1
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Obata T, Mizoguchi S, Greaney AM, Adams T, Yuan Y, Edelstein S, Leiby KL, Rivero R, Wang N, Kim H, Yang J, Schupp JC, Stitelman D, Tsuchiya T, Levchenko A, Kaminski N, Niklason LE, Brickman Raredon MS. Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration. bioRxiv 2024:2024.01.07.574469. [PMID: 38260691 PMCID: PMC10802449 DOI: 10.1101/2024.01.07.574469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Tissue homeostasis is controlled by cellular circuits governing cell growth, organization, and differentation. In this study we identify previously undescribed cell-to-cell communication that mediates information flow from mechanosensitive pleural mesothelial cells to alveolar-resident stem-like tuft cells in the lung. We find mesothelial cells to express a combination of mechanotransduction genes and lineage-restricted ligands which makes them uniquely capable of responding to tissue tension and producing paracrine cues acting on parenchymal populations. In parallel, we describe a large population of stem-like alveolar tuft cells that express the endodermal stem cell markers Sox9 and Lgr5 and a receptor profile making them uniquely sensitive to cues produced by pleural Mesothelium. We hypothesized that crosstalk from mesothelial cells to alveolar tuft cells might be central to the regulation of post-penumonectomy lung regeneration. Following pneumonectomy, we find that mesothelial cells display radically altered phenotype and ligand expression, in a pattern that closely tracks with parenchymal epithelial proliferation and alveolar tissue growth. During an initial pro-inflammatory stage of tissue regeneration, Mesothelium promotes epithelial proliferation via WNT ligand secretion, orchestrates an increase in microvascular permeability, and encourages immune extravasation via chemokine secretion. This stage is followed first by a tissue remodeling period, characterized by angiogenesis and BMP pathway sensitization, and then a stable return to homeostasis. Coupled with key changes in parenchymal structure and matrix production, the cumulative effect is a now larger organ including newly-grown, fully-functional tissue parenchyma. This study paints Mesothelial cells as a key orchestrating cell type that defines the boundary of the lung and exerts critical influence over the tissue-level signaling state regulating resident stem cell populations. The cellular circuits unearthed here suggest that human lung regeneration might be inducible through well-engineered approaches targeting the induction of tissue regeneration and safe return to homeostasis.
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Affiliation(s)
- Tomohiro Obata
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Satoshi Mizoguchi
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Allison M. Greaney
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of technology, Cambridge, MA, 02139
| | - Taylor Adams
- Pulmonary, Critical Care, & Sleep Medicine, Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Yifan Yuan
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
- Pulmonary, Critical Care, & Sleep Medicine, Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Sophie Edelstein
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Katherine L. Leiby
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Rachel Rivero
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Nuoya Wang
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Haram Kim
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
- Pulmonary, Critical Care, & Sleep Medicine, Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Junchen Yang
- Computational Biology and Biomedical Informatics, Yale University, New Haven, CT, 06511, USA
| | - Jonas C. Schupp
- Pulmonary, Critical Care, & Sleep Medicine, Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Respiratory Medicine, Hanover Medical School, Hanover, Germany
- Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Center for Lung Research (DZL), Hanover, Germany
| | - David Stitelman
- Department of Surgery, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Tomoshi Tsuchiya
- Department of Thoracic Surgery, University of Toyama, Toyama, 9300194, Japan
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Systems Biology Institute, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care, & Sleep Medicine, Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Laura E. Niklason
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
- Humacyte, Inc., Durham, North Carolina
| | - Micha Sam Brickman Raredon
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06511, USA
- Pulmonary, Critical Care, & Sleep Medicine, Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
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2
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Leiby KL, Yuan Y, Ng R, Raredon MSB, Adams TS, Baevova P, Greaney AM, Hirschi KK, Campbell SG, Kaminski N, Herzog EL, Niklason LE. Rational engineering of lung alveolar epithelium. NPJ Regen Med 2023; 8:22. [PMID: 37117221 PMCID: PMC10147714 DOI: 10.1038/s41536-023-00295-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/06/2023] [Indexed: 04/30/2023] Open
Abstract
Engineered whole lungs may one day expand therapeutic options for patients with end-stage lung disease. However, the feasibility of ex vivo lung regeneration remains limited by the inability to recapitulate mature, functional alveolar epithelium. Here, we modulate multimodal components of the alveolar epithelial type 2 cell (AEC2) niche in decellularized lung scaffolds in order to guide AEC2 behavior for epithelial regeneration. First, endothelial cells coordinate with fibroblasts, in the presence of soluble growth and maturation factors, to promote alveolar scaffold population with surfactant-secreting AEC2s. Subsequent withdrawal of Wnt and FGF agonism synergizes with tidal-magnitude mechanical strain to induce the differentiation of AEC2s to squamous type 1 AECs (AEC1s) in cultured alveoli, in situ. These results outline a rational strategy to engineer an epithelium of AEC2s and AEC1s contained within epithelial-mesenchymal-endothelial alveolar-like units, and highlight the critical interplay amongst cellular, biochemical, and mechanical niche cues within the reconstituting alveolus.
