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Zhu C, Yao M. Real-Time Monitoring of Air Pollution Health Impacts Using Breath-Borne Gaseous Biomarkers from Rats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4522-4534. [PMID: 38411076 DOI: 10.1021/acs.est.3c08629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Offline techniques are adopted for studying air pollution health impacts, thus failing to provide in situ observations. Here, we have demonstrated their real-time monitoring by online analyzing an array of gaseous biomarkers from rats' exhaled breath using an integrated exhaled breath array sensor (IEBAS) developed. The biomarkers include total volatile organic compounds (TVOC), CO2, CO, NO, H2S, H2O2, O2, and NH3. Specific breath-borne VOCs were also analyzed by a gas chromatography-ion mobility spectrometer (GC-IMS). After real-life ambient air pollution exposures (2 h), the pollution levels of PM2.5 and O3 were both found to significantly affect the relative levels of multiple gaseous biomarkers in rats' breath. Eleven biomarkers, especially NO, H2S, and 1-propanol, were detected as significantly correlated with PM2.5 concentration, while heptanal was shown to be significantly correlated with O3. Likewise, significant changes were also detected in multiple breath-borne biomarkers from rats under lab-controlled O3 exposures with levels of 150, 300, and 1000 μg/m3 (2 h), compared to synthetic air exposure. Importantly, heptanal was experimentally confirmed as a reliable biomarker for O3 exposure, with a notable dose-response relationship. In contrast, conventional biomarkers of inflammation and oxidative stress in rat sera exhibited insignificant differences after the 2 h exposures. The results imply that breath-borne gaseous biomarkers can serve as an early and sensitive indicator for ambient pollutant exposure. This work pioneered a new research paradigm for online monitoring of air pollution health impacts while obtaining important candidate biomarker information for PM2.5 and O3 exposures.
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Affiliation(s)
- Chenyu Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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2
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Bhattacharya S, Myers JA, Baker C, Guo M, Danopoulos S, Myers JR, Bandyopadhyay G, Romas ST, Huyck HL, Misra RS, Dutra J, Holden-Wiltse J, McDavid AN, Ashton JM, Al Alam D, Potter SS, Whitsett JA, Xu Y, Pryhuber GS, Mariani TJ. Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells. Genes (Basel) 2024; 15:298. [PMID: 38540357 PMCID: PMC10970229 DOI: 10.3390/genes15030298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/01/2024] Open
Abstract
While animal model studies have extensively defined the mechanisms controlling cell diversity in the developing mammalian lung, there exists a significant knowledge gap with regards to late-stage human lung development. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. Transcriptomic profiling at the single-cell level created a cellular atlas of newborn human lungs. Frozen single-cell isolates obtained from two newborn human lungs from the LungMAP Human Tissue Core Biorepository, were captured, and library preparation was completed on the Chromium 10X system. Data was analyzed in Seurat, and cellular annotation was performed using the ToppGene functional analysis tool. Transcriptional interrogation of 5500 newborn human lung cells identified distinct clusters representing multiple populations of epithelial, endothelial, fibroblasts, pericytes, smooth muscle, immune cells and their gene signatures. Computational integration of data from newborn human cells and with 32,000 cells from postnatal days 1 through 10 mouse lungs generated by the LungMAP Cincinnati Research Center facilitated the identification of distinct cellular lineages among all the major cell types. Integration of the newborn human and mouse cellular transcriptomes also demonstrated cell type-specific differences in maturation states of newborn human lung cells. Specifically, newborn human lung matrix fibroblasts could be separated into those representative of younger cells (n = 393), or older cells (n = 158). Cells with each molecular profile were spatially resolved within newborn human lung tissue. This is the first comprehensive molecular map of the cellular landscape of neonatal human lung, including biomarkers for cells at distinct states of maturity.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jacquelyn A. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Cameron Baker
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Minzhe Guo
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Soula Danopoulos
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - Jason R. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Stephen T. Romas
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Heidie L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Ravi S. Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jennifer Dutra
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
| | - Jeanne Holden-Wiltse
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Andrew N. McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - John M. Ashton
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - S. Steven Potter
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Jeffrey A. Whitsett
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Yan Xu
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Thomas J. Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
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3
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Dylag AM, Misra RS, Bandyopadhyay G, Poole C, Huyck HL, Jehrio MG, Haak J, Deutsch GH, Dvorak C, Olson HM, Paurus V, Katzman PJ, Woo J, Purkerson JM, Adkins JN, Mariani TJ, Clair GC, Pryhuber GS. New insights into the natural history of bronchopulmonary dysplasia from proteomics and multiplexed immunohistochemistry. Am J Physiol Lung Cell Mol Physiol 2023; 325:L419-L433. [PMID: 37489262 PMCID: PMC10642360 DOI: 10.1152/ajplung.00130.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a disease of prematurity related to the arrest of normal lung development. The objective of this study was to better understand how proteome modulation and cell-type shifts are noted in BPD pathology. Pediatric human donors aged 1-3 yr were classified based on history of prematurity and histopathology consistent with "healed" BPD (hBPD, n = 3) and "established" BPD (eBPD, n = 3) compared with respective full-term born (n = 6) age-matched term controls. Proteins were quantified by tandem mass spectroscopy with selected Western blot validations. Multiplexed immunofluorescence (MxIF) microscopy was performed on lung sections to enumerate cell types. Protein abundances and MxIF cell frequencies were compared among groups using ANOVA. Cell type and ontology enrichment were performed using an in-house tool and/or EnrichR. Proteomics detected 5,746 unique proteins, 186 upregulated and 534 downregulated, in eBPD versus control with fewer proteins differentially abundant in hBPD as compared with age-matched term controls. Cell-type enrichment suggested a loss of alveolar type I, alveolar type II, endothelial/capillary, and lymphatics, and an increase in smooth muscle and fibroblasts consistent with MxIF. Histochemistry and Western analysis also supported predictions of upregulated ferroptosis in eBPD versus control. Finally, several extracellular matrix components mapping to angiogenesis signaling pathways were altered in eBPD. Despite clear parsing by protein abundance, comparative MxIF analysis confirms phenotypic variability in BPD. This work provides the first demonstration of tandem mass spectrometry and multiplexed molecular analysis of human lung tissue for critical elucidation of BPD trajectory-defining factors into early childhood.NEW & NOTEWORTHY We provide new insights into the natural history of bronchopulmonary dysplasia in donor human lungs after the neonatal intensive care unit hospitalization. This study provides new insights into how the proteome and histopathology of BPD changes in early childhood, uncovering novel pathways for future study.
