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14 protocols using neopterin

1

Lipid, Protein, and Immune Markers Quantitation

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Lipid markers were measured by electrospray ionization tandem mass spectrometry as described previously (Haughey, Cutler et al. 2004 (link)). Protein carbonyls were quantitated using the OxyBlot Protein Oxidation Detection Kit as described previously (Schifitto, Yiannoutsos et al. 2009 (link)). Enzyme-linked immunosorbent assays (ELISA) were used to measure plasma Neopterin (GenWay Biotech), sCD14 (R&D Systems), sCD163 (from Trillium Diagnostics) and CSF sCD14, sCD163, neurofilament protein light chain (NFL) (UmanDiagnostics), and neurofilament protein heavy chain (NFH) (BioVendor) levels according to manufacturer’s protocols.
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2

CD4+ T cell and HIV biomarkers

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CD4+ T cell count and percentage and plasma HIV RNA were ascertained as
described [38 ]. Plasma concentrations of
sCD14, sCD163 and neopterin were assessed using commercially available kits
(sCD14 and sCD163, R&D Systems, Inc. Minneapolis, MN; neopterin, GenWay
Biotech Inc. San Diego, CA).
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3

Multiplex Cytokine Profiling of Plasma

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A custom multiplex cytokine array was used to quantify 16 analytes from cryopreserved plasma, including IFN-γ, IL-1α, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12p70, IL-15, IL-17, IP-10, MCP-1, TNF, and TNFRII, according to the manufacturer’s instructions (Quansys Biosciences, Logan, UT). Commercial single ELISAs were used to measure neopterin (GenWay Biotech, San Diego, CA), IFN-α, I-FABP, and sCD14 (R&D Systems). All samples were run in triplicate, and mean values were used for data analysis.
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4

Multiplex Cytokine Profiling of Plasma

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A custom multiplex cytokine array was used to quantify 16 analytes from cryopreserved plasma, including IFN-γ, IL-1α, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12p70, IL-15, IL-17, IP-10, MCP-1, TNF, and TNFRII, according to the manufacturer’s instructions (Quansys Biosciences, Logan, UT, USA). Commercial single ELISAs were used to measure neopterin (GenWay Biotech, San Diego, CA, USA), IFNα, I-FABP, and sCD14 (R&D Systems). All samples were run in triplicate and mean values were used for data analysis.
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5

Intestinal Biomarkers for Inflammation

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Intestinal inflammation was evaluated by measuring the levels of the biomarkers: alpha-1-anti-trypsin (Biovendor, Chandler, NC), neopterin (GenWay Biotech, San Diego, CA), and myeloperoxidase (Alpco, Salem, NH) in the stool samples collected from the study participants at the 3, 6, 9, 15, and 24 months of age time points by quantitative ELISA, using manufacturer’s guidelines45 (link).
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6

Biomarkers of Intestinal Dysfunction in EED

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A range of biomarkers were selected to characterise four domains of EED [12] (link). Briefly, we measured markers of (1) intestinal inflammation (stool neopterin and myeloperoxidase), (2) small intestinal damage and repair (plasma intestinal fatty acid binding protein (I-FABP), plasma citrulline, stool regenerating gene 1β (REG-1B)), (3) intestinal permeability (stool alpha-1 antitrypsin (A1AT)), and (4) microbial translocation and systemic inflammation (plasma soluble CD14, kynurenine:tryptophan ratio (KTR), and C-reactive protein (CRP)). Plasma samples were tested by ELISA according to manufacturers’ instructions for CRP (limit of detection (LOD) 0.01 ng/mL), soluble CD14 (LOD 125pg/mL) (both R&D Systems, Minneapolis, MN, USA); and I-FABP (LOD 47pg/mL) (Hycult Biotechnology, Uden, The Netherlands). Plasma citrulline (LOD 100 ng/mL), kynurenine (LOD 40 ng/mL), and tryptophan (200 ng/mL) were assayed by ultrahigh-performance liquid chromatography tandem mass spectrometry with electrospray ionisation (Waters, Wilmslow, U.K.) at Imperial College, London.
Stool samples were tested by ELISA according to manufacturers’ instructions for neopterin (LOD 0.7 nmol/L; GenWay Biotech Inc, San Diego, USA), myeloperoxidase (LOD 1.6 ng/mL; Immundianostik, Bensheim, Germany), A1AT (LOD 1.5 ng/mL; BioVendor, Brno, Czech Republic), and REG‐1β (LOD 0.625 ng/mL; TECHLAB Inc, Blacksburg, USA).
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7