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Affiliation(s)
- Katherine L Leiby
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Yifan Yuan
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Ronald Ng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Pavlina Baevova
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Karen K Hirschi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
- Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Stuart G Campbell
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Erica L Herzog
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA.
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3
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Greaney AM, Raredon MSB, Kochugaeva MP, Niklason LE, Levchenko A. SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection. iScience 2023; 26:106175. [PMID: 36788793 PMCID: PMC9912025 DOI: 10.1016/j.isci.2023.106175] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 01/05/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Despite much concerted effort to better understand severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection, relatively little is known about the dynamics of early viral entry and infection in the airway. Here we analyzed a single-cell RNA sequencing dataset of early SARS-CoV-2 infection in a humanized in vitro model, to elucidate key mechanisms by which the virus triggers a cell-systems-level response in the bronchial epithelium. We find that SARS-CoV-2 virus preferentially enters the tissue via ciliated cell precursors, giving rise to a population of infected mature ciliated cells, which signal to basal cells, inducing further rapid differentiation. This feedforward loop of infection is mitigated by further cell-cell communication, before interferon signaling begins at three days post-infection. These findings suggest hijacking by the virus of potentially beneficial tissue repair mechanisms, possibly exacerbating the outcome. This work both elucidates the interplay between barrier tissues and viral infections and may suggest alternative therapeutic approaches targeting non-immune response mechanisms.
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Affiliation(s)
- Allison Marie Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT 06511, USA
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT 06511, USA
- Medical Scientist Training Program, Yale University, New Haven, CT 06511, USA
| | - Maria P. Kochugaeva
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT 06511, USA
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06510, USA
- Humacyte Inc., Durham, NC 27713, USA
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Corresponding author
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4
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Raredon MSB, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason LE, Kluger Y. Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics 2023; 39:6865029. [PMID: 36458905 PMCID: PMC9825783 DOI: 10.1093/bioinformatics/btac775] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 10/31/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
MOTIVATION Recent years have seen the release of several toolsets that reveal cell-cell interactions from single-cell data. However, all existing approaches leverage mean celltype gene expression values, and do not preserve the single-cell fidelity of the original data. Here, we present NICHES (Niche Interactions and Communication Heterogeneity in Extracellular Signaling), a tool to explore extracellular signaling at the truly single-cell level. RESULTS NICHES allows embedding of ligand-receptor signal proxies to visualize heterogeneous signaling archetypes within cell clusters, between cell clusters and across experimental conditions. When applied to spatial transcriptomic data, NICHES can be used to reflect local cellular microenvironment. NICHES can operate with any list of ligand-receptor signaling mechanisms, is compatible with existing single-cell packages, and allows rapid, flexible analysis of cell-cell signaling at single-cell resolution. AVAILABILITY AND IMPLEMENTATION NICHES is an open-source software implemented in R under academic free license v3.0 and it is available at http://github.com/msraredon/NICHES. Use-case vignettes are available at https://msraredon.github.io/NICHES/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Neeharika Kothapalli
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Wesley Lewis
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Laura E Niklason
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
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5
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Sinha S, Sparks HD, Labit E, Robbins HN, Gowing K, Jaffer A, Kutluberk E, Arora R, Raredon MSB, Cao L, Swanson S, Jiang P, Hee O, Pope H, Workentine M, Todkar K, Sharma N, Bharadia S, Chockalingam K, de Almeida LGN, Adam M, Niklason L, Potter SS, Seifert AW, Dufour A, Gabriel V, Rosin NL, Stewart R, Muench G, McCorkell R, Matyas J, Biernaskie J. Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer. Cell 2022; 185:4717-4736.e25. [PMID: 36493752 PMCID: PMC9888357 DOI: 10.1016/j.cell.2022.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 09/21/2021] [Revised: 08/24/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022]
Abstract
Adult mammalian skin wounds heal by forming fibrotic scars. We report that full-thickness injuries of reindeer antler skin (velvet) regenerate, whereas back skin forms fibrotic scar. Single-cell multi-omics reveal that uninjured velvet fibroblasts resemble human fetal fibroblasts, whereas back skin fibroblasts express inflammatory mediators mimicking pro-fibrotic adult human and rodent fibroblasts. Consequently, injury elicits site-specific immune responses: back skin fibroblasts amplify myeloid infiltration and maturation during repair, whereas velvet fibroblasts adopt an immunosuppressive phenotype that restricts leukocyte recruitment and hastens immune resolution. Ectopic transplantation of velvet to scar-forming back skin is initially regenerative, but progressively transitions to a fibrotic phenotype akin to the scarless fetal-to-scar-forming transition reported in humans. Skin regeneration is diminished by intensifying, or enhanced by neutralizing, these pathologic fibroblast-immune interactions. Reindeer represent a powerful comparative model for interrogating divergent wound healing outcomes, and our results nominate decoupling of fibroblast-immune interactions as a promising approach to mitigate scar.
