1
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Burgess CL, Huang J, Bawa PS, Alysandratos KD, Minakin K, Ayers LJ, Morley MP, Babu A, Villacorta-Martin C, Yampolskaya M, Hinds A, Thapa BR, Wang F, Matschulat A, Mehta P, Morrisey EE, Varelas X, Kotton DN. Generation of human alveolar epithelial type I cells from pluripotent stem cells. Cell Stem Cell 2024; 31:657-675.e8. [PMID: 38642558 DOI: 10.1016/j.stem.2024.03.017] [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: 01/13/2023] [Revised: 01/31/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Alveolar epithelial type I cells (AT1s) line the gas exchange barrier of the distal lung and have been historically challenging to isolate or maintain in cell culture. Here, we engineer a human in vitro AT1 model system via directed differentiation of induced pluripotent stem cells (iPSCs). We use primary adult AT1 global transcriptomes to suggest benchmarks and pathways, such as Hippo-LATS-YAP/TAZ signaling, enriched in these cells. Next, we generate iPSC-derived alveolar epithelial type II cells (AT2s) and find that nuclear YAP signaling is sufficient to promote a broad transcriptomic shift from AT2 to AT1 gene programs. The resulting cells express a molecular, morphologic, and functional phenotype reminiscent of human AT1 cells, including the capacity to form a flat epithelial barrier producing characteristic extracellular matrix molecules and secreted ligands. Our results provide an in vitro model of human alveolar epithelial differentiation and a potential source of human AT1s.
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Affiliation(s)
- Claire L Burgess
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pushpinder S Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Kasey Minakin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Lauren J Ayers
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Michael P Morley
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apoorva Babu
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | | | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Bibek R Thapa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Adeline Matschulat
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Edward E Morrisey
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xaralabos Varelas
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA.
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2
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Tang W, Huang J, Pegoraro AF, Zhang JH, Tang Y, Bi D, Kotton DN, Guo M. Nuclear size-regulated emergence of topological packing order on growing human lung alveolospheres. bioRxiv 2024:2024.04.17.589951. [PMID: 38659777 PMCID: PMC11042317 DOI: 10.1101/2024.04.17.589951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Within multicellular living systems, cells coordinate their positions with spatiotemporal accuracy to form various structures, setting the clock to control developmental processes and trigger maturation. These arrangements can be regulated by tissue topology, biochemical cues, as well as mechanical perturbations. However, the fundamental rules of how local cell packing order is regulated in forming three-dimensional (3D) multicellular architectures remain unclear. Furthermore, how cellular coordination evolves during developmental processes, and whether this cell patterning behavior is indicative of more complex biological functions, is largely unknown. Here, using human lung alveolospheres as a model system, by combining experiments and numerical simulations, we find that, surprisingly, cell packing behavior on alveolospheres resembles hard-disk packing but with increased randomness; the stiffer cell nuclei act as the hard disks surrounded by deformable cell bodies. Interestingly, we observe the emergence of topological packing order during alveolosphere growth, as a result of increasing nucleus-to-cell size ratio. Specifically, we find more hexagon-concentrated cellular packing with increasing bond orientational order, indicating a topological gas-to-liquid transition. Additionally, by osmotically changing the compactness of cells on alveolospheres, we observe that the variations in packing order align with the change of nucleus-to-cell size ratio. Together, our findings reveal the underlying rules of cell coordination and topological phases during human lung alveolosphere growth. These static packing characteristics are consistent with cell dynamics, together suggesting that better cellular packing stabilizes local cell neighborhoods and may regulate more complex biological functions such as organ development and cellular maturation.
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3
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Basil MC, Alysandratos KD, Kotton DN, Morrisey EE. Lung repair and regeneration: Advanced models and insights into human disease. Cell Stem Cell 2024; 31:439-454. [PMID: 38492572 DOI: 10.1016/j.stem.2024.02.009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
The respiratory system acts as both the primary site of gas exchange and an important sensor and barrier to the external environment. The increase in incidences of respiratory disease over the past decades has highlighted the importance of developing improved therapeutic approaches. This review will summarize recent research on the cellular complexity of the mammalian respiratory system with a focus on gas exchange and immunological defense functions of the lung. Different models of repair and regeneration will be discussed to help interpret human and animal data and spur the investigation of models and assays for future drug development.
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Affiliation(s)
- Maria C Basil
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Edward E Morrisey
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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4
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Rodriguez LR, Alysandratos KD, Katzen J, Murthy A, Barboza WR, Tomer Y, Acin-Perez R, Petcherski A, Minakin K, Carson P, Iyer S, Chavez K, Cooper CH, Babu A, Weiner AI, Vaughan AE, Arany Z, Shirihai OS, Kotton DN, Beers MF. Impaired AMPK Control of Alveolar Epithelial Cell Metabolism Promotes Pulmonary Fibrosis. bioRxiv 2024:2024.03.26.586649. [PMID: 38585863 PMCID: PMC10996612 DOI: 10.1101/2024.03.26.586649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Alveolar epithelial type II (AT2) cell dysfunction is implicated in the pathogenesis of familial and sporadic idiopathic pulmonary fibrosis (IPF). We previously described that expression of an AT2 cell exclusive disease-associated protein isoform (SP-CI73T) in murine and patient-specific induced pluripotent stem cell (iPSC)-derived AT2 cells leads to a block in late macroautophagy and promotes time-dependent mitochondrial impairments; however, how a metabolically dysfunctional AT2 cell results in fibrosis remains elusive. Here using murine and human iPSC-derived AT2 cell models expressing SP-CI73T, we characterize the molecular mechanisms governing alterations in AT2 cell metabolism that lead to increased glycolysis, decreased mitochondrial biogenesis, disrupted fatty acid oxidation, accumulation of impaired mitochondria, and diminished AT2 cell progenitor capacity manifesting as reduced AT2 self-renewal and accumulation of transitional epithelial cells. We identify deficient AMP-kinase signaling as a key upstream signaling hub driving disease in these dysfunctional AT2 cells and augment this pathway to restore alveolar epithelial metabolic function, thus successfully alleviating lung fibrosis in vivo.
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5
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Eiken MK, Childs CJ, Brastrom LK, Frum T, Plaster EM, Shachaf O, Pfeiffer S, Levine JE, Alysandratos KD, Kotton DN, Spence JR, Loebel C. Nascent matrix deposition supports alveolar organoid formation from aggregates in synthetic hydrogels. bioRxiv 2024:2024.03.19.585720. [PMID: 38562781 PMCID: PMC10983987 DOI: 10.1101/2024.03.19.585720] [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: 04/04/2024]
Abstract
Human induced pluripotent stem cell (iPSC) derived alveolar organoids have emerged as a system to model the alveolar epithelium in homeostasis and disease. However, alveolar organoids are typically grown in Matrigel, a mouse-sarcoma derived basement membrane matrix that offers poor control over matrix properties, prompting the development of synthetic hydrogels as a Matrigel alternative. Here, we develop a two-step culture method that involves pre-aggregation of organoids in hydrogel-based microwells followed by embedding in a synthetic hydrogel that supports alveolar organoid growth, while also offering considerable control over organoid and hydrogel properties. We find that the aggregated organoids secrete their own nascent extracellular matrix (ECM) both in the microwells and upon embedding in the synthetic hydrogels. Thus, the synthetic gels described here allow us to de-couple exogenous and nascent ECM in order to interrogate the role of ECM in organoid formation.
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Affiliation(s)
- Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lindy K. Brastrom
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eleanor M. Plaster
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Orren Shachaf
- Department of Biomedical Engineering, University of Texas, Austin, TX, USA
| | - Suzanne Pfeiffer
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Justin E. Levine
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jason R. Spence
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
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6
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Montesi SB, Gomez CR, Beers M, Brown R, Chattopadhyay I, Flaherty KR, Garcia CK, Gomperts B, Hariri LP, Hogaboam CM, Jenkins RG, Kaminski N, Kim GHJ, Königshoff M, Kolb M, Kotton DN, Kropski JA, Lasky J, Magin CM, Maher TM, McCormick M, Moore BB, Nickerson-Nutter C, Oldham J, Podolanczuk AJ, Raghu G, Rosas I, Rowe SM, Schmidt WT, Schwartz D, Shore JE, Spino C, Craig JM, Martinez FJ. Pulmonary Fibrosis Stakeholder Summit: A Joint NHLBI, Three Lakes Foundation, and Pulmonary Fibrosis Foundation Workshop Report. Am J Respir Crit Care Med 2024; 209:362-373. [PMID: 38113442 PMCID: PMC10878386 DOI: 10.1164/rccm.202307-1154ws] [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: 07/06/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023] Open
Abstract
Despite progress in elucidation of disease mechanisms, identification of risk factors, biomarker discovery, and the approval of two medications to slow lung function decline in idiopathic pulmonary fibrosis and one medication to slow lung function decline in progressive pulmonary fibrosis, pulmonary fibrosis remains a disease with a high morbidity and mortality. In recognition of the need to catalyze ongoing advances and collaboration in the field of pulmonary fibrosis, the NHLBI, the Three Lakes Foundation, and the Pulmonary Fibrosis Foundation hosted the Pulmonary Fibrosis Stakeholder Summit on November 8-9, 2022. This workshop was held virtually and was organized into three topic areas: 1) novel models and research tools to better study pulmonary fibrosis and uncover new therapies, 2) early disease risk factors and methods to improve diagnosis, and 3) innovative approaches toward clinical trial design for pulmonary fibrosis. In this workshop report, we summarize the content of the presentations and discussions, enumerating research opportunities for advancing our understanding of the pathogenesis, treatment, and outcomes of pulmonary fibrosis.
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Affiliation(s)
| | - Christian R. Gomez
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael Beers
- Pulmonary and Critical Care Division, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert Brown
- Program in Neurotherapeutics, University of Massachusetts Chan Medical School, Worchester, Massachusetts
| | | | | | - Christine Kim Garcia
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, New York
| | | | - Lida P. Hariri
- Division of Pulmonary and Critical Care Medicine and
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Cory M. Hogaboam
- Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Grace Hyun J. Kim
- Center for Computer Vision and Imaging Biomarkers, Department of Radiological Sciences, David Geffen School of Medicine, and
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
| | - Melanie Königshoff
- Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Martin Kolb
- Division of Respirology, McMaster University, Hamilton, Ontario, Canada
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph Lasky
- Pulmonary Fibrosis Foundation, Chicago, Illinois
- Department of Medicine, Tulane University, New Orleans, Louisiana
| | - Chelsea M. Magin
- Department of Bioengineering
- Department of Pediatrics
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, and
| | - Toby M. Maher
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | | | | | | | - Anna J. Podolanczuk
- Division of Pulmonary and Critical Care, Weill Cornell Medical College, New York, New York
| | - Ganesh Raghu
- Division of Pulmonary, Sleep and Critical Care Medicine, University of Washington, Seattle, Washington
| | - Ivan Rosas
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, Texas; and
| | - Steven M. Rowe
- Department of Medicine and
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - David Schwartz
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Cathie Spino
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - J. Matthew Craig
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care, Weill Cornell Medical College, New York, New York
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7
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Miao Y, Tan C, Pek NM, Yu Z, Iwasawa K, Kechele DO, Sundaram N, Pastrana-Gomez V, Kishimoto K, Yang MC, Jiang C, Tchieu J, Whitsett JA, McCracken KW, Rottier RJ, Kotton DN, Helmrath MA, Wells JM, Takebe T, Zorn AM, Chen YW, Guo M, Gu M. Deciphering Endothelial and Mesenchymal Organ Specification in Vascularized Lung and Intestinal Organoids. bioRxiv 2024:2024.02.06.577460. [PMID: 38370768 PMCID: PMC10871227 DOI: 10.1101/2024.02.06.577460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
To investigate the co-development of vasculature, mesenchyme, and epithelium crucial for organogenesis and the acquisition of organ-specific characteristics, we constructed a human pluripotent stem cell-derived organoid system comprising lung or intestinal epithelium surrounded by organotypic mesenchyme and vasculature. We demonstrated the pivotal role of co-differentiating mesoderm and endoderm via precise BMP regulation in generating multilineage organoids and gut tube patterning. Single-cell RNA-seq analysis revealed organ specificity in endothelium and mesenchyme, and uncovered key ligands driving endothelial specification in the lung (e.g., WNT2B and Semaphorins) or intestine (e.g., GDF15). Upon transplantation under the kidney capsule in mice, these organoids further matured and developed perfusable human-specific sub-epithelial capillaries. Additionally, our model recapitulated the abnormal endothelial-epithelial crosstalk in patients with FOXF1 deletion or mutations. Multilineage organoids provide a unique platform to study developmental cues guiding endothelial and mesenchymal cell fate determination, and investigate intricate cell-cell communications in human organogenesis and disease. Highlights BMP signaling fine-tunes the co-differentiation of mesoderm and endoderm.The cellular composition in multilineage organoids resembles that of human fetal organs.Mesenchyme and endothelium co-developed within the organoids adopt organ-specific characteristics.Multilineage organoids recapitulate abnormal endothelial-epithelial crosstalk in FOXF1-associated disorders.