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Affiliation(s)
- Andrew M Dylag
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Ravi S Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Cory Poole
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Heidie L Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Matthew G Jehrio
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Jeannie Haak
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Gail H Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington, University of Washington, Seattle, Washington, United States
| | - Carly Dvorak
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Heather M Olson
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Vanessa Paurus
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Philip J Katzman
- Department of Pathology, University of Rochester Medical Center, Rochester, New York, United States
| | - Jongmin Woo
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Jeffrey M Purkerson
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Joshua N Adkins
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Geremy C Clair
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Gloria S Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
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4
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Camunas-Alberca SM, Moran-Garrido M, Sáiz J, Gil-de-la-Fuente A, Barbas C, Gradillas A. Integrating the potential of ion mobility spectrometry-mass spectrometry in the separation and structural characterisation of lipid isomers. Front Mol Biosci 2023; 10:1112521. [PMID: 37006618 PMCID: PMC10060977 DOI: 10.3389/fmolb.2023.1112521] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
It is increasingly evident that a more detailed molecular structure analysis of isomeric lipids is critical to better understand their roles in biological processes. The occurrence of isomeric interference complicates conventional tandem mass spectrometry (MS/MS)-based determination, necessitating the development of more specialised methodologies to separate lipid isomers. The present review examines and discusses recent lipidomic studies based on ion mobility spectrometry combined with mass spectrometry (IMS-MS). Selected examples of the separation and elucidation of structural and stereoisomers of lipids are described based on their ion mobility behaviour. These include fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. Recent approaches for specific applications to improve isomeric lipid structural information using direct infusion, coupling imaging, or liquid chromatographic separation workflows prior to IMS-MS are also discussed, including: 1) strategies to improve ion mobility shifts; 2) advanced tandem MS methods based on activation of lipid ions with electrons or photons, or gas-phase ion-molecule reactions; and 3) the use of chemical derivatisation techniques for lipid characterisation.
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Affiliation(s)
- Sandra M. Camunas-Alberca
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Maria Moran-Garrido
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Jorge Sáiz
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Alberto Gil-de-la-Fuente
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- Departamento de Tecnologías de la Información, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Ana Gradillas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- *Correspondence: Ana Gradillas,
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5
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The Landscape of Lipid Metabolism in Lung Cancer: The Role of Structural Profiling. J Clin Med 2023; 12:jcm12051736. [PMID: 36902523 PMCID: PMC10002589 DOI: 10.3390/jcm12051736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
The aim of this study was to explore the relationship between lipids with different structural features and lung cancer (LC) risk and identify prospective biomarkers of LC. Univariate and multivariate analysis methods were used to screen for differential lipids, and two machine learning methods were used to define combined lipid biomarkers. A lipid score (LS) based on lipid biomarkers was calculated, and a mediation analysis was performed. A total of 605 lipid species spanning 20 individual lipid classes were identified in the plasma lipidome. Higher carbon atoms with dihydroceramide (DCER), phosphatidylethanolamine (PE), and phosphoinositols (PI) presented a significant negative correlation with LC. Point estimates revealed the inverse associated with LC for the n-3 PUFA score. Ten lipids were identified as markers with an area under the curve (AUC) value of 0.947 (95%, CI: 0.879-0.989). In this study, we summarized the potential relationship between lipid molecules with different structural features and LC risk, identified a panel of LC biomarkers, and demonstrated that the n-3 PUFA of the acyl chain of lipids was a protective factor for LC.
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6
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Shakya S, Pyles KD, Albert CJ, Patel RP, McCommis KS, Ford DA. Myeloperoxidase-derived hypochlorous acid targets human airway epithelial plasmalogens liberating protein modifying electrophilic 2-chlorofatty aldehydes. Redox Biol 2023; 59:102557. [PMID: 36508858 PMCID: PMC9763693 DOI: 10.1016/j.redox.2022.102557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Neutrophil and airway epithelial cell interactions are critical in the inflammatory response to viral infections including respiratory syncytial virus, Sendai virus, and SARS-CoV-2. Airway epithelial cell dysfunction during viral infections is likely mediated by the interaction of virus and recruited neutrophils at the airway epithelial barrier. Neutrophils are key early responders to viral infection. Neutrophil myeloperoxidase catalyzes the conversion of hydrogen peroxide to hypochlorous acid (HOCl). Previous studies have shown HOCl targets host neutrophil and endothelial cell plasmalogen lipids, resulting in the production of the chlorinated lipid, 2-chlorofatty aldehyde (2-ClFALD). We have previously shown that the oxidation product of 2-ClFALD, 2-chlorofatty acid (2-ClFA) is present in bronchoalveolar lavage fluid of Sendai virus-infected mice, which likely results from the attack of the epithelial plasmalogen by neutrophil-derived HOCl. Herein, we demonstrate small airway epithelial cells contain plasmalogens enriched with oleic acid at the sn-2 position unlike endothelial cells which contain arachidonic acid enrichment at the sn-2 position of plasmalogen. We also show neutrophil-derived HOCl targets epithelial cell plasmalogens to produce 2-ClFALD. Further, proteomics and over-representation analysis using the ω-alkyne analog of the 2-ClFALD molecular species, 2-chlorohexadecanal (2-ClHDyA) showed cell adhesion molecule binding and cell-cell junction enriched categories similar to that observed previously in endothelial cells. However, in contrast to endothelial cells, proteins in distinct metabolic pathways were enriched with 2-ClFALD modification, particularly pyruvate metabolism was enriched in epithelial cells and mitochondrial pyruvate respiration was reduced. Collectively, these studies demonstrate, for the first time, a novel plasmalogen molecular species distribution in airway epithelial cells that are targeted by myeloperoxidase-derived hypochlorous acid resulting in electrophilic 2-ClFALD, which potentially modifies epithelial physiology by modifying proteins.
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Affiliation(s)
- Shubha Shakya
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA; Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Kelly D Pyles
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA; Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Carolyn J Albert
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA; Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Rakesh P Patel
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Kyle S McCommis
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA; Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - David A Ford
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA; Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
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7
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Gong Z, Li Q, Shi J, Liu ET, Shultz LD, Ren G. Lipid-laden lung mesenchymal cells foster breast cancer metastasis via metabolic reprogramming of tumor cells and natural killer cells. Cell Metab 2022; 34:1960-1976.e9. [PMID: 36476935 PMCID: PMC9819197 DOI: 10.1016/j.cmet.2022.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/21/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
While the distant organ environment is known to support metastasis of primary tumors, its metabolic roles in this process remain underdetermined. Here, in breast cancer models, we found lung-resident mesenchymal cells (MCs) accumulating neutral lipids at the pre-metastatic stage. This was partially mediated by interleukin-1β (IL-1β)-induced hypoxia-inducible lipid droplet-associated (HILPDA) that subsequently represses adipose triglyceride lipase (ATGL) activity in lung MCs. MC-specific ablation of the ATGL or HILPDA genes in mice reinforced and reduced lung metastasis of breast cancer respectively, suggesting a metastasis-promoting effect of lipid-laden MCs. Mechanistically, lipid-laden MCs transported their lipids to tumor cells and natural killer (NK) cells via exosome-like vesicles, leading to heightened tumor cell survival and proliferation and NK cell dysfunction. Blockage of IL-1β, which was effective singly, improved the efficacy of adoptive NK cell immunotherapy in mitigating lung metastasis. Collectively, lung MCs metabolically regulate tumor cells and anti-tumor immunity to facilitate breast cancer lung metastasis.