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Affiliation(s)
- Sarthak Sinha
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Holly D Sparks
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Elodie Labit
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Hayley N Robbins
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kevin Gowing
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Arzina Jaffer
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Eren Kutluberk
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Rohit Arora
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT, USA
| | - Leslie Cao
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Peng Jiang
- Morgridge Institute for Research, Madison, WI, USA
| | - Olivia Hee
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Hannah Pope
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Matt Workentine
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kiran Todkar
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Nilesh Sharma
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Shyla Bharadia
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Luiz G N de Almeida
- McCaig Institute, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Laura Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Antoine Dufour
- McCaig Institute, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Vincent Gabriel
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; McCaig Institute, University of Calgary, Calgary, AB, Canada; Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Nicole L Rosin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, USA
| | - Greg Muench
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Robert McCorkell
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John Matyas
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada; McCaig Institute, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada; Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada; Hotchkiss Brain Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.
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6
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Raredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome. Sci Rep 2022; 12:4187. [PMID: 35264704 PMCID: PMC8906120 DOI: 10.1038/s41598-022-07959-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns in a way that informs tissue biology are major computational and epistemological challenges. Here, we present Connectome, a software package for R which facilitates rapid calculation and interactive exploration of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. Connectome can be used with any reference set of known ligand-receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which signaling networks are compared between tissue systems. Connectome focuses on computational and graphical tools designed to analyze and explore cell-cell connectivity patterns across disparate single-cell datasets and reveal biologic insight. We present approaches to quantify focused network topologies and discuss some of the biologic theory leading to their design.
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Affiliation(s)
- Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA.
| | - Junchen Yang
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - James Garritano
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | - Meng Wang
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Dan Kushnir
- NOKIA Bell-Laboratories, Murray Hill, NJ, USA
| | - Jonas Christian Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Katherine L Leiby
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Applied Mathematics Program, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA.
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7
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Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nat Commun 2022; 13:440. [PMID: 35064122 PMCID: PMC8782894 DOI: 10.1038/s41467-021-27716-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/03/2021] [Indexed: 02/06/2023] Open
Abstract
Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100Ahi/HLA-DRlo classical monocytes and activated LAG-3hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8+ clones, unmutated IGHG+ B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19.
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MESH Headings
- Adaptive Immunity/drug effects
- Adaptive Immunity/genetics
- Adaptive Immunity/immunology
- Aged
- Antibodies, Monoclonal, Humanized/therapeutic use
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- COVID-19/genetics
- COVID-19/immunology
- Cells, Cultured
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/immunology
- Humans
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Male
- RNA-Seq/methods
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Single-Cell Analysis/methods
- COVID-19 Drug Treatment
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Affiliation(s)
- Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel.
| | - Tomokazu S Sumida
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA.
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA.
| | - Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Amy Y Zhao
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Hiromitsu Asashima
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Carlos Cosme
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Wenxuan Deng
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Ming Chen
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Micha Sam Brickman Raredon
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Guilin Wang
- Yale Center for Genome Analysis/Keck Biotechnology Resource Laboratory, Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Neal G Ravindra
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ningshan Li
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Patrick Wong
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - John Fournier
- School of Medicine, Yale University, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anthony Melillo
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Yan Stein
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Maksym Minasyan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - William E Ruff
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Inessa Cohen
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Khadir Raddassi
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Laura E Niklason
- Departments of Anesthesiology & Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Ruth R Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shelli F Farhadian
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - David van Dijk
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Steven H Kleinstein
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- West Haven Veterans Affair Medical Center, West Haven, CT, USA
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8
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Raredon MSB, Fisher C, Heerdt PM, Schonberger RB, Nargi A, Nivison S, Fajardo E, Deshpande R, Akhtar S, Greaney AM, Belter J, Raredon T, Zinter J, McKee A, Michalski M, Baevova P, Niklason LE. Pressure-Regulated Ventilator Splitting for Disaster Relief: Design, Testing, and Clinical Experience. Anesth Analg 2021; 134:1094-1105. [PMID: 34928890 DOI: 10.1213/ane.0000000000005825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has revealed that even the best-resourced hospitals may lack sufficient ventilators to support patients under surge conditions. During a pandemic or mass trauma, an affordable, low-maintenance, off-the-shelf device that would allow health care teams to rapidly expand their ventilator capacity could prove lifesaving, but only if it can be safely integrated into a complex and rapidly changing clinical environment. Here, we define an approach to safe ventilator sharing that prioritizes predictable and independent care of patients sharing a ventilator. Subsequently, we detail the design and testing of a ventilator-splitting circuit that follows this approach and describe our clinical experience with this circuit during the COVID-19 pandemic. This circuit was able to provide individualized and titratable ventilatory support with individualized positive end-expiratory pressure (PEEP) to 2 critically ill patients at the same time, while insulating each patient from changes in the other's condition. We share insights from our experience using this technology in the intensive care unit and outline recommendations for future clinical applications.