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8
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Sun YL, Hennessey EE, Heins H, Yang P, Villacorta-Martin C, Kwan J, Gopalan K, James M, Emili A, Cole FS, Wambach JA, Kotton DN. Human pluripotent stem cell modeling of alveolar type 2 cell dysfunction caused by ABCA3 mutations. J Clin Invest 2024; 134:e164274. [PMID: 38226623 PMCID: PMC10786693 DOI: 10.1172/jci164274] [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: 08/08/2022] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
Mutations in ATP-binding cassette A3 (ABCA3), a phospholipid transporter critical for surfactant homeostasis in pulmonary alveolar type II epithelial cells (AEC2s), are the most common genetic causes of childhood interstitial lung disease (chILD). Treatments for patients with pathological variants of ABCA3 mutations are limited, in part due to a lack of understanding of disease pathogenesis resulting from an inability to access primary AEC2s from affected children. Here, we report the generation of AEC2s from affected patient induced pluripotent stem cells (iPSCs) carrying homozygous versions of multiple ABCA3 mutations. We generated syngeneic CRISPR/Cas9 gene-corrected and uncorrected iPSCs and ABCA3-mutant knockin ABCA3:GFP fusion reporter lines for in vitro disease modeling. We observed an expected decreased capacity for surfactant secretion in ABCA3-mutant iPSC-derived AEC2s (iAEC2s), but we also found an unexpected epithelial-intrinsic aberrant phenotype in mutant iAEC2s, presenting as diminished progenitor potential, increased NFκB signaling, and the production of pro-inflammatory cytokines. The ABCA3:GFP fusion reporter permitted mutant-specific, quantifiable characterization of lamellar body size and ABCA3 protein trafficking, functional features that are perturbed depending on ABCA3 mutation type. Our disease model provides a platform for understanding ABCA3 mutation-mediated mechanisms of alveolar epithelial cell dysfunction that may trigger chILD pathogenesis.
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Affiliation(s)
- Yuliang L. Sun
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Erin E. Hennessey
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hillary Heins
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, Missouri, USA
| | - Ping Yang
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, Missouri, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Julian Kwan
- Departments of Biology and Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Krithi Gopalan
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Marianne James
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Andrew Emili
- Departments of Biology and Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - F. Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, Missouri, USA
| | - Jennifer A. Wambach
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, Missouri, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
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9
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Hume AJ, Olejnik J, White MR, Huang J, Turcinovic J, Heiden B, Bawa PS, Williams CJ, Gorham NG, Alekseyev YO, Connor JH, Kotton DN, Mühlberger E. Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality. Pathogens 2024; 13:62. [PMID: 38251369 PMCID: PMC10818917 DOI: 10.3390/pathogens13010062] [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: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies are instrumental to improving our understanding of virus-host interactions in cell culture infection studies and complex biological systems because they allow separating the transcriptional signatures of infected versus non-infected bystander cells. A drawback of using biosafety level (BSL) 4 pathogens is that protocols are typically developed without consideration of virus inactivation during the procedure. To ensure complete inactivation of virus-containing samples for downstream analyses, an adaptation of the workflow is needed. Focusing on a commercially available microfluidic partitioning scRNA-seq platform to prepare samples for scRNA-seq, we tested various chemical and physical components of the platform for their ability to inactivate Nipah virus (NiV), a BSL-4 pathogen that belongs to the group of nonsegmented negative-sense RNA viruses. The only step of the standard protocol that led to NiV inactivation was a 5 min incubation at 85 °C. To comply with the more stringent biosafety requirements for BSL-4-derived samples, we included an additional heat step after cDNA synthesis. This step alone was sufficient to inactivate NiV-containing samples, adding to the necessary inactivation redundancy. Importantly, the additional heat step did not affect sample quality or downstream scRNA-seq results.
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Affiliation(s)
- Adam J. Hume
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Judith Olejnik
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Mitchell R. White
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
- The Pulmonary Center and Department of Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Baylee Heiden
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Pushpinder S. Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
| | - Christopher J. Williams
- Department of Medicine, Single Cell Sequencing Core Facility, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Nickolas G. Gorham
- Microarray and Sequencing Resource Core Facility, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Yuriy O. Alekseyev
- Department of Pathology and Laboratory Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - John H. Connor
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
- The Pulmonary Center and Department of Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
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10
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Yampolskaya M, Herriges MJ, Ikonomou L, Kotton DN, Mehta P. scTOP: physics-inspired order parameters for cellular identification and visualization. Development 2023; 150:dev201873. [PMID: 37756586 PMCID: PMC10629677 DOI: 10.1242/dev.201873] [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: 04/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Advances in single-cell RNA sequencing provide an unprecedented window into cellular identity. The abundance of data requires new theoretical and computational frameworks to analyze the dynamics of differentiation and integrate knowledge from cell atlases. We present 'single-cell Type Order Parameters' (scTOP): a statistical, physics-inspired approach for quantifying cell identity given a reference basis of cell types. scTOP can accurately classify cells, visualize developmental trajectories and assess the fidelity of engineered cells. Importantly, scTOP does this without feature selection, statistical fitting or dimensional reduction (e.g. uniform manifold approximation and projection, principle components analysis, etc.). We illustrate the power of scTOP using human and mouse datasets. By reanalyzing mouse lung data, we characterize a transient hybrid alveolar type 1/alveolar type 2 cell population. Visualizations of lineage tracing hematopoiesis data using scTOP confirm that a single clone can give rise to multiple mature cell types. We assess the transcriptional similarity between endogenous and donor-derived cells in the context of murine pulmonary cell transplantation. Our results suggest that physics-inspired order parameters can be an important tool for understanding differentiation and characterizing engineered cells. scTOP is available as an easy-to-use Python package.
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Affiliation(s)
| | - Michael J. Herriges
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Laertis Ikonomou
- Department of Oral Biology, University at Buffalo, The State University of New York, Buffalo, NY 14215, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14215, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- Faculty of Computing and Data Science, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
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11
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Werder RB, Berthiaume KA, Merritt C, Gallagher M, Villacorta-Martin C, Wang F, Bawa P, Malik V, Lyons SM, Basil MC, Morrisey EE, Kotton DN, Zhou X, Cho MH, Wilson AA. The COPD GWAS gene ADGRG6 instructs function and injury response in human iPSC-derived type II alveolar epithelial cells. Am J Hum Genet 2023; 110:1735-1749. [PMID: 37734371 PMCID: PMC10577075 DOI: 10.1016/j.ajhg.2023.08.017] [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: 03/31/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023] Open
Abstract
Emphysema and chronic obstructive pulmonary disease (COPD) most commonly result from the effects of environmental exposures in genetically susceptible individuals. Genome-wide association studies have implicated ADGRG6 in COPD and reduced lung function, and a limited number of studies have examined the role of ADGRG6 in cells representative of the airway. However, the ADGRG6 locus is also associated with DLCO/VA, an indicator of gas exchange efficiency and alveolar function. Here, we sought to evaluate the mechanistic contributions of ADGRG6 to homeostatic function and disease in type 2 alveolar epithelial cells. We applied an inducible CRISPR interference (CRISPRi) human induced pluripotent stem cell (iPSC) platform to explore ADGRG6 function in iPSC-derived AT2s (iAT2s). We demonstrate that ADGRG6 exerts pleiotropic effects on iAT2s including regulation of focal adhesions, cytoskeleton, tight junctions, and proliferation. Moreover, we find that ADGRG6 knockdown in cigarette smoke-exposed iAT2s alters cellular responses to injury, downregulating apical complexes in favor of proliferation. Our work functionally characterizes the COPD GWAS gene ADGRG6 in human alveolar epithelium.
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Affiliation(s)
- Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Kayleigh A Berthiaume
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carly Merritt
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marissa Gallagher
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Vidhi Malik
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn M Lyons
- Biochemistry Department, Boston University School of Medicine, Boston, MA 02118, USA
| | - Maria C Basil
- School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edward E Morrisey
- School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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12
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Herriges MJ, Yampolskaya M, Thapa BR, Lindstrom-Vautrin J, Wang F, Huang J, Na CL, Ma L, Montminy MM, Bawa P, Villacorta-Martin C, Mehta P, Kotton DN. Durable alveolar engraftment of PSC-derived lung epithelial cells into immunocompetent mice. Cell Stem Cell 2023; 30:1217-1234.e7. [PMID: 37625412 PMCID: PMC10529386 DOI: 10.1016/j.stem.2023.07.016] [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: 07/13/2022] [Revised: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
Durable reconstitution of the distal lung epithelium with pluripotent stem cell (PSC) derivatives, if realized, would represent a promising therapy for diseases that result from alveolar damage. Here, we differentiate murine PSCs into self-renewing lung epithelial progenitors able to engraft into the injured distal lung epithelium of immunocompetent, syngeneic mouse recipients. After transplantation, these progenitors mature in the distal lung, assuming the molecular phenotypes of alveolar type 2 (AT2) and type 1 (AT1) cells. After months in vivo, donor-derived cells retain their mature phenotypes, as characterized by single-cell RNA sequencing (scRNA-seq), histologic profiling, and functional assessment that demonstrates continued capacity of the engrafted cells to proliferate and differentiate. These results indicate durable reconstitution of the distal lung's facultative progenitor and differentiated epithelial cell compartments with PSC-derived cells, thus establishing a novel model for pulmonary cell therapy that can be utilized to better understand the mechanisms and utility of engraftment.
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Affiliation(s)
- Michael J Herriges
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Bibek R Thapa
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Feiya Wang
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Cheng-Lun Na
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Liang Ma
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - McKenna M Montminy
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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13
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Ma L, Thapa BR, Le Suer JA, Tilston-Lünel A, Herriges MJ, Berical A, Beermann ML, Wang F, Bawa PS, Kohn A, Ysasi AB, Kiyokawa H, Matte TM, Randell SH, Varelas X, Hawkins FJ, Kotton DN. Airway stem cell reconstitution by the transplantation of primary or pluripotent stem cell-derived basal cells. Cell Stem Cell 2023; 30:1199-1216.e7. [PMID: 37625411 PMCID: PMC10528754 DOI: 10.1016/j.stem.2023.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/31/2022] [Revised: 06/13/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
Life-long reconstitution of a tissue's resident stem cell compartment with engrafted cells has the potential to durably replenish organ function. Here, we demonstrate the engraftment of the airway epithelial stem cell compartment via intra-airway transplantation of mouse or human primary and pluripotent stem cell (PSC)-derived airway basal cells (BCs). Murine primary or PSC-derived BCs transplanted into polidocanol-injured syngeneic recipients give rise for at least two years to progeny that stably display the morphologic, molecular, and functional phenotypes of airway epithelia. The engrafted basal-like cells retain extensive self-renewal potential, evident by the capacity to reconstitute the tracheal epithelium through seven generations of secondary transplantation. Using the same approach, human primary or PSC-derived BCs transplanted into NOD scid gamma (NSG) recipient mice similarly display multilineage airway epithelial differentiation in vivo. Our results may provide a step toward potential future syngeneic cell-based therapy for patients with diseases resulting from airway epithelial cell damage or dysfunction.
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Affiliation(s)
- Liang Ma
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Bibek R Thapa
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biology, Boston University, Boston, MA 02215, USA
| | - Jake A Le Suer
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrew Tilston-Lünel
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Michael J Herriges
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrew Berical
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mary Lou Beermann
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Pushpinder S Bawa
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Anat Kohn
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alexandra B Ysasi
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Hirofumi Kiyokawa
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Taylor M Matte
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Center, Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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14
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Hoffman ET, Uriarte JJ, Uhl FE, Eckstrom K, Tanneberger AE, Becker C, Moulin C, Asarian L, Ikonomou L, Kotton DN, Weiss DJ. Human alveolar hydrogels promote morphological and transcriptional differentiation in iPSC-derived alveolar type 2 epithelial cells. Sci Rep 2023; 13:12057. [PMID: 37491483 PMCID: PMC10368739 DOI: 10.1038/s41598-023-37685-x] [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: 02/24/2023] [Accepted: 06/26/2023] [Indexed: 07/27/2023] Open
Abstract
Alveolar type 2 epithelial cells (AT2s) derived from human induced pluripotent stem cells (iAT2s) have rapidly contributed to our understanding of AT2 function and disease. However, while iAT2s are primarily cultured in three-dimensional (3D) Matrigel, a matrix derived from cancerous mouse tissue, it is unclear how a physiologically relevant matrix will impact iAT2s phenotype. As extracellular matrix (ECM) is recognized as a vital component in directing cellular function and differentiation, we sought to derive hydrogels from decellularized human lung alveolar-enriched ECM (aECM) to provide an ex vivo model to characterize the role of physiologically relevant ECM on iAT2 phenotype. We demonstrate aECM hydrogels retain critical in situ ECM components, including structural and basement membrane proteins. While aECM hydrogels facilitate iAT2 proliferation and alveolosphere formation, a subset of iAT2s rapidly change morphology to thin and elongated ring-like cells. This morphological change correlates with upregulation of recently described iAT2-derived transitional cell state genetic markers. As such, we demonstrate a potentially underappreciated role of physiologically relevant aECM in iAT2 differentiation.
