1
|
Karmaus PWF, Tata A, Meacham JM, Day F, Thrower D, Tata PR, Fessler MB. Meta-Analysis of COVID-19 BAL Single-Cell RNA Sequencing Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates. Am J Respir Cell Mol Biol 2023; 69:623-637. [PMID: 37523502 DOI: 10.1165/rcmb.2023-0077oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of BAL cells has provided insights into coronavirus disease (COVID-19). However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-seq data from healthy control subjects (n = 13) and patients with COVID-19 (n = 20), sourced from six independent studies (167,280 high-quality cells in total). Consistent with the source reports, increases in infiltrating leukocyte subtypes were noted, several with type I IFN signatures and unique gene expression signatures associated with transcellular chemokine signaling. Noting dramatic reductions of inferred NKX2-1 and NR4A1 activity in alveolar epithelial type II (AT-II) cells, we modeled pseudotemporal AT-II-to-AT-I progression. This revealed changes in inferred AT-II cell metabolic activity, increased transitional cells, and a previously undescribed AT-I state. This cell state was conspicuously marked by the induction of genes of the epidermal differentiation complex, including the cornified envelope protein SPRR3 (small proline-rich protein 3), upregulation of multiple KRT (keratin) genes, inferred mitochondrial dysfunction, and cell death signatures including apoptosis and ferroptosis. Immunohistochemistry of lungs from patients with COVID-19 confirmed upregulation and colocalization of KRT13 and SPRR3 in the distal airspaces. Forced overexpression of SPRR3 in human alveolar epithelial cells ex vivo did not activate caspase-3 or upregulate KRT13, suggesting that SPRR3 marks an AT-I cornification program in COVID-19 but is not sufficient for phenotypic changes.
Collapse
Affiliation(s)
| | - Aleksandra Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
| | | | - Frank Day
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - David Thrower
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - Purushothama Rao Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
| | | |
Collapse
|
2
|
Ajayi T, Rai P, Shi M, Gabor KA, Karmaus PWF, Meacham JM, Katen K, Madenspacher JH, Schurman SH, Fessler MB. Race-specific association of an IRGM risk allele with cytokine expression in human subjects. Sci Rep 2023; 13:12911. [PMID: 37558924 PMCID: PMC10412543 DOI: 10.1038/s41598-023-40313-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Immunity-related GTPase family M (IRGM), located on human chromosome 5q33.1, encodes a protein that promotes autophagy and suppresses the innate immune response. The minor allele of rs13361189 (-4299T>C), a single nucleotide polymorphism in the IRGM promoter, has been associated with several diseases, including Crohn's disease and tuberculosis. Although patterns of linkage disequilibrium and minor allele frequency for this polymorphism differ dramatically between subjects of European and African descent, studies of rs13361189 have predominantly been conducted in Europeans and the mechanism of association is poorly understood. We recruited a cohort of 68 individuals (30 White, 34 African American, 4 other race) with varying rs13361189 genotypes and assessed a panel of immune response measures including whole blood cytokine induction following ex vivo stimulation with Toll-like Receptor ligands. Minor allele carriers were found to have increased serum immunoglobulin M, C-reactive protein, and circulating CD8+ T cells. No differences in whole blood cytokines were observed between minor allele carriers and non-carriers in the overall study population; however, minor allele status was associated with increased induction of a subset of cytokines among African American subjects, and decreased induction among White subjects. These findings underline the importance of broad racial inclusion in genetic studies of immunity.
Collapse
Affiliation(s)
- Teminioluwa Ajayi
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Prashant Rai
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Min Shi
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Kristin A Gabor
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Peer W F Karmaus
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Julie M Meacham
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Kevin Katen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Jennifer H Madenspacher
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Shepherd H Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
- Clinical Research Unit, National Institute on Aging, Baltimore, MD, 21225, USA
| | - Michael B Fessler
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA.