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Affiliation(s)
- Zheng Gong
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Qing Li
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Jiayuan Shi
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Guangwen Ren
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Tufts University School of Medicine, Boston, MA 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA.
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8
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Lukowski JK, Olson H, Velickovic M, Wang J, Kyle JE, Kim YM, Williams SM, Zhu Y, Huyck HL, McGraw MD, Poole C, Rogers L, Misra R, Alexandrov T, Ansong C, Pryhuber GS, Clair G, Adkins JN, Carson JP, Anderton CR. An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. Front Mol Biosci 2022; 9:1022775. [PMID: 36465564 PMCID: PMC9709465 DOI: 10.3389/fmolb.2022.1022775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/02/2022] [Indexed: 04/23/2024] Open
Abstract
Human disease states are biomolecularly multifaceted and can span across phenotypic states, therefore it is important to understand diseases on all levels, across cell types, and within and across microanatomical tissue compartments. To obtain an accurate and representative view of the molecular landscape within human lungs, this fragile tissue must be inflated and embedded to maintain spatial fidelity of the location of molecules and minimize molecular degradation for molecular imaging experiments. Here, we evaluated agarose inflation and carboxymethyl cellulose embedding media and determined effective tissue preparation protocols for performing bulk and spatial mass spectrometry-based omics measurements. Mass spectrometry imaging methods were optimized to boost the number of annotatable molecules in agarose inflated lung samples. This optimized protocol permitted the observation of unique lipid distributions within several airway regions in the lung tissue block. Laser capture microdissection of these airway regions followed by high-resolution proteomic analysis allowed us to begin linking the lipidome with the proteome in a spatially resolved manner, where we observed proteins with high abundance specifically localized to the airway regions. We also compared our mass spectrometry results to lung tissue samples preserved using two other inflation/embedding media, but we identified several pitfalls with the sample preparation steps using this preservation method. Overall, we demonstrated the versatility of the inflation method, and we can start to reveal how the metabolome, lipidome, and proteome are connected spatially in human lungs and across disease states through a variety of different experiments.
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Affiliation(s)
| | - Heather Olson
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Marija Velickovic
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Juan Wang
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Jennifer E. Kyle
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Young-Mo Kim
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Sarah M. Williams
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Ying Zhu
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Heidi L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Matthew D. McGraw
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Cory Poole
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Lisa Rogers
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Ravi Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Charles Ansong
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Geremy Clair
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Joshua N. Adkins
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - James P. Carson
- Texas Advanced Computing Center (TACC), University of Texas at Austin, Austin, TX, United States
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9
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Bartolacci C, Andreani C, Vale G, Berto S, Melegari M, Crouch AC, Baluya DL, Kemble G, Hodges K, Starrett J, Politi K, Starnes SL, Lorenzini D, Raso MG, Solis Soto LM, Behrens C, Kadara H, Gao B, Wistuba II, Minna JD, McDonald JG, Scaglioni PP. Targeting de novo lipogenesis and the Lands cycle induces ferroptosis in KRAS-mutant lung cancer. Nat Commun 2022; 13:4327. [PMID: 35882862 PMCID: PMC9325712 DOI: 10.1038/s41467-022-31963-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/06/2022] [Indexed: 12/22/2022] Open
Abstract
Mutant KRAS (KM), the most common oncogene in lung cancer (LC), regulates fatty acid (FA) metabolism. However, the role of FA in LC tumorigenesis is still not sufficiently characterized. Here, we show that KMLC has a specific lipid profile, with high triacylglycerides and phosphatidylcholines (PC). We demonstrate that FASN, the rate-limiting enzyme in FA synthesis, while being dispensable in EGFR-mutant or wild-type KRAS LC, is required for the viability of KMLC cells. Integrating lipidomic, transcriptomic and functional analyses, we demonstrate that FASN provides saturated and monounsaturated FA to the Lands cycle, the process remodeling oxidized phospholipids, such as PC. Accordingly, blocking either FASN or the Lands cycle in KMLC, promotes ferroptosis, a reactive oxygen species (ROS)- and iron-dependent cell death, characterized by the intracellular accumulation of oxidation-prone PC. Our work indicates that KM dictates a dependency on newly synthesized FA to escape ferroptosis, establishing a targetable vulnerability in KMLC.
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Affiliation(s)
- Caterina Bartolacci
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Cristina Andreani
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Gonçalo Vale
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Stefano Berto
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Margherita Melegari
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Anna Colleen Crouch
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dodge L Baluya
- Tissue Imaging and Proteomics Laboratory, Washington State University, Pullman, WA, 99164, USA
| | | | - Kurt Hodges
- Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | | | - Katerina Politi
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Sandra L Starnes
- Department of Surgery, Division of Thoracic Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Daniele Lorenzini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, via Venezian 1, 20133, Milan, Italy
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic H&N Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boning Gao
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Pier Paolo Scaglioni
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA.
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Oyeniyi EA, Sorgi CA, Gardinassi LG, Azevedo LF, Adeyemi JA, Omotoso OT, Faccioli LH, Greggi Antunes LM, Barbosa F. Phospholipids modifications, genotoxic and anticholinesterase effects of pepper fruit (Dennettia tripetala G. Baker) extract in Swiss mice. Food Chem Toxicol 2022; 165:113189. [PMID: 35636641 DOI: 10.1016/j.fct.2022.113189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022]
Abstract
The toxicity of D. tripetala fruit extract to mice was investigated using data obtained from lipidomic analyses, comet and Acetylcholinesterase (AChE) assays. Mice (n = 8) were exposed for 30 days via oral gavage to vehicle (5% Tween 80) (negative control), D. tripetala extract (100, 200 and 400 mg/kg) and 40 mg/kg methyl methanesulfonate (MMS) (positive control). The profile of compounds in the fruit extract was analyzed using gas chromatography-mass spectrometry. Out of the total of 32 compounds identified, considerable amount of established insecticidal compounds such as 2-phenylnitroethane, cis-vaccenic acid, linalool and linoleic acid were detected. Fruit extract did not induce DNA damage relative to negative control. Percentage gain in body weights differed significantly across the four weeks. Significantly highest and lowest brain AChE activity was observed in animals exposed to 200 and 400 mg/kg D. tripetala, respectively. Fruit extract modulated the brain phospholipid profile due to significant fold changes of 48 lipid species out of the total of 280 lipid species. High number of differentially expressed phosphatidylcholine (PC) species and significant levels of phosphatidylethanolamine (PE) at 400 mg/kg suggests that activation of inflammation and methylation pathways are the most plausible mechanisms of D. tripetala toxicity to mouse brain tissue.