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Affiliation(s)
- Evan T Hoffman
- Department of Medicine, Larner College of Medicine, University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Juan J Uriarte
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Franziska E Uhl
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Alicia E Tanneberger
- Department of Medicine, Larner College of Medicine, University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Chloe Becker
- Department of Medicine, Larner College of Medicine, University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Chloe Moulin
- Department of Medicine, Larner College of Medicine, University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Loredana Asarian
- Department of Medicine, Larner College of Medicine, University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Laertis Ikonomou
- Department of Oral Biology, University of Buffalo, The State University of New York, Buffalo, NY, 14260, USA
- Cell, Gene and Tissue Engineering Center, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Daniel J Weiss
- Department of Medicine, Larner College of Medicine, University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
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15
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Alber AB, Marquez HA, Ma L, Kwong G, Thapa BR, Villacorta-Martin C, Lindstrom-Vautrin J, Bawa P, Wang F, Luo Y, Ikonomou L, Shi W, Kotton DN. Directed differentiation of mouse pluripotent stem cells into functional lung-specific mesenchyme. Nat Commun 2023; 14:3488. [PMID: 37311756 PMCID: PMC10264380 DOI: 10.1038/s41467-023-39099-9] [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: 06/25/2022] [Accepted: 05/30/2023] [Indexed: 06/15/2023] Open
Abstract
While the generation of many lineages from pluripotent stem cells has resulted in basic discoveries and clinical trials, the derivation of tissue-specific mesenchyme via directed differentiation has markedly lagged. The derivation of lung-specific mesenchyme is particularly important since this tissue plays crucial roles in lung development and disease. Here we generate a mouse induced pluripotent stem cell (iPSC) line carrying a lung-specific mesenchymal reporter/lineage tracer. We identify the pathways (RA and Shh) necessary to specify lung mesenchyme and find that mouse iPSC-derived lung mesenchyme (iLM) expresses key molecular and functional features of primary developing lung mesenchyme. iLM recombined with engineered lung epithelial progenitors self-organizes into 3D organoids with juxtaposed layers of epithelium and mesenchyme. Co-culture increases yield of lung epithelial progenitors and impacts epithelial and mesenchymal differentiation programs, suggesting functional crosstalk. Our iPSC-derived population thus provides an inexhaustible source of cells for studying lung development, modeling diseases, and developing therapeutics.
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Affiliation(s)
- Andrea B Alber
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hector A Marquez
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Liang Ma
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - George Kwong
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Bibek R Thapa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | | | - Pushpinder Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Yongfeng Luo
- Department of Surgery, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90027, USA
| | - Laertis Ikonomou
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY, 14260, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14215, USA
| | - Wei Shi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA.
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA.
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16
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Wang R, Simone-Roach C, Lindstrom-Vautrin J, Wang F, Rollins S, Bawa PS, Lu J, Tang Y, Beermann ML, Schlaeger T, Mahoney J, Rowe SM, Hawkins FJ, Kotton DN. De Novo Generation of Pulmonary Ionocytes from Normal and Cystic Fibrosis Human Induced Pluripotent Stem Cells. Am J Respir Crit Care Med 2023; 207:1249-1253. [PMID: 36857488 PMCID: PMC10161739 DOI: 10.1164/rccm.202205-1010le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Affiliation(s)
- Ruobing Wang
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Chantelle Simone-Roach
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
| | - Stuart Rollins
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Pushpinder Singh Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
| | - Junjie Lu
- Cystic Fibrosis Foundation Therapeutics Laboratories, Lexington, Massachusetts
| | - Yang Tang
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mary Lou Beermann
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine and
| | | | - John Mahoney
- Cystic Fibrosis Foundation Therapeutics Laboratories, Lexington, Massachusetts
| | - Steven M. Rowe
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Finn J. Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine and
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine and
- Department of Pathology & Laboratory Medicine, Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts; and
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17
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Pradhan A, Che L, Ustiyan V, Reza AA, Pek NM, Zhang Y, Alber AB, Kalin TR, Wambach JA, Gu M, Kotton DN, Siefert ME, Ziady AG, Kalin TV, Kalinichenko VV. Novel FOXF1-Stabilizing Compound TanFe Stimulates Lung Angiogenesis in Alveolar Capillary Dysplasia. Am J Respir Crit Care Med 2023; 207:1042-1054. [PMID: 36480964 PMCID: PMC10112450 DOI: 10.1164/rccm.202207-1332oc] [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: 07/14/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
Rationale: Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is linked to heterozygous mutations in the FOXF1 (Forkhead Box F1) gene, a key transcriptional regulator of pulmonary vascular development. There are no effective treatments for ACDMPV other than lung transplant, and new pharmacological agents activating FOXF1 signaling are urgently needed. Objectives: Identify-small molecule compounds that stimulate FOXF1 signaling. Methods: We used mass spectrometry, immunoprecipitation, and the in vitro ubiquitination assay to identify TanFe (transcellular activator of nuclear FOXF1 expression), a small-molecule compound from the nitrile group, which stabilizes the FOXF1 protein in the cell. The efficacy of TanFe was tested in mouse models of ACDMPV and acute lung injury and in human vascular organoids derived from induced pluripotent stem cells of a patient with ACDMPV. Measurements and Main Results: We identified HECTD1 as an E3 ubiquitin ligase involved in ubiquitination and degradation of the FOXF1 protein. The TanFe compound disrupted FOXF1-HECTD1 protein-protein interactions and decreased ubiquitination of the FOXF1 protein in pulmonary endothelial cells in vitro. TanFe increased protein concentrations of FOXF1 and its target genes Flk1, Flt1, and Cdh5 in LPS-injured mouse lungs, decreasing endothelial permeability and inhibiting lung inflammation. Treatment of pregnant mice with TanFe increased FOXF1 protein concentrations in lungs of Foxf1+/- embryos, stimulated neonatal lung angiogenesis, and completely prevented the mortality of Foxf1+/- mice after birth. TanFe increased angiogenesis in human vascular organoids derived from induced pluripotent stem cells of a patient with ACDMPV with FOXF1 deletion. Conclusions: TanFe is a novel activator of FOXF1, providing a new therapeutic candidate for treatment of ACDMPV and other neonatal pulmonary vascular diseases.
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Affiliation(s)
| | | | | | | | - Nicole M. Pek
- Division of Neonatology and Pulmonary Biology
- Center for Stem Cells and Organoid Medicine
| | | | - Andrea B. Alber
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts
| | - Timothy R. Kalin
- College of Arts and Sciences, University of Cincinnati, Cincinnati, Ohio; and
| | - Jennifer A. Wambach
- Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children’s Hospital, St. Louis, Missouri
| | - Mingxia Gu
- Division of Neonatology and Pulmonary Biology
- Center for Stem Cells and Organoid Medicine
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts
| | | | - Assem G. Ziady
- Division of Bone Marrow Transplantation and Immune Deficiency, and
| | | | - Vladimir V. Kalinichenko
- Center for Lung Regenerative Medicine
- Division of Neonatology and Pulmonary Biology
- Center for Stem Cells and Organoid Medicine
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
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18
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Chen DY, Chin CV, Kenney D, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Adams S, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation. Nature 2023; 615:143-150. [PMID: 36630998 DOI: 10.1038/s41586-023-05697-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
The SARS-CoV-2 Omicron variant is more immune evasive and less virulent than other major viral variants that have so far been recognized1-12. The Omicron spike (S) protein, which has an unusually large number of mutations, is considered to be the main driver of these phenotypes. Here we generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron (BA.1 lineage) in the backbone of an ancestral SARS-CoV-2 isolate, and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escaped vaccine-induced humoral immunity, mainly owing to mutations in the receptor-binding motif; however, unlike naturally occurring Omicron, it efficiently replicated in cell lines and primary-like distal lung cells. Similarly, in K18-hACE2 mice, although virus bearing Omicron S caused less severe disease than the ancestral virus, its virulence was not attenuated to the level of Omicron. Further investigation showed that mutating non-structural protein 6 (nsp6) in addition to the S protein was sufficient to recapitulate the attenuated phenotype of Omicron. This indicates that although the vaccine escape of Omicron is driven by mutations in S, the pathogenicity of Omicron is determined by mutations both in and outside of the S protein.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Chue Vin Chin
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Manish C Choudhary
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K O'Connell
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott Adams
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexandra Herrmann
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Markus Bosmann
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jonathan Z Li
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yachana Kataria
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
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19
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Burgess CL, Huang J, Bawa P, Alysandratos KD, Minakin K, Morley MP, Babu A, Villacorta-Martin C, Hinds A, Thapa BR, Wang F, Matschulat AM, Morrisey EE, Varelas X, Kotton DN. Generation of human alveolar epithelial type I cells from pluripotent stem cells. bioRxiv 2023:2023.01.19.524655. [PMID: 36711505 PMCID: PMC9882278 DOI: 10.1101/2023.01.19.524655] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the distal lung, alveolar epithelial type I cells (AT1s) comprise the vast majority of alveolar surface area and are uniquely flattened to allow the diffusion of oxygen into the capillaries. This structure along with a quiescent, terminally differentiated phenotype has made AT1s particularly challenging to isolate or maintain in cell culture. As a result, there is a lack of established models for the study of human AT1 biology, and in contrast to alveolar epithelial type II cells (AT2s), little is known about the mechanisms regulating their differentiation. Here we engineer a human in vitro AT1 model system through the directed differentiation of induced pluripotent stem cells (iPSC). We first define the global transcriptomes of primary adult human AT1s, suggesting gene-set benchmarks and pathways, such as Hippo-LATS-YAP/TAZ signaling, that are enriched in these cells. Next, we generate iPSC-derived AT2s (iAT2s) and find that activating nuclear YAP signaling is sufficient to promote a broad transcriptomic shift from AT2 to AT1 gene programs. The resulting cells express a molecular, morphologic, and functional phenotype reminiscent of human AT1 cells, including the capacity to form a flat epithelial barrier which produces characteristic extracellular matrix molecules and secreted ligands. Our results indicate a role for Hippo-LATS-YAP signaling in the differentiation of human AT1s and demonstrate the generation of viable AT1-like cells from iAT2s, providing an in vitro model of human alveolar epithelial differentiation and a potential source of human AT1s that until now have been challenging to viably obtain from patients.
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Affiliation(s)
- Claire L Burgess
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Kasey Minakin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Michael P Morley
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Apoorva Babu
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Bibek R Thapa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Adeline M Matschulat
- Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Edward E Morrisey
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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20
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Chen DY, Kenney D, Chin CV, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron. bioRxiv 2023:2022.10.13.512134. [PMID: 36263066 PMCID: PMC9580375 DOI: 10.1101/2022.10.13.512134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The recently identified, globally predominant SARS-CoV-2 Omicron variant (BA.1) is highly transmissible, even in fully vaccinated individuals, and causes attenuated disease compared with other major viral variants recognized to date. The Omicron spike (S) protein, with an unusually large number of mutations, is considered the major driver of these phenotypes. We generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron in the backbone of an ancestral SARS-CoV-2 isolate and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escapes vaccine-induced humoral immunity, mainly due to mutations in the receptor binding motif (RBM), yet unlike naturally occurring Omicron, efficiently replicates in cell lines and primary-like distal lung cells. In K18-hACE2 mice, while Omicron causes mild, non-fatal infection, the Omicron S-carrying virus inflicts severe disease with a mortality rate of 80%. This indicates that while the vaccine escape of Omicron is defined by mutations in S, major determinants of viral pathogenicity reside outside of S.
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21
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Alysandratos KD, Garcia-de-Alba C, Yao C, Pessina P, Huang J, Villacorta-Martin C, Hix OT, Minakin K, Burgess CL, Bawa P, Murthy A, Konda B, Beers MF, Stripp BR, Kim CF, Kotton DN. Culture impact on the transcriptomic programs of primary and iPSC-derived human alveolar type 2 cells. JCI Insight 2023; 8:e158937. [PMID: 36454643 PMCID: PMC9870086 DOI: 10.1172/jci.insight.158937] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Dysfunction of alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of lung alveoli, is implicated in pulmonary disease pathogenesis, highlighting the importance of human in vitro models. However, AEC2-like cells in culture have yet to be directly compared to their in vivo counterparts at single-cell resolution. Here, we performed head-to-head comparisons among the transcriptomes of primary (1°) adult human AEC2s, their cultured progeny, and human induced pluripotent stem cell-derived AEC2s (iAEC2s). We found each population occupied a distinct transcriptomic space with cultured AEC2s (1° and iAEC2s) exhibiting similarities to and differences from freshly purified 1° cells. Across each cell type, we found an inverse relationship between proliferative and maturation states, with preculture 1° AEC2s being most quiescent/mature and iAEC2s being most proliferative/least mature. Cultures of either type of human AEC2s did not generate detectable alveolar type 1 cells in these defined conditions; however, a subset of iAEC2s cocultured with fibroblasts acquired a transitional cell state described in mice and humans to arise during fibrosis or following injury. Hence, we provide direct comparisons of the transcriptomic programs of 1° and engineered AEC2s, 2 in vitro models that can be harnessed to study human lung health and disease.
