Data from: Crystalline silica-induced proinflammatory eicosanoid storm in novel alveolar macrophage model quelled by docosahexaenoic acid
Data files
Jun 11, 2023 version files 544.54 KB
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Dryad_File_1_-_Oxylipin_Profiling_Data.xlsx
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README.md
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Oct 11, 2023 version files 934.85 KB
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Dryad_File_1_-_Oxylipin_Profiling_Data.xlsx
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Dryad_Zip_File_1_-_MS_Spectra_for_Representative_Oxylipins.zip
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README.md
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Nov 02, 2023 version files 934.96 KB
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Dryad_File_1_-_Oxylipin_Profiling_Data.xlsx
533.68 KB
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Dryad_Zip_File_1_-_MS_Spectra_for_Representative_Oxylipins.zip
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README.md
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Dec 13, 2023 version files 934.99 KB
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Dryad_File_1_-_Oxylipin_Profiling_Data.xlsx
533.68 KB
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Dryad_Zip_File_1_-_MS_Spectra_for_Representative_Oxylipins.zip
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README.md
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Abstract
Introduction: Workplace exposure to respirable crystalline silica (cSiO2) is associated with chronic inflammatory and autoimmune diseases. At the mechanistic level, cSiO2 particles are quickly phagocytosed by resident alveolar macrophages (AMs) in the lung, causing a robust cycle of proinflammatory cytokine release, lysosomal rupture, mitochondrial toxicity, and immunogenic cell death if the particle is not efficiently cleared by the lung. We and others have demonstrated in bone marrow-derived and transformed macrophage models that supplementation with the ω-3 polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA) contributes to increased membrane phospholipid content of DHA and subsequent suppression of cSiO2-triggered inflammatory responses. However, mechanistic exploration of ω-3 PUFA effects in AMs is challenging due to reliance on short-lived primary AMs derived from lung lavage fluid.
Methods: To address these limitations, we have employed a recently developed novel self-renewing AM model from C57BL/6 mice, fetal liver-derived alveolar-like macrophages (FLAMs), that is phenotypically representative of primary lung AM populations. We found that incubation of FLAMs with 25 µM DHA as ethanolic suspensions or as complexes with bovine serum albumin were equally effective at increasing ω-3 PUFA content of phospholipids at the expense of the ω-6 PUFA arachidonic acid (ARA) and the ω-9 monounsaturated fatty acid oleic acid. Based on these findings, FLAMs were treated with 25 µM DHA in EtOH or EtOH vehicle (VEH) for 24 h, with or without LPS for 2 h, and with or without cSiO2 for 1.5 or 4 h then proinflammatory cytokine release, lysosomal membrane permeabilization, and mitochondrial depolarization assessed. In addition, oxylipin metabolites were measured using a targeted LC-MS lipidomics panel of 156 metabolites.
Results: Regardless of whether FLAMs were LPS-primed, cSiO2-triggered lysosomal permeability, mitochondrial toxicity, and cell death were not impacted by DHA. LPS+cSiO2 elicited marked IL-1α, IL-1β, and TNF-α release after 1.5 and 4 h of cSiO2 exposure, which was significantly inhibited by DHA. In VEH-treated cells, cSiO2 alone and LPS+cSiO2 induced synthesis of ARA-derived proinflammatory oxylipins including prostaglandins, leukotrienes, and thromboxanes that was suppressed by DHA. In addition, DHA promoted synthesis of pro-resolving DHA-derived oxylipins at the expense of ARA-derived oxylipins.
Discussion: FLAMs were amenable to lipidome modulation by DHA, which suppressed cSiO2-triggered proinflammatory cytokine responses and ARA-derived oxylipins that potentially contribute to the particle’s toxicity in the lung. FLAMs are a promising in vitro alternative to primary AMs for investigating interventions against toxicant-triggered inflammation and autoimmunity in the lung.