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Affiliation(s)
- Emmanuel Ayobami Oyeniyi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil; Department of Biology, School of Life Sciences, Federal University of Technology, P.M.B. 704, Akure, Ondo State, Nigeria; Department of Zoology and Environmental Biology, Faculty of Sciences, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria.
| | - Carlos Arterio Sorgi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Luiz Gustavo Gardinassi
- Department of Biosciences and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lara Ferreira Azevedo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Joseph Adewuyi Adeyemi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil; Department of Biology, School of Life Sciences, Federal University of Technology, P.M.B. 704, Akure, Ondo State, Nigeria
| | - Olumuyiwa Temitope Omotoso
- Department of Zoology and Environmental Biology, Faculty of Sciences, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria
| | - Lucia Helena Faccioli
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Lusania Maria Greggi Antunes
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Fernando Barbosa
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
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11
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Lipid Peroxidation Produces a Diverse Mixture of Saturated and Unsaturated Aldehydes in Exhaled Breath That Can Serve as Biomarkers of Lung Cancer-A Review. Metabolites 2022; 12:metabo12060561. [PMID: 35736492 PMCID: PMC9229171 DOI: 10.3390/metabo12060561] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 02/06/2023] Open
Abstract
The peroxidation of unsaturated fatty acids is a widely recognized metabolic process that creates a complex mixture of volatile organic compounds including aldehydes. Elevated levels of reactive oxygen species in cancer cells promote random lipid peroxidation, which leads to a variety of aldehydes. In the case of lung cancer, many of these volatile aldehydes are exhaled and are of interest as potential markers of the disease. Relevant studies reporting aldehydes in the exhaled breath of lung cancer patients were collected for this review by searching the PubMed and SciFindern databases until 25 May 2022. Information on breath test results, including the biomarker collection, preconcentration, and quantification methods, was extracted and tabulated. Overall, 44 studies were included spanning a period of 34 years. The data show that, as a class, aldehydes are significantly elevated in the breath of lung cancer patients at all stages of the disease relative to healthy control subjects. The type of aldehyde detected and/or deemed to be a biomarker is highly dependent on the method of exhaled breath sampling and analysis. Unsaturated aldehydes, detected primarily when derivatized during preconcentration, are underrepresented as biomarkers given that they are also likely products of lipid peroxidation. Pentanal, hexanal, and heptanal were the most reported aldehydes in studies of exhaled breath from lung cancer patients.
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12
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Castañé H, Iftimie S, Baiges-Gaya G, Rodríguez-Tomàs E, Jiménez-Franco A, López-Azcona AF, Garrido P, Castro A, Camps J, Joven J. Machine learning and semi-targeted lipidomics identify distinct serum lipid signatures in hospitalized COVID-19-positive and COVID-19-negative patients. Metabolism 2022; 131:155197. [PMID: 35381232 PMCID: PMC8976580 DOI: 10.1016/j.metabol.2022.155197] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/11/2022] [Accepted: 03/28/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Lipids are involved in the interaction between viral infection and the host metabolic and immunological responses. Several studies comparing the lipidome of COVID-19-positive hospitalized patients vs. healthy subjects have already been reported. It is largely unknown, however, whether these differences are specific to this disease. The present study compared the lipidomic signature of hospitalized COVID-19-positive patients with that of healthy subjects, as well as with COVID-19-negative patients hospitalized for other infectious/inflammatory diseases. METHODS We analyzed the lipidomic signature of 126 COVID-19-positive patients, 45 COVID-19-negative patients hospitalized with other infectious/inflammatory diseases and 50 healthy volunteers. A semi-targeted lipidomics analysis was performed using liquid chromatography coupled to mass spectrometry. Two-hundred and eighty-three lipid species were identified and quantified. Results were interpreted by machine learning tools. RESULTS We identified acylcarnitines, lysophosphatidylethanolamines, arachidonic acid and oxylipins as the most altered species in COVID-19-positive patients compared to healthy volunteers. However, we found similar alterations in COVID-19-negative patients who had other causes of inflammation. Conversely, lysophosphatidylcholine 22:6-sn2, phosphatidylcholine 36:1 and secondary bile acids were the parameters that had the greatest capacity to discriminate between COVID-19-positive and COVID-19-negative patients. CONCLUSION This study shows that COVID-19 infection shares many lipid alterations with other infectious/inflammatory diseases, and which differentiate them from the healthy population. The most notable alterations were observed in oxylipins, while alterations in bile acids and glycerophospholipis best distinguished between COVID-19-positive and COVID-19-negative patients. Our results highlight the value of integrating lipidomics with machine learning algorithms to explore the pathophysiology of COVID-19 and, consequently, improve clinical decision making.
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Affiliation(s)
- Helena Castañé
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Simona Iftimie
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Gerard Baiges-Gaya
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Elisabet Rodríguez-Tomàs
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Andrea Jiménez-Franco
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Ana Felisa López-Azcona
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Pedro Garrido
- Intensive Care Unit, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Antoni Castro
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain.
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
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13
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Sun X, Perl AK, Li R, Bell SM, Sajti E, Kalinichenko VV, Kalin TV, Misra RS, Deshmukh H, Clair G, Kyle J, Crotty Alexander LE, Masso-Silva JA, Kitzmiller JA, Wikenheiser-Brokamp KA, Deutsch G, Guo M, Du Y, Morley MP, Valdez MJ, Yu HV, Jin K, Bardes EE, Zepp JA, Neithamer T, Basil MC, Zacharias WJ, Verheyden J, Young R, Bandyopadhyay G, Lin S, Ansong C, Adkins J, Salomonis N, Aronow BJ, Xu Y, Pryhuber G, Whitsett J, Morrisey EE. A census of the lung: CellCards from LungMAP. Dev Cell 2022; 57:112-145.e2. [PMID: 34936882 PMCID: PMC9202574 DOI: 10.1016/j.devcel.2021.11.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/19/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing and genetic lineage tracing have revealed novel cell types and enriched functional properties of existing cell types in lung. The time has come to take a new census. Initiated by members of the NHLBI-funded LungMAP Consortium and aided by experts in the lung biology community, we synthesized current data into a comprehensive and practical cellular census of the lung. Identities of cell types in the normal lung are captured in individual cell cards with delineation of function, markers, developmental lineages, heterogeneity, regenerative potential, disease links, and key experimental tools. This publication will serve as the starting point of a live, up-to-date guide for lung research at https://www.lungmap.net/cell-cards/. We hope that Lung CellCards will promote the community-wide effort to establish, maintain, and restore respiratory health.