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Affiliation(s)
- Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Carolina Garcia-de-Alba
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Changfu Yao
- Women’s Guild Lung Institute
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Patrizia Pessina
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jessie Huang
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Olivia T. Hix
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Kasey Minakin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Claire L. Burgess
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Aditi Murthy
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, and
- PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bindu Konda
- Women’s Guild Lung Institute
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michael F. Beers
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, and
- PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Barry R. Stripp
- Women’s Guild Lung Institute
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carla F. Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
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22
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Kee J, Thudium S, Renner DM, Glastad K, Palozola K, Zhang Z, Li Y, Lan Y, Cesare J, Poleshko A, Kiseleva AA, Truitt R, Cardenas-Diaz FL, Zhang X, Xie X, Kotton DN, Alysandratos KD, Epstein JA, Shi PY, Yang W, Morrisey E, Garcia BA, Berger SL, Weiss SR, Korb E. Publisher Correction: SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry. Nature 2023; 613:E5. [PMID: 36624294 PMCID: PMC9827436 DOI: 10.1038/s41586-022-05631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- John Kee
- grid.25879.310000 0004 1936 8972Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Samuel Thudium
- grid.25879.310000 0004 1936 8972Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - David M. Renner
- grid.25879.310000 0004 1936 8972Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Karl Glastad
- grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Katherine Palozola
- grid.25879.310000 0004 1936 8972Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Zhen Zhang
- grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Yize Li
- grid.25879.310000 0004 1936 8972Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Yemin Lan
- grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Joseph Cesare
- grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Andrey Poleshko
- grid.25879.310000 0004 1936 8972Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Anna A. Kiseleva
- grid.25879.310000 0004 1936 8972Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Rachel Truitt
- grid.25879.310000 0004 1936 8972Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Fabian L. Cardenas-Diaz
- grid.25879.310000 0004 1936 8972Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Xianwen Zhang
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX USA
| | - Xuping Xie
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX USA
| | - Darrell N. Kotton
- grid.189504.10000 0004 1936 7558Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | - Konstantinos D. Alysandratos
- grid.189504.10000 0004 1936 7558Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | - Johnathan A. Epstein
- grid.25879.310000 0004 1936 8972Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Pei-Yong Shi
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX USA
| | - Wenli Yang
- grid.25879.310000 0004 1936 8972Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Edward Morrisey
- grid.25879.310000 0004 1936 8972Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Benjamin A. Garcia
- grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Shelley L. Berger
- grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Susan R. Weiss
- grid.25879.310000 0004 1936 8972Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
| | - Erica Korb
- grid.25879.310000 0004 1936 8972Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
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23
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Torchia JA, Tavares AH, Carstensen LS, Chen DY, Huang J, Xiao T, Mukherjee S, Reeves PM, Tu H, Sluder AE, Chen B, Kotton DN, Bowen RA, Saeed M, Poznansky MC, Freeman GJ. Optimized ACE2 decoys neutralize antibody-resistant SARS-CoV-2 variants through functional receptor mimicry and treat infection in vivo. Sci Adv 2022; 8:eabq6527. [PMID: 36475798 PMCID: PMC9728973 DOI: 10.1126/sciadv.abq6527] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/01/2022] [Indexed: 05/14/2023]
Abstract
As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolves to escape natural antibodies, it also loses sensitivity to therapeutic antibody drugs. By contrast, evolution selects for binding to ACE2, the cell-surface receptor required for SARS-CoV-2 infection. Consistent with this, we find that an ACE2 decoy neutralizes antibody-resistant variants, including Omicron, with no loss in potency. To identify design features necessary for in vivo activity, we compare several enzymatically inactive, Fc effector-silenced ACE2-Fc decoys. Inclusion of the ACE2 collectrin-like domain not only improves affinity for the S protein but also unexpectedly extends serum half-life and is necessary to reduce disease severity and viral titer in Syrian hamsters. Fc effector function is not required. The activity of ACE2 decoy receptors is due, in part, to their ability to trigger an irreversible structural change in the viral S protein. Our studies provide a new understanding of how ACE2 decoys function and support their development as therapeutics to treat ACE2-dependent coronaviruses.
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Affiliation(s)
- James A. Torchia
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Alexander H. Tavares
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Laura S. Carstensen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Da-Yuan Chen
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University, Boston Medical Center, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Tianshu Xiao
- Division of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia Mukherjee
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Patrick M. Reeves
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Hua Tu
- LakePharma Inc., San Carlos, CA 94070, USA
| | - Ann E. Sluder
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Bing Chen
- Division of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University, Boston Medical Center, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Gordon J. Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
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24
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Kaserman JE, Werder RB, Wang F, Matte T, Higgins MI, Dodge M, Lindstrom-Vautrin J, Bawa P, Hinds A, Bullitt E, Caballero IS, Shi X, Gerszten RE, Brunetti-Pierri N, Liesa M, Villacorta-Martin C, Hollenberg AN, Kotton DN, Wilson AA. Human iPSC-hepatocyte modeling of alpha-1 antitrypsin heterozygosity reveals metabolic dysregulation and cellular heterogeneity. Cell Rep 2022; 41:111775. [PMID: 36476855 PMCID: PMC9780780 DOI: 10.1016/j.celrep.2022.111775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/23/2022] [Revised: 09/28/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Individuals homozygous for the "Z" mutation in alpha-1 antitrypsin deficiency are known to be at increased risk for liver disease. It has also become clear that some degree of risk is similarly conferred by the heterozygous state. A lack of model systems that recapitulate heterozygosity in human hepatocytes has limited the ability to study the impact of a single Z alpha-1 antitrypsin (ZAAT) allele on hepatocyte biology. Here, we describe the derivation of syngeneic induced pluripotent stem cells (iPSCs) engineered to determine the effects of ZAAT heterozygosity in iPSC-hepatocytes (iHeps). We find that heterozygous MZ iHeps exhibit an intermediate disease phenotype and share with ZZ iHeps alterations in AAT protein processing and downstream perturbations including altered endoplasmic reticulum (ER) and mitochondrial morphology, reduced mitochondrial respiration, and branch-specific activation of the unfolded protein response in cell subpopulations. Our model of MZ heterozygosity thus provides evidence that a single Z allele is sufficient to disrupt hepatocyte homeostatic function.
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Affiliation(s)
- Joseph E. Kaserman
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rhiannon B. Werder
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Taylor Matte
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Michelle I. Higgins
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Mark Dodge
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Jonathan Lindstrom-Vautrin
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University, Boston, MA 02118, USA
| | - Ignacio S. Caballero
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Hospital, Boston, MA 02118, USA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Hospital, Boston, MA 02118, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy,Department of Translational Medicine, Federico II University, 80131 Naples, Italy
| | - Marc Liesa
- Departments of Medicine, Endocrinology, and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA,Institut de Biologia Molecular de Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Anthony N. Hollenberg
- Joan and Sanford I. Weill Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrew A. Wilson
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA,Lead contact,Correspondence:
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25
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Kee J, Thudium S, Renner DM, Glastad K, Palozola K, Zhang Z, Li Y, Lan Y, Cesare J, Poleshko A, Kiseleva AA, Truitt R, Cardenas-Diaz FL, Zhang X, Xie X, Kotton DN, Alysandratos KD, Epstein JA, Shi PY, Yang W, Morrisey E, Garcia BA, Berger SL, Weiss SR, Korb E. SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry. Nature 2022; 610:381-388. [PMID: 36198800 PMCID: PMC9533993 DOI: 10.1038/s41586-022-05282-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [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: 12/28/2020] [Accepted: 08/26/2022] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and caused the devastating global pandemic of coronavirus disease 2019 (COVID-19), in part because of its ability to effectively suppress host cell responses1-3. In rare cases, viral proteins dampen antiviral responses by mimicking critical regions of human histone proteins4-8, particularly those containing post-translational modifications required for transcriptional regulation9-11. Recent work has demonstrated that SARS-CoV-2 markedly disrupts host cell epigenetic regulation12-14. However, how SARS-CoV-2 controls the host cell epigenome and whether it uses histone mimicry to do so remain unclear. Here we show that the SARS-CoV-2 protein encoded by ORF8 (ORF8) functions as a histone mimic of the ARKS motifs in histone H3 to disrupt host cell epigenetic regulation. ORF8 is associated with chromatin, disrupts regulation of critical histone post-translational modifications and promotes chromatin compaction. Deletion of either the ORF8 gene or the histone mimic site attenuates the ability of SARS-CoV-2 to disrupt host cell chromatin, affects the transcriptional response to infection and attenuates viral genome copy number. These findings demonstrate a new function of ORF8 and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Further, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19.
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Affiliation(s)
- John Kee
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel Thudium
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David M Renner
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Karl Glastad
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine Palozola
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zhen Zhang
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yize Li
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Cesare
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna A Kiseleva
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel Truitt
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fabian L Cardenas-Diaz
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Wenli Yang
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Edward Morrisey
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Susan R Weiss
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erica Korb
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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26
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Werder RB, Liu T, Abo KM, Lindstrom-Vautrin J, Villacorta-Martin C, Huang J, Hinds A, Boyer N, Bullitt E, Liesa M, Silverman EK, Kotton DN, Cho MH, Zhou X, Wilson AA. CRISPR interference interrogation of COPD GWAS genes reveals the functional significance of desmoplakin in iPSC-derived alveolar epithelial cells. Sci Adv 2022; 8:eabo6566. [PMID: 35857525 PMCID: PMC9278866 DOI: 10.1126/sciadv.abo6566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Genome-wide association studies (GWAS) have identified dozens of loci associated with chronic obstructive pulmonary disease (COPD) susceptibility; however, the function of associated genes in the cell type(s) affected in disease remains poorly understood, partly due to a lack of cell models that recapitulate human alveolar biology. Here, we apply CRISPR interference to interrogate the function of nine genes implicated in COPD by GWAS in induced pluripotent stem cell-derived type 2 alveolar epithelial cells (iAT2s). We find that multiple genes implicated by GWAS affect iAT2 function, including differentiation potential, maturation, and/or proliferation. Detailed characterization of the GWAS gene DSP demonstrates that it regulates iAT2 cell-cell junctions, proliferation, mitochondrial function, and response to cigarette smoke-induced injury. Our approach thus elucidates the biological function, as well as disease-relevant consequences of dysfunction, of genes implicated in COPD by GWAS in type 2 alveolar epithelial cells.
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Affiliation(s)
- Rhiannon B. Werder
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Tao Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kristine M. Abo
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Carlos Villacorta-Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anne Hinds
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nathan Boyer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marc Liesa
- Department of Medicine, Endocrinology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095, USA
- Institut de Biologia Molecular De Barcelona (IBMB-CSIC), Barcelona, Catalonia 08028, Spain
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew A. Wilson
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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27
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Posabella A, Undeutsch HJ, Alber AB, Kurmann A, Droeser R, Hollenberg A, Kotton DN. Derivation of thyroid progenitors from human induced pluripotent stem cells. Br J Surg 2022. [DOI: 10.1093/bjs/znac176.002] [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: 11/13/2022]
Abstract
Abstract
Objective
Despite the availability of synthetic thyroid hormone for therapeutic use, a significant number of patients with hypothyroidism do not feel well on replacement doses of thyroid hormones suggesting that better-individualized therapy is needed. For this reason, hypothyroidism resulting from congenital lack of functional thyrocytes, surgical tissue removal, or gland ablation, represents a particularly attractive endocrine disease target that may be conceivably cured by transplantation of long-lived functional thyroid progenitors or mature follicular epithelial cells.
Methods
To generate thyroid follicular progenitors from human induced pluripotent stem cells (hiPSCs), we sought to develop a directed differentiation approach by activating or inhibiting endogenous developmental signaling pathways previously identified in the mouse. To facilitate tracking and purification of candidate human thyroid progenitors, we engineered a hiPSC-line carrying a tdTomato reporter targeted to the PAX8 locus and a GFP reporter targeted to the NKX2-1 locus.
Results
We adapted our published in vitro differentiation protocol previously used to differentiate mouse PSCs into thyroid progenitors and observed tdTomato/GFP co-expressing cells first emerging from our hiPSC line by day 12 of culture and persisting for at least 2 months of further culture in thyroid maturation media, supplemented with TSH. Thus, we profiled all cells deriving from hiPSCs by single-cell RNA sequencing >6,000 cells captured on days 12 and 29 of in vitro differentiation. At day 12, tdTomato/GFP co-expression was observed in 12% of all cells and these cells appeared to be early thyroid follicular progenitors as they uniquely co-expressed the tetrad of thyroid lineage selective transcription factors, NKX2-1, PAX8, FOXE1, and HHEX. By day 29 tdTomato+/GFP+ cells represented 69% of all cells and had upregulated TG, TSHR, NIS and TPO expression in addition to the previously described four thyroid lineage markers, suggesting time-dependent differentiation and maturation of thyroid follicular epithelial cells.
Conclusion
Thus, we have employed a novel hiPSC line to optimize a protocol able to generate human thyroid progenitors and mature follicular epithelial cells, representing a purifiable source of human thyroid lineage cells whose functional and thyroid reconstituting potential can be tested in vivo in animal models of hypothyroidism.