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Affiliation(s)
- Micha Sam Brickman Raredon
- From the Department of Biomedical Engineering, Yale University, New Haven, Connecticut.,Medical Scientist Training Program
| | - Clark Fisher
- Department of Anesthesiology, Yale School of Medicine, New Haven, Connecticut
| | - Paul M Heerdt
- Department of Anesthesiology, Yale School of Medicine, New Haven, Connecticut
| | | | - Alyssa Nargi
- Division of Respiratory Care, Yale-New Haven Hospital, New Haven, Connecticut
| | - Steven Nivison
- Division of Respiratory Care, Yale-New Haven Hospital, New Haven, Connecticut
| | - Elaine Fajardo
- Division of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Ranjit Deshpande
- Department of Anesthesiology, Yale School of Medicine, New Haven, Connecticut
| | - Shamsuddin Akhtar
- Department of Anesthesiology, Yale School of Medicine, New Haven, Connecticut
| | - Allison M Greaney
- From the Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Joseph Belter
- Center for Engineering Innovation and Design, Yale University, New Haven, Connecticut
| | | | - Joseph Zinter
- Center for Engineering Innovation and Design, Yale University, New Haven, Connecticut
| | - Andrew McKee
- Headland Strategy Group, San Francisco, California
| | | | - Pavlina Baevova
- Department of Anesthesiology, Yale School of Medicine, New Haven, Connecticut
| | - Laura E Niklason
- From the Department of Biomedical Engineering, Yale University, New Haven, Connecticut.,Department of Anesthesiology, Yale School of Medicine, New Haven, Connecticut
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9
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Yuan Y, Leiby KL, Greaney AM, Raredon MSB, Qian H, Schupp JC, Engler AJ, Baevova P, Adams TS, Kural MH, Wang J, Obata T, Yoder MC, Kaminski N, Niklason LE. A Pulmonary Vascular Model From Endothelialized Whole Organ Scaffolds. Front Bioeng Biotechnol 2021; 9:760309. [PMID: 34869270 PMCID: PMC8640093 DOI: 10.3389/fbioe.2021.760309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
The development of an in vitro system for the study of lung vascular disease is critical to understanding human pathologies. Conventional culture systems fail to fully recapitulate native microenvironmental conditions and are typically limited in their ability to represent human pathophysiology for the study of disease and drug mechanisms. Whole organ decellularization provides a means to developing a construct that recapitulates structural, mechanical, and biological features of a complete vascular structure. Here, we developed a culture protocol to improve endothelial cell coverage in whole lung scaffolds and used single-cell RNA-sequencing analysis to explore the impact of decellularized whole lung scaffolds on endothelial phenotypes and functions in a biomimetic bioreactor system. Intriguingly, we found that the phenotype and functional signals of primary pulmonary microvascular revert back—at least partially—toward native lung endothelium. Additionally, human induced pluripotent stem cell-derived endothelium cultured in decellularized lung systems start to gain various native human endothelial phenotypes. Vascular barrier function was partially restored, while small capillaries remained patent in endothelial cell-repopulated lungs. To evaluate the ability of the engineered endothelium to modulate permeability in response to exogenous stimuli, lipopolysaccharide (LPS) was introduced into repopulated lungs to simulate acute lung injury. After LPS treatment, proinflammatory signals were significantly increased and the vascular barrier was impaired. Taken together, these results demonstrate a novel platform that recapitulates some pulmonary microvascular functions and phenotypes at a whole organ level. This development may help pave the way for using the whole organ engineering approach to model vascular diseases.
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Affiliation(s)
- Yifan Yuan
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Katherine L Leiby
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States.,Medical Scientist Training Program, Yale University, New Haven, CT, United States
| | - Allison M Greaney
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Micha Sam Brickman Raredon
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States.,Medical Scientist Training Program, Yale University, New Haven, CT, United States
| | - Hong Qian
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States.,Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Alexander J Engler
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Pavlina Baevova
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Mehmet H Kural
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Juan Wang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Tomohiro Obata
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Mervin C Yoder
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Laura E Niklason
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States
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10
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Raredon MSB, Engler AJ, Yuan Y, Greaney AM, Niklason LE. Microvascular fluid flow in ex vivo and engineered lungs. J Appl Physiol (1985) 2021; 131:1444-1459. [PMID: 34554016 PMCID: PMC8616606 DOI: 10.1152/japplphysiol.00286.2020] [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: 04/15/2020] [Revised: 08/23/2021] [Accepted: 09/15/2021] [Indexed: 11/22/2022] Open
Abstract
In recent years, it has become common to experiment with ex vivo perfused lungs for organ transplantation and to attempt regenerative pulmonary engineering using decellularized lung matrices. However, our understanding of the physiology of ex vivo organ perfusion is imperfect; it is not currently well understood how decreasing microvascular barrier affects the perfusion of pulmonary parenchyma. In addition, protocols for lung perfusion and organ culture fluid-handling are far from standardized, with widespread variation on both basic methods and on ideally controlled parameters. To address both of these deficits, a robust, noninvasive, and mechanistic model is needed which is able to predict microvascular resistance and permeability in perfused lungs while providing insight into capillary recruitment. Although validated mathematical models exist for fluid flow in native pulmonary tissue, previous models generally assume minimal intravascular leak from artery to vein and do not assess capillary bed recruitment. Such models are difficult to apply to both ex vivo lung perfusions, in which edema can develop over time and microvessels can become blocked, and to decellularized ex vivo organomimetic cultures, in which microvascular recruitment is variable and arterially perfused fluid enters into the alveolar space. Here, we develop a mathematical model of pulmonary microvascular fluid flow which is applicable in both instances, and we apply our model to data from native, decellularized, and regenerating lungs under ex vivo perfusion. The results provide substantial insight into microvascular pressure-flow mechanics, while producing previously unknown output values for tissue-specific capillary-alveolar hydraulic conductivity, microvascular recruitment, and total organ barrier resistance.NEW & NOTEWORTHY We present a validated model of pulmonary microvascular fluid mechanics and apply this model to study the effects of increased capillary permeability in decellularized and regenerating lungs. We find that decellularization alters microvascular steady-state mechanics and that re-endothelialization partially rescues key biologic parameters. The described model provides powerful insight into intraorgan microvascular dynamics and may be used to guide regenerative engineering experiments. We include all data and derivations necessary to replicate this work.