Title of Dataset: Data from: Omega-3 docosahexaenoic acid suppresses silica-induced proinflammatory cytokine release and oxylipin mediator production in novel fetal liver-derived alveolar-like macrophages
Author/Principal Investigator Information
Name: Dr. Olivia Favor
ORCID: 0000-0001-9164-7077
Institution: Michigan State University
Address: 567 Wilson Rd, Office 4183, East Lansing, MI 48824
Email: favoroli@msu.edu
Author/Associate or Co-Investigator Information
Name: Dr. James Pestka
ORCID: 0000-0003-4689-2756
Institution: Michigan State University
Address: 567 Wilson Rd, Office 4176, East Lansing, MI 48824
Email: pestka@msu.edu
Author/Alternate Contact Information
Name: Dr. Kathryn Wierenga
ORCID: 0000-0003-1725-4616
Institution: Utrecht University
Address: Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
Email: k.a.wierenga-royer@uu.nl
Author/Alternate Contact Information
Name: Dr. Lichchavi Rajasinghe
ORCID: 0000-0002-5136-7422
Institution: AstraZeneca
Address: 1800 Concord Pike, Wilmington, DE 19803
Email: lichchavi.rajasinghe@astrazeneca.com
Author/Alternate Contact Information
Name: Dr. Krishna Maddipati
ORCID: 0000-0003-1445-791X
Institution: Wayne State University
Address: 435 Chemistry Bldg., 5101 Cass Ave, Detroit, MI 48202
Email: maddipati@wayne.edu
Author/Associate or Co-Investigator Information
Name: Dr. Kin Sing Stephen Lee
ORCID: 0000-0003-4541-3063
Institution: Michigan State University
Address: Address: 1355 Bogue St, Room B330A, East Lansing, MI 48824
Email: sing@msu.edu
Author/Alternate Contact Information
Name: Dr. Andrew Olive
ORCID: 0000-0003-3441-3113
Institution: Michigan State University
Address: 567 Wilson Rd, Office 5198, East Lansing, MI 48824
Email: oliveand@msu.edu
Date of data collection: 2021
Geographic location of data collection: Wayne State University
Information about funding sources that supported the collection of the data: National Institute of Environmental Health Sciences, ES027353; National Institutes of Health/National Center for Research Resources, S10RR027926.
Description of the Data and File structure
File List:
File 1 - Oxylipin Profiling Data: contains area ratios, signal-to-noise (SN) ratios, chromatographic peak quality values, calculated quantities with validation, and final quantities for 143 unique oxylipins analyzed by LC-MS.
Zip File 1 - MS Spectra for Representative Oxylipins: contains mass spectrometry spectra for representative omega-6 eicosanoids (i.e., PGE2, LTB4, TXB2), hydroxy-fatty acids (i.e., 5-HETE, 5-HEPE, 4-HDoHE), epoxy-fatty acids (i.e., 14,15-EpETrE, 19,20-EpDPE), dihydroxy-fatty acids (i.e., 14,15-DiHETrE, 19,20-DiHDoPE), and specialized pro-resolving mediators (i.e., RvD6, MaR1[n-3 DPA]) in PDF format for Windows OS and Mac OS.
Relationship between files, if important:
Additional related data collected that was not included in the current data package:
Are there multiple versions of the dataset? No
If yes, name of file(s) that was updated:
Why was the file updated?
When was the file updated?
Methodological Information
MEASUREMENT OF INTRACELLULAR AND EXTRACELLULAR OXYLIPINS
SAMPLE PREPARATION
Following treatments, ice-cold methanol was added to each well, resulting in a final sample volume of 3 ml (1 ml cell culture supernatant + 2 ml methanol). To each sample, 60 l of antioxidant cocktail (0.2 mg/ml butylated hydroxytoluene, 0.2 mg/ml triphenylphosphine, 0.6 mg/ml EDTA) was added to achieve a total cocktail concentration of 5% (v/v). Cells and supernatants within each well were pooled together, then samples were frozen at -80 C until liquid chromatography-mass spectrometry (LC-MS) analysis.
LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY (LC-MS) ANALYSIS
Targeted LC-MS lipidomics for 156 lipid metabolites was conducted at the Lipidomics Core Facility at Wayne State University. 100 l aliquots of cellular samples were thawed and spiked with a cocktail of deuterated internal standards (5 ng each of PGE1-d4, RvD2-d5, LTB4-d4, and 15[S]-HETE-d8; Cayman Chemical, Ann Arbor, MI) for quantification of oxylipins and recovery. Then, fatty acyl lipid metabolites were extracted by using C18 extraction columns that were washed with 15% (v/v) methanol and subsequently hexane, dried in a vacuum, eluted with methanol containing 0.1% (v/v) formic acid, dried under nitrogen gas, and dissolved in a 1:1 mixture of methanol:25 mM aqueous ammonium acetate. Extracted fatty acyl metabolites were subjected to high-performance liquid chromatography (HPLC) using a Luna C18 (3 m, 2.1150 mm) column connected to a Prominence XR system (Shimadzu, Somerset, NJ) then analyzed with a QTrap5500 mass spectrometer (AB Sciex, Singapore) set to negative ion mode. Analyst 1.6 software (AB Sciex) and MultiQuant software (AB Sciex) were used to collect and quantify the data in units of ng, respectively.
DATA ANALYSIS AND STATISTICS
MetaboAnalyst Version 5.0 (Xia Lab, Quebec, Canada, www.metaboanalyst.ca/) was used to conduct statistical analyses. First, raw ng values were converted to corresponding pmol values in Microsoft Excel. Then, in MetaboAnalyst, the one factor statistical analysis module was chosen, and data were uploaded as a comma separated values (.csv) file with samples in unpaired columns and features (i.e., metabolites) in rows. Features with >70% missing data were removed from the dataset, and remaining missing values were estimated by replacing with the corresponding limits of detection (LODs; 1/5 of the minimum positive value of each variable). After the data was cleaned, the data was normalized by auto scaling only, then the data editor option was used to select experimental groups of interest to compare. For comparisons between experimental groups, one-way analysis of variance (ANOVA) (FDR = 0.05) followed by Tukeys honestly significant difference (HSD) post-hoc test was used, with FDR q < 0.05 considered statistically significant.
Instrument- or software-specific information needed to interpret the data: Microsoft Excel, MetaboAnalyst Version 5.0 (Xia Lab, Quebec, Canada, www.metaboanalyst.ca/)
Environmental/experimental conditions: Fetal liver-derived alveolar-like macrophages (FLAMs) were seeded in 6-well plates at a density of 4.5010^5 cells/well in complete FLAM medium (RPMI 1640, 10% fetal bovine serum, 1% penicillin-streptomycin, 30 ng/ml GM-CSF, 20 ng/ml TGF-beta). Cells were incubated overnight to achieve 70-90% confluency before beginning treatments. The next day, cells washed once with sterile PBS, fresh complete FLAM medium containing either 25 uM ethanolic DHA or ethanol vehicle (VEH) added, then cells incubated for 24 h. Following DHA or VEH treatment, cells were washed once with sterile PBS, treated with either 20 ng/ml lipopolysaccharide (LPS) or VEH in DPBS+/+ (DPBS containing calcium and magnesium) for 2 h, then exposed to 12.5 ug/cm2 crystalline silica (cSiO2) or VEH for 1.5 or 4 h. Cell culture supernatants and cells were pooled together and collected at t = 2 h (after 2 h LPS priming), 3.5 h (after 1.5 h cSiO2 exposure), and 6 h (after 4 h cSiO2 exposure). LPS and cSiO2 exposures were done in DPBS+/+ to minimize interference from fatty acids present in cell culture medium during oxylipin analyses.