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Affiliation(s)
- A Posabella
- Center for Regenerative Medicine, Boston University and Boston Medical Center , Boston, USA
- Clarunis - University Abdominal Center Visceral Surgery, , Basel, Switzerland
| | - H J Undeutsch
- Division of Endocrinology, Diabetes and Metabolism, Joan and Sanford I. Weill Department of Medicine , Weill Cornell Medicine, New York, USA
| | - A B Alber
- Center for Regenerative Medicine, Boston University and Boston Medical Center , Boston, USA
| | - A Kurmann
- Center for Regenerative Medicine, Boston University and Boston Medical Center , Boston, USA
| | - R Droeser
- Clarunis - University Abdominal Center Visceral Surgery, , Basel, Switzerland
| | - A Hollenberg
- Division of Endocrinology, Diabetes and Metabolism, Joan and Sanford I. Weill Department of Medicine , Weill Cornell Medicine, New York, USA
| | - D N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center , Boston, USA
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28
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Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M. SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.125.39] [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] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs, liver, kidneys, and gut. Angiotensin-converting enzyme 2 (ACE2), the best-characterized entry receptor for the disease-causing virus SARS-CoV-2, is highly expressed in the aforementioned tissues. However, the pathways that underlie the disease are still poorly understood. Here, we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi), indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients, distinct signatures of complement activation in myeloid, lymphoid, and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-κB as the main drivers of their expression. Ruxolitinib, a JAK1/2 inhibitor, normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines but did not affect NF-κB–regulated genes. Ruxolitinib, alone or in combination with the antiviral remdesivir, inhibited C3a protein produced by infected cells. Together, we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-κB signaling could potentially have clinical application for severe COVID-19.
This research was financed by the National Heart, Lung, and Blood Institute of the NIH (grant 5K22HL125593 to M. Kazemian; R01HL119215 to J.R.S.); National Institute of General Medical Sciences of the NIH (grant R35GM138283 to M. Kazemian); and Deutsche Forschungsgemeinschaft (fellowship FR3851/2-1 to T. Freiwald) and supported, in part, by the Intramural Research Program of the NIH; the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) (project number ZIA/DK075149 to B.A.); the National Heart, Lung, and Blood Institute (NHLBI) (project number ZIA/Hl006223 to C.K.); and the National Institute of Allergy and Infectious Diseases (NIAID) (project number ZIA/AI001175 to M.S.L.). T. Frum is supported by T32DE007057. Funding for part of the work was provided by the University of Michigan Biological Scholars Program (to C.E.W.), LifeARC Charity (to S.K.), and CRUK KHP Centre (to S.K.).
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Affiliation(s)
- Bingyu Yan
- 1Department of Biochemistry, Purdue University
| | - Tilo Freiwald
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
- 3Complement and Inflammation Research Section, NHLBI, NIH
- 4Department of Nephrology, University Hospital Frankfurt, Goethe-University, Germany
| | - Daniel Chauss
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
| | - Luopin Wang
- 5Department of Computer Science, Purdue University
| | - Erin West
- 3Complement and Inflammation Research Section, NHLBI, NIH
| | - Carmen Mirabelli
- 6Department of Microbiology and Immunology, University of Michigan
| | | | | | | | | | | | | | | | - Tristan Frum
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
| | - Jason R. Spence
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
- 10Department of Cell and Developmental Biology, University of Michigan
| | - Jonathan Z. Sexton
- 7Department of Medicinal Chemistry, University of Michigan
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
| | - Konstantinos D. Alysandratos
- 11Center for Regenerative Medicine of Boston University and Boston Medical Center
- 12Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Darrell N. Kotton
- 11Center for Regenerative Medicine of Boston University and Boston Medical Center
- 12Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | | | - Jack Bibby
- 3Complement and Inflammation Research Section, NHLBI, NIH
| | - Nathalie Niyonzima
- 14Center of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Norway
| | | | - Shahram Kordasti
- 16CRUK KHP Centre, Comprehensive Cancer Centre, King’s College London, United Kingdom
- 17Haematology Department, Guy’s Hospital, United Kingdom
| | - Didier Portilla
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
- 18Division of Nephrology and Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia
| | | | - Arian Laurence
- 19Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Michail S. Lionakis
- 20Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH
| | - Claudia Kemper
- 3Complement and Inflammation Research Section, NHLBI, NIH
- 21Institute for Systemic Inflammation Research, University of Lübeck, Germany
| | - Behdad Afzali
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
| | - Majid Kazemian
- 1Department of Biochemistry, Purdue University
- 5Department of Computer Science, Purdue University
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29
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Werder RB, Huang J, Abo KM, Hix OT, Minakin K, Alysandratos KD, Merritt C, Berthiaume K, Alber AB, Burgess CL, Kotton DN, Wilson AA. Generating 3D Spheres and 2D Air-Liquid Interface Cultures of Human Induced Pluripotent Stem Cell-Derived Type 2 Alveolar Epithelial Cells. J Vis Exp 2022. [PMID: 35499347 DOI: 10.3791/63875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In the lung, the alveolar epithelium is a physical barrier from environmental stimuli and plays an essential role in homeostasis and disease. Type 2 alveolar epithelial cells (AT2s) are the facultative progenitors of the distal lung epithelium. Dysfunction and injury of AT2s can result from and contribute to various lung diseases. Improved understanding of AT2 biology is, thus, critical for understanding lung biology and disease; however, primary human AT2s are generally difficult to isolate and limited in supply. To overcome these limitations, human induced pluripotent stem cell (iPSC)-derived type 2 alveolar epithelial cells (iAT2s) can be generated through a directed differentiation protocol that recapitulates in vivo lung development. iAT2s grow in feeder-free conditions, share a transcriptomic program with human adult primary AT2s, and execute key functions of AT2s such as production, packaging, and secretion of surfactant. This protocol details the methods for maintaining self-renewing iAT2s through serial passaging in three-dimensional (3D) culture or adapting iAT2s to air-liquid interface (ALI) culture. A single-cell suspension of iAT2s is generated before plating in 3D solubilized basement membrane matrix (hereafter referred to as "matrix"), where they self-assemble into monolayered epithelial spheres. iAT2s in 3D culture can be serially dissociated into single-cell suspensions to be passaged or plated in 2D ALI culture. In ALI culture, iAT2s form a polarized monolayer with the apical surface exposed to air, making this platform readily amenable to environmental exposures. Hence, this protocol generates an inexhaustible supply of iAT2s, producing upwards of 1 x 1030 cells per input cell over 15 passages while maintaining the AT2 program indicated by SFTPCtdTomato expression. The resulting cells represent a reproducible and relevant platform that can be applied to study genetic mutations, model environmental exposures, or screen drugs.
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Affiliation(s)
- Rhiannon B Werder
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine; QIMR Berghofer Medical Research Institute
| | - Jessie Huang
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Kristine M Abo
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Olivia T Hix
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Kasey Minakin
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Carly Merritt
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Kayleigh Berthiaume
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Andrea B Alber
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Claire L Burgess
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Andrew A Wilson
- Center for Regenerative Medicine, Boston University and Boston Medical Center; The Pulmonary Center and Department of Medicine, Boston University School of Medicine;
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30
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Basil MC, Cardenas-Diaz FL, Kathiriya JJ, Morley MP, Carl J, Brumwell AN, Katzen J, Slovik KJ, Babu A, Zhou S, Kremp MM, McCauley KB, Li S, Planer JD, Hussain SS, Liu X, Windmueller R, Ying Y, Stewart KM, Oyster M, Christie JD, Diamond JM, Engelhardt JF, Cantu E, Rowe SM, Kotton DN, Chapman HA, Morrisey EE. Human distal airways contain a multipotent secretory cell that can regenerate alveoli. Nature 2022; 604:120-126. [PMID: 35355013 PMCID: PMC9297319 DOI: 10.1038/s41586-022-04552-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
Abstract
The human lung differs substantially from its mouse counterpart, resulting in a distinct distal airway architecture affected by disease pathology in chronic obstructive pulmonary disease. In humans, the distal branches of the airway interweave with the alveolar gas-exchange niche, forming an anatomical structure known as the respiratory bronchioles. Owing to the lack of a counterpart in mouse, the cellular and molecular mechanisms that govern respiratory bronchioles in the human lung remain uncharacterized. Here we show that human respiratory bronchioles contain a unique secretory cell population that is distinct from cells in larger proximal airways. Organoid modelling reveals that these respiratory airway secretory (RAS) cells act as unidirectional progenitors for alveolar type 2 cells, which are essential for maintaining and regenerating the alveolar niche. RAS cell lineage differentiation into alveolar type 2 cells is regulated by Notch and Wnt signalling. In chronic obstructive pulmonary disease, RAS cells are altered transcriptionally, corresponding to abnormal alveolar type 2 cell states, which are associated with smoking exposure in both humans and ferrets. These data identify a distinct progenitor in a region of the human lung that is not found in mouse that has a critical role in maintaining the gas-exchange compartment and is altered in chronic lung disease.
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Affiliation(s)
- Maria C Basil
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabian L Cardenas-Diaz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jaymin J Kathiriya
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Michael P Morley
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Justine Carl
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexis N Brumwell
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jeremy Katzen
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine J Slovik
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Apoorva Babu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Su Zhou
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Madison M Kremp
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine B McCauley
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - Shanru Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph D Planer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shah S Hussain
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xiaoming Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Rebecca Windmueller
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yun Ying
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen M Stewart
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Oyster
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason D Christie
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua M Diamond
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edward Cantu
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Cardiovascular Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven M Rowe
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - Harold A Chapman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Edward E Morrisey
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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31
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Na E, Allen E, Baird LA, Odom CV, Korkmaz FT, Shenoy AT, Matschulat AM, Jones MR, Kotton DN, Mizgerd JP, Varelas X, Traber KE, Quinton LJ. Epithelial LIF signaling limits apoptosis and lung injury during bacterial pneumonia. Am J Physiol Lung Cell Mol Physiol 2022; 322:L550-L563. [PMID: 35137631 PMCID: PMC8957336 DOI: 10.1152/ajplung.00325.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/30/2021] [Revised: 12/17/2021] [Accepted: 02/02/2022] [Indexed: 11/22/2022] Open
Abstract
During bacterial pneumonia, alveolar epithelial cells are critical for maintaining gas exchange and providing antimicrobial as well as pro-immune properties. We previously demonstrated that leukemia inhibitory factor (LIF), an IL-6 family cytokine, is produced by type II alveolar epithelial cells (ATII) and is critical for tissue protection during bacterial pneumonia. However, the target cells and mechanisms of LIF-mediated protection remain unknown. Here, we demonstrate that antibody-induced LIF blockade remodels the lung epithelial transcriptome in association with increased apoptosis. Based on these data, we performed pneumonia studies using a novel mouse model in which LIFR (the unique receptor for LIF) is absent in lung epithelium. Although LIFR is expressed on the surface of epithelial cells, its absence only minimally contributed to tissue protection during pneumonia. Single-cell RNA-sequencing (scRNAseq) was conducted to identify adult murine lung cell types most prominently expressing Lifr, revealing endothelial cells, mesenchymal cells, and ATIIs as major sources of Lifr. Sequencing data indicated that ATII cells were significantly impacted by pneumonia, with additional differences observed in response to LIF neutralization, including but not limited to gene programs related to cell death, injury, and inflammation. Overall, our data suggest that LIF signaling on epithelial cells alters responses in this cell type during pneumonia. However, our results also suggest separate and perhaps more prominent roles of LIFR in other cell types, such as endothelial cells or mesenchymal cells, which provide grounds for future investigation.
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Affiliation(s)
- Elim Na
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Eri Allen
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Lillia A Baird
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Christine V Odom
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
| | - Filiz T Korkmaz
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Anukul T Shenoy
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Adeline M Matschulat
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts
| | - Matthew R Jones
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Darrell N Kotton
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts
| | - Xaralabos Varelas
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts
| | - Katrina E Traber
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Lee J Quinton
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts
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32
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Abo KM, Sainz de Aja J, Lindstrom-Vautrin J, Alysandratos KD, Richards A, Garcia-de-Alba C, Huang J, Hix OT, Werder RB, Bullitt E, Hinds A, Falconer I, Villacorta-Martin C, Jaenisch R, Kim CF, Kotton DN, Wilson AA. Air-liquid interface culture promotes maturation and allows environmental exposure of pluripotent stem cell-derived alveolar epithelium. JCI Insight 2022; 7:155589. [PMID: 35315362 PMCID: PMC8986076 DOI: 10.1172/jci.insight.155589] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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] [Indexed: 12/13/2022] Open
Abstract
Type 2 alveolar epithelial cells (AT2s), facultative progenitor cells of the lung alveolus, play a vital role in the biology of the distal lung. In vitro model systems that incorporate human cells, recapitulate the biology of primary AT2s, and interface with the outside environment could serve as useful tools to elucidate functional characteristics of AT2s in homeostasis and disease. We and others recently adapted human induced pluripotent stem cell–derived AT2s (iAT2s) for air-liquid interface (ALI) culture. Here, we comprehensively characterize the effects of ALI culture on iAT2s and benchmark their transcriptional profile relative to both freshly sorted and cultured primary human fetal and adult AT2s. We find that iAT2s cultured at ALI maintain an AT2 phenotype while upregulating expression of transcripts associated with AT2 maturation. We then leverage this platform to assay the effects of exposure to clinically significant, inhaled toxicants including cigarette smoke and electronic cigarette vapor.