Multiparametric Profiling of PBMC

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Peripheral blood mononuclear cells (PBMC), isolated and cryopreserved as previously described [9] , were thawed, washed, and stained with the LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Molecular Probes, Eugene, Oregon, USA), and monoclonal antibodies for CD3(SK7) PerCP-Cy5.5, CD8(SK1) PE-Cy7, CD38(HB7) APC, HLA-DR(L243) FITC, PD-1(EH12.1) PE, CD14(MΦP9) APC-H7, and CD16(3G8) Pacific Blue (all from BD Biosciences, San Jose, California, USA), as well as CD4 + (SFCI12T4D11) ECD (Beckman Coulter, Indianapolis, Indiana, USA). Fixed cells were run on a BD FACSARIA II SORP (BD Biosciences) where populations were sorted, and dry pellets stored. A multiplex array was used to quantify plasma levels of: IFNγ, IL-1α, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12p70, IL-15, IL-17, IP-10, MCP-1, TNF, and TNFRII (Quansys Biosciences, Logan, Utah, USA). ELISAs were used to measure neopterin (GenWay Biotech, San Diego, California, USA), as well as IFNα, I-FABP, and sCD14 (R&D Systems, Minneapolis, Minnesota, USA). Plasma was tested in triplicate and mean values used for data analysis.
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8

Assessing Zinc Status and Enteric Inflammation

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Monthly non-diarrheal stools were collected from each participant and venous blood was collected at 7, 15 and 24 months. The biological samples collected were subsequently processed following identical standardized protocols and were stored in −80 °C freezers, prior to further analyses. Plasma zinc, popularly considered to be a proxy indicator for assessment of zinc status in children was assessed by flame absorption spectrophotometry (Shimadzu AA-6501S, Tokyo, Japan). Alpha-1-acid glycoprotein (AGP), a systemic inflammation biomarker, was measured by an immunoturbidimetric assay using commercial kits and a chemistry analyzer (Roche, Munich, Germany). Enteric inflammation was assessed by measuring the levels of myeloperoxidase (Alpco, Salem, NH, USA), neopterin (GenWay Biotech, San Diego, CA, USA) and alpha-1-anti-trypsin (Biovendor, Brno, Czech Republic) at 3, 6, 9, 15, and 24 months by using quantitative ELISA. EED score, ranging from 0 to 10, was calculated from the three biomarkers, as described previously [17 (link)].
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9

Biomarkers of Intestinal Inflammation

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Intestinal inflammation was evaluated by measuring the levels of the biomarkers: alpha-1-anti-trypsin (Biovendor, Chandler, NC), neopterin (GenWay Biotech, San Diego, CA), and myeloperoxidase (Alpco, Salem, NH) in the stool samples collected from the study participants at the 3, 6, 9, 15, and 24 months of age time points by quantitative ELISA, using manufacturer’s guidelines34 (link).
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10

Multiplex Analysis of Inflammatory Biomarkers

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We evaluated the following circulating inflammatory biomarkers: neopterin, TNF-α, IL-6, IL-1β and MCP-1 in the plasma and CSF in this cohort. TNF-α, IL-6, IL-1β and MCP-1 were quantified in triplicate as part of a custom multiplex ELISA array according to the manufacturer's protocol (Quansys Biosciences, Logan, UT). Data were captured on the Odyssey infrared imaging system (Li-Cor Biosciences, Lincoln, NE) and analyzed using Quansys Q-view Plus software (Quansys Biosciences). Single-analyte ELISA was performed in duplicate to detect levels of neopterin (GenWay Biotech, San Diego, CA) and analyzed using SoftMax Pro (Molecular Devices, Sunnyvale, CA).
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