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Affiliation(s)
- Xin Sun
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Anne-Karina Perl
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Rongbo Li
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sheila M Bell
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Eniko Sajti
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vladimir V Kalinichenko
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA; Center for Lung Regenerative Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Tanya V Kalin
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Ravi S Misra
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Hitesh Deshmukh
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Geremy Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer Kyle
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Laura E Crotty Alexander
- Deparment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jorge A Masso-Silva
- Deparment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph A Kitzmiller
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Kathryn A Wikenheiser-Brokamp
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Gail Deutsch
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA; Department of Laboratories, Seattle Children's Hospital, OC.8.720, 4800 Sand Point Way Northeast, Seattle, WA 98105, USA
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Yina Du
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Michael P Morley
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael J Valdez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haoze V Yu
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kang Jin
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eric E Bardes
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jarod A Zepp
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Terren Neithamer
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria C Basil
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William J Zacharias
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Internal Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Jamie Verheyden
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Randee Young
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Gautam Bandyopadhyay
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sara Lin
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Ansong
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Gloria Pryhuber
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeff Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Edward E Morrisey
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Chorioamnionitis alters lung surfactant lipidome in newborns with respiratory distress syndrome. Pediatr Res 2021; 90:1039-1043. [PMID: 33531681 DOI: 10.1038/s41390-021-01371-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/29/2020] [Accepted: 01/01/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND Chorioamnionitis is associated with preterm delivery and morbidities; its role in lung disease is controversial. The aim of this study is to assess the effect of chorioamnionitis on metabolite and lipid profiles of epithelial lining fluid in preterm newborns with respiratory distress syndrome (RDS). METHODS The study involved 30 newborns with RDS, born from mothers with or without histological chorioamnionitis (HCA): HCA+, N = 10; HCA-, N = 20. Patients had a gestational age ≤30 weeks; the groups were matched for age and birth weights. Tracheal aspirates were collected within 24 h after birth and analyzed using liquid chromatography/mass spectrometry-based untargeted lipidomics. RESULTS According to Mann-Whitney U tests, 570 metabolite features had statistically significantly higher or lower concentrations (p < 0.05) in tracheal aspirates of HCA+ compared to HCA-, and 241 metabolite features were putatively annotated and classified. The most relevant changes involved higher levels of glycerophospholipids (fold change 2.42-17.69) and sphingolipids, with lower concentration of all annotated sphingomyelins in HCA+ (fold change 0.01-0.50). CONCLUSIONS Untargeted lipidomics of tracheal aspirates suggested the production of lipid mediators in the context of an ongoing inflammatory status in HCA+ babies. However, the effect of chorioamnionitis on epithelial lining fluid composition deserves further investigations on a larger group of infants. IMPACT Our lipidomics investigation on tracheal aspirates of preterm newborns at birth suggested that exposure to maternal histological chorioamnionitis may cause changes in epithelial lining fluid composition. This is the first description of epithelial lining fluid lipidomic profiles in preterm infants with and without exposition to chorioamnionitis. These results could provide novel link between placental membrane inflammation and newborns' respiratory outcome.
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15
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Szlenk CT, Gc JB, Natesan S. Membrane-facilitated receptor access and binding mechanisms of long-acting β2-adrenergic receptor (β2-AR) agonists. Mol Pharmacol 2021; 100:406-427. [PMID: 34334369 DOI: 10.1124/molpharm.121.000285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/20/2021] [Indexed: 11/22/2022] Open
Abstract
The drugs salmeterol, formoterol, and salbutamol constitute the frontline treatment for asthma and other chronic pulmonary diseases. These drugs activate the β2-adrenergic receptors (β2-AR), a class A G-protein-coupled receptor (GPCR) and differ significantly in their clinical onset and duration of actions. According to the "microkinetic model," the long duration of action of salmeterol and formoterol compared to salbutamol were attributed, at least in part, to their high lipophilicity and increased local concentrations in the membrane near the receptor. However, the structural and molecular bases of how the lipophilic drugs reach the binding site of the receptor from the surrounding membrane remain unknown. Using a variety of classical and enhanced molecular dynamics simulation techniques, we investigated the membrane partitioning characteristics, binding, and unbinding mechanisms of the ligands. The obtained results offer remarkable insight into the functional role of membrane lipids in the ligand association process. Strikingly, salmeterol entered the binding site from the bilayer through transmembrane helices 1 and 7. The entry was preceded by membrane-facilitated rearrangement and presentation of its phenyl-alkoxy-alkyl tail as a passkey to an access route gated by F193, a residue known critical for salmeterol's affinity. Formoterol's access is through the aqueous path shared by other β2-AR agents. We observed a novel secondary path for salbutamol that is distinct from its primary route. Our study offers a mechanistic description for the membrane-facilitated access and binding of ligands to β2-AR and establishes a groundwork for recognizing membrane lipids as an integral component in the molecular recognition process. Significance Statement The cell membrane's functional role behind the duration of action of long-acting β2-adrenergic receptor (β2-AR) agonists such as salmeterol has been a subject of debate for a long time. We investigated the binding and unbinding mechanisms of the three commonly used β2-AR agonists, salmeterol, formoterol, and salbutamol, using advanced simulation techniques. The obtained results offer unprecedented insights into the active role of membrane lipids in facilitating access and binding of the ligands, affecting the molecular recognition process and their pharmacology.
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Affiliation(s)
| | | | - Senthil Natesan
- Pharmaceutical Sciences, Washington State University, United States
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16
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Majewska M, Khan F, Pieta IS, Wróblewska A, Szmigielski R, Pieta P. Toxicity of selected airborne nitrophenols on eukaryotic cell membrane models. CHEMOSPHERE 2021; 266:128996. [PMID: 33288286 DOI: 10.1016/j.chemosphere.2020.128996] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/26/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Nitroaromatics belong to the group of toxic components of aerosol particles and atmospheric hydrometeors that enter the atmosphere through biomass burning and fuel combustion. In the present work, we report on the cytotoxic effects of a 2-, 3- and 4-nitrophenol mixture on a model eukaryotic-like cell membrane and compared it with in vitro cellular models BEAS-2B (immortalized bronchial epithelial cells) and A549 (cancerous alveolar epithelial cells). A selected model biomembrane comprised of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine), DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) was studied. The electrochemical-based method, combined with atomic force microscopy (AFM) and phase-contrast microscopy imaging, allowed to get insights into the mechanism of cellular function disruption caused by airborne nitrophenols. The efficacy of the method is supported by the data obtained from in vitro experiments performed on cell models. The nitrophenol mixture exhibited cytotoxic effects at concentrations above 100 μg mL-1, as demonstrated by phase-contrast microscopy in real lung cell lines. Electrochemical impedance spectroscopy (EIS) revealed the formation of membrane defects at a nitrophenol concentration of 200 μg mL-1. AFM imaging confirmed the model membrane disintegration and phospholipids rearrangement in the presence of nitrophenols. These observations indicate that particle-bound nitrophenols induce substantial changes in cell membranes and make them more permeable to aerosol, resulting in major cellular damage in the lungs when inhaled. The study provides initial evidence of cellular membrane damage induced by three important nitrated phenols present in the environment.