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Affiliation(s)
- Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Julio Sainz de Aja
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Lindstrom-Vautrin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Alexsia Richards
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Carolina Garcia-de-Alba
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Olivia T Hix
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University, Boston, Massachusetts, USA
| | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Isaac Falconer
- Boston University School of Medicine, Boston, Massachusetts, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
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33
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Gil CH, Chakraborty D, Vieira CP, Prasain N, Calzi SL, Fortmann SD, Hu P, Banno K, Jamal M, Huang C, Sielski MS, Lin Y, Huang X, Dupont MD, Floyd JL, Prasad R, Longhini ALF, McGill TJ, Chung HM, Murphy MP, Kotton DN, Boulton ME, Yoder MC, Grant MB. Specific mesoderm subset derived from human pluripotent stem cells ameliorates microvascular pathology in type 2 diabetic mice. Sci Adv 2022; 8:eabm5559. [PMID: 35245116 PMCID: PMC8896785 DOI: 10.1126/sciadv.abm5559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) were differentiated into a specific mesoderm subset characterized by KDR+CD56+APLNR+ (KNA+) expression. KNA+ cells had high clonal proliferative potential and specification into endothelial colony-forming cell (ECFCs) phenotype. KNA+ cells differentiated into perfused blood vessels when implanted subcutaneously into the flank of nonobese diabetic/severe combined immunodeficient mice and when injected into the vitreous of type 2 diabetic mice (db/db mice). Transcriptomic analysis showed that differentiation of hiPSCs derived from diabetics into KNA+ cells was sufficient to change baseline differences in gene expression caused by the diabetic status and reprogram diabetic cells to a pattern similar to KNA+ cells derived from nondiabetic hiPSCs. Proteomic array studies performed on retinas of db/db mice injected with either control or diabetic donor-derived KNA+ cells showed correction of aberrant signaling in db/db retinas toward normal healthy retina. These data provide "proof of principle" that KNA+ cells restore perfusion and correct vascular dysfunction in db/db mice.
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Affiliation(s)
- Chang-Hyun Gil
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dibyendu Chakraborty
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Cristiano P. Vieira
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Nutan Prasain
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Astellas Institute for Regenerative Medicine (AIRM), Westborough, MA 01581, USA
| | - Sergio Li Calzi
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Seth D. Fortmann
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
- Medical Scientist Training Program (MSTP), School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ping Hu
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Kimihiko Banno
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Mohamed Jamal
- Center for Regenerative Medicine, Pulmonary Center, and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Endodontics, Hamdan Bin Mohammed College of Dental Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 00000, UAE
| | - Chao Huang
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Micheli S. Sielski
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Yang Lin
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xinxin Huang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Zhongshan-Xuhui Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 310104, China
| | - Mariana D. Dupont
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Jason L. Floyd
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Ana Leda F. Longhini
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Trevor J. McGill
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Hyung-Min Chung
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Michael P. Murphy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Pulmonary Center, and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Michael E. Boulton
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Mervin C. Yoder
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Maria B. Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
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34
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Wang R, Hume AJ, Beermann ML, Simone-Roach C, Lindstrom-Vautrin J, Le Suer J, Huang J, Olejnik J, Villacorta-Martin C, Bullitt E, Hinds A, Ghaedi M, Rollins S, Werder RB, Abo KM, Wilson AA, Mühlberger E, Kotton DN, Hawkins FJ. Human airway lineages derived from pluripotent stem cells reveal the epithelial responses to SARS-CoV-2 infection. Am J Physiol Lung Cell Mol Physiol 2022; 322:L462-L478. [PMID: 35020534 PMCID: PMC8917936 DOI: 10.1152/ajplung.00397.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 02/01/2023] Open
Abstract
There is an urgent need to understand how SARS-CoV-2 infects the airway epithelium and in a subset of individuals leads to severe illness or death. Induced pluripotent stem cells (iPSCs) provide a near limitless supply of human cells that can be differentiated into cell types of interest, including airway epithelium, for disease modeling. We present a human iPSC-derived airway epithelial platform, composed of the major airway epithelial cell types, that is permissive to SARS-CoV-2 infection. Subsets of iPSC-airway cells express the SARS-CoV-2 entry factors angiotensin-converting enzyme 2 (ACE2), and transmembrane protease serine 2 (TMPRSS2). Multiciliated cells are the primary initial target of SARS-CoV-2 infection. On infection with SARS-CoV-2, iPSC-airway cells generate robust interferon and inflammatory responses, and treatment with remdesivir or camostat mesylate causes a decrease in viral propagation and entry, respectively. In conclusion, iPSC-derived airway cells provide a physiologically relevant in vitro model system to interrogate the pathogenesis of, and develop treatment strategies for, COVID-19 pneumonia.
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Affiliation(s)
- Ruobing Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
| | - Mary Lou Beermann
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Chantelle Simone-Roach
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Jake Le Suer
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University, Boston, Massachusetts
| | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Mahboobe Ghaedi
- Research and Early Development Respiratory & Inflammation (R&I), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Stuart Rollins
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts
| | - Finn J Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
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Miorin L, Mire CE, Ranjbar S, Hume AJ, Huang J, Crossland NA, White KM, Laporte M, Kehrer T, Haridas V, Moreno E, Nambu A, Jangra S, Cupic A, Dejosez M, Abo KA, Tseng AE, Werder RB, Rathnasinghe R, Mutetwa T, Ramos I, de Aja JS, de Alba Rivas CG, Schotsaert M, Corley RB, Falvo JV, Fernandez-Sesma A, Kim C, Rossignol JF, Wilson AA, Zwaka T, Kotton DN, Mühlberger E, García-Sastre A, Goldfeld AE. The oral drug nitazoxanide restricts SARS-CoV-2 infection and attenuates disease pathogenesis in Syrian hamsters. bioRxiv 2022:2022.02.08.479634. [PMID: 35169796 PMCID: PMC8845418 DOI: 10.1101/2022.02.08.479634] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A well-tolerated and cost-effective oral drug that blocks SARS-CoV-2 growth and dissemination would be a major advance in the global effort to reduce COVID-19 morbidity and mortality. Here, we show that the oral FDA-approved drug nitazoxanide (NTZ) significantly inhibits SARS-CoV-2 viral replication and infection in different primate and human cell models including stem cell-derived human alveolar epithelial type 2 cells. Furthermore, NTZ synergizes with remdesivir, and it broadly inhibits growth of SARS-CoV-2 variants B.1.351 (beta), P.1 (gamma), and B.1617.2 (delta) and viral syncytia formation driven by their spike proteins. Strikingly, oral NTZ treatment of Syrian hamsters significantly inhibits SARS-CoV-2-driven weight loss, inflammation, and viral dissemination and syncytia formation in the lungs. These studies show that NTZ is a novel host-directed therapeutic that broadly inhibits SARS-CoV-2 dissemination and pathogenesis in human and hamster physiological models, which supports further testing and optimization of NTZ-based therapy for SARS-CoV-2 infection alone and in combination with antiviral drugs.
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Hume AJ, Heiden B, Olejnik J, Suder EL, Ross S, Scoon WA, Bullitt E, Ericsson M, White MR, Turcinovic J, Thao TTN, Hekman RM, Kaserman JE, Huang J, Alysandratos KD, Toth GE, Jakab F, Kotton DN, Wilson AA, Emili A, Thiel V, Connor JH, Kemenesi G, Cifuentes D, Mühlberger E. Recombinant Lloviu virus as a tool to study viral replication and host responses. PLoS Pathog 2022; 18:e1010268. [PMID: 35120176 PMCID: PMC8849519 DOI: 10.1371/journal.ppat.1010268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/16/2022] [Accepted: 01/11/2022] [Indexed: 01/06/2023] Open
Abstract
Next generation sequencing has revealed the presence of numerous RNA viruses in animal reservoir hosts, including many closely related to known human pathogens. Despite their zoonotic potential, most of these viruses remain understudied due to not yet being cultured. While reverse genetic systems can facilitate virus rescue, this is often hindered by missing viral genome ends. A prime example is Lloviu virus (LLOV), an uncultured filovirus that is closely related to the highly pathogenic Ebola virus. Using minigenome systems, we complemented the missing LLOV genomic ends and identified cis-acting elements required for LLOV replication that were lacking in the published sequence. We leveraged these data to generate recombinant full-length LLOV clones and rescue infectious virus. Similar to other filoviruses, recombinant LLOV (rLLOV) forms filamentous virions and induces the formation of characteristic inclusions in the cytoplasm of the infected cells, as shown by electron microscopy. Known target cells of Ebola virus, including macrophages and hepatocytes, are permissive to rLLOV infection, suggesting that humans could be potential hosts. However, inflammatory responses in human macrophages, a hallmark of Ebola virus disease, are not induced by rLLOV. Additional tropism testing identified pneumocytes as capable of robust rLLOV and Ebola virus infection. We also used rLLOV to test antivirals targeting multiple facets of the replication cycle. Rescue of uncultured viruses of pathogenic concern represents a valuable tool in our arsenal for pandemic preparedness. Due to increasing utilization of high-throughput sequencing technologies, RNA sequences of many unknown viruses have been discovered in bats and other animal species. Research on the pathogenic potential of these viruses is hampered by incomplete viral genome sequences and difficulties in isolating infectious virus from the animal hosts. One example of these potentially zoonotic pathogens is Lloviu virus (LLOV), a filovirus which is closely related to Ebola virus. Here we applied molecular virological approaches, including minigenome assays, to complement the incomplete LLOV genome ends with sequences from related viruses and identify cis-acting elements required for LLOV replication and transcription that were missing in the published LLOV sequence. The resulting full-length clones were used to generate infectious recombinant LLOV. We used this virus for electron microscopic analyses, infection studies in human cells, host response analysis, and antiviral drug testing. Our results provide new insights into the pathogenic potential of LLOV and delineate a roadmap for studying uncultured viruses.
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Affiliation(s)
- Adam J. Hume
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
| | - Baylee Heiden
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Stephen Ross
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Whitney A. Scoon
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Maria Ericsson
- Department of Cell Biology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Mitchell R. White
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Program in Bioinformatics, Boston University; Boston, Massachusetts, United States of America
| | - Tran T. N. Thao
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - Ryan M. Hekman
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
| | - Joseph E. Kaserman
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Gabor E. Toth
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Ferenc Jakab
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston Medical Center; Boston, Massachusetts, United States of America
| | - Andrew A. Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
- Department of Biology, Boston University; Boston, Massachusetts, United States of America
| | - Volker Thiel
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Gabor Kemenesi
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
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Ng WH, Johnston EK, Tan JJ, Bliley JM, Feinberg AW, Stolz DB, Sun M, Wijesekara P, Hawkins F, Kotton DN, Ren X. Recapitulating human cardio-pulmonary co-development using simultaneous multilineage differentiation of pluripotent stem cells. eLife 2022; 11:67872. [PMID: 35018887 PMCID: PMC8846595 DOI: 10.7554/elife.67872] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 02/25/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
The extensive crosstalk between the developing heart and lung is critical to their proper morphogenesis and maturation. However, there remains a lack of models that investigate the critical cardio-pulmonary mutual interaction during human embryogenesis. Here, we reported a novel stepwise strategy for directing the simultaneous induction of both mesoderm-derived cardiac and endoderm-derived lung epithelial lineages within a single differentiation of human-induced pluripotent stem cells (hiPSCs) via temporal specific tuning of WNT and nodal signaling in the absence of exogenous growth factors. Using 3D suspension culture, we established concentric cardio-pulmonary micro-Tissues (μTs), and expedited alveolar maturation in the presence of cardiac accompaniment. Upon withdrawal of WNT agonist, the cardiac and pulmonary components within each dual-lineage μT effectively segregated from each other with concurrent initiation of cardiac contraction. We expect that our multilineage differentiation model will offer an experimentally tractable system for investigating human cardio-pulmonary interaction and tissue boundary formation during embryogenesis. Organs begin developing during the first few months of pregnancy, while the baby is still an embryo. These early stages of development are known as embryogenesis – a tightly organized process, during which the embryo forms different layers of stem cells. These cells can be activated to turn into a particular type of cell, such as a heart or a lung cell. The heart and lungs develop from different layers within the embryo, which must communicate with each other for the organs to form correctly. For example, chemical signals can be released from and travel between layers of the embryo, activating processes inside cells located in the different areas. In mouse models, chemical signals and cells travel between developing heart and lung, which helps both organs to form into the correct structure. But it is unclear how well the observations from mouse models translate to heart and lung development in humans. To find out more, Ng et al. developed a human model of heart and lung co-development during embryogenesis using human pluripotent stem cells. The laboratory-grown stem cells were treated with chemical signals, causing them to form different layers that developed into early forms of heart and lung cells. The cells were then transferred into a specific growing condition, where they arranged into three-dimensional structures termed microtissues. Ng et al. found that lung cells developed faster when grown in microtissues with accompanying developing heart cells compared to microtissues containing only developing lung cells. In addition, Ng et al. revealed that the co-developing heart and lung tissues automatically separate from each other during later stage, without the need for chemical signals. This human cell-based model of early forms of co-developing heart and lung cells may help provide researchers with new strategies to probe the underlying mechanisms of human heart and lung interaction during embryogenesis.