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Affiliation(s)
- Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Vascular Biology and Therapeutics, Yale University, New Haven, Connecticut
- Medical Scientist Training Program, Yale University, New Haven, Connecticut
| | - Alexander J Engler
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Vascular Biology and Therapeutics, Yale University, New Haven, Connecticut
| | - Yifan Yuan
- Vascular Biology and Therapeutics, Yale University, New Haven, Connecticut
- Department of Anesthesiology, Yale University, New Haven, Connecticut
| | - Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Vascular Biology and Therapeutics, Yale University, New Haven, Connecticut
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Vascular Biology and Therapeutics, Yale University, New Haven, Connecticut
- Department of Anesthesiology, Yale University, New Haven, Connecticut
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11
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Manning EP, Ramachandra AB, Schupp JC, Cavinato C, Raredon MSB, Bärnthaler T, Cosme C, Singh I, Tellides G, Kaminski N, Humphrey JD. Mechanisms of Hypoxia-Induced Pulmonary Arterial Stiffening in Mice Revealed by a Functional Genetics Assay of Structural, Functional, and Transcriptomic Data. Front Physiol 2021; 12:726253. [PMID: 34594238 PMCID: PMC8478173 DOI: 10.3389/fphys.2021.726253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/19/2021] [Indexed: 01/08/2023] Open
Abstract
Hypoxia adversely affects the pulmonary circulation of mammals, including vasoconstriction leading to elevated pulmonary arterial pressures. The clinical importance of changes in the structure and function of the large, elastic pulmonary arteries is gaining increased attention, particularly regarding impact in multiple chronic cardiopulmonary conditions. We establish a multi-disciplinary workflow to understand better transcriptional, microstructural, and functional changes of the pulmonary artery in response to sustained hypoxia and how these changes inter-relate. We exposed adult male C57BL/6J mice to normoxic or hypoxic (FiO2 10%) conditions. Excised pulmonary arteries were profiled transcriptionally using single cell RNA sequencing, imaged with multiphoton microscopy to determine microstructural features under in vivo relevant multiaxial loading, and phenotyped biomechanically to quantify associated changes in material stiffness and vasoactive capacity. Pulmonary arteries of hypoxic mice exhibited an increased material stiffness that was likely due to collagen remodeling rather than excessive deposition (fibrosis), a change in smooth muscle cell phenotype reflected by decreased contractility and altered orientation aligning these cells in the same direction as the remodeled collagen fibers, endothelial proliferation likely representing endothelial-to-mesenchymal transitioning, and a network of cell-type specific transcriptomic changes that drove these changes. These many changes resulted in a system-level increase in pulmonary arterial pulse wave velocity, which may drive a positive feedback loop exacerbating all changes. These findings demonstrate the power of a multi-scale genetic-functional assay. They also highlight the need for systems-level analyses to determine which of the many changes are clinically significant and may be potential therapeutic targets.