| |
Collapse
|
3
|
Madenspacher JH, Morrell ED, McDonald JG, Thompson BM, Li Y, Birukov KG, Birukova AA, Stapleton RD, Alejo A, Karmaus PW, Meacham JM, Rai P, Mikacenic C, Wurfel MM, Fessler MB. 25-Hydroxycholesterol exacerbates vascular leak during acute lung injury. JCI Insight 2023; 8:e155448. [PMID: 36821369 PMCID: PMC10132150 DOI: 10.1172/jci.insight.155448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Cholesterol-25-hydroxylase (CH25H), the biosynthetic enzyme for 25-hydroxycholesterol (25HC), is most highly expressed in the lung, but its role in lung biology is poorly defined. Recently, we reported that Ch25h is induced in monocyte-derived macrophages recruited to the airspace during resolution of lung inflammation and that 25HC promotes liver X receptor-dependent (LXR-dependent) clearance of apoptotic neutrophils by these cells. Ch25h and 25HC are, however, also robustly induced by lung-resident cells during the early hours of lung inflammation, suggesting additional cellular sources and targets. Here, using Ch25h-/- mice and exogenous 25HC in lung injury models, we provide evidence that 25HC sustains proinflammatory cytokines in the airspace and augments lung injury, at least in part, by inducing LXR-independent endoplasmic reticulum stress and endothelial leak. Suggesting an autocrine effect in endothelium, inhaled LPS upregulates pulmonary endothelial Ch25h, and non-hematopoietic Ch25h deletion is sufficient to confer lung protection. In patients with acute respiratory distress syndrome, airspace 25HC and alveolar macrophage CH25H were associated with markers of microvascular leak, endothelial activation, endoplasmic reticulum stress, inflammation, and clinical severity. Taken together, our findings suggest that 25HC deriving from and acting on different cell types in the lung communicates distinct, temporal LXR-independent and -dependent signals to regulate inflammatory homeostasis.
Collapse
Affiliation(s)
- Jennifer H. Madenspacher
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Eric D. Morrell
- Section of Pulmonary, Critical Care, and Sleep Medicine, Harborview Medical Center, Seattle, Washington, USA
| | - Jeffrey G. McDonald
- Center for Human Nutrition and
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Yue Li
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Konstantin G. Birukov
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anna A. Birukova
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Renee D. Stapleton
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Aidin Alejo
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Peer W. Karmaus
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Julie M. Meacham
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Prashant Rai
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Carmen Mikacenic
- Section of Pulmonary, Critical Care, and Sleep Medicine, Harborview Medical Center, Seattle, Washington, USA
| | - Mark M. Wurfel
- Section of Pulmonary, Critical Care, and Sleep Medicine, Harborview Medical Center, Seattle, Washington, USA
| | - Michael B. Fessler
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| |
Collapse
|
4
|
Madenspacher JH, Morrell ED, Gowdy KM, McDonald JG, Thompson BM, Muse G, Martinez J, Thomas S, Mikacenic C, Nick JA, Abraham E, Garantziotis S, Stapleton RD, Meacham JM, Thomassen MJ, Janssen WJ, Cook DN, Wurfel MM, Fessler MB. Cholesterol 25-hydroxylase promotes efferocytosis and resolution of lung inflammation. JCI Insight 2020; 5:137189. [PMID: 32343675 DOI: 10.1172/jci.insight.137189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Alveolar macrophages (AM) play a central role in initiation and resolution of lung inflammation, but the integration of these opposing core functions is poorly understood. AM expression of cholesterol 25-hydroxylase (CH25H), the primary biosynthetic enzyme for 25-hydroxycholesterol (25HC), far exceeds the expression of macrophages in other tissues, but no role for CH25H has been defined in lung biology. As 25HC is an agonist for the antiinflammatory nuclear receptor, liver X receptor (LXR), we speculated that CH25H might regulate inflammatory homeostasis in the lung. Here, we show that, of natural oxysterols or sterols, 25HC is induced in the inflamed lung of mice and humans. Ch25h-/- mice fail to induce 25HC and LXR target genes in the lung after LPS inhalation and exhibit delayed resolution of airway neutrophilia, which can be rescued by systemic treatment with either 25HC or synthetic LXR agonists. LXR-null mice also display delayed resolution, suggesting that native oxysterols promote resolution. During resolution, Ch25h is induced in macrophages upon their encounter with apoptotic cells and is required for LXR-dependent prevention of AM lipid overload, induction of Mertk, efferocytic resolution of airway neutrophilia, and induction of TGF-β. CH25H/25HC/LXR is, thus, an inducible metabolic axis that programs AMs for efferocytic resolution of inflammation.
