktail (P-8340; Sigma). Samples were then sonicated using an ultrasonic device, centrifuged at 14,000 × g for 10 min at 4°C; the extracts were denatured (10 min, 70°C), and 18 μg was loaded onto 10% bistris SDS-polyacrylamide gels (Thermo Fisher Scientific, Vienna, Austria), separated for 35 min at 200 V and finally electrotransferred to nylon-PVDF Immobilon-PSQ membranes for 20 min at 30 V in 20% methanol blotting buffer. Next, blots were blocked for 30 min in blocking buffer; incubated with primary antibody against APP (Abcam ab32136, 1:2,000, Cambridge, UK), or CD41 (Abcam ab63323, 1:2,000), or actin (1:1,000, A2066; Sigma, Vienna, Austria) at 4°C overnight; washed; and then incubated in alkaline phosphatase–conjugated anti–rabbit IgG for 30 min. After washing, bound antibodies were detected using an enhanced chemiluminescence system and visualized by using a cooled CCD camera (SearchLight; Thermo Fisher Scientific).
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7

Western Blot Analysis of Serpinin

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Western blots were performed as described by us previously [14 (link)]. Briefly, the tissue was dissolved in 200 µL ice-cold PBS with a protease inhibitor cocktail (P8340, Sigma, Hamburg, Germany), homogenized by using an ultrasonic device (Branson sonifier 250, Danburry) and centrifuged at 16,000× g at 4 °C for 10 min. Protein was determined by the Bradford assay. The non-denatured supernatants (25 µg) were loaded onto a 10% Bis-Tris polyacrylamide gel (Invitrogen, Waltham, MA, USA) and were electrophoresed for 25 min at 200 V. Samples were electrotransferred to nylon PVDF (Immobilon-PSQ membranes (Millipore, Burlington, MA, USA) for 90 min at 30 V with 20% methanol blotting buffer (Invitrogen). Blots were blocked for 30 min with blocking buffer, then incubated overnight at 4 °C with the primary serpinin antibody (1:1000; gift from Peng Loh, National Institutes of Health, Bethesda, MD, USA; polyclonal antibody, raised in rabbits) or overnight at 4 °C with a rabbit anti-actin antibody (1:1000, Sigma-Aldrich, St. Louis, MO, USA). Blots were washed and incubated with alkaline phosphatase-conjugated anti-rabbit antibodies for 30 min at room temperature. After washing, blots were incubated (free-floating) in CDP-Star chemiluminescent substrate solution (Invitrogen) for 10 min and the signal was visualized (exposure time 1200 s) with a cooled CCD camera (SearchLight, Thermoscience).
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8

Western Blot Analysis of Cell Extracts

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Western blot analysis was performed as previously described by us [16 (link)]. Twenty µl of the cell/vessel extracts were loaded onto 10% Bis-Tris SDS-polyacrylamide gels (Thermo Fisher Scientific), separated for 35 min at 200 V and finally electro-transferred to nylon-PVDF Immobilon-PSQ membranes for 90 min at 30 V in 20% methanol blotting buffer. Briefly, blots were blocked for 30 min in blocking buffer, incubated with primary antibodies against PDGFRβ clone Y92 (C-terminal, amino acid (aa)1050-1150) (1:3000, Novus Biologicals NB110-57343), alpha-smooth muscle actin (1:1000, abcam ab119952), actin (1:1000, Sigma A2066) or laminin (1:500, Sigma) at 4°C overnight, washed, and then incubated in alkaline phosphatase conjugated anti-rabbit IgG or anti-mouse IgG for 30 min. After washing, bound antibodies were detected using an enhanced chemiluminescence (ECL) system and visualized by using a cooled CCD camera (SearchLight; Thermo Fisher Scientific).
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9

Quantitative Western Blot Analysis of Tau Phosphorylation

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Western blot analysis was performed for tau and phospho-tau396 as described by us in detail [35] . Platelet extracts (80 µg per lane total protein) were denatured (70 °C for 10 min) and loaded onto 4-12% Bis-Tris polyacrylamide gels (Invitrogen Life Tech, Darmstadt, Germany) and separated by electrophoresis for 60 min at 200 V. Consecutively, samples were electrotransferred to nylon PVDF Immobilon-PSQ membranes (Millipore, Vienna, Austria) at 30 V for 90 min with 20% methanol transfer buffer (Invitrogen). Protein detection was performed with Western Breeze Chemiluminescent System (Invitrogen). Thus, membranes were blocked for 30 min with blocking solution at RT on the shaker, then incubated with the primary antibody tau-5 (Thermo AHB0042, 1:1000) or phospho-tau-396 (pTau396, BioLegend 807401, 1:10,000) or HT7 antibody (1:500, Thermo MN1000) overnight at 4 °C. Subsequently, blots were washed and incubated with anti-mouse (tau-5, HT7) or anti-rabbit (pTau396) antibodies for 30 min at room temperature (RT), again washed and incubated with CDP-Star chemiluminescent substrate solution (Invitrogen). Imaging was performed with a cooled CCD camera (SearchLight, ThermoScientific, Austria).
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