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Affiliation(s)
- Edward P Manning
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States.,VA Connecticut Healthcare System, West Haven, CT, United States
| | - Abhay B Ramachandra
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Jonas C Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States.,Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Cristina Cavinato
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States.,Vascular Biology and Therapeutics Program, Yale University, New Haven, CT, United States.,Department of Anesthesiology, Yale School of Medicine, New Haven, CT, United States
| | - Thomas Bärnthaler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States.,Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Carlos Cosme
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Inderjit Singh
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - George Tellides
- VA Connecticut Healthcare System, West Haven, CT, United States.,Vascular Biology and Therapeutics Program, Yale University, New Haven, CT, United States.,Department of Surgery, Yale School of Medicine, New Haven, CT, United States
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Jay D Humphrey
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States.,Vascular Biology and Therapeutics Program, Yale University, New Haven, CT, United States
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12
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Sphabmixay P, Raredon MSB, Wang AJS, Lee H, Hammond PT, Fang NX, Griffith LG. High resolution stereolithography fabrication of perfusable scaffolds to enable long-term meso-scale hepatic culture for disease modeling. Biofabrication 2021; 13. [PMID: 34479229 DOI: 10.1088/1758-5090/ac23aa] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022]
Abstract
Microphysiological systems (MPS), comprising human cell cultured in formats that capture features of the three-dimensional (3D) microenvironments of native human organs under microperfusion, are promising tools for biomedical research. Here we report the development of a mesoscale physiological system (MePS) enabling the long-term 3D perfused culture of primary human hepatocytes at scales of over 106cells per MPS. A central feature of the MePS, which employs a commercially-available multiwell bioreactor for perfusion, is a novel scaffold comprising a dense network of nano- and micro-porous polymer channels, designed to provide appropriate convective and diffusive mass transfer of oxygen and other nutrients while maintaining physiological values of shear stress. The scaffold design is realized by a high resolution stereolithography fabrication process employing a novel resin. This new culture system sustains mesoscopic hepatic tissue-like cultures with greater hepatic functionality (assessed by albumin and urea synthesis, and CYP3A4 activity) and lower inflammation markers compared to comparable cultures on the commercial polystyrene scaffold. To illustrate applications to disease modeling, we established an insulin-resistant phenotype by exposing liver cells to hyperglycemic and hyperinsulinemic media. Future applications of the MePS include the co-culture of hepatocytes with resident immune cells and the integration with multiple organs to model complex liver-associated diseases.
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Affiliation(s)
- Pierre Sphabmixay
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America.,Whitehead Institute of Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States of America.,Vascular Biology and Therapeutics, Yale University, New Haven, CT, United States of America
| | - Alex J-S Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Howon Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Paula T Hammond
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Nicholas X Fang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Linda G Griffith
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America.,Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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13
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Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021; 144:286-302. [PMID: 34030460 PMCID: PMC8300155 DOI: 10.1161/circulationaha.120.052318] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cellular diversity of the lung endothelium has not been systematically characterized in humans. We provide a reference atlas of human lung endothelial cells (ECs) to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium. METHODS We reprocessed human control single-cell RNA sequencing (scRNAseq) data from 6 datasets. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by fluorescent microscopy and in situ hybridization. scRNAseq of primary lung ECs cultured in vitro was performed. The signaling network between different lung cell types was studied. For cross-species analysis or disease relevance, we applied the same methods to scRNAseq data obtained from mouse lungs or from human lungs with pulmonary hypertension. RESULTS Six lung scRNAseq datasets were reanalyzed and annotated to identify >15 000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including panendothelial, panvascular, and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial, and venous ECs, we found previously indistinguishable subpopulations; among venous EC, we identified 2 previously indistinguishable populations: pulmonary-venous ECs (COL15A1neg) localized to the lung parenchyma and systemic-venous ECs (COL15A1pos) localized to the airways and the visceral pleura; among capillary ECs, we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1, and TBX2 and general capillary EC. We confirmed that all 6 endothelial cell types, including the systemic-venous ECs and aerocytes, are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. scRNAseq of commercially available primary lung ECs demonstrated a loss of their native lung phenotype in culture. scRNAseq revealed that endothelial diversity is maintained in pulmonary hypertension. Our article is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com). CONCLUSIONS Our integrated analysis provides a comprehensive and well-crafted reference atlas of ECs in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice.
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Affiliation(s)
- Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Taylor S. Adams
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Carlos Cosme
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering (M.S.B.R., L.E.N.), Yale University, New Haven, CT
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Yifan Yuan
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
- Department of Anesthesiology (Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Sergio Poli
- Department of Medicine, Baylor College of Medicine, Houston, TX (S.P., I.O.R.)
- Division of Internal Medicine, Mount Sinai Medical Center, Miami Beach, FL (S.P.)
| | - Maurizio Chioccioli
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Kadi-Ann Rose
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Edward P. Manning
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
- VA Connecticut Healthcare System (E.P.M.), West Haven
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Giuseppe DeIuliis
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Nir Neumark
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (A.C.H., J.A.K.)
| | - Austin J. Gutierrez
- Translational Genomics Research Institute, Phoenix, AZ (A.J.G., L.T.B., N.E.B.)
| | - Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ (A.J.G., L.T.B., N.E.B.)
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, PA (R.L.)
| | - Richard W. Pierce
- Department of Pediatrics (R.W.P.), Yale University School of Medicine, New Haven, CT
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (K.B.M., S.A.T.)
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology (M.C.N.), University Medical Center Groningen, University of Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (M.C.N.), University Medical Center Groningen, University of Groningen, The Netherlands
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (K.B.M., S.A.T.)
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, UK (S.A.T.)
| | | | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (A.C.H., J.A.K.)
- Department of Veterans Affairs Medical Center, Nashville, TN (J.A.K.)
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN (J.A.K.)
| | - Laura E. Niklason
- Department of Biomedical Engineering (M.S.B.R., L.E.N.), Yale University, New Haven, CT
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
- Department of Anesthesiology (Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Dana Pe’er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (D.P.)