Collapse
Affiliation(s)
- Jennifer H Madenspacher
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| | - Eric D Morrell
- Section of Pulmonary, Critical Care, and Sleep Medicine, Harborview Medical Center, Seattle, Washington, USA
| | - Kymberly M Gowdy
- Division of Pulmonary, Critical Care and Sleep Medicine, and.,Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bonne M Thompson
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ginger Muse
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| | - Jennifer Martinez
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| | - Seddon Thomas
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| | - Carmen Mikacenic
- Section of Pulmonary, Critical Care, and Sleep Medicine, Harborview Medical Center, Seattle, Washington, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Edward Abraham
- Department of Medicine, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Stavros Garantziotis
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| | - Renee D Stapleton
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Julie M Meacham
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| | - Mary Jane Thomassen
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - William J Janssen
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Donald N Cook
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| | - Mark M Wurfel
- Section of Pulmonary, Critical Care, and Sleep Medicine, Harborview Medical Center, Seattle, Washington, USA
| | - Michael B Fessler
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, North Carolina, USA
| |
Collapse
|
5
|
Binkley MM, Cui M, Li W, Tan S, Berezin MY, Meacham JM. Design, modeling, and experimental validation of an acoustofluidic platform for nanoscale molecular synthesis and detection. Phys Fluids (1994) 2019; 31:082007. [PMID: 31462888 PMCID: PMC6711656 DOI: 10.1063/1.5100149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/28/2019] [Indexed: 05/30/2023]
Abstract
Microfluidic technologies are increasingly implemented to replace manual methods in biological and biochemical sample processing. We explore the feasibility of an acoustofluidic trap for confinement of microparticle reaction substrates against continuously flowing reagents in chemical synthesis and detection applications. Computational models are used to predict the flow and ultrasonic standing wave fields within two longitudinal standing bulk acoustic wave (LSBAW) microchannels operated in the 0.5-2.0 MHz range. Glass (gLSBAW) and silicon (siLSBAW) pillar arrays comprise trapping structures that augment the local acoustic field, while openings between pillars evenly distribute the flow for uniform exposure of substrates to reagents. Frequency spectra (acoustic energy density E ac vs frequency) and model-predicted pressure fields are used to identify longitudinal resonances with pressure minima in bands oriented perpendicular to the inflow direction. Polymeric and glass particles (10- and 20-µm diameter polystyrene beads, 6 µm hollow glass spheres, and 5 µm porous silica microparticles) are confined within acoustic traps operated at longitudinal first and second half-wavelength resonant frequencies (f 1,E = 575 kHz, gLSBAW; f 1,E = 666 kHz; and f 2,E = 1.278 MHz, siLSBAW) as reagents are introduced at 5-10 µl min-1. Anisotropic silicon etched traps are found to improve augmentation of the acoustic pressure field without reducing the volumetric throughput. Finally, in-channel synthesis of a double-labeled antibody conjugate on ultrasound-confined porous silica microparticles demonstrates the feasibility of the LSBAW platform for synthesis and detection. The results provide a computational and experimental framework for continued advancement of the LSBAW platform for other synthetic processes and molecular detection applications.
Collapse
Affiliation(s)
- M M Binkley
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - M Cui
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - W Li
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - S Tan
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | | | | |
Collapse
|
6
|
Cui M, Binkley MM, Shekhani HN, Berezin MY, Meacham JM. Augmented longitudinal acoustic trap for scalable microparticle enrichment. Biomicrofluidics 2018; 12:034110. [PMID: 29937950 PMCID: PMC5991967 DOI: 10.1063/1.5036923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/30/2018] [Indexed: 05/06/2023]
Abstract
We introduce an acoustic microfluidic device architecture that locally augments the pressure field for separation and enrichment of targeted microparticles in a longitudinal acoustic trap. Pairs of pillar arrays comprise "pseudo walls" that are oriented perpendicular to the inflow direction. Though sample flow is unimpeded, pillar arrays support half-wave resonances that correspond to the array gap width. Positive acoustic contrast particles of supracritical diameter focus to nodal locations of the acoustic field and are held against drag from the bulk fluid motion. Thus, the longitudinal standing bulk acoustic wave (LSBAW) device achieves size-selective and material-specific separation and enrichment of microparticles from a continuous sample flow. A finite element analysis model is used to predict eigenfrequencies of LSBAW architectures with two pillar geometries, slanted and lamellar. Corresponding pressure fields are used to identify longitudinal resonances that are suitable for microparticle enrichment. Optimal operating conditions exhibit maxima in the ratio of acoustic energy density in the LSBAW trap to that in inlet and outlet regions of the microchannel. Model results guide fabrication and experimental evaluation of realized LSBAW assemblies regarding enrichment capability. We demonstrate separation and isolation of 20 μm polystyrene and ∼10 μm antibody-decorated glass beads within both pillar geometries. The results also establish several practical attributes of our approach. The LSBAW device is inherently scalable and enables continuous enrichment at a prescribed location. These features benefit separations applications while also allowing concurrent observation and analysis of trap contents.
Collapse
Affiliation(s)
- M Cui
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - M M Binkley
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - H N Shekhani
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | | | | |
Collapse
|