Describe any quality-assurance procedures performed on the data:
People involved with sample collection, processing, analysis, and/or submission: Olivia Favor, Dr. Lichchavi Rajasinghe, Dr. Krishna Maddipati, Dr. James Pestka
DATA-SPECIFIC INFORMATION FOR: Oxylipin Profiling Data
Number of variables: Three variables - 1) exposure (VEH, LPS, cSiO2, LPS+cSiO2), 2) treatment (VEH, DHA), and 3) timepoint (2, 3.5, 6)
Variable list:
VEH - PBS vehicle
LPS - lipopolysaccharide, 20 ng/ml
cSiO2 - crystalline silica, 12.5 ug/cm^2
DHA - docosahexaenoic acid, 25 uM
SHEET 1 - Key
Description: Contains Sample ID numbers and corresponding exposure/treatment groups with timepoints
Number of cases/rows: 61
Missing data codes: None
Specialized formats of other abbreviations used:
VEH - PBS vehicle
LPS - lipopolysaccharide, 20 ng/ml
cSiO2 - crystalline silica, 12.5 ug/cm^2
LPS+cSiO2 - simultaneous LPS (20 ng/ml) and cSiO2 (12.5 ug/cm^2) exposure
DHA - docosahexaenoic acid, 25 uM
SHEET 2 - Area Ratio
Description: Ratio of the chromatographic peak area to that of the Internal Standard added to the sample at the start of sample processing for analysis.
Number of cases/rows: 147
Missing data codes: N.D. - not determined
Specialized formats of other abbreviations used:
VEH - PBS vehicle
LPS - lipopolysaccharide, 20 ng/ml
cSiO2 - crystalline silica, 12.5 ug/cm^2
LPS+cSiO2 - simultaneous LPS (20 ng/ml) and cSiO2 (12.5 ug/cm^2) exposure
DHA - docosahexaenoic acid, 25 uM
SHEET 3 - SN
Description: Signal to noise ratio of the detected peak in the chromatogram. Minimum acceptable for quantitation: 3.
Number of cases/rows: 147
Missing data codes: N.D. - not determined
Specialized formats of other abbreviations used:
VEH - PBS vehicle
LPS - lipopolysaccharide, 20 ng/ml
cSiO2 - crystalline silica, 12.5 ug/cm^2
LPS+cSiO2 - simultaneous LPS (20 ng/ml) and cSiO2 (12.5 ug/cm^2) exposure
DHA - docosahexaenoic acid, 25 uM
SHEET 4 - Quality
Description: Chromatographic peak quality based on symmetry, noise, data points,
etc. Range 0 1. Minimum accepted for quantitation 0.2.
Number of cases/rows: 147
Missing data codes: N.D. - not determined
Specialized formats of other abbreviations used:
VEH - PBS vehicle
LPS - lipopolysaccharide, 20 ng/ml
cSiO2 - crystalline silica, 12.5 ug/cm^2
LPS+cSiO2 - simultaneous LPS (20 ng/ml) and cSiO2 (12.5 ug/cm^2) exposure
DHA - docosahexaenoic acid, 25 uM
SHEET 5 - Validity\&Calc
Description: Calculated data of each analyte after validating that the SN > 3 and Quality > 0.2. The calculation includes multiplication of the Area Ratio with the quantity of internal standard used and adjustment to any dilutions.
Number of cases/rows: 147
Missing data codes: #VALUE! - value that fails validation (SN < 3 and/or Quality < 0.2)
Specialized formats of other abbreviations used:
VEH - PBS vehicle
LPS - lipopolysaccharide, 20 ng/ml
cSiO2 - crystalline silica, 12.5 ug/cm^2
LPS+cSiO2 - simultaneous LPS (20 ng/ml) and cSiO2 (12.5 ug/cm^2) exposure
DHA - docosahexaenoic acid, 25 uM
SHEET 6 - ng per sample
Description: Provides quantities of oxylipins in each sample in units of ng/sample. This worksheet is essentially the same as Validity&Calc data but without the formulas and other qualification information.