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Robert J. Homer
- Department of Pathology (R.J.H.), Yale University School of Medicine, New Haven, CT
- Pathology and Laboratory Medicine Service (R.J.H.), West Haven
| | - Ivan O. Rosas
- Department of Medicine, Baylor College of Medicine, Houston, TX (S.P., I.O.R.)
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
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14
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Greaney AM, Adams TS, Brickman Raredon MS, Gubbins E, Schupp JC, Engler AJ, Ghaedi M, Yuan Y, Kaminski N, Niklason LE. Platform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing. Cell Rep 2020; 30:4250-4265.e6. [PMID: 32209482 PMCID: PMC7175071 DOI: 10.1016/j.celrep.2020.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/24/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-based therapies have shown promise for treating myriad chronic pulmonary diseases through direct application of epithelial progenitors or by way of engineered tissue grafts or whole organs. To elucidate environmental effects on epithelial regenerative outcomes in vitro, here, we isolate and culture a population of pharmacologically expanded basal cells (peBCs) from rat tracheas. At peak basal marker expression, we simultaneously split peBCs into four in vitro platforms: organoid, air-liquid interface (ALI), engineered trachea, and engineered lung. Following differentiation, these samples are evaluated using single-cell RNA sequencing (scRNA-seq) and computational pipelines are developed to compare samples both globally and at the population level. A sample of native rat tracheal epithelium is also evaluated by scRNA-seq as a control for engineered epithelium. Overall, this work identifies platform-specific effects that support the use of engineered models to achieve the most physiologic differential outcomes in pulmonary epithelial regenerative applications.
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Affiliation(s)
- Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA.
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Medical Scientist Training Program, Yale University, New Haven, CT 06511, USA
| | - Elise Gubbins
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Alexander J Engler
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA
| | - Mahboobe Ghaedi
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Yifan Yuan
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
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15
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Abstract
The pulmonary blood-gas barrier represents a remarkable feat of engineering. It achieves the exquisite thinness needed for gas exchange by diffusion, the strength to withstand the stresses and strains of repetitive and changing ventilation, and the ability to actively maintain itself under varied demands. Understanding the design principles of this barrier is essential to understanding a variety of lung diseases, and to successfully regenerating or artificially recapitulating the barrier ex vivo. Many classical studies helped to elucidate the unique structure and morphology of the mammalian blood-gas barrier, and ongoing investigations have helped to refine these descriptions and to understand the biological aspects of blood-gas barrier function and regulation. This article reviews the key features of the blood-gas barrier that enable achievement of the necessary design criteria and describes the mechanical environment to which the barrier is exposed. It then focuses on the biological and mechanical components of the barrier that preserve integrity during homeostasis, but which may be compromised in certain pathophysiological states, leading to disease. Finally, this article summarizes recent key advances in efforts to engineer the blood-gas barrier ex vivo, using the platforms of lung-on-a-chip and tissue-engineered whole lungs. © 2020 American Physiological Society. Compr Physiol 10:415-452, 2020.
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Affiliation(s)
- Katherine L. Leiby
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
- Department of Anesthesiology, Yale University, New Haven, Connecticut, USA
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16
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Raredon MSB, Adams TS, Suhail Y, Schupp JC, Poli S, Neumark N, Leiby KL, Greaney AM, Yuan Y, Horien C, Linderman G, Engler AJ, Boffa DJ, Kluger Y, Rosas IO, Levchenko A, Kaminski N, Niklason LE. Single-cell connectomic analysis of adult mammalian lungs. Sci Adv 2019; 5:eaaw3851. [PMID: 31840053 PMCID: PMC6892628 DOI: 10.1126/sciadv.aaw3851] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 09/18/2019] [Indexed: 05/17/2023]
Abstract
Efforts to decipher chronic lung disease and to reconstitute functional lung tissue through regenerative medicine have been hampered by an incomplete understanding of cell-cell interactions governing tissue homeostasis. Because the structure of mammalian lungs is highly conserved at the histologic level, we hypothesized that there are evolutionarily conserved homeostatic mechanisms that keep the fine architecture of the lung in balance. We have leveraged single-cell RNA sequencing techniques to identify conserved patterns of cell-cell cross-talk in adult mammalian lungs, analyzing mouse, rat, pig, and human pulmonary tissues. Specific stereotyped functional roles for each cell type in the distal lung are observed, with alveolar type I cells having a major role in the regulation of tissue homeostasis. This paper provides a systems-level portrait of signaling between alveolar cell populations. These methods may be applicable to other organs, providing a roadmap for identifying key pathways governing pathophysiology and informing regenerative efforts.
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Affiliation(s)
- Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Taylor Sterling Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
| | - Yasir Suhail
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jonas Christian Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
| | - Sergio Poli
- Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nir Neumark
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Katherine L. Leiby
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Allison Marie Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
| | - Yifan Yuan
- Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Corey Horien
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA
| | - George Linderman
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT 06510, USA
- Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
| | - Alexander J. Engler
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
| | - Daniel J. Boffa
- Thoracic Surgery, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yuval Kluger
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
- Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Ivan O. Rosas
- Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT 06520, USA
- Corresponding author. (N.K.); (L.E.N.)