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Affiliation(s)
- Wai Hoe Ng
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
| | - Elizabeth K Johnston
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
| | - Jun Jie Tan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Jacqueline M Bliley
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
| | - Adam W Feinberg
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
| | - Donna B Stolz
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, United States
| | - Ming Sun
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, United States
| | - Piyumi Wijesekara
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
| | - Finn Hawkins
- Center for Regenerative Medicine, Boston University, Boston, United States
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University, Boston, MA, United States
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
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Kotton DN, Nilsson M. Editorial: Progenitors and Stem Cells in Thyroid Development, Disease, and Regeneration. Front Endocrinol (Lausanne) 2022; 13:848559. [PMID: 35211095 PMCID: PMC8861071 DOI: 10.3389/fendo.2022.848559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, United States
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- *Correspondence: Mikael Nilsson, ; Darrell N. Kotton,
| | - Mikael Nilsson
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, University of Gothenburg, Göteborg, Sweden
- *Correspondence: Mikael Nilsson, ; Darrell N. Kotton,
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Ding J, Lugo-Martinez J, Yuan Y, Huang J, Hume AJ, Suder EL, Mühlberger E, Kotton DN, Bar-Joseph Z. Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection. bioRxiv 2021:2020.06.01.127589. [PMID: 33083801 PMCID: PMC7574259 DOI: 10.1101/2020.06.01.127589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several molecular datasets have been recently compiled to characterize the activity of SARS-CoV-2 within human cells. Here we extend computational methods to integrate several different types of sequence, functional and interaction data to reconstruct networks and pathways activated by the virus in host cells. We identify key proteins in these networks and further intersect them with genes differentially expressed at conditions that are known to impact viral activity. Several of the top ranked genes do not directly interact with virus proteins. We experimentally tested treatments for a number of the predicted targets. We show that blocking one of the predicted indirect targets significantly reduces viral loads in stem cell-derived alveolar epithelial type II cells (iAT2s).
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Affiliation(s)
- Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, Quebec, H4A 3J1, Canada
| | - Jose Lugo-Martinez
- Department of Computer Science, University of Puerto Rico, San Juan, Puerto Rico, 00925, USA
| | - Ye Yuan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam J. Hume
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ellen L. Suder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Elke Mühlberger
- National Emerging Infectious Diseases Laboratory (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
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40
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Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, Ren B, Kotton DN, Sander M. Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Nat Commun 2021; 12:6636. [PMID: 34789735 PMCID: PMC8599738 DOI: 10.1038/s41467-021-26950-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 10/29/2020] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: first, FOXA facilitates signal-dependent lineage initiation via enhancer priming, and second, FOXA enforces organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.
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Affiliation(s)
- Ryan J. Geusz
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Biomedical Graduate Studies Program, University of California San Diego, La Jolla, San Diego, CA 92037 USA
| | - Allen Wang
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Dieter K. Lam
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Nicholas K. Vinckier
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Konstantinos-Dionysios Alysandratos
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - David A. Roberts
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA
| | - Jinzhao Wang
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Samy Kefalopoulou
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Araceli Ramirez
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Yunjiang Qiu
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA
| | - Joshua Chiou
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Biomedical Graduate Studies Program, University of California San Diego, La Jolla, San Diego, CA 92037 USA
| | - Kyle J. Gaulton
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA
| | - Bing Ren
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, San Diego, CA 92093-0653 USA
| | - Darrell N. Kotton
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - Maike Sander
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA, 92093, USA. .,Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA, 92093, USA.
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41
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Moreira JD, Gopal DM, Kotton DN, Fetterman JL. Gaining Insight into Mitochondrial Genetic Variation and Downstream Pathophysiology: What Can i(PSCs) Do? Genes (Basel) 2021; 12:1668. [PMID: 34828274 PMCID: PMC8624338 DOI: 10.3390/genes12111668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/19/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized organelles involved in energy production that have retained their own genome throughout evolutionary history. The mitochondrial genome (mtDNA) is maternally inherited and requires coordinated regulation with nuclear genes to produce functional enzyme complexes that drive energy production. Each mitochondrion contains 5-10 copies of mtDNA and consequently, each cell has several hundreds to thousands of mtDNAs. Due to the presence of multiple copies of mtDNA in a mitochondrion, mtDNAs with different variants may co-exist, a condition called heteroplasmy. Heteroplasmic variants can be clonally expanded, even in post-mitotic cells, as replication of mtDNA is not tied to the cell-division cycle. Heteroplasmic variants can also segregate during germ cell formation, underlying the inheritance of some mitochondrial mutations. Moreover, the uneven segregation of heteroplasmic variants is thought to underlie the heterogeneity of mitochondrial variation across adult tissues and resultant differences in the clinical presentation of mitochondrial disease. Until recently, however, the mechanisms mediating the relation between mitochondrial genetic variation and disease remained a mystery, largely due to difficulties in modeling human mitochondrial genetic variation and diseases. The advent of induced pluripotent stem cells (iPSCs) and targeted gene editing of the nuclear, and more recently mitochondrial, genomes now provides the ability to dissect how genetic variation in mitochondrial genes alter cellular function across a variety of human tissue types. This review will examine the origins of mitochondrial heteroplasmic variation and propagation, and the tools used to model mitochondrial genetic diseases. Additionally, we discuss how iPSC technologies represent an opportunity to advance our understanding of human mitochondrial genetics in disease.
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Affiliation(s)
- Jesse D. Moreira
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
| | - Deepa M. Gopal
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
- Cardiovascular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Boston Medical Center, Center for Regenerative Medicine of Boston University, Boston, MA 02118, USA;
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessica L. Fetterman
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
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42
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Fuchs SY, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway. J Virol 2021; 95:e0086221. [PMID: 34260266 PMCID: PMC8428404 DOI: 10.1128/jvi.00862-21] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we generated a panel of phenotypically diverse, SARS-CoV-2-infectible human cell lines representing different body organs and performed longitudinal survey of cellular proteins and pathways broadly affected by the virus. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cells and primary-like cardiomyocytes, and found that SARS-CoV-2 targeted the proximal pathway components, including Janus kinase 1 (JAK1), tyrosine kinase 2 (Tyk2), and the interferon receptor subunit 1 (IFNAR1), resulting in cellular desensitization to type I IFN. Detailed mechanistic investigation of IFNAR1 showed that the protein underwent ubiquitination upon SARS-CoV-2 infection. Furthermore, chemical inhibition of JAK kinases enhanced infection of stem cell-derived cultures, indicating that the virus benefits from inhibiting the JAK-STAT pathway. These findings suggest that the suppression of interferon signaling is a mechanism widely used by the virus to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19. IMPORTANCE SARS-CoV-2 can infect various organs in the human body, but the molecular interface between the virus and these organs remains unexplored. In this study, we generated a panel of highly infectible human cell lines originating from various body organs and employed these cells to identify cellular processes commonly or distinctly disrupted by SARS-CoV-2 in different cell types. One among the universally impaired processes was interferon signaling. Systematic analysis of this pathway in diverse culture systems showed that SARS-CoV-2 targets the proximal JAK-STAT pathway components, destabilizes the type I interferon receptor though ubiquitination, and consequently renders the infected cells resistant to type I interferon. These findings illuminate how SARS-CoV-2 can continue to propagate in different tissues even in the presence of a disseminated innate immune response.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Brianna J. Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Raghuveera K. Goel
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Benjamin Blum
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Alexander H. Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hasahn L. Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Vipul C. Chitalia
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Boston Veterans Affairs Healthcare System, Boston, Massachusetts, USA
- Institute of Medical Engineering and Sciences, MA Institute of Technology, Cambridge, Massachusetts, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Susan C. Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Serge Y. Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John H. Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
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43
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Alysandratos KD, Russo SJ, Petcherski A, Taddeo EP, Acín-Pérez R, Villacorta-Martin C, Jean JC, Mulugeta S, Rodriguez LR, Blum BC, Hekman RM, Hix OT, Minakin K, Vedaie M, Kook S, Tilston-Lunel AM, Varelas X, Wambach JA, Cole FS, Hamvas A, Young LR, Liesa M, Emili A, Guttentag SH, Shirihai OS, Beers MF, Kotton DN. Patient-specific iPSCs carrying an SFTPC mutation reveal the intrinsic alveolar epithelial dysfunction at the inception of interstitial lung disease. Cell Rep 2021; 36:109636. [PMID: 34469722 PMCID: PMC8432578 DOI: 10.1016/j.celrep.2021.109636] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/28/2021] [Accepted: 08/06/2021] [Indexed: 01/08/2023] Open
Abstract
Alveolar epithelial type 2 cell (AEC2) dysfunction is implicated in the pathogenesis of adult and pediatric interstitial lung disease (ILD), including idiopathic pulmonary fibrosis (IPF); however, identification of disease-initiating mechanisms has been impeded by inability to access primary AEC2s early on. Here, we present a human in vitro model permitting investigation of epithelial-intrinsic events culminating in AEC2 dysfunction, using patient-specific induced pluripotent stem cells (iPSCs) carrying an AEC2-exclusive disease-associated variant (SFTPCI73T). Comparing syngeneic mutant versus gene-corrected iPSCs after differentiation into AEC2s (iAEC2s), we find that mutant iAEC2s accumulate large amounts of misprocessed and mistrafficked pro-SFTPC protein, similar to in vivo changes, resulting in diminished AEC2 progenitor capacity, perturbed proteostasis, altered bioenergetic programs, time-dependent metabolic reprogramming, and nuclear factor κB (NF-κB) pathway activation. Treatment of SFTPCI73T-expressing iAEC2s with hydroxychloroquine, a medication used in pediatric ILD, aggravates the observed perturbations. Thus, iAEC2s provide a patient-specific preclinical platform for modeling the epithelial-intrinsic dysfunction at ILD inception.
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Affiliation(s)
- Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Scott J Russo
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Anton Petcherski
- Departments of Medicine, Endocrinology and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Evan P Taddeo
- Departments of Medicine, Endocrinology and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Rebeca Acín-Pérez
- Departments of Medicine, Endocrinology and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - J C Jean
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Surafel Mulugeta
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Luis R Rodriguez
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Benjamin C Blum
- Departments of Biology and Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ryan M Hekman
- Departments of Biology and Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Olivia T Hix
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Kasey Minakin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Marall Vedaie
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Seunghyi Kook
- Department of Pediatrics, Monroe Carell Jr. Children's Hospital, Vanderbilt University, Nashville, TN 37232, USA
| | - Andrew M Tilston-Lunel
- Departments of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Xaralabos Varelas
- Departments of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jennifer A Wambach
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - F Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - Aaron Hamvas
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lisa R Young
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marc Liesa
- Departments of Medicine, Endocrinology and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Andrew Emili
- Departments of Biology and Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Susan H Guttentag
- Department of Pediatrics, Monroe Carell Jr. Children's Hospital, Vanderbilt University, Nashville, TN 37232, USA
| | - Orian S Shirihai
- Departments of Medicine, Endocrinology and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Michael F Beers
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; PENN-CHOP Lung Biology Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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Abstract
Airway basal cells play an essential role in the maintenance of the airway epithelium. Here, we provide a detailed directed differentiation protocol to generate ‘‘induced basal cells (iBCs)’’ from human pluripotent stem cells. iBCs recapitulate biological and functional properties of airway basal cells including mucociliary differentiation in vitro or in vivo in tracheal xenografts, facilitating the study of inherited and acquired diseases of the airway, as well as potential use in regenerative medicine. For complete details on the use and execution of this protocol, please refer to Hawkins et al. (2021). This protocol enables differentiation of human iPSCs into airway basal cells (iBCs) The derived iBCs can give rise to well-differentiated airway epithelium Expansion and cryopreservation of iBCs is possible without loss of BC characteristics This protocol is applicable to both reporter and non-reporter iPSCs
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Affiliation(s)
- Shingo Suzuki
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.,The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Cristina Barillà
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Mary Lou Beermann
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.,The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.,The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
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45
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Sun YL, Hurley K, Villacorta-Martin C, Huang J, Hinds A, Gopalan K, Caballero IS, Russo SJ, Kitzmiller JA, Whitsett JA, Beers MF, Kotton DN. Heterogeneity in Human iPSC-derived Alveolar Epithelial Type II Cells Revealed with ABCA3/SFTPC Reporters. Am J Respir Cell Mol Biol 2021; 65:442-460. [PMID: 34101541 DOI: 10.1165/rcmb.2020-0259oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of lung alveoli, are typically identified through the use of the canonical markers, SFTPC and ABCA3. Self-renewing AEC2-like cells have been generated from human induced pluripotent stem cells (iPSCs) through the use of knock-in SFTPC fluorochrome reporters. However, developmentally, SFTPC expression onset begins in the fetal distal lung bud tip and thus is not specific to mature AEC2s. Furthermore, SFTPC reporters appear to identify only those iPSC-derived AEC2s (iAEC2s) expressing the highest SFTPC levels. Here, we generate an ABCA3 knock-in GFP fusion reporter (ABCA3:GFP) that enables the purification of iAEC2s while allowing visualization of lamellar bodies, organelles associated with AEC2 maturation. Using a SFTPCtdTomato and ABCA3:GFP bi-fluorescent line for in vitro distal lung directed differentiation, we observe later onset of ABCA3:GFP expression and broader identification of the subsequently emerging iAEC2 population based on ABCA3:GFP expression compared to SFTPCtdTomato expression. Comparing ABCA3:GFP/SFTPCtdTomato double positive (DP) to ABCA3:GFP single positive cells (SP) by RNA sequencing and functional studies reveals iAEC2 cellular heterogeneity with both populations functionally processing surfactant proteins but the SP cells exhibiting faster growth kinetics, increased clonogenicity, increased expression of progenitor markers, lower levels of SFTPC expression, and lower levels of AEC2 maturation markers. Over time, we observe each population (DP and SP) gives rise to the other and each can serve as the parents of indefinitely self-renewing iAEC2 progeny. Our results indicate iAEC2s are a heterogeneous population of cells with differing proliferation vs maturation properties, the majority of which can be tracked and purified using the ABCA3:GFP reporter or surrogate cell surface proteins, such as SLC34A2 and CPM.