Number of cases/rows: 147
Missing data codes: N.D. - not determined
Specialized formats of other abbreviations used:
VEH - PBS vehicle
LPS - lipopolysaccharide, 20 ng/ml
cSiO2 - crystalline silica, 12.5 ug/cm^2
LPS+cSiO2 - simultaneous LPS (20 ng/ml) and cSiO2 (12.5 ug/cm^2) exposure
DHA - docosahexaenoic acid, 25 uM
DATA-SPECIFIC INFORMATION FOR: MS Spectra for Representative Oxylipins
Description: Zip file provides mass spectrometry (MS) spectra for representative omega-6 eicosanoids (i.e., PGE2, LTB4, TXB2), hydroxy-fatty acids (i.e., 5-HETE, 5-HEPE, 4-HDoHE), epoxy-fatty acids (i.e., 14,15-EpETrE, 19,20-EpDPE), dihydroxy-fatty acids (i.e., 14,15-DiHETrE, 19,20-DiHDoPE), and specialized pro-resolving mediators (i.e., RvD6, MaR1[n-3 DPA]). Each MS spectrum contains an abbreviation for a representative oxylipin (e.g., 4-HDoHE), blue peaks labeled with mass-to-charge (m/z) ratios (given in Daltons, Da) for the most characteristic molecular ion fragments, negative enhanced product ion (-EPI) scan with m/z ratio for specific molecular ion fragment analyzed, charge, collision energy (CE), collision energy spread (CES), fourier transform (FT), and counts per second (cps).
Number of cases/rows: 12 oxylipins: 4-HDoHE, 5-HEPE, 5-HETE, 14(15)-EpETrE, 14-15-DiHETrE, 19(20)-EpDPE, 19-20-DiHDoPE, LTB4, MaR1(n-3-DPA), PGE2, RvD6, TxB2
Missing data codes: N/A
Specialized formats of other abbreviations used:
4-HDoHE: 4-hydroxydocosahexaenoic acid
5-HEPE: 5-hydroxyeicosapentaenoic acid
5-HETE: 5-hydroxyeicosatetraenoic acid
14(15)-EpETrE: 14,15-epoxyeicosatrienoic acid
14-15-DiHETrE: 14,15-dihydroxyeicosatrienoic acid
19(20)-EpDPE: 19,20-epoxydocosapentaenoic acid
19-20-DiHDoPE: 19,20-dihydroxydocosapentaenoic acid
LTB4: leukotriene B4
MaR1(n-3-DPA): maresin-1, derived from omega-3 DPA
PGE2: prostaglandin E2
RvD6: resolvin D6
TxB2: thromboxane B2
m/z: mass-to-charge ratio, given in Daltons (Da)
Rel. Int.: relative intensity or abundance of molecular ion fragments, given in percentage (%)
-EPI: negative enhanced product ion scan
CE: collision energy
CES: collision energy spread
FT: fourier transform
cps: counts per second
Sharing/access Information
Licenses/restrictions placed on the data: None
Links to publications that cite or use the data: https://doi.org/10.3389/fimmu.2023.1274147
Links to other publicly accessible locations of the data: None
Links/relationships to ancillary data sets: None
Was data derived from another source? No
If yes, list source(s):
Recommended citation for this dataset: doi: 10.3389/fimmu.2023.1274147
CC0 license waiver: The uploaded supplemental files are compatible with the CC0 license waiver required by Dryad for publication and are not included within the related manuscript.