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06520, USA
- Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
- Corresponding author. (N.K.); (L.E.N.)
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17
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Raredon MSB, Rocco KA, Gheorghe CP, Sivarapatna A, Ghaedi M, Balestrini JL, Raredon TL, Calle EA, Niklason LE. Biomimetic Culture Reactor for Whole-Lung Engineering. Biores Open Access 2016; 5:72-83. [PMID: 27088061 PMCID: PMC4827315 DOI: 10.1089/biores.2016.0006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Decellularized organs are now established as promising scaffolds for whole-organ regeneration. For this work to reach therapeutic practice, techniques and apparatus are necessary for doing human-scale clinically applicable organ cultures. We have designed and constructed a bioreactor system capable of accommodating whole human or porcine lungs, and we describe in this study relevant technical details, means of assembly and operation, and validation. The reactor has an artificial diaphragm that mimics the conditions found in the chest cavity in vivo, driving hydraulically regulated negative pressure ventilation and custom-built pulsatile perfusion apparatus capable of driving pressure-regulated or volume-regulated vascular flow. Both forms of mechanical actuation can be tuned to match specific physiologic profiles. The organ is sealed in an elastic artificial pleura that mounts to a support architecture. This pleura reduces the fluid volume required for organ culture, maintains the organ's position during mechanical conditioning, and creates a sterile barrier allowing disassembly and maintenance outside of a biosafety cabinet. The combination of fluid suspension, negative-pressure ventilation, and physiologic perfusion allows the described system to provide a biomimetic mechanical environment not found in existing technologies and especially suited to whole-organ regeneration. In this study, we explain the design and operation of this apparatus and present data validating intended functions.
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Affiliation(s)
- Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Department of Anesthesia, Yale University, New Haven, Connecticut
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Kevin A. Rocco
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Department of Anesthesia, Yale University, New Haven, Connecticut
| | - Ciprian P. Gheorghe
- Department of Obstetrics, Gynecology, and Reproductive Services, Yale University, New Haven, Connecticut
| | - Amogh Sivarapatna
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Department of Anesthesia, Yale University, New Haven, Connecticut
| | - Mahboobe Ghaedi
- Department of Anesthesia, Yale University, New Haven, Connecticut
| | - Jenna L. Balestrini
- Department of Anesthesia, Yale University, New Haven, Connecticut
- Department of Pathology, Yale University, New Haven, Connecticut
| | | | - Elizabeth A. Calle
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Department of Anesthesia, Yale University, New Haven, Connecticut
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Department of Anesthesia, Yale University, New Haven, Connecticut
- Address correspondence to: Laura E. Niklason, MD, PhD, Department Biomedical Engineering, Yale University, 10 Amistad Street, Room 301D, New Haven, CT 06511, E-mail:
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18
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Raredon MSB, Ghaedi M, Calle EA, Niklason LE. A Rotating Bioreactor for Scalable Culture and Differentiation of Respiratory Epithelium. Cell Med 2014; 7:109-21. [PMID: 26858899 DOI: 10.3727/215517914x681794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Respiratory epithelium is difficult to grow in vitro, as it requires a well-maintained polarizing air-liquid interface (ALI) to maintain differentiation. Traditional methods rely on permeable membrane culture inserts, which are difficult to work with and are ill-suited for the production of large numbers of cells, such as the quantities required for cell-based clinical therapies. Herein, we investigate an alternative form of culture in which the cells are placed on a porous substrate that is continuously rolled, such that the monolayer of cells is alternately submerged in media or apically exposed to air. Our prototype bioreactor is reliable for up to 21 days of continuous culture and is designed for scale-up for large-scale cell culture with continuous medium and gas exchange. Normal human bronchial epithelial (NHBE) cells were cultured on an absorbent substrate in the reactor for periods of 7, 14, and 21 days and were compared to static controls that were submerged in media. Quantification by immunohistochemistry and quantitative PCR of markers specific to differentiated respiratory epithelium indicated increased cilia, mucous production, and tight junction formation in the rolled cultures, compared to static. Together with scanning electron microscopy and paraffin histology, the data indicate that the intermittent ALI provided by the rolling bioreactor promotes a polarized epithelial phenotype over a period of 21 days.
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Affiliation(s)
| | - Mahboobe Ghaedi
- Department of Biomedical Engineering, Yale University , New Haven, CT , USA
| | - Elizabeth A Calle
- Department of Biomedical Engineering, Yale University , New Haven, CT , USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; †Department of Anesthesia, Yale University, New Haven, CT, USA
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19
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Abstract
Educational institutions must begin training tissue engineers to think as both biomedical investigators and fabricators.
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Affiliation(s)
- Micha Sam Brickman Raredon
- Department of Biomedical Engineering and Department of Anesthesia, Yale University, New Haven, CT 06520, USA
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