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Affiliation(s)
- Yuliang L Sun
- Boston University School of Medicine, 12259, Center for Regenerative Medicine, Boston, Massachusetts, United States.,Boston University School of Medicine, 12259, The Pulmonary Center and Department of Medicine, Boston, Massachusetts, United States
| | - Killian Hurley
- Boston University School of Medicine, 12259, Center for Regenerative Medicine, Boston, Massachusetts, United States.,Royal College of Surgeons in Ireland, 8863, Beaumont Hospital, Dublin, Ireland.,Boston University School of Medicine, 12259, The Pulmonary Center and Department of Medicine, Boston, Massachusetts, United States.,Royal College of Surgeons in Ireland, 8863, Tissue Engineering Research Group, Dublin, Ireland
| | - Carlos Villacorta-Martin
- Boston University School of Medicine, 12259, Center for Regenerative Medicine, Boston, Massachusetts, United States
| | - Jessie Huang
- Boston University School of Medicine, 12259, Center for Regenerative Medicine, Boston, Massachusetts, United States.,Boston University School of Medicine, 12259, The Pulmonary Center and Department of Medicine, Boston, Massachusetts, United States
| | - Anne Hinds
- Boston University School of Medicine, 12259, The Pulmonary Center and Department of Medicine, Boston, Massachusetts, United States
| | - Krithi Gopalan
- Boston University School of Medicine, 12259, Center for Regenerative Medicine, Boston, Massachusetts, United States
| | - Ignacio S Caballero
- Boston University School of Medicine, 12259, Center for Regenerative Medicine, Boston, Massachusetts, United States
| | - Scott J Russo
- University of Pennsylvania Perelman School of Medicine, 14640, Department of Medicine, Philadelphia, Pennsylvania, United States
| | - Joseph A Kitzmiller
- Cincinnati Children's Hospital Medical Center, 2518, Neonatology and Pulmonary Biology, Cincinnati, Ohio, United States
| | - Jeffrey A Whitsett
- Cincinnati Children's Hospital Medical Center, 2518, The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati, Ohio, United States
| | - Michael F Beers
- University of Pennsylvania Perelman School of Medicine, 14640, Department of Medicine, Philadelphia, Pennsylvania, United States
| | - Darrell N Kotton
- Boston University, 1846, Medicine, Boston, Massachusetts, United States.,Boston University School of Medicine, 12259, The Pulmonary Center and Department of Medicine, Boston, Massachusetts, United States;
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46
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Undeutsch HJ, Posabella A, Kurmann AA, Kotton DN, Hollenberg AN. Generation and Transplantation of HiPSC-Derived Thyroid Follicular Cells. J Endocr Soc 2021. [DOI: 10.1210/jendso/bvab048.1735] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Abstract
Despite the availability of synthetic thyroid hormone (TH) for therapeutic use, many patients with hypothyroidism do not feel well on replacement doses of TH. Indeed, hypothyroid children may develop various behavioral issues if under- or overtreated for hypothyroidism, suggesting the need of better individualized therapy. The development of stem cell-based models of thyroid replacement would greatly facilitate the treatment of post-surgical and congenital hypothyroidism and our understanding of the causes of congenital hypothyroidism. To generate thyroid follicular cells from human induced pluripotent stem cells (hiPSCs), we utilize a directed differentiation approach by activating endogenous signaling pathways we have previously identified in the mouse. We are employing a hiPSC-line with a GFP reporter targeted to the NKX2-1 locus allowing us to identify and purify cells positive for the transcription factor NKX2-1. Using these cells, we confirmed that BMP4 and FGF2 led to the induction of thyroid progenitors from foregut endoderm, expressing the four transcription factors in thyroid development NKX2-1, PAX8, HHEX and FOXE1. Subsequent differentiation of the purified, NKX2-1-positive progenitors led to follicular cell maturation, expressing genes related to TH synthesis, such as TG, TSHR, NIS (SLC5A5) and TPO. To assess the in vivo function of these hiPSC-derived thyroid follicular cells, we grafted the cells under the kidney capsule of radioablated, immunocompromised mice. First, hypothyroidism was confirmed 4 weeks post-ablation by increased TSH and low T4 levels. Next, mice received matured hiPSC-derived follicular cells, undifferentiated hiPSCs or sham surgery and were monitored for 8 weeks. In this preliminary test, no difference in TH levels was detected between the three groups. However, the grafted follicular cells formed a distinct cell population with thyroid-like histology. In order to optimize our directed differentiation protocol further and obtain a purer thyroid progenitor population, we generated a hiPSC line carrying a tdTomato reporter targeted to the PAX8 locus in addition to the NKX2-1-GFP-reporter. After directed differentiation cells sorted for NKX2-1-GFP and PAX8-tdTomato showed high induction of NKX2-1, PAX8, HHEX and FOXE1 expression, as well as expression of TG and TPO. Utilizing this double-reporter hiPSC line will enhance our ability to generate mature follicular cells for transplantation.
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Affiliation(s)
| | - Alberto Posabella
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | | | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
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47
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Basil MC, Katzen J, Engler AE, Guo M, Herriges MJ, Kathiriya JJ, Windmueller R, Ysasi AB, Zacharias WJ, Chapman HA, Kotton DN, Rock JR, Snoeck HW, Vunjak-Novakovic G, Whitsett JA, Morrisey EE. The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future. Cell Stem Cell 2021; 26:482-502. [PMID: 32243808 PMCID: PMC7128675 DOI: 10.1016/j.stem.2020.03.009] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The respiratory system, which includes the trachea, airways, and distal alveoli, is a complex multi-cellular organ that intimately links with the cardiovascular system to accomplish gas exchange. In this review and as members of the NIH/NHLBI-supported Progenitor Cell Translational Consortium, we discuss key aspects of lung repair and regeneration. We focus on the cellular compositions within functional niches, cell-cell signaling in homeostatic health, the responses to injury, and new methods to study lung repair and regeneration. We also provide future directions for an improved understanding of the cell biology of the respiratory system, as well as new therapeutic avenues.
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Affiliation(s)
- Maria C Basil
- Department of Medicine, Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeremy Katzen
- Department of Medicine, Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna E Engler
- Center for Regenerative Medicine of Boston University and Boston Medical Center, The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Minzhe Guo
- Division of Pulmonary Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Michael J Herriges
- Center for Regenerative Medicine of Boston University and Boston Medical Center, The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Jaymin J Kathiriya
- Division of Pulmonary Medicine, Department of Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Rebecca Windmueller
- Department of Medicine, Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexandra B Ysasi
- Center for Regenerative Medicine of Boston University and Boston Medical Center, The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - William J Zacharias
- Division of Pulmonary Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Hal A Chapman
- Division of Pulmonary Medicine, Department of Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Jason R Rock
- Center for Regenerative Medicine of Boston University and Boston Medical Center, The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Hans-Willem Snoeck
- Center for Human Development, Department of Medicine, Columbia University, New York, NY 10027, USA
| | - Gordana Vunjak-Novakovic
- Departments of Biomedical Engineering and Medicine, Columbia University, New York, NY 10027, USA
| | - Jeffrey A Whitsett
- Center for Regenerative Medicine of Boston University and Boston Medical Center, The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Edward E Morrisey
- Department of Medicine, Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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48
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Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M. SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation. Sci Immunol 2021; 6:6/58/eabg0833. [PMID: 33827897 PMCID: PMC8139422 DOI: 10.1126/sciimmunol.abg0833] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/31/2021] [Indexed: 12/26/2022]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs, liver, kidneys and gut. Angiotensin converting enzyme (ACE) 2, the best-characterized entry receptor for the disease-causing virus SARS-CoV-2, is highly expressed in the aforementioned tissues. However, the pathways that underlie the disease are still poorly understood. Here, we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi), indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients, distinct signatures of complement activation in myeloid, lymphoid and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-B as the main drivers of their expression. Ruxolitinib, a JAK1/2 inhibitor, normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines, but did not affect NF-B-regulated genes. Ruxolitinib, alone or in combination with the antiviral remdesivir, inhibited C3a protein produced by infected cells. Together, we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-B-signaling could potentially have clinical application for severe COVID-19.
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Affiliation(s)
- Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Tilo Freiwald
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.,Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA.,Department of Nephrology, University Hospital Frankfurt, Goethe-University, Frankfurt, Germany
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Erin West
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Charles J Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | | | - Tristan Frum
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 1702118, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 1702118, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA
| | - Jack Bibby
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nathalie Niyonzima
- Center of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Matthew R Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shahram Kordasti
- CRUK-KHP Centre, Comprehensive Cancer Centre, King's College London, London, UK.,Haematology Department, Guy's Hospital, London, UK
| | - Didier Portilla
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.,Division of Nephrology and the Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, VA, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Arian Laurence
- Nuffield Department of Medicine, University of Oxford, UK
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Claudia Kemper
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA. .,Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA. .,Department of Computer Science, Purdue University, West Lafayette, IN, USA
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49
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Dobrindt K, Hoagland DA, Seah C, Kassim B, O'Shea CP, Murphy A, Iskhakova M, Fernando MB, Powell SK, Deans PJM, Javidfar B, Peter C, Møller R, Uhl SA, Garcia MF, Kimura M, Iwasawa K, Crary JF, Kotton DN, Takebe T, Huckins LM, tenOever BR, Akbarian S, Brennand KJ. Common Genetic Variation in Humans Impacts In Vitro Susceptibility to SARS-CoV-2 Infection. Stem Cell Reports 2021; 16:505-518. [PMID: 33636110 PMCID: PMC7881728 DOI: 10.1016/j.stemcr.2021.02.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/05/2023] Open
Abstract
The host response to SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, demonstrates significant interindividual variability. In addition to showing more disease in males, the elderly, and individuals with underlying comorbidities, SARS-CoV-2 can seemingly afflict healthy individuals with profound clinical complications. We hypothesize that, in addition to viral load and host antibody repertoire, host genetic variants influence vulnerability to infection. Here we apply human induced pluripotent stem cell (hiPSC)-based models and CRISPR engineering to explore the host genetics of SARS-CoV-2. We demonstrate that a single-nucleotide polymorphism (rs4702), common in the population and located in the 3' UTR of the protease FURIN, influences alveolar and neuron infection by SARS-CoV-2 in vitro. Thus, we provide a proof-of-principle finding that common genetic variation can have an impact on viral infection and thus contribute to clinical heterogeneity in COVID-19. Ongoing genetic studies will help to identify high-risk individuals, predict clinical complications, and facilitate the discovery of drugs.
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Affiliation(s)
- Kristina Dobrindt
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carina Seah
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bibi Kassim
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Callan P O'Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aleta Murphy
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Iskhakova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samuel K Powell
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - P J Michael Deans
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ben Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cyril Peter
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rasmus Møller
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Skyler A Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Meilin Fernandez Garcia
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Masaki Kimura
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Center for Stem Cell and Organoid Medicine (CuSTOM), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Center for Stem Cell and Organoid Medicine (CuSTOM), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John F Crary
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Center for Stem Cell and Organoid Medicine (CuSTOM), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education and Clinical Centers, James J. Peters Department of Veterans Affairs Medical Center, Bronx, NY 10468, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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50
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Abstract
The mammalian lung epithelium is composed of a wide array of specialized cells that have adapted to survive environmental exposure and perform the tasks necessary for respiration. Although the majority of these cells are remarkably quiescent during adult lung homeostasis, a growing body of literature has demonstrated the capacity of these epithelial lineages to proliferate in response to injury and regenerate lost or damaged cells. In this review, we focus on the regionally distinct lung epithelial cell types that contribute to repair after injury, and we address current controversies regarding whether elite stem cells or frequent facultative progenitors are the predominant participants. We also shed light on the newly emerging approaches for exogenously generating similar lung epithelial lineages from pluripotent stem cells.
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Affiliation(s)
- Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts 02118, USA;
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Michael J Herriges
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts 02118, USA;
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts 02118, USA;
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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