Experimental design
Fetal liver-derived alveolar-like macrophages (FLAMs) were seeded in 6-well plates at a density of 4.50×105 cells/well in complete FLAM medium (RPMI 1640, 10% fetal bovine serum, 1% penicillin-streptomycin, 30 ng/ml GM-CSF, 20 ng/ml TGF-β). Cells were incubated overnight to achieve 70-90% confluency before beginning treatments. The next day, cells washed once with sterile PBS, fresh complete FLAM medium containing either 25 µM ethanolic DHA or ethanol vehicle (VEH) added, then cells incubated for 24 h. Following DHA or VEH treatment, cells were washed once with sterile PBS, treated with either 20 ng/ml lipopolysaccharide (LPS) or VEH in DPBS+/+ (DPBS containing calcium and magnesium) for 2 h, then exposed to 12.5 µg/cm2 crystalline silica (cSiO2) or VEH for 1.5 or 4 h. Cell culture supernatants and cells were pooled together and collected at t = 2 h (after 2 h LPS priming), 3.5 h (after 1.5 h cSiO2 exposure), and 6 h (after 4 h cSiO2 exposure). LPS and cSiO2 exposures were done in DPBS+/+ to minimize interference from fatty acids present in cell culture medium during oxylipin analyses.
Measurement of intracellular and extracellular oxylipins
Sample preparation
Following treatments, ice-cold methanol was added to each well, resulting in a final sample volume of 3 ml (1 ml cell culture supernatant + 2 ml methanol). To each sample, 60 µl of antioxidant cocktail (0.2 mg/ml butylated hydroxytoluene, 0.2 mg/ml triphenylphosphine, 0.6 mg/ml EDTA) was added to achieve a total cocktail concentration of 5% (v/v). Cells and supernatants within each well were pooled together, then samples were frozen at -80 °C until liquid chromatography-mass spectrometry (LC-MS) analysis.
Liquid chromatography-mass spectrometry (LC-MS) analysis
Targeted LC-MS lipidomics for 156 lipid metabolites was conducted at the Lipidomics Core Facility at Wayne State University. Briefly, 100 µl aliquots of cellular samples were thawed and spiked with a cocktail of deuterated internal standards (5 ng each of PGE1-d4, RvD2-d5, LTB4-d4, and 15[S]-HETE-d8; Cayman Chemical, Ann Arbor, MI) for quantification of oxylipins and recovery. Then, fatty acyl lipid metabolites were extracted by using C18 extraction columns that were washed with 15% (v/v) methanol and subsequently hexane, dried in a vacuum, eluted with methanol containing 0.1% (v/v) formic acid, dried under nitrogen gas, and dissolved in a 1:1 mixture of methanol:25 mM aqueous ammonium acetate. Extracted fatty acyl metabolites were subjected to high-performance liquid chromatography (HPLC) using a Luna C18 (3 µm, 2.1×150 mm) column connected to a Prominence XR system (Shimadzu, Somerset, NJ) then analyzed with a QTrap5500 mass spectrometer (AB Sciex, Singapore) set to negative ion mode. Analyst 1.6 software (AB Sciex) and MultiQuant software (AB Sciex) were used to collect and quantify the data in units of ng, respectively.
Data analysis and statistics
For oxylipin data, MetaboAnalyst Version 5.0 (Xia Lab, Quebec, Canada, www.metaboanalyst.ca/) were used to conduct statistical analyses. First, raw ng values were converted to corresponding pmol values in Microsoft Excel. Then, in MetaboAnalyst, the one factor statistical analysis module was chosen, and data were uploaded as a comma separated values (.csv) file with samples in unpaired columns and features (i.e., metabolites) in rows. Features with >70% missing data were removed from the dataset, and remaining missing values were estimated by replacing with the corresponding limits of detection (LODs; 1/5 of the minimum positive value of each variable). After the data was cleaned, the data was normalized by auto scaling only, then the data editor option was used to select experimental groups of interest to compare. For comparisons between experimental groups, one-way analysis of variance (ANOVA) (FDR = 0.05) followed by Tukey’s honestly significant difference (HSD) post-hoc test was used, with FDR q < 0.05 considered statistically significant.
Applications needed: Microsoft Excel, MetaboAnalyst Version 5.0 (Xia Lab, Quebec, Canada, www.metaboanalyst.ca/).