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Affiliation(s)
- Marta Majewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Faria Khan
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Izabela S Pieta
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Aleksandra Wróblewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Rafal Szmigielski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Piotr Pieta
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
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17
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Barklis E, Alfadhli A, Kyle JE, Bramer LM, Bloodsworth KJ, Barklis RL, Leier HC, Petty RM, Zelnik ID, Metz TO, Futerman AH, Tafesse FG. Ceramide synthase 2 deletion decreases the infectivity of HIV-1. J Biol Chem 2021; 296:100340. [PMID: 33515546 PMCID: PMC7949126 DOI: 10.1016/j.jbc.2021.100340] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/01/2023] Open
Abstract
The lipid composition of HIV-1 virions is enriched in sphingomyelin (SM), but the roles that SM or other sphingolipids (SLs) might play in the HIV-1 replication pathway have not been elucidated. In human cells, SL levels are regulated by ceramide synthase (CerS) enzymes that produce ceramides, which can be converted to SMs, hexosylceramides, and other SLs. In many cell types, CerS2, which catalyzes the synthesis of very long chain ceramides, is the major CerS. We have examined how CerS2 deficiency affects the assembly and infectivity of HIV-1. As expected, we observed that very long chain ceramide, hexosylceramide, and SM were reduced in CerS2 knockout cells. CerS2 deficiency did not affect HIV-1 assembly or the incorporation of the HIV-1 envelope (Env) protein into virus particles, but it reduced the infectivites of viruses produced in the CerS2-deficient cells. The reduced viral infection levels were dependent on HIV-1 Env, since HIV-1 particles that were pseudotyped with the vesicular stomatitis virus glycoprotein did not exhibit reductions in infectivity. Moreover, cell-cell fusion assays demonstrated that the functional defect of HIV-1 Env in CerS2-deficient cells was independent of other viral proteins. Overall, our results indicate that the altered lipid composition of CerS2-deficient cells specifically inhibit the HIV-1 Env receptor binding and/or fusion processes.
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Affiliation(s)
- Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA.
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Lisa M Bramer
- Computing and Analytics Division, National Security Directorate PNNL, Richland, Washington, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Hans C Leier
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - R Max Petty
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Iris D Zelnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA.
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18
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When polyphenols meet lipids: Challenges in membrane biophysics and opportunities in epithelial lipidomics. Food Chem 2020; 333:127509. [DOI: 10.1016/j.foodchem.2020.127509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/25/2020] [Accepted: 07/04/2020] [Indexed: 12/14/2022]
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19
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Odenkirk MT, Zin PPK, Ash JR, Reif DM, Fourches D, Baker ES. Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems. Analyst 2020; 145:7197-7209. [PMID: 33094747 PMCID: PMC7695036 DOI: 10.1039/d0an01638a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Since its inception, the main goal of the lipidomics field has been to characterize lipid species and their respective biological roles. However, difficulties in both full speciation and biological interpretation have rendered these objectives extremely challenging and as a result, limited our understanding of lipid mechanisms and dysregulation. While mass spectrometry-based advancements have significantly increased the ability to identify lipid species, less progress has been made surrounding biological interpretations. We have therefore developed a Structural-based Connectivity and Omic Phenotype Evaluations (SCOPE) cheminformatics toolbox to aid in these evaluations. SCOPE enables the assessment and visualization of two main lipidomic associations: structure/biological connections and metadata linkages either separately or in tandem. To assess structure and biological relationships, SCOPE utilizes key lipid structural moieties such as head group and fatty acyl composition and links them to their respective biological relationships through hierarchical clustering and grouped heatmaps. Metadata arising from phenotypic and environmental factors such as age and diet is then correlated with the lipid structures and/or biological relationships, utilizing Toxicological Prioritization Index (ToxPi) software. Here, SCOPE is demonstrated for various applications from environmental studies to clinical assessments to showcase new biological connections not previously observed with other techniques.
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Affiliation(s)
- Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
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20
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Shon JC, Lee SM, Jung JH, Wu Z, Kwon YS, Sim HJ, Seo JS. Integrated metabolomics and lipidomics reveals high accumulation of polyunsaturated lysoglycerophospholipids in human lung fibroblasts exposed to fine particulate matter. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110896. [PMID: 32622306 DOI: 10.1016/j.ecoenv.2020.110896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Exposure to fine particulate matter (PM) comprising toxic compounds arising from air pollution is a major human health concern. It is linked to increased mortality and incidence of various lung diseases. However, the mechanisms underlying the toxic effects of PM on lung fibroblasts have not been fully explored. We used targeted quantitative metabolomics and lipidomics analysis along with cytotoxicity studies to comprehensively characterize the alterations in the metabolite profiles of human lung fibroblasts (HEL 299) upon exposure to PM2.5 and PM10. This exposure at 50 μg/mL for 72 h induced an abnormally high apoptotic response via triggering intracellular reactive oxygen species (ROS) production and mitochondrial dysfunction through an imbalance between pro- and anti-apoptotic signaling pathways. The cytotoxic effects of PM2.5 were more severe than those of PM10. Metabolomics and lipidomics analyses revealed that PM exposure triggered substantial changes in the cellular metabolite profile, which involved reduced mitochondria-related metabolites such as tricarboxylic acid (TCA) cycle intermediates, amino acids, and free fatty acids as well as increased lysoglycerophospholipids (LPLs) containing polyunsaturated fatty acids. The decrease in mitochondria-related metabolites suggested that PM exposure led to reduced TCA cycle capacity and energy production. Apoptotic and inflammatory responses as well as mitochondrial dysfunction were likely to be accelerated because of excessive accumulation of LPLs, contributing to the disruption of membrane rafts and Ca2+ homeostasis and causing increased mitochondrial ROS formation. These results provide valuable insights regarding the toxic effects of PM exposure. Our study also provides a new direction for research on PM exposure-related health disorders using different cell lines.
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Affiliation(s)
- Jong Cheol Shon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Seon Min Lee
- Biological Resources Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Jung-Hoon Jung
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Zhexue Wu
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Young Sang Kwon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Hee-Jung Sim
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Jong-Su Seo
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea.
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21
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Reis A, Perez-Gregorio R, Mateus N, de Freitas V. Interactions of dietary polyphenols with epithelial lipids: advances from membrane and cell models in the study of polyphenol absorption, transport and delivery to the epithelium. Crit Rev Food Sci Nutr 2020; 61:3007-3030. [PMID: 32654502 DOI: 10.1080/10408398.2020.1791794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Currently, diet-related diseases such as diabetes, obesity, hypertension, and cardiovascular diseases account for 70% of all global deaths. To counteract the rising prevalence of non-communicable diseases governments are investing in persuasive educational campaigns toward the ingestion of fresh fruits and vegetables. The intake of dietary polyphenols abundant in Mediterranean and Nordic-type diets holds great potential as nutritional strategies in the management of diet-related diseases. However, the successful implementation of healthy nutritional strategies relies on a pleasant sensory perception in the mouth able to persuade consumers to adopt polyphenol-rich diets and on a deeper understanding on the chemical modifications, that affect not only their chemical properties but also their physical interaction with epithelial lipids and in turn their permeability, location within the lipid bilayer, toxicity and biological activity, and fate during absorption at the gastro-intestinal epithelium, transport in circulation and delivery to the endothelium. In this paper, we review the current knowledge on the interactions between polyphenols and their metabolites with membrane lipids in artificial membranes and epithelial cell models (oral, stomach, gut and endothelium) and the findings from polyphenol-lipid interactions to physiological processes such as oral taste perception, gastrointestinal absorption and endothelial health. Finally, we discuss the limitations and challenges associated with the current experimental approaches in membrane and cell model studies and the potential of polyphenol-rich diets in the quest for personalized nutritional strategies ("personalized nutrition") to assist in the prevention, treatment, and management of non-communicable diseases in an increasingly aged population.
