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Bramer LM, Hontz RD, Eisfeld AJ, Sims AC, Kim YM, Stratton KG, Nicora CD, Gritsenko MA, Schepmoes AA, Akasaka O, Koga M, Tsutsumi T, Nakamura M, Nakachi I, Baba R, Tateno H, Suzuki S, Nakajima H, Kato H, Ishida K, Ishii M, Uwamino Y, Mitamura K, Paurus VL, Nakayasu ES, Attah IK, Letizia AG, Waters KM, Metz TO, Corson K, Kawaoka Y, Gerbasi VR, Yotsuyanagi H, Iwatsuki-Horimoto K. Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections. Heliyon 2023; 9:e13795. [PMID: 36915486 PMCID: PMC9988701 DOI: 10.1016/j.heliyon.2023.e13795] [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: 05/10/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics and correlative analysis of an immunologically naïve SARS-CoV-2 clinical cohort from blood plasma of uninfected controls, mild, and severe infections. Consistent with previous observations, severe patient populations showed an elevation of pulmonary surfactant levels. Intriguingly, mild patients showed a statistically significant elevation in the carnosine dipeptidase modifying enzyme (CNDP1). Mild and severe patient populations showed a strong elevation in the metabolite L-cystine (oxidized form of the amino acid cysteine) and enzymes with roles in glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both mild and severe populations, and NET formation was higher in severe vs. mild samples. Our correlative analysis suggests a potential protective role for CNDP1 in suppressing PSPB release from the pulmonary space whereas NET formation correlates with increased PSPB levels and disease severity. In our discussion we put forward a possible model where NET formation drives pulmonary occlusions and CNDP1 promotes antioxidation, pleiotropic immune responses, and vasodilation by accelerating histamine synthesis.
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Affiliation(s)
- Lisa M Bramer
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert D Hontz
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | - Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Amy C Sims
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | | | | | - Osamu Akasaka
- Emergency Medical Center, Fujisawa City Hospital 2-6-1 Fujisawa, Fujisawa, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Morio Nakamura
- Department of Pulmonary Medicine, Tokyo Saiseikai Central, Tokyo, Japan
| | - Ichiro Nakachi
- Pulmonary Division, Department of Internal Medicine, Utsunomiya Hospital, Utsunomiya, Japan
| | - Rie Baba
- Pulmonary Division, Department of Internal Medicine, Utsunomiya Hospital, Utsunomiya, Japan
| | - Hiroki Tateno
- Department of Pulmonary Medicine, Saitama City Hospital, Saitama, Japan
| | - Shoji Suzuki
- Department of Pulmonary Medicine, Saitama City Hospital, Saitama, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, University School of Medicine, Yokohama, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, University School of Medicine, Yokohama, Japan
| | | | - Makoto Ishii
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Mitamura
- Division of Infection Control, Eiju General Hospital, Tokyo, Japan
| | | | | | - Isaac K Attah
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrew G Letizia
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | | | - Thomas O Metz
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karen Corson
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.,Department of Microbiology and Immunology, Japan.,International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo
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Whittamore JM, Hatch M. Oxalate Flux Across the Intestine: Contributions from Membrane Transporters. Compr Physiol 2021; 12:2835-2875. [PMID: 34964122 DOI: 10.1002/cphy.c210013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epithelial oxalate transport is fundamental to the role occupied by the gastrointestinal (GI) tract in oxalate homeostasis. The absorption of dietary oxalate, together with its secretion into the intestine, and degradation by the gut microbiota, can all influence the excretion of this nonfunctional terminal metabolite in the urine. Knowledge of the transport mechanisms is relevant to understanding the pathophysiology of hyperoxaluria, a risk factor in kidney stone formation, for which the intestine also offers a potential means of treatment. The following discussion presents an expansive review of intestinal oxalate transport. We begin with an overview of the fate of oxalate, focusing on the sources, rates, and locations of absorption and secretion along the GI tract. We then consider the mechanisms and pathways of transport across the epithelial barrier, discussing the transcellular, and paracellular components. There is an emphasis on the membrane-bound anion transporters, in particular, those belonging to the large multifunctional Slc26 gene family, many of which are expressed throughout the GI tract, and we summarize what is currently known about their participation in oxalate transport. In the final section, we examine the physiological stimuli proposed to be involved in regulating some of these pathways, encompassing intestinal adaptations in response to chronic kidney disease, metabolic acid-base disorders, obesity, and following gastric bypass surgery. There is also an update on research into the probiotic, Oxalobacter formigenes, and the basis of its unique interaction with the gut epithelium. © 2021 American Physiological Society. Compr Physiol 11:1-41, 2021.
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Affiliation(s)
- Jonathan M Whittamore
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marguerite Hatch
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
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Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist. Appl Environ Microbiol 2021; 87:e0054421. [PMID: 34190610 DOI: 10.1128/aem.00544-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Oxalobacter formigenes, a unique anaerobic bacterium that relies solely on oxalate for growth, is a key oxalate-degrading bacterium in the mammalian intestinal tract. Degradation of oxalate in the gut by O. formigenes plays a critical role in preventing renal toxicity in animals that feed on oxalate-rich plants. The role of O. formigenes in reducing the risk of calcium oxalate kidney stone disease and oxalate nephropathy in humans is less clear, in part due to difficulties in culturing this organism and the lack of studies which have utilized diets in which the oxalate content is controlled. Herein, we review the literature on the 40th anniversary of the discovery of O. formigenes, with a focus on its biology, its role in gut oxalate metabolism and calcium oxalate kidney stone disease, and potential areas of future research. Results from ongoing clinical trials utilizing O. formigenes in healthy volunteers and in patients with primary hyperoxaluria type 1 (PH1), a rare but severe form of calcium oxalate kidney stone disease, are also discussed. Information has been consolidated on O. formigenes strains and best practices to culture this bacterium, which should serve as a good resource for researchers.
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Chamberlain CA, Hatch M, Garrett TJ. Extracellular Vesicle Analysis by Paper Spray Ionization Mass Spectrometry. Metabolites 2021; 11:metabo11050308. [PMID: 34065030 PMCID: PMC8151837 DOI: 10.3390/metabo11050308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/23/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022] Open
Abstract
Paper spray ionization mass spectrometry (PSI-MS) is a direct MS analysis technique with several reported bacterial metabolomics applications. As with most MS-based bacterial studies, all currently reported PSI-MS bacterial analyses have focused on the chemical signatures of the cellular unit. One dimension of the bacterial metabolome that is often lost in such analyses is the exometabolome (extracellular metabolome), including secreted metabolites, lipids, and peptides. A key component of the bacterial exometabolome that is gaining increased attention in the microbiology and biomedical communities is extracellular vesicles (EVs). These excreted structures, produced by cells in all domains of life, contain a variety of biomolecules responsible for a wide array of cellular functions, thus representing a core component of the bacterial secreted metabolome. Although previously examined using other MS approaches, no reports currently exist for a PSI-MS analysis of bacterial EVs, nor EVs from any other organism (exosomes, ectosomes, etc.). PSI-MS holds unique analytical strengths over other commonly used MS platforms and could thus provide an advantageous approach to EV metabolomics. To address this, we report a novel application representing, to our knowledge, the first PSI-MS analysis of EVs from any organism (using the human gut resident Oxalobacter formigenes as the experimental model, a bacterium whose EVs were never previously investigated). In this report, we show how we isolated and purified EVs from bacterial culture supernatant by EV-specific affinity chromatography, confirmed and characterized these vesicles by nanoparticle tracking analysis, analyzed the EV isolate by PSI-MS, and identified a panel of EV-derived metabolites, lipids, and peptides. This work serves as a pioneering study in the field of MS-based EV analysis and provides a new, rapid, sensitive, and economical approach to EV metabolomics.
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Chamberlain CA, Hatch M, Garrett TJ. Oxalobacter formigenes produces metabolites and lipids undetectable in oxalotrophic Bifidobacterium animalis. Metabolomics 2020; 16:122. [PMID: 33219444 DOI: 10.1007/s11306-020-01747-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/11/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the search for new potential therapies for pathologies of oxalate, such as kidney stone disease and primary hyperoxaluria, the intestinal microbiome has generated significant interest. Resident oxalate-degrading bacteria inhabit the gastrointestinal tract and reduce absorption of dietary oxalate, thereby potentially lowering the potency of oxalate as a risk factor for kidney stone formation. Although several species of bacteria have been shown to degrade oxalate, select strains of Oxalobacter formigenes (O. formigenes) have thus far demonstrated the unique ability among oxalotrophs to initiate a net intestinal oxalate secretion into the lumen from the bloodstream, allowing them to feed on both dietary and endogenous metabolic oxalate. There is significant interest in this function as a potential therapeutic application for circulating oxalate reduction, although its mechanism of action is still poorly understood. Since this species-exclusive, oxalate-regulating function is reported to be dependent on the use of a currently unidentified secreted bioactive compound, there is much interest in whether O. formigenes produces unique biochemicals that are not expressed by other oxalotrophs which lack the ability to transport oxalate. Hence, this study sought to analyze and compare the metabolomes of O. formigenes and another oxalate degrader, Bifidobacterium animalis subsp. lactis (B. animalis), to determine whether O. formigenes could produce features undetectable in another oxalotroph, thus supporting the theory of a species-exclusive secretagogue compound. METHODS A comparative metabolomic analysis of O. formigenes strain HC1 (a human isolate) versus B. animalis, another oxalate-degrading human intestinal microbe, was performed by ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS). Bacteria were cultured independently in anaerobic conditions, harvested, lysed, and extracted by protein precipitation. Metabolite extracts were chromatographically separated and analyzed by UHPLC-HRMS using reverse phase gradient elution (ACE Excel 2 C18-Pentafluorophenyl column) paired with a Q Exactive™ mass spectrometer. OBJECTIVES The purpose of this study was to assess whether O. formigenes potentially produces unique biochemicals from other oxalate degraders to better understand its metabolic profile and provide support for the theoretical production of a species-exclusive secretagogue compound responsible for enhancing intestinal oxalate secretion. RESULTS We report a panel of metabolites and lipids detected in the O. formigenes metabolome which were undetectable in B. animalis, several of which were identified either by mass-to-charge ratio and retention time matching to our method-specific metabolite library or MS/MS fragmentation. Furthermore, re-examination of data from our previous work showed most of these features were also undetected in the metabolomes of Lactobacillus acidophilus and Lactobacillus gasseri, two other intestinal oxalate degraders. CONCLUSIONS Our observation of O. formigenes metabolites and lipids which were undetectable in other oxalotrophs suggests that this bacterium likely holds the ability to produce biochemicals not expressed by at least a selection of other oxalate degraders. These findings provide support for the hypothesized biosynthesis of a species-exclusive secretagogue responsible for the stimulation of net intestinal oxalate secretion.
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Affiliation(s)
- Casey A Chamberlain
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Marguerite Hatch
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA.
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