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Affiliation(s)
- Ana Reis
- Department Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Rosa Perez-Gregorio
- Department Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nuno Mateus
- REQUIMTE/LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal
| | - Victor de Freitas
- REQUIMTE/LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal
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22
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Clair G, Reehl S, Stratton KG, Monroe ME, Tfaily MM, Ansong C, Kyle JE. Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data. Bioinformatics 2020; 35:4507-4508. [PMID: 30977807 DOI: 10.1093/bioinformatics/btz250] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/27/2019] [Accepted: 04/06/2019] [Indexed: 12/12/2022] Open
Abstract
SUMMARY Here we introduce Lipid Mini-On, an open-source tool that performs lipid enrichment analyses and visualizations of lipidomics data. Lipid Mini-On uses a text-mining process to bin individual lipid names into multiple lipid ontology groups based on the classification (e.g. LipidMaps) and other characteristics, such as chain length. Lipid Mini-On provides users with the capability to conduct enrichment analysis of the lipid ontology terms using a Shiny app with options of five statistical approaches. Lipid classes can be added to customize the user's database and remain updated as new lipid classes are discovered. Visualization of results is available for all classification options (e.g. lipid subclass and individual fatty acid chains). Results are also visualized through an editable network of relationships between the individual lipids and their associated lipid ontology terms. The utility of the tool is demonstrated using biological (e.g. human lung endothelial cells) and environmental (e.g. peat soil) samples. AVAILABILITY AND IMPLEMENTATION Rodin (R package: https://github.com/PNNL-Comp-Mass-Spec/Rodin), Lipid Mini-On Shiny app (https://github.com/PNNL-Comp-Mass-Spec/LipidMiniOn) and Lipid Mini-On online tool (https://omicstools.pnnl.gov/shiny/lipid-mini-on/). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah Reehl
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kelly G Stratton
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.,Soil, Water, and Environmental Science Department, Tuscon, AZ, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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23
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Anderson M, Youngner S, Smith RD, Nandyal RR, Orlowski JP, Jessie Hill B, Barsman SG. Neonatal Organ and Tissue Donation for Research: Options Following Death by Natural Causes. Cell Tissue Bank 2020; 21:289-302. [PMID: 32166424 PMCID: PMC7223177 DOI: 10.1007/s10561-020-09822-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
The donation of organs and tissues from neonates (birth to 28 days) for transplantation has been a relatively infrequent occurrence. Less common has been the use of neonatal organs and tissues for research. Specific ethical and legal questions beg for rational and transparent guidelines with which to evaluate referrals of potential donors. Donation of organs and tissues from a neonate can play a key role in the care and support provided to families by health care professionals around the time of a neonate's death. We report on the recovery of neonatal organs and tissues for research. A working group made up of bioethicists, neonatologists, lawyers, obstetric practioners as well as organ procurement and tissue banking professionals evaluated legal, ethical and medical issues. Neonatal donor family members were also consulted. Our primary goals were (a) to ensure that referrals were made in compliance with all applicable federal and state laws, regulations and institutional protocols, and (b) to follow acceptable ethical standards. Algorithms and policies designed to assist in the evaluation of potential neonatal donors were developed. Neonatal donation is proving increasingly valuable for research into areas including diabetes, pulmonary, gastrointestinal, genitourinary and neurological development, rheumatoid arthritis, autism, childhood psychiatric and neurologic disorders, treatment of MRSA infection and pediatric emergency resuscitation. The development of policies and procedures will assist medical professionals who wish to offer the option of donation to family members anticipating the death of a neonate.
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Affiliation(s)
| | - Stuart Youngner
- Department of Bioethics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4976 USA
| | - Regina Dunne Smith
- International Institute for Advancement of Medicine, Romansville, PA USA
| | - Raja R. Nandyal
- Department of Neonatology, Oklahoma University Health Sciences Center, Oklahoma City, OK USA
| | | | - B. Jessie Hill
- School of Law, Case Western Reserve University, Cleveland, OH USA
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24
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Adeyemi JA, Sorgi CA, Machado ART, Ogunjimi AT, Gardinassi LGA, Nardini V, Faccioli LH, Antunes LMG, Barbosa F. Phospholipids modifications in human hepatoma cell lines (HepG2) exposed to silver and iron oxide nanoparticles. Arch Toxicol 2020; 94:2625-2636. [PMID: 32474618 DOI: 10.1007/s00204-020-02789-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/20/2020] [Indexed: 12/25/2022]
Abstract
Metallic nanoparticles such as silver (Ag NPs) and iron oxide (Fe3O4 NPs) nanoparticles are high production volume materials due to their applications in various consumer products, and in nanomedicine. However, their inherent toxicities to human cells remain a challenge. The present study was aimed at combining lipidomics data with common phenotypically-based toxicological assays to gain better understanding into cellular response to Ag NPs and Fe3O4 NPs exposure. HepG2 cells were exposed to different concentrations (3.125, 6.25, 12.5, 25, 50 and 100 µg/ml) of the nanoparticles for 24 h, after which they were assayed for toxic effects using toxicological assays like cytotoxicity, mutagenicity, apoptosis and oxidative stress. The cell membrane phospholipid profile of the cells was also performed using shotgun tandem mass spectrometry. The results showed that nanoparticles exposure resulted in concentration-dependent cytotoxicity as well as reduced cytokinesis-block proliferation index (CBPI). Also, there was an increase in the production of ROS and superoxide anions in exposed cells compared to the negative control. The lipidomics data revealed that nanoparticles exposure caused a modulation of the phospholipidome of the cells. A total of 155 lipid species were identified, out of which the fold changes of 23 were significant. The high number of differentially changed phosphatidylcholine species could be an indication that inflammation is one of the major mechanisms of toxicity of the nanoparticles to the cells.
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Affiliation(s)
- Joseph A Adeyemi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil. .,Department of Biology, School of Sciences, Federal University of Technology, P.M.B. 704, Akure, Ondo State, Nigeria.
| | - Carlos Arterio Sorgi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Ana Rita Thomazela Machado
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Abayomi T Ogunjimi
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Avenue, Iowa City, Iowa, USA
| | - Luiz Gustavo Araujo Gardinassi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Viviani Nardini
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | | | - Lusania Maria Greggi Antunes
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Fernando Barbosa
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil.
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25
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Titz B, Szostak J, Sewer A, Phillips B, Nury C, Schneider T, Dijon S, Lavrynenko O, Elamin A, Guedj E, Tsin Wong E, Lebrun S, Vuillaume G, Kondylis A, Gubian S, Cano S, Leroy P, Keppler B, Ivanov NV, Vanscheeuwijck P, Martin F, Peitsch MC, Hoeng J. Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke. Comput Struct Biotechnol J 2020; 18:1056-1073. [PMID: 32419906 PMCID: PMC7218232 DOI: 10.1016/j.csbj.2020.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/19/2020] [Indexed: 12/15/2022] Open
Abstract
Multi-omics systems toxicology study, comprising five omics data modalities. Multi-Omics Factor Analysis and multi-modality functional network interpretation. Cigarettes smoke (CS) induced complex immunoregulatory interactions across molecular layers. Aerosols from two heat-not-burn tobacco products had less impact on lungs than CS.
Cigarette smoke (CS) causes adverse health effects and, for smoker who do not quit, modified risk tobacco products (MRTPs) can be an alternative to reduce the risk of developing smoking-related diseases. Standard toxicological endpoints can lack sensitivity, with systems toxicology approaches yielding broader insights into toxicological mechanisms. In a 6-month systems toxicology study on ApoE−/− mice, we conducted an integrative multi-omics analysis to assess the effects of aerosols from the Carbon Heated Tobacco Product (CHTP) 1.2 and Tobacco Heating System (THS) 2.2—a potential and a candidate MRTP based on the heat-not-burn (HnB) principle—compared with CS at matched nicotine concentrations. Molecular exposure effects in the lungs were measured by mRNA/microRNA transcriptomics, proteomics, metabolomics, and lipidomics. Integrative data analysis included Multi-Omics Factor Analysis and multi-modality functional network interpretation. Across all five data modalities, CS exposure was associated with an increased inflammatory and oxidative stress response, and lipid/surfactant alterations. Upon HnB aerosol exposure these effects were much more limited or absent, with reversal of CS-induced effects upon cessation and switching to CHTP 1.2. Functional network analysis revealed CS-induced complex immunoregulatory interactions across the investigated molecular layers (e.g., itaconate, quinolinate, and miR-146) and highlighted the engagement of the heme–Hmox–bilirubin oxidative stress axis by CS. This work exemplifies how multi-omics approaches can be leveraged within systems toxicology studies and the generated multi-omics data set can facilitate the development of analysis methods and can yield further insights into the effects of toxicological exposures on the lung of mice.
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Key Words
- CHTP, Carbon Heated Tobacco Product
- COPD, chronic obstructive pulmonary disease
- CS, cigarette smoke
- Cigarette smoking
- Inhalation toxicology
- LC, liquid chromatography
- MOFA, Multi-Omics Factor Analysis
- MS, mass spectrometry
- Modified risk tobacco product (MRTP)
- Multi-omics
- PCSF, prize-collecting Steiner forest
- ROS, reactive oxygen species
- Systems toxicology
- THS, Tobacco Heating System
- cMRTP, candidate modified risk tobacco product
- sGCCA, sparse generalized canonical correlation analysis
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Justyna Szostak
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Alain Sewer
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Thomas Schneider
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Sophie Dijon
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Oksana Lavrynenko
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Stefan Lebrun
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Grégory Vuillaume
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Athanasios Kondylis
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Sylvain Gubian
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Stephane Cano
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Patrice Leroy
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | | | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | | | - Florian Martin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
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26
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Abstract
Lipidomics data generated using untargeted mass spectrometry techniques can offer great biological insight to metabolic status and disease diagnoses. As the community's ability to conduct large-scale studies with deep coverage of the lipidome expands, approaches to analyzing untargeted data and extracting biological insight are needed. Currently, the function of most individual lipids are not known; however, meaningful biological information can be extracted. Here, I will describe a step-by-step approach to identify patterns and trends in untargeted mass spectrometry lipidomics data to assist users in extracting information leading to a greater understanding of biological systems.
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Misra RS, Nayak JL. The Importance of Vaccinating Children and Pregnant Women against Influenza Virus Infection. Pathogens 2019; 8:pathogens8040265. [PMID: 31779153 PMCID: PMC6963306 DOI: 10.3390/pathogens8040265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022] Open
Abstract
Influenza virus infection is responsible for significant morbidity and mortality in the pediatric and pregnant women populations, with deaths frequently caused by severe influenza-associated lower respiratory tract infection and acute respiratory distress syndrome (ARDS). An appropriate immune response requires controlling the viral infection through activation of antiviral defenses, which involves cells of the lung and immune system. High levels of viral infection or high levels of inflammation in the lower airways can contribute to ARDS. Pregnant women and young children, especially those born prematurely, may develop serious complications if infected with influenza virus. Vaccination against influenza will lead to lower infection rates and fewer complications, even if the vaccine is poorly matched to circulating viral strains, with maternal vaccination offering infants protection via antibody transmission through the placenta and breast milk. Despite the health benefits of the influenza vaccine, vaccination rates around the world remain well below targets. Trust in the use of vaccines among the public must be restored in order to increase vaccination rates and decrease the public health burden of influenza.
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Affiliation(s)
- Ravi S Misra
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14623, USA
- Correspondence:
| | - Jennifer L Nayak
- Department of Pediatrics Division of Pediatric Infectious Diseases, The University of Rochester Medical Center, Rochester, NY 14623, USA;
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Zalis EA, Nuxoll AS, Manuse S, Clair G, Radlinski LC, Conlon BP, Adkins J, Lewis K. Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells. mBio 2019; 10:e01930-19. [PMID: 31530676 PMCID: PMC6751062 DOI: 10.1128/mbio.01930-19] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Chronic bacterial infections are difficult to eradicate, though they are caused primarily by drug-susceptible pathogens. Antibiotic-tolerant persisters largely account for this paradox. In spite of their significance in the recalcitrance of chronic infections, the mechanism of persister formation is poorly understood. We previously reported that a decrease in ATP levels leads to drug tolerance in Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus We reasoned that stochastic fluctuation in the expression of tricarboxylic acid (TCA) cycle enzymes can produce cells with low energy levels. S. aureus knockouts in glutamate dehydrogenase, 2-oxoketoglutarate dehydrogenase, succinyl coenzyme A (CoA) synthetase, and fumarase have low ATP levels and exhibit increased tolerance of fluoroquinolone, aminoglycoside, and β-lactam antibiotics. Fluorescence-activated cell sorter (FACS) analysis of TCA genes shows a broad Gaussian distribution in a population, with differences of over 3 orders of magnitude in the levels of expression between individual cells. Sorted cells with low levels of TCA enzyme expression have an increased tolerance of antibiotic treatment. These findings suggest that fluctuations in the levels of expression of energy-generating components serve as a mechanism of persister formation.IMPORTANCE Persister cells are rare phenotypic variants that are able to survive antibiotic treatment. Unlike resistant bacteria, which have specific mechanisms to prevent antibiotics from binding to their targets, persisters evade antibiotic killing by entering a tolerant nongrowing state. Persisters have been implicated in chronic infections in multiple species, and growing evidence suggests that persister cells are responsible for many cases of antibiotic treatment failure. New antibiotic treatment strategies aim to kill tolerant persister cells more effectively, but the mechanism of tolerance has remained unclear until now.
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Affiliation(s)
- Eliza A Zalis
- Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts, USA
| | - Austin S Nuxoll
- Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts, USA
| | - Sylvie Manuse
- Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts, USA
| | - Geremy Clair
- Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lauren C Radlinski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Brian P Conlon
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Joshua Adkins
- Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kim Lewis
- Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts, USA
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